ATG Newsletter issue 7

ATG Newsletter Issue 07

June 2018

Welcome to another edition of the ATG Member Newsletter

Science without Borders ATG Newsletter

Filipa Ferreira

Issue 07 June, 2018 Contributors: Ana Rita Araújo Bruno Fontinha Catarina Nogueira Catarina Seabra Filipa Ferreira Ligia Tavares Helder F. Araújo André Sousa Joana Wilton Mafalda Azevedo Maria De Sousa Pedro Resende Raquel Sousa Cover: Mafalda Azevedo and Filipa Ferreira Editors: Filipa Ferreira and Mafalda Azevedo

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

Editor-in-Chief

The world is currently changing. With borders actually getting bigger. In Europe we are dealing with a migrant crisis, the rising of extreme nationalism, and the European alliance faces major difficulties that resulted in Brexit for example. Here in the U.S. there is an exponential growing distortion of the world and a negative attitude towards immigration. However, as scientists, most of us are expatriates, living in a parallel world - without borders. GABBA gave an opportunity to explore the world to hundreds of students. Most of these students are still living abroad. In this issue of the ATG newsletter we will examine the reasons that may have kept GABBAs abroad – the opportunities and difficulties they face. And the unfortunate reality of Portugal still not being able to attract back all the brains that it helped develop. To finish on a positive note – by being spread all around the world, GABBAs are forming an outstandingly diverse international scientific network. If we are motivated and organize ourselves around our common goals, we can only imagine what we could achieve. ***

ATG - GABBA i3S, R. Alfredo Allen, 4200-135 Porto, Portugal

Contents Message from the President of the Executive Board Pedro Resende 6 De Sousa et al. Maria de Sousa (Helder AraĂşjo) 8 Science without borders Raquel Sousa Catarina Nogueira Andre Sousa Bruno Fontinha 19 City of Knowledge Part I. Knowledge Ana Rita AraĂşjo & Catarina Seabra 31 Part II. Citizens Joana Wilton 38 ATG News Mafalda Azevedo Pedro Resende Ligia Tavares Catarina Seabra 47

Have you already become a member? 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 find the form on the ATG website: www.atg.up.pt 5

Message from the President of the Executive Board Pedro Resende

Dear ATG readers,

“GABBA alumni were able to attract more than 20M of Euros to Portuguese scientific Institutions”

“… we should all be “fighting” not to be discontinued”

On the 7th edition of our newsletter we catch a glimpse on how the GABBA community found a place to dwell all over the world. After 20 years, GABBA students and alumni can now be found in more than 19 countries, wow! Beyond a shadow of doubt, it stems from one of GABBA´s hallmarks: the freedom given to the students to pick any lab in the world to pursue their professional or personal goals. Please don´t be fooled by those who argue this is a waste of economic investment from the perspective of the Portuguese scientific community. Some GABBA students choose to do their PhDs in Portugal and some of those who have chosen to do it abroad do return. GABBA alumni were able to attract more than 20M of Euros to Portuguese scientific Institutions and 8 ERC grants were awarded to GABBA alumni (40% of the total sum brought into the country in Life Sciences!)1. Like Professor Maria de Sousa points out “we know that Science doesn´t exist without freedom” and I would add that freedom comes in different flavors. The “geographic freedom” seems to be rewarding GABBA and ATG (and FCT...and ICBAS…and the University of Porto…and i3S) with something we should all be quite proud of, and we should all be “fighting” not to be discontinued. Wish you all a sunny summer! 1. “ERC in Portugal. Beyond the First Decade”. url: https://www.fct.pt/documentos/ERC10years.pdf

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We know you are really busy with other impact factors, but your help would really have a major impact on ATG! ATG really needs your help! Send us an email when you are ready to help us, will you?

DE SOUSA et al. Science, Society’s Intangible Good

Maria de Sousa Translated from Portuguese by Helder F. Araújo

When

the Science Minister invited me to participate in the

remembrance of the “Jornadas da Ciência”, an event to which Mariano Gago summoned all Portuguese scientists precisely 30 years ago, on May 11, 1987, I decided to give this talk the title "Science, citizenship’s intangible good” for one reason: in the last 30 years, Portugal introduced science into the country’s conception of its intellectual and productive fabric. But the country is still far, far away, from producing the same level of knowledge that we see in older and more established places such as universities and/or university hospitals and traditional businesses. And above all, the country is far from what Mariano Gago imagined and aspired to: a country in which science’s social fabric summons society as a whole (1). By professional default, I organized this talk in four parts: I. What we already knew before 1987 II. The predictable III. The unpredictable “(Portugal) is far from what IV. The Strange flame of the unlikely Mariano Gago imagined and aspired to: a country in which science’s social fabric summons I. What we already knew before 1987 society as a whole.” We knew that science cannot exist without freedom. Why? Because the essence of science is to ask, to doubt established knowledge and power, and to move forward by showing and demonstrating temporary answers (if not the true answers) to new questions, using methods and tools that we have never seen before. The creative process of science requires demonstration and proof; it is therefore different from the creative process in the arts, and to a certain extent, more threatening to the established power.

This event is a great opportunity to ask ourselves who we are today, where and with what arms and allies we are going.

II. The predictable In all generations, it is foreseeable that someone will stand out “The creative process of science even in a setting of great adversity. In the case of history of science, this requires demonstration and consisted of political and/or religious persecution, lack of financial proof; it is therefore different support or institutional understanding, and so on and so forth. from the creative process in the In each generation, there will always be men and women who arts, and to a certain extent, are endowed with enough perseverance, determination, conviction and more threatening to the strength to achieve their goals. They will fulfill what they believe in established power.” regardless of how precarious that might be, regardless of how much recognition they will receive. The examples I know best in Portugal come from the biological (2) and biomedical sciences. They include men who have already died, like Corino de Andrade and others, who were determined in assuring that the causes they believed in would outlive them. I will highlight four people who are very different but comparable in their ability to affirm what they believe.

Odete Santos Ferreira I chose Odete Santos Ferreira for her determination in believing that the virus that “In each generation, there will she found in the blood always be men and women samples of patients of African who are endowed with enough origin was different from the perseverance, determination, virus that was then known as conviction and strength to HIV, and later known as HIV-1. achieve their goals.” Her determination and ability to convince Luc Montagnier's team at the Pasteur institute in Paris led to the identification of a new virus, which is now known as HIV-2 (3).

Arselio Pato de Carvalho A man who contributed to the establishment of biochemistry and scientific research not only at the University of Coimbra but in the country. By creating a school and merging it with IBILI (a product of another fighter, José Cunha Vaz), he helped create what is today the CNC.IBILI. Also, worth of note, is Biocant, a company managed by Carlos Faro, one of his students. Finally, he proved that there is no age limit for social commitment to a scientific education, by creating an institution, the Institute for Education and Citizenship, which gives scientific training in high schools, and is located, of all the places, in Mamarrosa, which few will know where it is.

Claudina Rodrigues Pousada

“… it does not really matter where one comes from; what matters is where we can go, and that we do not accept limits as to what we can do.”

There is another person that I want to highlight, a survivor in the literal sense of the term, Claudina Rodrigues Pousada. For 30 years, she was one of the driving forces behind higher education in molecular biology in Portugal (4).

Rosalia Vargas Rosalia Vargas and “Ciência Viva” (4) are a natural choice for the reasons that everyone knows. I always like to highlight that Rosalia Vargas has a philosophy degree. This illustrates that in a truly scientific culture, it does not really matter where one comes from; what matters is where we can go, 10

and that we do not accept limits as to what we can do. We place importance not only on what we have but also on who you are. In each generation it is therefore foreseeable that exceptional people will appear. Exceptional people are important, but as Mariano Gago tells us "science’s social fabric summons the entire society” (1). The examples of the Institute for Education and Citizenship, and “Ciência Viva” represent well social acts of constructing science, which summons the whole society and extends beyond the circle of people around one exceptional individual.

III. The unpredictable

“The huge expansion in the world of communication has brought libraries to our houses, scientific articles to the palm of the hand.”

The topic of the session I chaired in 1987 was "Immunology and Molecular Genetics". Its report is, what we would see today as a black and white photograph, more black than white, of the scientific country we were in at the time, especially in the area of health sciences. The invited speakers highlighted the large deficiencies in that area. The country did not have good libraries, the country had only one “animal house, there was little support to travelling abroad, there was a lack of adequate equipment, research in the university and/or in hospitals was not stimulated or encouraged. I decided to organize the unpredictable events into two groups: 1. outside the country, 2. within the country.

1. Outside the country

“(…) whoever is awarded with an ERC scholarship is likely to be one among the best in Europe. In the last 10 years Portuguese scientists have received 64 ERC scholarships.”

The huge expansion in the world of communication has brought libraries to our houses, scientific articles to the palm of the hand. Europe has become an open geography in which we move and cross borders without passports. In 2007, the European Research Council was created and scientists started being able to apply for large ERC scholarships. The application process requires several layers of evaluation, which means that whoever is awarded with an ERC scholarship is likely to be one among the best in Europe. In the last 10 years Portuguese scientists have received 64 ERC scholarships.

2. Within the country The emergence of new research institutes in the 1990s increased the level of quality and quantity of research laboratories in all areas, improved the quality of the equipment, and increased the level of quality and the number of animal houses, etc. Within the country, the biggest challenge was posed by opportunities to apply for individual doctoral scholarships and later to apply for funding of doctoral programs. This eventually brought the post-graduation to the twentieth century and represented an explosion of the offer of postgraduate studies. What was truly unpredictable to me, was the extraordinary way in which young college graduates, men and women, responded to this challenge. By the time young Portuguese people began to realize that they could be scientists, young people in countries with a long scientific tradition were generally making other career choices, choices that they knew would give money and some stability and even wealth. Becoming a scientist was not a particularly popular choice in countries like England or even the United States, where young people's choices leaned more toward the world of financial markets, City in London or Wall Street in New York, and more recently towards the Silicon Valley. I think the country itself did not expect that young college graduates would respond that way. Although we have contributed to many of world's acknowledged achievements as discoverers in past centuries, we probably did not know that we had so many of our young people with the quality of falling in love with wanting to know and asking new questions. Traditionally, we thought of ourselves as a country of poets. Surely, we did not think of ourselves as scientists. From that new population of young Portuguese scientists arose a group of scientists that are now winning ERCs and other European scholarships such as the Marie Curie and also North American scholarships. With our success being tested by the rigorous evaluation required by these great international scholarships, we would expect a great transformation and renewal in Portuguese university and business institutions. We had publicly lamented in 1987 that we were not â&#x20AC;&#x153;Traditionally, we thought of stimulating research - I am referring once again to what I know best: the ourselves as a country of poets. schools of medicine and university hospitals. Surely we did not think of It was difficult to imagine that a great number of young people would ourselves as scientists.â&#x20AC;? decide to pursue a scientific career, but it is even more unthinkable that universities in the country did not go to great lengths to renew and refresh themselves, to transform departments into universities, and 12

services into hospitals, especially when so many of their professionals were very old and on the verge of retirement.

The Champalimaud Foundation Another unpredictable event was Antonio Champalimaud’s will, a rare event of philanthropy in Portugal that led to the creation of the Champalimaud Foundation, which includes a large research laboratory and clinical services in the areas of neuroscience and cancer.

Exodus As a result of what I will call incomprehensible blindness that seems to affect our universities and entrepreneurial fabric, many universities in other countries are naturally offering great opportunities and places at the highest ranks to Portuguese researchers. Relatives and close friends experience both joy and sorrow with their children and friends’ emigration. In fairness, this redistribution shows that we scientists failed science’s social fabric and that we were not able to summon the whole society as Mariano Gago aspired (1).

Who can be our allies to reverse the situation? I have always demarked science from politics. Perhaps with the naiveté of a scientist, I thought my contemporary scientists, the old ones, would share the enthusiasm and pride I have experienced in seeing the success of our young scientists. I thought that they would be “head hunting” for their departments, similar to what other colleagues do in other countries. Moreover, the integration of these young researchers, many awarded with millionaire grants and scholarships, into their departments would help their departments’ budgets.

But my view reflects the ignorance of a person who seems to have forgotten the "cleansing" that the universities suffered almost a hundred years ago. First by a decree-law of May 13th, 1936, then by another in 1947, men who wanted to do research, were forced out of their institutions because they were considered a threat to the established (then political) power.

We needed a revolution to change political power Perhaps time has come for another revolution, one that takes place in universities and demands for better research funding. “Better” may not mean much more money, but most of all it needs to mean a rigorous evaluation of the quality and purpose of the research. It needs to mean allocation of time for research in medical careers and valuing research more in academic performance. - More funding for scientific research?! Persuade me. – every finance minister will say. - What if the greatest result of scientific training is to improve the quality of citizenship, Minister? - That's not enough, Dear Professor. We need to understand what the research is for. - Isn’t that what Pato de Carvalho is trying to do in his Institute for Education and Citizenship? The most important aspects in scientific education are a careful preparation of “the question”, the power that comes from demanding for accurate knowledge, from respecting our adversaries’ opinions, from not cheating because great part of the scientific education trains you to promptly uncover and exclude those who cheat. “Perhaps time has come for another revolution, one that takes place in universities and demands for better research funding.”

For a finding to become a scientific fact it needs to be replicated by peers. Regardless of its size, any contribution can only exist if confirmed by others. Although not immediately noticeable, scientific training of good quality creates citizens with great respect for life and for each other, even when we know that people have used and continue to use science and scientists for destruction of lives throughout history. 14

If it is true that scientific education is an intangible good, fundamental to citizenship, we scientists have the obligation to persuade politicians like the finance ministers that, ultimately, their countries will be more appreciated and even richer because they have different citizens. Although the plumber, the piano tuner, or the driver look the same, they will all be better prepared to welcome tourists, with increasing levels of education, from other countries. Tourism is just one example of great opportunity for the country. But of course, the cultural offer in general is an intangible engine for the economy that can but should not be ignored.

What the dictator thinks But if all that I have said so far is not enough, I can borrow arguments from our great and astute dictator, Antonio de Oliveira Salazar. For him, any man of science was a threat: men like Abel Salazar, Aurélio Quintanilha or Augusto Celestino da Costa, who were motivated only by wanting to know more, without being able to predict what they would find out. What would Salazar say today about those people in Champalimaud Foundation who created the Center for the Unknown? He probably would say that they are dangerous. It is dangerous not knowing what they might discover. It is dangerous that they do not even want to work for money, because, in that case, we cannot “buy” them. It is dangerous because they will not be silent or satisfied with the alternative truths that we want to disseminate. He probably would propose a law decree (6) that would take those people out of circulation today and that would make it very difficult for similar people to appear in the many years to come!

“… we should seek a different plan. We need to identify weapons and other comrades to fight along with us. We need to try to keep fighting, even when we know that winning is unlikely.”

Nothing of what I said today is new or something I had not thought of before. But never have I had the opportunity to say it in the way that is only allowed to the elder, who are now considered irrelevant. Today and from now on, I have to recognize that scientists until now have worked alone. Alone, they have managed to change themselves. They managed to dramatically increase the size of their funding and the funding they have brought to their institutions. They managed to improve their curricula and to increase the quality and the number of their publications. They managed to make their families proud. However, by 2017, we should seek a different plan. We need to identify weapons and other comrades to fight along with us. We need to try to keep fighting, even when we know that winning is unlikely. 15

In this context it seems appropriate to mention part of a recent message from the Union of Higher Education (7): “If we believe that the March for Science was important, it is fundamental to begin the mobilization by a March for Knowledge, that allows to claim the necessary conditions for Portugal to become a country of knowledge and qualification”

Before I finish, I would like to cite Hélia Correia (8) What weapons will we have, if not these That are within the body: the thought. […] A beginning […] A beginning of 30 and many more years After which there will be a collection of feats […] Which you cannot see, which you cannot hear, But, which, quiet inside the scientist within We proved to be, We will transform Portugal Into that strange blaze of the unlikely.

“We may not make great discoveries, but we will share this strange passion of the poet and, with that passion, we will transform what is now unlikely.”

I will end by reiterating the following. The intangible part of knowing, of doubting, of asking, will create citizens who may or may not have great inventions, but who will be different citizens wherever they may work. Dangerous in the eyes of any dictator similar to what is happening today in Hungary, or in eyes of any other administrative or academic autocrat in a position of power. We may not make great discoveries, but we will share this strange passion of the poet and, with that passion, we will transform what is now unlikely. Ideally, we should have politicians as allies, who are able to surprise us by paying attention to those who, like me, have nothing material to offer. 16

Thank you, Mr. Prime Minister, for honoring us with your presence on this occasion. Thank you, Mr. Minister, for inviting me to take part in the memory of May 87 which I can hardly forget. We were so few. We thought we were so unlikely. But above all, we did not know how Mariano Gago vehemently believed in us and in the science we represented. Thirty years, seeking to deserve his vehemence.

New York, 17 de Abril de 2017 Maria de Sousa

References

1. Gago, JM 2004 Prefacio. In M. Heitor (ed.), (2004), “Pensar e fazer engenharia com os mais novos: um ensaio sobre cultura tecnológica para pais e educadores”, Lisboa: Dom Quixote 2. De Sousa, M. 2009 A personal account of the development of modern biological research in Portugal. Int. J. Dev Biol. 53:1253-1259 3. Clavel F, Mansinho K, Chamaret S, Guetard D, Favier V, Nina J, Santos-Ferreira MO, Champalimaud JL, Montagnier L Human immunodeficiency virus type 2 infection associated with AIDS in West Africa. 1987 N Engl J Med. May 7;316(19):1180-5. 4. http://www.dn.pt/tag/claudina-rodrigues-pousada.html 5. http://www.cienciaviva.pt/centroscv/rede/ 6. de Sousa, M. 2014 . A liberdade é indispensável mas não suficiente para o desenvolvimento científico. In Meu Dito Meu escrito. Gradiva. 7. Sindicato do Ensino Superior. Valorização do Emprego Clentífico e Académico. 2 de Maio de 2017 8. Helia Correia. A Terceira Miseria. Relogio de Agua

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Science without Borders â&#x20AC;&#x153;Faculdade sem paredesâ&#x20AC;?

GABBA community around the world: Portugal, France, Qatar, Italy, U.K., Netherlands, Switzerland, Mozambique, Cape Vert, U.S.A., Spain, Israel, Austria, Germany, Australia, Ireland, Canada, Sweden.

United States of America

Catarina Nogueira GABBA 7th edition

My name is Catarina Nogueira. I am a GABBA alumna (7

edition-

2003) and am currently a Senior Scientist at Neon Therapeutics in Cambridge, MA, U.S.A. Neon Therapeutics focuses on the development of personalized neoantigen vaccines and autologous T cell therapies against cancer. I currently lead the vaccine technology group, a team responsible for the in vivo pre-clinical studies designed to support and improve the neoantigen vaccine products at Neon. I moved to the United States in the Fall of 2004 to start my PhD thesis work in the laboratory of Craig Roy at Yale University. Craig Royâ&#x20AC;&#x2122;s research focuses on host-pathogen interface. Specifically, the lab has discovered many novel mechanisms used by intracellular pathogens, such as Legionella pneumophila and Coxiella burnetii to modulate host pathways, which allow these pathogens to evade the immune system in order to replicate and survive in the host. My interest in immune responses to intracellular pathogens, however, started while working as a research technician at Instituto Nacional de SaĂşde Doutor Ricardo Jorge. At the institute, I worked in the laboratory of water analysis, developing culture and sequencing methodologies that would allow for the comparison of environmental and clinical Legionella pneumophila strains. These methods would then allow for the identification of the environmental source of contamination during Legionella outbreaks. During these years, it always struck me how Legionella could be so easily cleared by some individuals, while leading to severe pneumonia and death in others. Clearly, immunosuppressed individuals were the ones who succumbed to infection. When I joined Craig Royâ&#x20AC;&#x2122;s laboratory, I was interested in understanding innate immune pathways triggered during 19

Legionella infection. I believed that by understanding the first line of immune defense to this pathogen, we could try to tackle infection and avoid dissemination. Specifically, I was able to demonstrate that “Looking back, I can say I was dendritic cells are capable of restricting intracellular replication of very fortunate to be exposed to different fields in the beginning Legionella pneumophila by activating a “self-destruct” pathway called of my career and that Boston is apoptosis when they are infected. The discovery of this immunological a great city to pursue a career in detection pathway could be leveraged to develop new strategies to protect humans against multiple intracellular pathogens. Biotech.” After completing my PhD, I moved to Boston and I continued to investigate host immunity to bacterial infection as a postdoctoral fellow in Michael Starnbach’s laboratory at Harvard Medical School. Here, I expanded my studies to other clinically important pathogens, including Shighella flexneri and Chlamydia trachomatis. I had particular interest in elucidating T cell responses required to induce a protective immune response to Chlamydia trachomatis genital infections to ultimately develop a vaccine against this devastating sexually transmitted disease. The ability to be a mentor to Graduate students, as well as the collaborative environment at Harvard were amongst the things I appreciated the most during my postdoctoral work. In terms of research, the science was “top notch”, but we were still far from developing a product that could actually help patients. At this point, I started realizing that if I moved into industry, I would be able to do more applied research, and I would be closer to helping patients. My postdoctoral advisor, and the Harvard network as a whole, provided me the ability to establish connections within the biotech world of Boston. I started attending seminars and workshops to explore other career opportunities outside of academia and soon realized that Boston is one of the largest biotech industry “hubs” in the country. “I have now been in the U.S. for 13 years, and I am thankful every day to GABBA for opening doors for me and facilitating the development of my scientific career.”

I began hearing the name “Genocea Biosciences” at a number of the workshops I attended. Genocea, a small company just outside of Boston, develops T cell-based vaccines against multiple intracellular pathogens, including Chlamydia. After talking to the founder of the company about my current postdoctoral work and my future plans, he invited me to give a presentation at Genocea. A few months later, I was hired as a scientist in the vaccine development group. During my first year at Genocea, I worked on the Chlamydia vaccine project and 20

developed my mentorship skills by managing two research associates. After just a year on the project, Genocea decided to pause all infectious disease programs to focus entirely on cancer vaccines and I was asked to join the new team. At this point, I took a few days to reflect on my passion for fighting infectious disease and to consider the pros and cons of the opportunity that was now in front of me. I discovered, however, that I was quite eager to try this new field of Cancer Immunotherapy. It was hard in the beginning, but my manager and colleagues helped me to get up to speed. The literature was vast, and there was so much to learn. Confronting cancer immunotherapy is daunting and demanding, but just as fascinating as tackling a bacterial infection. Looking back, I can say I was very fortunate to be exposed to different fields in the beginning of my career and that Boston is a great city to pursue a career in Biotech. The networking and scientific resources provided by academic institutions such as MIT and Harvard, and the presence of so many local biotech companies makes Boston a fantastic city to be a scientist. I have now been in the U.S. for 13 years, and I am thankful every day to GABBA for opening doors for me and facilitating the development of my scientific career. Thanks to the support and guidance of this program, I have found myself at one of the most pioneering personalized cancer vaccine companies in the country. In my current position at Neon Therapeutics, I am able to continue my passion of mentoring young scientists, while also witnessing the direct impact our research has in the lives of patients. I look forward to many more years of advocacy for the GABBA program and will always strive to be a role model for students who wish to pursue a career in science either in or outside Portugal. ***

Israel

Raquel Sousa GABBA 16th edition

Shalom!

“The WIS campus resembles a fancy urbanization enclosing student housing, family residences, research and lectures buildings, gym, swimming pool, and plenty of gardens. All accessible to the academic community of the Institute.”

Israel has never been part of my travel or research plans, until recently. And here I am now. For the last 4 years, I have focused my PhD research in honey bee nutrition and behaviour in the Wright’s Lab in Newcastle Upon Tyne, north east UK. Not only have we been motivated to explore novel dimensions of bee feeding behaviour and taste, but also to evoke the entrepreneurial realm of the scientific knowledge this lab has produced over the years. Last August I arrived in Israel for the first time. Rehovot is a city about 20 km south of Tel Aviv in the Central District of Israel. Rehovot is home of the Faculty of Agriculture, Food and Environment in The Hebrew University of Jerusalem Israel (HUIJ) and The Weizmann Institute of Science (WIS). While the HUJI offers undergraduate studies, the Weizmann Institute conducts exclusively postgraduate research. The plan was to join The Shafir Lab in the B. Triwaks Bee Research Center at HUJI as a visiting researcher to assist developing a pollen substitute and use the outdoor lab amenities to test it. This campus and bee facilities offer unparalleled advantages over the UK. Outdoor temperatures fluctuate between mild and hot throughout the year, thus permitting field work with dozens of strong bee colonies all year round. Although, HUJI in Rehovot is a good university for animal sciences, WIS is the key place for Israeli and most international researchers. This is a highly-regarded institution founded by Chaim Weizmann, a Zionist leader and Ein Bobek, Dead Sea (Israel) Chemist, before the recognition of the State of Israel in 1948, of which he became the 1st President. Here, even Masters scholarships attributed to foreigner students include 2 years of accommodation. The WIS campus resembles a fancy urbanization enclosing student housing, family 22

“Israel is a country of cultural diversity and of contrasts. It’s double face switches from progressive to very conservative. For example, Tel Aviv is a social escape in Israel and a technological spin out core.”

residences, research and lecture buildings, gym, swimming pool, and plenty of gardens. All accessible to the academic community of the Institute. Historically, group leadership positions across scientific areas in this Institute have been largely attributed to Jewish/Israeli academics. Recently, and perhaps one of the first, a non-Jewish Portuguese, Filipe Natálio, has been invited to start his own group in Bioinorganic and Biomimetic Chemistry. Professor Carlos Caldas is another Portuguese academic and honorary lecturer in WIS, though based in the Cancer Research UK Cambridge Institute. A little far-fetched comparison between HUJI and Weizmann academics could be “hippies vs. posh”. Truth is that renting an apartment in this town can be easier if you work in the WIS.

The word Weizmann serves as a trust/money certificate. Sometimes, one would need an innocent lie only to be granted an opportunity to visit an apartment for renting. Otherwise, the advertiser may literally hang up the phone without further notice. This example leads us to one apparent downside of daily life in Israel: unnecessary rudeness in customer assistance/general services and some lack of politeness and professional pride. This is mostly striking after one has lived in the UK and compared to the European standards. Israel is a country of cultural diversity and of contrasts. It’s double face switches from progressive to very conservative. For example, Tel Aviv is a social escape in Israel and a technological spin out core. This coastal city transpires youth “The Middle Eastern food (e.g. Falafel, Tahini, Humus) is tasty and a European and suitable for vegetarians. lifestyle, though Israel is a green oasis in the has recently been Middle East.” ranked amongst the top 10 cities with the highest costs of living around the Globe (Worldwide cost of The Shafir Lab in the B. Triwaks Bee Research Center, living 2018). In Office (Rehovot, Israel) contrast, the historical city of Jerusalem, which attracts several religious creeds can also be rough for the heedless tourists. In some highly conservative (Orthodox Jews) neighborhoods, if someone is caught driving a car during Shabbat (Judaism's day of rest and 7th day of the week), is no surprise if the car is hit by stones. In Israel you work 6 days a week from Sunday to Friday. In Judaism, Saturday (Shabbat) is the day of rest (e.g. 23

“However, it is sad to observe that there is still a lack of environmental awareness among people. Beaches, camping and picnic sites end up with kilos of litter left behind”

no working, no driving, no cooking). If you are oblivious of religion and come to Israel to work, you should expect plenty of bank holidays. One of the most striking is the Yom Kippur (mid-late September), the “Day of Atonement” and the holiest and most solemn day of the Jewish year. Adults are expected to fast and the country literally stops. No cars in the streets, no trains, no buses and no airplanes departures nor arrivals. Over 24h, Israeli streets and highways are a communal playground for people, especially for children. In general, social life and bonding with likeminded people (i.e. non-religious) is straight forward and easy. The level of spoken English in the streets is average to very good. Yet, in some services across town (e.g. supermarket, gas and water companies) is not as good and can become difficult to communicate clearly. For example, if you register as a foreigner customer, your gas bill is still likely to arrive in Hebrew. The same for a rental contract. The Middle Eastern food (e.g. Falafel, Tahini, Humus) is tasty and suitable for vegetarians. Israel is a green oasis in the Middle East. After all, the drop irrigation system is a remarkable Israeli innovation. Access to fresh fruit and vegetables is good. Besides the blooming nature, the Holy Land has plenty of archaeological and hiking sites. However, it is sad to observe that there is still a lack of environmental awareness among people. Beaches, camping and picnic sites end up with kilos of litter left behind. Places to visit should include: West Bank (Cis Jordan), for example, The Banksy's Walled Off Hotel in Bethlehem; Dead Sea and Masada; and Jerusalem. For research purposes, there are several routes to apply for Government and International funding: Israel Science Foundation (ISF), Bi-national and International Funds and Research Centers such as WIS. Moreover, there are several other organizations and charities in Israel and abroad to finance research. For example, the Israel Research Fund is a charity in North America devoted to support cancer research in Israel. Private donations from Jews overseas are huge contributions for research labs in Israel. One of the main hurtles about traveling to and living in Israel is security checks. The political and military situation imposes a clear suspicious atmosphere. This translates into airport security hassles that can take hours, especially if you are travelling by Israeli airlines or if you arrive in Israel from Muslim cities (e.g. via Istanbul). Rehovot is a family-oriented city and safe to live in even if it sounds odd to hear the fighter aircrafts (possibly going to Syria); it is central for scientific research as it is home of the HUJI and the WIS; it is close to Tel Aviv (20 min by car) and to Jerusalem (45 min by car).

United States of America Andre Sousa GABBA 11th edition

I came to the United States in 2009 after a long deliberation of my options. I remember being the last one in my class to choose the laboratory and, consequently, the last one to start my studies. Why? Because choosing the laboratory where we want to do our doctoral research is likely one of the most important decisions of our scientific careers. As such, it is a decision that will have an overarching and significant impact on our personal lives. After visiting two laboratories in the U.S. and one in the U.K., I decided to come to the U.S. and join the Sestan lab at Yale. Today, I can say that it was a very good decision. I joined the lab because its line of research aligned with my interests, and also because during my visit I understood that the university had resources beyond my imagination. Doing research with little to no budgetary concerns opens the possibility for asking and pursuing the answer to daring scientific questions, and that was very attractive to me. Therefore, there are considerable advantages in being a researcher here: I can get all the reagents I need very quickly, the funding scheme is very stable, and, more importantly, there is an amazing network of researchers with whom to foster interesting and fruitful exchange of ideas, and who can help me solving some of the problems I find. My choice in coming to this Yale University Campus particular university also included consideration of aspects other than the purely scientific ones. There is life beyond the lab and I also considered what the city had to offer culturally. Yale and New Haven have a cultural agenda busy enough â&#x20AC;&#x153;Doing research with little to no to keep one off the couch (and the bench) almost every day of the year. budgetary concerns opens the I have attended concerts, plays, films screenings, and seminars on a possibility for asking and pursuing the answer to daring myriad of topics, all by top musicians, directors, and researchers, and all free of charge! I have visited the art museums and the museum of natural scientific questions, and that history, and I have enjoyed the books and manuscripts that the Sterling was very attractive to me.â&#x20AC;? Memorial Library and the Beinecke Rare Book & Manuscript Library have to offer. I have also indulged in the eclectic restaurant choices around the city. New Haven feeds you well! The environment is perfect for me. 25

Additionally, New Haven is very well located, being 1h30m from NYC and 2h30m from Boston. I found myself on the train to NYC very often, even to attend concerts after a day of work in the lab. This might sound perfect but it may not be easy for everyone to adapt to this country. The first thing I noticed was that I needed to change my daily rhythm. Here, everything is done earlier. The day starts at 6am, lunch begins at 11am, and by 5.30pm people are gathering for dinner. Strolls after dinner to relax? Forget about that. By 9pm the streets are empty, and by 10pm restaurants are about to close (NYC is an exception, of course!). It was also hard to develop any personal relationship with the other members of the lab; they are all very focused on work and family, leaving no space for a social life outside the lab. People here are usually polite but they engage with those outside of their inner circle in a superficial manner. This has proven to be a significant cultural clash, but one with which I quickly learned to live with. I decided to continue my postdoctoral training in the same lab for several reasons, the most important being that my lab was basically the only one that had all the resources I needed to continue to develop my research interests. I am now approaching the final steps of my training and will likely apply to academic positions in the U.S.. I spent most of my time as a researcher here, I know how the system works and, even though â&#x20AC;&#x153;Yale and New Haven have a there are, as is often the case, advantages and disadvantages, I think the cultural agenda busy enough to funding structure is more stable and clear, and that gives me assurances keep one off the couch (and the for the future that are currently very hard to find elsewhere. There are bench) almost every day of the many aspects of the socio-political structure that I also like in the U.S., year.â&#x20AC;? and others that I despise, but this text is probably not the most appropriate place to discuss them. I have to finish by mentioning that this short text reflects my perspective, which, of course, is very narrow by virtue of being personal. If you are considering studying in the U.S., my advice is that you visit the institution, talk to people, learn about the city, consider its location and offer in light of what is important to you, and pay attention to the subtleties. In the end, the decision you make should be one that better balances your professional and personal goals. ***

Austria 26

Bruno Fontinha GABBA 10th edition

Die Grenzen, die nicht wahr sind* And then comes the language. Words that have no meaning. People in the street that you can’t grasp. The inability to communicate. Without words and correct understanding, the message is lost. And being lost is such an unattractive place to be in. Ten (almost) full years have passed since the first day. The PhD is done. The PostDoc soon will be. And the knowledge of a total uncanny idiom is (almost) mastered. Austria is not, indeed, the top choice to do science. Fact. There’s a “public relation” issue with this land that is very palpable, that makes people squint. The politics also does not help. Too much of a recent Past on its shoulders. Fact. But here I am, a Portuguese immigrant (words are important and, once again, count a lot) who did his doctorate studies in a top excellency research institute (it is not unrelated to being an institute with private funds; a different story, for a different newsletter). Here I am, a Portuguese foreigner (a dangerous expression in these refugee times) about to finish his own Postdoc at one of the oldest and most renowned Universities in Europe, which houses 15 Nobel Prize winners. Not too bad for a place that fortunately stayed at the other side Vienna Giant Wheel (´Riesenrad´), of the Iron Curtain. Another fact with at the Prater`s amusement park. a transcendental significance.

“Austria is not, indeed, the top choice to do science. Fact. There’s a “public relation” issue with this land that is very

I did my PhD in the field of Neurobiology. Looking into how the mammalian brain perceives, assimilates and reacts to stimuli. Now, I am finishing my Postdoc on the field of the vertebrate inner brain photoreception, with a strong evolutionary and ecological focus. There was never any barrier, any constraint, and limitation to my work. Academically and financially. Being an EU citizen has its own advantages, where being European is deeply engraved in this country. 27

palpable, that makes people squint.”

Ground / basic science is indeed nourished here. In this topic, there is not a difference between other destinations. After all, Science is done by people. And smart people also gather in Vienna. Science is done with the help of money. And money exists here. There are in-house doctoral programs. There are fellowships. There are sponsorships from private companies. There’s philanthropy. Not in such large scales as in other stops, but nevertheless, is here and alive. And more and more private companies are flocking to Vienna. When you are right between East and West, geography plays a lot at your favour. The mention to my (our) nationality is not innocent. Although behind the safe walls (another word full of meaning in this

“Ground / basic science is indeed nourished here. In this topic, there is not a difference between other destinations. After all, Science is done by people.”

Sunset at the Augarten park

neighborhood of Europe) of the research institute and lab, with your colleagues and friends, with whom one speaks always in English, there is a world (or a lot of them) outside. A world that might not be as welcoming if you do not speak the language, with its immense implications on a daily basis. But I do believe that this sentence can easily apply to other places where English is not the native tongue. Nothing that a couple of after-work language courses don’t fix. Fact. Vienna is an incredibly well-organized city. A city that can grow in any direction. A city that houses several international organizations. A safe city to live. Fact. But forget about Haydn, Liszt or even Mozart (I am already seeing André Sousa rolling his eyes in disapproval). A lot in Science is happening here. Slowly, as it is the case for a country where research is mainly based in its capital. But happening. It is another fact that Austria will not be a powerhouse for research, like the US or the UK are… But there’s freedom and smart people doing research. That counts a lot. I was asked by Filipa Ferreira, who organises this ATG Newsletter, why am I living in Austria and not in Portugal, and interestingly, if I imagine myself staying here in the future or head to other destination. One deals

with the Present; the other deals with the Future. I answer with the help of the Past and Rachel Kushner “A lot in Science is happening here. Slowly, as it is the case for a country where research is mainly based in its capital. But happening.”

“To be young was to be more closely rooted to the thing that forms you” -The Flamethrowers *The borders that are not true

***

ATG: A City of Knowledge. Letâ&#x20AC;&#x2122;s take another look at a few of our citizens and some of their knowledge published since our last issue!

Part I. Knowledge Catarina Seabra & Ana Rita Araújo

In this edition of the ATG Newsletter, we are proud to share with this community the original scientific contributions of the GABBA students and alumni published so far in 2018 (first or last authorship). In this edition, matching the theme of the newsletter, we highlight the countries where these publications were originated, to show the diversity and quality of the GABBA community worldwide.

Portugal

“This work highlights the importance of adaptive changes in kinetochore size for mitotic fidelity in humans.”

From Portugal, 15th GABBA edition student Danica Drpic disclosures that differential chromosome missegregation can be dictated by the size of the 31

centromere-kinetochore that is the chromosome site specialized for interaction with microtubules of the mitotic spindle. Chromosome missegregation during mitosis or meiosis is a hallmark of cancer and the main cause of prenatal death in humans. By taking advantage of the unique features of the chromosomes of the Indian muntjac, the authors were able to present convincing evidence that in this species’ chromosomes, the greater surface area of large kinetochores allows for more microtubule interactions, greater chance of forming erroneous attachments, and hence greater chance of chromosome missegregation compared to chromosomes with smaller kinetochores. This work highlights the importance of adaptive changes in kinetochore size for mitotic fidelity in humans. “To have a paper is great, but to have the cover is even better!” by Danica

Drpic, D., Almeida, A. C., Aguiar, P., Renda, F., Damas, J., Lewin, H. A., … Maiato, H. (2018). Chromosome Segregation Is Biased by Kinetochore Size. Current Biology: CB, 28(9), 1344–1356.e5. Bastos, N., & Melo, S. A. (2018). Quantitative Analysis of Precursors MicroRNAs and Their Respective Mature MicroRNAs in Cancer Exosomes Overtime. Methods in Molecular Biology (Clifton, N.J.), 1733, 137–143. Pinho, S., Marchand, T., Yang, E., Wei, Q., Nerlov, C., & Frenette, P. S. (2018). Lineage-Biased Hematopoietic Stem Cells Are Regulated by Distinct Niches. Developmental Cell, 44(5), 634–641.e4. Veiga-Fernandes, H., & Artis, D. (2018). Neuronal-immune system cross-talk in homeostasis. Science (New York, N.Y.), 359(6383), 1465–1466. Rodrigues, P. M., Ribeiro, A. R., Serafini, N., Meireles, C., Di Santo, J. P., & Alves, N. L. (2018). Intrathymic Deletion of IL-7 Reveals a Contribution of the Bone Marrow to Thymic Rebound Induced by Androgen Blockade. Journal of Immunology (Baltimore, Md. : 1950), 200(4), 1389–1398. Cerqueira-Rodrigues, B., Mendes, A., Correia-Neves, M., & Nobrega, C. (2018). Ag85-focused T-cell immune response controls Mycobacterium avium chronic infection. PloS One, 13(3), e0193596.

United States of America

“… T. brucei causes an advanced circadian rhythm disorder (…), which leads to changes in the timing of sleep.”

From the United States of America, we would like to highlight Filipa RijoFerreira’s latest contribution to the field of parasitology and infection research. This was a result of a collaboration between the iMM, Lisbon, and the University of Texas Southwestern Medical Center, USA. In this elegant article in Nature Communications, Filipa proposes that T. brucei causes an advanced circadian rhythm disorder, previously associated only with mutations in clock genes, which leads to changes in the timing of sleep. Indeed, they show that the circadian rhythms of mice become phase advanced upon infection, with abnormal activity occurring during the rest phase. Filipa Rijo-Ferreira, GABBA 14th, is currently a HHMI postdoctoral associate at University of Texas Southwestern Medical Center, USA. Rijo-Ferreira F, Carvalho T, Afonso C, Sanches-Vaz M, Costa RM, Figueiredo LM, Takahashi JS. Sleeping sickness is a circadian disorder. Nat Commun. 2018 Jan 4;9(1):62.

Corvelo, A., Clarke, W. E., Robine, N., & Zody, M. C. (2018). taxMaps: Comprehensive and highly accurate taxonomic classification of short-read data in reasonable time. Genome Research. da Silva, J. A., Tecuapetla, F., Paixao, V., & Costa, R. M. (2018). Dopamine neuron activity before action initiation gates and invigorates future movements. Nature, 554(7691), 244–248. Athalye, V. R., Santos, F. J., Carmena, J. M., & Costa, R. M. (2018). Evidence for a neural law of effect. Science (New York, N.Y.), 359(6379), 1024–1029.

United Kingdom

“… defroxamine can protect bone marrow areas from being overtaken by leukaemia cells…”

One of our recent graduates in the United Kingdom, Delfim Duarte just reported in Cell Stem Cell that a drug that treats iron overload could improve treatment for patients with acute myeloid leukaemia (AML). The drug defroxamine can protect bone marrow areas from being overtaken by leukaemia cells, allowing blood stem cells to survive. The team discovered that the specialised vascular regions of bone marrow that house stem cells (vascular niches) are particularly impacted in AML. Deferoxamine could have a protective effect on these structures, allowing healthy blood stem cells to be rescued. Since the drug is already approved for human use for a different condition, the researchers now hope to team up with clinicians to begin human trials of the drug for AML. Duarte, D., Hawkins, E. D., Akinduro, O., Ang, H., De Filippo, K., Kong, I. Y., … Lo Celso, C. (2018). Inhibition of Endosteal Vascular Niche Remodeling Rescues Hematopoietic Stem Cell Loss in AML. Cell Stem Cell, 22(1), 64–77.e6. 34

Sa-Pereira, I., Roodselaar, J., Couch, Y., Consentino Kronka Sosthenes, M., Evans, M. C., Anthony, D. C., & Stolp, H. B. (2018). Hepatic acute phase response protects the brain from focal inflammation during postnatal window of susceptibility. Brain, Behavior, and Immunity, 69, 486–498.

Other Countries

“a mode of neurogenesis where two sequential Notchdependent divisions (…) produce matching sets of two T4 and two T5 neurons”

Apart from the countries most populated by the GABBA community, we highlight here the contribution from other countries. In particular we would like to mention the contribution of Filipe Pinto-Teixeira, GABBA 9th, in the field of developmental biology. This work combines efforts of researchers from the New York University Abu Dhabi, in the United Arab Emirates, and the New York University, in the USA. Reported in Cell, Filipe discovered a mode of neurogenesis where two sequential Notch-dependent divisions of either a horizontal or a vertical progenitor produce matching sets of two T4 and two T5 neurons retinotopically coincident with pairwise opposite direction selectivity. They show that retinotopy is an emergent characteristic of this neurogenic program and derives directly from neuronal birth order.

United Arab Emirates / USA Pinto-Teixeira, F., Koo, C., Rossi, A. M., Neriec, N., Bertet, C., Li, X., … Desplan, C. (2018). Development of Concurrent Retinotopic Maps in the Fly Motion Detection Circuit. Cell, 173(2), 485–498.e11.

Austria Kelemen, R. K.,& Vicoso, B. (2018). Complex History and Differentiation Patterns of the t-Haplotype, a Mouse Meiotic Driver. Genetics, 208(1), 365–375.

Germany Neto, F., Klaus-Bergmann, A., Ong, Y. T., Alt, S., Vion, A.-C., Szymborska, A., … Gerhardt, H. (2018). YAP and TAZ regulate adherens junction dynamics and endothelial cell distribution during vascular development. eLife, 7.

Brazil Zucca, L. E., Morini Matushita, M. A., da Silva Oliveira, R. J., Scapulatempo-Neto, C., de Lima, M. A., Ribeiro, G. G., … Reis, R. M. (2018). Expression of tyrosine kinase receptor AXL is associated with worse outcome of metastatic renal cell carcinomas treated with sunitinib. Urologic Oncology, 36(1), 11.e13-11.e21. Cruvinel-Carloni, A., Yamane, L., Scapulatempo-Neto, C., Guimaraes, D., & Reis, R. M. (2018). Absence of TERT promoter mutations in colorectal precursor lesions and cancer. Genetics and Molecular Biology, 0. Linhares, P., Viana-Pereira, M., Ferreira, M., Amorim, J., Nabico, R., Pinto, F., … Reis, R. M. (2018). Genetic variants of vascular endothelial growth factor predict risk and survival of gliomas. Tumour Biology : The Journal of the International Society for Oncodevelopmental Biology and Medicine, 40(3), 1010428318766273.

***

Part II. Citizens Joana Wilton Delfim Duarte, PhD GABBA 17th edition, class 2013 Clinician, IPO and Teaching Assistant, i3S

What did you study during your PhD?

“… GABBA nurtured my critical thinking and allowed me to meet fantastic scientists and fantastic people and to build a sort of scientific network that will most likely help me in the future…”

I studied how blood cancer cells interact with their surrounding microenvironment. I used intravital microscopy to investigate this crosstalk. During my PhD I asked two main questions: are specific bone marrow niches relevant for acute leukaemia expansion and chemoresistance? And does acute leukaemia change the microenvironment that sustains non-malignant haematopoiesis? This is relevant because acute leukaemias are aggressive diseases and patients often present with cytopenias that lead to fatigue, infection and bleeding. The main conclusions were that T-cell acute lymphoblastic leukaemia is niche-agnostic and that acute myeloid leukaemia selectively remodels endosteal blood vessels.

LONDON PORTO

2014 2 2018

How did the GABBA PhD affect your career so far? It might be too soon to judge that but it’s unquestionable that among other things GABBA nurtured my critical thinking and allowed me to meet fantastic scientists and fantastic people and to build a sort of scientific network that will most likely help me in the future, through collaborations for example. A good example of such a ‘network’ is the All Time GABBA (ATG) association. 38

In what way did your background as a medical doctor impact your choice of field/lab for the PhD project?

“… in the end, it all comes down to ‘the question’ and the biology, which for me was cool and kept me going during the PhD…”

Our previous education and past experiences are always key for decision making. In my case, I had just chosen Haematology as my field of specialization when I started GABBA. This was obviously very important for choosing a project and a lab. I also wanted to positively impact the life of patients, which is probably associated with having done medical school. But in the end, it all comes down to ‘the question’ and the biology, which for me was cool and kept me going during the PhD.

At the time of writing, you’re right at the finish line for the defense. What are your plans for the future? I want to complete my clinical training in Haematology and to continue my research. At the moment I’m working as a clinician at IPO-Porto and developing the research at i3S in Graça Porto’s group. The new consortium Porto Comprehensive Cancer Centre will hopefully facilitate the balance between the two. My main focus will be the role of blood vessels and iron on cancer and haematopoiesis.

Your PhD project was based in the UK, one of the top 3 countries chosen by GABBA students. How did this choice influence you as a scientist? Were you affected by Brexit at an institutional and/or professional level during the project?

“The atmosphere in London was very strange when Brexit won. It was like a bank holiday full of zombies.”

The UK has a very long scientific history. When you look at their scientific institutions and output, it shows the critical mass and the scientific melting pot (despite the Brexit). You’re surrounded by good science. This is very stimulating! I loved the experience and would always recommend the UK. The atmosphere in London was very strange when Brexit won. It was like a bank holiday full of zombies. This is to say that London is very anti-Brexit. It didn’t affect me but it might affect others in the future.

What advice would you give to the 21st edition students? Take the opportunity to do something very different during the PhD. Do something risky in a very good lab, with a good mentor. And spend as much time as you can abroad, somewhere out of Portugal where you’ll need to learn and adapt.

Favorite Sunday activity: Brunch and beach. Dream vacation: Tavira and Praia Verde. Favorite non-Portuguese cuisine: Indian. Sport: Football. TV show that you binge watched recently: La Casa de Papel. Android or iOS: iOS. Pipet tip box usage method (in order, the ones in same area or random): It varies but most frequent might be â&#x20AC;&#x2DC;the ones in same areaâ&#x20AC;&#x2122; ahah. Friday night drink: With friends, anywhere.

Patrícia Oliveira, PhD Postdoc at Expression Regulation in Cancer (ERIC), IPATIMUP (PI Carla Oliveira, GABBA 2nd) GABBA 10th edition, class of 2006

What did you study during your PhD? During my PhD, I studied the role and relevance of introns present in cadherin genes. It all started because of the presence of a massive 70 Kb intron in CDH1, the gene encoding E-cadherin, which in turn is a protein deregulated in 90% of epithelial cancers. Previous studies had shown that the removal of this intron led to E-cadherin expression loss in several tissues in mouse embryos. During my PhD and using bioinformatics analysis of genomes of several species, we showed that cadherin genes (over 100 in the human genome) globally possessed longer introns than other genes and gene families. These longer introns were found in the 5’ region of cadherin “… cadherin genes (over 100 in the human genome) genes, emphasizing that the structural conservation of these longer introns, globally possessed longer rather than the sequence itself, was a mean to carry relevant information introns than other genes necessary for proper cadherin expression/function. In addition, we saw that and gene families.” the longest introns in human cadherin genes revealed a significant enrichment in several putative regulatory elements, such as complex repetitive sequences. These findings underlie current studies in our group, which are focused on the function of particular intronic sequences that impact E-cadherin expression. As the work evolved, we also developed an in vitro model of epithelial to mesenchymal transition (EMT), a normal biological process crucial for embryogenesis and with increasing (yet controversial) relevance during cancer progression. This model fit with my PhD given that one of the hallmarks of EMT is the loss of E-cadherin already at the mRNA level. With this model we studied the de novo transcription arising from cadherin (longest) introns, showing that exonization events could also trigger cadherin expression deregulation.

VANCOUVER

PORTO TRIESTE

2007 2018

In what way did the GABBA PhD affect your career? GABBA was my way into Science. I applied to GABBA blindly, recommended by a friend. Back then, I was very confused on what to do after finishing Biochemistry in the University of Coimbra. I had very little knowledge on what was a PhD and suddenly I found myself in the (best) doctoral program in Portugal. In hindsight, I can see that it was purely blind luck, as I had never “… more than “affecting my done any type of Science work before GABBA. So, more than “affecting my career”, GABBA made my career”, GABBA made my career! career!”

As a bioinformatician, how is your perception of current PhDs and PhD candidates and their attitudes towards wet vs. dry science? Things have changed a lot since I started doing bioinformatics in my PhD. I was very lucky to train in an Italian lab split 50/50 between people working with bioinformatics and wet lab, supporting each other. I had a great teacher (Dr. Remo Sanges), with incredible patience and continuous support, as I had literally zero experience in programming or using any type of bioinformatics tools. When I came back to Portugal, I was an oddball, working on my own and trying to show everyone what bioinformatics could do to help those working in the bench. Back then, we were less than 10 people working with bioinformatics in the entire institute! With time, our team became more and more knowledgeable in bioinformatics (as I did in wet lab techniques) and now we happily work together, bringing dry and wet science together.

“… the general feeling I have is that now, everyone knows that dry and wet science are complementary and equally necessary to move Science forward.”

Looking back, in the early stages of my PhD, bioinformatics was not a familiar term in Portugal. But now everyone knows about it, from our group leaders, to our PhD students, to our Master students. Even students from high school that come to our lab have heard about bioinformatics! The general feeling I have is that now, everyone knows that dry and wet science are complementary and equally necessary to move Science forward.

Your PhD project ended up spanning three countries (Portugal, Italy and Canada). What were the main differences in the day-today environment (if there were any at all)? Do you have any anecdotes from that time? Life was very different in the 3 countries. In Italy, where I started, we had a great ambience, as we routinely went out for drinks together, as Italians like to do. Although Trieste (where I was), was the least Italian city (architecturally), the ‘dolce vita’ mood was there, brought by all the Neapolitans that filled the lab where I was working in. Dr. Elia 42

Stupka, our group leader, was great in getting everyone involved and I never felt alone there. The 18 months I spent there were truly special. Back in Portugal, the day to day was always great, as Ipatimup was more a family than a formal institute, at times. We all got along, with many social events happening that made my return to our country easier.

“… I realize that it is pivotal to hear/see the others’ point of view, as only with team work can Science truly advance.”

In Canada, although I only visited for a few months, the vibe was completely different. Dr. David Huntsman, our group leader in Vancouver, was most hospitable, bringing me into the heart of his family in the most endearing manner. He truly made me feel welcome! However, the lab was a quiet place, unlike the rumbustious Italians back in Trieste and my friends in Portugal. I had to work on my social skills (for the first time in my life) to prevent loneliness… One of the most out-of-character things for me, was that I had to force myself to watch every single soccer game of the 2010 World Cup (that was going on while I was in Vancouver), so that I could establish a conversation with a German guy that was seated next to me in the lab. I had tried different conversation angles prior to this, and the guy was very monosyllabic…until I discovered that he was crazy for soccer… and suddenly I saw that he was capable of enunciating more than the usual ‘Good Morning’ and ‘See you tomorrows’ I was getting thus far …

After your PhD, you trained as a postdoc at IPATIMUP. What do you consider as the most useful transferable skills you gained during the PhD? In two words, perseverance and plasticity. First, the ability to keep trying to get answers even if we have to change the original question and nothing is going as planned. Second, the capacity of adapting our approach and our mindset to what the Science is showing without fear of failing. I have also learned that listening is one of the best features that a scientist can have. As an only child, I have struggled with this (and still do!), but I realize that it is pivotal to hear/see the others’ point of view, as only with team work can Science truly advance.

Your lab has recently hosted high school students, also under the Ciência Viva umbrella. Can you share any stories about mentoring early-career scientists? Our work with students is something that fills me with pride, as I believe that as researchers, we have a duty to pass our knowledge forward, being it for a scientific-oriented audience or to lay people. High school students are a curious breed, as they are somewhere in the middle of this, with some 43

knowledge on Science. Since the beginning of my PhD, I have been lucky enough to help in the hosting of some very special kids in our lab, always with curious minds and an eagerness to learn that put a lot of Master students to shame. However, with time, I have come to rely more and more on the younger members of our group to help us host the Ciência Viva students. “Every year is different, and it is hard to pinpoint any story… and more than stories, what stands out are the characters of the students that intern with us.”

“… 1) never lose your curiosity; 2) be openminded and; 3) embrace failure…”

Every year is different, and it is hard to pinpoint any story… and more than stories, what stands out are the characters of the students that intern with us. One of the most recent student pairs we have hosted was very particular: Zé Pedro and Diogo, two boys, a rare event in itself, as we receive girls more often. These guys were very peculiar: they started out the internship with an extreme formality in the way they addressed us at the lab, and demonstrated a strong respect for our daily work. As the days went on, the formality faded and they developed an interesting dynamic with myself and Sara Teles, the Master student that was more hands-on with this internship. At the time of the final presentation, they spoke of the work they were involved in as their own, a mark that fills me with pride. In the end, some weeks after the internship had ended, they decided to apply for the ATG award and contacted us to inquire whether it was possible. Gladly we said yes and they produced a report, that was way beyond my expectations for any given high school student. In fact, they came in second place that year! Even cooler is the fact that Diogo has contacted us asking to come back to our lab as a 2nd year University student during this Summer to continue to see what goes on in our lab and Zé Pedro re-applied to Ciência Viva! These guys stood out and we still keep in touch with them.

What advice would you give to the 21st edition students? The best advice I could give them is to enjoy your time as a PhD student, as it is a time of learning like no other in your life. The second-best advice is to celebrate your victories, even the small ones. They will be your emotional trampoline later on, when things don’t go your way (and they will often, it’s life!). The third best advice are in fact three: 1) never lose your curiosity; 2) be open-minded and; 3) embrace failure, as it often hides new avenues of research that can be the most interesting ones.

Favorite Sunday activity: Horror movies with Catarina Carona. Dream vacation: After Patagonia (done!), now Africa. Favorite non-Portuguese cuisine: Japanese. Sport: Swimming. TV show that you binge watched recently: La Casa de Papel. Android or iOS: iOS. Pipet tip box usage method (in order, the ones in same area or random): Back when I used them: random. Favorite Programming language: Perl. Friday night drink: Beer.

It would be great to count with your help for the next ATG Newsletter If you are willing to help, just write us an email. We will take all the help & ideas you may have.

ATG News Mafalda Azevedo RECENT GRADUATES

Joana Neves, GABBA 15th Thesis: The hepcidin/ferroportin regulatory circuitry in lung iron homeostasis. Mentor: Martina Muckenthaler, PhD (University of Heidelberg). Defense date: 01-09-2018.

Ana Luisa Neves, GABBA 16th Thesis: Indoles as gut microbial pharmaco-metabolites: Targets, mechanisms and consequences for obesity and cardiometabolic diseases. Mentor: Dr. MarcEmmanuel Dumas (Imperial College London). Defense date: 01-23-2018.

Lara Marques, GABBA 16th Thesis: Nucleic acid structures as transcriptional and epigenetic regulators in health and disease. Mentor: Prof Matthew Wood (University of Oxford). Defense date: 03-20-2018.

Ana Rita Araújo, GABBA 17th Thesis: Temporal Control Principles in Cell Cycle Regulation. Mentor: Dr. Sílvia Santos (Imperial College London). Defense date: 03-23-2018.

Vera Lemos, GABBA 16th Thesis: Liver Receptor Homolog-1 and control of mitochondrial function. Mentor: Kristina Schoonjans and Johan Auwerx (École Polytechnique Fédérale de Lausanne). Defense date: 04-24-2018.

Delfim Duarte, GABBA 17th Thesis: In vivo imaging of the dynamic interactions of acute leukaemias with the bone marrow microenvironment. Mentor: Cristina Lo Celso (Imperial College London/ The Francis Crick Institute). Defense date: 05-08-2018.

Raquel Sousa, GABBA 16th Thesis: Exploring Mineral Salt Feeding Preferences and Regulation of the European Worker Honey Bee. Mentor: Dr. Geraldine Wright (Newcastle University). Defense date: 06-13- 2018.

TRIBUTE TO PROFESSOR MARIA DE SOUSA Pedro Resende

Last April, the lifetime scientific contributions of Professor Maria de Sousa, cofounder of the GABBA program, were highlighted by ICBAS during a 3-hours symposium. The session was moderated by Professor Manuel Sobrinho Simões and counted with the presence of the new recently elected rector of the University of Porto, Professor António Sousa Pereira. Inspired by Professor Maria’s words “Queremos para a afirmação da nossa identidade reconhecer os cientistas como antepassados que nos orgulhamos?”, from her book Meu Dito Meu Escrito, several topics were discussed. The session started with Professor Maria Carmo Fonseca, director of iMM, talking about her view on professor Maria’s distinct personality, her character and her values. Then, Professor Graça Porto, group leader at i3S, guided the audience through Professor Maria’s research on hemochromatosis. ICBAS Professor Manuel Correia, talked about the genesis of ICBAS and how professor Maria joined it and has contributed for the success of this institution. Professor Mario Barbosa, director of i3S reminded us of how the merging of IPATIMUP, INEB and IBMC happened and how professor Maria de Sousa helped this ambitious project. As part of this discussion, the GABBA program could not be forgotten. For this purpose, Pedro Resende, president of ATG, All Time GABBAs, shared a few personal notes on how Professor Maria has served both as mentor and role model ever since he joined GABBA as a student, revealed a few reasons that make GABBA a unique PhD program and finished by highlighting the outstanding achievements of the GABBA alumni in the past 20 years. This symposium was part of a 3-day series of ICBAS on History of Medicine, where 3 personalities were chosen due to their lifetime contributes to ICBAS: professor Corino de Andrade, professor Maria de Sousa and professor Nuno Grande. 49

CIÊNCIA VIVA AWARD Lígia Tavares

This year we are launching the 3

edition of The ATG – Ciência Viva award! This is

a partnership between the ATG association (All Time GABBAs) and Ciência Viva (national agency for scientific and technological culture). Ciência Viva in the laboratory allows students to do an internship in a lab from a R&D Institute across Portugal. At the end of the internship students have to do a report to apply to the ATG – Ciência Viva award. With this award we recognize the best reports in order to enthuse students for science and the scientific questions. http://www.cienciaviva.pt/estagios/jovens/ocjf2018/index.asp

MARIA DE SOUSA SUMMER RESEARCH PROGRAM 2nd Edition

Catarina Seabra ATG has the pleasure to announce the second edition of the "Maria de Sousa Summer Research Program". The program was designed for undergraduate and graduate students, enrolled in a higher education institution in Portugal, interested in doing summer internships in a laboratory, with the supervision of an All Time GABBA member.

This edition has the goal of giving the opportunity to students from Portuguese universities to develop an internship in one of four laboratories in the country. The internships will have a duration of two weeks and will be carried out at research institutes in Aveiro, Coimbra, Porto and Braga. A "Maria de Sousa Research Program" monetary award will be awarded to all students to help support travel and accommodation costs during the internship. This program counts on the kind support of the sponsors, namely Fundação Eng. António de Almeida and the American Portuguese Biomedical Research Fund. The second edition had a total of 63 eligible applications from students of all over the country. The selected candidates will be announced by the end of this month. 51

What the first edition students had to say:

"The summer program "Maria de Sousa Summer Research Program" allowed me to deepen my knowledge about some subjects with which I had had little or no previous contact. Especially at the laboratory level I feel that I learned more techniques and work routine. In addition, being integrated into such a motivating, cooperative team and with a lot of patience and confidence in myself and in my work, I ended up understanding how research teams work and felt my work being valued." - Eduardo Pinho

"The Maria de Sousa Summer Research Program has proved to be a unique learning opportunity that has contributed very positively to my personal growth, where I have been able to develop hands-on skills, immersed in the laboratory environment. I cannot fail to highlight the availability of the tutors who accompanied us throughout the program and of the entire research team that also helped make this program a remarkable experience." - JoĂŁo Gomes

For more information, please visit: www.facebook.com/mdsresearchprogram https://atg.up.pt/news/mds-research-program-2018

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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

ATG Newsletter issue 7

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