Research Outreach Issue 101

The outreach quarterly connecting science with society ISSN 2517-7028 ISSUE 101

FEATURING RESEARCH FROM:

Columbia University, Boise State University, University of Leeds, University of Strathclyde, University of Southampton, West Virginia University, Research Experiences and Exploration in Materials Science (REEMS) , The Leadership Alliance, Synapse Neurobiology Training Program (SNTP), University of Michigan, University of Nottingham, Purdue University, University of Louisville, Green Biologics, European Society for Evolutionary Research Features 3 Biology (ESEB) , Florida International University (FIU), University of Minnesota, Fresno City College, University of Wisconsin, Cornell University

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We abide by the Creative Commons (CC) license terms to ensure widespread, open-access dissemination of all the work featured across our various platforms.

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RPI has over 30 years of collective expertise in science communications. Our know-how ensures that we work efficiently and cost-effectively, boosting the impact of your research globally.

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RESEARCH OUTREACH ISSUE 101

WELCOME

The public outreach quarterly for the research community ISSN 2517-7028 ISSUE 101

TO ISSUE 101

FEATURING RESEARCH FROM:

For those not immersed in it every day, the world of research can seem dauntingly distant. At Research Outreach, we are committed to closing that gap. We want to open up the research community so that readers around the world can understand the value of the work being carried out in diverse subject areas.

Whether you are interested in Physical Sciences, Education & Training, Engineering & Technology or Biology, this issue of Research Outreach will have plenty to interest you. In addition to detailed articles on research projects, we also hear from the scientists themselves, to gain an insight into the people behind the research.

We speak to Professor Laurent Keller from the European Society for Evolutionary Biology (ESEB) about all things evolution as well as his experience as president of the society. The ESEB has approximately 1,400 members who it supports through a networking platform, conferences, funding and two journals.

It was a pleasure to work on this issue and I hope that you enjoy reading it.

Columbia University, Boise State University, University of Leeds, University of Strathclyde, University of Southampton, West Virginia University, Research Experiences and Exploration in Materials Science (REEMS) , The Leadership Alliance, Synapse Neurobiology Training Program (SNTP), University of Michigan, University of Nottingham, Purdue University, University of Louisville, Green Biologics, European Society for Evolutionary Research Features 3 Biology (ESEB) , Florida International University (FIU), University of Minnesota, Fresno City College, University of Wisconsin, Cornell University

THIS ISSUE Published by: Research Outreach Publisher: Simon Jones Editorial Director: Emma Feloy emma@researchoutreach.org Operations Director: Alastair Cook audience@researchoutreach.org Editor: Hannah Fraser hannah@researchoutreach.org Designer: Craig Turl Project Managers: Kate Cooper (Senior) kate@researchoutreach.org Tobias Jones tobias@researchoutreach.org Ben Phillips ben@researchoutreach.org James Harwood james@researchoutreach.org Contributors: Patrick Bawn, Abigail Beall, Alex Davey, Agnieszka Dygus, Leanne Edermaniger, Rachel Goddard, Rebecca Ingle, Jacek Krywko, Kate Porter, Ila Sivarajah, Paul Smith, Victoria Stanley Tsui, Rebecca White. /ResearchOutreach /ResOutreach

Editor Please feel free to comment or join the debate. Follow us on twitter @ResOutreach or find us on Facebook https://www.facebook.com/ ResearchOutreach/

Copyright Š and ™ 2018 Research Outreach

CC BY This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons. org/licenses/by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.

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A NEEDLE IN A HAYSTACK – THE FUTURE OF BIG DATA Dr Yang Feng Using network modelling to detect communities using available nodal information.

LYSENIN CHANNELS AS SINGLE-MOLECULE SENSORS, CONTROLLED NANO-VALVES, AND MEMORY ELEMENTS Professor Daniel Fologea How cells interact with their environment by selective transportation.

CRYSTAL CLEAR: HOW TOPOGRAPHY AFFECTS CRYSTAL FORMATION Dr Hugo Christenson Why crystals first form in topographical defects like cracks and crevices.

FROM EARS TO ENGINEERING Professor James Windmill Learning from insect hearing to develop new microphones and transducers.

BUILDING ARTIFICIAL INTELLIGENCE FOR SOCIAL GOOD Dr Long Tran-Thanh Harnessing AI to solve the most important societal challenges of our age.

PUSHING THE BOUNDARIES – INTERROGATING MAGNETISM AT MATERIAL INTERFACES Dr Mikel Holcomb Understanding the behaviour of ions at the boundaries between two materials.

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THE REEMS PROGRAMME: DISCOVERING UNTAPPED TALENT Mr Bartlett Sheinberg Contextualising materials science for community college students.

SUPPORTING TOMORROW’S ROLE MODELS: HOW THE LEADERSHIP ALLIANCE IS ENCOURAGING STUDENTS FROM UNDERREPRESENTED GROUPS Dr Medeva Ghee Developing a workforce reflective of the diverse fabric of our society.

THE SYNAPSE NEUROBIOLOGY TRAINING PROGRAM, TRAINING THE NEXT GENERATION OF NEUROSCIENTISTS

Professor Michele Jacob Provides predoctoral students with individualised, in-depth, multidisciplinary research training.

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EXPANDING CAPACITY OF NON-COMMUNICABLE DISEASE RESEARCH AND TRAINING IN THAILAND Dr Kathleen Potempa Helping improve the capability of the Thai healthcare system in managing chronic diseases.

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TAKING INSPIRATION FROM NATURE FOR A NEW GENERATION OF QUIET AEROFOILS Professor Phil Joseph Reducing noise pollution through the development of new aerofoil design.

I see the Leadership Alliance as a model for diversity on the global stage.

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EVADING THE RISE OF RANSOMWARE Professor Elisa Bertino Designing tools to prevent ransomware infections from ever taking hold.

BIASES FROM BIG DATA: THE PREJUDICED COMPUTER Professor Olfa Nasraoui Developing tools to lift the lid on ‘black box’ algorithms and create truly fair alternatives.

FOSSILISING FOSSIL FUELS WITH GREEN ALTERNATIVES Dr Liz Jenkinson Developing an alternative to fossil fuels based on three key components – bacteria, genetic engineering and sugar.

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ESEB: HELPING EVOLUTIONARY BIOLOGY EVOLVE IN EUROPE Professor Laurent Keller Uniting and supporting evolutionary biology researchers.

DEVELOPMENT OF IMMUNITY IN BASAL METAZOANS Dr Mauricio Rodriguez-Lanetty Investigating immunological priming in corals and anemones.

SYNTHETIC CELLS HAVE SENSES TOO Professor Allen Liu Constructing prototypes of synthetic cells displaying the minimal characteristics of life.

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CAPTURING IMAGES AND DATA BEFORE THE SLIDES DEGRADE INTO USELESSNESS Professor Carl Johansson Documenting the amazing diversity of tardigrades – the mysterious ‘water bears’.

PEATLANDS’ PAST SUGGESTS FAST-CHANGING FUTURE Professor Sara Hotchkiss Investigating the effects of climate change on kettle hole ecosystems of the northern US. CROSSING KINGDOMS BETWEEN PLANTS, FUNGI AND BACTERIA Professor Teresa Pawlowska Investigating the complex interrelationship between endobacteria and their host plants.

COMMUNICATION The media’s manipulation of scientific perception.

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RESEARCH AREAS

Physical Sciences

Education & Training

Engineering & Tech

Biology

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Physical Sciences ︱ Dr Yang Feng

A needle in a haystack – the future of big data Dr Yang Feng is Associate Professor of Statistics at Columbia University. His research aims to structure, into a useful form, the voluminous data available from many areas of science, humanity, industry and governments, like social networks, the study of the genome, understanding economics or finance and health sciences. Using network modelling, he has focused on novel ways of detecting “communities” more accurately by using available nodal information.

Dr Feng’s approach is underpinned by rigorous theory and its effectiveness is demonstrated using simulated and real networks.

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network is a way to represent information and is underpinned by mathematical methods that are well understood. Networks are groups of nodes interconnected by links, or edges, that can be directed (from one node to another) or undirected (two way). Web pages are examples of directed networks with the page representing a node and a hyperlink as an edge. Dr Feng uses networks to find “communities” more accurately. These are nodes that are densely connected as a group but have few connections to other groups, like people in social networks with similar interests or researchers collaborating within a scientific field. Of interest to Dr Feng are “covariates” from the data under study as they may help to improve the accuracy for identifying communities.

Figure 1: Community detection results when considering school, ethnicity, and gender as the ground truth. Predicted communities are separated by the middle dash line.

School

COMMUNITIES AND NODAL INFORMATION Recognising communities within networks clarifies their structure, offering practical benefits; for example, social network groups share similar interests so recommendations can be better targeted. Broadly, current methods for identifying communities within data sets are either algorithmic, relying on derived computer programs, or model based, using statistical methods, a common one being the stochastic block model. This is a model that assumes the nodes inside the same community behave identically when interacting with other nodes. For example, if persons A and B belong to the same community, they would exhibit similar behaviour when communicating with any other person C. In real networks, nodes contain properties that can help pinpoint community structures within the data.

As examples, social networks have their user profiles attached to nodes and cited scientific papers contain author information, keywords and abstracts.

Dr Feng considered that this kind of covariate information, combined with edges, could better infer the existence of communities, through the two different relationships described in Figure 1.

ASYMPTOTIC APPROACH Dr Feng’s work introduces a flexible statistical model, tuned to identify communities using the structure of the network, its nodes and edges, and nodal properties that represent the covariate information. The model uses a grounding of network mathematics to create matrices for the network and its connections, plus the nodal properties (the covariates) and uses an iterative approach to identify the

Ethnicity

Gender

Recognising communities within networks clarifies their structure, offering practical benefits, like better recommendations in web searches communities. One challenge was that a pure likelihood-based approach was sensitive to the initial solutions so an alternative had to be developed. This involved finding well-behaved initial values for the model using optimisation techniques. These worked better than random initialisation.

NOW, TO REAL LIFE It was time to test the model on some real data so an example was chosen comprising a research team of 77 employees working in a manufacturing company. To create a network, consider the employees as nodes with their links, or edges, being how much they interact to allow them to do their work. These

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X

A A

c

(a) Covariates-adjusted

links are weighted; if Helen co-operates with Joseph then the weight might be based upon their interaction: 0: none, 1: very infrequent, 2: infrequent, 3: somewhat infrequent, 4: somewhat frequent, 5: frequent and 6: very frequent. The dataset contained other attributes about each employee, in particular their country location and level in the organisation.

The data represented a weighted, directed network and needed to be converted to a binary undirected network. The final model used the frequency of communication to isolate those who didn’t communicate often and included properties from the database to seed it. The attribute “location” was a “ground truth” as disparate location implies lower interaction and this could be used to test the effectiveness of the process. Dr Feng found that by incorporating the nodal properties, community detection accuracy was improved and semidefinite programming performed as well as two of the newly proposed likelihoodbased methods.

Another more complex example used a ‘friend network’ at a USA high school, taken from the National Longitudinal Study of Adolescent to Adult Health comprising 795 students between nine and 12 years of age at the high school and between seven and eight

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c (b) Covariates-confounding

X

Figure 2: Two different relationships among nodal information X, community information c and the observed adjacency matrix A.

In real networks, nodes contain properties that can help pinpoint community structures within the data years at the feeder middle school.

The collection had multiple covariate properties of grade, gender, ethnicity and number of friends nominated (up to ten). In communities like these the nodal information (like age or ethnicity) can often infer a ‘ground truth’ for the community identifier.

The final dataset, after removing those with missing covariates, had 777 nodes and 4,124 edges. Dr Feng and his team used their model with this dataset as it contained multiple category variables; anyone could be considered as the community of interest with the other variables controlled to make a prediction. School, race and gender were used as the ground truth (students at the same school are more likely to be friends, for example) and the other two properties were controlled when detecting a community. The results presented in Figure 2 suggested an accurate community detection for school and ethnicity but did not perform as well when using gender as the true label.

Dr Feng concluded that the gender result

was no better than random and that there was the possibly of another covariate available that had not been identified.

Finally, Dr Feng examined community detection of this dataset using standard network models (like the stochastic block model) and concluded that detection is poor; naively applying them to detect communities would lead to unreliable findings.

LOOKING AHEAD Dr Feng’s work has demonstrated the viability of using statistical models to detect communities in networks that are built from network data that includes attributes provided at each node, like a person’s interests or location. It has real world applications in many disciplines or industries, like forensics or drug selection from genetic data, and holds promise when using a wider family of node properties or a greater number of them and in networks that have low densities of communities.

Behind the Bench Dr Yang Feng

E: yang.feng@columbia.edu T: +1 (212) 851 2139 W: http://www.stat.columbia.edu/~yangfeng/

Research Objectives Dr Feng’s research focuses on proposing statistical models for networks and developing efficient estimation methods. He is currently interested in finding out how the available nodal information can help with community detection in networks.

Funding • NSF Collaborators • Sihan Huang • Haolei Weng Bio Yang Feng is an associate professor of statistics at Columbia University.

His current research interests include high-dimensional statistical learning, network models, nonparametric and semiparametric methods and bioinformatics. He is currently an associate editor for Statistica Sinica, Computational Statistics & Data Analysis, and Statistical Analysis & Data Mining.

Contact Dr Yang Feng Associate Professor Department of Statistics Columbia University 1255 Amsterdam Ave. 10th Floor, MC 4690 New York, NY 10027 USA

Q&A

What would you say was the strength of the approach taken by your team in comparison to that taken by others in your field?

Compared with the existing approaches, the proposed approach is intuitive, can be computed efficiently, and has solid theoretical justification of its performance.

Why did you choose semi-definite programming and how did you ensure that the computational load was achievable?

The semi-definite programming (SDP) approach is a popular method for relaxing a NP hard problem to a convex one. By using SDP, the computation becomes feasible through a wellknown algorithm called ADMM. At the same time, we provide theoretical justification on the solution of SDP. Empirically, we observe using the SDP solution as the initial solution to our likelihood-based methods can improve the estimation accuracy significantly.

How do you see your research being used in health care and its services?

I see this research framework to be potentially useful in the health care domain, where precision medicine is the current trend to ensure everyone receives the personalised treatment that is best for each individual. If we can collect the network information among different patients along

with their personal information, the proposed method may be used to detect different communities among patients. It is possible that we may want to use different treatments for patients that are in different groups.

There’s a great deal of mathematics in your papers. Could you summarise how the mathematics helped you develop your solution and test the accuracy of your findings?

Indeed, a lot of math was used in this research project. We use likelihood-based approaches to detect communities and this naturally leads to the study for the maximisers of the likelihood functions. Quantifying the theoretical properties of those MLEs requires various techniques from mathematics and statistics.

How would you like to see your research developed further and to what practical benefit?

Currently, I am working to further develop this project by integrating the network information to improve prediction. This would require us to study the regression problem under dependent sample where the dependency is characterised by the network. I hope this research will lead to improvements in personalised recommendation and advertisement targeting.

I hope this research will lead to improvements in personalised recommendation and advertisement targeting

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Physical Sciences ︱ Professor Daniel Fologea

Lysenin channels as single-molecule sensors, controlled nano-valves, and memory elements Professor Daniel Fologea, an associate professor at Boise State University, studies the way cells interact with their environment by selective transportation of ions and molecules through the cell membrane. His research group examines these interactions in order to understand how diseases occur, and how to use them for biosensing, early diagnosis, and to cure diseases like cancer.

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ny cell in your body, whether it is in your brain, blood, muscles, or heart, interacts with its environment and allows for the selective passage of ions and molecules through its membrane. To decipher the functionality of cells in health and disease, the intimate mechanisms by which ions and molecules make their way into and out of cells through their membranes must be better understood.

Under the umbrella of membrane transportation, there are several different topics of research that Prof Daniel Fologea’s membrane biophysics group at Boise State University is looking into. One of these uses a special protein found in an unusual organism – a red earthworm.

WHAT IS LYSENIN? Lysenin is the name of a pore-forming toxin that can be found in fluids from the main body of an earthworm called redworm or Eisenia fetida. The worm, typically found in Europe, lives on decaying organic material and can be used for composting household and industrial waste – like sheep manure, coffee pulp, and even wood chips.

Despite its origins, this protein inside the earthworm might be the key to the better diagnosis and treatment of deadly diseases, according to Prof Fologea’s research.

Lysenin destroys cells through cytolysis, a process by which a cell bursts due to excess water flowing into the cytosol

The experimental setup for single molecule analysis consists of single lysenin channels inserted into planar lipid membranes produced in a thin Teflon film.

When the analyte molecule is electrophoretically driven through the channel it impedes the ionic flow and yields a drop in the current (IB) for the time (T) the analyte resides within the channel’s lumen. The electronic signature recorded during the passage depends on the size and charge of the translocated molecule.

(the fluid within the cell). Once lysenin is inserted into the membrane, it forms stable nano-sized channels, or pores, through the hydrophobic, or waterrepelling, cell wall. Prof Fologea and his colleagues use these channels to their advantage, by recreating the way the protein forms the pores in the cell wall.

LYSENIN: CHANNEL, SENSOR, OR MEMORY ELEMENT? In earlier works published in 2010 and 2011, Prof Fologea and his team focused on understanding the biophysical properties of lysenin channels by reconstituting them in artificial membrane systems and investigating their response to physical and chemical stimuli. Their findings have shown a pore-forming

toxin that deviates considerably from its previously assumed killer role.

Unlike any other pore-forming toxins, lysenin channels are highly regulated by transmembrane voltage, multivalent metal ions, and temperature. His research group proposed using these channels as cheap and reliable sensors for detecting toxic metals in water by monitoring the changes in the electric currents through channels in the presence of tiny amounts of metal cations (positively charged ions).

When Prof Fologea’s team investigated the response of lysenin channels to variable external voltages they recorded a striking feature: lysenin channels responded to the applied voltages in a history-dependent manner. In simple

Lysenin channels are temporarily blocked during the passage of angiotensin II (Ang ii). a) The insertion of a single channel in the bilayer membrane at -60 mV is observed as a sudden change in the ionic current through the supporting bilayer lipid membrane. No transient changes in the ionic current established through two open lysenin channels were observed at -80 mV in the absence of Ang II (b) and when Ang II was added to the negatively biased reservoir. d) Addition of Ang II to the positively biased reservoir yielded multiple transient changes in the ionic current, indicative of translocation of electrophoretically driven peptides.

terms, lysenin channels are molecules with memory, capable of “remembering” the last state they were in. This work demonstrated beyond any doubt that memory in biological systems is not necessarily a function of evolved organs like the brain, but may be achieved at single molecule levels.

Prof Fologea and his team discovered that lysenin, similar to other poreforming toxins, is a great way to create a ‘bio-sensing device’ to study the way molecules move through membranes.

If they pass an electric current through the lysenin channel, that current is affected by any tiny changes caused by molecules passing through the channel.

The team can monitor the current, and watch for these tiny changes, enabling the detection of even a single molecule as it passes through the channel in the membrane. In one of the latest studies Prof Fologea and his team published in 2017, they found that lysenin channels can act as nanosensors, by allowing the hormone angiotensin II to pass through channels when an electric field is applied.

Angiotensin II is a peptide that causes vasoconstriction, the tightening of blood vessels, and a consequent increase in blood pressure. In contrast to other pore-forming proteins that may be used for similar studies, lysenin has the advantage of a large pore, therefore allowing analysis of bigger molecules.

This work is expected to advance our ability to characterise and even sequence important biomolecules such as DNA and proteins. In addition, by endowing the channel with biorecognition elements capable of recognising and binding disease-specific biomarkers in

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Lysenin channels can be used to temporary permeabilise cell membranes. Left panel: Lysenin addition to the solution bathing ATDC5 cells provides access to the cytosol for otherwise non-permeant fluorescent molecules (red color). Right panel: Subsequent addition of chitosan, an irreversible lysenin channel blocker, preserves cell viability as demonstrated by the green fluorescence of the live-cell indicator. In the absence of chitosan, the lysenin-permeabilised cells die within the same time frame.

complex biological fluids, this technique enables early diagnosis of cancer and other diseases.

LYSENIN AS A CONTROLLED NANOVALVE FOR DRUG DELIVERY ‘The remarkable biophysical properties of lysenin channels present a tremendous potential for multiple scientific, technological, and biomedical applications,’ says Prof Fologea. The large pore size may accommodate the passage of large molecules, and the ability to open and close the pores at will is a feature uncommon among pore-forming toxins. To exploit these capabilities, one of the group’s goals is to transport drugs to diseased sites through lipid-made nano-sized carriers mimicking a spherical membrane, and release them by controlling the opening and closing of the lysenin channels inserted into it. Similarly, the channels can be reconstituted directly into live cell membranes and used to

Lysenin, a protein found inside earthworms, might be the key to early diagnosis and treatment of deadly diseases such as cancer transport foreign molecules into and out of the cells. Not only drugs, but genes could also be introduced into cells to manipulate their functionality or correct other deficient genes. Prof Fologea’s group demonstrated that whether or not a molecule can pass through the channels can be controlled by external electric fields, multivalent cations, pH, temperature, and even adenosine triphosphate (ATP), which transports chemical energy within cells. Currently, the team is focused on using X-rays to trigger the release of anti-cancer drugs only at the diseased site, which can be easily targeted with focused ionising

Lysenin channels behave like memory elements and present a strong hysteresis in conductance (measured in nS) when exposed to variable external voltages. Lysenin channels closed by ascending voltages (red line) re-open at lower voltages when the transmembrane voltage decreases (blue line).

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radiation. Such achievement would enable concomitant highly localised radio and chemotherapy while significantly reducing the remote effects associated with systemic chemotherapy.

LYSENIN RESEARCH PROVIDES OPPORTUNITIES FOR MULTIDISCIPLINARY MENTORING AND LEARNING While Prof Fologea and his colleagues are making great strides towards developing cures for diseases like cancer, he also recognises the importance of mentoring future generations of scientists. With this in mind, Prof Fologea dedicates a great amount of his time to mentoring students in the Biomolecular Sciences Graduate Program at Boise State University. ’My affiliation with the Biomolecular Sciences Graduate Program at Boise State University provides unique opportunities for fruitful collaborations with faculty from Biology, Chemistry, Physics, and Engineering,’ he says. ‘The program provides a constant flow of graduate students for which multidisciplinary approaches are crucial for gaining insights into the functionality of transmembrane transporters and developing novel applications.’ In this way, Prof Fologea’s work will continue to greatly impact the field long after he stops undertaking his own research.

Behind the Bench Dr Daniel Fologea

E: danielfologea@boisestate.edu T: +1 (208) 426 2664 W: http://physics.boisestate.edu/fologea/

Research Objectives Prof Fologea’s work aims to discover more detail on the functionality of lysenin channels.

Funding • National Science Foundation • National Aeronautics and Space Administration • Idaho State Board of Education Collaborators • Dr Greg Salamo and Dr Ralph Henry, University of Arkansas

Q&A

You studied physics and biophysics, why did you choose to go into research about cell membranes?

The cell membrane plays a fundamental role in the functionality of any cell, beyond the obvious function as a physical barrier between the interior of the cells and their external environment.

The cell membrane participates in crucial physiological functions such as nutrition, controlled transport of ions and molecules, creating and maintaining electrical and chemical gradients, communication, information storage, and many others. Any attempt to produce an artificial cell must start by creating the membrane and replicating its functions. The cell membrane is one of those organelles for which a complete understanding of functionality requires a truly multidisciplinary approach.

Your research has a broad remit. How do you decide what each of your students studies and what you will focus on next?

That is always the student’s decision.

Each student joining my group comes with a certain background, knowledge, skills, and dreams. The research focus of their choice must appeal to their background, challenge them to advance in their discipline, and motivate them to embrace multidisciplinary approaches.

•D r David Pink, St. Francis Xavier University • Dr Robert Woodburn, Provena St. Mary Hospital • Dr Charles Hanna, Dr Denise Wingett, Dr Juliette Tinker, and Dr Julie Oxford, Boise State University

His research is focused on membrane biophysics with a special emphasis on using transmembrane transporters as single molecule sensors, bioelectronics elements, and for controlled transport across artificial and natural membranes.

Bio Dr Daniel Fologea is an associate professor of Biophysics with the Department of Physics and the Biomolecular Sciences Graduate Program at Boise State University.

He graduated with a PhD in Biophysics from the University of Bucharest in Romania.

Contact Daniel Fologea, PhD Physics Department Boise State University 1910 University Drive Boise, ID 83725-1570 USA

Their future plans are important as well.

Students interested in biomedical studies are more prone to focus on developing novel approaches for diagnosis or drug delivery, students from Math and Physics are more interested in developing quantitative models of biological functionality, while students from Biology are more inclined towards physiological insights from a multidisciplinary perspective.

With regards to graduates, they are required to demonstrate excellent knowledge of Biology, Chemistry, Physics, and Math as a condition for admission into our graduate program.

What kind of interdisciplinary backgrounds do your students, whether they are undergraduates, PhD students or post-docs, have? Is experience in both physics and biology a must?

Biophysics is interdisciplinary by definition, therefore advanced knowledge from Physics and Biology is a must for advancing the field. However, this is not a requirement for undergraduate students interested in starting their research career in my lab. Nonetheless, all the undergraduate students who have worked in my lab ended up taking relevant classes outside their home department, which demonstrates a strong motivation for gaining multidisciplinary knowledge and skills.

To what extent do you have to develop new experimental tools and equipment to go alongside your research?

Sometimes we are unable to purchase what is required for our investigations because what is available does not satisfy our needs. Many of our small tools and devices are homemade, and the students bring great contributions to such developments. I can say that many devices, tools, and software packages developed by our students are outperforming their commercially available counterparts with respect to fulfilling our needs.

What is the ultimate goal for your research, in your own personal opinion?

If the results of my research will improve someone else’s life, I shall consider my research goal achieved.

Through his mentoring activities, Prof Fologea’s work will continue to greatly impact the field long after he stops undertaking his own research

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Physical Sciences ︱ Dr Hugo Christenson

CRYSTAL CLEAR: how topography affects crystal formation Dr Hugo Christenson is a Reader in the Molecular and Nanoscale Physics Group at the University of Leeds. His present research interests lie in crystallisation – an important process across multiple areas of science. Specifically, Dr Christenson’s work provides in-depth insight into why crystals first form in topographical defects, like cracks and crevices.

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ave you ever sat on a park bench on a frosty cold morning? Did you notice that the ice crystals seem to form first on the chipped parts of the surface? Did you wonder why?

The answer to this observation has been the topic of extensive scientific research.

Ice is the crystallised form of water and crystallisation is an important process in nature and industry. It is an intricate part of subjects as wide-ranging as geology, meteorology, materials science and medicine and many technological advances apply crystallisation processes.

Understanding this naturally occurring phenomenon allows better control of the process and more efficient uses of its end product. The fundamentals

of crystallisation and the environmental conditions that promote crystal growth are therefore of great interest.

It has long been known that crystal nucleation (the first process in the formation of a crystal) almost always occurs on a surface. For example, ice crystals in cirrus clouds in the upper atmosphere will form on a small aerosol particle rather than in the air itself.

However, the physical and chemical properties of surfaces that are conducive to crystal nucleation are still not clearly understood. Dr Christenson’s recent work seeks a clearer “picture” of the underlying topographical properties that promote nucleation.

Figure 1. Typical images of mica surfaces showing nucleation density of (a) neo-C5OH crystals on unscratched mica and on (b) mica scratched with 10 nm diamond powder.

START THE TRANSFORMATION When a substance transforms from one form of matter to another, like water (a liquid) changing to ice (a solid), it goes through a phase change. Nucleation is the initial process of the phase change that progresses to crystallisation.

When molecules self-assemble in an ordered structure they become what we generally refer to as crystals.

Crystal nucleation can happen from solution, from vapour, or from liquid. Dr Christenson’s research has concentrated on heterogeneous nucleation, which occurs when a particular surface assists the process.

Dr Christenson has extensively studied various aspects of phase change dynamics, investigating what variables affect crystal nucleation. Drawing on the Classical Nucleation Theory (CNT),

substances [neo-pentanol (neo-C5OH) and carbon tetrabromide (CBr4)] was studied on flat surfaces of glass and mica using optical microscopy. They were also studied on identical surfaces that had been scratched with diamond powders.1 The particle size of these diamond powders can be carefully chosen, giving experimental control over the size of the grooves on the surface and allowing the team to look at the effect a change in size has. The scratched surfaces were then imaged via scanning electron microscopy (SEM).

The results from this experiment clearly demonstrated that nucleation increased on the scratched surfaces (see Figure 1). Induction time, which is measured from first exposure to the vapour to the first appearance of a crystal visible in the microscope, was also studied. The induction times on unscratched glass

Understanding crystallisation allows better control of the process and more efficient uses of its end product which describes how physical attributes, such as defects or crevices on a surface, foster nucleation, Dr Christenson devised several experiments to study precisely the effect of these physical features. His research associate Dr James Campbell has contributed significantly to the design of the experiments and carried out most of the experimental work.

CONTROLLING THE SURFACE DEFECTS Dr Christenson designed a test to investigate the idea that defects on a surface could help control crystal nucleation. For this experiment, the nucleation from vapour of two organic

and mica were similar. However, the induction time significantly decreases when the surface is scratched and, the larger the particle diameter (and therefore the larger the defect), the quicker the crystallisation occurs.

The effects were more pronounced on mica, probably because the scratching gives rise to a greater number of very small and sharply acute topographical features, whereas on glass the grooves tended to be less deep and more rounded in form.

NATURALLY PRESENT DEFECTS In an alternative experiment to investigate the same problem,

Dr Christenson and his team studied nucleation of four different crystals (carbon tetrabromide, camphor, norbornane, and hexachloroethane) from vapour on mica. Instead of manufacturing surface features, naturally present defects on the mica surface were studied.2 These natural defects are much easier to characterise than most manufactured features.

Repeat experiments were performed to identify the best nucleation sites on each surface. SEM could then be used to image and characterise these favourable sites.

All four compounds were allowed to nucleate repeatedly on a number of mica substrates. All four were seen to nucleate preferentially on the same types of sites which were typically characterised by an acute wedge geometry. Figure 2 shows crystals of carbon tetrabromide growing in naturally occurring defects on mica.

DEEP POCKETS In a third experiment, the formation of ice and organic crystals were observed in mica.3 Well-defined topographical features with sharp acute wedges, referred to as “pockets,” which naturally occur when Muscovite

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Figure 2 (above). Optical microscopy images of typical defects on a cleaved mica surface (a) and with crystals of carbon tetrabromide growing from vapour in the defects (b).

Figure 3. Optical micrographs showing crystals of various compounds crystallising inside pockets and from the two corners of one or more mica pockets.

mica is cleaved, were studied. Optical microscopy was used to characterise (describe) the geometry of the surface as well as image the nucleation sites.

The results of this experiment showed that crystals were more likely to form inside and from the corners of these “pockets”. Figure 3 depicts the images of various compounds crystallising in the mica pockets. Often, the crystals are seen to form in supercooled liquid which first condenses in the pockets.

Although the defect features prepared on the mica surface for this test were in the order of micrometres in size it can be inferred that the nucleation would be attracted to the acute crevices even in naturally occurring or manufactured nano-scale sites.

ALL BECOMES CLEAR Using three different experimental approaches, Dr Christenson has demonstrated the dependency of nucleation on surface defects. In agreement with CNT expectations, the cracks on a surface reduce the height of the energy barrier to nucleation. In simple terms, these cracks allow molecules to congregate for longer than they would be able to on a flat surface, increasing the likelihood that they will nucleate.

The results from Dr Christenson’s work show that mechanically produced surface defects can increase both the rate and density of crystal formation.

Dr Christenson’s research has now extended to include crystal nucleation

The results from Dr Christenson’s work show that surface defects can increase both the rate and density of crystal formation

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from solutions and pure liquids with results that correspond to his work on vapours. This has increased our basic understanding of how crystals form.

Importantly though, it also suggests that the engineering of nanoscale topographical features has real potential for control of heterogeneous nucleation, although this remains a significant challenge. Careful implementation of crystallisation techniques would allow for applications in industry (e.g., chemical vapour deposition) and medical diagnostics (e.g., understanding how kidney stones form) among others.

References 1 J. L. Holbrough, J. M. Campbell, F. C. Meldrum and H. K. Christenson, Cryst.

Growth Des. 12, 750-755 (2012).

2 J. M. Campbell, F. C. Meldrum and H. K. Christenson, Cryst. Growth Des. 13, 1915–1925 (2013).

3 J. M. Campbell, F. C. Meldrum and H. K. Christenson. Proc. Natl. Acad. Sci. USA, 114, 810-815 (2017).

Behind the Bench Dr Hugo Christenson

E: h.k.christenson@leeds.ac.uk T: +44 (0) 113 343 3879 W: http://www1.mnp.leeds.ac.uk/hchristenson/

Research Objectives Dr Christenson’s work focuses on showing that crystals initially form on small surface defects and proving why this is so.

Funding The Leverhulme Trust Collaborators Dr Christenson would like to acknowledge invaluable discussions with and input from Dr Richard Sear from the Department of Physics, University of Surrey, over many years.

Q&A

Defects on surfaces are physical changes. How does chemical change on a surface promote nucleation?

This is a much-debated question. In the case of nonpolar substances like norbornane and other hydrocarbons, surface chemistry is unlikely to be important. It is a different matter in the case of water, or ionic compounds like calcium carbonate and calcium phosphate, both important biominerals. Particularly ice nucleation, both from vapour and from liquid water, is often discussed in terms of “lattice matching”, meaning that there is a correspondence between the positions of water molecules on the surface of the ice crystal and those of surface atoms on the substrate surface. Also, it has been shown that many organic crystals with hydroxyl groups on the surface are particularly good at nucleating ice from water vapour (a surprising example is testosterone!), but it is notable that the ice crystals are often seen to form in surface cracks on these crystals.

Perhaps a synergistic effect of surface chemistry and topography?

In addition: • Fiona Meldrum (Chemistry, Leeds) • Tamas Kovacs, Jack Holbrough, James Campbell and Angela Bejarano-Villafuerte (Physics, Leeds) • Mark Holden (Chemistry and Earth and Environment, Leeds), Ben Murray and Tom Whale (Earth and Environment, Leeds) Bio Hugo Christenson is Reader in the School of Physics and Astronomy at the University of Leeds. He received his PhD from the Australian National University, where he spent 20 years

This is a very important question, and one that we wish to explore in more detail in the near future.

Is high resolution imaging the most critical limiting technology in determining whether direct nucleation from vapour or the 2-step crystal nucleation takes precedence?

Yes, I think so. One can use light microscopy or interferometric techniques, which are both limited by the resolution of light – of the order of one micron. Various more sophisticated optical techniques can improve slightly upon this. There is also environmental scanning electron microscopy, which allows imaging in dilute vapour, but the resolution is limited and we have not found it better than optical microscopy.

If the nucleation process is reversed, is it expected to follow the same path in reverse? For example, as ice melted, would it stay frozen for longer in the areas where the initial crystal formed?

Short answer is no, there should be no connection.

doing experimental research on surface forces and phase behaviour in confinement. He is now working on nucleation and crystal growth, particularly on surfaces and in confinement.

Contact Dr Hugo Christenson E. C. Stoner Building 8.36 School of Physics and Astronomy University of Leeds LS2 9JT UK

What do you enjoy most about this area of your research?

It is the beauty and variety of the crystalline structures that you can see with your own eyes, albeit often with the help of a microscope. It is also the thought of how order and symmetry are created almost instantaneously as a crystal grows from a disordered liquid or gaseous phase. Crystallisation is a truly amazing phenomenon.

Would it be possible to spray a diamond-like particle into the atmosphere to induce rain on command to stall a cricket match?

Silver iodide has been extensively studied as a cloud-seeding agent to induce precipitation. The results of large-scale trials have been mixed.

See http://cen.acs.org/articles/94/i22/ Does-cloud-seeding-really-work.html.

I have not heard of diamond being used.

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Physical Sciences ︱ Professor James Windmill

From ears to engineering M Sometimes the solutions to engineering questions have already been answered – by animals! Rather than ‘reinvent the wheel,’ therefore, Professor James Windmill and his lab team at the University of Strathclyde choose to learn from some of the remarkable feats of engineering found in the natural world. In particular, his research focuses on using ideas from insect hearing to develop new microphones and transducers for use in fields as wide-ranging as medicine and materials science.

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odern microphones, such as those used in hearing aids, and transducers such as ultrasound scanners, are remarkably sensitive.

However, they still struggle to deal with issues such as background noise, which may need to be removed by downstream digital processing, or identifying the direction from which a sound originates.

Electronics engineer Prof Windmill’s highly multi-disciplinary team provide solutions to these problems, taking their inspiration from the natural world, in particular the insects.

INSPIRING INSECTS With about a million species known

to science, insects are an extremely varied group of organisms, and have evolved a diverse array of different hearing organs. Previous research into insect hearing has largely focused on the noisiest groups: the grasshoppers, crickets, locusts, and cicadas; however, Prof Windmill’s research covers a wide range of other insects including flies and moths. In the course of their work, Prof Windmill and colleagues have discovered some remarkable insects, including a moth, the greater wax moth, with the ability to hear sounds up to 300 kilohertz, higher than any other animal; the insect with the highest frequency call – a genus of katydid dubbed

waves) and transducers (instruments that can both generate and sense sound – such as are used in hospital ultrasound scanners) based on these findings.

Comparing their experimental data with the computer models gives the researchers a thorough understanding of how the organism’s hearing works ‘Supersonus,’ from the South American rainforest; and the loudest (relative to its size) animal on earth – a water boatman that generates a mating call by rubbing its penis against its abdomen.

To elucidate the mechanisms of hearing in an insect, Prof Windmill’s lab use an array of techniques, including behavioural observation, microscopy and X-ray microtomography, 3D laser vibrometry, and electrical examination of the signals passing through the auditory nerve. The results are translated into a three-dimensional

computer model of the ear’s structure, which can then be used to simulate how it responds to sound. Comparing their experimental data with the computer models gives the researchers a thorough understanding of how the organism’s hearing works – both in terms of its mechanics, and downstream signal processing at the neural level.

Then, the baton is passed to the engineers, physicists, mathematicians and material scientists of the team who develop new microphones (instruments for sensing acoustic and ultrasonic

NAVIGATING BY SOUND While larger animals can detect the direction of a sound source by the difference in timing and amplitude as sound waves are received at each of their two ears, for smaller animals such as insects, the distance between their two hearing organs is likely too small for this to work. Thus, smaller organisms have come up with a variety of innovative techniques that are now coming to the interest of engineers.

Ormia ochracea is a tiny, nocturnal fly which lays its eggs on crickets.

It therefore needs to locate its cricket hosts in the dark, which it does by the sound of the male cricket’s mating call.

Since the mid-nineties, it has been known that the Ormia’s two tympanic membranes (ear drums) which are located around the base of their front legs, are directly coupled to each other by a strut.

In effect, the structure forms a tiny, highly sensitive see-saw which rocks if the sound waves reaching the two tympanic membranes are in any way different in intensity or timing. This ingenious system amplifies minute differences in sound reaching the two membranes, enabling the insect to detect the direction a sound is coming from.

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MEMS directional microphone in a 3D-printed housing (UK five-pence coin for scale)

Left: Multi-band silicon piezoelectric MEMS directional microphone inspired by Ormia ochracea

A hearing aid could focus on the frequency range of human speech and fade out the ‘noise’ from other sources In Prof Windmill’s lab, their threedimensional computer models and simulations of the Ormia system have been used to develop tiny acoustic sensors for use in hearing aids. Until recently, the sensors were built from silicon using standard Microelectromechanical Systems (MEMS, or ‘micromachine’) techniques – but now the team are moving into the realm of 3D-printing. This is enabling them to more easily design complex three-dimensional structures and to use more flexible materials, simulating more closely the mechanical properties of biological structures.

More recently, Prof Windmill, with colleagues from the Université François Rabelais de Tours, France, has identified a tiny moth, Achroia grisella, the lesser wax moth, which is able to determine the directionality of sound with just one ear, which has a maximum response to sound arising from a particular angle. These moths

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then use their behaviour – scanning with their head to search for the source of a sound, and then maintaining the same angle between themselves and the sound as they move – to locate their singing partners for mating.

BLOCKING OUT THE NOISE In fact, it is in the butterflies and moths (Lepidoptera) that the greatest number of ‘acoustic’ insects are found. Around 55% of Lepidoptera have tympanal ears, and many use ultrasound for mating.

To enable them to hone in on the mating call of their own species, these moths are able to physically adapt the response of their eardrums to focus on particular frequencies of sound.

There are many situations in which this property could be useful: for instance, a hearing aid could focus on the frequency range of human speech and fade out the ‘noise’ from other sources. Like the Lepidoptera, our own ears, and those of many animals, do this

automatically through a feedback system – the nature of the sounds heard changes the response of the ear. Until now, however, engineered microphones have relied on downstream digital processing of all the sound signals received, which can cause time delays as well as using energy and increasing the total size of the microphone system.

Now Prof Windmill’s team, after studying the hearing system of the large yellow underwing (Noctua pronuba), have developed a MEMS microphone which can adapt its sensitivity to different frequencies depending on the sound received. This may be particularly good news to users of hearing aids or cochlear implants who struggle with background noise. Thanks to Prof Windmill’s multidisciplinary team and the combination of fundamental biology with applied engineering, the amazing adaptations of the insect world could be coming to a microphone near you.

Behind the Bench Professor James Windmill E: james.windmill@strath.ac.uk T: +44 (0)141 548 2694 W: http://www.cue.ac.uk W: http://www.strath.ac.uk/staff/windmilljamesdr/ W: http://www.sasatin.eu

Research Objectives Prof Windmill’s research focuses on the investigation of hearing systems in insects to inspire the development of new acoustic and ultrasonic sensors and systems. He is also interested in sustainable engineering through the process of remanufacturing, the development of new biomedical sensors, and the use of ultrasound in manufacturing.

Funding European Research Council - https://erc. europa.eu/

Q&A

How did you first become aware of the potential of biological systems to inform engineering questions?

My background is electronic engineering, which led to a PhD that involved sensing at the nanoscale. I wanted to do something a little different following my PhD, and that led me to biological research into insect hearing systems as a postdoctoral researcher. This gave me the opportunity to discover just how many different hearing systems there are in the insect world. I went back into an engineering department as an academic, but I wanted to continue biological research as well as develop my engineering work. So the natural thing to do was to bring the two together.

What techniques do you use to study such tiny organisms?

We use a variety of microscopy techniques to study their morphology, including optical and scanning electron microscopy, and more recently X-ray 3D microtomography. We use electrophysiological techniques to measure auditory nerve signals, and have also worked with colleagues to study the behaviour of some insects. We use a 3D microscanning laser Doppler vibrometer to measure how things move, i.e., how does an insect eardrum

Collaborators •D r Fernando Montealegre-Z, University of Lincoln, UK • Dr Jerome Sueur, Muséum national d’Histoire naturelle de Paris, France • Prof Michael Greenfield, Université François-Rabelais, Tours, France Bio Prof James Windmill is a Professor of Electronic and Electrical Engineering at the University of Strathclyde. He gained a PhD in nanotechnology from the University of Plymouth (UK) in 2002, and then worked as a researcher on insect auditory systems at the School of Biological Sciences, University

move in response to sound. We need the vibrometer because the insect hearing systems usually move only tiny amounts, typically nanometers or less. Finally, we tie this all together using powerful computer modelling to explore and explain how these auditory systems function.

What is your favorite or most exciting biological discovery so far?

My favourite is the discovery of travelling waves on the tympanal membrane (eardrum) of the locust. This was my first discovery, and led to my first biological sciences paper. The waves appear on one side of the eardrum, and then their direction and the point they stop moving changes depending on the sound frequency. This allows the locust to distinguish different frequencies, and is very similar to how the basilar membrane in the human inner ear works. But the locust was doing this all on the eardrum. This led me to realise that there could be many interesting insect hearing systems phenomena that we could use to inspire engineering.

What impact do you think the advent of 3D printing will have on this kind of research?

The main impact is speed for the researcher.

A device can be computer designed, 3D printed, then tested and characterised in hours, or at the most a few days. Working with standard silicon microfabrication, particularly for smaller labs and institutions,

of Bristol (UK), from 2003 to 2008. He joined the University of Strathclyde as a lecturer in 2008. He is an academic member of the Centre for Ultrasonic Engineering at Strathclyde, and has featured in more than 50 journal publications. He is also the managing editor of the Journal of Remanufacturing (Springer).

Contact Prof James Windmill Electronic and Electrical Engineering Royal College Building University of Strathclyde 204 George St, Glasgow G1 1XW UK

can stretch this process out to months.

So, 3D printing provides a research team with many iterations in the same time that standard microsystem fabrication provides just one. But there are some notes of caution. 3D printing has many challenges as there are many things it’s difficult to do with this technology.

And, standard microsystem fabrication is very easy to scale up to produce millions of the same unit, while generally 3D printing isn’t.

What benefits and challenges are there from working in such an interdisciplinary team?

The major benefits are that researchers not only bring different skills and expertise, but have been trained to think and utilise different scientific methods.

For example, biologists may want to explore something that already exists in nature, and engineers are used to creating something to solve a problem.

Add to this physicists, mathematicians and materials scientists, and the mix can produce very intriguing ideas.

Of course, it can be very challenging, as you must ensure that everyone has some understanding of what the others are doing, why, and also how. But the experience is then a great positive, as the researchers can use what they’ve learnt from others in their own work.

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Physical Sciences ︱ Dr Long Tran-Thanh

Building artificial intelli Artificial intelligence is one of the most disruptive technologies nowadays and as such is considered both an opportunity and a threat to society. On the one hand, it could make us vulnerable as we trust machines to make more and more decisions that so far have been reserved for humans. On the other hand, it has the potential to revolutionise large-scale energy management, traffic control, the job market, and countless other areas of our economy. For this reason, Dr Long Tran-Thanh, a Lecturer at Southampton University, aims to harness AI to solve the most important societal challenges of our age.

A

s artificial intelligence becomes more and more ubiquitous, we need to learn how to live and interact with it. And of course, this goes both ways: AI systems also need to learn how to interact with humans, and take their preferences or choices into account.

Dr Long Tran-Thanh calls this making AI more “human-aware” – something that so far has not been fully exploited. Often, AI researchers will design a beautifully efficient and rational digital system, only for it to fail when faced with the unpredictability of its human users.

Dr Tran-Thanh wants to change this and develop AI platforms that can be used to tackle some of society’s biggest problems. He wants AI to take into account that human users are not perfectly efficient nor perfectly rational, that we are creatures of habit and are often stubbornly stuck in our ways.

SMOOTHING OUT THE ENERGY PEAKS One of the first attempts he made at making this vision a reality was a home energy management system. The main

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igence for social good issue with operating a nationwide electricity grid is that the demand for energy varies throughout the day: there are peaks and troughs all the time. For the supplier, this translates into keeping so-called “peak plants” up and running at all times just in case there is a sudden peak in energy consumption. In practice, such plants are rarely used but need to be manned and supplied with fuel nonetheless which leads to increased costs and greenhouse gas emissions.

One possible way of dealing with this is smoothing those peaks out by convincing people to change their energy consumption habits. To quantify the problem, a team of researchers at Massachusetts Institute of Technology fitted a few households with sensors monitoring the energy consumption of every home appliance. After that, numerous other teams tried to unleash AI

– and come up with the most efficient energy consumption plan within such derived constraints. However, another issue quickly came to light. People, bombarded every day with hundreds of incoming emails, phone calls and social media notifications didn’t want to be bothered by yet another set of queries eating up their time and attention.

INNOVATIVE AI DESIGN This is where Dr Tran-Thanh’s innovation shone out. His AI was programmed to do as much as possible on its own, and query the user only when necessary.

To achieve this, Dr Tran-Thanh’s team had their algorithm take into account the “bother cost”, which reflected the increasing annoyance caused by asking questions. The result was a system designed to take preferences into account and maximise energy efficiency while minimising the “bother cost” at the same

Dealing with traffic management in a big city like Singapore or London is crucial – make one mistake and you cause instant mayhem on the gathered data to find the most efficient ways of reducing energy costs in homes. But it quickly transpired that algorithms which had been super-efficient in simulations, proved nearly useless in the real world. The reason was simple – people rejected their recommendations as incompatible with their daily routines.

If you have been doing your laundry on Saturday afternoon all your life, it will take more than a machine’s recommendation to reschedule for 3am on Tuesday.

Dr Tran-Thanh and his team then thought about a system that would simply ask users about their preferences – for example, “Would you mind turning your kettle on an hour later on Wednesdays?”

time. And it worked. Overall, it has managed to reduce the participating households’ energy consumption by 35%.

In the not-so-distant future, Dr TranThanh’s AI will be implemented in Schoonschip, an experimental floating neighbourhood in Amsterdam.

There were a few other projects where Dr Tran-Thanh’s team sought to apply their human-aware AI idea. One of them was built to cost-efficiently assign tasks to workers, each with his or her own hourly rate and skill level, hired through expert crowdsourcing platforms. Another dealt with applying AI to fight drug trafficking and other situations where networks needed to defend themselves

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against adapting and malicious adversaries. This combined experience allowed Dr Tran-Thanh and his colleagues to take on one of the biggest challenges facing developed countries – traffic management.

INTELLIGENT TRAFFIC CONTROL Thousands of sensors measuring traffic are fitted along streets and avenues to provide real-time data about how many cars drive past them and how quickly.

This data is then transferred to data centres and processed by AI algorithms making decisions about managing the traffic lights all over the area. Solutions much like the one used in Dr Tran-Thanh’s home energy management system will keep human operators in the loop without overloading them with information and systems resembling those Dr Tran-Thanh designed to tackle drug trafficking will protect the network from cyber attacks.

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It turned out algorithms that had been super-efficient in simulations proved nearly useless in real world applications What makes this project stand out is the huge consequences of a potential failure.

Bad design in a home energy management system, or even letting a drug trafficker escape, causes a relatively small-scale, local problem. But dealing with traffic management in a big city like Singapore or London is different – make one mistake and you cause instant mayhem. That’s why there are numerous teams working on different aspects of the AI system being built to take on this challenge. Professor Nicholas R. Jennings, a vice-provost at Imperial College London leads a team responsible for the system’s cyber security and Dr Bo An, Nanyang

Assistant Professor at NTU Singapore, is working on the game theory approach to eventual attacks. Dr Tran-Thanh’s team is responsible for making algorithms which can recognise patterns in the vast amounts of traffic data generated by the sensors. Making an enterprise this huge a reality will take years. But with people like Professor Jennings, Dr Bo An, and Dr Tran-Thanh in charge, we can rest assured we will be well taken care of.

Behind the Bench Dr Long Tran-Thanh

E: ltt08r@ecs.soton.ac.uk T: +1 442380593715 W: https://www.ecs.soton.ac.uk/people/ltt1m09

Research Objectives Professor Tran-Thanh develops AI algorithms aimed at tackling societal problems and his work focuses on increasing security for AI. Funding EPSRC (EP/N02026X/1) Collaborators • Professor Nicholas R. Jennings (viceprovost of Imperial College London) • Professor Alex Rogers (Oxford University) • Professor Milind Tambe (University of Southern California Center for Artificial Intelligence in Society) • Dr Sebastian Stein and Dr Sarvapali D. Ramchurn (University of Southampton)

Q&A

How much more efficient will traffic control get once the system you’re working on is implemented?

Our system makes the smart traffic control more secure against malicious and adversarial behaviour, while keeping the traffic control efficiency at the same level (i.e., we protect the traffic system without compromising on its quality).

What are the possible consequences of a successful cyber attack carried out against the traffic management system?

A possible consequence is that terrorists can take over the traffic control system and create chaos, significantly increasing the casualty tally in case of a terrorist attack. Another example is a heist, in which the robbers, by being able to control the traffic system, will block the routes of the police while freeing up their escape

• Dr Henry Ngoc Cuong Truong (SenseEye) and Dr Tim Baarslag (CWI Amsterdam) • Dr Bo An (Nanyang Assistant Professor at NTU Singapore) • Dr Vinh Thong Ta (University of Central Lancashire) • Dr Matteo Venanzi, Dr Valentin Robu, Dr The Anh Han, Dr Avi Rosenfeld, Dr Trung Dong Huynh, Dr Michael Kaisers, Dr Marcin Waniek, Haifeng Xu Bio Long Tran-Thanh is a Lecturer (Assistant Professor equivalent) at the University of Southampton, UK. He obtained his PhD in Computer Science in 2012 at the same university, under the supervision of Nick Jennings and route (see, for example, the Ocean’s 11 movie).

How is your AI for home energy management system going to work at Schoonschip?

We are planning to continue our collaboration with Kaiser’s team at CWI to run a set of experiments at Schoonschip to collect data about different user behaviours. Once we have this data, we will be able to model these behaviours and fine-tune our energy management system against these models. Once this is done we aim to deploy the system in these real homes.

How do algorithms like yours help fight drug trafficking and what are the results so far?

This is still in a theoretical research stage.

However, in the (near) future, we aim to introduce our results to the appropriate authorities to initiate a collaboration with them in order to deploy our algorithm in real life.

Alex Rogers. He has been conducting active research in a number of key areas of Artificial Intelligence. His results have been published at top AI conferences and journals and he has received a number of prestigious awards.

Contact Dr Long Tran-Thanh University of Southampton University Road Southampton SO17 1BJ United Kingdom

To what extent do you want to incorporate affective computing in your “human-aware” AIs and do you think they should take into account users’ emotional states, such as asking questions when they are less stressed or angry?

Affective computing is definitely an important tool in order to achieve efficient human-aware AI. In the future, I am planning to incorporate it into my research. I am working closely with Dr Klaus-Peter Zautner (bio-inspired robotics) and Dr Hedwig Eisenbarth (psychology), both from Southampton, to combine emotion detection, robotics, and sequential machine learning, to make robots more aware of human annoyance/stress level, so they will know when it is appropriate to approach their human trainers for further guidance and instructions.

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Physical Sciences ︱ Dr Mikel Holcomb

Pushing the boundaries – interrogating magnetism at material interfaces In order to keep improving electronic devices, whether it be computers or sensors, researchers must understand what is going on, on an atomic level.

Understanding the behaviour of ions within materials is difficult enough, but when you put two materials together it gets much more complicated.

Dr Mikel Holcomb, Associate Professor from West Virginia University, has dedicated her work to finding out exactly what happens at these boundaries.

M

agnetism is extremely important to our everyday lives. Without it, we would not have computers, credit cards, or the inevitable fridge magnets, to name a few. But our understanding of magnetism remains limited. When a material that is normally magnetic becomes too thin, or even at the boundary between two different materials, the magnetic properties can be lost – and this area of physics is not very well understood.

Dr Mikel Holcomb, from West Virginia University, has dedicated her career to better understanding magnetism, specifically looking at one interesting class of materials, complex oxides.

A complex oxide is any compound that contains oxygen along with typically at least two other elements. They make up some of the most abundant minerals on Earth, and complex oxides show a huge variety of interesting properties, from superconductivity to dielectrics.

In particular, Dr Holcomb’s group (and many collaborators including Romero, LeBeau, Stanescu and several national facility scientists) has made progress looking into thin films of a particular complex oxide called lanthanum strontium manganite, or LSMO. LSMO is an important material because it has the potential to be used in a variety of applications, including computers and sensors. It exhibits a range of interesting properties, including ferromagnetism – when a material maintains its magnetism even after a magnetic field has been removed. Dr Holcomb has developed and combined new methods to study the interfaces of these thin films, with

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an aim to learn more about magnetism and other types of interface properties.

WHY INTERFACES? In thin films in general, the properties at the boundary of two materials are often extremely different from the bulk of the materials. Many devices use boundaries, which can be the surface of a material – the boundary between it and the air – or the interface between layers of two different materials. This is because many properties like spin, charge, and orbital degrees of freedom, depend on the ions’ surroundings within a material.

While all of these properties can be affected in different ways, they all link together to cause different magnetic effects in a ‘complicated web’ according to Dr Holcomb, who tries to shed light on these effects by measuring as much as possible, to compare all factors.

For example, she examines the different ways strain, thickness of materials and choice of materials can affect the magnetic properties. She uses a variety of methods including X-ray absorption spectroscopy, which uses synchrotron

The lab team: (from left to right) Navid Mottaghi, Justin Bowman, Professor Holcomb, Saeed Yousefi, Rob Trappen, Ghadendra Bhandari, Jonathan Cramer, Shalini Kumari. Not shown: Guerau Cabrera, Chih-Yeh Huang, Madelene Blackwell, Brandon Howard, Liam Mcgoldrick, Troy Williams, Viraat Das.

When a material that is normally magnetic becomes too thin, or even at the boundary between two different materials, the magnetic properties can be lost radiation to excite core electrons, to probe the inner structure of the materials. Dr Holcomb’s group combines this kind of technique with others like neutron reflectivity – which uses the reflection of neutrons (at the National Institute of Standards and Technology, NIST) to determine the strength and direction of the magnetism at every layer of the material.

FERROELECTRIC AND FERROMAGNETIC MATERIALS In recent years, Dr Holcomb and her team have studied what happens when LSMO, a ferromagnetic material, is placed adjacent to a ferroelectric layer. Ferroelectric materials can

become electrically polarised, with one side positively charged and the other negatively, which can switch under an electric field. When placing a thin film of LSMO on this kind of material, Dr Holcomb discovered some curious properties.

At the interface between ferroelectric and ferromagnetic materials, something called magnetoelectric coupling occurs.

This means there is a link between the magnetic and electric properties of the material. For example, the magnetic properties of LSMO thin films with a layer of lead zirconate titanate (PZT) on top can be controlled by the presence of an external electric field.

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Surface Thin film Interface

Starting material or underlying layer

Electrical control of magnetism could revolutionise computing (and other devices) by removing the constant need for current in transistors.

By varying the thickness of the LSMO film, Dr Holcomb and her team found that the thicker the layers of LSMO and PZT, the higher the valence (the capacity of the ion to combine with others) of manganese ions within the LSMO. The valence of these ions is linked to the magnetic properties of LSMO, and understanding what affects it can help to create more efficient devices in the future.

The properties of materials can be very different at their boundaries compared to the bulk of the material. A boundary can be an interface between two materials or the surface where the material meets the air.

especially when the data about each material is not always readily available.

Dr Holcomb and her team are in the process of developing a unique kind

but we’d like to expand it to include others’ samples’, says Dr Holcomb.

‘We are probably going to pull a lot from published literature, but that takes a lot of time and people don’t publish all data on a sample.

The more help we can get from others, the better.’

Dr Holcomb’s vision for the database is that anyone using it will be able to plot various properties of a material and see how they change for a variety of samples that meet a given search criterion.

Everything from the dependence of magnetism with temperature to the chemical spectrum could be included.

‘I’ve seen something similar done for simple semiconductors, but I’ve not seen it for complex oxides,’ she says.

Dr Holcomb examines the different ways strain, thickness of materials and the conditions under which materials are grown can affect the magnetic and other properties

A MATERIALS DATABASE Although Dr Holcomb has focussed much of her work on LSMO, there are a huge number of materials that exhibit interesting properties on their own and at the interface with other materials. Because of this, keeping on top of the possibilities is a difficult task,

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of database that will give researchers a simple way to compare different materials, using machine learning.

At the moment, the database focuses only on the materials the group’s expertise lies with, like LSMO, but they are hopeful they can expand it to include many others. To do this, however, they will need the help of colleagues who will eventually benefit from the database. ‘Our database currently includes our own samples,

Behind the Bench Dr Mikel “Micky” Holcomb

E: mikel.holcomb@mail.wvu.edu T: +1 304 293 5196 W: http://holcombphysics.wixsite.com/home Research Objectives Dr Holcomb’s work focuses on the properties of the boundaries of two materials. These are often very different to the properties of the bulk of the material and Dr Holcomb aims to develop methods for studying the boundaries specifically.

Funding NSF, DOE and American Chemical Society Collaborators • Theorists Aldo Romero, WVU, Tudor Stanescu, WVU, Shaui Dong, Southeast University

Q&A

Why are you interested in the interfaces between materials?

Over time, devices have become smaller and smaller. One advantage of this is that we have smaller and faster computers.

However, materials on the small scale (whether they be thin films or nanoparticles) do not behave the same as their big counterparts. As we approach these small scales, we will need to understand how these interface effects will change the properties of our devices. Nobel Prize winner Herbert Kroemer said in his acceptance speech in 2000 that “the interface is the device”. He might have meant that eventually devices will take advantage of the physics at the interface only when there is no more bulk left.

How thick are these interfaces, is it just one layer of atoms thick or do the layers merge in a more messy way?

It depends on how you make the material; some methods are messier than others.

We grow our films with pulsed laser deposition (PLD) with in-situ measurement that allows us to more easily optimise our film quality. We can observe our layers growing one by one, and our interfaces are very sharp. Molecular beam epitaxy is another method to grow high quality films.

However, these techniques are not the easiest for industry to scale up, so some researchers specialise in other growth methods which have varying quality. It all depends on what researchers do to verify the quality of their growth process.

Why did you choose to focus on LSMO? Lots of reasons. First of all, it is one of the few complex oxides that are ferromagnetic

• National Facility Collaborators Alpha N’Diaye, ALS; Matthew Marcus, ALS; John Freeland, APS; Alex Grutter, NIST; Brian Kirby, NIST

Tolk) and did an internship at IBM Almaden.

While she enjoys collaborating on a variety of topics, her main projects involve magnetic thin films and magnetoelectric heterostructures.

• Others James LeBeau, NCSU; Norman Tolk, Vanderbilt; Ying-Hao Chu, National ChiaoTung University; Alejandro Cabrera, Pontificia Universidad Católica de Chile

Contact Dr Mikel “Micky” Holcomb Associate Professor of Physics, WVU Office: 437 White Hall Mailing Address: Physics Department West Virginia University 135 Wiley Street, PO Box 6315 Morgantown, WV 26506 USA

Bio Dr Mikel “Micky” Holcomb is an Associate Professor of Physics at West Virginia University.

She got her PhD at UC Berkeley (advisor: Ramesh), Bachelors at Vanderbilt (advisor: at room temperature. While I have studied many different kinds of materials, I really enjoy studying those that have their properties at room temperature. First, they are easier to measure because they do not have to be cooled (though their low temperature properties might also be interesting). But, more importantly, it is more likely they can be used in a real device. I also like LSMO because it has been proposed for a lot of different types of technology. So, even if one does not work out, hopefully another will and we will have already started to understand the important physics. LSMO is also just a good model system. It is in a class of complex oxides called perovskites that have a simple structure, even though their physics can be complex.

When scientists try to understand something complex, it can be helpful to start out with something as simple as possible.

How do you decide what parameters you change, e.g. thickness?

For every new material a grower makes, they should optimise their growth process. Ideally, you get a reasonable starting recipe from the literature or a similar material. Then, you have to tweak it. What you tweak depends partly on the growth method. In PLD, the most common variables to adjust are the growth temperature and pressure, but you might also change the laser frequency, fluence, cooling rate or after growth pressure. Sadly, no two chambers seem to be exactly the same, so every recipe has to be optimised if quality is critical. However, all of this tweaking takes a lot of time and money. Everyone has their own standard and this is one of the common things reviewers look out for when reviewing papers.

Where did the idea for the materials database come from?

I was reading an article from WIRED magazine that was talking about using machine learning

to aid in cancer research. The general idea was why not let computers take a crack at solving cancer. There is a ton of data in the field and maybe unbiased computers might pick up on something we are missing, particularly since so many variables affect each other. I realised that a similar argument could be made for the materials I study and many others.

Will people have to pay to use your database once it is up and running?

No, but without help it might take us a long time for it to be very useful. We are eager to partner with people that can help make this a good resource. The initial feature will run like a searchable database. You can input what types of materials you want to search, and various parameters (such as thickness and/or growth details). Then you can plot and compare anything you like that meets your search criteria. It will include information on what lab and/or paper the data comes from, so that you can look that up or reference it if you like. How can you help? We need people for a variety of tasks. 1. Just entering data (either from your own work or pulling from published work). I have trained high school students how to do this so even non-scientists could help. If you know how to automate this process, please let me know! This is the biggest hurdle right now. 2. Helping us create a nice website for people to use. I am a physicist, so it might not surprise you that organised programming that is really easy for anyone to understand and use is not my speciality. 3. Aid in implementing machine learning. There is going to be a LOT of data in this database and a lot of it will be graphs. What will be the best things to have the computers compare? I expect there will be a lot of trial and error in the initial analysis.

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Education & Training︱ Mr Bartlett Sheinberg

The REEMS Programme: discovering untapped talent To many, materials science represents a fairly inaccessible, complicated topic of science requiring a highly academic approach. Mr Bartlett Sheinberg’s Research Experiences and Exploration in Materials Science (REEMS) Programme aims to overcome this – contextualising materials science for community college students. The programme’s approach also aims to instil confidence in these students and provide them with skills to help them progress in their academic careers.

The REEMS programme gives students an opportunity to see first-hand the broad scope of materials science. Academic and career exploration is the key objective

M

aterials science is a topic involved in every facet of life.

From the car you drive to work, to the clay on the white cliffs of Dover, materials are everywhere and have a significant impact on life as we know it.

Understanding the extent of this impact is critical and should be accessible to whomever is interested, regardless of academic background or financial status.

Delivering materials science to seriousminded students is vital not only for developing the next generation of materials scientists and engineers, but for generating a technically prepared workforce. The study of materials provides an academic umbrella under which community college students can appreciate concepts in the physical and biological sciences, engineering and computational science. An introduction to materials provides an important context for appreciating their coursework and generates an invaluable self-confidence as they move forward to complete their undergraduate degree and transition to graduate school or into the technical workforce. It is in this area that Houston Community College’s (HCC) Mr Bartlett Sheinberg, and his increasingly popular REEMS Programme, prevail.

OPENING DOORS This programme – entitled Research Experiences and Exploration in Materials Science (REEMS) – is funded by the Division of Materials Research at the National Science Foundation (NSF) and is aimed

Dr Rafael Verduzco giving a tour of his lab to REEMS participants

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at bridging the gap between community college and university for talented students at HCC who will be transferring primarily into engineering, the physical and biological sciences, and computational analysis.

As Mr Sheinberg describes it himself: “The REEMS programme gives students an opportunity to see first-hand the broad scope of materials science. These experiences combine academic experience with recognition of the roles which materials can play in solving important societal issues and lay the foundation for the identification of interesting and meaningful career opportunities. Academic and career exploration really is the key objective of the REEMS programme. We provide the means for students to take the first steps towards exploring academic pathways and potential careers.”

FINDING THAT SPECIAL SOMETHING Following the programme’s success since its inception in 2015, Mr Sheinberg’s role as mentor, ambassador and principal investigator has become ever more important in identifying ideal candidates.

Each autumn, students are recruited and, through a highly competitive process, are selected for the following year’s summer research experience. During the autumn semester an additional cohort of students is recruited to apply for entry into the seminar series “Impact of Materials on Society” (IMOS). Over the autumn semester, REEMS staff provide a series of seminars on university transfer opportunities, networking opportunities with materials professionals, and oneon-one transfer guidance. The REEMS programme welcomes students across all academic interests and majors.

During the recruitment process, for either the summer research experiences or into the IMOS seminar, students’ grades are an important indicator. However, their attitude towards their study and a demonstrated interest in discovery are critical selection criteria.

REEMS student Raymond McCoy presents his poster from the 2016 REU

“Many students come into my office and say, ‘I really want to do such-and-such’, and one of the things I’ve always tried to do is identify those students who possess that intangible gleam in their eye. One of the objectives of the REEMS programme is to quantify what that gleam in the eye means in terms of their future academic pursuits and their ability to appreciate the opportunities which the REEMS programme provides as they consider their futures.”

THE IMPORTANCE OF DIVERSITY HCC is an open admission institution which provides students with a cost-effective education during their time at Houston Community College and supplies a second chance for those students to prove themselves academically, as well as the opportunity to enhance their maturity level, so that they can succeed in their upper division work. Community colleges, across the United States, are home to a highly diverse population of individuals from different nationalities, backgrounds and situations. Many of these students do

The programme forced me to become a better, more vigorous student and, although I found it hard at first, I truly appreciate what it, and Dr Sheinberg, has done for me

REEMS students at the West Houston Center with staff members Dr Yibran Pereramercado and Dr Gizelle Davis – they are working on the scanning electron microscope, on loan for the REEMS Programme from JEOL, USA

not realise their own potential talent and abilities – REEMS provides that opportunity.

Because of this, Mr Sheinberg offers an individual approach to interviewing each REEMS applicant to ensure that there will be a demonstrated mutual benefit for the student and opportunities provided by the programme. He said: “Applicants might have a great academic background and our selection of students is based upon why they want to become involved in the REEMS programme and what their expectations are from it. I like to make sure that there is an overlap between what the programme can offer, and what the student hopes to take out of it.

IMPACT OF MATERIALS ON SOCIETY During the spring term, the IMOS seminar provides a significant emphasis on contextualising and teaching students about the impacts of materials on society. This includes “broadening students’ horizons” in terms of how materials have shaped cultures, geo-politics and technology advances over the past three to four thousand years.

“At HCC, you have a population of roughly one third African-Americans, one third Hispanics and the final third made up of both Caucasians and Asians. Funding agencies, universities and employers are interested in looking at students who originate from diverse cultures, are highly motivated and have demonstrated a strong work ethic. REEMS plays a role in identifying these talented students.”

He said: “As an example, IMOS begins by exploring the cultural aspects of clay and the impact of it on cultures, and the evolution of the material to include superconductive materials. It’s interesting to see how the transition changes student perceptions as we explore both technology, cultural developments and impacts.

“One of the results of this seminar is that students start to ask themselves: if I want to have a career in science, engineering or even materials research, what impact can I have on society as an engineer or a scientist?

How am I going to impact society? What problems can I solve? The identification of societal problems and challenges and a realisation of the importance of materials science in solving those challenges is one of the key objectives of the seminar series.”

For Dr Megan Robertson at the University of Houston, one of REEMS’ partner institutions, having this diversity is a real benefit. She said: “My university has a significant number of students who transfer from community colleges, so this is an important avenue for us. We have a lot of students who work while they’re at school, or maybe they’re the first person in the family to go to university – that sort of experience.

“Having this diversity is a really nice aspect of being in such a multicultural city, as it can offer new perspectives to research – I think there are only advantages to having that level of diversity in the programme.”

Topics in this seminar series discuss the intersection of materials, technology, anthropology, economics and politics.

Mr Sheinberg notes that IMOS plays an important role in helping students to realise their career path.

TEAMWORK MAKES THE DREAM WORK Mr Sheinberg also highlights the concept of teamwork as a key benefit from the programme, through the IMOS seminar series and preparation for the summer research experiences.

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Dr Megan Robertson’s research group and REEMS students

“Students who participate in the REEMS programme have an opportunity to participate in teamwork. One of the objectives of the programme is to demonstrate the value of working and contributing to team activities. The structure of the IMOS seminars incorporates lectures and group presentations by REEMS students. These presentations are based upon contributions from each team member, incorporating and articulating their results to fellow students, faculty and guests during the seminar and responding effectively to questions, on an individual basis and as a member of a team effort.

These experiences are important for those REEMS students who participate in summer research and present their findings at the REEMS REU poster session at the end of each summer.”

Mr Sheinberg noted that the REU experiences provide the first formal participation in team experiences for many of these students. They learn the importance of sharing results, seeking assistance from research staff and a realisation of their respective individual roles in addressing research challenges.

The REEMS programme is unique among conventional REU activities. REUs are generally sponsored by research universities and recruit lower and upper division students, often from community colleges. Students participating in the REEMS REU are recruited and placed in university research projects by REEMS staff, in close collaboration with research faculty. REEMS has established partnerships with regional universities and faculty from the University of Houston, Rice University and the University of Texas Health Science Center – Houston. In 2016 twelve students participated in the REEMS REU and in 2017,

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with the addition of a new faculty member at Rice University, fourteen students will be participating in the REEMS REU. IDENTIFYING TALENT Mr Sheinberg describes how almost all REEMS REU students finish their summer research experiences with a high level of self-confidence, and the realisation that they have both academic potential and the talent to consider new and challenging academic and career pathways. The increase in confidence, tied with the realisation of their talent, are strongly influenced by each of the seven research faculty during their summer experiences. One of the objectives of the REEMS programme is to provide each student with the ability to determine their own academic and career futures.

This self-confidence is something Zeshan Rizvi, a member of the 2016 REEMS REU and the forthcoming 2017 REEMS REU, has experienced. He said: “When I first started the programme, I wasn’t too sure exactly what I would get out of it – it seemed a little too good to be true, but it turned out to be the real deal. Initially, I found it a bit overwhelming with the duties and responsibility given to you. I also found it hard to get used to the workload and the vigorous routine of being part of a research programme and a research group, but eventually I learned to really enjoy it.

“For me, the experience I gained just from being a part of the research group, learning about what they do on the front lines of research on a daily basis, was the most important thing. The IMOS seminar and REU forced me to become a better, more vigorous student and, although I found it hard at first, I truly appreciate what it has done for me.”

Mr Sheinberg is like a father to us – you cannot put a price on what he has done for me. No one will help me in the same way he did MAKING UNIVERSITY ACCESSIBLE Another former REEMS student, Raymond McCoy, even said that without the programme, he would never have even considered going to university – seeing a life in the workforce for himself instead.

He said: “I wasn’t planning on going any further than my associate degree, but the programme sets you up with some great university contacts. It really amplifies the opportunities you receive going into the next stage of your academic career, and it sets you up with skills that make you distinct from other candidates going for jobs, positions, internships – whatever it may be.”

However, Dr Robertson believes the programme does not only benefit the REEMS students themselves, but her lab as well. In fact, she was so impressed by the quality of the students she mentored last year, that she decided to keep them on.

She said: “The students I had last year were excellent and I managed to find a way to continue their work in my lab even after the summer programme was done. After all, the REEMS programme doesn’t just provide an opportunity for them, it provides an opportunity for us as well. In the end, we could continue the work they had done over the summer, and we’re even going to get a research publication out of their work.”

FUTURE PLANNING Mr Sheinberg looks forward to other community colleges and university partnerships emulating part of the REEMS programme. Part of his job is to work with interested community college and university partnerships to discuss funding and structural and programmatic aspects which are unique to each partnership.

Mr Sheinberg mentioned that while he and his staff play an important role in

administration of the programme, one of the critical components of the programme are the multi-faceted roles which each of the REEMS research faculty play in the process.

Sheinberg’s fatherly persona, stating that his “really friendly personality … [and] helpful approach throughout the programme” had made it a “blessing getting to know him”.

He said: “What has made it successful are the research faculty members. These are the people who really inspire the students – the linchpins that make this thing work. Students get a chance to meet with them, work in their labs, and it’s sort of a double-edged sword in a way – on the one hand, the students feel a little bit intimidated, but on the other, they get to say, ‘wow, this is really interesting’ and eventually, ‘I can do this’.”

Similarly, Dr Zachary Cordero, the new research faculty mentor for two additional REEMS students at Rice University, agrees that the programme’s success is down to Mr Sheinberg, predominantly due to his ability to identify and place candidates.

He said: “I think credit is due to Bartlett (Mr Sheinberg) for attracting good students and for trying to put them on placements that he thinks are appropriate to them and their personalities. I specifically requested students who have an interest in tinkering, working with their hands, and have a natural proclivity for doing experiments, and Bartlett tried to connect me with students who aligned with those criteria.

The programme has been successful mainly due to him.”

MR BARTLETT SHEINBERG: MENTOR Gelareh Nobakht, a current REEMS student, somewhat disagrees with Mr Sheinberg’s characterisation of his role, stating that Mr Sheinberg’s tenacious energy and fatherly care for students is the reason the programme has proved so successful over the years.

She said: “He’s like a father to us. He’s the one who encouraged me to go to university and he has a lot of hope for me, and all his students. He provided recommendations for me, he focused me on universities that would be right for me – you cannot put a price on what he has done for me in the past two years. No one will help me in the same way he did.”

Sogol Gharaeimoghadam, another current REEMS student, can also vouch for Mr

ADDITIONAL BENEFITS For Professor James Meen, the programme has been a positive not only for the REEMS students that he mentors, but also for the graduate and postdoctoral students he oversees at the University of Houston.

He said: “It is a positive for the graduate students especially, because they have to explain to somebody with a limited amount of background what they’re doing in the lab.

It forces them to think about it and it makes them much better teachers in the future.”

Dr Rafael Verduzco of Rice University

agreed as well, stating: “The REEMS programme helps me and my graduate students in that it actually forces us to explain our science in a way that makes sense to somebody who isn’t an expert in the field, because we are explaining it to people who are completely new to the topic. It is always helpful for us to learn how to do that more generally and more broadly.”

REACHING OTHERS In addition to his responsibility administering REEMS, and providing stewardship of existing West Houston collaborations and programmes, he is continually seeking new partnerships with community colleges, universities, professional societies and businesses to participate in a wide array of programmes focused on materials science education.

Mr Sheinberg serves as the lead for the 2017 Materials Research Society Educational Symposium at the MRS autumn meeting that will focus on strategies for community college and university partnerships to develop lower division materials science educational programmes.

For information on attending or submitting a presentation abstract: http://www.mrs. org/fall2017/call-for-papers?code=BI1 If you would like to view the students’ research posters or the abstracts from their projects, please contact Mr Sheinberg who will be happy to forward them to you.

Behind the Bench Mr Bartlett Sheinberg

E: bart.sheinberg@hccs.edu T: +1 (713) 718 5617 (Direct Line) T: +1 (713) 569 4046 (Mobile Number) F: +1 (713) 718 6884 W: www.hccs.edu/whc West Houston Center for Science and Engineering Houston Community College 2811 Hayes Road MC 1524 Houston, TX 77082 USA Bio Mr Bartlett Sheinberg is the founding Director at the West Houston Center for Science and Engineering at Houston Community College which was established in 2006. He has served as a physics and engineering faculty member, and several administrative positions at Houston

Community College for over thirty years.

He currently serves as the Principal Investigator on Houston Community College’s REEMS programme.

Collaborators Professional Societies: • Materials Research Society Research Faculty Collaborations: • University of Houston: Dr Jakoah Brgoch; Dr James Meen; Dr Megan Robertson • Rice University: Dr Zachary Cordero; Dr Margaret Cheung; Dr Rafael Verduzco • University of Texas Health Science Center – Houston: Dr Laura Smith Callahan

Research Objectives Mr Sheinberg’s current research objectives focus on identifying, educating and serving as the Principal Investigator for students involved in Houston Community College’s REEMS programme.

Funding The REEMS project acknowledges financial support from the National Science Foundation, Division of Materials Research (Award 1460564) and additional financial support from the Houston Community College District Office.

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Education & Training︱ Dr Medeva Ghee

Supporting tomorrow’s role models:

how the Leadership Alliance is encouraging students from underrepresented groups If the balance of underrepresented groups in American academic institutions and the research workforce is to be effectively addressed, it is imperative that young people have role models. For over 25 years, The Leadership Alliance, a consortium of over 30 institutions, has provided support in the shape of encouragement, mentorship and training. This effort has directly resulted in the achievement of over 450 PhDs/MD-PhDs

by Alliance alumni. So how are they tipping the scales and, in Executive Director Dr Medeva Ghee’s words, populating a ‘workforce reflective of the diverse fabric of our society’?

D

espite making up almost 40% of the United States population (a proportion which is on the rise), underrepresented ethnic and racial minorities receive a much smaller proportion of university degrees, especially in the fields of science, technology, engineering and mathematics (STEM) (around 20% of undergraduate degrees and less than 8% of doctorates). In addition, women remain hugely underrepresented in STEM subjects across the world. Despite these challenges, students and researchers from diverse ethnic and cultural backgrounds make massively valuable contributions; fresh perspectives and diverse experiences are a positive force for research and necessary for tackling challenging problems. Indeed, the United States needs a competitive research workforce that explicitly understands the David Stout, PhD, AAAS Science and Technology Policy Fellow.

complex societal needs of its diverse population if it is to remain a key player on the global, political and economic stage.

To address this critical need, broader and more reliable pathways must be opened for students and researchers from underrepresented groups to enter and stay in the research workforce. A positive trend for historically underrepresented groups in academia in the United States is gaining momentum, with the number of degrees overall for this demographic slowly increasing over the last 20 years.

More recently, academics have focused on what actions institutions can take to break down barriers preventing students from underrepresented groups from realising their potential. Critically, it is necessary to overturn stereotypes and prejudices, provide continuous social support and to address identity development. It is through these processes that organisations like The Leadership Alliance have been promoting inclusion and diversity in the STEM disciplines as well as the humanities and social sciences for over 25 years.

FORWARD TOGETHER The Leadership Alliance is a national consortium of more than 35 institutions (including prominent Minority Serving Institutions (MSIs), PhD granting institutions and private industry) headed

by Executive Director Dr Medeva Ghee, who maintains that the solution to underrepresentation is not fundamentally a difficult one: talent should be promoted for talent’s sake. What is needed is persistence and presence throughout a young person’s career, with support provided at critical transition points along

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Victoria Cole, undergraduate student.

Justin Holmer, Associate Professor of Mathematics (left), and Mamikon Gulian, undergraduate (right).

It is necessary to overturn stereotypes and prejudices, provide continuous social support and to address identity development the academic pathway. One Leadership Alliance alumna, Scharri Walker PhD, now Chair of the Biology Department at Tougaloo College, which is also her alma mater, noted that when she was most struggling with her PhD studies, the Alliance provided an internship and mentors that inspired her to continue: ‘they were the living, breathing examples of who I wanted to become’.

The Leadership Alliance has developed a number of programmes designed to bring together and motivate students.

The Summer Research Early Identification Program (SR-EIP), established in 1993, brings undergraduate students from all (not just science) subject fields together for intense research experiences at some of the United States’ top institutions; 50% of these students have never participated in a summer research event before.

Believing that the future of research relies upon connecting with young scholars as early as possible, the Alliance launched the First Year Research Experience (FYRE) programme for first year students from Alliance MSIs. To increase opportunities for students in the humanities and social sciences, the Leadership Alliance started the Leadership Alliance Mellon Initiative in 2009. In 1995, the first Leadership Alliance National Symposium (LANS) was held, bringing SR-EIP participants, Doctoral Scholars (SR-EIP alumni who have obtained a PhD or MD-PhD degree),

faculty mentors and administrators together to celebrate the summer research of the undergraduates, who make either oral or poster presentations, many for the first time. The LANS also provides activities designed to improve postgraduate skills and inform career decisions, as well as showcasing work of emerging scholars and alumni who act as role models for the undergraduates.

The Leadership Alliance’s most recent project is the SYnergistic Network to Enhance Research that Grows Innovation (SYNERGI). This multi-institutional network aims to extend the Alliance’s programme throughout the academic year, hosting regional conferences to advise faculty and teachers, workshops for students to prepare for academic and research development, and making online and in-person mentoring available at all times, with an especial focus on professional development for graduate students.

Perhaps the most significant part of the whole programme process is the fact that alumni become part of the mentorship cycle, consolidating the pathway for new students. Undergraduates are advised by graduates, graduates are mentored by doctoral candidates who become role models for the entire student body and who are supported themselves by the Alliance’s professional and academic guides. The Leadership Alliance works by the African proverb, ‘If you want to go

fast, go alone. If you want to go far, go together’.

DEGREES OF SUCCESS So what impact has the Alliance had?

The Leadership Alliance celebrated more than 450 Doctoral Scholar alumni with PhD/MD-PhD degrees in 2017, of whom 60% are women in STEM. Its success is perhaps most attributable to its measured and consistent approach to inspiring students to pursue research careers and then connecting them with the means to do so. There has been a steadily increasing demand from students to take part in the programmes.

In post-programme surveys, up to 75% of participants consistently say that the summer programme has strengthened their ‘commitment to pursue a research career’, suggesting that the activities

Student Chloe Edmonds in the library.

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The solution to misrepresentation is not fundamentally a difficult one: talent should be promoted for talent’s sake Valentina Alvarado, undergraduate at University of Puerto Rico, Biological Sciences lab.

are effective in building confidence and instilling enthusiasm. The most successful workshops at the LANS (as judged by the surveys) are those on the graduate school application process and graduate school experience, implying that career development is high on the list of priorities for the attendees and that the Alliance has succeeded in its endeavour to inspire. This is evidenced by 37% enrollment into PhD programmes.

Doctoral Scholar alumni are diversifying the research workforce with 54% having already obtained faculty positions at colleges and universities across the US and poised to mentor the next generation. The Leadership Alliance membership institutions have also benefitted; they recruit nearly a quarter of the Doctoral Scholars for faculty positions.

As important, alumni are populating

Micah Holness, undergraduate at Xavier University of Louisiana, Cognitive Science lab.

leadership positions in industry, public and private sectors, fulfilling the Alliance’s promise of developing underrepresented students into outstanding leaders and role models.

The Leadership Alliance has long recognised the need for the ‘best and the brightest’ young people of the United States to reach their potential in research and academia, regardless of whether they form part of an ethnic, racial or

gender minority. Despite the scale of the problem, the Leadership Alliance has identified a straightforward mission: give more undergraduates the opportunity to link their academic curiosity with research experience, provide support along the whole of their career pathway and let them become the role models who positively shape the lives of the generations behind them. These are changes, Dr Ghee suggests, that we can believe in and depend on.

The solution to misrepresentation is not fundamentally a difficult one: talent should be promoted for talent’s sake LEADERSHIP ALLIANCE MEMBER INSTITUTIONS Members of the Leadership Alliance include thirty-five of the nation’s leading research and teaching academic institutions and one associate member from industry:

Kevin Trinh, undergraduate at Bowdoin College, Earth Sciences lab.

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• Brooklyn College • Brown University • Chaminade University of Honolulu • Claflin University • Columbia University • Cornell University • Dartmouth College • Dillard University • Harvard University • Heritage University • Howard University • Hunter College • Johns Hopkins University • Montana State University • Morehouse College • Morgan State University • New York University • North Carolina Agricultural and Technical State University

• Princeton University • Spelman College • Stanford University • Tougaloo College • Tufts University • University of Chicago • University of Colorado Boulder • University of Maryland, Baltimore County • University of Miami • University of Pennsylvania • University of Puerto Rico • University of South Florida • University of Virginia • Vanderbilt University • Washington University in St. Louis • Xavier University of Louisiana • Yale University • [Associate Member] Novartis Institutes for BioMedical Research

Behind the Bench Dr Medeva Ghee

E: TheLeadershipAlliance@Brown.edu T: +1 401 863 1474

The Leadership Alliance 133 Waterman St. Providence, RI 02912 USA Bio Dr Medeva Ghee is the Executive Director of the Leadership Alliance and a faculty member in the Department of Behavioral and Social Sciences at Brown University. As Director of the Leadership Alliance, she is responsible for leading the 36-member consortium dedicated to increasing the participation of underrepresented students in competitive graduate and doctoral training programmes and ultimately developing leaders and role models in academia, the public and private sectors.

Q&A

Academia and research institutions have a reputation for being traditional and stuck in their ways.

With regards to underrepresented groups do you think attitudes are changing/have changed?

Attitudes are changing. Over the years, we have developed and sustained strategic partnerships between Minority-Serving Institutions and PhD granting institutions that have contributed to this change. This has resulted in a heightened awareness of institutional cultures and values that have provided opportunities for students from underrepresented groups to be exposed to competitive training environments and have resulted in the sharing of best practices

Research Objectives The Leadership Alliance is a partnership of institutions that aims to develop students from underrepresented groups into the leaders and role models of tomorrow.

Funding Funding for Alliance programmes is provided through institutional resources and membership fees, grant awards from federal agencies and private foundations, private gifts and conference fees. The Leadership Alliance programmes are currently supported by grants from the following: • The Andrew W. Mellon Foundation • The National Institute of General

among faculty and administrators from diverse institutional types that inform discussions on institutional transformation. These collaborative efforts speak to the power of the partnership.

The Leadership Alliance has just celebrated its 25th birthday; where would you like to see the organisation at its 50th birthday?

I would like to see the Leadership Alliance reach its goal of achieving equity and equality in academia and the broader research workforce, that is to say, the workforce is truly representative of the national population of underrepresented groups. There is also the capacity for the Alliance to expand its partnership and provide opportunities for students to conduct research internationally. I see the

W: www.theleadershipalliance.org

Medical Sciences • The Titus Foundation • National Institutes of Health • National Science Foundation In the past, Alliance programmes have also been supported by: • The National Science Foundation • The Council for Undergraduate Research Collaborators The Leadership Alliance collaborates with several organisations including: UNCF/ Mellon; Keystone Symposia; American Physiological Society; American Society of Microbiology

Alliance as a model for diversity on the global stage.

The Leadership Alliance has clearly helped so many individuals, but is there a particular ‘success story’ you would like to briefly mention?

I recently attended a job talk of a Leadership Alliance alumnus, who participated in the summer programme in 1999, interviewing for a faculty position at an Alliance institution. As I sat in the lecture, I was beaming with pride as I considered how the Alliance community cultivated and nurtured his talent throughout the years to produce a scholar who is transforming the academy by way of his scholarship and cultural background.

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Education & Training︱ Professor Michele Jacob

The Synapse Neurobiology Training Program, training the next generation of neuroscientists Research into the functions of synapses is crucial to understanding the mechanisms of highly prevalent brain disorders such as epilepsy, autism and Alzheimer’s disease. Professor Michele Jacob is the director of the Synapse Neurobiology Training Program (SNTP), located at Tufts Sackler School of Graduate Biomedical Sciences in Boston. SNTP provides predoctoral students with individualised, in-depth, multidisciplinary research training to investigate critical areas of synaptic function associated with disease and behaviour. Alumni of SNTP have gone on to receive recognition for both their research discoveries and their impressive contribution to various public engagement initiatives.

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esearch into synaptic functions is key to understanding many neurological diseases including Alzheimer’s, Parkinson’s, ALS, autismspectrum disorders, depression, anxiety, epilepsy and insomnias. Synapses are specialised contact sites between single nerve cells and their target cells that function in rapid information processing.

They form the basis of our central nervous system’s functions.

Institute of Neurological Diseases and Strokes (NINDS), part of the National Institute of Health (NIH). Each student is co-mentored by two SNTP faculty members that provide training in distinct yet complementary areas, equipping the student with multidisciplinary research skills.

Dye filled neurons after electrophysiological recording of their activity in the hypothalamus in acute mouse brain slices. Generated by Dominique Ameroso, in the lab of Maribel Rios.

Mechanisms that alter synaptic activity affect our behaviours, learning and memory formation. Many disorders of the nervous system involve fundamental alterations in synaptic function, and hundreds of mutations in synaptic proteins have been implicated in human diseases such as epilepsy, autism and cognitive impairments.

Additionally, synaptic receptors and channels represent over half of the pharmaceutical industry’s drug development targets, making research both medically and industrially impactful.

Founded by Professor Kathleen Dunlap, SNTP is now in its nineth year of training students. The program is now under the directorship of Professor Michele Jacob, an expert in synapse neurobiology.

Her research has focused on defining molecular mechanisms that direct the proper maturation and function of

Students are also given one-on-one training in areas such as imaging, bioinformatics, electrophysiology and animal behaviour methods, provided via state-of-the-art core facilities and PhDlevel managers in the NINDS-funded Center for Neuroscience Research at Tufts. SNTP training emphasises critical thinking and multidisciplinary approaches for effective and influential research.

STUDENT RESEARCH AREAS Since 2009, the SNTP has helped augment the neuroscience community by generating a cohort of highly skilled researchers able to produce key breakthroughs in the diagnosis, prevention and treatment of neurological diseases.

SNTP students contribute to a wide range of research areas, from synaptic studies investigating appetite and wakefulness to examining the synapse activity associated with disorders such as autism, epilepsy and anxiety.

Students graduate with the multi-faceted research skills necessary to address some of the critical neurological problems that have direct consequence to human health

THE FUTURE OF SYNAPTIC NEUROBIOLOGY RESEARCH Future approaches to treating these brain disorders will involve further indepth investigation of the mechanisms that govern synaptic function, and will also require a community of welltrained synaptic physiologists equipped to carry out research in a complex field.

To improve the research skills of their predoctoral students, the Neuroscience faculty at Tufts Sackler School of Graduate Biomedical Sciences in Boston developed the Synapse Neurobiology Training Program (SNTP), with the objective that students graduate with the multi-faceted research skills necessary to address some of the critical neurological problems that have direct consequence to human health.

neuronal and sensory cell synapses, and the role that their dysfunction plays in intellectual disabilities, autism, childhood epilepsy, and hearing loss.

The SNTP is run in the Department of Neuroscience, which is Chaired by Professor Philip Haydon, a world class expert in the key role of non-neuronal glial cells, the major cell type in the brain, in modulating synaptic function.

THE PROGRAM Drawing on the expertise of 20 neuroscience faculty researchers from the Tufts Sackler School of Graduate Biomedical Sciences, located on the Health Sciences campus of Tufts University in Boston, and working in conjunction with Tufts Medical Center, mentors guide each student through a thesis study of synaptic functions in both the healthy and diseased states. Since its inception in 2009 the program has been funded annually by the National

Working with SNTP mentor Dr Leon Reijmers, Patrick Davis, PhD conducted a study looking at the neuronal mechanisms that control the balance between the opposing systems that regulate the brain’s expression and suppression of fear. Dysfunction of these synaptic mechanisms can lead to ‘inappropriate’ fear responses and have been linked to anxiety disorders, PostTraumatic Stress Disorder (PTSD) and specific phobias. This work has led to a publication in the high impact Nature Neuroscience journal.

Jonathan Alexander, PhD completed his project under the mentorship of SNTP

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director Dr Michele Jacob. The research involved identifying novel molecular changes that lead to autistic behaviours, learning disabilities and chronic seizures, and resulted in publications in Nature’s Molecular Psychiatry, a chapter in Springer’s Encyclopaedia of Signalling Molecules 2nd Edition, and Elsevier’s Neurobiology of Disease Journal.

Elizabeth Hanson, PhD worked on a study of glial cell modulation of excitatory synaptic activity in the normal developing cortex, compared to a cortex associated with epilepsy caused by a traumatic brain injury.

Guided by Dr Chris Dulla, Hanson’s work has been published in Wiley’s Glia Journal, Elsevier’s Neurobiology of Disease and the high impact Journal of Neuroscience.

Michaela Tolman, currently working with Dr Phil Haydon, is identifying how nonneuronal glial cells modulate synaptic activity to regulate wakefulness, and has published this work in Cell Press’s Neuron.

New SNTP trainee Dominique Ameroso is working with Dr Maribel Rios to elucidate regulatory mechanisms that govern synaptic functions associated with appetite, energy status and glucose balance control within the body.

STUDENT OUTREACH INITIATIVES As well as conducting their own doctoral thesis research, engaging with the academic literature in journal clubs, and attending weekly seminars by leaders in the field, SNTP students have also undertaken an impressive range of outreach activities to enhance public understanding and increase interest in learning and careers in science. Current students have taken the opportunity to teach science sessions in local Boston high schools and colleges, engaging with underserved groups within the population. This has involved assisting high school classes with experimental design and data analysis, teaching UMass Boston undergraduate students valuable modern research techniques and talking to students about the wide range of career paths available

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Measuring the levels of D-serine in the hippocampus in vivo by microdialysis and HPLC, the levels correlate with wakefulness and activity of the mouse. Generated by Michaela Tolman, in the lab of Phil Haydon.

Inhibitory interneurons fail to mature properly in the absence of proper activation and brain function is permanently disrupted. Generated by Elizabeth Hanson, in the lab of Chris Dulla.

SNTP students have undertaken an impressive range of outreach activities to enhance public understanding and increase interest in learning and careers in science to neuroscience students, and the pathways to obtaining PhD training.

SNTP trainees also staffed the recruitment both at the Annual Biomedical Research Conference for Minority Students (ABRCMS), engaging with students from under-represented communities within STEM. Other activities include talking to students at the Annual Northeast Scientific Training Programs (NEST) retreat about how best to develop their scientific careers, membership of the Boston Chapter of Women in Bio, and various student mentorship programs. Alumni of the SNTP who are currently completing thesis research at Tufts continue to contribute to outreach efforts, with students volunteering with the Boston Brain Bee, the Museum of Science and the Science Communication Collaborative with Emerson University.

Alumni also contribute to mentorship programs at Tufts and to directing and lecturing a graduate studentrun Neuropsychiatry course for Tufts Medical Center psychiatry residents.

With a need for a new generation of synaptic neuroscientists to tackle the growing health issues of Alzheimer’s, Parkinson’s and autism, as well as to explain disorders such as anxiety and insomnia, training in modern research techniques and multifaceted skillsets are crucial to progress. Tufts’ SNTP continues to develop multi-skilled neuroscience doctorates, as well as maintain a notable contribution by its trainees towards outreach events, engaging both the scientific community and the wider public in synapse and brain research.

Behind the Bench Professor Michele Jacob

E: Michele.Jacob@tufts.edu T: +1 617 636 2429 W: http://sackler.tufts.edu/Faculty-and-Research/ Faculty-Profiles/Michele-Jacob-Profile W: http://sackler.tufts.edu/Academics/Neuroscience-Welcome

Sackler School of Graduate Biomedical Sciences Dept. of Neuroscience Tufts University 136 Harrison Avenue Boston, MA 02111 USA Bio The director of the Synapse Neurobiology Training Program (SNTP), Professor Michele Jacob, received her PhD degree from Yale University School of Medicine, and completed postdoctoral training at Columbia

Q&A What qualities do you look for in students when considering applications to SNTP? The SNTP benefits from a large and high-quality pool of graduate students interested in neuroscience, and in particular the synapse. A committee of SNTP faculty mentors selects the trainees. Qualities that distinguish top candidates for the SNTP are outstanding performance in all coursework and research, strong recommendations from their thesis research mentor and thesis advisory committee, high quality of the thesis project, and demonstration of a willingness to assume an active role in one’s education (e.g., inquisitiveness, taking leadership positions).

How does participation in SNTP help prepare your students for a career in the field?

The SNTP is designed to provide students with the rigorous, multidisciplinary research training and critical thinking skills they need to compete for research jobs in academia

University School of Medicine and the University of California, San Diego. She headed a research lab at the Worcester Foundation for Biomedical Research, and, in 1997, joined Tufts University Sackler Biomedical Graduate School, where she is currently Professor of Neuroscience.

Collaborators The twenty SNTP faculty mentors are experts in multifaceted research approaches for investigating synaptic function in the healthy brain and in

identifying the synaptic alterations that impair brain function and behaviour.

Research Objectives The goals of the SNTP are to produce graduates who are exceptional research scientists addressing critical neurological problems of consequence to human health.

Funding • National Institutes of Health (NIH) • National Institute of Neurological Diseases and Strokes (NINDS)

or industry and maintain successful, independent research programs. Dual mentorship is required to provide each SNTP trainee with in-depth exposure to multiple mentoring styles and to techniques and approaches beyond those available through the primary mentor’s lab. To further improve trainees’ chances of success, the training plan also provides opportunities to acquire effective written and oral communication skills, engage in activities that develop mentoring skills, interact with clinical faculty to gain the clinical perspective on their thesis research, and interact as hosts with seminar and symposium speakers to develop a personal contact network with experts in the field.

attest to SNTP trainees’ intellectual curiosity, interactive attitude, sense of community responsibility, and love of science.

One of your aims is to get SNTP trainees heavily involved in outreach initiatives and mentoring of younger students. Why do you consider this to be important?

SNTP trainees are capable, proactive, and motivated young scientists. They have independently engaged in an impressive array of outreach activities that include teaching workshops at high schools and colleges with large populations of students from underserved groups. These activities

What plans do you have for the future of SNTP going forward? Are you looking to make any changes to the structure or aims of the program?

The goal of the SNTP is to keep developing talented well-trained young investigators necessary for a vibrant neuroscience research community capable of developing new approaches for disorders caused by synaptic dysfunction.

Your students have studied disorders such as epilepsy, Alzheimer’s and autism. What do you see as the long-term future of research and treatment for some of these major disorders?

New therapeutic approaches for preventing or treating these diseases in the future will be facilitated by continued in-depth exploration of the mechanisms that drive synaptic function, through the work of welltrained neuroscience researchers.

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Education & Training︹ Dr Kathleen Potempa

Expanding capacity of non-communicable disease research and training in Thailand Dr Kathleen Potempa is Professor at the School of Nursing in the University of Michigan, where she served as Dean from 2006 to 2016. A globally renowned leader in nursing, education and science, she has a long academic career focusing on cardiovascular fitness in physically impaired populations, nursing, leadership, and community-based approaches to improving health.

She is currently collaborating with Dr Benjaporn Rajataramya to improve the capability of the Thai healthcare system in managing chronic diseases.

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ases of non-communicable diseases (i.e., illnesses such as diabetes or cancer – NCDs) are growing worldwide, and are responsible for an increasing number of mortalities each year. This growth coincides with rapid globalisation and urbanisation in developing countries, which have brought about changes in lifestyles and eating habits: from traditional food and high levels of physical activity to western-style foods and lower levels of physical activity.

The growing rates of NCDs pose a threat

to the global population. In Thailand, noncommunicable diseases have become the leading cause of morbidity and mortality.

Yet most NCDs are preventable or treatable, which strongly indicates a need for improved healthcare and improved NCD training and research for healthcare professionals, such as nurses.

Dr Kathleen Potempa’s research background and collaboration with Thailand’s public health services in managing HIV/AIDS and their policies for NCD management led to the

Growth of NCDs is occurring globally, causing an increasing number of mortalities every year

collaboration for this current project with Thai collaborator Dr Benjaporn Rajataramya. The project aims to provide a five-year training program to enhance the NCD research capabilities of Thai scientists including nurses and other health professionals. Additionally, the programme supports translation of NCD research into practice, enabling better care for people with NCDs and reduction in the incidence of NCDs in Thailand.

PAST SUCCESSES As is the case with many developing countries, HIV/AIDS is a significant cause of mortality. However, the Thai government was one of the first to significantly advance their control of this disease. In 2003, a collaboration between Thai and American academic institutions was formed to manage the expansion of HIV/AIDS into more populations as well as to provide the opportunity to treat HIV more widely because of a new government policy instituting a universal health plan. This effort aimed to empower nurses within the country’s health infrastructure, ultimately expanding the capacity of the public health service to manage the rising number of cases of HIV/AIDS. This collaboration was successful – by 2009 it had expanded the capability of Thailand’s healthcare system to cope with the challenges created by infectious diseases, particularly HIV and AIDS. The infrastructure created an opportunity to consider other projects that would leverage this expanded capacity such as the rising occurrence of NCDs. RISING NCDs In 2011, Thailand’s public health landscape was shifting towards a growing incidence of NCDs, with a concomitant increase in mortality.

As with other developing countries, this rise in NCDs was associated with urbanisation and globalisation, which promote a shift from traditional, high activity/low calorie lifestyles towards more western lifestyles, which are associated with lower physical activity and higher calorie intake. Along with this shift comes increasing risk of developing chronic diseases, such as heart disease, cancer and diabetes, which are some of the illnesses categorised as NCDs. Prior to 2012, training for treating NCDs had not been emphasised because of the

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primary focus on infectious diseases, injuries and other more prevalent causes of illness at that time. A study

by Dr Potempa and Thai collaborators, however, found that nurses and other health professionals were not confident in their ability to care for those with cancer and heart disease, and less than half of the nurses surveyed were confident in their ability to treat more common NCDs like hypertension and diabetes. The need for more information about how to prevent and treat NCDs in Thailand was apparent.

For nurses and other health professionals, the need to refocus their research on NCDs was of increasing importance to provide evidence-based guidance to clinicians and public health policy makers in the new era of NCD prevalence. Because nurses and other health professionals with PhDs were an important part of the research workforce in Thailand, Dr Potempa and Dr Rajataramya embarked on this current programme to advance research training for expanded NCD research.

NCD RESEARCH AND TRAINING To ameliorate the threat of NCDs, Dr Potempa and Dr Rajataramya’s work aims to improve the research training of nurses and other scientists by proposing a five-year post-doctoral training programme. The programme aims to provide two years of post-doctoral NCD research training for ten PhDs, offer short term NCD training for 20 investigators, and provide forums for researchers and administrators to discuss and identify ways to further NCD research in Thailand, thus strengthening the existing foundation for NCD research.

This project will increase the capacity of the Thai health infrastructure to manage the increasing burden of NCDs and promote efforts to reduce and prevent their growth, ultimately improving the prevention and treatment of these diseases in the long-term.

CONCLUSION Growth of NCDs is occurring globally, causing an increasing number of mortalities every year. This growth is influenced by a shift in many developing countries, associated with urbanisation and westernisation, from high activitylow calorie intake to low activity-high

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The global community will benefit from countries working together to share knowledge and effective practices calorie intake lifestyles. To address this, improved training and research into NCDs needs to occur, which would allow countries to refocus their health systems and health policy on the prevention and treatment of such diseases.

If you would like to find out more about the training programme please visit the website http://postdoctoratencd.umich. edu/

Behind the Bench Dr Kathleen Potempa

E: potempa@med.umich.edu T: +1 734 615 0085 W: https://postdoctoratencd.wordpress.com/

University of Michigan School of Nursing 426 North Ingalls Ann Arbor MI 48109-5482 USA Research Objectives Dr Kathleen Potempa’s research program has focused on fatigue, exercise, and cardiovascular fitness in physically impaired populations.

She directs the Training Program for Strengthening Non-Communicable Disease Research and Training Capacity in Thailand.

Q&A

What are the main challenges that you expect to face in your current work?

We are finishing year three of this five-year project and find that the enthusiasm for this work is strong. A big challenge has involved choosing our trainees from among the many highly capable applicants. Going forward we want to support those who complete the training to continue their research in Thailand. Finding financial support for research is always a challenge. However, we prepare our fellows to be highly competitive in obtaining research grants both in Thailand and from international research support institutions.

What prompted your interest in this project?

The Thai people are forward thinking and committed to finding solutions to health care challenges through policy, research and practice. As one of the first countries to effectively address infectious disease challenges such as HIV, malaria and others, we knew they would be wonderful collaborators in addressing the rapid growth in NCDs. We are committed to working together

Funding National Institutes for Health, Fogarty International Center Collaborators • Dr Benjaporn Rajataramya, Praboromarajchanok Institute for Health Workforce Development, Thailand • Dr Philip Furspan, University of Michigan School of Nursing • Dr Debra Barton, University of Michigan School of Nursing • Dr Naruemol Singha-Dong, Suranaree University of Technology, Thailand to find mutually beneficial solutions to prevention and treatment of NCDs through research. Our work will not only benefit Thailand and the US, but the growing number of countries who also are facing this global challenge.

To what extent do you feel that urbanisation is a cause of increasing cases of NCDs in developing countries?

While the changing patterns of work and lifestyle that urbanisation often brings undoubtedly contribute to the rising prevalence of NCDs, the ageing of populations also contributes. As infectious disease prevalence and other sources of acute disease decline people are living longer. A longer life leads to more exposure to conditions that give rise to NCDs – unhealthy diet, smoking, lack of exercise, stress, etc., all acting on genetic predispositions. Our research is aimed at finding ways to prevent the occurrence of disease or to help people stay healthy even with chronic exposure to adverse health conditions. As well, we aim to find culturally appropriate interventions for treatment of NCDs which typically require life-long management.

Do you expect that we will continue to see a rise in the prevalence of NCDs as

Bio Dr Kathleen Potempa, Professor at the University of Michigan, is an internationally recognised leader in nursing, education, and science, as well as the integration of education, practice, and research in clinical settings. Former positions include progressive leadership in health systems and in higher education. She is a member of the National Academy of Medicine and the American Academy of Nursing.

developing countries continue their development?

NCDs are clearly on the rise globally with parallel increases in urbanisation and ageing populations. The global community will benefit from countries working together to share knowledge and effective practices as they are developed through research and innovation.

Do you think that projects similar to the one you are currently conducting could be applied to healthcare systems in other countries?

The Fogarty International Center of the National Institutes of Health provides support to many countries by addressing research and research training capacity. We are grateful for their funding and support of this project. The US itself benefits from these activities as we learn a great deal through these research efforts that can be applied here at home.

Countries with similar issues may have novel solutions that can be shared and translated effectively to other cultures and circumstances. We think that our approach, building capacity for NCD research and training, with its associated translation of findings into health care practice, is essential for all countries with rising NCD.

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Engineering & Technology ︱ Professor Phil Joseph

Taking inspiration from nature for a new generation of quiet aerofoils Constant exposure to noise is an increasing problem in developed countries, with impacts not only on industry but also our health. Key culprits often accused of creating noise include airports and wind farms. Professor Phil Joseph from University of Southampton is heading up a team of scientists focused on reducing noise pollution through the development of new aerofoil design. The team, from a consortium of four universities (Nottingham, Southampton, City (London) and Brunel) with industrial support from Airbus and Vestas, have achieved noticeable noise reductions of about 10dB – far surpassing previous designs.

A

ccording to health studies, loud noise is not only responsible for hearing loss but also causes psychological and physical stress, and can contribute to reduced workplace productivity. It is also the biggest workrelated problem affecting workers in the construction and manufacturing sectors. Those who live near airports and wind turbines frequently complain of dizziness, headaches and sleep disturbance. The noise generated by wind farms or aeroplanes taking off and landing is emitted across a wide area and is difficult to eliminate. One group of scientists directed by Prof Phil Joseph and including Dr Tze Pei Chong, Professor Kwing-So Choi, Professor Alfredo Pinelli and Dr Mohammad Omidyeganeh, is focused on overcoming this problem.

They plan to introduce new designs of aerofoils which are more efficient in reducing noise and can be applied in a wide range of conditions, conserving their performances.

CAUSES OF NOISE The precise mechanisms behind noise generation on aerofoils are not wholly understood, although it is known that the dominant sound source is located on the aerofoil surface (the blade of a wind turbine or an aeroplane’s wing). Aerofoils generally have a rounded leading edge (that hits the air first) and a sharp trailing edge (from which the air flows off). When the leading edge of the aerofoil interacts with a turbulent fluid flow (this can be a liquid or a gas e.g., the atmosphere), an aerodynamic force is produced.

Aerodynamic force is composed of drag and lift, both generated when an aerofoil (e.g., an aircraft’s wings) interacts with a fluid (e.g., the atmosphere). We can think about drag as friction between the

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surface of the aircraft’s wings and the air molecules. Lift is the force generated by the wings deflecting the air molecules downwards. It acts perpendicular to the direction of flow and is what holds the plane in the air.

The aerodynamic force is heavily influenced by the ‘angle of attack’ – the angle between the aerofoil and the direction of flow of the fluid.

For example, think of an aeroplane moving along a runway.

The angle of the aerofoil (the wings of the aircraft) in relation to the direction of flow (in this case, the aircraft’s movement means the air is flowing parallel to the aircraft but in the opposite direction) is very important for lift off.

helped them understand the mechanisms of undulations better. The scalloped edges of these whales’ flippers give them an enormous advantage in underwater acrobatics. Their technique of hunting is called bubble net fishing. Whales make sharp U-turns and pirouettes to concentrate their prey inside a ‘net’ of bubbles which the fish cannot cross. The

performance but can also diminish unwanted noise. The group based their research on this fact and presented a detailed experimental study in which they tested the combination of sinusoidal leading edge undulations and trailing edge serrations interacting with a turbulent flow. Their experiments proved that a drastic noise reduction can be achieved by combining the two modifications.

An important finding of the study is that the serration can change the hydrodynamical and acoustical fields simultaneously.

Noise reduction by serration is found to be a collective effort underpinned by the reduction of the turbulent energy of the flow, as well as the acoustical destructive interference across the edges.

Replicating the scalloped design of humpback whale flippers on wind turbine blades resulted in reduced drag, quieter functioning, and increased efficiency scalloped edges of their flippers allow them to make a more acute angle of turn than would be possible with smooth edges: it allows for an abrupt change of the position without the so-called stall.

The idea of serrated leading edges is passing now from the test phase into the production process: replicating this scalloped design on wind turbine blades resulted in reduced drag, quieter functioning, and increased efficiency.

As a side effect of the unsteady aerodynamic force acting on the aerofoil, noise is also produced. This noise increases when the unsteady force is acting on the wings or blades at large angles of attack. As a result of OWL-INSPIRED TURBINE BLADES regions of turbulent air passing over Owls are well-known for their noiseless the aerofoil leading and trailing edges, technique of hunting: they can silently acoustic waves are created. Acoustic approach their prey without being waves can bend around obstacles and detected thanks to the unique serration spread out from small openings. The feature at the edges of their wings. creation of noise by rotating aerofoils is Modification of both leading-edge more complex than air passing over a and trailing-edge geometries using stationary aerofoil. The faster the blades serrations, as in the owl’s wings, can cut the air, the higher the frequency not only improve the aerodynamical of the noise generated there. The trailing eddies Vortical flow around an aerofoil at high loading condition generate random noise, the frequency of which is higher at the tip of a wind turbine for example, because it is moving faster.

SECRETS OF SHARK SKIN Another promising technology that the group is planning to work on involves using ‘riblets’ to reduce noise. Riblets are longitudinal raised grooves on the surface which successfully reduce drag in pipework systems and wind turbines.

Riblets have been used by America’s Cup yachts and for swim suits to improve speed in competition. Flight tests of riblets have been carried out using Airbus A320 to show reduction of drag by two percent. The pattern used is similar to that present on shark skin, which is not smooth but covered with tooth-like

HUMPBACK WHALE AND WIND TURBINES Nature has always been an inexhaustible source of ideas for technological innovations. For the team of scientists aiming to reduce noise generated by aerofoils, the observation of the humpback whale’s flipper

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Close-up of wing structure of a barn owl Curved leading-edge serration

Trailing edge fringes

Trailing edge

Curved aeration

Leading edge

Owl-inspired aerofoil with curved-serrated leading edge

scales called denticles. This skin with its tiny V-shaped scales, decreases both turbulence and drag. As a result, sharks can swim faster and more quietly.

COMPUTER SIMULATIONS The team’s research project combines these three nature-inspired technologies using computer modelling with promising results.

They are developing and optimising these technologies to be available for a wider range of loading conditions and flow speeds.

The team run a computer simulation of fluids to recreate turbulent flows appearing in oceans or the atmosphere.

The simulations use Navier-Stokes equations governing the motion of fluids: these are similar to Newton’s second law but are applied to fluids (gas or liquids). The computer calculates the solutions to these equations for a specific set of conditions and allows the team to predict the velocity and pressure of the fluid in a particular area.

The parameter that determines the computational cost for finding a numerical solution of the NavierStokes equation is Reynold’s number (Re), describing the ratio of inertial to viscous forces. In more simple

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Simulation of a turbulent detached flow on a wing at high angle of attack. Colours highlight the presence and strength of vortices in the flow.

The noise generated by wind turbines or aeroplanes taking off and landing is emitted across a wide area and is difficult to eliminate terms, it determines whether fluid flow is laminar or turbulent. Low Re characterises smooth and slow flow; high Re describes chaotic and unstable fluid movement.

The crucial requirement for the reduction of aerofoil noise is that flow along the boundary should remain in direct contact with the aerodynamic surface. Using a simulation called Large eddy numerical simulation, the team were able to demonstrate that aerofoils with leading-edge undulations had boundary layer-flows that remained attached to the surface under higher angles of attack than in previous designs. During the past decade, they have demonstrated that leading-edge undulations could increase the lift by 60 percent and reduce drag by the same amount. They also showed that undulations can dramatically decrease the produced noise with a reduction of about 10dB.

Currently, the group’s work is supported by an EPSRC grant. The main goal is to integrate all of their findings in order to reduce noise in aircraft engines, aircraft wings, wind turbines and cooling fans.

The increasing popularity of unmanned air vehicles (drones) in a wide range of fields (military operations, humanitarian aid) also motivates increased research of aerofoils under large angles of attack and at reduced size. The team’s research shows that for noise reduction, the best strategies involve the modification of the noise source – the turbine blades.

Integrating three innovative leadingedge profiles – double-wavelength, chopped-peak and slit-root serrations – simultaneously provides reduction of noise and enhances the general aerodynamic performance. Thanks to these discoveries, we are closer to obtaining clean energy from quiet wind farms and reducing noise pollution from airports.

Behind the Bench Professor Phillip Joseph Professor of Acoustics at the Institute of Sound and Vibration Research, University of Southampton

Dr Tze Pei Chong

Senior Lecturer at the Department of Mechanical, Aerospace and Civil Engineering, Brunel University

Professor Kwing-So Choi Professor of Fluid Mechanics at the Department of Mechanical, Materials and Manufacturing Engineering, University of Nottingham

Professor Alfredo Pinelli Professor of Fluid Simulation at the School of Engineering and Mathematical Sciences, City University London

Dr Mohammad Omidyeganeh

Lecturer at the School of Engineering and Mathematical Sciences, City University London

E: kwing-so.choi@nottingham.ac.uk T: +44 0115 95 13792 W: www.southampton.ac.uk/engineering/research/centres/isvr.page W: www.nottingham.ac.uk/engineering/

Research Objectives The team’s work aims to reduce the noise generated by aerofoils through three separate technologies.

The results have applications in the aerospace and renewable energy sectors.

Funding EPSRC

Q&A

Can you describe how Large eddy simulation works and why exactly you are using this method?

In the majority of industrial and natural turbulent flows the size ratio between the smallest and the largest vortices may become huge to an extent where it becomes impossible to computationally resolve all the eddies embedded in the flow. To overcome this problem a filter that separates the small eddies from the large ones is applied to the Navier-Stokes equations leading to a new set of equations that model the motion of the large eddies only. These equations incorporate a model that mimics the drainage of energy exerted by the filtered smallscale motions from the resolved large scales.

Collaborators • Professor Ugo Piomelli (Queen’s University, Canada) • Dr Oksana Stalnov (Technion, Israel) Industrial partners • Vestas Technologies UK • Airbus Group Limited

Are any of your technologies currently in use?

No, not yet.

What was the most surprising finding you made during your research?

Although the history of aircraft and associated aerofoil development is old, yet we were able to find a new shape of aerofoil that is more efficient and reduces noise at the same time.

What parts of your work do you find the most interesting and why?

We find it very interesting that nature has developed the best aerofoil that

Contact Prof Kwing-So Choi Faculty of Engineering University Park Nottingham NG7 2RD UK

reduces noise (see owls), increases the lift force (see hump-back whales) and reduces skin-friction drag (see sharks). We – humans are learning from them for industrial applications.

What are the next steps to further improve the designs that you have proposed?

To further improve the aerofoil designs, our next step is to test our new aerofoils and blades on aircraft and gas turbines to see if they work as well as in laboratories.

We were able to find a new shape of aerofoil that is more efficient and reduces noise at the same time

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Engineering & Technology ︱ Professor Elisa Bertino

Evading the rise o Ransomware, malicious software that takes users’ files “hostage” and demands payment from users to get back their files, has become a popular income stream for cybercriminals. While not all ransomware attacks are effective money earners, they often cause immense disruption for key services such as the healthcare industry.

In the case of ransomware, prevention is often better than cure, and Professor Elisa Bertino at Purdue University is designing tools to do exactly that – prevent the ransomware infection from ever taking hold with the possibility of stopping the millions of pounds of damage these attacks can cause.

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ansomware dominated the daily news in May 2017, with the arrival of WannaCry. An unwelcome arrival on personal and company computers alike, the software took files hostage and demanded payment for users to be able to get their files back. WannaCry is probably one of the most famous examples of ransomware, malicious software that makes the victim’s files inaccessible through encryption.

Encryption ‘locks’ the data, making it unreadable to anyone without a very specific ‘key’.

What made WannaCry such an exceptional attack was the sheer number of infected computers (thought to be around 200,000) and also the nature of some of the organisations affected. Alarmingly, one high-profile victim was the UK’s National Health Service hospital computer systems.

This affected not just the computers relied upon for administrative tasks, but those responsible for the analysis of test

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of ransomware results and the operation of equipment like MRI scanners.

While the prevalence of ransomware in the media may seem like a recent phenomenon, the first ransomware attack occurred in 1989, also targeting the healthcare industry. However, this attack was largely a failure due to a design flaw: rather than encrypting files, it simply renamed them, making it easily reversible. Now though, attacks have become more technologically sophisticated and the availability of anonymous currencies, like Bitcoin, has made it harder than ever to trace the source of such attacks.

Researchers like Professor Elisa Bertino and her group at Purdue University are now fighting back. Breaking the ransomware encryption to recover files is often nearly impossible but Professor Bertino has another clever trick. Rather than trying to break the encryption on affected files, she focuses on prevention approaches that stop the initial encryption process, rendering the ransomware essentially useless.

Her research group have already demonstrated this approach to be highly successful in stopping ransomware infections and these tools may be the answer to avoiding a repeat of the WannaCry events.

KEEPING SECRETS The encryption process is at the heart of how malicious software or ‘malware’, like ransomware, operates. Encryption is a way of hiding information so that anyone who wants to read the real information must possess a special kind of key.

Reversing the encryption processes on a file, or ‘decrypting’ it, is not always a trivial or easy task. Encryption

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Reversing the encryption processes on a file, or ‘decrypting’ it, is not always a trivial or easy task comes in many flavours and strengths.

Some keys are kept entirely secret, so only the ‘sender’ and ‘receiver’ of the information have a copy. Others, counterintuitively, are publicly available and rely on the generation of a paired private, or secret, key for encryption.

The generation process relies on an algorithm that can be used to generate more simple or complex keys depending on the security requirement.

Breaking encryption could be done by interception of the keys or by trying to guess the correct key. A brute force approach, where a computer tries to guess all the possible combinations that could comprise the key, means that a correct guess on a reasonable timescale is highly implausible.

Where things get even harder is that some malware can require a unique decryption key for each infected computer.

This is why Professor Bertino’s approach is so successful. Her tool essentially lies in wait for the signs of a malicious attack. This could be the sudden encryption of a large number of files, resulting in a change to the

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computer’s filesystem. In conjunction with this, it looks for any anomalies in the processes that read and write to the filesystem, that are the signals for the encryption process to occur. This early warning detection system allows the tool to spot an attack very early and halt the encryption.

PREVENTION TACTICS Professor Bertino is not the first to attempt the search for warning signs to stop ransomware. However, approaches that either just look for file encryption events or anomalous process requests tend to flag a large number of false positives and are generally ineffective in halting real attacks. They can be fooled by the ransomware encrypting files more slowly or trigger when the user is trying to encrypt their own files.

The joint approach of Professor Bertino has proved highly effective for 15 different types of ransomware attack.

When the early warning system triggers in the event of an attack, it can stop further encryption but, if some files are already encrypted before the process is blocked, the tool can record the parameters used for the process and,

depending on the specific ransomware, recover even the decryption keys. This makes it incredibly straightforward to undo any damage caused by the malware and restore the files to operation.

THE FUTURE FIGHT Professor Bertino and two of her PhD students in the Computer Science Department at Purdue University, Anand Mudgerikar and Shagufta Mehnaz, are working to further develop this approach. One strategy is to deploy decoy files, that would be of no interest to the user but equally likely to be targeted by the ransomware, as another part of the early warning detection system. Attempts to encrypt those files would be a strong indication of a ransomware attack as users would not usually encrypt such files. She and her students are also focusing on ransomware attacks aimed at different targets, such as IoT (Internet of Things) devices.

Given the increasing volume of sensitive data stored on systems and networks that are connected to the internet, it is likely that ransomware will continue to seem a lucrative tactic for cybercriminals. However, with tools like Professor Bertino’s, malware will need to become even more sophisticated to be effective.

Behind the Bench Professor Elisa Bertino

E: bertino@cs.purdue.edu T: +1 765 496 2399 W: www.cs.purdue.edu/people/bertino

Cyber2SLab Purdue University Department of Computer Science 305 N. University Street West Lafayette, IN 47907 USA

Collaborators • Shagufta Mehnaz (CS Dept. Purdue University) • Anand Mudgerikar (CS Dept. Purdue University)

Q&A Do you think having ‘antiransomware’ software will become as common as an antivirus?

Today there is awareness that data security is a key requirement. Therefore tools for in-depth protection of data are being developed and deployed by industry in many different application domains. A notable example of such tools is represented by data leakage protection tools aimed at preventing data from being stolen by skilful adversaries. Blocking and recovering ransomware attacks is today another relevant frontier for data cybersecurity. Good practices involve frequent backup of files – so that files can be recovered in the event of a ransomware attack – and anomaly detection tools, like the ones we are developing. At present, state-of-the-art, anti-ransomware tools are still complex and are still in an early research stage. However, once these tools are engineered for wide-scale deployment, they will be used by organisations with important data assets.

Bio Elisa Bertino is the Samuel Conte Professor of Computer Science at Purdue University. She serves as Director of the Cyber Space Security Lab (Cyber2Slab). In her role as Director of the Cyber2Slab she leads multidisciplinary research in IoT security, data security and privacy, security for mobile systems and projects in the area of cyberinfrastructure for scientific research.

Research Objectives Professor Bertino’s work spans many areas in the fields of information security and database systems. In particular, she is currently working on an approach to combat ransomware attacks.

Are organisations like hospitals particularly vulnerable?

Organisations where timely access to data is critical are certainly vulnerable.

Also the vulnerability of organisations depends on their maturity status with respect to the adoption of security practices and tools, and the security training of their staff. In this respect, hospitals are a perfect target for ransomware as critical care for patients relies on timely access to up-to-date information from patient records.

Without real-time access to drug histories, surgery directives and other information, patient care can get delayed or halted, with serious consequences. In addition, medical information systems and networks are today very complex – thus making difficult their comprehensive protection, and hospitals often to do not have IT security staff. Therefore, it is not a surprise that many hospitals have been targeted by ransomware and have preferred to pay the ransom rather than endanger patients’ health.

– from encryption performed by ransomware, e.g. malicious encryption.

To understand such differences, we performed a user survey to better assess whether users encrypt their files, and which files they encrypt.

What is the most technically challenging aspect of creating your prevention tool?

The most challenging aspect has been to identify the features that allow our tool to distinguish between encryption performed by a user – and thus legitimate

Funding NSF

How do you think ‘better user behaviour’ can be encouraged to prevent some of the issues with malware?

Better user behaviour is always critical for enhancing security. As with all malware, it is important that users be aware of suspicious messages requiring for example the user to click on certain websites or to download and open an e-mail message attachment. Also installing an antivirus and backing up files are good practices that may drastically reduce the number of successful ransomware attacks.

Professor Bertino’s approach is highly successful in stopping ransomware infections

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Engineering & Technology ︱ Professor Olfa Nasraoui

Biases from Big Data: The prejudiced computer Big Data and Machine Learning seem to be the modern buzzword answers for every problem. Areas such as healthcare, fraud prevention and sales are just a few of the places that are thought to benefit from self-learning and improving machines that can be trained on huge datasets. However, how carefully do we scrutinise these algorithms and investigate possible biases that could skew results? Professor Olfa Nasraoui at the University of Louisville has demonstrated that this is done not nearly carefully enough and is developing tools to lift the lids on ‘black box’ algorithms and create truly fair alternatives.

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B

ig data is a generic term for any dataset that is large in volume or variety. It may also be large in ‘velocity’, a term for the rate at which new data is being added to the existing dataset. One example of a ‘big data’ dataset might be a census, with a huge number of entries (people) and a variety of information (age, gender, location).

Such large datasets are becoming increasingly common as large-scale data storage has become more practical as well as an increasing number of possibilities for tracking user behaviour on websites and app usage. While such complex datasets may contain valuable information on why customers choose to buy certain products and not others, the size and scale of the available data makes it unfeasible for a human being to analyse it and identify any patterns present.

This is why machine learning is often touted as the answer to the ‘Big Data Problem.’ Automation of the analysis is one approach to deconstructing such datasets, but conventional algorithms

Dedicated mentoring, teamwork, hard work, service, outreach and research dissemination are pillars at the Knowledge Discovery & Web Mining Lab. At a research symposium (left to right): Wenlong Sun, Mahsa Badami, Prof Olfa Nasraoui, Behnoush Abdollahi, Gopi Nutakki.

must be pre-programmed to compare particular factors and look for certain levels of significance. An automated algorithm capable of learning and adapting to the dataset offers much greater levels of flexibility in the analysis and can offer far deeper, and potentially original, insights into any trends. This is what is inspiring the use of machine learning in an increasing number of areas, such as education, justice and criminal investigation.

There is a pressing need for transparency in machine learning models Machine Learning Algorithms

Humans

Information

Humans and algorithms are tightly coupled within a feedback loop. They influence each other via the information or the data generated by humans and by algorithms who guide them,

While a self-teaching, developing algorithm may sound wonderful, machine learning algorithms are often only as good as the datasets on which they have been trained. It also appears that the computer may not be a dispassionate, impartial analysis tool either. With her students and collaborators, Professor Olfa Nasraoui at the University of Louisville has been investigating the issue of how bias can affect machine learning, rendering results unreliable, and how the behaviour of such algorithms can be monitored.

POLARISING DATA Bias in machine learning models is a crucial issue as such results are now being used in systems such as informational filtering and personalisation. This means there is a continuous feedback loop between the user and system and the algorithm can eventually restrict the information available to the user. This also raises questions about the ethics of using such models if they, even inadvertently, lead to the manipulation of users and perhaps to discrimination against others.

There are several ways that bias can creep into machine learning algorithms.

One is through biases in the sampling to create the dataset. For example, if the sampling for a dataset that was supposed to be representative of the population’s shopping habits was only performed at a university, the results from the final dataset would be inherently biased because the sampling would over-represent the student demographic.

Iterative bias, common in userrecommendation systems such as those found on most online shopping platforms, is created by a feedback loop between the

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Prof Olfa Nasraoui’s students at the Knowledge Discovery and Web Mining lab.

Rrom left to right: Wenlong Sun, Mahsa Badami, Gopi Nutakki.

user and system. For recommendation, it is impossible to train the algorithm on stale benchmark datasets which is why Professor Nasraoui and her students Wenlong Sun and Mahsa Badami, along with collaborator Prof Patrick Shafto, have created cognitive models to try and benchmark such rating systems and also what are called counter-polarising systems.

These break the positive feedback loop between the user and system and encourage the recommendation of items that will be genuinely new to the user, freeing them from their algorithmic chains and feedback loops.

OPENING THE BOX All of these factors are why Professor Nasraoui feels there is a pressing need for transparency in machine learning models.

Many models are ‘black boxes’, such

as deep learning networks and matrix factorisation. This means that the model cannot give explanations for why certain results are achieved. The results obtained may be accurate, but it is not clear how they were obtained so it is difficult to probe their reliability.

Open, or ‘white box’ systems, are typically less accurate but the rules and decision trees which are utilised in the process are interpretable. This offers several advantages. It is possible to assess the validity of a prediction or, if there are errors, understand why these prediction errors occurred. Professor Nasraoui and her former doctoral student Behnoush Abdollahi have been developing such a system for recommendations that continues to proactively learn to make explainable predictions, overcoming

Prof Nasraoui (centre) at the Doctoral hooding ceremony with her former PhD students, Behnoush Abdollahi (left) and Gopi Nutakki (right).

issues with accuracy, but tries to remain more explainable in its decisions and results than alternative black box methods.

CAREFUL DECISIONS Professor Nasraoui’s work as part of the Knowledge Discovery and Web Mining Lab has far-reaching implications in the Transparency Fairness fields of big data and machine learning.

The issue of bias in data, either through sampling or issues with feedback loops in the algorithm, means that the results Data ML Model Prediction of any machine learning approach should be carefully considered and Professor Nasraoui has been developing tool and algorithms to do that. She is also working on alternative approaches to black box Explainability methods that may help users make fully Module informed decisions about the data they are using, something that is becoming increasing critical with the growing reliance on the results of these types of Explainability plays a critical role in transparency. The latter is a pillar of fairness in machine learning models. analysis.

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Behind the Bench Professor Olfa Nasraoui

E: olfa.nasraoui@louisville.edu T: +1 901 491 3851 W: http://webmining.spd.louisville.edu

Knowledge Discovery & Web Mining Lab Dept. of Computer Engineering & Computer Science Speed School of Engineering University of Louisville Louisville, Kentucky 40292 USA Bio Olfa Nasraoui is a Professor of Computer Engineering and Computer Science, Endowed Chair of e-commerce, and the founding director of the Knowledge Discovery and Web Mining Lab at the University of Louisville. She received her PhD in

Q&A

Can you discuss an example of biased machine learning results causing poor decisions?

I can think of two cases: Filter bubbles: Suppose that an algorithm learns that you like a certain category of news simply because you happened to have clicked on a few popular items at some initial point, and then all news starts getting filtered through this narrow lens built by the model. If all the news you see happens to be visible to you because it passed through the algorithmic filter, and you therefore do not click on any alternative views, the algorithm will perceive your limitation in discovery as a narrow interest and will keep reinforcing its filter, hiding even more diverse options from your recommended items.

Computer Engineering and Computer Science from the University of MissouriColumbia in 1999. She has more than 160 refereed publications, including over 40 journal papers and book chapters and eight edited volumes.

Research Objectives Professor Nasraoui’s work focuses on Big Data. She examines how Machine Learning can lead to unreliable and biased models, problems around explainability and whether increased personalisation contributes to polarisation of opinions.

Unfair predictions: Suppose that an algorithm learns a predictive model for some risk scoring using data about people that includes certain demographic attributes. If the data itself hides some systemic societal biases, then the predictive model will simply learn and echo those biases. One example is a model to predict which individuals are likely to be indicted for consuming illegal drugs when people from certain ethnic backgrounds tend to be suspected, screened, arrested, and prosecuted at a higher rate.

Do users notice when extensive content filtering is occurring with feedback loops?

Most users are not aware that advanced algorithms act like gateways between them and the information they could potentially discover. Often users are missing out on information that could be discovered without even realising it. This is the biggest danger to discovery.

Funding • National Science Foundation • Kentucky Science & Engineering Foundation Collaborators Students: Wenlong Sun Former students: Behnoush Abdollahi , Mahsa Badami, Gopi Nutakki Colleague: Prof Patrick Shafto, Rutgers University, who collaborated with Professor Nasraoui on her work on filter bubbles.

Are white box algorithms more difficult to create than black box ones?

White box models are easier to create.

However they tend to be less powerful than black box models in making accurate predictions. This is one reason why black box models are popular.

Given the importance of machine learning algorithms, will there be standards and legislation around using ‘fair’ algorithms?

This has already started: the European Union recently passed a law requiring that algorithmic predictions that have an impact on humans must provide an explanation for the reasoning behind the prediction. The city of New York is also considering a bill that will assign a task force to monitor the fairness of predictive algorithms that influence decisions concerning people to try to prevent biased and unfair algorithms that discriminate.

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Engineering & Technology ︱ Dr Liz Jenkinson

Fossilising fossil fuels with green alternatives

Green Biologics are a renewable chemicals company who are not only changing the face of renewable chemicals, but are changing the world while they are at it. Dr Liz Jenkinson is one of the lead researchers at the company, and it is her work that is providing the answer to the question: is there an alternative to fossil fuels? Her work proves that the answer is yes, and that it only relies on three key components – bacteria, genetic engineering and sugar.

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ith the unprecedented threat of climate change making the planet’s temperature warmer year on year, there is a growing need for greener, environmentally-friendly alternative products. It has been well documented over the years that fossil fuels are in limited supply and yet, they are the source used to power the world.

They run our cars, heat our homes, and are even used to produce a variety of products such as medicines, cosmetics, plastics and lubricants. If you brushed your teeth this morning, or if you have ever played tennis, the toothpaste and balls you used were probably produced using fossil fuels.

This is where Green Biologics and the excellent work of a dedicated team of molecular microbiologists, analytical chemists and fermentation scientists comes in. The Oxford-based institution and its US-based subsidiary have recently opened the first renewable ABE manufacturing plant in the USA since the second World War, to convert the sugar from corn into the products acetone and n-Butanol along with by-products of corn oil and animal feed. These chemicals and their modified derivatives can then be used in a wide range of everyday products directly replacing the same chemicals that are currently made from fossil fuels.

So, the question is: if we are to reduce our dependency on fossil fuels, how are we going to continue our modern way of living?

FROM MANCHESTER TO OXFORD GBL’s research follows on from the original acetone–butanol–ethanol (ABE) fermentation work carried out

Green Biologics’s research follows on from the original acetone–butanol– ethanol fermentation work carried out in 1912, using a bacterium called Clostridium as a biocatalyst to create n-Butanol and acetone

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in Manchester back in 1912. This discovered a method that could use bacterial fermentation (the conversion of sugar into products) to produce acetone, n-Butanol, and ethanol from carbohydrates such as starch and glucose. Over a hundred years later, Green Biologics have taken this concept many steps further. Their research follows the same principle of bacterial fermentation, using a bacterium called Clostridium as a biocatalyst to create n-Butanol and acetone but Green Biologics have improved both the bacterium and the process to produce cost-effective, higher-quality chemicals when compared to the fossil-derived versions. These chemicals can then be used directly or reacted to make derivatives, before being used in products such as paints, fragrances, cosmetics, lubricants and even as ingredients for food.

JUST A SPOONFUL OF SUGAR‌ The whole process, in effect, revolves around breaking down sugar, and converting it into n-Butanol and acetone via bacterial fermentation using Clostridia microbial strains. The simpler and more accessible the sugars, the more efficient this process is. For example Clostridia will quite happily ferment glucose which is a C6 sugar or xylose which is a C5 sugar. However, the feedstocks used for a commercial fermentation process are rarely simple and without this, the Clostridia microbial strain is unable to ferment correctly to produce the required products quickly enough and at high enough concentrations. ...HELPS THE CLOSTRIDIA FERMENT‌ The team at Green Biologics have overcome this issue through a combination of advanced engineering and strain improvement methods. Using methods such as adaptive lab evolution, they have developed improved clostridial strains to use in the process of breaking down C5 and C6 sugars and for overcoming a number of other challenges associated with this type of fermentation. Not only that, but as these strains have been produced without the need for genetic modification (GM), they are natural and safe to use at the Minnesota plant.

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…IN THE MOST DELIGHTFUL WAY This plant – known as Central Minnesota Renewables – currently uses the ABE fermentation process with Clostridia to ferment sugars found in corn. However, it is hoped that future research and technological developments will move the process towards using sugars found in lignocellulosic feedstocks (i.e., corn stover, bagasse, woody biomass).

Currently, the C5 and C6 sugars contained within these feedstocks are inaccessible to Clostridia and are unable to be broken down directly. Future research will therefore look to establish hydrolysis pre-treatments that will allow the sugars to be accessed and converted.

This is just one of Green Biologics’s current research focuses, progressing in conjunction with Dr Jenkinson’s ground-breaking work using CLEAVE™ technology. This technology is a different way of applying CRISPR gene-editing technology, designed to make highly specific changes in the clostridial DNA (for example deleting a specific region of a gene or making a single base pair change). It can also be used to integrate specific genes into Clostridia microbial strains. These genes can be pinpointed, edited and developed to incorporate the new functionalities required.

In other words, CLEAVETM technology has provided Dr Jenkinson and her team with a breakthrough technology capable of expanding and diversifying their product range. Using this innovation, clostridial microbes can be effectively converted into small chemical factories which, with the application of genomic editing and synthetic biology techniques, can develop more products than the

butanol and acetone produced during ABE fermentation.

CLEAVING CLOSTRIDIA The ability to edit genomes and utilise synthetic biology within Clostridia enables new biological pathways to be added or removed. This, in turn, generates different products that can be utilised across different industries.

In one example of Dr Jenkinson’s work, a novel pathway was added to the fermentation process using CLEAVETM technology to produce a chemical particularly valuable within the food industry. In another example, CLEAVETM was used to alter the ratio of butanol and acetone produced during the ABE fermentation process, depending on the quantity required and the value of each product. Not only that, but by optimising and inserting new enzymatic genes into the Clostridia, the microbes can be modified to break down more complex carbohydrates, which supports and ties into Green Biologic’s other area of research – accessing sugars contained within lignocellulosic feedstocks.

A SWEET FUTURE Although the research undertaken by Dr Jenkinson and her team is yet to be published, the emergence of CLEAVETM technology as a potential, scientificallyproven, alternative method to fossil fuels is ground breaking work, and is likely to change the world as we know it. The ability to develop a diverse range of products using Green Biologics’ methods will not only help the environment, but it will also provide a platform on which further beneficial research can take place.

The emergence of CLEAVETM technology as a potential, scientifically-proven, alternative method to fossil fuels is groundbreaking work, and is likely to change the world as we know it 60

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The Biomass route to the consumer

Biomass

C5 and C6 sugars Bio-based n-butanol & acetone Bio-based esters and derivatives Formulated products Consumers

Behind the Bench Dr Liz Jenkinson

E: liz.jenkinson@greenbiologics.com T: +44 (0)1235 435710

Office: 80F Park Drive, Milton Park Abingdon, Oxford OX14 4RY UK Lab: 45A Western Avenue, Milton Park Abingdon, Oxford OX14 4RU UK Bio Dr Jenkinson received a Bachelor’s degree in Molecular Genetics in Biotechnology at Sussex University before undertaking a PhD in Biology at York University. She is currently the

Q&A

What made you decide to get involved with Green Biologics?

When I joined, the company was still working in many different areas, including research contracts, before focusing on Clostridia and chemical production. For me the interest was in the science – we were working with bacteria that are not standard lab strains therefore we had lots of challenges to overcome and that was what drew me in.

Why is finding green alternatives to products typically derived from fossil fuels so important to you?

There is a need to find alternative ways of making these chemicals. Using microbial fermentation is one way to do this whereby we can take waste and convert it into something useful.

Ultimately these processes can be both renewable and sustainable, they can reduce greenhouse gas emissions, and they can provide some security regarding supply chains.

How likely is it that your technology could replace fossil fuels as a power source (rather than as a source of chemicals to use in products) in the future?

Right now the challenge with using the bio-butanol from our process as a

W: www.greenbiologics.com

head of the strain development team at Green Biologics, utilising her expertise in molecular biology to develop key tools capable of manipulating Clostridia microbial strains. She is also in charge of several Innovate UK funded grant projects, primarily focused on synthetic biology.

Research Objectives Dr Jenkinson’s research focuses on using microbial engineering and synthetic biology techniques to utilise Clostridia microbial strains as biocatalysts. She and her team at Green Biologics aim to provide

biofuel is related to cost. Butanol can be used instead of petrol and the founder of Butylfuel, Dave Ramey, has shown this by driving a Buick across the US powered by 100% n-butanol (http://www.butyldude. com/the-2005-trip.html). At the moment, our production costs cannot compete with petrol, primarily due to the cost of feedstocks. In an ideal process our feedstock costs would be minimal, using waste that would otherwise be burnt or left to breakdown naturally. However right now, the sugars contained in these lignocellulosic feedstocks are generally inaccessible to our strains and the pre-treatment processes are either not efficient or economic to use at scale. As these technologies mature, the costs of production will come down and in the future it is feasible that bio-butanol could be used as a fuel to power our cars.

Why did you choose to use Clostridium as the bacterium in the fermentation process?

Solventogenic Clostridia have previously been used as industrial microbes for the production of ABE; therefore, we know they are robust enough to be scaled up.

The process itself, however, fell out of favour when it could no longer compete economically with petrochemical-derived products. In the last 15–20 years our understanding of these microbes, the advances made in genomics and in genetic manipulation technologies and

@GreenBioLtd

customers with more sustainable, green alternatives for everyday products such as paints, cosmetics and food ingredients.

Funding Green Biologics has benefitted from private and public funding including investors Swire Pacific, Sofinnova, Capricorn Ventures, Morningside and Oxford Capital partners, and UK, European and American agencies including Innovate UK, Horizon2020, ERANET, and US Department of Energy

the advances made with fermentation technology development mean we can be competitive again, especially in the high-value market sectors.

Synthetic biology has great potential for engineering organisms to make products that we need, but if we can work with nature to give us a head start, as we have with Clostridia, then we are more likely to be successful.

With the recent purchase of a manufacturing plant in America, will Green Biologics continue to expand in the future?

That is the idea. Our first commercial plant at Little Falls, Minnesota began production in 2016. We are currently producing butanol and acetone and selling them to chemical companies and directly blended into consumer products. Our first product, Greenflame™ charcoal lighter fluid is now available in stores in the US (www.greenflame.com). Over the next 12–18 months, production of acetone and butanol will be ramped up and in the meantime we are looking for potential new plants in the US or Europe. Ultimately, we will introduce new products developed through CLEAVETM to develop biorefineries making a range of renewable chemicals.

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Thought Leader

ESEB: Helping evolutionary biology evolve in Europe Evolution has been shaping our planet’s inhabitants for billions of years, and it continues to do so. Since its inception in 1987, the European Society for Evolutionary Biology (ESEB) and its members have worked to further our understanding of the complex subject, and its president Professor Laurent Keller is no exception. Professor Keller spoke with us at Research Outreach about the society, his experience as president, and where he sees evolutionary biology in the future.

T

he European Society for Evolutionary Biology (ESEB) has approximately 1,400 members mainly from across Europe. From students to professors, members of the society share a passion for evolutionary biology. Since it began 30 years ago, the society has shaped the direction of research into evolution throughout Europe. It has helped researchers by providing a networking platform, conferences and funding and introduced

useful suggestions and help implement all our decisions.

How has ESEB evolved over the years since its inception back in 1987, and what are the society’s current main strategic focuses?

There has been a large increase both in our membership and our finances.

We receive more money now, which has allowed us to develop quite a few different products. For example,

student meetings every two years. In addition to this, we provide special topic networks if people want to develop a new topic and so, they have a meeting to do that which we will also sponsor.

Do you think research for evolutionary biology receives as much funding and attention as it should?

I’d say it depends on which countries. In some countries, there are good funding opportunities like here in Switzerland,

The incentive to develop this journal and the society was to develop the research and study of evolutionary biology in Europe two academic journals. At the forefront of the ESEB is Professor Laurent Keller a Swiss evolutionary biologist.

Research Outreach spoke to Prof Keller about all things evolution, from what it is like to be president of the society to where the future of evolutionary biology is heading. He discusses why evolution should play a part in medical research, and the countries that are leading the way in evolutionary biology.

Hi Laurent! Could you please describe for us your role as President within the European Society for Evolutionary Biology?

The society has an executive committee, which consists of a president, a vice president, a secretary, and so forth. This executive committee is key to the central decisions of the society. As president, I try to make

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ESEB is financing outreach projects for more than five years. This has turned out to be one of our most successful and popular initiatives, through which members are proposing highly creative concepts to bring the topic of evolution to the general public.

A more recent and related activity is called the Global Training Initiative.

This is slightly different. It is designed more for scientists, but for countries where there is little research on evolution or a bad perception of evolution. We try to help scientists in these countries to meet and communicate together. This will typically be in countries where the topic of evolution and its research is limited, like in Turkey.

We provide the opportunity to develop different meetings and we also sponsor

for instance. However, there are many countries in the world that tend to fund more applied research. In these countries, it’s more difficult to get money to conduct evolution-based research than in other countries.

The ESEB produces the wonderful Journal of Evolutionary Biology. What difference does it make in terms of spreading ideas and data?

The original aim of this journal was to aid the development of evolutionary biology research in Europe as this was more underdeveloped in comparison to the US. While evolutionary biology research was prevalent in some countries in Europe, like the UK, it was very limited or non-existent in other countries. I think the journal and the society have been very useful and successful in further developing the field of evolutionary research in Europe.

What do you make of the open access movement?

That is a difficult issue but a very important one. Editors and publishers of scientific journals make a lot of profit. I truly believe in the concept of open access and the movement itself. Although, at some point, people must pay to publish and you have two options. The first option is where the researcher will pay to publish or the second option being that the readers pay an article access or subscription fee.

I think neither of these two options are

perfect. However, the worst case can be journals which are not open access but allow authors to pay to have their articles open access. Although they claim the contrary, I believe those journals get paid twice (by libraries which subscribe to the journal and by authors who want to make their article open access). In my opinion, it should be either those publishing or those reading who pay – not both.

Award in which you have a large say in whom the award goes to. How difficult is it making that decision?

The Presidents’ Award is a new award, so there’s only been one person who has received it. We have our next meeting in the summer of 2018 in Montpelier where myself, the previous president and the president-elect must select a researcher for the award.

ESEB offers several award initiatives to show recognition for evolutionary biologists, including the Presidents’

We also have the Maynard Smith’s Award, which is given to young researchers, and this has been quite

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successful. There’s a special committee where people can nominate researchers for the award and then the committee selects from the nominees.

From a more personal perspective, your research has seen you win numerous awards yourself over the years, including the Marcel Benoist Prize in 2015. Does winning these awards make all your work feel worthwhile or are they just an extra bonus for you?

I always enjoy conducting research and my work was already recognised before receiving the award, so I see it more as an added bonus. I think it is a fantastic recognition and every researcher naturally likes to be recognised.

ESEB hold a congress once every two years. How successful are these events and how important are they to ESEB as a society as well?

These events are extremely successful.

The previous ESEB congress was in Lausanne, and we had to limit the number of participants. We are now reaching a stage where we have approximately 1,400 people applying, and for many places, it’s difficult to host an event with such a large number of people. Therefore, those meetings are extremely successful to the point that they become almost too large.

Fast-forwarding ten years into the future, what kind of state would you like the field of evolutionary biology to be in? Are there any areas you are particularly excited about over the coming years?

I would hope to see that there’s more interaction between different fields and evolutionary biology. I can think of at least three different fields. One is primarily medicine. When talking to a medical practitioner, I would point out that, “Humans have evolved; therefore, we must understand evolution and our interaction with other species to obtain

a better basis of understanding”. For example, with the AIDS virus, people have now realised it’s evolving. We need phylogenies (a phylogenetic tree is a branching diagram or “tree” showing the inferred evolutionary

relationships among various biological species or other entities) to understand where viruses come from. So that’s one field that is developing – the interaction between evolution and medicine.

Humans have evolved; therefore, we must understand evolution and our interaction with other species, to obtain a better basis of understanding

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Thought Leader

The same is also true with agriculture.

The animal species we are consuming have greatly evolved over the last thousands of years because us humans have selected species to be more productive.

regulate gene expression. All these processes evolved by natural selection, and I am sure there is still a lot to learn about the selective forces acting on gene regulation and the evolution of our genomes.

The third field linked to evolutionary biology that is also very interesting, is molecular biology. I think there is a lot to benefit by having more interaction between evolutionary biologists and molecular biologists. People have started to realise that there are many ways in which an organism can

• For more information on evolutionary biology and the European Society for Evolutionary Biology (ESEB), please visit their website at www.eseb.org.

Contact

Professor Laurent Keller Department of Ecology and Evolution Biophore University of Lausanne 1015 Lausanne Switzerland E: Laurent.Keller@unil.ch W: http://eseb.org/

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Biology ︱ Dr Mauricio Rodriguez-Lanetty

Development of immunity in basal metazoans Dr Mauricio RodriguezLanetty from Florida International University (FIU), is currently conducting research that focuses on immunological priming in corals and anemones, a process by which an animal can resist pathogens through repeated, non-lethal exposure.

As corals are at risk due to climate change, this is an important project to help further our understanding of their immunology. The project also includes an outreach programme to motivate minority students to pursue science as a career.

C

oral reefs are one of the most important ecosystems on the planet as they support a wide and diverse array of organisms and human activities. Unfortunately, however, they are also one of the most vulnerable.

Corals are categorised as anthozoans, a class shared by anemones, and are made up of small, colonial animals which come together to create reefs. As coral tissues contain symbiotic algae, they can only live within a “goldilocks zone”, where the waters are suitably warm and where the algae receive enough light to photosynthesise and support their coralline hosts. Climate change has reduced the size of the area habitable by corals due to ocean warming, and has caused further issues that include ocean acidification and an increased prevalence of coral diseases.

As such, swathes of reef are being lost

cause. Dr Mauricio Rodriguez-Lanetty is currently leading a programme to research immunological priming in anthozoans and determine if these animals can be inoculated against disease. His programme will also provide educational and research experiences to high school, undergraduate, and postgraduate students to inspire the next generation of scientists.

CORAL DISEASE Not only are corals very visually appealing, attracting thousands of tourists every year, they provide numerous services to local populations.

They act as nurseries for fish, support fisheries, and protect coastlines from facing the full force of storms. They are also home to thousands of animals and are areas of high biodiversity. As such, it is vital that we find ways to

Research suggests that immunological priming could have developed much earlier in the evolutionary tree around the world due to bleaching (when symbiotic algae leave their coral host).

It is imperative that we find ways to improve corals’ resilience against worsening environmental conditions and the range of problems they can

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protect them against the changing environment.

One recent problem faced by corals is the prevalence of pathogens, which has been exacerbated by climate change.

As corals are very long-lived (some can survive for hundreds of years), it

is expected that they will encounter the same pathogens at several points during their lives. Therefore, it is believed that, through repeated lowlevel exposure, corals may build up a resistance against disease-causing pathogens. However, this area of science is highly under-researched.

ANEMONES AS MODELS To further our understanding of disease resistance in corals, Dr RodriguezLanetty studies the immune response of anemones as a model system.

Anemones are easier to cultivate in laboratories, where they also have symbiotic algae and undergo bleaching, making them suitable replacements for coral species in research.

The brown anemone, called Exaiptasia pallida, is used in the “CAREER: Exploring the Immunological Priming in a Basal Metazoan (Anthozoan)” programme. This species is found in the western Atlantic Ocean, sharing the same waters as Caribbean reefs.

It is likely to encounter the same pathogens as corals in this area, making it susceptible to certain diseases that allow it to be used in place of corals in this research. By studying immunological priming in brown anemones, our understanding of the processes behind immunological defence in anthozoans, and the evolution of immunity in basal metazoans (species that diverged early on in evolution and have remained relatively unchanged since) will expand.

IMMUNOLOGICAL PRIMING Immunological priming is a process by which the immune response of an organism is strengthened by repeated exposure to a pathogen. This is common in more advanced species, such as humans and other vertebrates, but research suggests that priming could have developed much earlier in the evolutionary tree.

In his initial research proposal for the CAREER programme, Dr RodriguezLanetty hypothesised that sub-lethal exposure to a pathogen could result in anthozoans establishing a defensive response that they will be able to express more effectively when they encounter the pathogen again in the future.

To determine if this is the case, brown anemones were repeatedly exposed to Vibrio coralliilyticus – a bacterial species known to cause morbidity and bleaching in both corals and anemones.

It was found that three days of exposure to the bacterium could be considered “sub-lethal”, and anemones exposed to the pathogen twice were more likely to survive future encounters to it, than those naïve to it. This is an exciting finding that suggests learnt

Anemones exposed to the pathogen twice were more likely to survive future encounters to it than those naïve to it

immune responses such as this are not limited to complex vertebrates. As a result, this has opened many doors for further research into the immunological processes of anthozoans.

Differences in proteins between unexposed and exposed anemones were also identified, suggesting that this defensive mechanism is controlled at a molecular level. The identified proteins were similar to genes associated with immune responses in other organisms. One in particular was similar to inotropic glutamate receptors (iGluR), which are associated with neurotransmissions in animals with a nervous system, and are common in exposed anemones. Again, using brown anemones as a model system, nine iGluR-like genes were identified and found to change when the animal was exposed to a pathogen. This is a particularly interesting finding, as it suggests these types of receptors are more widespread than previously thought, and that they originated as mechanisms for sensing cues early on in evolutionary history.

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HSP

Binding of peptides to HSPs

TLR

1

HSP

2 Complement system

3

4 6 HSP

Pathogen taken up

by Phagocytosis

Lyosome

8

Capthesin

?

DAMP

CAREER DEVELOPMENT Inspiring future generations is a vital part of the scientific process. An important component of the CAREER programme is outreach to students from high school to postgraduate levels, and particularly to minorities who are underrepresented in science. This is highly important as it encourages those that may not pursue careers in science to consider entering the field.

By 2050, 60% of the US’ population growth is expected to originate from the Hispanic community, however, Hispanic people are the least likely to enter higher education. For this reason, the

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Transcription factors NF KappaB

7

TLR

5

iGluR

Based on these findings, future research will assess whether host responses to repeated infectious agent exposure are pathogen-specific, and how symbiotic microbes respond to immunological priming. These are exciting areas that with further improve our understanding of disease resistance in anthozoans.

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Increased expression of pro-inflammatory mediators

Proposed model of Heat Shock Proteins (HSP), Capthesin and Glutamate Receptor (iGluR) roles in cnidarian molecular defense priming: (1) HSP are up regulated and some are extracellularly secreted where bind to peptides and act as DAMPs; (2) as DAMPs, HSP help with a faster activation of the innate complement system, and/or (3) interact and cause a quicker activation of outer host cell membrane TLRs; (4) intracellularly, up-regulated HSP proteins can be delivered into lysosomes in which they can also interact and activate endosomal cell membrane TLRs; (5) higher production of Capthesin are delivered into lysosomes in which they can also interact and activate endosomal cell membrane TLRs; (6) activated TLRs either from the outer membrane or endosomal membranes will trigger cell signaling pathways that will converge in the activation of transcription factors (likely NF-kappa β) that will ultimately induce the expression of immune-related genes (7) resulting in the production of potential pro-inflammatory molecules; (8) Higher expression of iGluR expressed on the outer membrane will also facilitate a faster sensing of potential DAMPs upon secondary exposure of pathogens. Adapted from a figure originally published in SCIENTIFIC REPORTS under the Creative Commons CC BY 4.0 license.

educational aspect of the programme focuses on engaging Hispanic students and other minorities.

Conducting a summer science programme entitled “Aventura Cientifica”, Dr Rodriguez-Lanetty hopes to motivate minority high school students to consider scientific research as a career. This is inspired by his own experiences, attributing a large part of his success to the positive role models he encountered throughout school and extra-curricular activities.

Aventura Cientifica is a four-week long experience held at Florida International University that will involve high school students in subjects included in the CAREER programme, improving their confidence and appreciation for science.

This is vital to ensure that people from all backgrounds have opportunities to advance their interests in science and ultimately pursue a career in research.

It will also enable the future generation to continue protecting the environment, which will become increasingly more important over the coming years.

Behind the Bench Dr Mauricio Rodriguez-Lanetty

E: rodriguezlanetty@gmail.com; rodmauri@fiu.edu T: +1 337 254 7136 W: http://imageslab.fiu.edu W: http://biology.fiu.edu/portfolio/mauricio-rodriguez-lanetty/ Research Objectives Dr Rodriguez-Lanetty’s research programme will elucidate the specificity, memory and molecular basis of the defence response of corals upon repetitive encounters with pathogens. Understanding how the immune system of these organisms responds to pathogens may offer insights into the resilience of these ecosystems, and potentially may inform remediation of them.

Funding National Science Foundation (NSF)

Q&A

What first sparked your interest in corals?

Coral reefs encompass one if not the most productive and diverse ecosystems within the marine realms, housing hundreds of thousands of species from single-cell microorganisms to spectacular colourful fish vertebrates. What is incredible, is that a symbiotic association between reefbuilding coral hosts and photosynthetic microalgae living inside the corals powers the foundation of such ecological success. The mysteriously intricate cellular communication of these mutualistic associations in which both host and symbionts benefit from each other, caught my research interest early on during my career as scientist. Unfortunately, coral reef ecosystems are in decline because of the threats of local man-made disturbances and global climate factors such as ocean warming and acidification. Many maladies linked to these stressors such a coral bleaching and diseases are on the rise.

My current motivation is to find solutions and remedies to mitigate the problems currently affecting corals.

What must be considered when using anemones as proxies for studying corals?

Coral species are very slow-grower organisms that on average, extend their calcareous skeleton a few centimetres per year, and consequently, this poses a challenge to set up well replicated experiments that can be conducted in a reasonable timeframe to study how corals function and how they respond to biotic and abiotic factors around their changing environments. Hence, a surrogate model to study corals has been

Collaborators The work and experiments of cnidarian immunology is being conducted in collaborations with Biologists from Florida International University. Graduate students: Tanya Brown and Ellen Dow. Postdoctoral Fellow: Dr Anthony Bellantuono.

Bio Dr Mauricio Rodriguez-Lanetty is an Associate Professor at Florida International University (FIU, Miami). After obtaining a bachelor degree in Biology in Venezuela, Dr Rodriguez-Lanetty achieved a PhD

in need. Over the last ten years, several of us in the field of coral biology have proposed and are actively working using the sea anemone Exaiptasia pallida, as a model organism to study corals. The important features considered in this selection were attributed to the fact that these anemones engage symbiotically with similar microorganisms as corals do and therefore, make them good proxies to study coral biology and ecology.

Furthermore, these anemones are fast growers and easy to culture in captivity and in laboratory conditions. A great advantage of this system is that clonal populations of anemones can be raised from a dozen of individuals to a population of hundreds in a matter of a months in the lab. All these features make the anemones the right ‘laboratory mouse’ to study corals.

How similar are the immune responses of anemones to our own immunological priming mechanisms?

In many cellular and molecular aspects, there are considerable differences between the immune system of anemones and those from humans, however, we have also learned they share more similarities that we once considered the long evolutionary history separating anemones from us.

Anemones, and all invertebrates lack of the cellular components of the adaptive immune system, such as T cell and B cells (Lymphocytes), has led to the assumption that evolutionary early diverged invertebrates do not have the capability to develop a trained or acquired immunity. Nevertheless, our recent phenomenological findings, in concordance with results from insects, have revealed that the defence system

in Marine Studies from the University of Queensland (Australia) and is now the Principal Investigator of the IMAGES lab at FIU. Contact Dr Mauricio Rodriguez-Lanetty Associate Professor and Director QBIC Programme (Quantifying Biology in the Classroom) Department of Biological Sciences Florida International University 11200 SW 8th St; Miami, FL 33199 USA

of sea anemones display some degree of acquired immunity with a mechanism yet to be fully understood. Also, anemones and humans share many components of first line of defence, the innate immune system, composed of conserved Pathogen Recognition Receptors (PRRs) that sense and distinguish large groups of PathogenAssociated Molecular Patterns (PAMPs) found on many infectious microbial pathogens.

Is there much crossover between the pathogens encountered by anemones and corals?

We do not know yet the degree in which natural populations of sea anemones are affected by the same pathogens causing infections on corals, and this type of research exploration is currently being undertaken. Having said that, we have shown that many identified infectious pathogens affecting coral species also cause disease sign development on E. pallida anemones, which adds strength to our model system for studying cnidarian immunology.

How successful has the outreach programme been so far?

The educational summer scienceexperience workshop (Aventura Cientifica) tailored for high school students has been very successful. We have run it twice with a total of 40 students that have already participated in the programme. We even have some students continuing their science involvement after completing the workshop either in their high schools or in University research laboratories. Our plan is to expand and enlarge the participation of students over the next three remaining years of the programme.

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Biology ︱ Professor Allen Liu

Synthetic cells have senses too What defines a living cell?

How to capture the molecular essence of life? These fundamental questions underpin the collaborative research programme led by Prof Allen Liu at the University of Michigan and Prof Vincent Noireaux at the University of Minnesota. The pair uses molecular components to construct prototypes of synthetic cells displaying the minimal characteristics of life.

Their ‘cell analogs’ shed light on basic biological processes, and also provide new tools for biotechnology and medicine.

B

iologists and philosophers have long pondered the question, “What are the hallmarks of life?”

Whilst many scientists attempt a topdown approach to the issue based on the organisms we see around us, Prof Liu and Prof Noireaux are pioneers of an alternative, bottom-up approach. Their long-term goal is to construct a functional, living cell from scratch, something that has never been done before but now through their efforts appears conceivable.

LIFE AT A MINIMUM To build a synthetic cell, Liu and Noireaux have identified three essential ‘modules’ that they consider define a functional living cell. Their aim is to bring these modules together in the lab to first construct models of ‘minimal cell’ capable of recapitulating complex biological functions. It is an essential step before moving towards a full minimal cell (a cell that displays only the minimum requirements for life), and, in doing so, characterise the essential elements needed to sustain life.

The three essential modules are information (the instructions for building cellular components, held

Foundation (NSF) project, ‘Construction of DNA Programmed Minimal Cells with Membrane Mechanosensitive Functions.’

Although construction of synthetic biological cells now appears plausible, no functional minimal cells have yet been constructed from basic molecules. Liu and Noireaux believe that their modular approach should enable the integration of multiple molecular components through carefully characterised connections, to create the artificial cells capable of incorporating multiple cellular functions.

INFORMATION IS POWER Using elements of the molecular machineries of the bacterium Escherichia coli, Liu and Noireaux have developed a cell-free system that can transcribe and translate the information in a DNA sequence into the proteins that carry out cellular functions.

Transcription (the copying of the DNA code onto a template RNA molecule) and translation (the construction of proteins using this RNA template) are both achieved in the team’s unique

Phospholipid bilayers are direct analogues of the membranes surrounding cells in nature in a DNA sequence), metabolism (energy generation, building blocks synthesis and cycling), and selforganisation (encapsulate information and metabolism within a physical boundary). All three are included in Liu and Noireaux’s National Science

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cell-free transcription-translation (TXTL) system, which forms the basis for their minimal cells. The TXTL system is already being taken up by industry as an alternative means for synthesising proteins, but its role in the lab is even more exciting.

ORGANISATION IS KEY In the Michigan-Minnesota system, the TXTL machinery is encased in a small, cell-sized compartment called a liposome. Liposomes make use of the simple fact that fats (lipids) do not dissolve in water. A double layer of molecules, each comprising a hydrophilic (water-loving) group such as a phosphate and a hydrophobic (lipid) component, when placed in water, will spontaneously orient itself to form a membrane-bound sphere, with the lipids pointing into the centre of the membrane, shielded from the water on either side by the phosphate groups. These phospholipid bilayers are direct analogues of the membranes surrounding cells in nature. Once the TXTL system is encapsulated into liposomes, this system fulfils the first two modules required for life: enabling execution of genetic programmes to stimulate cell construction and function in a controlled environment.

MAKING METABOLISM POSSIBLE Having encased the information system inside a liposome, the final, and perhaps most challenging part of building a minimal cell is to enable it to communicate with the outside world.

To metabolise, grow, and reproduce, the minimal cell must be able to take in sources of energy across its membrane, expel waste products in the opposite direction, and respond to signals received from the surrounding environment.

Liu and Noireaux’s current work is focused on integrating molecular channels in the membrane of the liposome, which respond to environmental stimuli by opening or closing. Modelled on another system found in Escherichia coli, they have built a DNA sequence that encodes a membrane channel protein called MscL. MscL is ‘mechanosensitive,’ that is, it opens and closes in response to

osmotic pressure (the pressure created by the difference in concentrations of the dissolved molecules in the surrounding water and the inside of liposomes).

To test the function of the MscL channel, they also encoded in the DNA of their minimal cell an engineered protein called G-GECO, which fluoresces in response to calcium ions.

Thus, when calcium molecules present only on the outside pass through the membrane via MscL, G-GECO responds by fluorescing.

A BIOLOGICAL ‘AND GATE’ Liu and Noireaux describe this minimal cell system as the synthetic, biosensitive ‘AND gate’ (a system that requires two inputs to produce a response). In this case, the two inputs are mechanical (osmotic pressure) and chemical (calcium ions). When osmotic pressure causes the MscL channel to

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osmotic pressure

external calcium

dsDNA mRNA

AND

biosensing membrane-active property

Ca2+

fluorescence

Lipid

G-GECO

Lipid

G-GECO

(Top left) Schematics of protein synthesis by TXTL in synthetic cells. (Top right) AND-gate output with osmotic pressure and external calcium as inputs. (Bottom) Increase in osmotic pressure triggers mechanosensitive channel activation leading to G-GECO fluorescence.

Figure adapted from Majumder, Garamella et al., Chemical Communications, 52, 7349-7352, 2017.

G-GECO iso-osmotic Ca2+

G-GECO hypo-osmotic shock open, calcium ions flow through the liposome and activate G-GECO. Thus, say the pair, “We have generated a DNA-programmed cell-sized artificial cell that senses osmotic pressure and external calcium ion concentration.”

Their aim now is to couple this activation to the physical growth of the lipid bilayer (and therefore the cell as a whole) by linking it to the geneticallycontrolled synthesis of lipids from smaller precursor molecules. In this way, the mechanosensitive membrane will facilitate key linkages between the cell’s structure and its DNA, a crucial further development towards true synthetic life.

BETTER THAN BIOLOGY? Liu and Noireaux’s research paves the way for the creation of minimal cells capable of sensing and responding to their environment, a central step in synthetic biology that has been

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The research paves the way for the creation of minimal cells capable of sensing and responding to their environment until now hard to achieve. Their system provides an experimental platform enabling rapid and reliable quantification of the effect of manipulating any aspect of the minimal cell system: the membrane, surrounding solution, and genetic machinery. This should speed up future advances in minimal cell engineering, which may ultimately be able to expand upon the properties found in the cells of natural organisms.

This project relies heavily upon collaboration between laboratories, institutions, and disciplines, to solve

what Noireaux terms the “challenging but conceivable goal” of synthesising the minimal cell. Lying at the interface of biology and engineering, this research increases our basic knowledge of life, stimulates advances in medicine – such as drug delivery – and biotechnology, and provides future scientists studying across these institutions with an exciting introduction to cutting-edge research based on fundamental biological and physical principles. It is not, says Noireaux, “just an exercise,” but a “forward engineering approach.”

Behind the Bench Prof Allen Liu

E: allenliu@umich.edu T: +1 734 764 7719 W: http://liulab.engin.umich.edu Research Objectives Prof Liu and Prof Noireaux’s project aim is to construct synthetic cells, consisting of a cell-free expression system encapsulated into a cell-sized phospholipid vesicle, capable of sensing the environment through its lipid bilayer by expressing mechanosensitive channels.

Funding National Science Foundation (NSF) Collaborators • Sagardip Majumder, PhD student, University of Michigan • Jonathan Garamella, PhD student, University of Minnesota

Q&A

What led you to start researching the idea of the ‘minimal cell’?

The idea of assembling a synthetic cell from molecular components became experimentally conceivable during the 80s and 90s. At that time, these projects were motivated by questions related to the origin of life. The bottom-up construction of cell analogs, using engineering approaches, gained considerable credibility in the past 15 years. This engineering approach to synthetic cell is one of the many outcomes of the post-genome era. Several labs demonstrated that basic biological functions can be recapitulated in liposomes. Allen and I developed interests in these ideas in some of these multidisciplinary labs where novel approaches to studying cells were endeavoured.

How does the TXTL system differ from previous methods of building minimal cells?

TXTL recapitulates the process of gene expression, like in a living cell, but in vitro. This contrasts with two alternative and complementary approaches of building minimal cells. The protocell approach posits the use of self-organised vesicles of essential components of primitive

Bio Allen Liu received his PhD in Biophysics in 2007 from the University of CaliforniaBerkeley. Since 2012, he has been an Assistant Professor in the Department of Mechanical Engineering at the University of Michigan.

Vincent Noireaux received his PhD in Biophysics in 2000 from the University Paris XI. Since 2005, he has been an Assistant, Associate and now Full Professor in the Physics Department at the University of Minnesota.

cells. These bottom-up systems have been attractive for origin of life studies. A more top-down approach is to take full genome in living cells and systematically truncate the genome. This has led to the synthesis of a minimal bacterial genome smaller than any known living organisms. Our approach can be considered as an intermediate of both approaches.

Why is the incorporation of a membrane channel so important?

In living cells, the membrane is the physical boundary that separates the external medium and the cytoplasm.

Engineering membrane is currently the bottleneck in bottom-up synthetic cell engineering for two main reasons.

Firstly, it is hard to develop an active interface that contains functional membrane proteins, for sensing and nutrients exchanges. The second reason is mechanical robustness.

The current synthetic cell models are made of a simple phospholipid bilayer that are not mechanically robust. It is therefore essential to construct synthetic cells with mechanosensitive channels capable of responding to mechanical stress.

What genes or functions would you like to incorporate in your minimal cell next?

The minimal set of genes to get a synthetic cell capable of self-

Vincent Noireaux E: noireaux@umn.edu T: +1 612-624-6589 W: http://www.noireauxlab.org

Contact Prof Allen Liu Assistant Professor of Mechanical Engineering University of Michigan 2350 Hayward Street, Ann Arbor, MI 48109, USA Prof Vincent Noireaux University of Minnesota – Twin Cities Physics and Nanotechnology 115 Unions Street SE Minneapolis, MN 55455-2070 USA

reproduction has been estimated to be on the order of 300-400 genes.

This estimation has been made by several independent studies. It’s a lot of genes and all of them are interesting to incorporate into the current prototypes of synthetic cells. The Liu and Noireaux labs are primarily interested in some aspects of cell mechanics. That is why our work focuses on mechanosensitivity and cytoskeleton, in relation to mechanical robustness, cell shape and division.

Where do you see this research leading in ten years’ time?

It is a growing research area. New approaches to synthetic cells are proposed every year. Many things are going to be done in the next ten years. The most important achievements will be those that really solve the current bottlenecks: mechanical robustness, assembly of a minimal genome in a unique plasmid, successful integration of gene circuits and metabolism into cell-sized liposomes, physical expansion and division of the compartments. To be called synthetic cells, all of these aspects have to be achieved through the inner expression of gene circuits.

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Biology ︱ Professor Carl Johansson

Capturing images and data before the slides degrade into uselessness Microscopic and enigmatic, the tardigrades are little known to science. However, their remarkable ability to enter suspended animation and withstand extreme conditions may support important medical advances. Prof Carl Johansson of Fresno City College, California, and Dr Lynn Kimsey of the Bohart Museum at UC Davis are documenting the amazing diversity of these secretive animals, and at the same time training students from deprived areas to become expert biologists. Together, they have digitised over 40,000 tardigrade specimens, bringing the mysterious ‘water bears’ into the limelight.

A

s we hasten to document the Earth’s species before human activities extinguish them for good, our biggest challenge lies in those that are too small to be seen with the naked eye, and the microscopic tardigrades (or, more endearingly, ‘water bears’ or ‘moss piglets’) are a perfect example. It is rapidly becoming apparent that all species, as well as their intrinsic right to survive, may provide us with vital ecosystem services or economic uses. Yet we can neither use nor protect species if we cannot identify or locate them. Thus, using modern digital techniques, Prof Johansson is among those seeking to transform our knowledge of the tardigrades.

ENTER THE WATER BEARS An ornithologist by training, Johansson challenged himself to study the tardigrades precisely because they were so little known. First discovered in the nineteenth century by German pastor Johann Goeze, an estimated 1150 species of this unique invertebrate

group are now known to science, with more being added every year. However, they remained under-researched until their remarkable properties became apparent.

The water bears live up to their nickname, with short, plump, cylindrical bodies usually less than a millimetre long, and eight legs each ending in multiple claws. Found on every continent, in environments ranging from damp moss to sand dunes or the ocean depths, terrestrial species have the ability to enter a suspended animation known as ‘cryptobiosis,’. This enables the water bears to survive extreme conditions including temperatures from close to absolute zero to over 150 degrees centigrade, immense pressures, almost complete vacuums, and ionising radiation strong enough to kill a human several times over.

During cryptobiosis, a water bear’s body goes through extraordinary changes: its head and legs retract, and it shrivels into Dactylobiotus grandipes (Schuster, Toftner & Grigratick, 1978) from between the grains of sand on Pope Beach, Lake Tahoe, NV, USA.

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Below: Milnesium sp. From California, USA.

what looks like a tiny raisin, known as a ‘tun’. Its metabolism slows dramatically, it loses 97% of its body fluid, and stops feeding, moving and growing, yet its cells remain perfectly intact. When conditions become more habitable, sometimes years later; in one reported case it was 125 years later, the animals reanimate with the simple reintroduction of water into their habitat. Within minutes or hours of rehydration, the tardigrade will leave the ‘tun’ stage and simply pick up life where they left off.

SUSPENDED ANIMATION The cryptobiotic abilities of the water bears are now targets of research that may prolong the life of human organs donated for transplantation, or help preserve live vaccines being transported to areas without refrigeration. The tardigrades’ capacity to resist or repair DNA damage under intensely mutagenic conditions also has fascinating potential applications. And the list goes on. But the foundation of all tardigrade research rests on our ability to find and identify them, and this requires specimens.

many specimens preserved using old techniques and materials are now rapidly degrading, becoming useless for scientific study. Because the name of each species is usually linked to one of the oldest specimens collected, many of these designated ‘type’ specimens are particularly at risk. Thus, it is crucial to

preserve both the specimens and their associated data as best we can.

America’s largest collection of tardigrade specimens – 26,800 specimens held at the Bohart Museum of Entomology in Davis, CA. Nothing if not ambitious, they then added 17,000 specimens collected

by Fresno College as part of an earlier NSF grant, making a total of almost 44,000 permanent water bear records, associated with an incredible 120,000 digital images of the beasts. Alongside the digitisation, Dr Kimsey’s team developed a new method to recover and remount the most important specimens in their collection, which will hopefully now preserve them permanently.

One of the best ways to do this is with high quality digital photographs, alongside digitised label data. With a grant from the US National Science Foundation (NSF), Prof Johansson, Dr Kimsey and their students set about the mammoth task of digitising North

But even the best digital records are useless if they remain isolated in individual museums where they cannot be compared. As Prof Johansson believes, data is only valuable if it can be accessed freely and easily by anyone, anywhere on the planet. For this reason,

Dr Johansson’s students are provided with training which enables them to graduate from Fresno College with a sound knowledge of research, database management and digital imaging

Properly preserved, catalogued and curated, zoological specimens are a mine of information, both in the organisms themselves and the associated ‘label data’ (notes on where and when the animal was collected, what it looked like when alive, and so on). Sadly,

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A new species discovered by Johansson’s students, Oreella chugachii. Calloway, Miller, Johansson & Whiting, 2011 from southern Alaska, USA.

Echiniscus testudo (Doyére, 1840) from Utah, USA.

many natural history museums are now pushing to share their data in online databases. However, standardised databases require standardised data.

Because museums around the world evolved in relative isolation until recently, each has their own specimen cataloguing system, incompatible with others, and that means investing a huge amount of time, money and energy re-cataloguing specimens in a universal framework. Fortunately for the water bears, Johansson and Kimsey’s students have provided that energy, resulting in a complete specimen collection now online, searchable and freely accessible in the database iDigBio. INSPIRING A COMMUNITY One of the greatest beneficiaries of this project is not tardigrade taxonomy at all, but the community of Fresno and beyond. California’s oldest community college, Fresno prides itself on giving economically and/or culturally challenged students a chance: many are the first in their family to attend college, ninety percent receive financial aid, the majority are from minority groups, and most have no scientific background.

Yet Johansson calls them to work on a

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SEM of mouth and front claws of a tardigrade

There is a real sense of community surrounding the project, everyone involved has strived to make the project a success top-level NSF-funded project, receive sound training in research methods, database management and digital imaging, and even publish peer reviewed papers naming new species; not many undergraduates can claim that! The students work with top scientists, receiving genetic support from Byron Adams at Brigham Young University, databasing expertise from Ed Gilbert of Symbiota (the software that supports iDigBio), and the immense tardigrade knowledge of Dr William Miller at Baker University, Kansas.

And their success is phenomenal:

compared to an average graduation rate of just 30%, Johansson’s is closer to 100%. Youngsters who once aspired to work in fashion, media or finance are now inspired to pursue advanced degrees in research biology. What’s more, they can be proud of their part in bringing knowledge of the water bears to researchers and enthusiasts across the world. The full benefits of this level of accessibility, to biodiversity conservation, medical research and human health, remain to be seen. But one thing is certain: this pioneering project will ensure the water bears are no longer overlooked.

Behind the Bench Professor Carl Johansson

E: carl.johansson@fresnocitycollege.edu T: +1 559 367 7156 W: http://mwww.fresnocitycollege.edu/ index.aspx?recordid=1186&page=1096 W: http://www.sciencefriday.com/person/carl-johansson/ W: http://www.therampageonline.com/news/2017/05/03/instructor-magnifies-little-known-organism/ W: http://mywaterbears.org

Research Objectives Carl Johansson studies the tardigrades (Tardigrada, or the ‘water bears’) and is offering the opportunity for Fresno City College students to join him in his exciting research on this intractable group of organisms. The aim is not only to find out more about these little-known species and their relevance to the human population, but to also engage students’ interest in and passion f or science.

Funding National Science Foundation (NSF)

Q&A

What attracted you to study such an obscure group as the tardigrades?

When I became eligible to apply for a sabbatical, I asked myself: “What do I know absolutely nothing about?”

Tardigrades were an answer to that question, and they truly intrigued me, so I wrote an application aimed at researching tardigrades of California.

That opened up Pandora’s box for me – in a very good way!

How might research into the tardigrades make a difference to human health?

Based on John Crow’s pioneering work in the 1970’s, clinical trials are currently examining the effectiveness of “Dried Blood’ preserved with Trehalose – a sugar used by tardigrades in their process of cryptobiosis, which plays a huge role in protecting cells from damage caused by dehydration. Essentially a soldier or other person could carry small packets of their blood as a dried powder and, if needed, rapidly rehydrate their dried blood to give them matching blood available – anywhere, anytime.

Collaborators • Dr Lynn Kimsey (Director of the Bohart Museum located at UC Davis) • Dr Byron Adams (Brigham Young University - BYU) • Dr Ed Gilbert (Symbiota) • Dr William Miller (Baker University) Bio Carl Johansson is a Professor of Biology at Fresno City College in Fresno, California. He trained as a classical ornithologist and ecologist at BYU, previously developing nesting prediction models for the northern

The recently discovered DNA repair and protection mechanisms that tardigrades seem to excel at, are also obviously hugely important. Not only that, but the newly uncovered glass proteins and Trehalose will be key in extending the shelf life of organs or tissues – facilitating a much higher transplant rate.

I am also very interested in pursuing the idea that wind born Tardigrades could be vectors for the spread of disease globally. There is currently some poorly known research into this area that indicates there could be an issue.

How important is it that scientific data is freely accessible to all?

If funding is from a public source or sources, it should be mandatory that those findings are released in a timely manner. Many scientists believe that they need to hold their research close to their chest to stop someone else from “scooping them”, publishing their work before they do.

I personally find that to be a totally arrogant approach. If your findings are important, you need to make them available as soon as possible. There are

goshawk, and radar tracking systems for birds and bats. He is now studying the toughest living organisms on Earth, the tardigrades.

Contact Carl Johansson, MS Professor of Biology Fresno City College Fresno City College

probably hundreds of thousands of files and computer hard drives loaded with what might be very important data that end up never being released because the researcher retired, died, lost interest, or lost funding.

What advice would you give to students who want to pursue a career in scientific research but feel they are not able to?

If it is truly your passion, it is the greatest career you can ever imagine.

If, however, you think that it could be your pathway to fame, wealth or stardom, don’t waste your time!

What does the future hold for this project?

We have now finished the cataloguing and digitisation of the collection.

You can visit IDigBio to see our results. Currently we have students working on writing several new species descriptions, based on slides found in the database. We also have students writing up the re-mounting methodology they have now perfected.

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Biology ︱ Professor Sara Hotchkiss

Peatlands’ past suggests fast-changing future Minimising and mitigating the effects of global climate change rely on accurate predictions of future climate, vegetation changes, and feedbacks between the Earth and its atmosphere.

Prof Sara Hotchkiss, of the University of Wisconsin – Madison, and Prof Robert Booth, of Lehigh University, Pennsylvania, have investigated the effects of climate change on an overlooked landscape, the kettle hole ecosystems of the northern US. Their work suggests that increasingly frequent and severe droughts could trigger sudden transitions from lake to peatland, with dramatic consequences for this ecosystem and potential feedbacks to the broader Earth system.

Figure 1: The classic model of kettle peatland development invokes expansion of pioneering plants across the lake surface, leading to the gradual encroachment of Sphagnum peatland.

In contrast, empirical data support episodic expansion of the floating mat during & after major changes in water level (Ireland & Booth 2011, Ireland et al. 2013). Modified from (Ireland et al.2012) & Ricklefs & Relyea (2014).

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s global climate change intensifies, many of the Earth’s ecosystems are threatened with irreversible change. Some will change gradually and predictably; others may undergo sudden, dramatic state shifts when one or more ecological parameters reach a tipping point, resulting in abrupt transitions from one ecosystem to another.

PREDICTIONS FROM PEAT Such sudden state shifts are notoriously difficult to predict under conventional forward modelling approaches. However, rapid ecosystem transformations have occurred in the past and investigating these events may allow scientists to explore the conditions under which they happen, trace their ecological impacts, and estimate the likelihood of future shifts in similar ecosystems. Few relevant historical datasets have been explored so far, but Prof Sara Hotchkiss and Prof Robert Booth have identified one ecosystem that may be a useful model system for studying state shifts – the kettle hole-peatland mosaics of northern Wisconsin, US. Peatlands cover only around 2% of the

world’s land area, but punch far above their weight in terms of carbon capture, making them crucial weapons in the fight against climate change. Compared to other carbon sinks such as oil, which are held deep below ground, peat lies within a few metres of the atmosphere, making it highly responsive to changes in climate. Furthermore peat, comprising partially decayed vegetation, provides a uniquely high-resolution record of the past flora and climate of an area which can be extracted as sediment cores, often dating back tens of thousands of years. Such a record is well-suited to investigating past time periods of abrupt change.

HOW BOGS BECOME Kettle holes are created when buried blocks of ice melt as a glacier retreats, leaving lakes. Over time, the lakes are overgrown, and eventually filled, by floating mats of peat. Conventional wisdom suggests that the peat mats develop through gradual and inevitable inward encroachment of plants, independent of a lake’s shape, location, or climate. However, several recent studies suggest that much more rapid and discrete transitions from open water

to peatland may have occurred, more characteristic of sudden state shifts.

formation, roughly coincident with independently-verified drought events.

Palaeoecologists Robert Booth of Lehigh University, Pennsylvania, and Sara Hotchkiss of the University of WisconsinMadison have used Wisconsin’s kettle holes to test the hypothesis that peatland develops suddenly, triggered by intermittent drought conditions.

Prof Booth and his students had already documented similar transitions in a Pennsylvania bog system using radiocarbon dating and detailed sediment core analyses, finding discrete and rapid episodes of peatland

Together, Booth, Hotchkiss, and their students have developed a new conceptual model, in which fluctuating water levels drive peatland establishment and expansion. For example, falling water levels during droughts cause rapid colonisation of kettle hole lakes by plants such as sedges. During subsequent wetter conditions, lake levels recover, uprooting the vegetation to produce

floating mats of peat and plants, which are further colonised by typical peatland plants such as Sphagnum mosses.

Beneath the mats, peat accumulates rapidly to infill the lake. They have been testing this model using sediment cores from the kettle hole peats.

ALL KETTLE HOLES ARE NOT EQUAL In Hotchkiss and Booth’s model, climate is not the only factor determining how kettle hole lakes are converted to peatland: shallow kettle holes would be more susceptible to colonisation during short or low magnitude drought

Peatlands cover only 2% of the world’s land area, but punch far above their weight in carbon capture

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events, while deeper ones would require more prolonged periods of drought. It also follows that kettle lakes at higher altitude – which are generally rainfallfed – would be more susceptible to colonisation than lower altitude lakes supplied by more reliable groundwater.

If these hypotheses are correct, they may be able to predict which kettle holes are most susceptible to peat encroachment over coming decades. Integrated with regional climate forecasts, their projections could help anticipate and even mitigate the effects of climate change on these ecosystems.

This is important because kettle hole landscapes provide a range of ecosystem services including biogeochemical cycling, habitats for aquatic and wetland flora and fauna, areas for human recreation, and of course carbon sequestration. Although the end appearance of kettle holes is identical regardless of whether their creation was slow and steady or rapid and episodic, the contrasting paradigms have markedly different implications.

As Hotchkiss and colleagues put it in a recent paper, “From an ecological perspective, the important question is, at what rate do these variables change? Are these lake systems responding linearly to peatland expansion over millennia or do they experience abrupt, threshold effects?” (Ireland et al., 2012: 996). For example, the aquatic communities supported by kettle hole lakes differ depending on whether or not they are peat-bordered because the presence of peat has substantial biogeochemical and hydrological effects on the lake itself. Under the slow and gradual model, lakes would be peat-bordered for a considerable time, and effects on the aquatic ecosystem would be gradual over many millennia. However, under the new model rapid changes would be expected.

Hotchkiss and Booth’s research may also predict how sudden transitions from lake to peatland could alter the whole ecosystem’s carbon storage capacity. Peatlands accumulate carbon much faster than lake sediments do, but they occupy sensitive transition zones between aquatic and terrestrial ecosystems on the landscape. Although good at storing carbon, peatlands can

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Figure 2: Fallison Kettle has had three major phases: a lake phase before 5300 years ago, a dynamic peatland expansion phase 5300 to 2000 years ago, and isolation of the lake by peatland during the past 2000 years. Prior to peatland establishment the basin accumulated about half as much carbon per year as it did during the past 2000 years.

Their projections could help anticipate and even mitigate the effects of climate change on these ecosystems also release carbon to the atmosphere if they begin to decompose. Thus, this research has implications for the total net carbon that can be fixed in kettle hole landscapes, an urgent parameter for those seeking to mitigate climate change through maximising carbon sequestration.

Even in regions of moderate climate, the future is expected to feature significantly more frequent and intense periods of drought. If the new model is correct,

kettle hole ecosystems will therefore undergo increasing numbers of abrupt community changes over coming decades – posing new challenges to mitigating the effects of future climate change. And kettle holes are unlikely to be the only ecosystem prone to abrupt state shifts. Hotchkiss and Booth’s research provides a tantalising glimpse of our potential future and a long-term prediction of how our actions can trigger rapid and permanent changes in the natural world upon which we depend.

Behind the Bench

Prof Sara C. Hotchkiss

E: shotchkiss@wisc.edu T: +1 808 895 0442 W: http://www.botany.wisc.edu/hotchkiss.htm W: http://www.botany.wisc.edu/hotchkiss/index.html

Research Objectives Prof Booth and Hotchkiss’ research uses the paleoecological record preserved in kettle hole ecosystems of northern Wisconsin to assess the potential for climate-induced ecosystem state shifts, as well as the ecological effects of these events.

Funding National Science Foundation (NSF) Bio Sara Hotchkiss is a professor in the Department of Botany and a member of

Q&A

What first drew you to the kettle hole ecosystem as somewhere both prone to the impacts of climate change and vital to attempts to mitigate it?

To be honest, we were drawn to kettles because they are so beautiful!

Scientifically, we are both interested in the effects of climate variability on their development, and in the ways in which the small hills and valleys in hummocky kettle landscapes can maintain higher levels of biodiversity in a region. Of course, because they leave a record of their own development in the form of peat and lake sediments, they are particularly well-suited to paleoecological studies.

What do peatlands do for us?

Peatlands provide a vast array of ecosystem services, including flood control, habitat for biodiversity, and global climate regulation through their ability to sequester carbon from the atmosphere. And of course, they also provide us with delicious cranberries!

Why do you think the paradigm of slow, gradual colonisation of kettle hole lakes by peatlands has been so pervasive, until now?

It’s appealing, and it’s a simpler

Prof Robert K Booth E: rkb205@lehigh.edu T: +1 610 758 6580 W: http://www.lehigh.edu/~rkb205

the Nelson Institute for the Environment’s Centers for Climatic Research and Culture, History, and Environment. She earned an AB in Biology from Oberlin College and a PhD in Ecology from the University of Minnesota-Twin Cities.

Contact Prof Sara C. Hotchkiss, PhD Department of Botany University of Wisconsin – Madison 132 Birge Hall, 430 Lincoln Drive, Madison, WI 53706 USA

Bob Booth is an associate professor in the Earth and Environmental Science Department at Lehigh University. He earned a BS in Biology from the Pennsylvania State University, an MS in Biology from Georgia Southern University, and a PhD in Botany from the University of Wyoming.

Prof Robert K Booth, PhD Earth & Environmental Science Department Lehigh University, 1 West Packer Ave Bethlehem, PA 18015 USA

explanation than one that demands a dramatic change in conditions. We examine how the plants that live there now support one another physically, and we infer a slow process of expansion of that support across the surface of the water. To explain the kind of sudden state change that our observations support requires an interval of much drier conditions in the past, without which current conditions can’t be explained.

Occam’s Razor is useful in science, but sometimes upon closer observation a more complicated explanation actually fits the data much better than the simple one. In these cases, it can take a long time for the simpler explanation to fade from popular use.

If we began to study a kettle ecosystem during a drought period, we would quickly begin to think of those conditions as ‘normal’, and we would be surprised if it were suddenly inundated with water.

If you expand your time frame and think of glacial-interglacial cycles, we are quite comfortable with thinking of our current interglacial conditions as normal, but over the past million years interglacial conditions have actually only lasted 10 or 20,000 years out of every 100,000 years.

We live in anomalously warm conditions, nested within a broader period of earth history in which it is much more normal to have major continental ice sheets growing.

How can we manage the kettle hole ecosystem better?

We need to think about managing for diversity of landscape features, including kettles that are deep and shallow, high and low in the local watershed, isolated and connected to other lakes and peatlands. Taking this approach to maintaining landscapelevel variety can buffer our land management against our ignorance of how these sensitive ecosystems respond to extreme events and unforeseen stressors.

How widespread do you think these sudden state shifts will turn out to be as climate change intensifies?

Will the kettle holes turn out to be an anomaly, or will they be the first of many?

We can expect many sudden state shifts as the frequency of extreme climatic events increases, and we may also see sudden shifts due to internal feedbacks in ecosystems as average climatic conditions slowly drift out of the range in which those internal feedbacks operate. As climate continues to change, there will also certainly be surprises.

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Biology ︱ Professor Teresa Pawlowska

Crossing kingdoms between plants, fungi and bacteria Professor Teresa Pawlowska and her team from the School of Integrative Plant Science at Cornell University have performed an in-depth study on the evolutionary genomics of the recently discovered mycoplasma-related endobacteria (MRE). They are currently in the process of investigating the complex interrelationship between these endobacteria, arbuscular mycorrhizal fungi (AMF) and their host – terrestrial plants. This is one of the oldest examples of symbiosis on our planet and a full understanding is essential for us to support both natural and agricultural global ecosystems.

AMF spore with CaMg. A crushed spore of the arbuscular mycorrhiza fungus Claroideoglomus claroideum, stained with the fluorescent dyes SYTO BC and propidium iodide. The image shows a cloud of endobacteria (in green) being released from the spore together with fungal nuclei (in red). Photograph by Maria Naumann and Paola Bonfante, University of Torino (Italy).

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very living organism is connected in the web of life. Complex and dynamic interactions can span across different species, families, kingdoms, and domains of life. This inspired Professor Pawlowska, and her team, to study one of the most common relationships seen in nature – the connection between terrestrial plants and mycorrhizal fungi.

This is known as a symbiotic relationship, in which an association exists between two (or more) organisms. Interactions can range from antagonistic to beneficial for one or both the species involved.

Symbiotic relationships are unique and are essential in maintaining a delicate balance in ecosystems all over the world.

ARBUSCULAR MYCORRHIZAL FUNGI (AMF) AND PLANTS Incredibly, the majority of all studied plant families have a beneficial association with their mycorrhizal fungi and are sometimes completely dependent on the fungus.

80% of vascular plant families, including crops, have a mutualistic symbiotic relationship (thought to have originated around 400-460 million years ago) with Arbuscular Mycorrhizal Fungi (AMF), part of the Glomeromycotina group.

This important partner acts as a natural biofertiliser, harvesting from the soil essential nutrients, such as phosphorus and nitrogen, and translocating them to plant hosts. AMF colonise plant roots, using specialised structures known as arbuscules to penetrate root cortical cells. This physical connection allows the passage of nutrients from the AMF to the plant. In return, the AMF receive approximately 20% of the plant’s photosynthetic carbon.

Remarkably, research has shown that AMF have an additional symbiotic relationship with mycoplasma-related endobacteria (part of the Mollicutes

Root with AMF. A plant root surrounded by hyphae and spores of Claroideoglomus etunicatum.

class of bacteria), which reside in the cytoplasm of AMF cells. Our knowledge regarding the biology and life-cycle of MRE is relatively limited. To address this lack of understanding, Professor Pawlowska and her team have conducted a series of in-depth studies, focusing on the evolution and genetic make-up of these endobacteria. As it has been suggested that AMF could be an effective alternative to potent chemical fertilisers, understanding the effects of MRE on AMF function, and the subsequent consequences for the host plant, is of vital importance.

them with research experience in the fields of microbiology, molecular genetics, and bioinformatics.

This project, sponsored by the National Science Foundation and the National Institute of Food and Agriculture, was highly collaborative, involving scientists from Cornell University, West Virginia University, and the University of Turin, and offered training opportunities for undergraduate, graduate and postdoctoral students.

Mentoring throughout the study inspired and engaged students and provided

Results indicated that MRE genomes are greatly reduced – their genomic capacities being minimal and limited to

ENDOSYMBIONTS DEPEND ON FUNGALÂ HOSTS Professor Pawlowska conducted a metagenomic study by analysing different populations of MRE, associated with three different AMF species. Metagenomics is the study of genetic material, obtained from environmental samples. This allows researchers to examine the complex genetic composition and diversity within natural populations and communities.

in metabolites such as amino and nucleic acids. As a result, endobacterial genes that also encode these products, essentially become unnecessary and MRE become completely reliant on AMF. VERTICAL TRANSMISSION Some endosymbionts, including MRE, are vertically transmitted between host generations. This means that when AMF asexually reproduces (the offspring contains the exact same genes as the parent and are effectively clones) only some of the endobacteria are inherited by the next generation. A reduction in endobacteria population size could therefore limit genetic diversity, meaning that deleterious mutations can become more frequent in the population, potentially leading to extinction.

Symbiotic relationships are unique and are essential in maintaining a delicate balance in ecosystems all over the world the most basic cellular functions. This is a consequence of living in the cytoplasm of host AMF cells. The intracellular environment is relatively safe and rich

However, Professor Pawlowska and her team showed that within each of the three studied MRE populations, genetic diversity was unusually high, enabling the different populations to adapt to specific host conditions. Typically, mutualistic

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or beneficial bacteria are characterised by genetic similarity, whereas parasitic bacteria have a greater level of diversity, enabling them to adapt to potential host resistance. Therefore, these results suggest that MRE could be parasitic.

WHY ARE MRE SO GENETICALLY DIVERSE? Rapid accumulation of both beneficial and deleterious mutations is common in heritable endosymbionts (including MRE). This is due to the loss of the ‘proofreading’ ability of DNA polymerase to use its exonuclease activity to remove erroneously introduced bases and to replace them with the correct ones.

However, the team showed that MRE uses recombination to overcome the risk of degenerative evolution and restore high fitness MRE genotypes. In fact, recombination rates are higher than mutation rates, which makes MRE one of the fastest evolving bacteria on the planet. Recombination is the process of rearranging genetic material, by exchanging genes between different organisms. Not only can this ‘repair’ gene copies carrying harmful mutations, but it also enhances genetic diversity.

Results also indicated that 5% of the MRE genome comprises mobile genetic elements (MGE). These are DNA sequences, encoding enzymes that enable the movement of DNA within and between genomes. Ultimately MGEs can introduce novel genes, or disrupt existing ones. The movement of MGE and amplification of sequences on a single chromosome, increases the number of available recombination sites, thereby further promoting genetic diversity.

Furthermore, the team showed that a significant part of the MRE genome encodes proteins mainly used for interacting with AMF – for example, the SUMO protease, which controls postranslation modifications of host proteins. This provides evidence for horizontal gene transfer; whereby genetic material is exchanged between organisms of different species or populations. In fact, genes that originate from AMF represent 3-5% of the total coding DNA sequences in the three different MRE populations.

A NEW SPECIES? Overall, the research conducted

by Professor Pawlowska and her

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Fungal hyphae Root hair Epidermis

Arbuscules Fungal vesicle

Cortex

Endobacterial genes that also encode these products (essential metabolites), become unnecessary and MRE become completely reliant on AMF colleagues has shown that MRE are truly unique in terms of their high level of genetic diversity, as a result from genetic recombination and horizontal gene transfer, which increases this endosymbiont’s adaptive ability. In fact, to acknowledge their distinctive biology, the team have developed a taxonomic proposal to accommodate MRE in the new species ‘Candidatus Moeniiplasma glomeromycotorum’.

The team also discovered that within a single AMF host, CaMg can coexist with another endobacterium, ‘Candidatus Glomeribacter gigasporarum’ (CaGg).

This was the first study to highlight the co-existence of two endosymbionts within a single fungal host. CaGg is entirely nutritionally dependant on the fungal host, and in return, primes host energy metabolism. Unlike MRE, CaGg populations have a much lower level of genetic diversity, which suggests that these two endosymbionts may have distinctly different lifestyles. Interestingly, in all samples, MRE was much more abundant than CaGg, further supporting differences between their biologies.

Furthermore, results indicated both

endosymbionts retain their genetic and lifestyle characteristics, regardless of whether they are present in the fungal host alone or together.

However, much more research is still needed to fully understand the complex relationship between MRE, AMF and the host plant. Are MRE a friend or foe of their fungal host? And, if the effects are antagonistic, how will this impact the life of the plant?

Understanding this complex relationship is vital for the future of agriculture. Soil tilling disrupts delicate mycorrhizal networks, necessitating the increased use of chemical fertilisers such as phosphates.

However, researchers predict that the world’s phosphate supply will be exhausted within the next 100 years. AMF, as a natural biofertiliser, could be the answer. However, we will need to greatly increase the prevalence of sustainable farming practises before this becomes a viable option.

Behind the Bench Professor Teresa Pawlowska

E: tep8@cornell.edu T: +1 607 342 3866 W: https://pppmb.cals.cornell.edu/people/teresa-pawlowska

Research Objectives Professor Pawlowska and her team’s aim was to understand the life history and evolutionary genomics of recently discovered mycoplasma-related endobacteria (MRE) of arbuscular mycorrhizal fungi (AMF, subphylum Glomeromycotina).

Funding National Science Foundation (NSF) Collaborators PhD advisees: Mizue Naito (Cornell University), Olga Lastovetsky (Cornell University), and Stephen Mondo (DOE Joint Genome Institute).

Q&A

Why are arbuscular mycorrhizal fungi (AMF) so important for plant health?

Dependence on AMF for soil mineral nutrients appears to be an ancestral feature of terrestrial plants. Some plants, such as brassicas, have evolved to be independent of AMF but most other plants relay on AMF for mineral nutrition. Mineral nutrient deficiencies are debilitating to plant growth and development. Plants deficient in phosphorus, the key element translocated by AMF, experience stunting.

How did endobacteria, such as mycoplasma-related endobacteria (MRE) evolve to become so dependent on their fungal host?

Our data suggest that MRE, or better

Undergraduate mentees: Toomer, Kevin (Cornell University), Zhang, Aolin (Brown University), Ahn, Ezekiel (Cornell University).

Co-authors: Bonfante, Paola (University of Torino), Chen, Xiuhua (Huazhong Agricultural University), Desirò, Alessandro (Michigan State University), Gonzalez, Jonathan (Cornell University), Morton, Joseph (West Virginia University), Olsson, Stefan (University of Copenhagen), Tao, Gang (Guizhou Agricultural Academy).

Bio Prof Pawlowska is a fungal biologist with interests in the evolution of

CaMg, is a product of an ancestral host switch from animals to fungi. Presentday animal-infecting mycoplasmas are entirely dependent on host metabolites.

Availability of costly metabolites from the host reduces selective pressures on genes responsible for their biosynthesis.

These genes accumulate deleterious mutations and, in bacteria, they are eliminated from the genome, leading to permanent dependency on the host.

In what ways are MRE different from other endobacteria?

CaMg is vertically transmitted and yet it retains mechanisms that generate genetic diversity in its populations, such as recombination and MGE. These mechanisms are lost in other heritable endobacteria.

symbioses between fungi and bacteria. She received her PhD from the University of Minnesota and is an Associate Professor in the Section of Plant Pathology & Plant-Microbe Biology in the School of Integrative Plant Science at Cornell University.

Contact Teresa E. Pawlowska, PhD School of Integrative Plant Science Plant Pathology & Plant-Microbe Biology 334 Plant Science Building, 236 Tower Rd Cornell University Ithaca, NY 14850 USA

Why is it important to study the relationship between AMF, MRE and plants?

Once rock phosphate deposits, which are the source of phosphate fertilisers, are exhausted, AMF with their ability to translocate phosphorus from the soil into plant roots will become critical to food production.

It has been suggested that MRE could be a parasite of AMF. How could this impact both the fungi and the plant hosts?

As a parasite, CaMg would inflict a metabolic cost on AMF, which themselves are obligately dependent on plants for energy. Consequently, mycorrhizal symbioses involving CaMg would become costlier to plants.

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COMMUNICATION

The media’s manipulation of scientific perception Take your mind back to 1998 – the year the two-pound coin was introduced in Britain, the year DVDs made their debut and the year Andrew Wakefield was involved in one of the most scandalous examples of science journalism to date. Take your mind back to 1998 – the year the two-pound coin was introduced in Britain, the year DVDs made their debut and the year Andrew Wakefield was involved in one of the most scandalous examples of science journalism to date.

D

uring the late 1990s, Andrew Wakefield and 12 other researchers published fraudulent research highlighting an apparent link between the measles-mumps-rubella (MMR) vaccine and autism.

This ‘research’ sent mainstream news media into overdrive, publishing the falsified results extensively and encouraging parents to avoid vaccinating their children with the MMR vaccine. This had the desired effect and resulted in a substantial decline of vaccination rates amongst children – leading to several preventable deaths from subsequent mumps and measles epidemics.

AN INJECTION OF DISTRUST Wakefield’s research was in fact highly biased, featuring only a small sample of 12 autistic children throughout his study.

He also subjected the children involved to unnecessary, painful invasive medical procedures without any ethical approval.

The aim of his falsified research was to create an association between vaccines and autism, to gain publicity and further his medical funding – and boy, did the media fall for it.

By the time the truth was revealed about his research, following a thorough investigation by Brian Deer at The Sunday Times, the media’s influence in broadcasting Wakefield’s claims had almost irreversibly damaged the public’s perception of vaccines.

Even to this day, the public remain distrustful of vaccines, which has caused a potential re-emergence of certain previously controlled diseases, including tuberculosis.

Science and the media can therefore be enemies to each other: scientists can make fabricated claims that the media broadcast to the public, while the media can misrepresent research through sensational claims, tarnishing public perception. It is important to overcome this and ensure that science is received by the public in an accessible and accurate format.

THE TRUMP CARD Rather worryingly, despite the numerous failed attempts to replicate Wakefield’s work and prove the damaging reputation of vaccines, large numbers of people, including the President of the USA, remain convinced that his research is, in

The public remain distrustful of vaccines, which has caused a potential re-emergence of certain previously controlled diseases

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fact, viable – 19 years after it first came out, and 13 years after it was proved false.

This kind of ignorance and refusal of scientific expertise is so damaging.

Vaccines have proved over and over again that they offer a vital, fundamental defence against disease. Without them, the global population as a whole would only be more susceptible to disease.

If we and our leaders, as an international society, cannot understand that for ourselves, and learn to appreciate scientific, peer-reviewed evidence, then we risk exposing ourselves to increasing epidemics of fatal, yet avoidable, diseases.

Social Media for Scientists RSM was born out of multiple conversations with researchers who see a real benefit in connecting with a broad audience over an ongoing basis. Social Media can now be considered one of the most prominent and important engagement tools of the modern era. We help you get the ball rolling and can even provide long term Social Media Management support.

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