ATG Newsletter 12

ATG Newsletter Issue 12

December 2020

Welcome to another edition of the ATG Newsletter Contents 3 • Message from the President of the Executive Board Lígia Tavares 4 • de Sousa et al. 5 • In a Pandemic World 14 • City of Knowledge 16• Part I. Citizens Marta Madureira 19 • Part II. Knowledge Ana Rita Araújo & Telmo Catarino 25 • What can I be with a PhD in Biology? Pedro Resende & Catarina Seabra from Chaperone

any of us are experiencing the pandemic in different ways, while living in different countries. In this edition of the ATG newsletter, we interviewed seven GABBAs/ATGs to have a sense of how they are dealing with the restrictions, how their work has been affected, and what has been keeping them busy. Additionally, we interviewed Manuel Vicente and Pedro Beltrão, who are actively working on COVID-related projects. We created a new section called “What can you be with a PhD in Biology?”. In this edition, we collaborated with Pedro Resende and Catarina Seabra from Chaperone to deliver information on career options for doctorates and identify a few myths often associated with career development. If you are a regular reader of this newsletter, you are most likely noticing that something looks different. We redesigned the newsletter and we hope you enjoy reading it in the new format. If you want to contribute with beautiful scientific images or artwork for the newsletter, see page 24. One of the submissions will be the cover of the next issue. Last but not least, on behalf of the editorial team, I would like to thank everyone who contributed to the newsletter and welcome anyone who wants to join. Happy Holidays! Stay safe!

27 • ATG News

Mafalda Azevedo Editor-in-Chief

ATG Newsletter • Issue 12 • December 2020 Editors Mafalda Azevedo, Marta Madureira, Telmo Catarino Cover Mafalda Azevedo Contributors Afonso Bravo, Ana Luísa Neves, Ana Rita Araújo, Anaísa Valido Ferreira, André Sousa, Anna Brito (Maria de Sousa), Bruno Fontinha, Catarina Seabra, Francisca Soares da Silva, Iliona Wolfowicz, Hélder Araújo, Lígia Tavares, Manuel Vicente, Marta Madureira, Pedro Beltrão, Pedro Resende, Rita Gomes, Telmo Catarino

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 • i3S, R. Alfredo Allen, 4200-135 Porto, Portugal

Message from the President of the Executive Board the pandemic is certainly making it worse. In Portugal the scientific community is shrinking, getting smaller and poorly funded. The idea ear GABBA community and ATG newsletter behind GABBA, that we need freedom, we need readers, to empower people, to train them at the best places because not all but a few will be truly successful and will have an impact in science is I hope this newsletter finds you well as long gone. We are funding very few people with your families. 2020 has been a strange year that very low budgets and very safe projects. We is now approaching the end. For our scientific should know from the past, from other countries GABBA community it was a sad year due to the that this is not the way forward. Of course, the loss of our mentor Prof. Maria de Sousa (subject country is going through a huge economic crisis, of our last newsletter). We are dedicating this but shouldn’t this pandemic have made us aware newsletter to the COVID-19 pandemic. Since of the importance of science, the importance February/March, when the spread through the of all the science and not just the fancy one? world started, we went into a global lockdown Scientific problems never arrive where we expect as we knew nothing about the virus. But since them. All the viruses are different, maybe next then we learned a lot, we learned about the time it is a bacterium… What are we doing virus, the infection, how its spread and how wrong that we are not making it clear that we we can protect ourselves need to invest in science. Or at and others. The scientific least we should know and the “...(1) science must be community combined efforts population should know that done in a community, with to work in several fronts: from the government does not want interdisciplinarity, as in this way a healthy scientific community testing, data collection and findings are more robust and have and see if the population analysis, study the infection, consequences of the virus, a true effect; (2) science takes time! agrees with that. treatments and a vaccine. We We can speed up things but we need I know my words are not that went through a calm summer to be sure of the results, to use the encouraging but with that I that made us believe that proper methods, to analyse data want to spike the community we had figured it out but to make pressure, to tell your carefully; (3) most of the world as October came along the picture changed again. Even leaders have no idea what science family, your neighbours, your though we made massive is, and they do not make an effort to audience whatever that is that we need science and that we findings we still know very know more, to learn and take advice are not in the right track. little. From my perspective from scientists.” the lessons we need to take Despite all the grey shades are: (1) science must be done from a pandemic and science I wish you a in a community, with interdisciplinarity, as in this wonderful Christmas and a 2021 full of hope for way findings are more robust and have a true better days to come. I am sure we all learned a effect; (2) science takes time! We can speed up lot with 2020 and 2021 will be different, hopefully things but we need to be sure of the results, better! to use the proper methods, to analyse data carefully; (3) most of the world leaders have no idea what science is, and they do not make an effort to know more, to learn and take advice Cheers, from scientists. This should prompt us to have a more prominent role in our society, an active Lígia Tavares ¤ role instead of a passive one. Portugal is going through difficult times. I do not know if due to the closure of the scientific community on its own or due to bad politician’s science, but 3

de Sousa et al. A Most Forgotten Thing: The Biology of Imagination “In the abismal ignorance of the biology of imagination many squashed XX chromosomes shall, one day, be found under the unpublished silence of women” (for O. A.)

Anna Brito We forget that words unlike cells differentiate in the bodies of men with no antigens telling their sex of origin; that word squashes unlike cell squashes shall yield no visible chromosomes under microscopes; that love, in print, shall remain the permanent symbol of expressed human feeling but noone from reading it will know I-she wrote it you-he wrote it Auden in love with it wrote it Byron in love with thee wrote it. For only a few among all male and female creatures carry wombs on their shoulders

and their words, unlike their cells, shall shed no telling antigens shall hear no visible chromosomes, their words like their thoughts shall keep multiplying helplessly into poem into prose at dawn at night behind drawn curtains in the bath in the bed waiting for the bus watching the bank managers and the ways of other devourers multiplying helplessly into theories we all shall share for the most part, unaware, until the day, in nuclear horror, we all shall die; words forever silenced chromosomes forever damaged a few intact molecules scattered perhaps among ashed bones holding on to futile telephones. March, 5 (1981)

Poem written by Anna Brito, Professor Maria de Sousa’s pseudonym. It can be found in Gávea-Brown, A Bilingual Journal of Portuguese-American Letters and Studies, Vol. II, Number 2, July-Dec 1981.

In a Pandemic World

GABBAs and ATGs around the world answer questions about what’s been keeping them busy during this pandemic.

Afonso Bravo 20th edition

At the beginning of the year I had also decided to switch a bit my current Ph.D. research direction, to start finishing things up. This obviously would involve a lot of bench work, that I have hardly managed to perform this year. As useful shiftbased lab work is difficult to achieve, I would say that I have only seriously dedicated about 4 non continuous months of lab work to research this year. This has somewhat affected my research, but I think it is something that I can recover until I am ready to defend (and who knows when that will be…). What is the current situation? The second wave COVID cases seem to be going down now. At the time of writing we are having 4.5K daily cases in

Where do you live? Lausanne, Switzerland. What restrictive measures did the country/city you live in implement? Despite the number of cases (population normalized) being one of the highest in Europe, we had/have a lot of freedom. During the first wave, back in March, we had a 4-month lockdown where we weren’t allowed to go to the work place. We were allowed to leave our homes and walk around/travel though. By June, lab work was possible again, albeit only a few times per week due to the university implemented mandatory shift system. This continued until August, when “non-shift” work resumed. By October the COVID-19 second wave started. This time almost no measures were taken. Currently, all the restaurants and shops are closed, and masks are mandatory in public and workspaces (like the lab/office). That is about it. I guess this partially explains why Switzerland is experiencing so many cases.

“When lockdown started, I took my work computer setup home. I essentially used the lockdown time to advance a lot of data analysis, improve my coding skills, and start writing possible paper stories.” Switzerland (coming down from a 10K cases/day peak). Besides what I mentioned before, I don’t think there are any intentions of implementing more lockdown measures. Even mandatory quarantine has been removed when coming to Switzerland from most countries.

Did you start any new hobbies? If yes, tell which one(s)? I started exercising a lot. First, I would only do stay-at-home own-body weight exercise routines. But like I said before, during “lockdown” there were no restrictions to leaving your house, so I started running as well. This was back in March and I hated running. In “I had never run more than 3km in fact, I had never run more than my life. Now, 9 months later, I am 3km in my life. Now, 9 months later, I am proud to say I ran my proud to say I ran my first marathon first marathon back in October. back in October.” I still continue to run, and most importantly, I enjoy it now.

How was your work affected by the pandemic, if at all? When lockdown started, I took my work computer setup home. I essentially used the lockdown time to advance a lot of data analysis, improve my coding skills, and start writing possible paper stories. I didn’t have enough material to keep me busy the entire time, so eventually I ran out of useful work to do.

Did this pandemic bring something positive into your life? I became fitter and physically healthier. I think this was the only upside. ¤ 5

ATG Newsletter 12 • December 2020

Ana Luísa Neves 16th edition Where do you live? London, UK.

healthcare service delivery, there was a major drive to move to remote digital care (i.e., video, telephone consultations, online triage). I have started a few projects to understand the impact of these new ways of delivering care on patients, healthcare professionals and organisations, and I was lucky to be awarded my first two grants as PI on this subject during the summer.

What restrictive measures did the country/ city you live in implement? We are now in the second lockdown. We are advised to work from home, unless that is not possible. We can leave home to provide voluntary or charitable services, where we cannot do this from home. In general, we must not meet with another person socially or undertake any activities with another person. Most services have been closed since Nov 5th, except essential services (schools, pharmacy, supermarket). However, we can exercise or meet in a public, outdoors space with people you live with, with our support You do what you have to do... or childcare bubble, or with one other person.

Did you start any new hobbies? If yes, tell us which one(s)? I wish I had some fancy answer here, but honestly, I feel I have been in survival mode over the last months. The only creative thing I learned during the first lockdown was to play ukulele to entertain my kids, and not sure if that’s something to be proud about! Above all, just trying to make sure I remain positive and a positive influence for those around me, keeping up with the professional opportunities that come across, and being quite strict with my work-personal life hours. It’s really easy to get dragged by work when our home becomes our workplace too...

How was your work affected by the pandemic, if at all? Since March 2020, I have been working remotely. The first months, Did this pandemic bring when the schools closed, were something positive into your a bit challenging, juggling my life? Professionally, there were full-time work while taking care opportunities that I wouldn’t of my twin toddlers at home. have had otherwise. The fact that I suppose that was the major my research was aligned with an challenge. At the same time, I area that experienced a great feel quite lucky as I can do most expansion during the pandemic of my work from home – as I do data analytics and health policy, I Writing one of the grants over did bring some unexpected was not particularly impacted by summer. The babies in the pram are opportunities and made me grow faster than I had anticipated. being prevented from going to not interested at all. Personally, I remember how the office. I do miss working in an stressful the first months were, open space, the informal discussions with other and my frustration of not being able to do team members, and I do believe that enhanced anything as well as I would like (i.e., researchcollaboration at a deeper level. wise, motherhood-wise). Looking back, I can only see that as a family we were really privileged What have you been up to during the pandemic? we remained healthy, our salaries and job roles In such a difficult situation, there were some silver remained intact, and I was able to see my kids linings. I was already working on digital health, becoming tiny humans in ways that would be and the COVID-19 pandemic forced some major impossible in our ‘normal’ lives. ¤ advances in this area. In particular, in what concerns 6

In a Pandemic World

Anaísa Valido Ferreira 21st edition

the vacancies.

What is the current situation? Currently a partial lockdown is in place. People may have a maximum of three visitors at home and groups of no more than four people are allowed outside. Restaurants are closed, and events are prohibited. The laboratory is working at a 50% capacity and so spots must be booked two weeks in advance to make sure one is able to perform an experiment. The measures in place are leading to a decrease Hello little visitor. Spring does not of cases so there is some hope care about the pandemic. for Sinterklaas and Christmas celebrations.

Where do you live? I returned to Portugal in October but for the last two years I have been in Nijmegen, the Netherlands. What restrictive measures did the country/city you live in implement? Different restrictive measures were applied over time. The most restrictive were the closing of non-essential businesses, and permission to leave the house only for groceries and exercise. Travel was strongly discouraged, specially to high-risk countries as was the case of Portugal. The hospital where I worked even started suspending the salary of those who travelled. Curiously, wearing masks in closed spaces was only implemented in the last couple of months. How was your work affected by the pandemic, if at all? Unfortunately, my work was affected. The laboratory that I frequented is inside a hospital, where contact with patients and medical care professionals is unavoidable, and so the measures applied were stricter. For a bit more than two months studies not related to COVID-19 were suspended. I honestly felt quite fortunate in the middle of this situation. I was granted permission to finish an ongoing mouse experiment and I was included in a small COVID-19 study (an obviously relevant topic and a great reason to leave the house!). After that period, the lab opened at a 25% capacity. Again, I was lucky because the PhD students that had limited time left had priority when booking

Did you start any new hobbies? If yes, tell which one(s)? After two weeks at home, I felt the relevance of the expression “Sound mind in a sound body”. To keep myself accountable, my sister and I started exercising together while on videocall. I also bought some plants, but my green thumb remained underdeveloped. The plants have been adopted into better homes now.

Neighbours’ PhD defence lunch celebration. I do not remember the name, let’s just call it spicy goodness.

Did this pandemic bring something positive into your life? I got to know my wonderful neighbours better and taste their new and international recipes. I also learned a lot about myself. I now know that working from home is only efficient when scarcely used. Also, I need to up my pastel de nata making game! Even the small pastry from a shop in Estação de Oriente felt like heaven when I returned. ¤

Beach in Nijmegen. Social distance guaranteed. 10/10 would recommend. 7

ATG Newsletter 12 • December 2020

Bruno Fontinha 11th edition

Where do you live? Vienna, Austria. What restrictive measures did the country/ city you live in implement? All trade, schools, restaurants, bars, night clubs, theaters and cinemas are closed, all cultural indoor and outdoor events are canceled, full recommendation to work from home (if possible), a strict curfew during the entire day, only allowed to leave home to fulfill basic life needs (including food shopping and the necessary walk for fresh air) and travel to and from work, strict rules on how many people are allowed to mingle together, mandatory usage of face masks in closed spaces and public transportation.

our workforce. That “My work hasn’t been combined with a fully much affected by the implemented SOP, pandemic. We are now gives me and my living in our second colleagues the feeling that the situation can decreed lockdown and be better managed. our work routine has But all the meetings learned a lot since the with collaborators are first lockdown back now shifted to the in March. I continue virtual world, which causes a bit more of a to travel daily to work calendar organization and interact with my as compared with colleagues.” before. And we all wear masks all day during working hours. What have you been up to during the pandemic? Reading a lot, talking daily with friends (and missing them a lot!), long walks outside, cleaning the flat more than often and definitely eating more sweets than average. And the level of physical exercise also rose considerably. Did you start any new hobbies? If yes, tell which one(s)? No, I did not start any new hobbies.

Did this pandemic bring something positive into your life? Only the feeling that one should nurture friendships on a daily basis. Besides that, for me, this pandemic did not bring anything positive... I think that the level of social, economical and How was your work financial destruction that affected by the pandemic, “The global level of human empathy should it brought is something if at all? My work hasn’t be revisited and cherished more often. The super scary, super been much affected by sense of community and close relationships raging, and should be the pandemic. We are on everyone’s mind for now living in our second should be a priority. To have more respect for the years to come. The decreed lockdown and your neighbour. To treat this Earth in a totally global level of human our work routine has empathy should be different way as it has been treated.” learned a lot since the first revisited and cherished lockdown back in March. I more often. The sense continue to travel daily to work and interact with of community and close relationships should be a my colleagues. Our “remote” communications priority. To have more respect for your neighbour. stopped existing and home-office is just a terrible To treat this Earth in a totally different way as it memory from the past. We do have the luxury of has been treated. ¤ having the possibility to be weekly tested for the Sars-CoV-2 at our campus, which helps to manage rapidly the occurrence of any positive cases and also gives a sense of “comfort” and “security” to know about the epidemiological situation around 8

In a Pandemic World

Francisca Soares da Silva 19th edition

How was your work affected by the pandemic, if at all? I am in the final year of the PhD and we were finishing some experiments for the paper that would allow me to finally defend the thesis (Hurray!). Unfortunately, I wasn’t allowed to get into the lab and we had to stop all experimental work from March though June. From July onwards the people in the lab re-started the experiments slowly and eventually we finished what we needed for submission of the paper in September. So I guess that the major impact was on the submission of the paper that completely delayed my thesis submission. But thankfully all went well!

Where do you live? Paris, France. What restrictive measures did the country/ city you live in implement? When COVID cases started to increase in Paris in the beginning/ middle of March, Pasteur Institute asked everyone to do a 2-week preventive quarantine at home. In the morning of March 16, I woke up ready to spend 2 weeks self-isolating in the room of the student residence I was staying. In the same morning, we started receiving e-mails from the director of the house informing us that the borders would be closing in 2 days, there would be a city lockdown and advising everyone to return to their home country. In that same morning, Pasteur Institute sent an e-mail that prevented international students from entering the campus (that included me!). No one knew how long this lockdown would last, neither when international students would be allowed to enter the Pasteur campus again. So that same morning, I booked flights to get back to Portugal before borders would close and flights were cancelled. After March 17th, Paris went through a complete lockdown, with research institutions closing completely, with the exception of the teams working with COVID.

What is the current situation? Currently, the city is in total lockdown, with the exception that those who cannot perform telework, can still go to work. Pasteur institute prioritised access to the campus to PhD students and post-docs, so it really did not affect my work this time around. What have you been up to during the pandemic? The pandemic was good for “computer work”: analysing data, writing review articles, writing the thesis; but also for taking time for myself and just do yoga, exercise and cook.. cook a lot... Did you start any new hobbies? If yes, tell which one(s)? I did not start new hobbies but I spent more time doing the hobbies I already had: Yoga, exercising, cooking, photography. Did this pandemic bring something positive into your life? Sure, it made me understand how important our mental health is and made me more aware of the importance of our little daily pleasures. ¤ 9

ATG Newsletter 12 • December 2020

Iliona Wolfowicz 16th edition

Where do you live? Braga, Portugal.

told me about this “Luckily, I had the UK consultancy chance to spend the first company offering confinement period proposal writing for at my family house in the EIC accelerator the seaside and could program. They were looking for easily go for a short a grant writer at walk in nature. As I was that time and starting this new job as contacted Bebiana. consultant, I had a lot to She referred them learn. Those times were to me and after the first interview, probably the busiest I had March this year, I so far.” started with them as a consultant. This is a fully remote position where I have to manage clients, learn about their technologies, business/financial plans, and put all those aspects together in a proposal format.

What restrictive measures did the country/city you live in implement? The first confinement What is the current situation? Braga is considered felt very strict. We couldn’t red zone for covid. Wearing really go anywhere besides the “(...) March this year, I started with a mask became mandatory groceries. Nowadays, different them (EIC) as a consultant. This is everywhere, streets/outdoors rules apply depending on the a fully remote position where I have as well. As I understand, so far, status of each municipality. it has been disturbing the lack to manage clients, learn about their of resources and care for the How was your work affected technologies, business/financial most vulnerable. by the pandemic, if at all? plans, and put all those aspects Unexpectedly, this was a great together in a proposal format.” What have you been up to working phase. Right before during the pandemic? Luckily, the pandemic, I had decided to leave a project I had the chance to spend the first confinement in Madeira islands and was actively looking for a period at my family house in the seaside and new job as grant writer. I had done grant writing could easily go for a short walk in nature. As I was for Madeira, remotely, and this was something I starting this new job as a consultant, I had a lot to would like to continue doing. I shared this with learn. Those times were probably the busiest I had Bebiana Moura (GABBA 12th edition) and she so far. I was acquiring many new skills, including business and financials plus proving myself within the company. My first client was a food-tech with a platform to produce lab-grown steaks, and so I was reading a lot about cultivated meat and carbon-neutral ways for producing animal protein. Did you start any new hobbies? If yes, tell us which one(s)? Not really, but I could enjoy daily strolls by the sea and felt very appreciative of that. Throwing stone. Esposende. 10

Did this pandemic bring something positive into your life? Silent streets. It was great to have silent empty streets with absolutely no cars…! ¤

In a Pandemic World

Rita Gomes 19th edition

In those few times, I decided to bike instead of taking the public transport to reach the lab, and it felt so good!

Where do you live? Milan, Italy. What restrictive measures did the country/city you live in implement? As you might be aware, Italy and more specifically Milan was the center of the Covid-19 outbreak in Europe in March this year. At the time, as in many other places, the country went in total lockdown. For 2 months, we were locked at home, being able only to leave the house to buy groceries (with long waiting lines) or to go to the pharmacy. We had to bring with us a self-certification, justifying every movement, in case the police stopped us. When finally the lockdown was finished, people started to get back to their “normal” day life and trying to adapt to the new reality. Masks were mandatory not only in closed places but also in the streets. People were working in shifts, and the public transport was working only at 50% of capacity. Slowly, and with the numbers of infected people decreasing, the measures became less restrictive during summer.

Second attempt of homemade bread... first successful one! When the lockdown was finished, we started to work by shifts, but we were still not able to work at 100%. In my case, I needed buffy coats to isolate human monocytes, but this service was totally blocked for several months. When finally we were able to work with buffy coats or other fresh human samples, we had to perform all the experiments in a modified BSL2 Lab, where the Covid samples were also being prepped. Several of our experiments were extremely delayed. What is the current situation? With the beginning of the second wave of infection, new measures have been implemented in November. Milan was considered again as “red zone” and therefore, besides the curfew from 10pm to 5am, we had to carry again a self-certification to justify any movement (people were allowed to move from the house mainly to go to work or buy groceries). Movements between cities are forbidden, unless for work reasons.

How was your work affected by the pandemic, if at all? During the lockdown, I couldn’t work on the bench at all. The institute was open, but only few people were allowed to work. Mainly those people working directly with Covid-19 patient samples. I went to the lab only 2 or 3 times during this period, to help a friend. Biking from the lab during the lockdown.

Last weekend Milan was considered out of the “red zone”, and therefore we are allowed to move a little bit more and some shops are now reopening. 11

ATG Newsletter 12 â&#x20AC;˘ December 2020

What have you been up to during the pandemic? During the lockdown in March, I was luckily living with a friend. It made everything a little bit easier. We tried to have more Lab meetings, read papers we havenâ&#x20AC;&#x2122;t had time to before, etc. Did you start any new hobbies? If yes, tell which one(s)? I did not start new hobbies, but had more time to cook and exercise. We were all trying to maintain a little bit sane and healthy. A lot of bread, cakes or cookies were baked in our house, and a lot of new recipes were tested.

Lab meetings at home...

Enjoying sunsets from the balcony! Did this pandemic bring something positive into your life? It made me see that even after a long time far away, people still remembered and cared about me. I received messages and calls from people I was not expecting at all. I would say that the distance and the lack of social contact made people more prone to interact, talk and think about their relationships with others. Â¤

It would be great to count on you for the next ATG Newsletter We know your time is short, but we are sure you can spare some of it to help us. Email mafaldamcazevedo@gmail.com to send any comments you might have, to suggest a topic for the next newsletter, if you want to be interviewed or to actively participate in creating the newsletter. All help is welcome and appreciated!

ATG (All Time GABBAs) is a non-profit organization gathering previous and current students of GABBA, as well as professors involved with the program and all who had or have a relationship with GABBA. ATG was created to develop a community spirit expressed in the sentence “once a GABBA always a GABBA”, where responsibilities should be shared and an active team effort should be in action to foster the program growth and ultimately benefit all members.

Are you an ATG member? The ATG membership fee is currently set at 20 euros per year. Fill out this membership form at www.atg.up.pt, pay the fee and send us your payment confirmation along with the form.

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We are deeply grateful for your contribution! The more, the merrier! 13

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!

ATG Newsletter 12 • December 2020

Part I. Citizens - Efforts to tackle a Global Pandemic Marta Madureira Name: Manuel Vicente GABBA Edition: 21st Edition PhD Thesis: Dynamics and functions of N-glycans in T cell development Current location: i3S - Porto This ATG Newsletter is focused on the global pandemic of Covid-19. In this Edition of Citizens, we want to get to know some Dream vacation: Snorkeling and sailing in the Phi Phi of the GABBAs that volunteered their time islands to Covid-related efforts. How did you get involved? Why did you make that decision? Favourite non-Portuguese cuisine: Chinese Friday the 13th of March was the day the TV show that you binge-watched recently: The Last Dance pandemic hit me. My research institute announced that it would close and the Best thing you’ve done during lockdown: Indoor gardening portuguese government imposed the confinement of the population in that Worst thing you’ve done during lockdown: Overeating weekend. By Monday, I was home thinking First thing you will do as soon as the covid pandemic about the potential of this pandemic, both in is behind us: Visit my family in Macau the global population and in my life. Pipet tip box usage method (in order, the ones in The Chinese word for “crisis” is composed by same area or random): As random as it gets two main concepts, “danger” and “change Friday night drink (do we even have Fridays point”. The idea that I could take a humane anymore?): Home-made margaritas part in the resolution of the pandemic, to drive, in my scale, a “change point” away from “danger”, was all I could think about. I thought of 3 ways I could make a difference: practicing social and hygienic distancing (“reachable” to any human), 3D printing protective gear (“reachable” to any human that owns a 3D printer) and volunteer in the diagnosis taskforce in my institute (“reachable” to any human with P2 biosafety training). Afterwards, there was the opportunity in the group I am in, to participate in a funded COVID19-related research project, which I saw as the perfect 4th parallel effort for me to embrace. Favourite Sunday activity: Movie and a blanket or a drive near the sea

Could you briefly explain the Covid-related projects where you were a volunteer? Are there any new developments you would like to highlight from those projects? I volunteered in a diagnosis taskforce that i3S created, where I essentially was doing one of the steps of sample viral inactivation. The research project is related to peripheral immune features, detected at diagnosis, that can provide insights on the initial response to infection. After 16

Part I. Citizens

a longitudinal analysis, we were able to detect some variables with prognostic potential. What would you hope could be achieved using the output/data generated from the research that you have helped produce? Given the timing of sample collection, near the infectious event, the initial immune response to a danger signal was something I found extremely interesting and I hope the results generated bring more knowledge to peripheral immune behaviour. Moreover, I would be extremely proud if the prognostic predictive variables found would help patient care and hospital resources management. In your experience, was there anything more the scientific community could have done to help fight this crisis? The efforts done by the scientific community were unprecedented. I truly believe that all was done in the best way possible. The only thought that comes to mind would be a better communication of scientific knowledge regarding the pandemic to the general public. ¤

Name: Pedro Beltrão GABBA Edition: 6th Edition PhD Thesis: Computational tools for the study of cellular networks Current location: European Bioinformatics Institute – Cambridge UK Favourite Sunday activity: Taking our 2 year old daughter to the park Dream vacation: Exploring a new country, jumping from place to place every few days Favourite non-Portuguese cuisine: Sushi TV show that you binge-watched recently: Queen’s Gambit Best thing you’ve done during lockdown: Spent more time with my daughter Worst thing you’ve done during lockdown: Stressed out for about not being able to work at home efficiently First thing you will do as soon as the covid pandemic is behind us: Probably a long vacation somewhere Pipet tip box usage method (in order, the ones in same area or random): There would probably be a robot involved and it would likely be all tips in one go Friday night drink (do we even have Fridays anymore?): Decaf with some chocolate at home after the little one falls asleep

This ATG Newsletter is focused on the global pandemic Covid-19. In this Edition of Citizens, we want to get to know some of the GABBAs that volunteered their time to Covid-related efforts. How did you get involved? Why did you make that decision? I supervise a research group doing primarily computational work. When we started to work from home and the situation in Italy in particular was becoming clearly catastrophic, I decided that our research group could contribute to help find potential drug treatments. I emailed a few other groups that I though could be already working on this and offered assistance. This is when our group joined an international consortium that was trying to find potential human targeting drugs that could reduce viral proliferation and ideally would be already in the clinic for some other purpose. 17

ATG Newsletter 12 • December 2020

Could you briefly explain the Covid-related projects you were involved in? Are there any new developments you would like to highlight from those projects? My research group has now been involved in 4 research projects, 3 of these are published and 1 is currently under review. All of these projects have the same objective: to understand how the virus takes over the target cell, find the human proteins that are needed for the virus to work and identify drugs that can counteract the infection by changing the function of these human proteins. These projects have involved over 200 scientists from all over the world and the main tasks from our group have been the computational analysis of the data. To give examples, in one project the viral proteins were pulled-down to find the human proteins that physically interact with the virus (Gordon et al. Nature 2020) and in another project we tracked the changes in protein phosphorylation along the time course of infection to find kinases required for viral proliferation (Bouhaddou et al. Cell 2020). What would you hope could be achieved using the output/data generated from the research that you have helped produce? The aim is really to find drugs that target human proteins that can reduce viral proliferation that could be followed up in clinical trials. From the different projects we have found over 30 drugs that reduce viral proliferation in cell based models. From these we think around 10 are now being followed up in clinical trials for safety and efficacy. Not all of these have necessarily directly started because of our studies but some were driven by our findings. We all hope that additional treatment options are not needed but even if the vaccines are very successful it will be useful to have additional drugs that can have some effect for those patients that still get ill. In your experience, was there anything more the scientific community could have done to help fight this crisis? Honestly, I think it is hard to ask for more from either the scientific or medical communities. Having been a part of some of the molecular studies I have been living a scientific roller-coaster with research happening at what feels like science fiction speed. Each of our published projects has compressed something like 3 to 4 years of work into 3 months and this is all due to hundreds of scientists stopping what they were doing to focus on this one single thing for a span of several months. Channelling these resources has been an unbelievable experience and I hope we will all learn to be more collaborative once this is all over. There has been some overlap in efforts at all levels (e.g. multiple vaccines, many repeated molecular experiments and drug screens, etc) but I think this is a good thing. It would have been impossible to try to coordinate this much science from the top down. Instead, several funding agencies allowed their grantees some freedom with their grants or quickly allocated emergency funds to free up more scientific resources in a way that was not too restrictive. I think we will look back at this period of time and be very proud of how the scientific community dealt with this crisis What disappoints me is that politicians appear on TV flanked by scientists and we keep hearing on the news how science is the light at the end of the tunnel, but we still don’t get the increase in science funding that we would expect to see. If governments don’t increase science funding now, when will they? ¤

Part II. Knowledge

Part II. Knowledge Telmo Catarino & Ana Rita Araújo

e are proud to share the great scientific contributions of the GABBA students and alumni, since the last newsletter. Among the list of publications, there are several articles that were published in prestigious high impact journals (original publications as first or last author) that we will highlight here. SARS-CoV-2

Pedro Beltrão and his collaborator Nevan Krogan recently coordinated two studies about SARSCoV-2 and its interaction with human proteins. In one of the studies, published by Science, they were able to map the interactions between host and virus proteins for SARS-CoV-2 and related viruses (SARS-CoV-1 and MERS-CoV), and in Cell, they showed that SARS-CoV-2 infection leads to a dramatic rewiring of phosphorylation, in both human and viral proteins. These studies highlight molecular mechanisms and potential drug treatments, which can be relevant as COVID-19 therapies. Pedro is from the 6th edition of GABBA and is currently a group leader at EMBL-EBI. Gordon, D. E., Hiatt, J., Bouhaddou, M., Rezelj, V. V, Ulferts, S., Braberg, H., … Beltrao, P., & Krogan, N. J. (2020). Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science (New York, N.Y.).

Bouhaddou, M., Memon, D., Meyer, B., White, K. M., Rezelj, V. V, Correa Marrero, M., … Beltrao, P., & Krogan, N. J. (2020). The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell, 182(3), 685712.e19.

ATG Newsletter 12 • December 2020

Immunology

Nuno Alves is from GABBA 4th and runs his own group at i3S. He and his team have recently developed a method to segment a subset of Autoimmune regulator+ (Aire) medullary thymic epithelial cells (mTECs) - mTEChi - taking advantage of the expression of CD24 and Sca1 markers, which was published by European Journal of Immunology. By transcriptomic analysis, they confirmed that the populations identified based on these markers mirrored the specific genetic programs of early-, late- and post-Aire mTECs, providing a new and simple approach to study late stages of mTEC differentiation. Ferreirinha, P., Ribeiro, C., Morimoto, J., Landry, J. J. M., Matsumoto, M., Meireles, C., … Alves, N. L. (2020). A novel method to identify Post-Aire stages of medullary thymic epithelial cell differentiation. European Journal of Immunology.

White, L. A., Siva-Jothy, J. A., Craft, M. E., & Vale, P. F. (2020). Genotype and sexbased host variation in behaviour and susceptibility drives population disease dynamics. Proceedings. Biological Sciences, 287(1938), 20201653.

Perro, M., Iannacone, M., von Andrian, U. H., & Peixoto, A. (2020). Role of LFA-1 integrin in the control of a lymphocytic choriomeningitis virus (LCMV) infection. Virulence, 11(1), 1640–1655

Oncobiology Carmen Jerónimo is from the 2nd edition of GABBA and is currently the head of Cancer Biology & Epigenetics Group at IPO, Porto. Recently, Carmen and her group tackled the urgent need to discover novel treatment options for patients with testicular germ cell tumors, which are resistant to standard chemotherapy. They discovered two new compounds that inhibit histone deacetylases and were effective in reducing tumor cell viability, by decreasing cell proliferation and increasing cell death. These results are promising and will improve the care of germ cell tumor patients. 20

Part II. Knowledge

Lobo, J., Guimarães-Teixeira, C., Barros-Silva, D., Miranda-Gonçalves, V., Camilo, V., Guimarães, R., … Jerónimo, C. (2020). Efficacy of HDAC Inhibitors Belinostat and Panobinostat against CisplatinSensitive and Cisplatin-Resistant Testicular Germ Cell Tumors. Cancers, 12(10).

Arantes, L. M. R. B., Cruvinel-Carloni, A., de Carvalho, A. C., Sorroche, B. P., Carvalho, A. L., Scapulatempo-Neto, C., & Reis, R. M. (2020). TERT Promoter Mutation C228T Increases Risk for Tumor Recurrence and Death in Head and Neck Cancer Patients. Frontiers in Oncology, 10, 1275.

Leal, L. F., Laus, A. C., Cavagna, R., de Paula, F. E., de Oliveira, M. A., Ribeiro, D. M., … Reis, R. M. (2020). EGF+61 A>G polymorphism does not predict response to first-generation EGFR tyrosine kinase inhibitors in lung cancer patients. Thoracic Cancer, 11(10), 2987–2992.

Pinto, F., Costa, Â. M., Andrade, R. P., & Reis, R. M. (2020). Brachyury Is Associated with Glioma Differentiation and Response to Temozolomide. Neurotherapeutics: The Journal of the American Society for Experimental NeuroTherapeutics.

Physiology and Cell Biology Pedro Carvalho is a 3rd edition alumnus and is the EP Abraham Professor of Cell Biology at the University of Oxford and established his lab at the Sir William Dunn School of Pathology. Recently Pedro and his team identified a new branch of endoplasmic reticulum-associated degradation (ERAD) that is required for quality control of a subset of membrane proteins. Using a combination of biochemical and mass spectrometry approaches they compared the degradation of two shortlived ER proteins, and identified an ERAD complex composed of RNF185, TMUBs, and Membralin, a membrane protein essential to neuronal function. These results revealed that ERAD branches have remarkable specificity for their membrane substrates, suggesting that multiple determinants are involved in substrate selection.

ATG Newsletter 12 • December 2020

van de Weijer, M. L., Krshnan, L., Liberatori, S., Guerrero, E. N., Robson-Tull, J., Hahn, L., … Carvalho, P. (2020). Quality Control of ER Membrane Proteins by the RNF185/ Membralin Ubiquitin Ligase Complex. Molecular Cell, 79(5), 768-781.e7. Valente, R., Alves, L. Q., Nabais, M., Alves, F., Sousa-Pinto, I., Ruivo, R., & Castro, L. F. C. (2020). Convergent Cortistatin losses parallel modifications in circadian rhythmicity and energy homeostasis in Cetacea and other mammalian lineages. Genomics. Leite, J., Chan, F.-Y., Osório, D. S., Saramago, J., Sobral, A. F., Silva, A. M., … Carvalho, A. X. (2020). Equatorial Non-muscle Myosin II and Plastin Cooperate to Align and Compact F-actin Bundles in the Cytokinetic Ring. Frontiers in Cell and Developmental Biology, 8, 573393. Bessa-Gonçalves, M., Silva, A. M., Brás, J. P., Helmholz, H., Luthringer-Feyerabend, B. J. C., Willumeit-Römer, R., … Santos, S. G. (2020). Fibrinogen and magnesium combination biomaterials modulate macrophage phenotype, NF-kB signaling and crosstalk with mesenchymal stem/ stromal cells. Acta Biomaterialia, 114, 471–484.

Ventura, G., Moreira, S., Barros-Carvalho, A., Osswald, M., & Morais-de-Sá, E. (2020). Lgl cortical dynamics are independent of binding to the Scrib-Dlg complex but require Dlg-dependent restriction of aPKC. Development (Cambridge, England), 147(15). Cattaneo, P., Mukherjee, D., Spinozzi, S., Zhang, L., Larcher, V., Stallcup, W. B., … Guimarães-Camboa, N. (2020). Parallel Lineage-Tracing Studies Establish Fibroblasts as the Prevailing In Vivo Adipocyte Progenitor. Cell Reports, 30(2), 571-582.e2. Chen, A., Elia, N., Dunaiceva, J., Rudiger, A., Walder, B., & Bollen Pinto, B. (2020). Effect of ivabradine on major adverse cardiovascular events and mortality in critically ill patients: a systematic review and meta-analyses of randomised controlled trials with trial sequential analyses. British Journal of Anaesthesia, 124(6), 726–738. Maia, J., Batista, S., Couto, N., Gregório, A. C., Bodo, C., Elzanowska, J., … Costa-Silva, B. (2020). Employing Flow Cytometry to Extracellular Vesicles Sample Microvolume Analysis and Quality Control. Frontiers in Cell and Developmental Biology, 8, 593750.

Part II. Knowledge

Genetics and Gene expression

Margarida Cardoso-Moreira is from the 7th edition and will start her own group very soon at the Francis Crick Institute. In this work Margarida and her co-workers showed that there are associations between disease genes’ developmental profiles and clinical phenotypes. They also compared the similarity of spatiotemporal expression between human genes and their orthologs in rhesus macaque, mouse, rat, and rabbit and found out that organ temporal trajectory differences are common and include many disease genes. This work highlights the importance of choosing the adequate mammalian species to model the action of specific genes or processes in both healthy and pathological human organ development. Cardoso-Moreira, M., Sarropoulos, I., Velten, B., Mort, M., Cooper, D. N., Huber, W., & Kaessmann, H. (2020). Developmental Gene Expression Differences between Humans and Mammalian Models. Cell Reports, 33(4), 108308.

Klobučar, T., Kreibich, E., Krueger, F., Arez, M., Pólvora-Brandão, D., von Meyenn, F., … Teixeira da Rocha, S., & EckersleyMaslin, M. (2020). IMPLICON: an ultradeep sequencing method to uncover DNA methylation at imprinted regions. Nucleic Acids Research, 48(16), e92.

Neurosciences

Rui Costa, GABBA 2nd, is currently a group leader at Columbia University, NY, and has recently published a paper in Neuron. Using calcium imaging and optogenetics and submitting mice to a sequential decision task, he and his team reported that the anterior cingulate cortex (ACC) is able to predict the outcome of a given action and to monitor whether or not the predictions are correct. Their results show ACC as a central node for model-based control, with a particular role in the prediction of future outcomes in response to chosen actions. Akam, T., Rodrigues-Vaz, I., Marcelo, I., Zhang, X., Pereira, M., Oliveira, R. F., â&#x20AC;Ś Costa, R. M. (2020). The Anterior Cingulate Cortex Predicts Future States to Mediate ModelBased Action Selection. Neuron.

Margarido, A. S., Le Guen, L., Falco, A., Faure, S., Chauvet, N., & de Santa Barbara, P. (2020). PROX1 is a specific and dynamic marker of sacral neural crest cells in the chicken intestine. The Journal of Comparative Neurology, 528(5), 879â&#x20AC;&#x201C;889.

Would you like to showcase your scientific work or artistic skills in the next ATG newsletter? Email your submissions to mafaldamcazevedo@gmail.com along with a legend. You can submit as many images as you want. We accept all sorts of science-related images (not just microscopy). One of the submissions will be selected to be the cover of the next issue of this newsletter.

Be creative!

What can I be with a PhD in Biology? In collaboration with Chaperone

Pedro Resende, GABBA 11th, Co-Founder and Director at Chaperone Catarina Seabra, GABBA 16th, Business Developer at Chaperone

uring our academic career, we acquire many transferable skills that can be applied in different roles, such as analytical thinking, complex problem-solving, time management, leadership, and resilience. Being fully aware of these skills and aligning them with our interests and job options, is essential to a successful career exploration post-PhD. A PhD will open doors to a wide range of careers, here are a few of the most common examples: ¬ Academic paths (e.g. Research Assistant, Principle Investigator, Professor, Lab Manager, Grants Officer); ¬ Pharma / Biotech / Health industry (e.g. Medical Science Liaison, Scientist at different levels, Regulatory Affairs, Consultant, Market Access Specialist); ¬ Entrepreneurial or Business paths (e.g. CEO, Business Developer, Project Manager, Community Manager, Customer Success Manager, Data Scientist); ¬ Other creative paths (e.g. Policy Advisor, Science Communication Officer, Public Engagement, Science and/or Medical Writing).

can be provided by different people throughout our lives. As academics, we tend to think about our supervisors and mentors as the only people that can help us with our career. Although our supervisor and mentors should play an important role, other career specialists are very important actors, acting in an external and personalized manner, to help us develop career management skills. Who else, other than my supervisor or mentor, can help us?

¬ Career Advisors - Advisors have experience in achieving the goal or career you also want to achieve and will give you their insights (e.g. Professor, Senior Scientist, CEO, Consultant, Medical Science Liaison, Communication Specialist); ¬ Career Counselors or Career Development Specialists - These professionals have studies or official training in career guidance and will help you explore your strengths and interests, taking into account your career options; ¬ Career Coaches - Coaches have a coaching certification and are experienced in leading scientists to their career goals and excel at the highest level.

Myths about Career Development #1 Career development is planning a career change

How to plan my career? The importance of career management skills. Studies suggest that only a minority of academic researchers will stay in academia in the longterm1,2. The transition from academic research to roles outside Universities or Research Institutions is neither easy nor a fast process to do. Thus, we, scientists, must develop career management skills to navigate the current job market. Career support can be found in several formats and

#2 Career development is only for people starting their careers #3 Supervisors and Mentors are the only people that help us develop career management skills References 1. Royal Society (Great Britain). The scientific century. (Royal Society, 2010). 2. Kaminski, D. & Geisler, C. Survival Analysis of Faculty Retention in Science and Engineering by Gender. Science 335, 864–866 (2012).

How can Chaperone help you? At Chaperone (www.chaperone.online), we are developing the first online marketplace of personalized career development for scientists, with the mission to democratize access to high quality career development. In our platform, you can book online 1-to-1 sessions with experienced international career consultants (advisors, specialists and coaches), covering more than 50 career topics and many country-specific job markets. Our average user rating is 4.9 (out of 5 stars), and in just 8 months we have already supported scientists from 7 different countries, coming from prestigious institutions such as Karolinska Institutet or CERN.

Different areas of career development. Through Chaperone you can have access to career information, career advice, career counseling and career coaching.

Scientists who experienced our services mentioned they felt more empowered regarding their career management and revealed very positive changes in their well-being, productivity and also helped make job transitions more effectively. ATG - All Time GABBAs and Chaperone have recently signed a partnership. ATG members can benefit from a discount on online career development sessions by sending and email to alumnigabba@gmail.com.

ATG News

The lateste news, the most recent GABBA graduates and dates to keep in mind

Rosa Barreira da Silva, GABBA10th, was recently named STAT Wunderkind. The program searches for the next generation of scientific superstars and distinguishes the most impressive researchers at the beginning of their careers, among hundreds of nominations from across North America. Find out more about the work Rosa has been developing at Genentech here: https://www.statnews.com/wunderkinds/rosa-barreira-da-silva/

` Recent Graduates ¬ None since the last issue of the newsletter.

Dates to keep in mind

¬ January 1, 2021 to May 31, 2021 Application for Prémio Maria de Sousa Guidelines and Forms at www.ordemdosmedicos.pt and www.fundacaobial.com

¬ October 18, 2021

The school without walls by Maria de Sousa Tribute to Professor Maria de Sousa

At Biblioteca Almeida Garrett no Porto. In partnership with I3S, APBRF and Câmara do Porto. Email geral@atg.up.pt if you wish to join the organizing committee.

ATG - All Time GABBA The Alumni Association of the Graduate Program in Areas of Basic and Applied Biology University of Porto - Portugal

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