After a short break, our first ‘Developing news’ post of 2023 focusses on disruption in science.
How good is ChatGPT?
One of the main talking point on Twitter in December was ChatGPT, a chatbot from OpenAI that interacts with the user in a conversational tone. The success of ChatGPT has prompted worries of how the technology could affect student assessment and even write scientific papers!
U.S. universities are starting to overhaul classrooms in response to the new AI chatbot ChatGPT, prompting a potentially huge shift in teaching. Some professors are redesigning their courses, even choosing handwritten assignments over typed ones. https://t.co/5B6eEPyBS1
First article with ChatGPT as coauthor 🤨. Next article: Word, M., Excel, M., and GPT, C. (2023). 'Does Adding Software as Authors Result in More Citations? An Ongoing Experiment' pic.twitter.com/M8IfabC1Tu
A new paper analysing the frequency of major new directions (or disruption) of science over time prompted discussions on i) whether this is true, ii) the causes and iii) whether we should be worried. We have picked out some examples of the chat below and recommend that you click the links for the full discussion.
New Nature paper provides evidence that science has become less innovative since the 1950s. The authors suggest reversing the trend by: 1. reading widely, 2. focusing less on quantity of papers, & more on research quality, 3. taking year-long sabbaticals.https://t.co/oYV5JCXRl8pic.twitter.com/viN2IJ0cSn
This is a thought provoking article, If it is not the quality of published work than what is causing it! 🧐😶🙄🤔thread below 👇🏻 Papers and patents are becoming less disruptive over time | Nature https://t.co/RIwG1VuiMu
Piping hot morning coffee take: if there really is a decline in "disruptive" science, could it be linked to our easy, finger-tip access to *all* the literature? Maybe out-of-the-box thinking is correlated with naivety and ingnorance?
Victoria Deneke, a postdoc in Andi Pauli’s lab at the Vienna BioCenter, was the winner of the 2022 Society of Developmental Biology (SDB) Trainee Science Communication Award. Victoria is passionate about developing communities within the science world and creating opportunities for scientists from low-income countries. We caught up with Victoria to find out about her outreach and communication work, as well as her research career.
Where are you originally from and when did you first get interested in science?
I was born and raised in San Salvador, the capital city of El Salvador in Central America. Whilst growing, I was lucky enough to have access to school, and received a very good education. When I was 18, I applied for university places in the United States and that was when I really picked up science academically, but I’ve always been interested in the natural world. For example, I remember being fascinated by snake scales as a child and one of my favourite experiments in middle school was to dissect a frog to study the vasculature and the amazing organisation of the organism. Despite this early interest in biology, I decided to study chemical engineering as an undergraduate, as I thought that degree would be more versatile, either allowing me to return to my home country, or to develop elsewhere. Biology is not a very developed topic in El Salvador, but after my undergraduate degree I found myself being drawn back to biology. I decided to apply for umbrella PhD programmes, which give you access to a broad range of biology departments. You do rotations in different laboratories and then choose one for your PhD. This was an important aspect of the programme for me, particularly as I didn’t have a strong background in biology as an undergraduate. That’s how I ended up joining Stefano Di Talia’s lab, which was my fourth laboratory rotation. I very quickly fell in love with the research that was ongoing at the lab, which had just started at Duke. I was one of the first two graduate students that joined and the first graduate student that joined a fruit fly project. During my rotation, I was imaging early Drosophila embryos, and in particular the nuclear divisions that occur in the first few hours of development. These events are remarkably synchronous, and the waves of division spread through the embryo. My first PhD project was trying to figure out how these divisions are synchronised in the syncytial embryo. We found that there are waves of chemical activity via cyclin dependent kinase 1 (Cdk1), and through a combination of diffusion and positive feedback, these waves can synchronise the whole cytoplasm within minutes. It was the perfect project for me because it was very visual – I got to see and make these beautiful movies every day of my PhD! At the same time, the project involved not only biological concepts, like kinases and cell cycle regulation, but also concepts from physics and maths. For example, how the signal spreads, and the dynamics and the kinetics of chemical waves. This meant I got to collaborate with physicists, and indeed Stefano is a physicist by training, so I felt this project really suited my engineering background.
You said this was your first PhD project, can you tell us what you worked on for the rest of your PhD?
For the second half of my PhD, I decided to look at the role of cytoplasmic flows in spreading nuclei in the Drosophila embryo. So, originally these nuclei are all clustered in one part of the embryo and then there are beautiful contractions and subsequent flows that emerge and appear to move the nuclei. The regulation of the contractions is fascinating, and we assumed they must be tightly regulated for the nuclei to become so uniformly spaced through self-organisation. I started out by making movies of both the nuclei and the flows, trying to correlate these two movements. I went on to use optogenetics to perturb the contractions and monitor how that affects the nuclear spreading. Another beautiful, visual project where we really benefited from the application of quantitative biology methods. We tracked the cytoplasm and the nuclei and established quantitative relationships between these two movements to build a model. From the model, we made predictions that we then tested experimentally. I loved both of these projects, they allowed me to combine both imaging techniques and mathematical modelling, to address questions about fundamental developmental processes. Overall, I couldn’t have picked a better place for my PhD given my background and the kind of biology that excites me.
For your postdoc, you moved to Andi Pauli’s lab in Vienna, Austria, can you tell us about this move and your research in the Pauli lab?
In the final year of my PhD, I started reading more broadly to find other scientific topics that interest me, and I always seemed to be coming back to oocyte and sperm biology. I’ve always thought that those cells are really fascinating and really special, and I was particularly drawn to the process of fertilisation, whereby these two cells have to bind specifically to each other and then fuse. I came across the first paper from Andi Pauli’s lab describing the discovery of a protein called Bouncer, which is on the surface of zebrafish eggs, and is an essential fertilisation factor. The other really cool thing that the Pauli lab found was that if you replace the zebrafish Bouncer with the medaka homologue, you can now fertilise the zebrafish eggs with medaka sperm, changing the compatibility of sperm and egg by just switching this one protein on the surface of the eggs. I thought this was amazing, so I reached out to her, keen to come for a visit. I was excited by the science and felt a good connection with Andi, so I decided to take a plunge and change completely scientific field, change model organism, change continents! It was quite a 180-degree change. I have been here for three years now, and I’ve really had such a good time. I think that picking an area of science that you’re just completely fascinated by for your postdoc is definitely the way to go. I don’t think I’ve ever had a day where I’m bored by my projects, I’m always wondering, what is really going on? How could we figure this out? So, I have been studying the process of fertilisation, mostly using zebrafish, and specifically I’m working on trying to decipher, which proteins, at the molecular level, are mediating this process, both on the sperm side and on the egg side. I love thinking about how these two cells come together and how they can achieve specific cell fusion between them. That’s a concept that really fascinates me and is my research interest in a nutshell!
Did you find switching model organisms a big change, or was that quite easy to do?
It was easier than I expected. I think it helped that the lab here (in Vienna) was already established and there were a lot of people in the lab that helped me pick up the zebrafish model organism. One of the biggest advantages of working with zebrafish is that the embryos are transparent. This means that you can look through a bright field microscope and watch development unfold. You can watch the embryo gastrulating and you can see even the somites forming, which was so exciting to me.
Congratulations on being awarded the 2022 SDB Trainee Science Communication Award, can you tell us what winning this award means to you?
This award means so much to me. I think oftentimes, this kind of work is considered extracurricular, and is overlooked. It’s wonderful that the SDB is recognising that outreach and communication are important aspects of academic science, and I think it shows the direction that we’re moving in. I think that being a well-rounded scientist is not just about making exciting discoveries in biology, but also about mentoring the next generation of scientists, and building an inclusive space for everyone. My short story of how I got involved into outreach work was when, after being in the US for a few years, I realised that I was in a unique position to contribute to my home country of El Salvador. I started doing simple outreach activities whenever I was back in El Salvador in the summertime. I would reach out to a local university and got involved with a workshop encouraging middle school girls to consider STEM fields. I would volunteer to give one of the Saturday morning workshops they do as part of a 12-week programme. One year I organised a workshop on pulleys. I borrowed some material from my high school and we ran this workshop together. So, that’s how it started and then eventually, as I got more involved with the Salvadoran community, I started reaching out to universities to also give motivational talks, to share my story. Then the next step was the fellowship that I created with my postdoc advisor Andi. But as you can hopefully see, the projects started very small, but through the years I built bigger and bigger initiatives.
Can you tell us a little more about the Austria-El Salvador Research Fellowship that you founded?
The idea originated from a yearly mentoring meeting I was having with Andi. We were talking about the Vienna BioCenter Summer School, which is open for students from all over the world to apply to come for a summer research internship at the Vienna BioCenter. It’s an amazing programme, but the realities are that students from lower income countries do not have access to the same opportunities as applicants from other parts of the world. This means that they usually don’t make the cut for the normal programme that we run here. I suggested to Andi that we could try to fill this gap by inviting one person for the summer, see how it goes and take it from there. Since I am very connected to the community in El Salvador, it was easy for me to broadcast the application within El Salvador and then find a student who would be motivated to come join us for a summer. We extended an offer to a student called Eduardo. He was here for three months and I was his direct supervisor. One thing that really stood out was that he was always so eager to come to the lab, and so grateful and amazed by the facilities. He loved the library and would go in the evenings to read books, access that we take for granted. It was really fascinating and inspiring for me as a mentor and made me really start appreciating the resources that we have here. Even though he had never had any research experience, he quickly picked up a lot of concepts. Eduardo is a very talented scientist, and it was a treat to mentor him. I also became aware of a lot of barriers within developing countries that kind of inhibit the progression of science. I’ve heard a lot of stories of having to use makeshift reagents and delayed services to developing countries, which means that science moves a lot slower because you just don’t have access to the same resources. For Eduardo, the fellowship was his first research experience, his first opportunity to try out the techniques he had read about, and it allowed him to be immersed in science. He has also taken his knowledge back to El Salvador. He has started a molecular biology club within his university, where they read papers together and they are creating a scientific community of students back home. It’s a small thing, starting with just one person, but I think in the long run it could really have an impact in how biology develops in in low-income countries, and in El Salvador, in particular.
The bulk of the funding for the fellowship was from the Vienna BioCenter, but I also made a GoFundMe page to have additional funds to use to cover Eduardo’s travel, as well as a small stipend to cover living costs during the three months. I think it is important to remember that if we’re going to bring someone from a low-income country, you cannot expect that that person will be able to cover a roundtrip flight from across the world. We really wanted to be as accommodating as we could and consider the reality of the applicant, including funding travel, visa, but also being aware of access to opportunities when considering the strength of the application. As we move forward in creating an inclusive scientific environment, we have to consider, are we missing out on talent because of barriers to access these kinds of opportunities?
I saw that you also ran a do-it-yourself workshop for teachers in El Salvador, how did this course work and did you intentionally target teachers rather than students?
The do-it-yourself microscopes is a workshop that was developed by Bob Goldstein at UNC Chapel Hill. The premise of his programme was to offer this workshop to teachers, in his case in North Carolina. I came across Bob’s work in a conference where he had a stand with these microscopes. I talked to him about the idea of bringing this workshop to a low-income or an underprivileged country. I thought it would be a perfect fit to introduce both teachers and students to science because it was very affordable, the microscopes are easy to make, but nonetheless, give you access to the microscopic world. I think that all of those factors make it a perfect outreach tool for low-income countries. I saw the value in Bob’s programme to target teachers so that they could expand their knowledge and amplify that effect to their students, so we decided to implement this programme in El Salvador in a very similar fashion. I translated all the material, but Bob has this ‘Ikea-like’ drawing of how to build this microscope, so you don’t need a lot of text. I was also lucky to partner with a local university and we recruited around 40 to 50 teachers from across the country. It was such a good workshop; everyone came out so happy and so proud that they built this microscope. It was fun watching people’s first reaction, when they put say a leaf under this microscope, and all of a sudden, they could see the cells. A lot of these teachers had never seen that, not even in a textbook. The teachers wanted to take the microscopes into to the classroom, but they also wanted to show their families because they were so excited by it!
How can we, as a community, better support and promote scientists from low- and middle-income countries?
We’ve touched on some aspects already, and I think that we are in a very unique position to be able to provide opportunities to students from disadvantaged backgrounds. As a community, we should support open calls, specifically to recruit people from low-income countries, or we could reserve spots within our existing programmes to include talent from disadvantaged backgrounds. And we need to think about the barriers could prevent people from participating in such programmes. The exercise of putting yourself in other people’s shoes could really transform the way that we run a lot of our research programmes and we are currently discussing how we could implement this here at the Vienna BioCenter. We are discussing how, within our current summer programme, we can reserve spots for students from low-income countries, and what would we need to provide to really support the students participating in the programme.
It’s exciting to think that something can start with a small project, inviting one person into the lab, but then if that could be amplified to say 20% of institutes offering a few weeks in the lab, there would be a huge number of scientists benefiting from this kind of experience.
Yes, that’s a really good way of thinking about it. It could be applied to any research institute across the world and could really have an impact. But I think it is good to start with a small ‘experiment’ and then really pitch for implementing something bigger. That’s my hope. I hope that for next summer we can already reserve ~20% of the spots on our research programme for students from underprivileged backgrounds with the idea that we recognise that talent is everywhere, and that science also benefits from a diverse talent pool. And so, in that effort, we have restructured the programme to allow for this enrichment.
You’ve spoken about Andi Pauli and Bob Goldstein as mentors. Do you have any mentors or role models either in research or science communication and outreach?
One person that comes to mind was someone that I intersected with during my time at Duke. I was really lucky to be part of this programme called the Biocore Scholars programme, and this programme is led by an amazing scientist, advocate, and communicator, Sherilynn Black. Sherilynn created this graduate student programme that’s designed to build a supportive community for PhD students of diverse backgrounds. I applied to be part of this programme and remained in the programme throughout my PhD. It became my scientific home during my PhD. It was a cohort of really diverse students that were in the programme to come together and support each other and collectively move through our PhD experiences. I really owe my PhD to this community. It has made me passionate about community building within scientific spaces that allow people to thrive. If I could be a fraction of Sherilynn Black, I will have made it in life!
What’s next for you, both short term and longer term?
In the short term, I’m really enjoying my postdoc here at the Pauli lab. I love mentoring students and I think that the scientific world is the perfect ground for building communities, for mentoring people and for coming together and communicating our science broadly. In the long term, it’s hard to say, but I would be looking for something that allows me to continue this role of creating community, communicating science, and mentoring students. I think that my future role could take shape in many ways for me.
Where do you think developmental biology will be in ten years?
During my PhD, I was introduced to the field of quantitative biology and the additional insights that quantitative methods can provide into the dynamics and the regulation of biological processes within developing organisms. I’m curious to see how this field is going to keep evolving. And not only that, but how interdisciplinary projects that use concepts from physics or concepts from computer science, can bring new insights to biological questions that have been studied for a long, long time. At the SDB meeting, for example, we started seeing how people are using AI to be able to predict differentiation cascades – I think that that is truly fascinating. And combining that with detailed data sets of transcriptional states of cells can really propel the developmental biology field forward. So, those are the things that I’m really excited about, but whether that actually ends up being the crux of developmental biology in 10 years, who knows, but that’s something that I look forward to reading about!
When you’re not in the lab, what do you do for fun?
I really love going on walks. I have a sister that lives with me here in Vienna and every weekend we pick a different district or a different neighbourhood in Vienna to walk around. I think it is a great way to know a city. I also love travelling, and one of the biggest advantages of being in Central Europe is that I have access to a lot of beautiful cities, just amazing historical places. When I travel, I enjoy getting to know the culture and the food of different countries. Those are two of my big ones, but I also really enjoyed dancing, so that’s something I like to do on the weekend.
The diversity and complexity of shape in uni- and multicellular organisms has long been a source of fascination and interrogation. Since the seminal work of D’Arcy Wentworth Thompson, the study of the emergence of shape, so called morphogenesis, has been strongly influenced by the concept of emergence whereby complex pattern/shape can be explained by relatively simple mechanical and mathematical laws. In parallel, the rapid progress of the biochemical characterisation of the regulators of cell signalling has opened the possibility to compare developmental programs and dissect the molecular basis of evolution. Yet, how mechanics and mathematical laws may constrain the evolution of new shapes and morphogenesis has only come back to light recently. For two days (12 and 13th of December 2022), the symposium MeMoDEvo taking place in Institut Pasteur in Paris tried to discuss this issue by gathering interdisciplinary speakers and participants on site and online and organising two mornings of open discussions. The discussions and talks covered a large range of approaches (mathematics, fluid mechanics, soft matter physics, genetics, evolution, developmental biology, epistemology…) showcasing a diverse set of organisms, from mammals, birds, reptiles, insects, choanoflagellates, plants, algae, yeasts, and bacteria.
This fully hybrid meeting gathered close to 100 participants on site (mostly from Europe) and 100 participants online and its unusual format led to very interesting discussions and interactions. The conference was possible thanks to the support of several sponsors, including The Company of Biologists, the French Society of Developmental Biology, the Qbio initiative in Pasteur and the Pasteur Institute, as well as the DIM Elicit initiative
“Unconference” morning sessions and open discussions
One of the best parts of conferences that we had been missing over the past two years is the free time and open discussions in between sessions. We therefore dedicated a significant amount of time to open discussions and round tables during mornings with a subset of participants and the speakers (roughly 40 people). In line with the spirit of the meeting, we relied on a mixture of programmed schedule and self-organization.This engaging time involved first a quick introduction by each participant on their background and interest, followed by open discussions on the first day. This was followed the next morning by three round table discussions.
The first round table addressed constraints on the evolution of shape and how to reveal them experimentally. How can an organ evolve from one shape into another? Are there any limitations regarding shape innovation? The discussion included the distinction between pure physical/environment constraints and developmental hard-wired constraints related to the evolution history of the organism. Exploring the distribution of organ shape in the morphospace (using landmarks and dimension reduction) using intra and inter-specific variability can reveal such constraints by looking at non-occupied zones in the morphospace. The cause of these unoccupied areas can be either selective pressure or funnelling of evolutionary change by developmental constraints. A combination of description of natural variation and exploration of shape variability in the laboratory (including direct perturbation of developmental processes by mutagenesis and experimental evolution) may help to disentangle them. The discussion ended (as expected) with more questions than answers concluding on the mysterious cases of abrupt shape evolution/innovation which have to bypass strong developmental constraints while maintaining proper adaptation.
The second discussion was centred on the emergence of multicellularity comparing a large range of organisms which combine single cell and aggregate life mode. By comparing the mode of multicellularity (clonal/aggregative), the signals/conditions triggering aggregation or dissociation and the components that can structure and organise the aggregates (adhesion, contractility, matrix), a very complex pictures emerge with all sort of combination of strategies found in nature, outlining again the diversity of evolutionary path leading to multicellularity (see the table below summarising the comparison).
Finally, the last discussion was centered on sharing experience with various methodologies for mechanical simulation of tissues, ranging from continuous model, object based modeling and finite element modeling.
Afternoon hybrid sessions
The two afternoon sessions were following a more classic conference format alternating talk on site and online with an hybrid crowd. You will find hyperlinks connected to the published works that were discussed during these sessions (preprint and peer-reviewed articles). The meeting was launched by Thibaut Brunet (Institut Pasteur) who made a quick historical overview of the evolution of approaches to understand development and the various phases that brought to the front stage the role of mechanical constraints in shape evolution and its recent rejuvenation. The first talk was then given by Bruno Vellutini from Max Planck CBG who illustrated how the appearance of the cephallic furrow during evolution in Drosophila embryo may have helped to buffer mechanical constraints generated by ectoderm movements and cell division during gastrulation. Marie Monniaux, from the ENS RDP lab in Lyon, described the morphogenesis of petunia petals and sepals and how the comparison of mutants can help to disentangle the regulation of growth and shape by different epidermal layers. Jean-Léon Maître from Institut Curie then provided a quantitative comparison of the mechanisms of embryo compaction in different mammals, illustrating how qualitatively similar mechanisms can yet rely on quite different absolute mechanical properties. Arghyadip Mukherjee from the ENS in Paris described how topological transition through different modes of epithelial fusion can help to describe neuroepithelial organoid shape evolution. This was followed by Jose Bico, from the ESPCI, who illustrated how living matter can be used as an inspiration for generating complex inflatable shape based on local differences of inflation/growth (with a live illustration on stage with cup, saddle or helix shape generating devices). We then came back to insects with Steffen Lemke (from Heidelberg University) who compared gastrulation between different fly species (including Drosophila) and identified essential genes sufficient to explain several morphogenetic innovation in flies (including the mode of mesoderm invagination, cell elongation and the requirement for cephalic furrow). We then finished the first afternoon session with Annemiek Cornelissen from LMSC laboratory in Université Paris Cité, who used cracking theory and differential mechanical properties of tissues to explain the morphogenesis of jellyfish canal network.
The second afternoon session started with Arkhat Abzanof from Imperial College London who illustrated the power of morphospace analysis for the understanding of craniofacial shape evolution in vertebrates (from bats, Darwin finches and crocodiles). He was then followed by Hélène de Maleprade from Sorbonne Université who described various collective and single cell swimming strategies in Chlamydomonas, Volvox and Gonium. We then had an online talk from Lakshminarayanan Mahadevan from Harvard university describing fluid mechanics model of multicellular movements occurring during chick gastrulation and how the variation of initial conditions can recapitulate different modes of gastrulation across Vertebrates. This was followed by conceptual and theoretical considerations from Ana Soto and Maël Montevil from the Centre Cavaillès on the concept of autonomy in living systems and the definition of core principles (default state, variation and organisation) allowing proper understanding of a living system. We then came back to plants with Etienne Couturier from the LMSC lab who applied the Lockhart model (describing cell growth as a function of turgor pressure and viscoelastic deformation of the wall) to describe the dynamics of maïze root growth against a physical obstacle. This was then followed by an online talk from Peter Yunker from Georgia Tech describing his work in collaboration with Will Ratcliff on the ‘long-term experimental evolution’ of multicellular development in yeast. Remarkably, experimentally evolved yeast colonies were recently reported to have acquired macroscopic sizes after years of selection in the lab. The talk dissected the cellular and physical basis of this transition, which turned out to rely on mutations promoting elongated cell shape and reducing the mechanical stress that can cause colony fission. The meeting ended with a broad theoretical view of the evolution of multicellularity and morphogenetic innovation by Stuart Newman from New York Medical College, introducing the concept of dynamical pattern modules (integrating gene regulatory network and associated physical/spatial constraints) and their contribution to developmental and morphological innovation during evolution.
Conclusion: a lively and environmentally friendly format promoting discussions and connections
The meeting managed to gather a diverse crowd leading to a very refreshing and eclectic program. The relative “self-organisation” of the morning sessions actually led to very vivid interactions and deepening of the questions related to the meeting topic. All the participants came to conclusion that we should be ready for a MeMoDEvo#2 ! Of note, the symposium was the living proof of the possibility to organise a diverse, inclusive and very dynamics meeting while limiting environmental impact. Every speakers used the train to commute to the meeting and we could yet gathered a diverse crowd from Europe as well as many online attendees and speakers from other continents. Despite the usual technical hiccup associated with the hybrid format, we can only recommend the application of the same recipe !
Romain Levayer, Thibaut Brunet, Katja Heuer and Roberto Toro, organisers of the MeMoDEvo symposium.
Our next Development presents… webinar will be chaired by Associate Editor Paul François (who recently moved to the University of Montreal from McGill University). Paul has invited three talks on the topic of theoretical and computational modelling of developmental biology.
Kirsten ten Tusscher (Professor of Computational Developmental Biology at Utrecht University) ‘Reverse engineering lateral root formation’
Simon Freedman (Senior Bioinformatics Scientist at Illumina presenting Postdoctoral work from Madhav Mani‘s group at Northwestern University) ‘A dynamical systems approach to cell fate decisions’
Mindy Liu Perkins (Postdoctoral Fellow in Justin Crocker‘s lab at EMBL) ‘A bistable autoregulatory module in the developing embryo commits cells to binary fates’
June 25 – 30 Mount Holyoke College, Massachusetts, USA
It’s back! After 4 years and a global pandemic, the Developmental Biology GRC is on.
This is the premier, international scientific conference for the presentation of cutting-edge and unpublished developmental biology research. The format prioritises discussion and informal interactions among scientists of all career stages after talks, at poster sessions, and during the meeting. We have a great range of speakers, concentrating on the latest developments in the field.
Full speaker list and venue details are also available on the website.
Developmental Biology covers molecular, cellular, tissue and organismal levels, as well as theoretical concepts from physics and mathematics. The 2023 Gordon Conference topics include metabolic fluxes in development, transgenerational inheritance, gene regulation, dynamics of signaling at tissue scale, lineage tracing in the single-cell era, regeneration and tissue mechanics. We have also included a session highlighting the relevance of Developmental Biology to the development of diseases later in life. Because progress in Developmental Biology depends on cross-fertilization of ideas from complementary organisms, presentations will include studies in standard invertebrates such as Drosophila and C. elegans, classic vertebrate models including zebrafish, Xenopus and the mouse, as well as plants, non-classical models and humans. Afternoons and late evenings will be reserved for presentation of posters and informal interactions. The relaxed atmosphere and the rural setting of the meeting will encourage stimulating discussions between established and junior investigators in all aspects of the field.
Our lab is seeking PhD and POSTDOC candidates to apply to various calls that are NOW OPEN, so hurry up and do not miss any of these opportunities and contatct us ASAP if you are interested in the fields of Genomics, Embryo Development, Bioinformatics, Evolution and Molecular Ecology.
Our lab currently has different research lines ranging from muscle and heart development and the evolutionary impact of gene loss (see an example https://go.nature.com/3E83Lw8), as well as EcoEvoDevo investigations studying the genetic response of the defensome of marine embryos to environmental threats such as biotoxins produced by harmful algal blooms of diatoms in the context of global warming or the effect of noise contamination from human activities on embryo development of marine invertebrate species (see an example in https://go.nature.com/2O82VY8).
Our research focus on the study of the appendicularian tunicate specie Oikopleura dioica as our favourite animal model (see this “A day in our lab” post in the node https://thenode.biologists.com/day-life-oikopleura-lab/lablife/ and embryo microinjection, CRISPR, RNAi, DNAi, fluorescent and confocal imaging, RNAseq, ATACseq, population genomics and bioinformatics are among the techniques we use in our lab. Among candidate postdocs, experience in some of those techniques will positively considered, and specially candidates willing to develop new tools based on CRISPR, as well as candidates willing to develop single-cell omics approaches to Oikopleura dioica to address some of the topics we currently work in the lab or new questions that candidates might be interested.
For PhD, there are varios calls already open, so please contact us as soon as possible, since the dealine is very soon.
For POSTDOCS, there is a call for a 3-year position to be open next week (required to have defended the PhD between 1/1/2021 and 31/12/2022; 30.000 EUR/year), and some other calls are coming in the next moths, some including starting-grants.
CONTACT: Interested candidates, please send an email ASAP to Cristian Cañestro (canestro@ub.edu), including a brief letter of interest, a brief CV, including list of publications with their impact, and technical skills all together in ONE single pdf file.
Recent publication from our lab about massive gene losses and the deconstruction of the cardiopharyngeal gene regulatory network in appendicularians and the origin of the free-living and sessile styles in ancestral tunicates that was highlighted in the cover of nature
“The placenta is unique amongst organs in that you have two individuals contributing to a single organ.”
Dr Courtney Hanna
In the latest episode of the Genetics Unzipped podcast, we’re going back to the womb to explore the genetics of how to make babies – from finding out how birthweight is linked to the risk of diabetes to investigating the multifaceted role of the hormone prolactin in pregnancy and the role of epigenetics in the placenta.
The International Zebrafish Society (IZFS) is pleased to announce the call for nominations for our two prestigious annual awards – The George Streisinger and the Chi-Bin Chien Awards. Members of the zebrafish community are invited to submit nominations by February 2, 2023.
About the Awards
The George Streisinger Award recognizes senior investigators in the zebrafish community who have made outstanding and continued contributions to the advancement of the field.
Among the criteria that may be considered:
Contributions in the form of conceptual advances that have opened important new research directions
Development of tools or resources that have been transformative in enabling new research possibilities
Service to the Zebrafish research community
Nominations should be submitted by e-mail with the subject line “George Streisinger Award” to info@izfs.org. The email should include a single PDF file that contains:
A statement (up to one page) written by the nominators describing the key contributions of the nominee to the field.
The statement must be co-signed by two or more IZFS members who support the nomination.
A list of up to ten publications or links to online resources or databases that illustrate the central contributions of the nominee to the field.
The Chi-Bin Chien Award recognizes outstanding graduate students, postdoctoral trainees, or recently appointed faculty members from any country who have made significant contributions to the field of zebrafish research and have exhibited the generosity and openness that characterized and motivated Chi-Bin Chien.
Mentors of PhD or post-doctoral trainees of the zebrafish community are invited to submit nominations for the Chi-Bin Chien Award.
Nominations should be submitted by e-mail with the subject line “Chi-Bin Chien Award” to info@izfs.org. The email should include a single PDF file that contains:
A one-page statement from the nominee describing his/her research and its importance to the advancement of zebrafish research.
The nominee’s CV
Letter of recommendation from the mentor.
Letter of recommendation from one additional scholar who is familiar with the research being described in the application
We asked you to select your favourite Development cover from 2022* and after all the votes were counted, the Node community has chosen the mouse lung lobe from Issue 21. The image is linked to the Open Access Research Article from Prashant Chandrasekaran, Nicholas Negretti, Aravind Sivakumar, Jennifer Sucre, David Frank and colleagues on the role of CXCL12 in defining lung endothelial heterogeneity and promoting vascular growth.
Issue 21: Mouse lung lobe
In second place were the astrocytic cells in the mouse spinal cord from Maria Micaela Sartoretti, Carla Campetella and Guillermo Lanuza featured on Issue 15. Third place went to the Arabidopsis hypocotyl graft junction from Phanu Serivichyaswat, Kai Bartusch ,Charles Melnyk and colleagues in Issue 5.
Issue 15Issue 5
Interestingly, it wasn’t any of these entries that won the in-house team at Development the box of chocolates on offer for the most popular cover from The Company of Biologists in 2022. In this competition, the winning cover image was the stages of Xenopus development from Natalya Zahn, Christina James-Zorn, Aaron Zorn and colleagues in Issue 14.
Congratulations to the winners and thanks to everyone who submitted cover art in 2022. We are delighted to have had another year filled with wonderful cover images and we are now looking forward to seeing what 2023 brings!
During the first year of my course in biological sciences, I became interested in developmental biology. I am mesmerized by the exploration of the beginnings of life through the complex interactions and changes that are taking place from the moment of fertilization. Furthermore, I realized the potential applications that scientific advancements in this area may have for disease prevention and treatment. This is especially interesting to me as a wildlife health student, aiming to conduct research on wildlife conservation in the future.
Research led by Dr. Denis Larkin found a mutation in the amino acid sequence (AA) of the NRAP gene in Yakut Cattle, resulting in a single nucleotide polymorphism (SNP resulting in a Glutamine to Histidine substitution (H100Q) at position 100) (Larkin et al., 2021). Yakut cattle are resistant to the low temperatures of the Siberian arctic and exhibit features such as efficient thermoregulation, a slow metabolic rate, and resistance to diseases. Nebulin-Related-Anchoring Protein (NRAP) is an actin-binding gene responsible for producing proteins to connect actin filaments in skeletal and cardiac muscle (GeneCards, 2022). The NRAP gene AA sequence is evolutionary conserved, however, this specific H100Q mutation was found in other cold-adapted, hibernating species and those entering periods of extreme bradycardia.
The expression of this particular SNP in those specific animal species prompted us to start this study. My summer project aimed to create the H100Q NRAP single-point mutation in the human gene and clone it into a suitable vector for in-vivo expression. This construct will then be used for microinjections into zebrafish embryos to observe potential changes in their heart development, heart rate, and muscle function.
I was keen to start the project and started by gathering information about zebrafish heart development, as well as molecular biology techniques. Together with my team, we created a well-thought-out cloning and mutation strategy to substitute a single nucleotide from the human NRAP gene from CAC (H) to CAA (Q) to recreate the H100Q mutation found in Yakut cattle.
However, I soon learned that theory and practice are two very different sides of the same coin. The world of molecular biology seemed to be unpredictable at first! After the first couple of ligations that didn’t produce any colonies, it was difficult to believe that getting enough material to mutate this gene was even possible. But that didn’t stop us. We troubleshot, experimented with enzymes and buffers, made our own competent cells and bacteria plates, changed reaction conditions, consulted papers, and of course, could always rely on the advice of our helpful supervisors. Having an amazing and experienced team around us at all times was key to our success. Not only could they provide valuable insights through their many years of experience in molecular biology but also offered constant encouragement: “it will be fine” turned out to be right. I was determined to make it work and this experience strengthened my resilience and problem-solving skills.
I acquired many useful laboratory skills which will be very invaluable as a researcher. I learned how to read vector maps, how to clone, use publicly available software, and how to design primers for PCR… just to name a few. Understanding the science behind molecular biology techniques allowed me to modify protocols to troubleshoot efficiently. Finally, the Sanger-sequencing results came back, and excitingly, we validate our single-point mutation H100Q of the human-NRAP gene in pBluescript II SK (+) (Figure 1).
Figure 1: Sanger-sequencing read from nucleotide 253 to 294 by T3 polymerase. CAA mutation highlighted in yellow with C substituted to A at position 285.
Apart from generating the mutation, I learned how to conduct research on live animals during my work in the fish facility. I bred and cared for zebrafish embryos until up to 5 days post-fertilisation period during which they are not regulated under a Home Office licence. I practiced my microinjection skills into one-cell stage embryos. My fascination only grew stronger and I found myself peaking at the embryos throughout the day to witness the one cell splitting into 4-, 8- and 16-cells forming a plate on top of the yolk and was amazed how, in the span of only 48 hours, I could make out the heart structure and observe the heartbeat under a stereomicroscope. Another interesting aspect of this project was to investigate the H100Q-NRAP mutation in Pinniped and hypothesize its origin in Otariids and Odobenidae.
Overall, I was thrilled to discover how different aspects of biology, from molecular biology, and genetics to developmental biology and physiology came together in this project. It reminded me once again of the importance to follow a big-picture approach and that scientific understanding can seldom follow from isolated observations. The point is, however, to put them into the context of constant change interplay with each other and the environment. A continuation of this project would on the one hand be useful to further aid the scientific understanding of cold adaptations and hibernations to conserve ecosystems and species being threatened by climate change and on the other hand understand the physiological implication of heart mutations in humans.
I would like to thank my supervisor Dr. Claire Russell, Dr. Caroline Pellet-Many, Dr. Steve Allen, and Dr. Denis Larkin for their support, insights, well-stocked freezers full of enzymes, and encouragement throughout the whole process. I am also kindly thanking the British Society for Developmental Biology for granting me this fantastic opportunity and opening the doors to the world of scientific research for me. Thank you!
References
Buggiotti, L.; Yurchenko, A.A.; Yudin, N.S.; Vander Jagt, C.J.; Vorobieva, N.V.; Kusliy, M. A.; Vasiliev, S.K.; Rodionov, A.N.; Boronetskaya, O.I.; Zinovieva, N.A.; Graphodatsky, A.S.; Daetwyler, H.D; Larkin, D.M. (2021) ‘Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia’, Molecular Biology and Evolution, V(38), Issue(8), pp. 3093–3110, https://doi.org/10.1093/molbev/msab078
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