Gaia Pigino: Inside the cell

Gaia Pigino studies the molecular mechanisms and principles of self-organization in cilia using 3D cryo-EM.

Gaia Pigino was only 3 yr old when she became fascinated with nature in the beautiful countryside of Siena, Italy, where she grew up. The neighbor’s daughter showed her a hen in the chicken coop, and they caught it in the act of laying an egg. Gaia remembers, “This was for me almost a shock, as my experience about eggs was that they come directly out of paper boxes!” Her father was also an important part of awakening Gaia’s curiosity for the amazing things in nature. He used to bring home the award-winning magazine Airone, the Italian equivalent of National Geographic. Gaia never missed an issue; even before learning to read, she could spend hours looking at the captivating photos of the wildlife. She wanted to understand what she was seeing, and maybe because of that, she was determined to do science.Gaia Pigino. Photo courtesy of Human Technopole.Gaia took her first “scientific” steps with Professor Fabio Bernini and Professor Claudio Leonzio at the University of Siena, where she studied bioindicators of soil contamination and detoxification strategies of soil arthropods as part of her PhD project. But it was later, when she joined the laboratory of Professor Pietro Lupetti and met Professor Joel Rosenbaum, a pioneer of cilia research, that Gaia discovered the world of 3D EM and felt her place was “inside a single cell.” She solidified her interest in the structure of protein complexes of cilia and flagella and boosted her passion for cryo-electron tomography (ET) in the laboratory of Professor Takashi Ishikawa, first at the ETH Zurich and then at the Paul Scherrer Institut in Switzerland. In 2012, Gaia started her own laboratory at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany, with the vision of creating a truly interdisciplinary laboratory. Her team combines techniques from different fields such as biophysics, cell biology, and structural biology to answer open questions in the cilia field. Gaia recently moved countries again—this time to take over the position of Associate Head of the Structural Biology Research Centre, at the Human Technopole, Milan, Italy.We reached out to Gaia to learn more about her scientific journey and future research directions.What interested you about cilia?The first thing that attracted me toward cilia and flagella were some EM micrographs, by Professor Romano Dallai in Siena, that showed the beautiful geometrical microtubular structures of sperm flagella. I was intrigued by the apparent perfection of these organelles that clearly showed me that a cell is a coordinated system of complex molecular machines, the mechanism of many of which we do not understand. Soon after, Professor Joel Rosenbaum introduced me to the bidirectional transport of components inside cilia, which, he explained to me, is required for both assembly and function of virtually all cilia and flagella, from the motile cilia in our lungs to the primary cilium in our kidneys. He called it intraflagellar transport (IFT) and compared it to a Paternoster elevator, where the individual cabins were what we now call IFT trains. I was completely fascinated by the IFT system, the structure, the function, the dynamics, and the mechanism of which were still largely unknown. Quickly, I realized that in addition to IFT, cilia represent a virtually infinite source of open biological questions waiting to be solved, from the mechanics and regulation of the beating to the sensory function of primary cilia, and their importance for human health.What are some of the scientific questions currently of interest in your laboratory?In the past few years, we have made substantial contributions to the current understanding of the structure and the mechanism of the IFT (1, 2, 3). Currently, we are investigating how the structure of IFT trains relates to their functions by looking, in cryo-electron tomography, at how anterograde trains transform into retrograde trains and at how different ciliary cargoes are loaded on the trains. Beside this more classical line of research, we are exploring other approaches to study IFT, for instance we have developed a method to reactivate IFT trains in vitro on reconstituted microtubules. We want to use this approach to investigate the behavior of IFT trains, and their motors, in experimentally controllable conditions, e.g., in the presence of only certain tubulin posttranslational modifications. We have also made interesting discoveries about the distribution of tubulin posttranslational modifications on the microtubule doublets of the axoneme and how this spatially defined tubulin code affects the function of different ciliary components. We hope we will be able to share these new “stories” with the structural and cell biology community very soon!What kind of approach do you bring to your work?I believe that the main reason for why science became an integral, and dominant, part of my life is because it provides infinite riddles and continuous challenges. I have always been curious about how things work in nature, but I quickly realized that learning from books didn’t satisfy me. My desire was to be at the frontline, to be among the ones that see things happening in front of their eyes, at the microscope, for the first time. I wanted to be among the ones that make the discoveries that students read about in textbooks. Thus, what I bring to my work is an endless desire of solving biological riddles, curiosity, creativity, determination, and energy, with which I hope to inspire the members of my team. My laboratory uses an interdisciplinary approach; we use whatever method, technique or technology is needed to reach our goal, from the most basic tool to the most sophisticated cryo-electron microscope. And if the method we need does not yet exist, we try to invent it.A young Gaia Pigino (3 yr old) the day she discovered how eggs are made. Photo courtesy of Giancarlo Pigino.Could you tell us a bit about the Structural Biology Research Centre at the Human Technopole (HT)?At the HT Structural Biology Centre, we are working to create a vibrant and interdisciplinary scientific environment that will attract molecular, structural, cell, and computational biologists from all over the world. We are creating fantastic facilities, including one of the most well equipped and advanced electron microscopy facilities in Europe—and likely the world—headed by Paolo Swuec. My team, together with the teams of my colleague Alessandro Vannini and the research group leaders Ana Casañal, Francesca Coscia, and Philipp Erdmann, already cover a vast range of competences and know-how from classical molecular and structural biology approaches, such as crystallography and protein biophysics, to cryo-CLEM, cryo-FIB SEM and cryo-ET, all of which allow us to address questions in cell biology. Our goal is to create a scientific infrastructure and culture that will enable biologists to obtain a continuum of structural and functional information across scales.What did you learn during your PhD and postdoc that helped prepare you for being a group leader? What were you unprepared for?I learned that everyday research is mostly made of failures, but that with the right amount of obsession, persistence, curiosity, and creativity, it is always possible to succeed and discover new things. Being given the freedom to develop your own ideas and your own project very early in your career is a treat; science is not only about having good ideas! One needs to follow up on these ideas with intense work and troubleshooting to make them reality. In addition, I realized that being fearless and attempting what is considered too difficult by others, despite challenges, can turn into a worthy learning experience. Also, how you present your work to the scientific community matters for swinging the odds of success in your favor. Different places might work in very different ways, and conducting good science does not only depend on you, but also on the possibilities given to you by your environment.What was I unprepared for?—I guess several things, but one comes immediately to mind: I underestimated how much being responsible not only for my own life and career, but also the career of students, postdocs, and others in the laboratory, would affect me personally.Structure of the 96-nm axonemal repeat reconstructed by cryo-ET and subtomogram averaging. Image courtesy of Gonzalo Alvarez Viar, Pigino Lab.What has been the biggest accomplishment in your career so far?This is a tricky question for me... I tend to look into the future more than celebrating the past. I fight to succeed in something, but as soon as I conquer it, I find it less of an achievement than the thing I could conquer next. Nevertheless, I am happy about the discoveries and the papers published together with my students and postdocs (1, 2, 3, 4, 5). I am extremely excited about the fact that after many years of work I am now leading an interdisciplinary laboratory, where we combine techniques from different fields. I am also happy that three times my husband and I were able to move from one world class academic institution to the another to start exciting and fitting jobs and could still live together in the same place. We worked hard for this, but we also got lucky.What has been the biggest challenge in your career so far?I studied French in school; I had almost no exposure to spoken English until the end of my PhD. To avoid having to show my English insufficiencies, I did hide beside the board of my poster at the first international conference I attended in 2004! It took me a while to overcome this barrier and feel confident to express my thoughts and ideas in English.What do you think you would be if you were not a scientist?I had been a good fencer during my youth. I was a member of the Italian National Team between ages 14 and 19 and saw quite a bit of the world, which was cool! When my sporting career failed, due to diabetes, I was torn between art and science. I guess that in a parallel universe, I am a wildlife photographer and a potter specialized in wood kiln firing. [Gaia confesses that she misses “the amazing and addictive adrenaline rush of a good fencing match!”]Any tips for a successful research career?Do not compare your performances to the ones of the people at your career stage; compare yourself with people that are already successful one level higher than you currently are at. For example, if you are a PhD student, ask yourself what in your current performance separates you from being a good postdoc—once a postdoc, what is missing to be a good PI.     

Elda Grabocka: Stress-buffering comes in granules

Elda Grabocka investigates the role of stress granules in obesity and cancer.

When one thinks of high school, sharing hallways with students from 80 different countries is not the usual image that springs to mind. This was indeed Elda Grabocka’s experience. She grew up in Pogradec, a remote town in Albania—her parents, both physicians, were assigned to this location by the state. Elda won one of the two spots available for Albanian students in a national competition to attend the United World College of the Adriatic in Trieste, Italy, a high school focused on social change that brings together students from around the globe to promote intercultural understanding. Elda still remembers, with a smile on her face, the first glimpse at the laboratories as the senior students were working on their thesis projects: “That was exactly what I wanted to do!” She barely spoke English at the time and had to catch up to the level of her peers, but her perseverance and passion prevailed, and she obtained the International Baccalaureate Diploma (IBD). For the independent study of the IBD program, she submitted a research project in chemistry, which ended up being an important learning and life lesson: “That helped me understand that I was more suited to biology! In hindsight, it was great to have that experience so early; I certainly had no awareness then how essential failing and then learning from your failures is to science, but having a level of comfort with it from the beginning was probably a bonus.”Elda Grabocka. Photo courtesy of Chris Hamilton Photography.But science was not the only professional option Elda contemplated—her volunteering experience with relief organizations in various refugee camps made her consider a career in public health and humanitarian relief efforts. She finally sought a PhD degree in molecular pharmacology and structural biology in the laboratory of Phil Wedegaertner at Thomas Jefferson University. After studying heterotrimeric G-proteins and how the subcellular localization of their exchange factors regulates function, Elda felt the need to seek greener pastures. She went on to do a postdoc on one of longest-studied oncogenes, RAS—her choice wasn’t motivated by the field, but by the mentor, Dafna Bar-Sagi. Elda’s admiration for Dafna is notable when she speaks about her time at the New York University Langone Medical Center: “It’s remarkable how many novel aspects of RAS biology that have shaped and then re-shaped our thinking about this oncogene have come out of her lab; I felt there was a depth and breadth to her approach to scientific research that if I could learn, I’d be able to see more of the angles, so to speak, ask better questions; she has really expanded my mind in all those aspects.” Elda’s work focused on the interplay between the mutated forms of RAS and the wild-type isoforms, which she and others have shown is context dependent, with the wild-type isoforms acting as both tumor suppressors and tumor promoters (1). While still in Dafna’s laboratory, Elda pursued a more independent scientific interest: the role of stress granules in mutant KRAS cells. In 2016, Elda returned to her alma mater, joining the Department of Cancer Biology at the Sidney Kimmel Cancer Center at Jefferson as an assistant professor, with stress granules in cancer as the focus of her laboratory. We contacted her to learn more about her research journey.What interested you about stress granules and their connection with obesity and cancer?I became interested in stress granules and their potential role in cancer early in my postdoc. I read a review by Stephen Elledge’s group where they described the “stress phenotype” of cancer as an important player in tumorigenesis. I realized that cancer cells exist mostly in a state of stress—for example, mutated genes, like oncogenic RAS, are potent inducers of many types of cellular stresses. I was working on a RAS ubiquitination project, and one of the candidates for a RAS de-ubiquitinating enzyme we were looking at was implicated in stress granule formation. Little was known about stress granules at the time—they are induced by types of stresses associated with tumors (hypoxia, oxidative stress, osmotic pressure, proteotoxic stress, metabolic stress, etc.), so the question I asked was whether stress granules could function as a stress coping/adaptation mechanism in cancer. Indeed, I found that stress granules are prevalent in tissues from patients with pancreatic cancer and mouse models of pancreatic cancer. Remarkably, not all cancer cells are the same in their capacity to form stress granules—all cells will make stress granules under stress, but KRAS mutant cancer cells have a heightened ability to do so because signaling from mutant KRAS enhances the levels of a critical molecule to stress granule formation, 15-deoxy-prostaglandin J2 (2). This enhanced capacity to make stress granules, in turn, renders KRAS mutant cells more resistant to stress and more dependent on stress granules; inhibition of stress granules leads to increased cell death in KRAS mutant versus KRAS wild-type cancer cells.Immunofluorescence staining of pancreatic ductal adenocarcinoma tissue showing cancer cells in red, stress granules in green, and nuclei in blue. Image courtesy of the Grabocka laboratory.The work establishing this dependence was in vitro, so the primary goal when I started my laboratory was to determine their relevance in tumorigenesis, which led me to explore their connection to obesity and cancer for several reasons. First, obesity is a major predisposing factor for several cancers, including pancreatic and colon, which are prevalent KRAS-driven cancers for which treatment options are limited. Second, obesity is a complex pathology which likely impacts the pathobiology, the therapy response, and even the evolution of cancers that arise in this setting. Given that cell stress and inflammation are key features in obesity, this would make the ideal background to study the contribution of stress granules in tumorigenesis. I think this pre-existing stress [obesity] might necessitate the engagement of stress adaptive mechanisms from the early stages of tumorigenesis and may also lead to a high dependence on these processes.What are you currently working on, and what is up next for you?It’s a very exciting time to be working on stress granules! The field has grown significantly over the past 10 yr or so, especially with the renewed interest in phase separation. As organelles that form via phase separation when a cell is under stress, stress granules are perhaps one of the best examples of phase separation in vivo and a great platform to understand its relevance. The recent advances in defining the composition, as well as key molecular drivers and their functional domains in stress granule assembly, have been of great benefit. We are now better positioned to define the stress granule–specific functions in health and disease. Because stress granules are induced by various types of stresses, they could function as a pan-stress adaptation mechanism in cancer. This is a very appealing angle, as if we can solve how stress granules enable stress adaptation, which is a major focus of my laboratory, we could have better anti-cancer therapies.The composition of stress granules, comprising hundreds of proteins and mRNAs involved in several aspects of cell biology, prompted me to ask whether cytoprotection under stress is their main and/or only function. What other cellular processes stress granules regulate, whether these vary with the type of stress, and how such processes are integrated into the stress response of cancer cells are burning questions we are currently working on, as the answers will advance our understanding of the role of stress granules in cancer. The “chronic stress” of cancer is heterogenous in both spatial and temporal terms, as well as in the type of stress and intensity. I am also very curious to see if and how heterogeneity in stress stimuli impact the composition of stress granules and the processes they regulate, and how this may affect tumor evolution. Also, cancer cells are not the only cells in the tumor that make stress granules. As a matter of fact, we reported that KRAS mutant cells can stimulate stress granule formation in a paracrine manner. An ongoing project in the laboratory that I’m very excited about is focused on understanding the contribution of stress granules to the pro-tumorigenic microenvironment.What kind of approach do you bring to your work?My approach is very hypothesis and observation driven; the latter in the sense that it can often be that initial spark that inspires an idea, draws connections, and looks for context and meaning. I also find that sometimes the answer to my next question or the question I don’t know to ask yet is hidden right in front of my eyes, so paying careful attention to the data is key. It is also where objective and critical evaluation of experimental results starts. There’s one line that’s firmly ingrained in my mind from my postdoctoral training, which is “Science is self-correcting.” It’s a note of caution that if you don’t pay attention and see only what you want to see, it will still eventually prove you wrong, and you’d have wasted a lot of time in the process. So I try to minimize that waste as much as possible—unavoidable entirely, having a favorite hypothesis is part of the scientific thinking process, but crucial to remember to follow the data and not just convince yourself.What has been the biggest accomplishment in your career so far?I’m still quite early in my career to start listing accomplishments. I feel privileged to do the work I do; I essentially get funded to pursue ideas that I find interesting. So I have a hard time with this question because it has a hint of pride, and when you start adding pride to privilege, as a junior principal investigator especially, it gets a bit too self-serving. I hope that the work we are doing stands the test of time and leads to or helps lead to a meaningful impact on patients’ lives—that would be a great accomplishment.What has been the biggest challenge in your career so far?The past two years of COVID have certainly been a different reality, and a constantly shifting one at that. From a career perspective, so much of a scientific career happens at the bench: experiments happen at the bench, we train at the bench, animal work is long and requires multiple dedicated essential personnel and facilities, so inevitably, remote work, or shift work, limited occupancy, and the shortages we are now seeing in the supply chain have been a major challenge for everyone. I do think junior laboratories like mine experience that a bit harder. The bandwidth to absorb these challenges is much smaller if you’re just starting out, or if you’ve had a laboratory for a couple of years and are just ramping up. I must say though that it has made for stronger teamwork in the laboratory, and we’ve had to be really focused and efficient—so there’s an upside!Out for a paddle. Photo courtesy of Elda Grabocka.Any tips for a successful research career?Hard to say, because certainly it means different things to different people. The only tip I would give perhaps is to define what that means, what that success looks like for oneself, and be true to that. I expect how each one defines it also changes with time and experience, but I do think it’s very important to identify what success means as early as possible and let that be what you measure your efforts against. It’s easy to get distracted, overwhelmed, or even disheartened otherwise. My own definition is quite simple: success is doing what I love to do, working toward answering a meaningful scientific question, and enabling/supporting my trainees to reach their potential—keeping that in mind has been very important and helpful.     

Zooming in on the cell biology of disease

Today’s cell biology could be considered a fusion of disciplines that blends advanced genetics, molecular biology, biochemistry, and engineering to answer fundamental as well as medically relevant scientific questions. Accordingly, our understanding of diseases is greatly aided by an existing vast knowledge base of fundamental cell biology. Gunter Blobel captured this concept when he said, “the tremendous acquisition of basic knowledge will allow a much more rational treatment of cancer, viral infection, degenerative disease and mental disease.” In other words, without cell biology can we truly understand, prevent, or effectively treat a disease?

R. M. Perera     

Dr. Manners

Good manners make a difference—in science and elsewhere. This includes our social media etiquette as researchers. Subject Categories: S&S: History & Philosophy of Science, Methods & Resources, S&S: Ethics

Elbows off the table, please. Don’t chew with your mouth open. Don’t blow your nose at the table. Don’t put your feet up on the chair or table. And please, do not yuck my yum. These are basic table manners that have come up at some of our lab meals, and I have often wondered if it was my job to teach my trainees social graces. A good fellow scientist and friend of mine once told me it was absolutely our place as mentors to teach our trainees not only how to do science well, but also how to be well‐mannered humans. While these Emily Post‐approved table manners might seem old‐fashioned (I’m guessing some readers will have to look up Emily Post), I strongly believe they still hold a place in modern society; being in good company never goes out of style.Speaking of modern society: upon encouragement by several of my scientist friends, I joined Twitter in 2016. My motivation was mainly to hear about pre‐prints and publications, conference announcements and relevant news, science or otherwise. I also follow people who just make me laugh (I highly recommend @ConanOBrien or @dog_rates). I (re)tweet job openings, conference announcements, and interesting new data. Occasionally, I post photos from conferences, or random science‐related art. I also appreciate the sense of community that social media brings to the table. However, social media is a venue where I have also seen manners go to die. Rapidly.It is really shocking to read what some people feel perfectly comfortable tweeting. While most of us can agree that foul language and highly offensive opinions are generally considered distasteful, there are other, subtler but nonetheless equally—if not more—cringe‐worthy offenses online when I am fairly certain these people would never utter such words in real life. In the era of pandemic, the existence of people tweeting about not being able to eat at their favorite restaurant or travel to some destination holiday because of lockdown shows an egregious lack of self‐awareness. Sure it sucks to cancel a wedding due to COVID‐19, but do you need to moan to your followers—most of whom are likely total strangers—about it while other people have lost their jobs? If I had a nickel for every first‐world complaint I have seen on Twitter, I’d have retired a long time ago; although to be honest, I would do science for free. However, these examples pale in comparison with another type of tweeter: Reader, I submit to you, “the Humblebragger.”From the MacMillan Buzzword dictionary (via Google): a humblebrag is “a statement in which you pretend to be modest but which you are really using as a way of telling people about your success or achievements.” I would further translate this definition to indicate that humblebraggers are starved for attention. After joining Twitter, I quickly found many people using social media to announce how “humble and honored” they are for receiving grant or prize X, Y, or Z. In general, these are junior faculty who have perhaps not acquired the self‐awareness more senior scientists have. Perhaps the most off‐putting posts I have seen are from people who post photos of their NIH application priority scores right after study section, or their Notice of Awards (NOA). When did we ever, before social media, send little notes to each other—let alone to complete strangers—announcing our priority scores or NOAs? (Spoiler: NEVER)Some of you reading this opinion piece might have humblebragged at one or time or another, and might not understand why it is distasteful. Please let me explain. For every person who gets a fundable score, there are dozens more people who do not, and they are sad (I speak from many years of experience). While said fundable‐score person might be by someone we like—and I absolutely, positively wish them well—there are many more people who will feel lousy because they did not get funding from the same review round. When has anyone ever felt good about other people getting something that they, too, desire? I think as children, none of us liked the kid on the playground who ran around with the best new Toy of the Season. As adults, do we feel differently? Along these lines, I have never been a fan of “best poster/talk/abstract” prizes. Trainees should not be striving for these fleeting recognitions and should focus on doing the best science for Science’s sake; I really believe this competition process sets people up for life in a negative way—there, I’ve said it.Can your friends and colleagues tweet about your honors? Sure, why not, and by all means please let your well‐wishers honor you, and do thank them and graciously congratulate your trainees or colleagues for helping you to get there. But to post things yourself? Please. Don’t be surprised if you have been muted by many of your followers.It is notable that many of our most decorated scientists are not on Twitter, or at least never tweet about their accomplishments. I do not recall ever seeing a single Nobel laureate announce how humbled and honored they are about their prize. Of course, I might be wrong, but I am willing to bet the numbers are much lower than what I have observed for junior faculty. True humility will never be demonstrated by announcing your achievements to your social media followers, and I believe humblebragging reveals insecurity more than anything. I hope that many more of us can follow the lead of our top scientists both in creativity, rigor, and social media politeness.     

A Tale of Mother and Daughter

Loving science and nature and being a scientist can be very different, yet the two are so intertwined in a scientist''s life that you will certainly experience both aspects. This essay presents my perspective on how, as one who loves science and nature, I came to fall in love with centrosome behavior in stem cells and how I came to run a lab as a scientist. When I started, there was a big gap between my love for science and my experience as a scientist. I filled this gap by learning a “laid-back confidence.”Before the beauty of cell biology (or whatever you love), who you are (i.e., your age, gender, or race) is immaterial. Yet history shows that the ease with which you can pursue science is influenced by who you are. This has certainly been my experience. The key is to find a way to fill in the gap between who you are and what you are (i.e., a scientist), a goal in which we must all support each other. It is my hope that this essay will convey something helpful to those who are at early stages of their career and might be encountering obstacles because of who they are.     

Ye Tian: Surveilling stress to live longer

Ye Tian investigates how mitochondrial stress signaling pathways regulate longevity using C. elegans as a model system.

An avid reader, Ye Tian used to save up her child allowance with the sole purpose of buying science fiction books. Reading and solving mathematical problems were her favorite hobbies; indeed, she liked mathematics so much that she was about to enroll herself as an architecture major but finally chose biotechnology. Ye moved from her hometown in the Northwest of China, Baoji—famous for housing the Zhou dynasty’s bronzeware and being close to the Terracotta Army—to Beijing for her college and graduate studies.Ye is proud of being among the earliest researchers working on Caenorhabditis elegans in her country; for her PhD studies, she joined the lab of Hong Zhang, who at that time has just established the first C. elegans lab in China at the National Institute of Biological Sciences in Beijing. Ye identified epg-2 as an adaptor for cargo recognition during autophagy. In 2010, she crossed the Pacific toward the U.S. West Coast for her postdoctoral training in the aging field with Andrew Dillin, first at the Salk Institute in San Diego and then at the University of California, Berkeley. There, she discovered that mild mitochondrial stress during development in worms rewires their chromatin landscape to establish specific gene expression patterns throughout the lifespan and promote longevity.Ye Tian. Photo courtesy of Ye Tian.Ye came back to China at the end of 2016 to start her own lab at the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences. Her research team studies mitochondrial stress signaling pathways and their interplay with aging. We chatted with her to learn more about her next scientific plans.What interested you about the interplay between mitochondria and aging?I became interested in mitochondrial biology during my postdoc in Andrew Dillin’s lab. Since the origin of eukaryotic cells, mitochondria have been a driving force of evolution. During reproduction, mitochondria are passed from the mother to the offspring through egg cells and they exhibit a unique inheritance pattern. As essential hubs that dictate cellular metabolism, it is clear now that mitochondria and the nucleus maintain a bidirectional communication. Early life “stressed” mitochondria communicate with the nucleus to induce gene expression changes that are beneficial on longevity and persist throughout the lifespan. The fact that mitochondrial function is crucial to aging fascinated me; I wanted to continue exploring that topic further, and that’s why I established my lab around the question of how mitochondrial surveillance mechanisms regulate the aging process.What are you currently working on? What is up next for you?My research team focuses on the interplay between mitochondrial stress signaling pathways and aging. The first work that my lab published was a project that I started during my postdoc. The Dillin lab reported a phenomenon in which perturbations of mitochondria in neurons induced a mitochondrial stress response in the peripheral tissues and hypothesized that a secreted signal molecule, named after mitokine, is required for the cell non-autonomous regulation (1). The identity of this molecular signal remained elusive for almost ten years until we found that a secreted Wnt ligand, EGL-20, functions as the mitokine to coordinate mitochondrial stress signaling across tissues and promote longevity of the organism (2). We are also interested in how the crosstalk between mitochondria and the nucleus influences lifespan. We found that mitochondrial perturbations alter the nuclear epigenome to induce longevity via the histone deacetylation complex NuRD in response to cellular acetyl-CoA levels, the key metabolite at the entry point of the Krebs cycle (3).Lab group picture; current lab members (2021). Photo courtesy of Ye Tian.Our latest work stemmed from a serendipitous observation that neuronal mitochondrial stress is sensed by and transmitted through the mitochondria in the germline. Intergenerational, maternal inheritance of elevated levels of mitochondrial DNA via the mitokine Wnt/EGL-20, which causes the activation of the mitochondrial unfolded protein response (UPR^mt), provides descendants with a greater tolerance to environmental stress. This makes the offspring live longer (4).Among our short-term scientific plans, we’re determining how mitochondria functions during the aging process at both the genetic and biochemical levels and searching for ways to apply our findings from C. elegans to neurodegenerative disease models in mammals.What kind of approach do you bring to your work?The curiosity about how things work drives me; what I enjoy the most is when I see things happening in front of my eyes and when I figure out why they occur that way. That enthusiasm is what I try to spread to my team every day. In the lab, we rely on C. elegans as our model system and on genetics to dissect complex biological processes like aging. We have also adapted modern biochemical and imaging techniques as well as bioinformatics to complement our genetic studies. I’m a geneticist at heart, and I like to initiate a project with a well-designed genetic screen. The best part is that the screen often leads me to answers I was not expecting, and that’s genuinely inspiring!What did you learn during your PhD and postdoc that helped prepare you for being a group leader? What were you unprepared for?Like most scientists, my research career has gone through ups and downs. I had to change my research project in the last year of my graduate school; that was nerve-racking, but I eventually managed to redirect my thesis and get exciting results under time pressure, thanks in large to the support of my parents, mentors, and lab mates. That helped me prepare to become a principal investigator; I gained confidence in problem solving, and since I’ve experienced the stress of dealing with last-minute scope changes firsthand, I connect better with my students.I guess, as many other non-native English speakers, I wasn’t prepared for writing grants and papers fluently in English. This issue wasn’t obvious during my graduate and postdoctoral studies, as my mentors were always there for me and proofread and edited my writing. Now I have to stand up for myself. I spend most of my time writing; I’ve improved my writing skills but it’s still an ongoing process.Reconstruction of the nerve system of C. elegans by confocal microscopy. Green corresponds to YFP-labeled neuronal specific marker Q40, and red labels germline specific mitochondrial outer membrane protein TOMM-20::mkate2. Image courtesy of Ye Tian’s lab.What has been the biggest accomplishment in your career so far?My very first PhD student, Qian Zhang, graduated with two first-author papers and decided to pursue a research career in academia. Being responsible for someone else’s career is challenging but also rewarding.What has been the biggest challenge in your career so far?I use the model organism C. elegans for my research in aging, so from time to time, peers criticize the relevance of my work to human health. I’m used to justifying my scientific approach to funding agencies and peers in other fields, but sometimes it’s exhausting or not pleasant.Who were your key influences early in your career?My PhD mentor, Hong Zhang. He is very passionate about the science he does, and he is courageous to shift his research directions to answer new biological questions.What is the best advice you have been given?I think the best advice I’ve gotten is that “tomorrow is another day.” It reminds me to keep going and be optimistic.What hobbies do you have?I love art and music. When I was in San Diego, I used to play in the Chinese Music Band; I miss my musician friends over there. In my teens, I used to hike mountainside trails along the river with my parents. Now, running has become my new favorite hobby. I enjoy the tranquility and peace of mind while running; it’s soothing.     

In conversation with the Chief Editor

An interview with Facundo D Batista, The EMBO Journal new Editor‐in‐Chief.

An interview with Facundo D. Batista, The EMBO Journal new Chief Editor. Facundo D. Batista has shaped our understanding of the molecular and cellular biology of B‐cell activation. In 2016, he relocated his lab to Massachusetts General Hospital/M.I.T./Harvard’s Ragon Institute to explore the translational potential of two decades of basic research in B‐cell biology. The interview was conducted by Thiago Carvalho. Thiago Carvalho (TC): What inspired you to pursue a career in science? Facundo D Batista (FDB): I was very inspired by my undergraduate course on molecular biology at the University of Buenos Aires. The course was given for the first time, and we were taught the basic techniques of handling DNA, producing insulin, and so forth. Two professors in the course, Daniel Goldstein and Alberto Kornblihtt, really primed us to open our horizons and encouraged training in centers of excellence abroad. I did not speak any English at all, and applying to graduate school in the United States and doing the GRE was impossible for me. I would not have passed. Then, an opportunity to go to Italy and get experience in institutes that could provide me with better training came up. If I recall correctly, we were the first generation of Argentinian biology graduates—myself, Pablo Pomposiello, and many others—that left Argentina looking for a PhD. In general, people would try for a postdoc.I applied to a PhD program in Italy. I went with an open ticket for a year. If I had not passed the ICGEB/SISSA (Trieste) examination, I had three thousand dollars to travel around, and then I would go back to Argentina. I had never been in Europe before. So, for me it was an experience. What happened was that I was very lucky to be admitted in probably the first generation of this new institution, the International Centre for Genetic Engineering and Biotechnology in Italy. In three years, I finished my PhD, and then, to be honest, as an Argentinian in Europe, I did not have many postdoctoral funding opportunities either. TC: How did you move from Trieste to Cambridge’s Laboratory of Molecular Biology? FDB: I found Michael Neuberger’s laboratory to be very appealing, and I wrote to Michael. He replied to me, in a letter that I still keep, that—if I was able to obtain a fellowship—he would take me in his laboratory. A wonderful thing about EMBO was that it would recognize the country where you did your PhD when considering postdoctoral fellowship applications, giving me access to this important funding support. ¹ It was the very early days of diversity—the notion that people could be eligible for support based not only on their nationality, but also on their “scientific nationality”. It gave me a unique opportunity. TC: It was also an opportunity to meet another source of inspiration for you, César Milstein FDB: César was not well at the time, he had heart problems. But I met him, and I felt very close because Michael was working with César, and he worked next door. For me, walking in those corridors with César Milstein and several other Nobel Prize winners—you know, Aaron Klug and Max Perutz—it was a dream. I could not believe that you could have lunch with these wonderful people, and they would come and talk to you, not as Dr. Klug or Dr. Milstein, but they would be César, Aaron, and Max. That for me was totally mind‐changing, together with my relationship with Michael, whom I love. They completely changed my perspective on science. TC: What do you remember most about Michael Neuberger as a mentor? FDB: What was incredible about Michael was his clarity. You would present any biological problem to him, and he would crystallize in one sentence what the real question behind it was. He was amazing. Michael would enter into a state of thinking where he would stop looking at you and would start looking up at a wall and would start to concentrate for those 10, 20 minutes that you’d explain the problem. Then, he would come up with critical questions and he would be critical to the bones. I think that that is something that science has lost these days. I think that this notion of going deep into critically asking the right scientific questions has been lost as a tradition. It is something that I try to transmit to my postdocs and PhD students: Scientific criticism is not about personal or emotional evaluation. It is really about trying to nail down what the question is and how a project develops. I think that is what I remember most of Michael, his commitment to the people that worked with him and who surrounded him and that deep thinking and constant challenging about what is the next step. TC: In 2002, you started your laboratory at the London Research Institute FDB: I was at one stage considering staying at the LMB with my independent lab, and César and Michael were very supportive of that. But then came the opportunity to join the LRI—which at the time was still the ICRF. I was the last employee recruited (to the ICRF), and it was wonderful. The notion of changing environments again, changing colleagues. The LMB was not an immunology institute. It was a general research institute and the ICRF at that time was similar, with very little immunology. I have always valued the whole spectrum of biology from mathematical modeling to quantitative biology to biochemistry to technological inputs, to development, and so forth. TC: Your LRI laboratory revealed entirely new aspects of the molecular and cellular biology of B lymphocytes—one was the existence of organized membrane structures reminiscent of the immunological synapse first described in T cells that were crucial for activation. What are the implications of the immunological synapse for B‐cell function? FDB: It was a concept that was resisted by the B‐cell field. The notion at the time was that B cells would get activated by soluble antigens. But if you think about it, that does not make any sense. You will never reach a physiological concentration of a ligand that will allow you to engage a receptor in vivo at a low affinity. So in order to reach that concentration, you need to aggregate antigen on the surface of other cells first. And that makes the whole process much more efficient. It not only localizes the process into lymph nodes or spleens, but it also allows focusing the response into what the arrangement of a membrane is. I was not the first—the notion that antigens are on follicular dendritic cells was well‐established by early experiments. But I think our work transformed the field. A lot of laboratories have incorporated the notion that stimulating cells at the level of membranes changes the way that receptors perceive signals. This does not apply only to the B‐cell receptor, it applies to chemokines too, many of them are also coating the surface of other cells and that helps guide the signals that cells receive.I think that it is an important concept that is likely to be applicable to vaccines. There are several papers now showing that helping to aggregate antigens on the surface of macrophages or dendritic cells makes antigens more potent by driving them more efficiently into where they are used in follicles and lymph nodes. TC: What prompted your pivot to translational research? FDB: I had learned a lot about basic principles of B‐cell biology and antibody responses, but on model antigens. I felt at the time that translating that into humans and trying to understand how vaccines could be improved was an important step. I always like to recognize mentors or people who influenced me and one person who really influenced me in this thinking was Dennis Burton at Scripps. He was very early to incorporate into his HIV vaccine and antibody research people like me or Michelle Nussenzweig that were coming from basic B‐cell immunology to try to help to think about how vaccines can be improved. I decided to take a risk. I left a tenured, core‐funded position at the best institution in Europe to lead the Ragon Institute with Bruce Walker—I am the Associate Director and he is the Director—and brought my years of expertise at the ICGEB, LMB, LRI, and CRICK to a unique environment that is based on translational research. There is the incredible ecosystem of Harvard, MIT, and MGH, and the notion is to incorporate technologies and to incorporate immunology to tackle incredible challenges, like COVID‐19 is today. TC: Are there any major initiatives that you plan to focus on at The EMBO Journal? FDB: One of the things that I would really like to do is to involve the younger generations in the journal. I think that we have an opportunity for direct “translation”. I mean, EMBO has EMBO postdoctoral fellowships and EMBO young investigators, involving early career European scientists, but also scientists across the globe. We are discussing initiatives like, for example, inviting postdocs from different laboratories to present at the editorial meetings. The EMBO Journal has an open‐door policy in terms of people wanting to participate in the editorial meetings.I think that we have amazing scientists around the world that can really bring new views as to where the journal should be going. I feel strongly about that and about keeping a real sense of diversity in the journal, in terms of fields, in terms of gender, in terms of race, in getting people involved from Brazil, getting people involved from China, getting people involved from Japan, from across the globe. EMBO is no longer a European journal. EMBO is a journal whose office faces Europe, but it has a global outlook. TC: Early in their career, many researchers do not feel comfortable engaging with editors FDB: I sent one of my first papers as an independent P.I. to EMBO. That paper was editorially rejected. I replied to that rejection, saying that EMBO should stop publishing just biochemistry, and that they needed to appreciate the importance of quantitative cell biology. The paper was ultimately sent to review and accepted. What was also very positive was that a later review of the scope of The EMBO Journal came to a similar conclusion. That resulted in my appointment to the editorial advisory board of The EMBO Journal (I was not an EMBO member at the time). The positive message is that the journal very much welcomed receiving feedback. That was what made me like the journal. I felt that the journal was ready to listen, to change.This is not my journal. It is the community’s journal. I am just playing a role, putting in some time and effort. There are a lot of things that I do not see and other young people could see, and I am looking for inspiration there, to listen and translate those things into good policies for the journal. I think that this is important and I think that this is at the basis of what I want to be as a chief editor.     

Work life balance?

There is no perfect recipe to balance work and life in academic research. Everyone has to find their own optimal balance to derive fulfilment from life and work. Subject Categories: S&S: Careers & Training

A few years ago, a colleague came into my office, looking a little irate, and said, “I just interviewed a prospective student, and the first question was, ‘how is work‐life balance here?’”. Said colleague then explained how this question was one of his triggers. Actually, this sentiment isn''t unusual among many PIs. And, yet, asking about one''s expected workload is a fair question. While some applicants are actually coached to ask it at interviews, I think that many younger scientists have genuine concerns about whether or not they will have enough time away from the bench in order to have a life outside of work.In a nutshell, I believe there is no one‐size‐fits‐all definition of work–life balance (WLB). I also think WLB takes different forms depending on one''s career stage. As a new graduate student, I didn''t exactly burn the midnight oil; it took me a couple of years to get my bench groove on, but once I did, I worked a lot and hard. I also worked on weekends and holidays, because I wanted answers to the questions I had, whether it was the outcome of a bacterial transformation or the result from a big animal experiment. As a post‐doc, I worked similarly hard although I may have actually spent fewer hours at the bench because I just got more efficient and because I read a lot at home and on the six train. But I also knew that I had to do as much as I could to get a job in NYC where my husband was already a faculty member. The pressure was high, and the stress was intense. If you ask people who knew me at the time, they can confirm I was also about 30 pounds lighter than I am now (for what it''s worth, I was far from emaciated!).As an assistant professor, I still worked a lot at the bench in addition to training students and writing grant applications (it took me three‐plus years and many tears to get my first grant). As science started to progress, work got even busier, but in a good way. By no means did I necessarily work harder than those around me—in fact, I know I could have worked even more. And I’m not going to lie, there can be a lot of guilt associated with not working as much as your neighbor.My example is only one of millions, and there is no general manual on how to handle WLB. Everyone has their own optimal balance they have to figure out. People with children or other dependents are particularly challenged; as someone without kids, I cannot even fathom how tough it must be. Even with some institutions providing child care or for those lucky enough to have family take care of children, juggling home life with “lab life” can create exceptional levels of stress. What I have observed over the years is that trainees and colleagues with children become ridiculously efficient; they are truly remarkable. One of my most accomplished trainees had two children, while she was a post‐doc and she is a force to be reckoned with—although no longer in my laboratory, she still is a tour de force at work, no less with child number three just delivered! I think recruiters should view candidates with families as well—if not better—equipped to multi‐task and get the job done.There are so many paths one can take in life, and there is no single, “correct” choice. If I had to define WLB, I would say it is whatever one needs to do in order to get the work done to one''s satisfaction. For some people, putting in long days and nights might be what is needed. Does someone who puts in more hours necessarily do better than one who doesn''t, or does a childless scientist produce more results than one with kids? Absolutely not. People also have different goals in life: Some are literally “wedded” to their work, while others put much more emphasis on spending time with their families and see their children grow up. Importantly, these goals are not set in stone and can fluctuate throughout one''s life. Someone recently said to me that there can be periods of intense vertical growth where “balance” is not called for, and other times in life where it is important and needed. I believe this sentiment eloquently sums up most of our lives.Now that I''m a graying, privileged professor, I have started to prioritize other areas of life, in particular, my health. I go running regularly (well, maybe jog very slowly), which takes a lot of time but it is important for me to stay healthy. Pre‐pandemic, I made plans to visit more people in person as life is too short not to see family and friends. In many ways, having acquired the skills to work more efficiently after many years in the laboratory and office, along with giving myself more time for my health, has freed up my mind to think of science differently, perhaps more creatively. It seems no matter how much I think I’m tipping the balance toward life, work still creeps in, and that’s perfectly OK. At the end of the day, my work is my life, gladly, so I no longer worry about how much I work, nor do I worry about how much time I spend away from it. If you, too, accomplish your goals and derive fulfillment from your work and your life, neither should you.     

Hongyuan Yang: Tracking lipids,one droplet at a time

Hongyuan Yang investigates lipid trafficking and lipid droplet biogenesis.

Hongyuan Yang grew up in a small city east of Beijing, China. From his childhood, Hongyuan recalls that “food was not abundant, so I was hungry at times, but education was free and good.” Driven by his curiosity for science, after completing his undergraduate studies at Peking University Health Science Center, China, he enrolled at Columbia University, NY, for his doctoral training. Under the guidance of his advisor, Dr. Stephen Sturley, Hongyuan studied lipids in budding yeast. The laboratory’s research department fostered a strong interest in lipids and atherosclerosis, and after earning his PhD, Hongyuan obtained a faculty position at the National University of Singapore (NUS) in 1999. In 2007, he moved to the University of New South Wales (UNSW) in Sydney, Australia, to continue his scientific journey exploring lipids. We contacted Hongyuan to learn more about his career and interests.Hongyuan Robert Yang. Photo courtesy of UNSW.What interested you about lipids?My five-year doctoral study focused entirely on the enzymes Sterol O-Acyltransferases (SOAT, also known as ACAT, Acyl-CoA Cholesterol Acyltransferases), which catalyze the formation of sterol esters from sterols/cholesterol and fatty acyl CoAs (1). SOATs, integral membrane proteins of the ER, are potential therapeutic targets for heart disease and Alzheimer’s disease. Since then, I have been fascinated by two things related to SOAT: first, what happens upstream of SOAT, i.e., how exogenous cholesterol reaches SOAT/ER; and second, what happens downstream of SOAT, i.e., how its product—cholesterol esters—is stored in cells in the form of lipid droplets (LDs).These are fundamental questions in cell biology. While reading on how cholesterol arrives at the ER for esterification by SOAT/ACAT in the late 1990s, I realized that the trafficking of most lipids was poorly characterized with little molecular insight. Significant progress has been made in the last 20 years, but the lack of tools that track the movement of lipids has hampered our understanding of the selectivity, efficacy, and kinetics of lipid trafficking. Few cell biologists cared about LDs ∼20 years ago, even though LDs are prominent cellular structures in many disease conditions. Each LD comprises a hydrophobic core of storage lipids (triglycerides and sterol esters) wrapped by a monolayer of phospholipids. Largely considered inert lipid granules, LDs originate from the ER and are relatively simple cellular structures as compared with other organelles (see image). Now, we know that LDs are not that simple: their biogenesis is tightly regulated, they actively interact with other organelles, and they regulate many aspects of cellular function as well as disease progression. Astonishingly, we still have little understanding of how LDs originate from the ER. I am very much intrigued by the complexity of these two seemingly simple cellular processes, i.e., lipid trafficking and LD biogenesis.What are some of the scientific questions currently of interest in your laboratory?We are currently focusing on how LDs originate from the ER. The first significant paper from my own laboratory was the discovery of seipin as a key regulator of LD formation (2). Results from many groups have demonstrated that seipin can organize the formation of LDs; however, the exact molecular function of seipin remains mysterious. Our data suggest that seipin may directly impact the level and/or distribution of lipids such as phosphatidic acid near sites of LD biogenesis, and the effect of seipin deficiency on LD formation is secondary to changes in local lipids. We are now working hard to test this hypothesis. Moreover, data from my laboratory and others indicated that nonbilayer lipids may have a greater impact on the biogenesis of LDs than that of other ER-derived structures, such as COPII vesicles. This may result from the monolayer nature of the LD surface. We hope to dissect the dynamic changes of lipids at ER domains where LDs are born. More broadly, the ER is a fascinating organelle to me. The simple division of ER into sheets and tubules does not reflect the dynamic nature of this organelle. Dissecting the composition and organization of lipids and proteins of the ER would help answer key questions relating to LD biogenesis, and it is therefore one of our future directions.Another major focus is to understand how cholesterol and phosphatidylserine are moved between organelles. We have been working on how low-density lipoprotein (LDL)–derived cholesterol (LDL-C) reaches the ER for two decades. The release of LDL-C from lysosomes requires the Niemann Pick C1&2 proteins, whose malfunction causes lysosomal cholesterol accumulation and a lethal genetic disorder affecting young children. The Ara Parseghian Medical Research Foundation has led the way in supporting research into cholesterol trafficking, and I take this opportunity to thank their generous support. Once released from lysosomes, LDL-C is believed to reach the plasma membrane first and then the ER. We identified ORP2 as a possible carrier of LDL-C to the plasma membrane using a PI(4,5)P₂ gradient (3). There must be other carriers and/or pathways because ORP2 deficiency only causes a minor accumulation of cholesterol in lysosomes. Another interesting question is what prevents LDL-C from reaching the ER directly from lysosomes, given the close contact between lysosomes and the ER. We reported that ORP5 may bring LDL-C directly to the ER (4). However, it was later found that ORP5 binds and transfers phosphatidylserine, not cholesterol. Thus, our observed link between ORP5 and cholesterol is through some indirect yet unknown mechanism. We have been perplexed by these observations for many years, but a recent study demonstrated that phosphatidylserine is required for the trafficking of LDL-C, establishing a close link between cholesterol and phosphatidylserine (5). We are now trying to understand how the trafficking and distribution of cholesterol, phosphatidylserine, and PI(4,5)P₂ are interconnected. For a long time, I felt that it was impossible to figure out the molecular details governing the cellular trafficking of lipids due to redundant pathways and a lack of tools to track lipids. Recent progress in this field has given me hope.Lipid droplets in a HeLa cell are shown in red (BODIPY), with their surface in green. DAPI (blue) labels DNA. Image courtesy of Hongyuan Yang.What kind of approach do you bring to your work?Besides honesty and open-mindedness, we emphasize rigor and comprehensiveness. We often make our initial discoveries in cell-based screens. This approach has many advantages, but it also gives rise to artifacts and cell-line specific observations. We aim to complement our initial findings with biochemical and structural analyses in vitro as well as animal studies in vivo. To further establish the reproducibility of our data, I often ask my close friends and collaborators to independently repeat the key findings of a study before submission. It generally takes a long time for us to complete a study, but I believe the effort will pay off in the long run.What did you learn during your training that helped prepare you for being a group leader? What were you unprepared for?During my PhD at Columbia, I was most impressed with the general attitude of my mentors toward research. No matter how much they have achieved, they take every new experiment and every poster presentation seriously.As I did not have postdoctoral training, I was somewhat unprepared at the beginning of my independent career. One difficult challenge was knowing when to finish a paper and project. We often kept working and working. I have now gotten a lot better.You’ve done research on three continents throughout your career. Can you tell us about some of these transitions?During the last year of my doctoral studies at Columbia, I was offered a lecturer position by the Department of Biochemistry at NUS. It was a very hard decision to leave the United States, but I was excited by the prospect of starting my own laboratory at a top institution. Life at NUS was very good overall, despite some struggles. I had to make ∼700 slides for teaching during the first year and my start-up fund was 10,000 Singapore dollars (~6,000 USD). But the graduate students were fully supported by the university, and most of them are hard working and talented. The crucial screen that led to the discovery of seipin as a key regulator of LD formation was performed at NUS (2). I enjoyed my time at NUS, where I was promoted and tenured. However, my family and I could not get used to the heat and humidity. We looked for a place with better climate, and it happened that my current employer, UNSW, had an opening in 2006. Moving continents with two kids was very disruptive, and I had zero publications in 2007. Our work on seipin was delayed and almost got scooped. I was also very worried about funding in Australia since I hardly knew anyone and the funding system. It turned out that the Australian community was very supportive of our research from day one. I have also been very fortunate to receive generous support from the Ara Parseghian Medical Research Foundation, based in the United States, after my move to Sydney.Hongyuan’s “metabolism team” after a basketball game. Photo courtesy of Hongyuan Yang.What has been the biggest accomplishment in your career so far?While I am mostly recognized for discovering seipin’s role in lipid droplet formation, I am prouder of the work we have done on lipid trafficking and the oxysterol binding proteins. We struggled mightily for the first 15 years. At one point in 2015, I seriously considered abandoning this line of research. But we persisted and discovered their roles in regulating plasma membrane PI(4,5)P₂ and cholesterol, as well as in lipid droplet formation (3, 6).What has been the biggest challenge in your career so far?The biggest challenge has to do with the subject of my research topic: the fundamental cell biology of lipids. The sorting, distribution, and storage of cellular lipids are clearly very important topics in biology, but they are sometimes too fundamental to explain to funding agencies and new students. These days, lipid research is not as “sexy” as other topics. But there are so many unanswered questions in lipidology. I strongly believe that lipid research is going to be the next “big thing” as new techniques such as cryoEM now allow us to appreciate lipids and membrane proteins with unprecedented clarity.Who were your key influences early in your career?Besides mentors and teachers at Columbia, I really enjoyed reading and studying the works by Drs. Mike Brown and Joseph Goldstein, Ta-Yuan Chang, and Scott Emr. While they were not my teachers, their work inspired and impacted many young scientists, including me.What is the best advice you have been given?I have been given many pieces of great advice during my career. The best one in my view is “Less is more.” I was once told, “You would be better off with a lab of six than twelve.” Initially, I did not get it because I thought that a bigger group would allow me to explore more directions and be more productive. The reality is that, as a little-known junior researcher, few experienced people would join my laboratory. Funding is also a major limiting factor. Supervising a large number of students is fulfilling, but it also takes away some of my own time to think critically about the projects. I have largely kept my group under six, and this allows me to better supervise and guide the trainees. People say, “Once your team has more than 15 members, you become a manager instead of a scientist.” My own experience corroborates that statement because I struggled quite a bit when my group reached 12 at one point.What hobbies do you have?I am heavily into sports, especially basketball and tennis. I follow the NBA closely, and Jeremy Lin is my hero. I still play basketball at least twice a week. I am the captain of a basketball team comprised of scientists working on metabolism (see image). We play real, refereed basketball games against local teams during conferences. As I am getting older, I have also picked up tennis. I watch coaching videos on YouTube but still need a lot of work on my forehand. Through sports, I learned teamwork and the spirit of fighting to the last second. If I were not a scientist, I would probably run a sports-related business.What has been your biggest accomplishment outside of the laboratory?I got married and had children relatively early. Both of my kids are now in college and they appear to be decent human beings. I have been extremely lucky because my wife did most of the heavy lifting in looking after the kids. It was still a struggle for me to balance work and parental duties during the early days of my independent career. I am very proud and happy with where we are as a family right now.Any tips for a successful research career?Everyone is unique. Knowing your strengths and especially your weaknesses can be crucial to your success. My undergraduate training was in medicine and health management, and my PhD work focused on genetics and cell biology, so my understanding of physical chemistry is rather inadequate. I am also very bad at developing new methods. To alleviate these deficiencies, I constantly monitor new methods in my field and I purposefully look for collaborators with strong chemistry backgrounds. I have benefited immensely from such efforts.     

Spinning plates and juggling balls

A PhD thesis is a project with an established goal and a deadline. As such, the tools, strategies and insight of professional project management can be used effectively to improve both research success and personal well-being.A project is a “temporary endeavour undertaken to create a unique product, service or result” [1]. Although this is a generic definition, it pretty much describes any PhD research project. There are many ways to manage a project effectively and efficiently. Unfortunately, most of us are so busy with our science that we forget about the importance of planning and management to our own success, sanity and health. Instead, we approach our first three years of genuine scientific endeavour wide-eyed and unprepared to juggle the hundreds of tiny balls that make up a PhD. Several techniques from the realm of ‘project management'' might therefore be helpful for PhD students who need to plan and manage the many competing demands that doctoral research can place on them.A PhD comprises both the research itself and the acquisition of skills and knowledge that will facilitate your future career. As such, it is of paramount importance to establish your own objectives early on. For example, alongside dividing your project into work packages—smaller projects that might be discrete or might build on each other—it is also essential to define which so-called transferable skills—additional knowledge and experience that might improve your job prospects—you feel will be of greatest use to you, depending on what you want to do after your PhD. The importance of these skills is becoming more widely recognized and taken far more seriously, and you should find that your supervisor is willing to give you the time to pursue them—your institute or university usually requires that he or she does so. More importantly, you should give yourself the time to invest in these skills, as they are going to be vital to everything you do once your PhD project is over.Doctoral research requires a multitude of skills, most of which you will inevitably lack when you commence your PhD programme. The first step is to identify the gaps in your knowledge to plan what skills on which to focus. This will allow you to acquire them in good time, either through professional activities—shadowing a postdoc, teaching undergraduates, joining journal clubs and blogging—or through both internal and external courses and workshops to improve communication, presentation, writing, networking and other skills. In addition to your planned skills acquisitions, you will also have situations arise, in which you need to acquire new skills quickly. The more you plan training activities and skills acquisition in advance, however, the smoother this aspect will be of your PhD. By way of example, part of my own PhD project relates to statistical analysis of data. An early analysis highlighted several areas in which I had to improve my skills, including hierarchical cluster analysis, principal component analysis and χ² testing against standard distributions. Having identified these gaps in knowledge early on in my doctoral programme, I could plan ahead accordingly when and how to acquire these skills.The full scope of your PhD project is usually unknown at the outset, and even the direction of your research might well change before you are finished. ‘Rolling wave planning'' is a technique that allows you to take these facts into account and plan the short-term future in detail, with a high-level provision for medium- to long-term activities. For those new to developing project schedules, I advocate a simple five-step approach. First, make an ordered list of high-level activities needed to achieve your goal. Second, expand this list by adding lower-level activities for which you have a detailed understanding of the scope, for example work to be performed in the next six months. You now have a work breakdown structure. Third, turn this work breakdown structure into a dependency-driven list by adding associations between the activities, for example by adding links to precursor activities that need to be completed before another activity can be started. Fourth, estimate the duration of each activity and extrapolate the start and end dates beginning with the first scheduled activity. Finally, as you progress through your research, and the scope of future activities becomes clearer, update the project schedule with these low-level activities as they become known. This approach of generating a hybrid-level project schedule, and updating with detailed activities as the scope becomes clearer, is known as ‘rolling wave planning''.…we approach our first three years of genuine scientific endeavour wide-eyed and unprepared to juggle the hundreds of tiny balls that make up a PhDThere is a range of professional software to help develop project schedules, but there are also various freeware tools available. Alternatively, you can use one of the many word processing or spreadsheet applications to make a simple Gantt chart. Along with the technical scope of your doctoral research, it would also be useful to include milestones that your institution enforces; for example literature review submission, formal progress reports and thesis chapter outlines. Including these in your rolling wave planning will allow you to keep in mind the bigger picture and the formal aspects that must be completed for your PhD, in parallel with the progress you are making towards your specific research subject.It is of course a cliché, but it is true that ‘failing to plan is planning to fail''. Of course the fluid nature of research makes it difficult to estimate accurately the time that it will take to complete various experiments, especially as a novice researcher. I therefore believe that although experiments do overrun and PhD projects can change, developing a project schedule is not a futile activity. By having a plan, even if it is made up of ‘guesstimates'', you can forecast roughly how much time you have left for your research and roughly what you can realistically hope to achieve. After all, without a plan, how can you predict when you will complete your research, submit your thesis and ultimately gain your PhD?Doctoral research requires a multitude of skills, most of which you will inevitably lack when you commence your PhD programmeThe serious consideration of scope is necessary in any project, but even more when you are simultaneously project manager, research scientist and key stakeholder. This raises various crucial questions regarding scope management: what is my doctoral research all about (the goal), and what work do I need to do to meet this goal? Once this has been agreed between you and your supervisor(s), it is essential to manage the scope of your project—the breadth and number of experiments you will perform—and how this will achieve your goal(s). Furthermore, be specific—knowing exactly what you want to achieve will keep you motivated until you get there.Project managers often use the concept of the triple constraint to manage work: scope, time and cost are intricately linked in a project and the different level of focus that each is given affects the perceived quality (by others) of project deliverables (Fig 1). Project managers understand that any deviation in one of the triple constraints changes one or both of the others. This is where the project schedule really comes into its own by allowing you to forecast when you will complete the agreed goals of your PhD project. For example, is your doctoral programme for a fixed-term period? If so, then once a project schedule has been agreed that uses all of the time available, any project overruns will cause an overrun to the overall PhD. The two main possibilities for a PhD student to manage this situation and bring the projected completion back into acceptable timescales are either to work longer or to reduce the scope or goals of the project, either by conducting fewer experiments to answer the same question or by modifying the depth of the question being asked. This leads to the issue of whether there is a minimum set of goals that need to be achieved, or whether several agreed activities are ‘nice to haves'', but are not crucial for the overall PhD. I believe that your supervisor(s) are best suited to answer questions about the minimum goals and the scope needed to achieve them.Open in a separate windowFigure 1The project management triangle as applied to a PhD. Three competing constraints influence project management: time, scope and cost. The time constraint reinforces that projects are temporary endeavours, and that in most cases have defined timescales (absolute deadlines). The cost constraint refers to the budgeted amount allocated to the project that, from the perspective of doctoral research students, will predominantly be focused on the amount and duration of the stipend awarded, but might also incorporate various expenses such as bench fees, conference fees and consumables. For those changing career, the cost might also comprise an element of salary sacrifice. The scope constraint refers to what must be done, produced or developed to meet the objective of the project, which in the case of a PhD generally comprises the actual doctoral research to be performed, development (and submission) of the thesis, publication of one or more journal articles, presentation at conferences and potentially teaching. The triple constraint principle highlights that any change to one of the constraints will have an impact on one or both of the other constraints. For example, increased scope typically leads to increased time and cost; tight time constraints usually mean that an overrun in activities (such as experimentation) might have a knock-on effect of requiring the scope to be reduced to submit your thesis on time, or increasing the overall amount of time required to complete your PhD. Similarly, a tight budget could mean you cannot gain access to various resources, resulting in either increased time or a reduction in scope. Recently, a fourth component of the project management triangle has been introduced highlighting that along with the three constraints competing with each other, they also interact to form a fourth dimension of quality.If you need to complete your doctoral programme within a specified time frame, then you need to manage your goals and scope mercilessly—do not allow additional research questions or extra experiments to take away precious time. This does not mean that you cannot deviate, but any deviations need to be managed. Remember, whether you wish to remain in scientific research or not, the PhD is a stepping-stone to your future career and not the end goal in itself. Once you have achieved the goals agreed with your supervisor, it is more beneficial for you to write-up your doctoral thesis and move on [2].Good communication is essential in every area of work, but even more so for a PhD as you are simultaneously learning how to research along with doing the research. Often, access to your supervisor is limited by constraints on his/her or your time, which means that clear communication is vital. Do not assume that your supervisor knows every intricate detail of what you are doing; he or she might have a large group in which each member is looking at complementary aspects of a more general topic. It is, therefore, your responsibility to ensure that all your stakeholders—supervisors, postdoc leads and any others involved—know what you are doing and, more importantly, why you are doing it.This is another area in which the apt use of technology can maximize efficiency. Subject to institutional licensing, collaboration tools such as SkillsForge or Evernote can improve communication between stakeholders. For example, meeting minutes, action points to be followed and research results can be uploaded for sharing. Supervisors can then review the material at a convenient time to ensure that they stay up to date with the progress of each student within their research group.As PhD students usually aspire to become research scientists, it is of paramount importance that you learn the correct application of the scientific method and the context in which your work is being done. Before jumping into practical work—wet-lab experiments or computational modelling—it is important to understand the meaning and relevance of your project in relation to existing knowledge and the underlying science. For example, the hypothesis-driven research life cycle in systems biology [3,4]—my own field—advises that computational models should be developed on the basis of wet-lab data relating to the underlying biological system. Almeida-Souza and Baets state that a PhD in science is an opportunity to learn how to tackle problems scientifically and, as such, requires the development of skills in critical thinking, hypothesis formulation and experimental design [5]. I believe that the requirement for these skills is universal across the sciences, and that molecular biosciences and computational systems biology are no different.The serious consideration of scope is necessary in any project, but even more when you are simultaneously project manager, research scientist and key stakeholderTherefore, before the first wet-lab experiment is performed, or the first line of code is written, it is essential that we understand why the experiment is important and what results we might expect to support our initial hypotheses. Furthermore, regarding computational systems biology, I believe that it is also essential for wet-lab and computational researchers to collaborate to ensure both have a consistent understanding of the data and the purpose of the computational model. After all, for the most part, computational models are developed for their predictive capacities and to allow hypothesis generation for subsequent wet-lab experimentation. Baxter et al have extensively covered this area and advocate not only designing the project up-front, but also the need for quality control [6].You need to manage the scope and goals of your PhD mercilessly and, at the same time, be flexible enough to grasp new opportunities. Conversations at conferences, for instance, can open up opportunities for collaboration and take your research in a direction that you had not considered previously. In my case, I was invited to turn a conference paper relating to my masters degree into a full paper for a special issue of a well-known bioinformatics journal. Although it was not related to my doctoral research, the prospect was too good to turn down. I therefore discussed the idea with my PhD supervisor, and once we were in agreement, I updated the project schedule to incorporate this new activity, trying to mitigate as much as possible the resulting slippages to my doctoral research. In essence, I had performed an impromptu risk–reward analysis and decided that the reward that would be gained from publishing this work outweighed the risk of a slight overrun of my PhD thesis. It must be noted that I was lucky in this instance, as my PhD supervisor also supervised the research project during my master''s degree, so a full paper would be beneficial for both of us.A project risk is “an uncertain event or condition, that if it occurs, has an effect on at least one project objective” [1]. The positive side to risks is that the likelihood of their future occurrence can be mitigated by planning in the present. Once a risk is realized, however, and its effects begin to be felt, it has turned into a project issue. The first step in trying to manage risks is their identification. Risk identification in this context is the process of determining which events, if they occurred, would affect your research. In the context of a molecular biosciences PhD, I believe that general risks relate to access to resources, such as people—postdocs and collaborators, for example—reagents, cell lines and shared equipment. For example, if your work uses fluorescent proteins within single cell analysis, how would you be affected if the fluorescence microscope was booked out by another research lab? Similarly, in computational systems biology, if the design process for your computational model requires access to wet-lab data, what would the effect(s) be if this was not available?Once risks are identified, it is important to develop risk response plans. By using the above example of access to a microscope, what should your response be if you cannot gain access? The initial risk response would be to liaise with the other research lab to understand their requirements and ascertain whether you could gain access at a mutually convenient time. Alternatively, another approach might be to work outside normal office hours, either throughout the evenings or on the weekend, subject to health and safety procedures at your institution and your own health and well-being. I believe that a degree of creativity is often required when developing effective risk response plans.A PhD thesis is a hefty document that might run to many hundreds of pages. They are generally not written as a single large document from start to finish, but as chapters. In the molecular biosciences, a thesis consists of an initial literature review early in the doctoral programme, work-in-progress documents for materials and methods, experimental results throughout the middle section, which is followed by analysis and critical evaluation towards the end of your experimental work. Whether through software tools or through your own manual methods, such as keeping a configuration log and keeping a copy of each version of your working documents, it is essential that you maintain an up-to-date repository of all your notes. I have found through experience that it is beneficial to save not only the final versions, but also each of the working drafts of documents generated throughout your PhD. Ideas previously discounted, and thus removed from more recent versions of documents, might once again take centre stage at a later date.The positive side to risks is that the likelihood of their future occurrence can be mitigated by planning in the presentThis can be aided through the development and use of a project library with a logical folder structure to facilitate easy access to documentation. Noble [7] provides an in-depth discussion of organizing your computational biology project—in particular the value of version control—but the concepts are transferable across disciplines. Furthermore, do not forget to back-up your work, and without seeming too pessimistic, back-up your back-up!Finally, look after the most important resource: you. Exercise, diet, alcohol, caffeine and holidays all affect your well-being. Holidays and time away from the lab or office allow you to take a step back from the detail and reflect on your experiences and progress. Sometimes, time off allows you to process issues subconsciously and develop new approaches to overcome problems that you have been tackling for extended periods of time without success. Finally, holidays also help you recharge your batteries and enthusiasm to return to your project with fresh vigour. If you have sensibly and reasonably planned time off alongside your work, you will be able to enjoy it.Although a PhD requires consistent commitment, you simply cannot—and should not—work at full capacity all of the time. Issues arise periodically throughout any project, and if you have no reserves of energy—either mental or physical—you will be unable to tackle them head on with the step change of performance that is required. Furthermore, doctoral research is a marathon and not a sprint; we all experience the symptoms of burnout from time to time, and sometimes it is better to walk away for a short period to recharge than to carry on, become stale, and ultimately slow down.To conclude, I wish you good luck with your doctoral research, and I hope these techniques help you to manage your PhD project through to successful completion.? Open in a separate windowRichard Alun Williams     

Finding autophagy: It’s a question of how you look at it

To tell the truth, I find it difficult to work when flying, or even when sitting in an airport for an extended period of time. So, typically I take along a book to read. And when I truly cannot concentrate, for example when a flight is considerably delayed, I have even been known to resort to word puzzles. Depending on the type, they do not require much attention (that is, you can pick up right where you left off after you glance at the flight status screen for the twentieth or so time, even though you know nothing has changed), or effort (although you need to use a pen or pencil, not a keyboard), but nonetheless they can keep your mind somewhat occupied. I even rationalize doing them based on the assumption that they are sharpening my observational/pattern-finding skills. One type of word puzzle that is particularly mindless, but for that very reason I still enjoy in the above circumstances, is a word search; you are given a grid with letters and/or numbers, and a list of “hidden” terms, and you circle them within the grid, crossing them off the list as you go along. I do admit that the categories of terms used in the typical word searches can become rather mundane (breeds of dog, types of food, words that are followed by “stone,” words associated with a famous movie star, words from a particular television show, etc.). Therefore, on one of my last seminar trips I decided to generate my own word search, using the category of autophagy.     

Academic motherhood – what happens when you can't make it happen?

We need more openness about age‐related infertility as it is a particular risk for many female scientists in academia who feel that they have to delay having children. Subject Categories: S&S: Careers & Training, Genetics, Gene Therapy & Genetic Disease

Balancing motherhood and a career in academic research is a formidable challenge, and there is substantial literature available on the many difficulties that scientists and mothers face (Kamerlin, 2016). Unsurprisingly, these challenges are very off‐putting for many female scientists, causing us to keep delaying motherhood while pursuing our hypercompetitive academic careers with arguments “I’ll wait until I have a faculty position”, “I’ll wait until I have tenure”, and “I’ll wait until I’m a full professor”. The problem is that we frequently end up postponing getting children based on this logic until the choice is no longer ours: Fertility unfortunately does decline rapidly over the age of 35, notwithstanding other potential causes of infertility.This column is therefore not about the challenges of motherhood itself, but rather another situation frequently faced by women in academia, and one that is still not discussed openly: What if you want to have children and cannot, either because biology is not on your side, or because you waited too long, or both? My inspiration for writing this article is a combination of my own experiences battling infertility in my path to motherhood, and an excellent piece by Dr. Arghavan Salles for Time Magazine, outlining the difficulties she faced having spent her most fertile years training to be a surgeon, just to find out that it might be too late for motherhood when she came out the other side of her training (Salles, 2019). Unfortunately, as academic work models remain unsupportive of parenthood, despite significant improvements, this is not a problem faced only by physicians, but also one faced by both myself and many other women I have spoken to.I want to start by sharing my own story, because it is a bit more unusual. I have a very rare (~ 1 in 125,000 in women (Laitinen et al, 2011)) congenital endocrine disorder, Kallmann syndrome (KS) (Boehm et al, 2015); as a result, my body is unable to produce its own sex hormones and I don’t have a natural cycle. It doesn’t take much background in science to realize that this has a major negative impact on my fertility—individuals with KS can typically only conceive with the help of fertility treatment. It took me a long time to get a correct diagnosis, but even before that, in my twenties, I was being told that it is extremely unlikely I will ever have biological children. I didn’t realize back then that KS in women is a very treatable form of infertility, and that fertility treatments are progressing forward in leaps and bounds. As I was also adamant that I didn’t even want to be a mother but rather focus on my career, this was not something that caused me too much consternation at the time.In parallel, like Dr. Salles, I spent my most fertile years chasing the academic career path and kept finding—in my mind—good reasons to postpone even trying for a child. There is really never a good time to have a baby in academia (I tell any of my junior colleagues who ask to not plan their families around “if only X…” because there will always be a new X). Like many, I naïvely believed that in vitro fertilization (IVF) would be the magic bullet that can solve all my fertility problems. I accordingly thought it safe to pursue first a faculty position, then tenure, then a full professorship, as I will have to have fertility treatment anyhow. In my late twenties, my doctors suggested that I consider fertility preservation, for example, through egg freezing. At the time, however, the technology was both extravagantly expensive and unreliable and I brushed it off as unnecessary: when the time comes, I would just do IVF. In reality, the IVF success rates for women in their mid‐to‐late 30s are typically only ~ 40% per egg retrieval, and this only gets worse with age, something many women are not aware of when planning parenthood and careers. It is also an extremely strenuous process both physically and emotionally, as one is exposed to massive doses of hormones, multiple daily injections, tremendous financial cost, and general worries about whether it will work or not.Then reality hit. What I believed would be an easy journey turned out to be extremely challenging, and took almost three years, seven rounds of treatment, and two late pregnancy losses. While the driving factor for my infertility remained my endocrine disorder, my age played an increasing role in problems responding to treatment, and it was very nearly too late for me, despite being younger than 40. Despite these challenges, we are among the lucky ones and there are many others who are not.I am generally a very open person, and as I started the IVF process, I talked freely about this with female colleagues. Because I was open about my own predicament, colleagues from across the world, who had never mentioned it to me before, opened up and told me their own children were conceived through IVF. However, many colleagues also shared stories of trying, and how they are for various—not infrequently age‐related—reasons unable to have children, even after fertility treatment. These experiences are so common in academia, much more than you could ever imagine, but because of the societal taboos that still surround infertility and pregnancy and infant loss, they are not discussed openly. This means that many academic women are unprepared for the challenges surrounding infertility, particularly with advanced age. In addition, the silence surrounding this issue means that women lose out on what would have otherwise been a natural support network when facing a challenging situation, which can make you feel tremendously alone.There is no right or wrong in family planning decisions, and having children young, delaying having children or deciding to not have children at all are all equally valid choices. However, we do need more openness about the challenges of infertility, and we need to bring this discussion out of the shadows. My goal with this essay is to contribute to breaking the silence, so that academics of both genders can make informed choices, whether about the timing of when to build a family or about exploring fertility preservation—which in itself is not a guaranteed insurance policy—as relevant to their personal choices. Ultimately, we need an academic system that is supportive of all forms of family choices, and one that creates an environment compatible with parenthood so that so many academics do not feel pressured to delay parenthood until it might be too late.