ATG Newsletter Issue 03
April 2016
Welcome to another edition of the ATG Member Newsletter!
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Women In SCIENCE
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his issue is devoted to women in science. Are women treated differently from men in the world of science? If you were a screenwriter and you had to create a character who was a successful scientist, how would you describe the character? What would be, for example, the scientist’s gender, age, way of speaking and writing, clothes, likes and dislikes, hobbies, marital status?
ATG Newsletter
Issue 03 April, 2016 Contributors: Helder F. Araujo (Ed.), Maria De Sousa, Filipa Ferreira, Eurico Morais de Sá, Pedro Resende, Catarina Seabra & Andre Sousa. Cover: Hanna Damasio & Helder F. Araujo. Linguistic revision: Panthea Heydari www.agtnewsletter.up.pt atgsnewsletter@gmail.com ATG - All Time GABBA The Alumni Association of the Graduate Program in Areas of Basic and Applied Biology University of Porto - Portugal www.atg.up.pt ATG - GABBA IPATIMUP Rua Dr. Roberto Frias s/n 4200-465 Porto Portugal geral@atg.up.pt
Before entering the world of science, most people have a very romantic idea of science. Objectivity should reign over that realm. The main characters, the scientists, ought to be extremely knowledgeable individuals and endowed with unsurmountable levels of objectivity and sensibility. Scientists must, for example, never be influenced by all the factors that bias a regular person’s perception of other people. A more realist idea is that scientists are just like anyone else in relation to varied aspects. Is it really reasonable to expect that they are less vulnerable to the varied factors that Social Psychology has taught us to be relevant to the perception of oneself and other people? Should it shock us to know that many scientists do not treat all the other scientists equally even when there are not objective reasons for that differential treatment? And to go back to the initial question, should it shock us to learn about situations in which women are subject to some sort of differential treatment? As much as discrimination is still real in science and anywhere else, it is not inevitable. Implicit biases are difficult to correct; to do so, one needs, for example, time to introspect, which tends to be scarce. At any rate, it’s not hard to fight certain explicit expressions of discrimination. Many institutions impose strong policies against some forms of discrimination. Moreover, when both individuals and institutions work together, certain expressions of discrimination are eventually stigmatized and thus very unlikely to occur. I hope you, regardless of everything that makes up your uniqueness, enjoy this issue of our newsletter. As always, our sincere thanks to all of our contributors! This issue would not be possible without their help. Helder F. Araujo 2
Contents Message from the President of the Executive Board Andre Sousa 5 De Sousa et al. Maria de Sousa Hanna Damasio 7 City of Knowledge Part I. Citizens 12 Part II. Knowlegde 17 ATG News 25 GABBA News 27 Read and Highlighted 34
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Rumor has it that you haven’t become a member yet... Is it true?! For you to become a member, all you need to do is pay the annual dues, fill out the membership form, and email us the payment confirmation along with the membership form. You may please find the form on the website.
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Message from the President of the Executive Board Andre Sousa
Dear colleagues, We had our first annual meeting last December. I would like to thank all of you who were able to come and participate in our session. We organized two round-table discussions: “Coming back to Portugal” and “Alternative careers in Science”. Students and coordinators gave us good feedback, including some suggestions that we will take into consideration to improve our future meetings.
“We organized two discussions: ‘Coming back to Portugal’ and ‘Alternative careers in Science’
We are currently working on three projects: Prémio Mariano Gago Maria de Sousa Summer Research Program Gabba Student Handbook.
We are currently working on three projects. We have been in contact with Ciência Viva to implement the “Prémio Mariano Gago” for high school students and with Universidade do Porto to implement the Maria de Sousa Summer Research Program for undergraduate students. As you know, we are also preparing a student handbook. The book will cover several topics, ranging from the life as a graduate student, to defending their PhD thesis and professional choices after the PhD. In this newsletter, we share two texts from this handbook as supplement. They try to answer the question “When are you ready to read your thesis?”. I hope you enjoy reading them and feel inspired to contribute to this book with your own thoughts and advice. Although we have finished some chapters, we still need help to finish the book on time. Our goal is for it to be ready for the next GABBA class. We would greatly appreciate your help in writing some of the remaining chapters. We feel that this book will be very important to all of us. It would be a great way to help answer many of the questions students have. During our last GABBA meeting, we had an informal discussion about ways of assisting current students. As you may know, the path to graduation can be tortuous and some students may not be able to get to the finishing line without help. We would like to stress that we are always willing to help solve difficult situations. However, in order to do that, we need to know what kind of hurdles you are struggling to overcome. Please don’t hesitate to contact us if you are having problems. You can send us an email, or just schedule a phone call. Even if we cannot help you solve the situation ourselves, we probably know someone who can! I would like to finish by wishing good luck to all of you that are getting ready to defend your Ph.D. thesis. Please don’t forget to become a full member of ATG after you graduate. *** 5
So many projects, so little time... ATG needs your help to make all its dreams real. Send us an email when you are ready to help us, will you?
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DE SOUSA ET AL. GENDERLESS VALUES Maria de Sousa
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“[...] if we had to explain to a child what research is, the answer would be exactly that: questioning, try different answers until one is satisfactory and then, look at the answer and use it to formulate new questions”
This text is a reproduction of Maria de Sousa’s speech at the opening of a exhibit called “Women in Science” at Pavilhão do Conhecimento, on March 8, 2015. This exhibit was organized by Ciência Viva to honor Portuguese women who have devoted their lives to science, It is also available as a book. The photograph was taken by Luisa Ferreira. It is part of the work organized by Ciencia Viva, “Women in Science”. Courtesy of Ciência Viva (Rosalia Vargas).
osalia Vargas invited me to say a few words on this day. An invitation from Rosalia to celebrate this day, this place, and the memory of Mariano Gago is not really an invitation or an order to me, but it is rather a pleasure. I am very pleased to be here celebrating the 2016 International Women’s Day, on behalf of the science that we currently represent. The first words obviously go to Rosalia herself, to whom women and men, young and old, owe so much. Rosalia has been unwavering in her quest for maintaining science alive and for more and better knowledge, curiosity, questioning, solving, and then repeating this process ad eternum. I believe that if we had to explain to a child what research is, the answer would be exactly that: questioning, trying different answers until one is satisfactory and then, looking at the answer and using it to formulate new questions. This is a never-ending process that might be better explained to a child by comparing it to an endless carousel ride. The ticket for that ride has both a cost and very clear rules: 1.You shall not lie. 2.You will be open-minded to results that may or may not confirm your hypothesis. 3.You shall consider the results of the ride absolute. 4.Your peers, regardless of whether they work at a near bench or in a near continent, are your most important support. They are the ones who will try to corroborate your results. 7
5.If you did not fake your data or use intricate methods to get flashy (but far from the truth) results, your peers will reproduce your results. Knowledge is nothing more than that: a sum of truths. 6.Your findings may or may not be celebrated in places like this [Pavilhão do Conhecimento, Lisbon, Portugal]. However, if your peers corroborate your results, they will be included in the scientific body of knowledge and they will be written in books and other publications. This knowledge will pass on to future generations even if the name of the investigator who contributed to that knowledge is forgotten.
“When we follow the mentioned seven rules and our personal values, we usually do not think whether we are men or women or on how much our work is worth. Values have no gender!”
“If we treasured life the way it should always be treasured, [...] We would not need to have the International Women’s Day; we would rather have women receiving the same paycheck as men every day, everywhere.”
7.The Society of Knowledge demands several things from us: truth; tolerance from and to others; humility because time and new technologies might prove us wrong in the future; and pride for being the first to have seen the truth or fought for the truth. When we follow the mentioned seven rules and our personal values, we usually do not think whether we are men or women or on how much our work is worth. Values have no gender! Those who are worried about gender inequality and if women’s work is now rewarded equally to men’s, are also researchers; they research numbers. And the truth is that numbers favor men almost everywhere in the world. Today’s press is full of numbers that reveal that inequality. If we treasured life the way it should always be treasured, we would not need meetings and conferences to decide what do with the refugees. We would know what to do every day, the way those people who receive refugees on the beaches in Greece and Turkey seem to know. We would not need to have the International Women’s Day; we would rather have women receiving the same paycheck as men every day, everywhere. We would not have to watch the abhorrent demonstration of a book being burned, even if it were burned virtually, like the new Henrique Raposo’s book, which is being presented now by Henrique Monteiro.We would also not have the International Women’s Day in this place. But that would be unfortunate because we would not be able to repeat what Felix Ribeiro said so articulately few days ago, in an interview to Jornal Expresso, about the new maps of Portugal: we are confusing difference with inequality (Entrevista, Expresso, February 27 2016, page 6). There is no inequality on how creative women and men are, as the work of these first Women of Science clearly demonstrates. I will finish by saluting, on behalf of all these women and the women who are still entering the “Uma Ciência Viva” carousel, Rosalia Vargas and her collaborators for organizing this initiative.Thank you all, young and old men and women, for your exemplary and inspirational lives. 8
Maria de Sousa
WOMEN IN SCIENCE
Hanna Damasio
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hese days it is so natural and so frequent for women to have careers in science that I am rarely asked any question about the fact that I am a woman scientist. And yet, by coincidence, I have been recently asked about women and science, not once but twice.
“...the satisfaction of contributing to the solution of a problem, and mostly, for me, the complete and pleasurable immersion on THE problem, on the WAY to a certain place rather than on the arrival AT the certain place.”
“By now, there are few barriers and even fewer difficulties, at least in Western cultures. Women and men work side by side in research teams, respecting everyone’s opinion, collaborating towards a common goal.”
The photograph was taken by Antonio Pedro Ferreira. It is part of the work organized by Ciencia Viva, “Women in Science”. Courtesy of Ciência Viva (Rosalia Vargas).
One of the questions touched on a profound matter: what makes people, women and men, become scientists? What drives one into that path? The romance of research for people of my generation played a role, imagining a profession of people devoted seriously and nobly to solving mysteries that would help humanity. One has to imagine the glamour of Jonas Salk eradicating polio, or Einstein discovering relativity and playing the violin, apparently not so well, or Marie Curie, bravely dealing with the dangers of radiation. But the reality of life in science is a bit different from that idealized romance. I literally went into science because I was intrigued by animal and human behavior and more specifically because I wanted to understand structures. For me, it has been a rich life, one where days of joy and success can be followed by weeks of routine and even frustration, a life where there is satisfaction to be found not just in working in solitude but also working with a team in which everyone contributes differently but pulls in the same direction. And yes, there is the satisfaction of contributing to the solution of a problem, and mostly, for me, the complete and pleasurable immersion on THE problem, on the WAY to a certain place rather than on the arrival AT the certain place. One other question had to do with the specific difficulties faced by a woman who wants to be a scientist. The answer is fairly simple. By now, there are few barriers and even fewer difficulties, at least in Western cultures. Women and men work side by side in research teams, respecting everyone’s opinion, collaborating towards a common goal.
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*Hanna Damasio, MD University Professor, Dornsife Professor of Neuroscience, Director, Dornsife Cognitive Neuroscience Imaging Center, College of Letters, Arts and Sciences, University of Southern California, Los Angeles
Even the fact that women scientists may want to interrupt their careers to be mothers is now generally accepted and even legislated. Recently, in our group, three young colleagues have given birth to three babies and will be taking care of them at home, for a few months. There is no objection, no friction, and no complaining about this. Their pay will not be cut during their leave. We are all eager to have them visit with their infants and, later, welcome them back into our daily routines.
The world does get better, sometimes. Hanna Damasio*
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ATG: a City of Knowledge. Let’s take another look at a few of its citizens and some of its knowlegde published since our last issue! We should warn you that women are treated differentially in the following pages.
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City Of Knowledge Part I. Citizens Filipa Ferreira ANDREIA CARVALHO GABBA 9th edition, class 2005 Head of Scientific Affairs at Centre for Developmental Neurobiology, King’s College London
“Half way during my PhD I realized I wasn’t happy working at the bench.”
What was the topic of your PhD thesis and how do you think that defined your next steps? The topic of my PhD thesis was engineering spatial patterning in mammalian cells, employing entirely genetically encoded components. The topic itself didn’t influence much my next steps. Nonetheless, working in one of the best research institutes in Spain, perhaps even in the world, as well as having the independence to manage my research project, access to transferable skills workshops and the opportunity to get involved in some aspects of management of the Center, most definitely played a pivotal role in my future steps.
“ I became a PhD student representative [...] it opened my eyes to careers in science other than a postdoc.”
When and how did you decide you weren’t pursuing a postdoc when you graduate? Half way during my PhD I realized I wasn’t happy working at the bench. Around the same time I became a PhD student representative and had the amazing opportunity to be part of the Graduate Committee. Together with another PhD student, I represented and defended the student body’s interests. More importantly, this was an opportunity to think about different initiatives that could improve students’ experiences: small things such as increasing student thesis supervision and creating an alumni network. I also co-organized a conference and a career day. I very much enjoyed this experience. It opened my eyes to science careers other than a postdoc. 12
“Once you know what you want, you have to go for it. Everything is possible if you put your mind to it!”
“I joined the Centre for Developmental Neurobiology at King’s College London in June 2015.”
”GABBA [...] enabled me to pursue my PhD in an international biomedical research institute of excellence.”
“It is a real privilege to be part of the GABBA community!”
You shifted from the bench to science affairs. How did you prepare and how hard was this transition? Once I made up my mind to go into science management, I knew that I would only succeed in making this transition if I acquired work experience or formal training. I was doing my PhD, spending the whole day in the lab, so having a part-time job wasn’t really an option. I decided to do a Masters in Science Management, taking classes on Fridays and Saturdays. At the same time I started collaborating with the Pasqual Maragall Foundation, a newly created Alzheimer’s disease research center. I had the amazing opportunity to be involved in shaping the Foundation’s scientific strategy and policy. This experience helped me realize what I wanted to do. I joined the Foundation as Scientific Affairs Manager when I finished my PhD. I wouldn’t say the transition was hard although it did require hard work, dedication and a strong focus. Once you know what you want, you have to go for it. Everything is possible if you put your mind to it! How is a day as ‘Head of Scientific Affairs’? I joined the Centre for Developmental Neurobiology at King’s College London in June 2015. So far, every day has been different, which is one of the many reasons that I love my job! There is one constant thing though, I walk from one end of the hallway to the other several times throughout the day, talking to the researchers – it’s good exercise! My remit is very broad, I support the Director in providing input for scientific strategic decision and policy making, coordinate the Center’s research funding applications, provide support and advice to academic staff in the preparation of strategic bids, and coordinate the recruitment of senior scientific staff. I’m also responsible for all areas of communication and public engagement activities. This means that some days, as last week for British Science Week, I get to go with our researcher to schools and spend the whole day introducing children to the use of fluorescence in biomedical research, showing them fluorescently labeled zebra fish and fruit flies, among others!
In what way did the GABBA PhD program affect your career? GABBA enabled me to pursue my PhD in an international biomedical research institute of excellence. The opportunities, resources, people and environment I found there were instrumental to start a successful career in science management. It is a real privilege to be part of the GABBA community!
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Simão José Teixeira da Rocha GABBA 5th edition, class 2001 FCT investigator, Instituto de Medicina Molecular
“I don’t think the topic of a PhD thesis is necessarily deterministic for the future as a scientist. But obviously has an impact, at least the experience of living a PhD.”
What was the topic of your PhD thesis and how do you think that defined your next steps? I did my PhD at the University of Cambridge, on the subject of genomic imprinting, a mammalian epigenetic mechanism whereby a few genes (less than 1%) are rendered to be monoallelically expressed according to their parental origin (either maternal or paternal). I think this had a major impact on my career path. As a post-doc, I then move to the “cousin” field, the one of X-chromosome inactivation (XCI). XCI is another mammalian epigenetic mechanism that results in monoallelic expression of most of the genes on the X-chromosome in females to balance X-linked gene dosage differences between XX females and XY males. Nowadays, as a senior researcher, my interests still revolve around epigenetics, imprinting, and XCI, as well as around other interests that I developed in this path, such as long non-coding RNAs, stem cells, and reprogramming. Having said that, I don’t think the topic of a PhD thesis is necessarily deterministic for the future as a scientist. But obviously it has an impact, at least the experience of living a PhD. In my case, I think it really had! You are now transitioning from a postdoc to a fully independent position as a Principal Investigator. How long ago did you start planning this transition and what have been the major challenges? First of all, I found this transition harder than previous transitions (from undergraduate to PhD student or from PhD student to post-doc). It certainly feels more competitive and it also comes with a higher level of 14
“ I would say that I started thinking about the move two years ahead, however, only the last year, I was really pro-active at networking and applying for jobs and/or grants.”
responsibility. At this stage, our ideas and our capabilities are more important than ever, and we need to have leadership, mentoring and management skills. It almost comes with a feeling of loneliness, you have to believe in yourself and be fine with it! Therefore, before anything else, you have to be certain of this step.
“My recommendations to someone thinking about this move are to start networking very early...”
The challenges I encountered: on one hand, it was the competition, too few jobs for very qualified and high-profile candidates; on the other hand, my lack of experience, namely, during the first interviews.
I started planning this move around a year before the end of my post-doc. Fortunately, I prolonged my post-doc for another year. It is extremely difficult to try to have your post-doctoral papers out and, at the same time, think about the next step with an original line of research sufficiently independent from your previous work. All in all, I would say that I started thinking about the move two years ahead, but I was really pro-active at networking and applying for jobs and/or grants only the last year. It really felt like a full-time job at times.
My recommendations to someone thinking about this move are to start networking very early, practice interviewing with colleagues, and make sure you have a working program that reflects your scientific expertise from the past, that is innovative (but not too wild) and that has been well scrutinized by your scientific collaborators. After many years abroad you decided to move back to Portugal. What were your motivations? And how do you see Portuguese science in comparison with that you seen in other European institutions where you worked? When I stepped out to go abroad, I had the perception that one day I would come back to Portugal. This feeling kind of fell asleep over the years, but it would revive from time to time. I always felt a sense of commitment from the investment made by my country in my education. Obviously, I could still stay abroad and help advance Portuguese science community by actively connecting with the Portuguese research institutions and establishing collaborative projects as many other emigrant researchers do. However, as I was approaching a more senior and slightly more stable position, and after living in the UK, France, and Denmark, I thought the time was ripe to come back to Portugal. There were personal reasons that accounted for the decision to come back, but also scientific ones. Science in Portugal had improved significantly in the past years and started to become attractive to many renowned young scientists that established 15
“Science in Portugal had improved a lot in the past years and started to become attractive to many renowned young scientists that made significant part of their careers abroad.”
“Portuguese science [compared] with that in European Institutions where I worked [... is a] more peripheral position in the science galaxy.”
“GABBA provided me with the first serious interaction with international scientists and broaden my notion of the research conducted directly off the bench.”
significant part of their careers abroad. This is evident in the record number of ERC grants awarded to the country in recent years. The possibility to conduct good science in Portugal was reason number 1 for my decision to return to Portugal. Portuguese science still lags a bit behind other European countries, but this is the time of change in the philosophy of science in Portugal. To be able to contribute in loco to this change, it would be very gratifying and it was my reason number 2. Finally, being Portuguese, I felt that my voice speaks higher in Portugal than any other country in matters of scientific discussion and policy. Therefore, I could contribute greatly to issues involving society and science here at home (reason number 3). I returned back to Portugal one year ago. If I compare Portuguese science with that of the European Institutions where I worked, I see obvious differences. I feel I moved from the center towards to a more peripheral position in the science “galaxy”. This, per se, is not a limiting factor but requires that you strengthen your scientific collaborations abroad and establish tight links with national researchers. Another important issue is funding. What concerns me most is not the scarcity of funding, but rather the instability of the public funding system. The calls for different types of fellowships and project grants vary from year to year. There are no regular schedules throughout the year and constant criteria. Funding is also too dependent on the volatility of the political environment. The instability of the public funding sytem, along with the frequent delays, has negative implications on the quality of science we can produce. I hope this will change in the future. Such a change is a sign of respect to the Portuguese scientific community, whose role in modernizing the Portuguese society is more and more appreciated. In what way did the GABBA PhD affect your career? Greatly! GABBA provided me with the first serious interaction with international scientists and broadened my notion of the research conducted directly off the bench. GABBA was also crucial to my decision to go abroad for my PhD. The GABBA annual meetings, which I recall with special affection, always gave me a comfortable notion of community. Thank you, GABBA!
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City Of Knowledge Part II. Knowledge Catarina Seabra Because this issue is dedicated to Women in Science, we decided to feature our female contributors with a brief overview of their most recent paper, current research interests and scientific activity. Cell and Developmental Biology
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anica Drpic, GABBA 15th, member of the Chromosome Instability and Dynamics Group (i3S, Porto, Portugal), has published a paper in Cell Reports explaining how end-on kinetochore-microtubule attachments are first stabilized before the development of tension from spindle forces. She and other authors used Drosophila cells to model cell division and found that polar ejection forces promote the conversion from lateral to stable end-on kinetochore-microtubule attachments on mono-oriented chromosomes. These findings contribute to explain how initial end-on kinetochore-microtubule attachments are stabilized before bi-orientation
In this section, we highlight recent scientific publications in which GABBA Alumni or Students have contributed as first, second or senior authors.
Drpic, D., Pereira, A.J., Barisic, M., Maresca, T.J., and Maiato, H. (2015). Polar Ejection Forces Promote the Conversion from Lateral to End-on Kinetochore-Microtubule Attachments on Mono-oriented Chromosomes. Cell Rep. 13, 460–469.
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Other Publications Bucher, M., Wolfowicz, I., Voss, P.A., Hambleton, E.A., and Guse, A. (2016). Development and Symbiosis Establishment in the Cnidarian Endosymbiosis Model Aiptasia sp. Sci. Rep. 6, 19867. Pereira, C.-F., Chang, B., Gomes, A., Bernitz, J., Papatsenko, D., Niu, X., Swiers, G., Azzoni, E., de Bruijn, M.F.T.R., Schaniel, C., et al. (2016). Hematopoietic Reprogramming In Vitro Informs In Vivo Identification of Hemogenic Precursors to Definitive Hematopoietic Stem Cells. Dev. Cell 36, 525–539. Santos, A.J., Raote, I., Scarpa, M., Brouwers, N., and Malhotra, V. (2015). TANGO1 recruits ERGIC membranes to the endoplasmic reticulum for procollagen export. Elife 4. Grippa, A., Buxo, L., Mora, G., Funaya, C., Idrissi, F.-Z., Mancuso, F., Gomez, R., Muntanya, J., Sabido, E., and Carvalho, P. (2015). The seipin complex Fld1/Ldb16 stabilizes ER-lipid droplet contact sites. J. Cell Biol. 211, 829–844. Wagih, O., Sugiyama, N., Ishihama, Y., and Beltrao, P. (2016). Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks. Mol. Cell. Proteomics 15, 236–245.
Genetics and Molecular Biology Isabel Alves-Rodrigues, GABBA 6th, is a Postdoctoral Researcher at Universitat Pompeu Fabra (Barcelona, Spain). Her research focuses on the characterization of transcription factors required for meiosis progression in S. pombe. Isabel has recently published her work in Cell Reports showing that Fkh2, a forkhead transcription factor, is essential for mitotic cell-cycle progression, also plays a pivotal role in the control of meiosis. During meiosis, Fkh2 is phosphorylated in a CDK/Cig2-dependent manner, decreasing its affinity for DNA, which creates a window of opportunity for Mei4 to bind to its target genes. She and the other authors propose that Fkh2 serves as a placeholder until the later appearance of Mei4 with a higher affinity for DNA that induced the expression of a subset of meiotic genes.
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Alves-Rodrigues, I., Ferreira, P.G., Moldon, A., Vivancos, A.P., Hidalgo, E., Guigo, R., and Ayte, J. (2016). Spatiotemporal Control of Forkhead Binding to DNA Regulates the Meiotic Gene Expression Program. Cell Rep. 14, 885–895. Other Publications Alves, J.M., Lima, A.C., Pais, I.A., Amir, N., Celestino, R., Piras, G., Monne, M., Comas, D., Heutink, P., Chikhi, L., et al. (2015). Reassessing the Evolutionary History of the 17q21 Inversion Polymorphism. Genome Biol. Evol. 7, 3239–3248. Curado, J., Iannone, C., Tilgner, H., Valcarcel, J., and Guigo, R. (2015). Promoter-like epigenetic signatures in exons displaying cell type-specific splicing. Genome Biol. 16, 236. Dias, J.D., Rito, T., Torlai Triglia, E., Kukalev, A., Ferrai, C., Chotalia, M., Brookes, E., Kimura, H., and Pombo, A. (2015). Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells. Elife 4. Afreixo, V., Rodrigues, J.M.O.S., Bastos, C.A.C., and Silva, R.M. (2016). The exceptional genomic word symmetry along DNA sequences. BMC Bioinformatics 17, 59.
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Biology of Disease Clara Correia-Melo, GABBA 13th, along with another prestigious GABBA member JoĂŁo Passos (6th edition) at the Institute for Ageing and Health (Newcastle University, UK), have published their findings in the EMBO Journal, showing the role of mitochondria during cellular senescence. In this paper, they show that there is an increase in mitochondrial mass during cellular senescence. In addition, a vast number of senescence-associated phenotypes, particularly the pro-oxidant and pro-inflammatory phenotypes, are dependent on mitochondria. Genetic and chemical reduction of mitochondrial content prevented senescence not only in vitro but also in vivo. By linking DNA damage response to mTOR-PGC-1B dependent mitochondrial biogenesis, the authors revealed a mechanism by which mitochondrial content increases during senescence and place mitochondria as therapeutic targets for interventions to reduce the deleterious impact of senescence in ageing tissues.
Correia-Melo, C., Marques, F.D., Anderson, R., Hewitt, G., Hewitt, R., Cole, J., Carroll, B.M., Miwa, S., Birch, J., Merz, A., (‌), Passos, J.F. (2016). Mitochondria are required for pro-ageing features of the senescent phenotype. EMBO J. Other Publications Birch, J., Anderson, R.K., Correia-Melo, C., Jurk, D., Hewitt, G., Marques, F.M., Green, N.J., Moisey, E., Birrell, M.A., Belvisi, M.G., (‌), Passos, J.F. (2015). DNA damage response at telomeres contributes to lung aging and chronic obstructive pulmonary disease. Am. J. Physiol. 20
Lung Cell. Mol. Physiol. 309, L1124–L1137. Cunha, C., Lamas, S., Goncalves, R.M., and Barbosa, M.A. (2015). Joint analysis of IVD herniation and degeneration by rat caudal needle puncture model. J. Orthop. Res. Ribeiro, G., Santos, O., Camacho, M., Torres, S., Mucha-Vieira, F., Sampaio, D., and Oliveira-Maia, A.J. (2015). Translation, Cultural Adaptation and Validation of the Power of Food Scale for Use by Adult Populations in Portugal. Acta Med. Port. 28, 575–582.
Immunology, Microbiology and Parasitology
Cláudia Nóbrega, GABBA 8th, works at ICVS (Braga, Portugal) exploring the acquired immune response and the role of the thymus during chronic infections. Cláudia’s recent paper was published in AIDS Journal and addressed the fact that a sizeable percentage of individuals infected by the human immunodeficiency virus (HIV) under antiretroviral therapy fail to increase their CD4 T cells to satisfactory levels. The authors link that problem to profound alterations on Tregs subpopulations.
Nobrega, C., Horta, A., Coutinho-Teixeira, V., Martins-Ribeiro, A., Baldaia, A., Rb-Silva, R., Santos, C.L., Sarmento-Castro, R., and Correia-Neves, M. (2016). Longitudinal evaluation of regulatory T cells dynamics on HIV-infected individuals during the first two years of therapy. AIDS.
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Neurosciences Araujo, H.F., Kaplan, J., Damasio, H., and Damasio, A. (2015). Neural correlates of different self domains. Brain Behav. 5, e00409. Fox, G.R., Araujo, H.F., Metke, M.J., Shafer, C., and Damasio, A. (2015). How Does the Effort Spent to Hold a Door Affect Verbal Thanks and Reciprocal Help? Front. Psychol. 6, 1737. Barahona-Correa, J.B., Camacho, M., Castro-Rodrigues, P., Costa, R., and Oliveira-Maia, A.J. (2015). From Thought to Action: How the Interplay Between Neuroscience and Phenomenology Changed Our Understanding of Obsessive-Compulsive Disorder. Front. Psychol. 6, 1798. ONCOBIOLOGY Raquel Silva, GABBA 3rd, is a Researcher at the University of Aveiro, Portugal. She also collaborates with the Population Genetics and Evolution Group at i3S, Porto, Portugal. Her research encompasses the evolution and dynamics of the NAD metabolic networks and their roles in health and disease. Raquel’s most recent article in Oncotarget provides a comprehensive study of NAPRT and NAMPT expression across human tissues and tumor cell lines as the knowledge of the expression patterns of both genes is critical for the use of nicotinic acid as cytoprotective in therapies using NAMPT inhibitors
Duarte-Pereira, S., Pereira-Castro, I., Silva, S.S., Correia, M.G., Neto, C., da Costa, L.T., Amorim, A., and Silva, R.M. (2016). Extensive regulation of nicotinate phosphoribosyltransferase (NAPRT) expression in human tissues and tumors. Oncotarget 7, 1973–1983. 22
Other Publications Campanella, N.C., Penna, V., Abrahao-Machado, L.F., Cruvinel-Carloni, A., Ribeiro, G., Soares, P., Scapulatempo-Neto, C., and Reis, R.M. (2016). TERT promoter mutations in soft tissue sarcomas. Int. J. Biol. Markers 31, e62–e67. Carcano, F.M., Vidal, D.O., van Helvoort Lengert, A., Neto, C.S., Queiroz, L., Marques, H., Baltazar, F., da Silva Martinelli, C.M., Soares, P., da Silva, E.C.A., (…), Reis, R.M. (2015). Hotspot TERT promoter mutations are rare events in testicular germ cell tumors. Tumour Biol. Correia, N.C., Melao, A., Povoa, V., Sarmento, L., Gomez de Cedron, M., Malumbres, M., Enguita, F.J., and Barata, J.T. (2016). microRNAs regulate TAL1 expression in T-cell acute lymphoblastic leukemia. Oncotarget 7, 8268–8281. De Lima Vazquez, V., Vicente, A.L., Carloni, A., Berardinelli, G., Soares, P., Scapulatempo, C., Martinho, O., and Reis, R.M. (2016). Molecular profiling, including TERT promoter mutations, of acral lentiginous melanomas. Melanoma Res. 26, 93–99. Martinho, O., Campos, M., Ribeiro, G., Penna, V., Curcelli, E.C., Olivieri, M. V, Morini, S., Scapulatempo, C., Abrahao-Machado, L.F., and Reis, R.M. (2016). Raf Kinase Inhibitor Protein Expression and Prognostic Value in Soft Tissue Sarcomas. Pathobiology 83, 41–46. Pereira, M.S., de Almeida, G.C., Pinto, F., Viana-Pereira, M., and Reis, R.M. (2016). SPINT2 Deregulation in Prostate Carcinoma. J. Histochem. Cytochem. 64, 32–41. Silva-Oliveira, R.J., Silva, V.A.O., Martinho, O., Cruvinel-Carloni, A., Melendez, M.E., Rosa, M.N., de Paula, F.E., de Souza Viana, L., Carvalho, A.L., and Reis, R.M. (2016). Cytotoxicity of allitinib, an irreversible anti-EGFR agent, in a large panel of human cancer-derived cell lines: KRAS mutation status as a predictive biomarker. Cell. Oncol. (Dordr).
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The ATG Newsletter’s website is up! www.atgnewsletter.up.pt
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ATG News Pedro Resende & Eurico Morais de Sá DISTINCTIONS & AWARDS
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“The Pathologist”- top-100 most influencial pathologists Professor Sobrinho Simoes & Professor Fatima Carneiro
Liga Portuguesa Contra o Cancro Professor Sobrinho Simoes
Joana Correia Exogenous Therapeutics (Exo-T)
ecember last year, ATGs proudly received news that GABBA coordinator Professor Manuel Sobrinho Simoes was recognized by his international coleagues as the most influential laboratory medicine pathologist. The recognition results from an election of the top-100 most influencial pathologists and was organized by the “The Pathologist”. To our delight, we can find another another GABBA coordinator in the same list, Professor Fátima Carneiro. Professor Manuel Sobrinho Simoes was also in the news more recently because Liga Portuguesa contra o Cancro has named an award after him. This inaugural award honors individuals who have dedicated their lives to the “fight” against cancer. Last year, Joana Correia (GABBA´s 8th edition), received a splash of good news. Joana has always been keen on new challenges. She moved from a chemistry undergraduate degree into biology during her PhD. She has since moved away from basic science and is now the co-founder and Executive Director of the biotechnology startup Exogenous Therapeutics (Exo-T). This move has been utterly successful. First, Exo-T was awarded as Young Entrepreneur of the Year by ANJE - Associação Nacional de Jovens Empresários. It was also selected by Venture Capital partners Caixa Capital and Change Partners for a €900 000 round of investment. This generous funding enables the company to advance on the development of their first product, Exo-Wound, which will reach clinical trials in 2019 and become an efficient treatment for chronic wounds. Exo-T aims at other innovative cell-based therapies to treat skin lesions.
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OTHER NEWS
We had our first ATG meeting during GABBA’s 2015 Annual Meeting. In the first part of the meeting, Andre Sousa presented updates on the challenges and accomplishments of ATG during 2015, as well as a few hints on future short-term goals for our association. The second part of the meeting consisted of two lively round-table discussions: “Coming back home (Portugal): what to expect”, and “What to do with my PhD”.
“In the first part of the meeting, Andre Sousa presented updates on the challenges and acomplishments of ATG during 2015.”
“The second part of meeting consisted of two lively round-table discussions: Coming back home (Portugal): what to expect, and What to do with my PhD”
Eurico Morais de Sá (i3S Porto, GABBA 8th), Lígia Tavares (i3S Porto, GABBA 9th), Filipe Jacinto (University of Algarve, GABBA 7th) and Filipe Pereira (CNC Coimbra, GABBA 7th) participated in the first round-table, which was moderated by Carla Oliveira (i3S Porto, GABBA 2nd). This discussion gave us the opportunity to hear about the pros and cons of coming back to Portugal from different countries. Filipe Pereira and Filipe Jacinto moved from the United States, and Ligia and Eurico moved from the UK back to Portugal. They also discussed funding opportunities, life style and culture differences, and how to plan your move in advance. Pedro Resende (i3S Porto, GABBA 11th) moderated the second round-table discussion, in which Pedro Beltrão (EMBL-EBI, Cambridge, GABBA 6th), Nuno Marcos (i3S Porto, GABBA 7th), Sara Ribeiro (Faculty of Medicine, University of Porto, GABBA 11th) and Joana Correira (GABBA 8th) participated giving us their insight on the different options after the PhD, such as staying in academia and becoming a PI, going back to school to study Medicine, starting your own company, working on science communication. We all were very happy with the result of our inaugural meeting and we look forward to the next meeting this coming December! ***
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GABBA News GABBA ANNUAL meeting: You cannot start a fire without a spark. Helder F Araujo
GABBA’s 2015 annual meeting was full of fire!
We could experience the cozy fire of a fireplace in the winter. Dozens of scientists sharing a common origin – GABBA – reunited after one year, during which they lived in different countries and cultures. How comfortable to arrive to a familiar place! We could also experience the kind of fire that is used to transform and create. On one hand, we could observe tamed flames coming from the transformations that occurred since the year past: transformations pertaining to scientific knowledge and to the creators of that knowledge - changes that could never be fully summarized into a book of abstracts. On the other hand, we could detect more erratic and explosive flames coming from what is still under construction: the fire of building the future! As I drove to the second day of this meeting, the radio played the Hot Ship’s cover of “Dancing in the Dark”. By the time we were having our social dinner, this music was still playing in my head, reminding me that “You can’t start a fire without a spark”. And where were the sparks that started all that meeting’s fire? The answer was right at the center of the dinning room: Maria de Sousa and other Coordinators. We will always be grateful to them because we really cannot start any fire without a spark.
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Read ANd Highlighted Surely You’re Joking, Mr. Feynman! Adventures of a Curious Character Andre Sousa
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Feynman, Richard P. (1997) Surely You’re Joking Mr. Feynman! Adventures of a Curious Character. W. W. Norton & Company. New York.
“ n regard to education in Brazil, I had a very interesting experience. I was teaching a group of students who would ultimately become teachers, since at that time there were not many opportunities in Brazil for a highly trained person in science. These students had already had many courses, and this was to be their most advanced course in electricity and magnetism: Maxwell’s equations, and so on. […] I discovered a very strange phenomenon: I could ask a question, which the students would answer immediately. But the next time I would ask the question – the same subject, and the same question, as far as I could tell – they couldn’t answer it at all! […] After a lot of investigation, I finally figured out that the students had memorized everything, but they didn’t know what anything meant. When they heard “light that is reflected from a medium with an index”, they didn’t know that it meant a material such water. They didn’t know that the “direction of the light” is the direction in which you see something when you’re looking at it, and so on. Everything was entirely memorized, yet nothing has been translated into meaningful words. So if I asked, “What is Brewster’s Angle?” I’m going into the computer with the right keywords. But if I say, “Look at the water,” nothing happens – they don’t have anything under “Look at the water!” […]
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Finally, I said that I couldn’t see how anyone could be educated by this self-propagating system in which people pass exams, and teach others to pass exams, but nobody knows anything.”
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Inequality quantified: Mind the gender gap Helder F. Araujo
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“ he fraction of women gaining doctorates in science has more than doubled in the United States since 1980 and is now nearing equity. In some European countries, women outnumber men in science degrees but there is signicant variation between nations and felds. [...]
Shen, H. (2013) Inequality quantified: Mind the gender gap. Nature 495(7439):22-4 Pictures reproduced with permission provided by Nature Publishing Group.
A 2009 survey of postdoctoral fellows at the University of California showed that women who had children or planned to have them were more likely to consider leaving research. [...]
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A study of US science departments showed that women were more successful than men in gaining tenure between 2002 and 2004. [...
In Europe as in the United States, the gender gap is greater among senior than among junior faculty members
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ATG - All Time GABBA The Alumni Association of the Graduate Program in Areas of Basic and Applied Biology University of Porto - Portugal
Supplement GABBA Student Handbook Sample Chapter We are still working on this book and it would be great to count on you to help us finish it!
CHApTER 4 How do I know I am ready to defend? Nuno Camboa GABBA 10th edition University of California, San Diego, USA
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ow do I know I am ready to defend? On a first impulse, the answer seems obvious: when I publish at least one first authorship paper and have finalized putting together my thesis. In real life, however, the answer can be way more complex and, in my view, you are ready to defend whenever professional and/or personal events make you realize it’s time to turn the PhD page and move on to your new career or life goal. In addition to being a phase of learning and development of a scientific mind-set, your PhD should also be a period of introspection in which you analyse your personal priorities and define your short and long-term career goals. In some cases the question isn’t really when should I defend, but rather should I even defend? We all make wrong life choices and the best way to minimize their consequences is to assume and face them. Many graduate students will realize, sometime during their PhDs, they do not wish to pursue a career in science (in either academia or industry). If this is your case, my advice would depend on how far down the PhD road you are when this realization takes place. If you make this decision during your first two years, my advice would be to quit right away and focus your efforts and time on what you really want to do. Many would consider quitting a PhD a sign of weakness, I prefer to see it as a sign of determination – if it isn’t your goal, you shouldn’t feel ashamed for deciding not to pursue it! If this realization happens during your third or fourth year, then I think you should capitalize the time already invested and get your degree. Stop doing experiments, focus on putting your data together to create the most coherent story possible, get it published (no matter the journal’s impact factor) and defend as soon as you can. If you do want to stay in science (I’m hoping this applies to the majority of people reading this text) and feel like you have an interesting story in hands that can potentially lead to a relevant paper, then I’d suggest not being in a rush to defend. When you get admitted to GABBA, you automatically receive a four-year doctoral fellowship from FCT. Four years might sound like a lot of time, but it is not! Due to classes, lab visits and the challenges imposed by a move to a new culture, most of the students who chose to do their PhDs abroad don’t get to do any proper bench work before the beginning of their second year and, in nowadays biology, publishing a strong paper in three years is an extremely difficult task (even more if your work involves S1
animal models). As such, if you’re excited about your research and lucky enough to have a supervisor who is willing to support you after your FCT financing runs out, don’t let this deadline prompt an early termination of your project, likely jeopardizing the impact of your publication(s). It’s worth going the extra mile to get a strong first-authorship paper from your PhD, as it will greatly boost your short-term career for two main reasons: it opens the doors to “top-of-the-league” labs, in which PIs are usually more selective when it comes to hire new personnel, and it greatly increases your chances of receiving postdoctoral fellowships. If you do prolong your PhD past the four years of FCT founding and you are affiliated to ICBAS, please keep in mind that there is a limit on the number of years you can be enrolled as PhD student in University of Porto. When you reach that limit (contact the ICBAS secretariat to know exactly the legislation that applies), you’ll have to graduate or your registration will be cancelled. In some situations, it might be tempting to defend your thesis when your FCT fellowship ends and then stay in the same lab, as a postdoc, finalizing your ongoing project(s). The advantages are obvious – you avoid paying tuition fees and get a better salary – however, before you decide to do something like this, keep this important fact in mind: a very important countdown starts immediately after you graduate, as many junior investigator grants (first step of the path to independence after your postdoc) exclude all candidates who have been a postdoc for more than 4 years. However, please don’t misinterpret my words. I’m not trying to encourage all GABBA students to prolong their PhDs, nor claiming that a successful PhD must be long! I’m just defending that, if after evaluating your options, you face a situation where adding a couple of years to your initial plan would be beneficial to your career, you should not be afraid of doing so. I joined the GABBA program in January 2007 and since then I have learnt some important lessons from my own experience and from observing the scientific path of my colleagues. In this text, I tried to summarize these lessons the best I can, however, my analysis only covers the scientific component of your PhD. There is a lot more in life than science and no opinion article, no matter how exhaustive it might be, will ever be able to incorporate the impact of the unpredictable life events each one of you will face. As such, it will always be up to you to determine the exact moment to move on to your next challenge, but I sincerely hope the topics here explored might help you on your decision-making.
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Ricardo Ataide GABBA 10th edition Burnet Institute, Melbourne, Australia
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t the moment I’m writing to you from Melbourne, Australia, almost 5 years after my PhD defense. I will answer the main question of the text, but bear with me for a moment. I want you to try and imagine the scene: I am at my computer at home. The digital clock on the upper right corner of my iMac shows 10:13 pm. My 2-year old daughter is sleeping next door and my wife is reading in bed. After I finish writing this text I have to go back to writing a grant application that is due in 2 days. I have a manuscript to finalise in 4 days and a travel grant report due in 4 days also. My computer keyboard is surrounded by old batteries (from the wireless mouse), CDs, pens, stickers of weird animals that my daughter pastes everywhere, and a ton of legal papers for our tax returns and because we have just recently bought a house and we had to apply for a bank loan. I sometimes look at the guitar sitting in the corner of the room where I am and wonder if I can still play it (but there is no time to verify, and so I convince myself that yes, of course I can still play it!), or at the more than 100 books I have about the Maya civilization and wonder if I’ll ever have time to read and take notes like I used to do (or even open the last 5 books I bought but haven’t read yet!). Do you know what that means?... It means that ready or not, you are going to defend your PhD and then life goes on! Now, when did I know that I was ready to defend? To be honest, my case was more a case of ‘I want to defend” then a ‘I’m ready to defend’. When the time came to worry about being ready or not to defend it, I was more focused on the fact that the FCT had already stopped paying me, I was living in Australia (where I did my PhD) and I had to pay another year of Uni enrolment in Portugal (and that was not cheap). On top of that I had already been offered a position in Edinburgh as a postdoc. I wanted to finish my PhD! So I wrote, and re-wrote chapters furiously at an astonishing pace. I left the lab and went to a place where I could just focus on my writing. It is incredible how much you can achieve when your focus in all on one single goal. I just wanted to write enough of a story to make it coherent. I sent everything to Portugal and my mum delivered everything. This could have been time for me to think about the big question, right? Was I really ready to defend? Well, the question didn’t even cross my mind because I had no time for it. I guess that for me it was more a question of I was ready to move on. I had to focus on looking at accommodation in Edinburgh and finish writing papers and pack to go back to Portugal, and take my wife with me (oh, yes… I got married in Australia). Once in Portugal, with the date set and everything ready to defend I was busier trying to pack things for Edinburgh and making sure my wife got to know my family and friends. The day came. Was I ready to defend my PhD? I never thought about it. I went in, saw a few friendly faces, joked around with friends that came to watch (behind the scenes, because on stage serious business is required), defended my PhD and went out for drinks. S3
Only then, later that day did I realise fully what had happened. I had been ready to defend my PhD all along, but in all honesty I did not defend the PhD I wanted to defend. This may be more common than you think. You are so focused on moving on that you forget to enjoy the moment. I was ready to defend my position in Edinburgh, my will to start studying a new field of research, and I think I forgot to really focus and appreciate the work I had done. I ended up not including things in the thesis that I should and that would have complemented the story really well (easy to say when looking back, of course). In any case, my personal experience is: How did I know I was ready to defend my PhD? Well, with hindsight, if I was busy planning for a life after the PhD, then deep down, I must have known that I was ready. ***
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