Biotech World January 2015 by Biotech World

January 2015

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Itâ&#x20AC;&#x2122;s Ebola, on paper q Life in a test tube q Synthetic biology takes off q The web of the future

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As simple as ATCG. Connect with your customers. Biotech World brings together the best of the fast-moving biotechnology industry in one monthly digest. Revealing the latest discoveries and explaining developments in simple language, it offers a birds-eye view of a vast but interconnected industry. Advertising in Biotech World ensures your products and services reach the right people. Call Steve Fulford on +44 (0)1223 968 960 or email stevefulford@biotechworld.co

Contents

January 2015 5 News EDITOR Charlotte Niemiec T: +44 (0)1223 968 960 Email: editor@biotechworld.co ADVERTISING Steve Fulford T: +44 (0)1223 968 960 Email: stevefulford@biotechworld.co DESIGN & PRODUCTION T: +44 (0)1223 968 960 Email: production@biotechworld.co Biotech World is published 12 times a year by Biotech World magazine, 13 Prospects Court, 20 Holmesdale Road, Reigate, Surrey RH2 0BQ, UK. No part of this publication may be reproduced without the prior permission of Biotech World magazine, the copyright owners. Upon application, permission may be freely granted to copy abstracts of articles on condition that a full reference to the source is given. © 2015 Biotech World Views expressed by individual contributors in this issue are not necessarily those of Biotech World magazine. Equally, the inclusion of advertisements in this magazine does not constitute endorsement of the companies, products or services concerned by Biotech World magazine. The publisher reserves the right to refuse advertising. Website: www.biotechworld.co

17 Industry developments Researchers devise an enzyme that sheds light on the origin of life on Earth

For the first time, scientists have mapped the genomes of an entire species – birds

25 Synthetic biology Scientists create an Ebola sensor that differentiates between strains in seconds

Synthetic biology makes manned space travel, human organs grown in animals and rare flavourings possible

32 Industrial Spider silk inches towards becoming a commercial reality

38 Diary Round-up of industry conferences and exhibitions

Cover Ebola is in the media spotlight following the deadly outbreak in West Africa. While biotechnology companies scramble to provide vaccines and cures, scientists have developed an ‘Ebola sensor’ using synthetic biology (p25)

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Build momentum. Biotech World, covering the latest news and developments in the biotechnology industry, reaches thousands of readers each month. Advertising in the magazine ensures your products and services reach the right people. Call Steve Fulford on +44 (0)1223 968 960 or email stevefulford@biotechworld.co www.biotechworld.co

World news

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News & developments Comment “But I would like to sound one note of warning. Penicillin is, to all intents and purposes, non-poisonous, so there is no need to worry about giving an overdose and poisoning the patient. There may be a danger, though, in underdosage. It is not difficult to make microbes resistant to penicillin in the laboratory by exposing them to concentrations not sufficient to kill them, and the same thing has occasionally happened in the body ... there is the danger that the ignorant man may easily underdose himself and, by exposing his microbes to non-lethal quantities of the drug, make them resistant.” Thus warned Alexander Fleming in his Nobel Prize speech in 1945. Since then, penicillin and other antibiotics have been used extensively and effectively, saving millions of lives. However, Fleming’s warning proved prophetic: over the last few decades, some bacteria have built up resistance to our interventions, with MRSA and antibiotic-resistant tuberculosis (TB) the proof in the pudding. Antibiotic resistance is, according to the World Health Organization, “a growing public health threat of broad concern.” Overuse of antibiotics coupled with globalisation threatens the progress made so far within the medical community. National Health Service statistics show that, before antibiotics were introduced, TB was a major health problem in the UK. Today, the condition is much less common but, in the last 20 years, TB cases have gradually increased – particularly among ethnic minority communities originally from places where TB is more common. In 2011, it notes, 8,963 cases of TB were reported in the UK. Of those cases, more than 6,000 affected people were born outside the UK. It is of no surprise that biotechnologists are turning back to the drawing board, scratching their heads once again as they seek to defeat an enemy unimaginably smaller than us. A major breakthrough came late last year, when Northeastern University in Boston, Massachusetts, USA, revealed research that set the industry abuzz. The scientists involved had discovered a new antibiotic that killed pathogens without encountering any detectable resistance, signalling the first significant step forward for decades. The bacteria grown yielded 25 new antibiotics, including teixobactin – the most promising – which cleared a deadly dose of MRSA in tests on mice. Tests showed that teixobactin was toxic to bacteria but not mammalian tissue; it targets fats that are essential for building the bacterial cell wall. The scientists believe bacteria are unlikely to ever develop resistance to teixobactin. Professor Lewis, who worked on the study, said: “Here is an antibiotic that essentially evolved to be free of resistance. We haven’t seen that before. It has several independent different tricks that minimise resistance development.” For the biotech industry, it was a stellar way to begin the new year as we look towards a healthier, happier future. Charlotte Niemiec

HIV drug reduces prostate cancer metastases by 60% in mice Scientists at Thomas Jefferson University in the USA have discovered that maraviroc, a drug used to treat people with HIV, is also effective at stemming the speed of prostate cancer metastasis in mice. Although initially treatable, when prostate cancer metastasises to the bone, it is eventually lethal. The new discovery, however, “shows that we can dramatically reduce metastasis in preclinical models,” said Richard Pestell, director of the Sidney Kimmel Cancer Centre at the university. He added: “Because the drug is already FDA-approved for HIV treatment, we may be able to test soon whether this drug can block metastasis in patients with prostate cancer.” The work built on previous research by Pestell’s lab in 2012 that showed CCR5 signalling was key in the spread of aggressive forms of breast cancer to the lungs. Given that prostate cancer cells were attracted to the bone and brain, Pestell’s team investigated whether CCR5 could play a role in prostate cancer metastasis as well. The researchers developed a prostate cancer cell line,

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driven by an unregulated Src gene, that regularly caused bone metastases in immunecompetent mouse models. They found that the genes driving the cancer were also involved in the CCR5 signalling pathway. Investigating further, they administered the CCR5blocking drug maraviroc to the new prostate cancer mouse model. They found that, in comparison to control models, maraviroc dramatically reduced the overall metastatic load by 60% to the bone, brain and other organs. Finally, the researchers discovered that CCR5 was more highly expressed in human prostate cancer tissue compared with normal tissue – and even more highly expressed in metastases compared with primary tumours. “In fact, we noticed that patients who had a lower expression of these CCR5 genes had longer survival times, whereas high expression of these CCR5 genes was associated with a shorter overall survival,” said Xuanmao Jiao, PhD, an instructor in the department of Cancer Biology at Jefferson.

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Biotech World brings together the best of the fast-moving biotechnology industry in one monthly digest. Revealing the latest discoveries and explaining developments in simple language, it offers a birds-eye view of a vast but interconnected industry. The sectors of biotechnology are ever growing and Biotech World covers them all, from industrial biotech to bioterrorism, agriculture to ethics and regulations. To advertise, call Steve Fulford on +44 (0)1223 968 960 or email stevefulford@biotechworld.co www.biotechworld.co

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News & developments Vladimir Voronin/dollarphotoclub

Approval granted to biotech for diabetic macular edema treatment

US biotech company, pSivida Corp – a leader in the development of sustained release, drug delivery products

for treating eye diseases – has received Food and Drug Administration (FDA) approval for ‘Iluvien’, which helps in the

treatment of diabetic macular edema (DME). The approval entitles pSivida to US$25 million and 20% of the net profits from sales of Iluvien in the USA. Iluvien is an injectable micro-insert that provides sustained treatment through continuous delivery of a sub microgram dose of the corticosteroid fluocinolone acetonide for three years. Current standards require injection in the eye as frequently as monthly. The insert is injected in the back of the patient’s eye with an applicator that employs a 25-gauge needle, which allows for a self-sealing wound.

Freshidea/dollarphotoclub

Silk protein injections in joints eases osteoarthritis

Cocoon Biotech Inc has entered into an agreement with Tufts University to explore the commercialisation of new treatments for joint disease and arthritis using silk protein polymers. The silk biomaterial platform was developed in the laboratory of Professor David L Kaplin and spans many biomedical and industrial applications. Cocoon Biotech is in the formative stages of developing

products to treat osteoarthritis, a crippling disease affecting 27 million Americans and over 150 million people worldwide. Existing approaches to treating arthritis, especially in the knee joint, include frequent steroid injections and eventual surgical knee replacement that directly costs the US healthcare system over US$100 billion a year, according to the Center for Disease Control (CDC). Silk is a natural protein

with outstanding lubrication features for the joint. Silk has been used in sutures and other implants for many decades, demonstrating a favourable safety profile and has received prior FDA approval for certain medical devices. “Silk can also be engineered to biodegrade at desired rates and release a variety of medications locally into the joint space to facilitate tissue healing,” Kaplan said. Joint lubrication is a newer therapeutic option for osteoarthritis, in which a biomaterial is injected into damaged joints to reduce the friction between cartilage surfaces and relieve symptoms such as pain and inflammation. Cocoon Biotech Inc was founded in 2013 to bring treatments for arthritis and other debilitating diseases to market. The company has completed seed financing and is testing prototype products in the laboratory.

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Approximately 560,000 people in the USA alone are estimated to have clinically significant DME, the most frequent cause of vision loss in individuals with diabetes and the leading cause of blindness in young and middle-aged adults in developed countries. Iluvien is expected to be commercially available in the USA in early 2015. Paul Ahston, PhD, president and CEO of pSivida, said: “The US$25 million milestone will help finance our ongoing product development programme, including Medidur for posterior uveitis and Tethadur for the sustained delivery of biologics.” USA/China: China has officially approved the import of genetically modified (GM) crops, including a corn variety developed by Syngenta AG, a soyabean developed by DuPont Pioneer and a soyabean variety from Bayer CropScience AG, the International Service for the Acquisition of Agri-Biotech Applications announced late last year. The approval for Syngenta’s Viptera corn covers grain and processing byproducts, such as dried distillers’ grains, for human and animal consumption. The report said the US and Chinese governments had committed to synchronise policies – including those dealing with agricultural biotechnology – to encourage innovation in agriculture and ensure that regulatory frameworks are timely, predictable and protect US-China agricultural trade.

See the potential? We do. Let us help you grow. The sectors of biotechnology are ever growing and Biotech World covers them all, from industrial biotech to bioterrorism, agriculture to ethics and regulation. The magazine brings together the best of this fast-moving industry, revealing the latest discoveries and explaining developments in simple language, offering a birds-eye view of a vast but interconnected industry. Advertising in Biotech World ensures your products and services reach the right people.

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World news

News & developments Roll back time: skin ageing gene located after mice hit the sunbeds worsened by sunlight that can lead to disfiguring facial scarring. If the drug proves effective in preventing lupus-related skin lesions, there is potential for a cosmetic product to prevent the normal, gradual ageing of the skin, which is mostly caused by sun exposure. But the drug might also be used for lifethreatening conditions, such as aneurysms and chronic obstructive pulmonary disease, caused by the breakdown of collagen and other proteins that provide structure to blood vessels and lung passages. Granville, a professor in the Department of Pathology and Laboratory Medicine and a principal investigator in the Centre for Heart Lung Innovation of UBC and St Paul’s

Hospital, was investigating the role of Granzyme B in atherosclerosis and heart attacks. He and his team wanted to see if the blood vessels of mice lacking Granzyme B were more resistant to hardening and narrowing, which is a major cause of heart attacks in humans. In the process, they discovered that such mice retained youthful-looking skin compared to the aged skin on normal mice. Granville’s team constructed a device to simulate sun exposure on mice. Each mouse was put in a carousel that slowly turned under UV lamps, exposing them for three to four minutes, three times a week – enough to cause redness, but not to burn. After 20 weeks of repetitive

exposure, it became clear that the skin of mice lacking Granzyme B had aged much less – and their collagen was more intact – compared to the control groups.

Vladimir Voronin/dollarphotoclub

A scientific team at UCB and Providence Health Care have genetically engineered mice with less wrinkled skin, despite repeated exposure to wrinkleinducing ultraviolet (UV) light. The findings raise hope for a drug that would block the activity of Granzyme B in certain places and thus prevent the ageing and deterioration of tissues that depend on collagen – not just skin, but blood vessels and lung passages. ViDA Therapeutics, a company co-founded by Granville, is currently developing a Granzyme-B inhibitor based on technology licensed from UBC. The company plans to test a topically applied drug within two years on people with discoid lupus erythematosus, an autoimmune disease

Cephas/wikipedia

Non-profit project seeks to bring back extinct passenger pigeon

Using museum-specimen DNA, the ‘Revive & Restore’ project is working towards bringing back the extinct passenger pigeon using

the genome of the bandtailed pigeon and genomic technology. The data and analysis will begin with the process of

converting viable band-tailed DNA into viable passenger pigeon DNA, the project’s website explains. Later stages of the project will involve newly developed and advancing techniques for clustered regularly interspaced short palindromic repeats (CRISPR) genome editing and germ line transfer to generate live passenger pigeons from the DNA. According to its website, passenger pigeons were chosen because “the passenger pigeon is a model species poised at the optimal middle ground of ease and difficulty. It is a species that is not only feasible to successfully bring back, but also presents enough

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challenges to push the science forward and open up the possibility of de-extinction to many more species.” To study the ecology of the species requires not only multiple specimens, but old specimens; nearly complete mitochondrial genomes from 3,800-year-old passenger pigeons have been assembled and are helping to solve the species’ past. The researchers total data set includes mitochondrial and nuclear DNA from 40 specimens. Following years of human hunting, the last passenger pigeon disappeared in 1914. The project hopes to re-create the pigeon and successfully reintroduce it to the wild.

A global industry. One magazine. Biotech World, covering the latest news and developments in the biotechnology industry, reaches thousands of readers each month. Advertising in the magazine ensures your products and services reach the right people. Call Steve Fulford on +44 (0)1223 968 960 or email stevefulford@biotechworld.co www.biotechworld.co

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News & developments Scientists have discovered a protein in fat cells that could help produce drugs that treat obesity. In mammals, white adipose tissue stores excess calories as fat that can be released for use in other organs during fasting. But they also have small amounts of brown adipose tissue, which primarily acts as an effective fat burner for the production of heat. Now, researchers from the University of Southern Denmark have uncovered the mechanism by which fat cells from humans get programmed to become browner. Browning of white adipose tissue increases the energy consumption of the body and therefore constitutes a potential strategy for future treatment of obesity. The

challenge is to reprogramme the energy-storing white fat cells into so-called ‘brite’ (brown-in-white) fat cells in the body’s white adipose tissue and thus make adipose tissue burn off excess energy as heat, instead of storing it. The research team, from the Department of Biochemistry and Molecular Biology, was headed by professor Susanne Mandrup, who explained: “We have investigated how the genome of white adipocytes is reprogrammed during browning using advanced genome sequencing technologies.” “We stimulated browning in human white adipocytes by a drug used to treat type II diabetes and compared white and brite fat cells. This showed that brite fat cells have

University of Southern Denmark

Turning white fat cells brown could help beat obesity

distinct gene programmes which, when active, make these cells particularly energyconsuming.” She continued: “By identifying the areas of the genome that are directly involved in the reprogramming, we have also identified an important factor in the process – the gene regulatory protein KLF11 (Kruppel Like Factor-11), which is found in all fat cells, and we have shown that it is required for the reprogramming to take place.” One of the main forces

behind the project was PhD student Anne Loft, who pointed to the future prospects of the research on brite fat cells. She noted: “The discovery of the brite fat cell mechanisms and the specific regulatory areas brings us closer to understanding how reprogramming of white fat takes place. This knowledge potentially means that, in the future, we can target drugs to activate the genomic regions and browning factors like KLF11 in the treatment of obesity.”

Is it a food? Is it a poison? Protein reduces arsenic levels in rice plant Rice is notorious for its arsenic content which, if consumed in large amounts, can lead to cancer and skin lesions. Researchers in Japan and Korea have discovered that a transporter protein contained in rice prevents arsenic from damaging the plant. The scientists believe that genetically engineering rice to overexpress the protein would significantly reduce the amount of arsenic in rice. The protein, called OsABCC1, is found in the lipid membrane surrounding vacuoles, called the tonoplast, in rice cells, an October article from The Scientist explained. The protein pushes arsenic to other areas

of the plant, rather than gathering in the rice grains. The researchers found that, in unmodified wild rice, 3.4% of the plant’s total arsenic content ended up in rice grain. When the researchers knocked out the protein OsABCC1, 20-24% of arsenic made it to the rice grains, showing that the presence of the protein prevents arsenic from travelling to the rice. Overexpressing the protein, therefore, would further limit the amount of arsenic absorbed by rice and the amount passed on to humans by consumption. Study coauthor Jian Feng Ma, a professor at the Institute

of Plant Science and Resources at Okayama University in Japan, told The Scientist that he and his team would continue to look for other transporters that either help bring arsenic to the rice grain or sequester it. “Maybe there are a lot of transporters for arsenic in different cells. If you combine all of them, maybe you can get an arsenic-free rice.” Arsenic toxicity is a problem in areas of Southeast Asia, where people drink water containing high levels of arsenic and often grow rice in the same water. The Scientist article explains: “Rice accumulates arsenic both because of its growing

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conditions and biology. The crop is often grown in flooded rice paddy fields, where arsenic becomes arsenite, a compound that bears a strong chemical resemblance to silicic acid. The rice plants take up the silicic acid through transporters in their roots. Silicon makes rice plants stiff and sharp, allowing them to remain upright in damp conditions and to ward off pests. But, while rice is getting its needed dose of silicon, it’s accidentally drinking up arsenite. Arsenic is also found as arsenate, which mimics the key nutrient phosphate.”

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Printing 3D thermoplastic using squid ink

A team of researchers at Pennsylvania State University, USA, is printing 3D thermoplastic using squid ink – with no squid harmed in the making of the process. Melik C Demirel, professor of engineering science and mechanics, explained the significance: “Most of the companies looking into this type of material have focused on synthetic plastics.” However, “synthetic plastics are not rapidly deployable for field applications and, more importantly, they are not ecofriendly.” Demirel and his team looked at the protein complex that exists in the squid ring teeth (SRT). This naturally-made material is a thermoplastic, but obtaining it requires a large amount of effort and many squid. “We have the genetic sequence for the protein complex molecule and tried synthesising a variety of problems from the complex. Some were not thermoplastics, but others show stable thermal response – for example, the smallest known

molecular weight SRT protein was a thermoplastic.” Most plastics are currently manufactured from fossil fuel sources, such as crude oil, but some high-end plastics are made from synthetic oils. Thermoplastics are polymer materials that can melt, be formed and then solidify as the same material without degrading its properties. This particular thermoplastic can be fabricated either as a thermoplastic – heated, extruded or moulded – or the plastic can be dissolved in a simple solvent like acetic acid and used in film casting. The material can also be used in 3D printing machines as the source material to create complicated geometric structures. To manufacture this small, synthetic SRT molecule, the researchers used recombinant techniques. They inserted SRT protein genes into E.coli, so the bacteria produced the plastic molecules as part of its normal activity and the thermoplastic was then removed. “The next generation of materials will be governed

by molecular composition – sequence, structure and properties,” said Demirel. The thermoplastic the researchers created is semicrystalline and can be rigid or soft. It has a very high tensile strength and is a wet adhesive; it will stick to things even if it is wet. Furthermore, the thermoplastic protein has a variety of properties that can be adjusted to the individual requirements of different manufacturing processes. As it is a protein, it can be used for medical or cosmetic applications. “Direct extraction or recombinant expression of protein-based therapeutics opens up new avenues for materials fabrication and synthesis, which will eventually be competitive with the high-end synthetic oil-based plastics,” the researchers said. This thermoplastic protein has a variety of tunable properties, which can be adjusted to and used in the individual requirements of different manufacturing processes.

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USA: Dental and medical researchers from Case Western Reserve University in Cleveland, Ohio, have discovered that byproducts of bacteria in gum disease – called metabolic small chain fatty acids (SCFA) – can work together to wake up HIV in dormant T-cells and cause the virus to replicate. The findings help explain why people with both HIV and periodontal disease have higher levels of the HIV virus in their saliva than HIV patients with healthy gums. The researchers speculate that byproducts from other bacteria infections in other diseases might change gene expression using similar mechanisms. UK: Scientists at the University of Liverpool have sequenced the genome of the bowhead whale, estimated to live for more than 200 years with low incidence of disease. It it thought that large mammals, such as whales – with over 1,000 times more cells than humans – have a lower risk of developing cancer, suggesting that these creatures have natural mechanisms that can suppress disease more effectively than those of other animals. Sequencing of the bowhead whale showed changes in genetic information that related to cell division, DNA repair, disease and ageing that, with further analysis, could help inform future studies on longevity and cancer resistance. The research may also provide clues into why there is significant variance in the size of some mammals.

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News & developments

Two penguin genomes have been sequenced and analysed for the first time, revealing insights into how these birds have been able to adapt to the cold and hostile Antarctic environment. Antarctic penguins are subject to extremely low temperatures, high winds and profound changes in daylight. They have developed complicated biological systems to regulate temperature and store energy for long-term fasting. Most studies have focused on the physiological and behavioural aspects of their biology, but an international team of researchers has now analysed the DNA of two Antarctic penguins (Adélie and emperor) relative to other bird species, revealing the genetic basis of their adaptations and their evolutionary history in response to climate change. Using the historical genetic record within the DNA across bird species, the researchers estimate that penguins first appeared around 60 million years ago.

The study shows that the Adélie penguin population increased rapidly about 150,000 years ago when the climate became warmer, but later declined by 40% about 60,000 years ago during a cold and dry glacial period. In contrast, the emperor penguin population remained stable, suggesting that they were better adapted to glacial conditions, for example, by being able to protect their eggs from freezing temperatures and incubate them on their feet. Cai Li, team lead at BGIShenzhen, China, said: “These different patterns in historical population change also suggest that future climate change may have impacts on the two penguin species. For example, the fact that emperor penguins didn’t experience the same population boom as Adélie penguins in warm climates means that they could suffer more from global warming, and this needs to be considered in conservation efforts in Antarctica.” Both penguins were found

to have expanded genes related to beta-keratins – the proteins which make up 90% of feathers. They also had at least 13 genes responsible for a single type of beta-keratin, which is the highest number compared to all other known bird genomes. This would explain their importance in ensuring that penguin feathers are short, stiff and densely packed to minimise heat loss, remain waterproof and aid underwater flight. The team also identified a gene called DSG1, likely to be responsible for penguins’ thick skin and known to be involved in a human dermatological disease characterised by thick skin on the palms and soles. Packing on the fat Fat storage is critical for penguins to withstand the cold and survive long fasting periods – up to four months in emperor penguins. The two penguins were found to have exploited different adaptations for lipid metabolism in the course of their evolution. The researchers found eight genes involved in lipid metabolism in the Adélie penguin and three in the emperor penguin.

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During their evolutionary history, the wings (or forelimbs) of penguins changed profoundly for wing-propelled diving in the water. The team identified 17 forelimb-related genes in the penguin genomes that had unique changes. One of the genes in particular, EVC2, showed a larger number of genetic changes compared to other birds. Mutations of EVC2 in humans cause Ellis-van Creveld syndrome, characterised by short-limb dwarfism and short ribs. David Lambert, professor of evolutionary biology at Griffith University, Australia, said: “Although Adélie and emperor penguins both breed on the Antarctic continent, they do so in very different ways. By sequencing the genomes of two penguin species we have been able to compare many of the genes that are responsible for these different abilities to do the same thing – namely to survive and breed in Antarctica. This study is particularly important because it now provides us with the opportunity to conduct large scale evolutionary studies of both species.” Yvette Wharton, The University of Auckland

Yvette Wharton, The University of Auckland

Penguin genomes sequenced, reveal secret to success

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Fat could help protect against infection

Fat cells below the skin could help protect us from bacteria, according to new research from the San Diego School of Medicine at the University of California, USA. The researchers uncovered a previously unknown role for skin fat cells, known as adipocytes: they produce antimicrobial peptides that help fend off invading bacteria and other pathogens. “It was thought that, once the skin barrier was broken, it was entirely the responsibility of circulating (white) blood cells like neutrophils and macrophages to protect us from getting sepsis,” said Professor Richard Gallo, chief of dermatology at the school and the study’s principal investigator. “But it takes time to recruit these cells (to the wound site). We now show that the fat stem cells are responsible for protecting us. That was totally unexpected. It was not known that adipocytes could produce antimicrobials, let alone that they made almost as much as a neutrophil.” The human body’s defence against microbial infection is complex, multi-tiered and involves numerous cell types, culminating in the arrival of

neutrophils and monocytes – specialised cells that literally devour targeted pathogens. But, before these circulating white blood cells arrive at the scene, the body requires a more immediate response to counter the ability of many microbes to rapidly increase in number. That work is typically done by epithelial cells, mast cells and leukocytes residing in the area of infection. Staphylococcus aureus is a common bacterium and a major cause of skin and soft tissue infections in humans. The emergence of antibioticresistant forms of S. aureus is a significant problem worldwide in clinical medicine. Previously published work from Gallo’s lab had observed S. aureus in the fat layer of the skin, so the researchers looked to see if the subcutaneous fat played a role in preventing skin infections. Fat runs towards infection Researcher Ling Zhang, PhD, exposed mice to S. aureus and, within hours, detected a major increase in both the number and size of fat cells at the site of infection. More importantly, these fat cells produced high levels of an antimicrobial peptide (AMP) call cathelicidin

antimicrobial peptide (CAMP). AMPs are molecules used by the innate immune response to directly kill invasive bacteria, viruses, fungi and other pathogens. “AMPs are our natural firstline defence against infection. They are evolutionarily ancient and used by all living organisms to protect themselves,” said Gallo. “However, in humans, it is becoming increasingly clear that the presence of AMPs can be a double-edged sword, particularly for CAMP. Too little CAMP and people experience frequent infections. The best example is atopic eczema (a type of recurring, itchy skin disorder). These patients can experience frequent Staph and viral infections. But too much CAMP is also bad. Evidence suggests it can drive autoimmune and other inflammatory diseases like lupus, psoriasis and rosacea.” The scientists confirmed their findings by analysing S. aureus infections in mice unable to either effectively produce adipocytes or whose fat cells did not express sufficient antimicrobial peptides in general and CAMP in particular. In all cases, they found the mice suffered more

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frequent and severe infections. Further tests confirmed that human adipocytes also produce cathelicidin, suggesting the immune response is similar in both rodents and humans. Interestingly, obese subjects were observed to have more CAMP in their blood than subjects of normal weight. The potential clinical applications of the findings will require further study, said Gallo. Maintaining a balance “Defective AMP production by mature adipocytes can occur due to obesity or insulin resistance, resulting in greater susceptibility to infection, but too much cathelicidin may provoke an unhealthy inflammatory response.” “The key is that we now know this part of the immune response puzzle. It opens fantastic new options for study. For example, current drugs designed for use in diabetics might be beneficial to other people who need to boost this aspect of immunity. Conversely, these findings may help researchers understand disease associations with obesity and develop new strategies to optimise care.”

Ethics/policy/regulation Industry developments

Life in a test tube Mimicking natural evolution in a test tube, scientists at The Scripps Research Institute (TSRI) have devised an enzyme with a unique property that might have been crucial to the origin of life on Earth Aside from illuminating one possible path for life’s beginnings, the achievement is likely to yield a powerful tool for evolving new and useful molecules. “When I start to tell people about this, they sometimes wonder if we’re merely suggesting the possibility of such an enzyme – but no, we actually made it,” says Gerald F Joyce, professor in TSRI’s Department of Chemistry and Cell and Molecular Biology and director of the Genomics Institute of the Novartis Research Foundation.

The challenge of making copies

start to tell people about this, they sometimes wonder if we’re merely suggesting the possibility of such an enzyme – but no, we actually made it ” Professor Gerald F Joyce, TSRI Department of Chemistry and Cell and Molecular Biology, Director of the Genomics Institute of the Novartis Research Foundation

Gernot Krautberger/dollarphotoclub

The new enzyme is called a ribozyme because it is made from ribonucleic acid (RNA). Modern DNAbased life forms appear to have evolved from a simpler ‘RNA world’ and many scientists suspect that RNA molecules with enzymatic properties were Earth’s first self-replicators. The new ribozyme works essentially in that way. It helps knit together a ‘copy’ strand of RNA, using an original RNA strand as a reference or ‘template’. However, it doesn’t make a copy of a molecule completely identical to itself. Instead, it makes a copy of a mirror image of itself – like the left hand to

“ When I

its right – and, in turn, that ‘left-hand’ ribozyme can help make copies of the original. No one has ever made such ‘cross-chiral’ enzymes before. The emergence of such enzymes in a primordial RNA world – which the new study shows was plausible – could have overcome a key obstacle to the origin of life. Biology on Earth evolved in such a way that in each class of molecules, one chirality, or handedness, came to predominate. Virtually all RNA, for example, are right-handed and called D-RNA. That structural sameness makes interactions within that class more efficient – just as a handshake is more efficient when it joins two right or left hands, rather than a left and a right. “Scientists are generally taught to think that there has to be a common chirality among interacting molecules for biology to work,” says Joyce. It seems likely, however, that simple RNA molecules on the primordial Earth would have consisted of mixes of both right- and left-handed forms. Despite this reasoning, 30 years ago Joyce, then a graduate student, published a paper in Nature showing that self-replicators would have had a tough time evolving in such a mix. Any strand of RNA that gathered stray nucleotides onto itself would eventually have incorporated an RNA nucleotide of the opposite handedness, which would have blocked further assembly of that copy. “Since then, we’ve all been wondering how RNA replication could have started on the primitive Earth,” Joyce says.

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Industry developments

The research suggests that simple RNA molecules on primordial Earth would have consisted of mixes of both right- and left-handed forms

A looser grip One theory has been that a right-handed RNA enzyme emerged with the capacity to make copies of other right-handed RNA molecules, including itself, while ignoring left-handed L-RNA. Joyce and others have created such ribozymes in the laboratory, and have found that RNA’s propensity to form sticky base pairs with other RNA – which is a useful property for its various cellular functions – hampers its ability to work as a copier of other RNA molecules. In essence, these RNA-copying ribozymes work well with some RNA sequences, but not all. A general-purpose RNA replication enzyme would have less of a grip on the RNA it handles. “That’s how later-evolved protein enzymes that replicate RNA and DNA work – they’re not nucleic acids, so they can’t form base pairs with the nuclear acids they’re copying,” Joyce notes. But how could an RNA enzyme have worked like that, in a primordial world limited to RNA? Perhaps only if it worked on opposite-handed RNA, with which it is chemically prohibited from forming consecutive base pairs. “We started thinking: it feels a little weird but you can shake the wrong hand of somebody else,” Joyce explains.

Test tube evolution No one had ever made or even tried to make a ribozyme that worked cross-chirally, on oppositehanded RNA. But, in this new study, Joyce laboratory postdoctoral fellow Jonathan T Sczepanski used a technique called ‘test-tube evolution’ to come up with one. He started with a soup of about a quadrillion (1015) short RNA molecules. Their sequences were

essentially random, and all were of right-handed chirality. “We set it up so that the molecules that could catalyse a joining reaction with left-handed RNA could be pulled out of solution and then amplified,” Sczepanski said. After just 10 of these selection-and-amplification rounds, the researchers had a strong candidate ribozyme. They then expanded the size of its core region, put it through six more selection rounds and trimmed the extraneous nucleotides. The result: an 83-nucleotide ribozyme that was only moderately sequence-specific and could reliably knit a test segment of left-handed RNA to a template – about a million times faster than would have happened without enzyme assistance. The team also showed that the new ribozyme would work without hindrance, even when samehanded RNA nucleotides were present. In a last test, the new ribozyme successfully catalysed the assembly of 11 segments of RNA to make a complete copy of its left-handed counterpart ribozyme, which was able to join segments of right-handed RNA. The researchers are now working to put the right-handed ribozyme (and, by implication, its lefthanded partner) through more selection rounds, so that it can mediate the full replication of RNA, with essentially no sequence-dependence. That would make it a true general-purpose RNA-replication enzyme, capable in principle of turning a primordial nucleotide soup into a vast biosphere. “Ultimately, what one wants is to turn it loose – in the lab, of course, not in the wild – to let it start replicating and evolving and seeing what results,” t Joyce says.

Biotech World q January 2015 q 19

Industry developments

Ethics/policy/regulation

Mapping the bird tree of life takes flight A team of international researchers has completed the largest whole genome study of a single class of animals to date. Mapping the tree of life for birds involved sequencing, assembling and comparing full genomes of 48 bird species representing all major branches of modern birds over four years. Birds are some of the world’s most colourful animals, with a spectacular biodiversity of more than 10,000 species. Partly, this is because birds that survived the mass extinction experienced a rapid burst of evolution. For the first time, an international consortium of scientists – the Avian Phylogenomics Consortium*, comprising more than 200 scientists from 80 institutions across 20 countries – has mapped the largest whole genome study of a single class of animals (known as phylogeny). Previous attempts to reconstruct the avian family tree using partial DNA sequencing or anatomical and behavioural traits have met with contradiction and confusion. Because modern birds split into species early and in such quick succession, they did not evolve enough distinct genetic differences at the genomic level to clearly determine their branching order, the researchers say. To resolve the timing and relationships of modern birds, the consortium used whole-genome DNA sequences to infer the bird species tree. Neuroscientist Erich D Jarvis of Duke University explains: “In the past, people have been using 10 to 20 genes to try to infer the species relationships. What we’ve learned from doing this whole-genome approach is that we can infer a somewhat different phylogeny than that proposed in the past. We’ve figured out that protein-coding genes tell the whole story for inferring the species

“ The computational challenges in estimating the avian species tree of life used around 300 years of CPU time and some analyses required supercomputers with a terabyte of memory ” Computer scientist Tandy Warnow at the University of Illinois at Urbana-Champaign

tree. You need non-coding sequences, including the intergenic regions. The protein-coding sequences, however, tell an interesting story of proteomewide convergence among species with similar life histories.”

Mass extinction created biodiversity The whole-genome analysis dates the evolutionary expansion of modern birds (Neoaves) to the time of the mass extinction event 66 million years ago that killed off all dinosaurs except some birds. This contradicts the idea that Neoaves blossomed 10 to 80 million years earlier, as some recent studies suggest. Based on this new genomic data, only a few bird lineages survived the mass extinction, giving rise to the more than 10,000 Neoaves species that comprise 95% of all bird species living today. The freed-up ecological niches caused by the extinction event likely allowed rapid species radiation of birds in less than 15 million years, which explains much of modern bird biodiversity. The researchers analysed around 14,000 genes per species, requiring several new approaches to computing evolutionary family trees. “The computational challenges in estimating the avian species tree used around 300 years of CPU time and some analyses required supercomputers with a terabyte of memory,” says computer scientist

*Throughout this article, the word ‘consortium’ is used, although the various studies described were individually conducted by different groups all over the world. For more information on the individual studies, visit the consortium’s website www.avian.genomics.cn/en

Biotech World q January 2015 q 20

Industry developments

Tandy Warnow at the University of Illinois, who was involved in the project. For all their biological intricacies, birds are surprisingly light on DNA. One of the studies found that, compared to other reptile genomes, avian genomes contain less of the repetitive DNA and lost thousands of genes in their early evolution after birds split from other reptiles. “Many of these genes have essential functions in humans, such as in reproduction, skeleton formation and lung systems,” Dr Guojie Zhang, who led the study, notes. “The loss of these key genes may have had a significant effect on the evolution of many distinct phenotypes of birds. This is an exciting finding, because it is quite different from what people normally think, which is that innovation is normally created by new genetic material, not the loss of it. Sometimes, less is more.” From the whole chromosome level to the order of genes, this study found that the genomic structure of birds has stayed remarkably the same among species for more than 100 million years. The molecular evolution rate across all bird species is also slower compared to animals.

Answering key questions The various studies shed light on many other questions about birds. The researchers found that vocal learning evolved independently at least twice and was associated with convergent evolution in many proteins. They found that the specialised song-learning brain circuitry of vocal learning birds (songbirds, parrots and hummingbirds) and human brain speech regions have convergent changes in the activity of more than 50 genes. Most of these genes are involved in forming neural connections. They also found that singing is associated with the activation of 10% of the expressed genome, with diverse activation patterns in different song-learning

“ This is an

exciting finding, because it is quite different from what people normally think, which is that innovation is normally created by new genetic material, not the loss of it. Sometimes, less is more.” Dr Guojie Zhang, Beijing Genomics Institute, Shenzhen, China

regions of the brain, controlled by epigenetic regulation of the genome. They found that parrots have a song system-within-a-song system, with the surrounding song system unique to them. This might explain their greater ability to imitate human speech. More was revealed on the sex of birds; just as the sex of human beings is determined by the X and Y chromosomes, the sex of birds is controlled by the Z and W chromosomes. The W makes birds female, just as the Y makes humans male. Most mammals share a similar evolutionary history of the Y chromosome, which now contains many degenerated genes that no longer function and only a few active genes related to ‘maleness’. They also found that half of bird species still contain substantial numbers of active genes in their W chromosomes, challenging the classic view that the W chromosome is a ‘graveyard of genes’ like the human Y. The consortium also found that bird species are at drastically different states of sex chromosome evolution. For example, the ostrich and emu, which belong to one of the older branches of the bird family tree, have sex chromosomes resembling their ancestors. Yet, some modern birds such as the chicken and zebra finch have sex chromosomes that contain few active genes. This opens a new set of questions on how the diversity of sex chromosomes may drive the diversity of sex differences in the outward appearance of various bird species. Peacocks and peahens are dramatically different; male and female crows are indistinguishable. Another study focused on how and when birds lost their teeth. A comparison between the genome of living bird species and those of vertebrate species that have teeth identified key mutations in the parts of the genome that code for enamel and dentin, the building blocks of teeth. The evidence suggests that five tooth-related genes were disabled within

Biotech World q January 2015 q 21

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Photo: Eddy Perez, LSU University Relations

Industry developments

Scientists completed the largest whole genome study of a single class of animals to date by mapping the tree of life for birds. Avian genetic samples from Louisiana State Universityâ&#x20AC;&#x2122;s Museum of Natural Science, which has one of the largest vertebrate tissue collections in the world, were used for this study.

a short time period in the common ancestor of modern birds more than 100 million years ago.

Is it a bird? Is it a dinosaur? What is the connection between birds and dinosaurs? Unlike mammals, birds (along with reptiles, fish and amphibians) have a large number of tiny microchromosomes. These smaller packages of gene-rich material are thought to have been present in their dinosaur ancestors. A study of genome karyotype structure analysed whole genomes of the chicken, turkey, Peking duck, zebra finch and budgerigar. It found that the chicken has the most similar overall chromosome pattern to an avian ancestor, which was thought to be a feathered dinosaur. The consortium also analysed the connection between birds and crocodiles. It found that crocodiles have one of the slowest-evolving genomes. The researchers were able to infer the genome sequence of the common ancestor of birds and crocodiles (archosaurs) and, therefore, all dinosaurs, including those that went extinct 66 million years ago. Do bird genomes carry fewer virus sequences than other species? Mammalian genomes harbour a diverse set of genome fossils of past virus infections called â&#x20AC;&#x2DC;endogenous viral elementsâ&#x20AC;&#x2122; (EVEs). A study found that bird species had 6-13 times fewer EVE infections in their past than mammals. This finding is consistent with the fact that birds have smaller

Some of the diverse avian species that were analysed for the comparative genomics study. (Photos: AAAS/Carla Schaffer)

genomes than mammals. It also suggests birds may either be less susceptible to viral invasions or better able to purge viral genes. When did colourful feathers evolve? Elaborate, colourful feathers are thought to be evolutionarily advantageous, giving a male bird in a given species an edge over his competitors when it comes to mating. The consortium found that genes involved in feather colouration evolved more quickly than other genes in eight of 46 bird lineages. Waterbirds have the lowest number of beta keratin feather genes, land birds have more than twice as many and, in domesticated pet and agricultural bird species, there are eight times as many of these genes. Finally, what happens to species facing extinction or recovering from near-extinction? Birds are like proverbial canaries in the coal mine, because of their sensitivity to environmental changes that cause extinction. Researchers analysed the genomes of species that have recently nearly become extinct, including the crested ibis in Asia and the bald eagle in the Americas. They found that genes which break down environmental toxins have a higher rate of mutations in these species and there is a lower diversity of immune system genes in endangered species. In a recovering crested ibis population, genes involved in brain function and metabolism are evolving more rapidly. The researchers found more genetic diversity in the recovering population than was expected, giving greater hope for species conservation. t

Biotech World q January 2015 q 23

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Ethics/policy/regulation Synthetic biology

It’s Ebola, on paper If smart scrubs for healthcare workers that can sense exposure to a virus, bandages that signal when a wound is infected or clothing that tells a runner she’s getting dehydrated sounds like science fiction, think again Using synthetic biology, scientists have developed a pocket-sized slip of paper that could diagnose Ebola strains almost instantaneously and costs just US$21. The technology brings us one step closer to producing inexpensive, shippable and accurate test kits that use saliva or a drop of blood to identify specific disease or infection anywhere in the world, within minutes and without laboratory support. This technology could prove life-saving in third-world countries or during natural disasters, where disease must be quickly diagnosed before it spreads out of control. Putting a new spin on synthetic biology, a team at the Wyss Institute for Biologically Inspired Engineering has essentially packaged and freezedried the technology. James Collins, professor of Biomedical Engineering and Medicine at Boston University and co-director and co-founder of the Centre of Synthetic Biology, says: “In the last fifteen years, there have been exciting advances in synthetic biology. But, until now, researchers have been limited in their progress due to the complexity of biological systems and the challenges faced when trying to repurpose them. Synthetic biology has been confined to the laboratory,

operating within living cells or in liquid-solution test tubes.”

Synthetic biology on the up Of late, there has been a huge surge in media interest in synthetic biology, as it offers the potential to make manned space missions possible (see p29) or cheaply produce traditionally expensive products synthetically, such as saffron, lactose-free milk or civet coffee. Synthetic gene networks are built to carry out functions – similar to computer software applications – within a living cell or in a liquid solution, which is called the ‘operating system’. But, in this case, the team wanted to produce an operating system that did not rely on living cells or liquid, which take either too long to work or are too difficult to transport. Instead, Collins explains, they created an “in vitro, sterile, abiotic operating system upon which we can rationally design synthetic, biological mechanisms to carry out specific functions.” This operating system, astonishingly, is paper. “We’ve harnessed the genetic machinery of cells and

Biotech World q January 2015 q 25

Synthetic biology

Wyss Institute scientists have embedded effective synthetic gene networks in pocket-sized slips of paper. An array of RNA-activated sensors uses visible colour changing proteins to indicate presence of a targeted RNA, capable of identifying pathogens such as antibiotic-resistant and strain-specific Ebola virus (Photos: Wyss Institute at Harvard University)

embedded them in the fibre matrix of paper, which can then be freeze-dried for storage and transport. We can now take synthetic biology out of the lab and use it anywhere to better understand our health and the environment,” says Wyss staff scientist, Keith Pardee PhD. Using standard equipment at his lab bench and commercially-available, cell-free systems, Pardee designed and built a wide range of paper-based inks and printed patterns of small dots on uncoated filter paper. Each dot serves as a well or pit to hole a gene circuit and the cellular enzymes that make it work. He then used fluorescent and colour-changing proteins that signal when the mechanisms are working. Essentially, the strips of paper work in a similar way to a pregnancy test or pH strip – a colour or symbol will indicate if the test is positive or negative, alkali or alkaline.

The future of diagnostics? Crucially, once the strips have been produced, they can be freeze-dried and stored at room temperature for up to a year. To reactivate them, they need only be rehydrated and then immediately used. Will future doctors simply rehydrate these strips and use a saliva sample to diagnose mumps or the flu? Will patients be able to do this for themselves at home? Disturbingly, will employers be able to check their employees’ illnesses are real by checking for themselves? The technology saves a huge amount of time and cost in the lab compared to conventional laboratorybased methods of validating tools for cell-based research, Pardee says. “Where it would normally take two or three days to validate a tool inside of a living cell, this can be done using a synthetic biology paper-based platform in as little as 90 minutes.” Even

“ Where it

would normally take two or three days to validate a tool inside of a living cell, this can be done using a synthetic biology paperbased platform in as little as 90 minutes ” Keith Pardee, Wyss Institute research scientist

more encouragingly, the technology is significantly cheaper. Pardee adds: “We made 24 different Ebola sensors and tested them in a day, for US$21 each.” Had such technology been available in December 2013, would it have stemmed the tidal wave of Ebola in West Africa that authorities are still struggling to control? Could we have saved thousands of lives? The technology offers enormous potential in this area – it could help speed up diagnosis of any future outbreaks of Ebola and enable authorities to put immediate quarantines in place to prevent further spread and ensure proper medical care is available. The team’s ‘Ebola sensor’ was created using the paper-based method and utilised a novel gene regulator called a ‘toehold switch’, a new system for gene expression control. Although its inventors had designed the toehold switch to regulate genes inside living cells, its function was easily transferred to the convenience of ordinary freeze-dried paper. The Ebola sensor can differentiate between the Zaire and Sudan virus strains within an hour of exposure. When strain one has a 90% fatality rate and strain two a 55-65% fatality rate, the faster doctors know which strain they’re dealing with, the faster they can act. The sensor was conceived by Wyss Institute postdoctoral fellow Alex Green PhD, after the ongoing West Africa crisis brought the deadly pathogen into the global spotlight. Green reached out to Pardee and, together, they assembled the prototype Ebola sensor in less than a day.

The ‘toehold switch’ The toehold switch works as such an accurate biosensor because it can be programmed to only react with specific, intended targets, producing true ‘switch’ behaviour with an unprecedented ability to turn on targeted gene expression. It

Biotech World q January 2015 q 26

Synthetic biology

can be programmed to precisely detect an RNA signature of virtually any kind and then turn on production of a specific protein. Green developed the toehold switch with Yin, associate professor in the Department of Systems Biology at Harvard Medical School. “While conventional synthetic biology complicates accuracy and functionality because it relies on repurposing and re-wiring existing biological parts, the toehold switch is inspired by nature but is an entirely novel, de-novo-designed gene expression regulator,” says Yin. “We looked at our process to rationally design dynamic DNA nano devices in test tubes and applied that same fundamental principle to solve problems in synthetic biology.” The resulting toehold switch, an RNA-based organic nano device, is a truly ‘synthetic’ synthetic gene regulator with 40-fold better ability to control gene expression than conventional regulators. The toehold switch functions so precisely that many different toehold switches can be linked together, creating a complex circuit, which could be programmed to carry out multiple-step functions such as first detecting a pathogen and then delivering an appropriate therapy. “Instead of re-purposing an existing part that was evolved by nature, we wanted to change our way of thinking, leverage naturally-occurring principles and build from scratch,” says Green. His

“ We made

24 different Ebola sensors and tested them in a day, for US$21 each ” Keith Pardee, Wyss Institute research scientist

PhD in materials science and strong computer programming skills allowed him to approach biology with a fresh perspective and start from the ground up to engineer the toehold switch, rather than merely rewiring existing natural parts. “Whether used in vivo or in vitro, the ability to rationally design gene regulators opens many doors for increasingly complex synthetic biological circuits,” Green adds. Standing on their own, both paper-based synthetic gene networks and toehold switch gene regulators could each have revolutionary impacts on synthetic biology: the former brings synthetic biology out of the traditional confinement of a living cell, the latter provides a rational design framework to enable de-novo design of both the parts and the network of gene regulation. But combining the two technologies could truly set the stage for powerful, multiplex biological circuits and sensors that can be quickly and inexpensively assembled for transport and use anywhere in the world. Furthermore, now that we know it is possible to apply synthetic biology to physical ‘things’, endless opportunities are now open. Collins envisions a future with smart scrubs for healthcare workers that can sense exposure to a virus; bandages that signal when a wound is infected with antibiotic-resistant bacteria; or smart clothing that tells a runner she’s t getting dehydrated.

AN EYE ON THE FUTURE? Your buyers’ eyes. Here. Biotech World brings together the best of the fast-moving biotechnology industry in one monthly digest. Revealing the latest discoveries and explaining developments in simple language, it offers a birds-eye view of a vast but interconnected industry. Advertising in Biotech World ensures your products and services reach the right people. Call Steve Fulford on +44 (0)1223 968 960 or email stevefulford@biotechworld.co www.biotechworld.co

Biotech World q January 2015 q 27

DISCOVER

Sergey Drozdov/dollarphotoclub

Ethics/policy/regulation Synthetic biology

Synthetic biology ready for take-off A relatively new discipline, synthetic biology makes the impossible possible, be it manned space travel, growing human lungs in pigs, synthetically producing rare foods or making cells record their ‘life’ experiences Although not strictly biotechnology, synthetic biology is rapidly gaining ground in the scientific community. Stripping it down to basic principles, synthetic biology is either the design and construction of new biological systems in order to make them work unnaturally, or the redesign of existing biological systems for the purpose of modifying them to be more useful. For example, imagine a car. A car is constructed from numerous parts and car manufacturers have detailed knowledge of how each part works, as they have been engineered from scratch and purposebuilt. Manufacturers can select their preferred parts and assemble a car with specific qualities based on that knowledge. Synthetic biology applies a similar process at the microscopic level, except that scientists often have limited or no knowledge of how the individual parts work. In synthetic biology, scientists take a protein, analyse it, dissect it and attempt to recreate it synthetically – and then transplant it into a living cell to see if it ‘works’ (replicates) as the natural protein would.

“ Synthetic biology is

delivering some truly amazing advances that promise to change the way we understand and treat disease ”

Professor Patrick Maxwell, chair of the MRC’s Molecular and Cellular Medicine Board and Regis Professor of Physic, University of Cambridge, UK

This technology improves our understanding of natural systems and enables us to modify them for the benefit of humankind. If we can recreate the various parts that comprise a gene, we will one day be able to recreate and modify cells, viruses and bacteria without needing the natural versions. This would have many applications, but one example is recreating skin for burn victims. Current scientific methods allow us to clone skin cells in a Biotech World q January 2015 q 29

lab, but large skin pieces are difficult to come by and patient immune systems often reject skin grafts. Synthetic biology could offer us the opportunity to create skin cells from scratch, which could then be modified to ensure they are accepted by the body. Developments in synthetic biology have hit a high over the last few months. Globally, the market is expected to reach US$5,630.4 million in 2018 from US$1,923.1 million in 2013, a compound annual growth rate of 24%. In December 2014, Business Wire reported that the key factors expected to spur growth of the market were increasing research and development (R&D) expenditure in pharmaceutical and biotechnology companies, growing demand for synthetic genes, rising production of genetically modified crops and incessantly rising funding in the field. However, it noted, ethical and social issues such as biosafety and biosecurity of synthetic biology were hindering growth of the market. Key leaders in synthetic biology are

Synthetic biology viperagp/dollarphotoclub

Left: Scientists have rewritten the pig genome so it grows human-like lungs for transplant. Right: companies are synthetically producing flavourings such as saffron or vanilla

Canada and the UK. According to a November Concordia University article: “Since 2000, Genome Canada and partners have invested more than C$2.3 billion in deciphering the genomes of economically important plants, animals and microbes in order to understand how they function. A significant proportion of these funds has been invested in building the technological toolkits that can be applied to synthetic biology.”

Grow your own … on Mars One exciting application of the technology is the possibilities it offers for manned space travel. UC Berkeley and NASA scientists suggest synthetic biology could allow space travellers to use microbes to produce their own food, fuel, medicine and building materials from raw feedstocks readily available on Mars or the moon, instead of carrying all supplies aboard the spacecraft or making them at the destination with conventional nonbiological materials. Currently, any plans for manned space travel include carrying large amounts of food and other materials for a round-trip journey, which involves a lot of supply and equipment weight to lift off Earth and across the millions of miles between Earth and Mars. However, the scientists calculate that using biological production could reduce the mass of supplies sent with the expedition by between 26% and 85%, depending on the application, which would significantly reduce the cost of the mission. “Space synthetic biology is truly groundbreaking,” says Amor Menezes, a postdoctoral scholar at UC Berkeley’s California Institute for Quantitative Biosciences. “Abiotic [non-alive] technologies were developed for many, many decades before

“ Our work suggests

that, in principle, there are a number of possible alternatives to nature’s molecules that will support the catalytic processes required for life. Life’s ‘choice’ of RNA and DNA may just be an accident of prehistoric chemistry ” Dr Philipp Holliger, MRC Laboratory of Molecular Biology, University College London, UK

they were successfully utilised in space and biological technologies like synthetic biology are only now seeing development efforts. So, of course, these technologies have some catching-up to do when utilised in space. But, it turns out, this catching-up may not be that much and, in some cases, the technologies may already be superior to their abiotic counterparts.” Nevertheless, he notes: “In the future, the biological technologies will have to be deemed ‘safe’ for the astronauts and the extraterrestrial destination, with suitable containment efforts in place.” Other applications of synthetic biology are in the pharmaceutical/medical industry. In November, genome pioneer Craig Venter announced at the Synbiobeta 2014 conference that scientists were attempting to rewrite the pig genome so that it grew human-like lungs for transplant into humans. He said that, by changing as few as five genes, they had created lungs Biotech World q January 2015 q 30

that survived for a year in baboons. Other companies are looking at producing lactose-free milk or synthetically producing rare or traditionally expensive foods and flavourings such as saffron or vanilla.

An alternative to evolution? Scientific breakthroughs in synthetic biology are speeding up exponentially. In December, scientists at Cambridge University in the UK announced that they had created the world’s first enzymes from artificial genetic material. The synthetic enzymes, which are made from molecules that do not occur anywhere in nature, are capable of triggering chemical reactions in the lab. The researchers point out how significant the findings are when it comes to extraterrestrial life; they speculate that the study increases the range of planets that could potentially host life. All life on Earth, they explain, depends on the chemical transformations that enable cellular function and the performance of basic tasks, from digesting food to making DNA. These are powered by naturally-occurring enzymes that operate as catalysts, kick-starting the process and enabling such reactions to happen at the necessary rate. For the first time, however, the research shows that these natural biomolecules may not be the only option and that artificial enzymes could also be used to power the reaction that enables life to occur. Dr Alex Taylor, a post-doctoral researcher at St John’s College, University of Cambridge, explains that the results imply “our chemistry, of DNA, RNA and proteins, may not be special and that there may be a vast range of alternative chemistries that could make life possible.”

Synthetic biology Dr Philipp Holliger, from the MRC Laboratory of Molecular Biology at University College London, adds: “Until recently, it was thought that DNA and RNA were the only molecules that could store genetic information and, together with proteins, the only biomolecules able to form enzymes. “Our work suggests that, in principle, there are a number of possible alternatives to nature’s molecules that will support the catalytic processes required for life. Life’s ‘choice’ of RNA and DNA may just be an accident of prehistoric chemistry.” “The creation of synthetic DNA – and now enzymes – from building blocks that don’t exist in nature also raises the possibility that, if there is life on other planets, it may have sprung up from an entirely different set of molecules. [This would] widen the possible number of planets that might be able to host life.” Holliger says the enzymes could be an attractive candidate for long-lasting treatments that can disrupt diseaserelated RNAs. Professor Patrick Maxwell, chair of the MRC’s Molecular and Cellular Medicine Board and Regis Professor of Physic at the University of Cambridge, says: “Synthetic biology is delivering some truly amazing

I see, I remember, I record

Scientists have altered DNA to remember and record events

advances that promise to change the way we understand and treat disease. The UK excels in this field, and this latest advance offers the tantalising prospect of using designer biological parts as a starting point for an entirely new class of therapies and diagnostic tools that are more effective and have a longer shelf-life.”

Biotech World q January 2015 q 31

Another recent development is the success of synthetic biologist Timothy Lu of the Massachusetts Institute of Technology in Cambridge, Massachusetts, USA, whose team managed to give cells memories. Before the study, cells could remember or record a single piece of information, such as exposure to a certain toxin. However, Science magazine reported in November that Lu’s team created “a biological program that rewrites a living cell’s DNA when the cell senses a signal – from a flash of light to the presence of a chemical. “Once the DNA is altered, the information remains embedded in the genetic material even if the cell dies. By sequencing the genes of a population of cells that all contain the program, researchers can determine the magnitude and duration of the signal: the more cells that have the genetic mutation, the stronger or longer the signal was.” Lu says: “One [application of this technology] is being able to do long-term recording of a cell’s environment.” He told Science that living cells could be placed in an area of water and later collected to see if the cells had been exposed to bacteria or toxins in the water. t

BIOTECHNOLOGY? WEâ&#x20AC;&#x2122;VE GOT IT COVERED.

Industrial

The web of the future Stronger and lighter than steel, more durable than Kevlar, extremely elastic and able to stop a Boeing 747 in full flight with a strand as thin as a pencil, spider silk is the stuff of science fiction. Its unique properties have captured the imagination of thousands of scientists the world over. Many long to recreate it at commercial-scale for human use but the spider is holding onto its elusive secret. However, we are inching closer to making spider silk a commercial reality Humans have used spider silk since time immemorial. Peasants in the southern Carpathian Mountains used it to cover wounds, which reportedly facilitated healing and even connected with the skin. This is believed to be due to its antiseptic properties and high levels of vitamin K, which can be effective in clotting blood. Fishermen in the Indo-Pacific Ocean have used the web of the Nephila spider to catch small fish; it has been used as a thread for crosshairs in optical instruments; and it has been successfully formed into a set of violin strings. Today scientists lust after it for industrial applications ranging from super-strong bulletproof fabric to adhesives, gels, coatings, sponges and sealants. An article by Brian Barth published in Modern Farmer in November 2014 notes: â&#x20AC;&#x153;Interested parties have salivated for

years over the potential applications, which go far beyond fabrics: the US Navy wants spider silk for its ability to adhere to any material, even underwater; the US Department of Energy is hoping to make vehicles lighter and thus more fuel-efficient by integrating silk proteins into the manufacture of door panels; and the US Air Force is envisioning lightweight, bulletproof body armour that is easier to manoeuvre in during combat. The medical applications are all over the map: artificial skin for burn patients, better plasters, synthetic ligaments, micro-sutures for delicate organs like the eyes and a host of surgical implants and drug delivery mechanisms.â&#x20AC;? The silk is also able to absorb over 100,000 joules of kinetic energy, making it the ideal material for structural blast protection. Any future vision of large-scale spider silk

Biotech World q January 2015 q 33

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Industrial

Left: silkworms are being genetically modified to produce spider silk. Right: spiders cannot be farmed for their silk due to their cannibalistic natures

production does not, however, include spiders lining up in cages preparing to be milked. Spider farming is not possible due to the spider’s cannibalistic nature. Furthermore, milking a spider of its silk is a timeconsuming and expensive process. The longest piece of cloth made from spider silk – just 3.4m by 1.2m – was produced in 2009. It took 82 people four years to collect enough silk from the Golden Orb spider. Clearly, we need a faster way to produce this magical substance, but scientists have so far been unsuccessful in persuading the humble spider to share its secret. Nevertheless, there are ways of engineering the material without involving grumpy spiders and numerous companies are attempting to do just that.

Enter the silkworm The most successful approach has been that involving the silkworm, designed by nature to produce silk in significant quantities and apparently happy to do so. Around 40% of the silkworm’s weight is devoted to the silk glands, which produce large volumes of protein called fibroin, which is then spun into composite thread (silk). Barth explains that the silkworm has been farmed for centuries: “The Chinese perfected the art of harvesting the single, half-mile long thread that forms each cocoon, transforming worm silk into luxurious fabric at least 5,000 years ago.” Now, scientists are capitalising on the process, with a twist: they’re genetically engineering silkworms to produce spider silk. If that’s not enough, in the recent past, silkworms have been fed artificial colourants that have produced ‘pre-dyed’ versions of silk, which eliminates the costly and toxic silk dyeing process. Researchers in Japan have even engineered silkworms to spin glow-in-the-dark thread for use in high-end fashion. However, the technology is not perfect, yet. Dr Randy Lewis at the Synthetic Bioproducts Centre at

“ The worms

we have now make about five percent spider silk and 95% worm silk ... the gene is not as stable as we would like ... after several generations, the amount of spider protein starts to drop ” Dr Randy Lewis, Synthetic Bioproducts Centre, Utah State University, USA

Utah State University, USA, whose lab team is busy genetically modifying silkworms, says: “The worms we have now make about five percent spider silk and 95% silkworm silk,” but a threshold of 20-30% spider silk protein must be achieved before the technology becomes viable. He adds: “The gene is not as stable as we would like ... after several generations, the amount of spider protein starts to drop.” Even if 100% spider silk could be produced, scientists would face enormous regulatory hurdles, Lewis says. Despite this – and the larger question hovering over genetic modification on such a scale – he “can think of a lot of environmentallysound reasons to genetically engineer silkworms, [including the fact that] the enhanced fabric has potential to replace synthetics like nylon and Kevlar, which are petroleum-based products.”

Silkworms around the world Over in Japan, at Shinshu University, scientists are attempting a similar feat. Macao Nakagaki from the Faculty of Textile Science and Technology was the first person, in 2007, to implant spider genes in silkworms, according to the country’s Ashai newspaper. Today, they claim, they are producing silkworm silk that has nearly 20% of the components of spider webs, and several prototype socks have been manufactured using the material. Kraig Biocraft Laboratories in Michigan, USA, is also modifying silkworms. The company has created approximately 20 different genetically engineered spider silk fibres based on certain genetic sequences. Its lead product is ‘Monster Silk’, which the company believes “will make significant inroads in both technical textile and mundane silk and apparel markets”, adding that “the traditional silk market is estimated at approximately US$3-5 billion a year at the raw fibre level.” Another line of Kraig products is the ‘Gen 3

Biotech World q January 2015 q 35

yexela/dollarphotoclub

Wikipedia.com

Industrial

Figure 1: Tensile strength of Kevlar versus spider dragline silk

Right: spider silk thread is almost as strong as Kevlar, much lighter and significantly more durable, which makes it sought-after by the armed forces

technical and medical fibre’ line which, although at a relatively early stage of development, will incorporate such elements as antibacterial agents for medical use and metallic ions for use in industrial processes. Kraig claims it has a significant advantage over other companies, as it explains: “Teams of other scientists around the world have worked on other ways to produce spider silk using E.coli bacteria. That work is scientifically sound, but with production costs that could exceed US$100,000/kg, it is difficult to see how these programmes could capture a significant part of the textile market. [We’re] able to produce genetically engineered spider silks, including Monster Silk, at less than one percent of that cost.”

Goats and bacteria offer alternatives Elsewhere, silkworms are given a break, as production of these super-strands is not just limited to the amenable nature of the silkworm. In 2000, Canadian biotechnology company Nexia successfully produced spider silk protein in goat’s milk. A gene transplanted into the goat made it produce milk containing significant quantities of an extra protein – 1-2 grams of silk proteins per litre of milk – which was extracted and spun into spider silk thread. Moreover, beginning in Korea in March 2010, researchers from the Korea Advanced Institute of Science & Technology (KAIST) began genetically modifying the bacteria E.coli, crossing it with certain genes of the spider Nephila clavipes. The approach was pioneering: it eliminated the need to milk spiders and allowed the manufacture of spider silk in a cost-effective manner. The genius behind using bacteria is that its natural function is to reproduce; inject spider silk genes, therefore, and the bacteria sets about reproducing them. The idea was expanded last year by German

“ Our

discovery will revolutionise the conventional thought on the low thermal conductivity of biological materials ... There are only a few materials higher – silver and diamond ” Xinwei Wang, associate professor of mechanical engineering, Iowa State University, USA

company AMSilk, which crossed genetically modified E.coli with European garden cross spider DNA. The result was the production of four different varieties of silk in 20 different grades. Managing director of AMSilk said at the time: “This is scaleable technology. If someone ordered one tonne, we could make it. We have already made half a tonne.” He expects sales to hit US$10 million in the next couple of years and US$100 million when large-scale production begins. If spider silk is as sought-after as imagined, it seems certain that these are extremely conservative estimates. Adding further to spider silk’s superpower qualities, Xinwei Wang, associate professor of mechanical engineering at Iowa State University, USA, discovered that spider silk is also an incredible conductor of heat. He and his team found that it conducted heat better than most materials, including very good conductors such as silicon, aluminium and pure iron. It also conducts heat 1,000 times better than woven silkworm silk and 800 times better than other organic tissues. “Our discovery will revolutionise the conventional thought on the low thermal conductivity of biological materials,” he says. “This is very surprising, because spider silk is organic material. For organic material, this is the highest ever. There are only a few materials higher – silver and diamond.” If that’s not mind-boggling enough, when spider silk is stretched, its thermal conductivity increases. Wang says that stretching spider silk to its 20% limit also increases conductivity by 20%, whereas most materials lose thermal conductivity when they’re stretched. He adds: “That could lead to spider silk helping to create flexible, heat-dissipating parts for electronics, better clothes for hot weather, bandages that don’t trap heat and many other t everyday applications.”

Biotech World q January 2015 q 37

Events

Diary 11-16 January 2015 Precision Genome Engineering and Synthetic Biology Big Sky Resort, Big Sky, Montana, USA Contact: Heather Ford Tel: +1 800 253 0685 or +1 970 262 1230 E-mail: info@keystonesymposia.org Web: www.keystonesymposia.org/15A1 12-14 January 2015 7th Annual Conference Biotech Showcase 2015 Parc 55 Wyndham, San Francisco, California, USA Contact: Kelly Rogers, EBD Group Tel: +1 760 692 5917 E-mail: krogers@ebdgroup.com Web: www.ebdgroup.com 21-23 January 2015 National Conference on Genome Informatics ‘15 SRM University, Kattankulathur Campus, Tamil Nadu, India Contact: Dr Waheeta Hopper E-mail: hod.bioinfo@ktr.srmuniv.ac.in Web: www.srmuniv.ac.in/ncgi/ncgi.html 28-31 January 2015 2nd International Conference on Bioenergy, Environment and Sustainable Technologies Arunai Engineering College, Tiruvannamalai, Tamil Nadu, India Contact: BEST2015 Tel: +91 89038 88961 E-mail: icbest2015@gmail.com Web: www.best.biotechpage.com 1-6 February 2015 RNA Nanotechnology Conference Four Points Sheraton/Holiday Inn Express, Ventura, California, USA Tel: +1 859 218 0128 E-mail: peixuan.guo@uky.edu Web: www.nanobio.uky.edu/RNA2013 2-4 February 2015 BioAsia 2015 New Era of Life Sciences

Novotel Hyderabad Convention Centre, Hyderabad, India Contact: Ms Paridhi Gupta Tel: +91 40 6644 6477 / 6577 E-mail: paridhi@bioasia.in Web: www.2015.bioasia.in 5 February 2015 9th Swiss-Scandinavian Bio-Business Seminar SIX Stock Exchange building, Zurich, Switzerland Contact: Edin Erkocevic, Business Sweden E-mail: edin.erkocevic@business-sweden.se Web: www.b2match.eu/ssbbs2015 18-19 February 2015 The 3rd International Partnering of the Israeli BioMedTech Industry Life Sciences Israel 2015 Dan Panorama Hotel, Tel Aviv, Israel Contact: Gail Tito, Secretariat Tel: +972 3 5767753 E-mail: secretariat@gpcevents.com Web: www.lifesciencesisrael.com 23-24 February 2015 10th Annual Biomarkers Congress Manchester Central Convention Complex, Manchester, UK Contact: Oxford Global Conferences Tel: +44 (0)1865 248455 E-mail: a.pau@oxfordglobal.co.uk Web: www.biomarkers-congress.com 24-25 February 2015 Pharma CI Conference & Exhibition Hilton Amsterdam Hotel, The Netherlands Tel: +1 212 228 7974 E-mail: info@pharmaciconference.com Web: www.pharmaciconference.com 25-26 February 2015 Bitcom’s Global Life Science Partnering Conference The Lodge at Torrey Pines, La Jolla, California, USA Contact: Ashleigh Berry, Associate Manager of Events, Biocom

Tel: +1 858 455 0300 E-mail: aberry@biocom.org Web: www.biocom.org/event/index/ Partnering_Conference_2015 26-27 February 2015 Clinical applications of stem cells Singapore General Hospital, Singapore Contact: Select Biosciences Ltd Tel: +65 9186 3246 E-mail: sea@selectbio.com Web: www.selectbiosciences.com/ conferences/index.aspx?conf=CASC2015 24-25 March 2015 12th Annual BIO Asia International Conference Grand Hyatt, Tokyo, Japan Contact: Bernadette Blake E-mail: bd_registration@bio.org Web: www.bio.org/events/conferences/ bio-asia-international-conference 13-15 April 2015 8th International Conference on Biobased Materials Maternushaus, Cologne, Germany Tel: +49 (0) 2233 4814 49 E-mail: dominik.vogt@nova-institut.de Web: www.biowerkstoff-kongress.de 15-17 April 2015 International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO) 2015 Science Faculty of the University of Grenada, Grenada, Spain E-mail: iwbbio@ugr.es Web: www.iwbbio.ugr.es 12-15 May 2015 11th Annual World Congress on Industrial Biotechnology Montreal, Canada Contact: Simon Englhart, EBD Group Tel: +49 89 2388 756 0 E-mail: senglhart@ebdgroup.com Web: www.ebdgroup.com/bioeurope/ index.php

For more diary listings, visit www.biotechworld.co If you’d like your event listed here or on the website, email editor@biotechworld.co

Biotech World q January 2015 q 38

DISCOVER

Call Steve Fulford on +44 (0)1223 968 960 or email stevefulford@biotechworld.co