Recently, Brent Foster and I published an article on non-model organism (NMO) research, where we interviewed several researchers working across the globe on the challenges, rewards, and the particular questions they investigate while working on (relatively) little-studied organisms. Although we aimed to provide a bird’s-eye view of NMO research in a pot pourri-style article, we found that they each of our interviewees had many interesting things to say that we thought it was a shame not to share with a wider audience. For this reason, we decided to publish the full interviews as well, which we will be doing over the next several weeks.
This interview is with Dr. Claudia Patricia Ornelas-García, investigator at the National Autonomous University of Mexico (Universidad Nacional Autónoma de México, UNAM), who works on the Mexican cavefish (Astyanax mexicanus) and other freshwater fish, looking at their systematics and speciation. The full transcript of the interview is below:
Can you summarise your work in a few sentences?
I work mainly with the systematics and speciation mechanisms in freshwater fish species. Since my PhD, I have worked with Astyanax, a very interesting genus because it is distributed from Argentina [all the way] to the Mexico-US border. During my PhD we reconstructed the evolutionary history of the genus in a particular region identified as Mesoamerica. But in general terms, what we were doing in that project was to analyse four molecular markers, three mitochondrial and one nuclear, to recover the systematics of the group. During the development of the project, I was very interested in the lacustrine systems of Central American Lakes in Nicaragua and Mexico. In these lacustrine systems there are a pair of morpho-species that were sympatric and we were very interested in the correlation between the morphology and the genetic differentiation, because when we were doing this systematic group, they at least seemed to be sharing some haplotypes in the mitochondria. We continued working on the ecological divergence, ecomorphological divergence, and some morphometrics in this pair of species, and more recently with RadSeq Data.
Years later, when I came to Mexico and established my own lab, we started working with cavefish. Actually, when I started, my first job was in Querétaro, very close to the caves in San Luis Potosí. I started working on the caves and I fell in love immediately because the environment is so amazing. It’s very particular. And the system is also very interesting. As you know, there are a lot of genomic resources available nowadays. In the beginning, when I started working with this group, there were maybe 10 or 11 cave populations already analysed from [a] phylogenetic perspective, but not from an evolutionary or developmental perspective. So in the beginning, I just wanted to include as many caves as we could, so we could test these hypotheses of how many times the fish has been able to adapt to the caves. There were several hypotheses, some of them say that it happened only once and there has been a lot of drift. The other says that there’s two independent lineages. I’m in that group that would suggest that there are two independent lineages that came to the caves and adapted to them. Actually, in our most recent paper, by a master’s student of mine, we assess this question, using not only the complete genomes that are already available, but also including some caves that were never analysed before. So we have a very, very exhaustive sampling. And in our results, we have at least three independent colonisation events of the caves, which for some is crazy, it’s not possible. But from our point of view, we are really relying on exhaustive sampling of the caves, and that is what we’re suggesting.
Nowadays, we are starting to move to some developmental analyses, because we were able to capture some fish from the caves, and we are reproducing them here in the lab. So far, we have been able to reproduce five different populations, different from the common ones like Pachón or Tinaja. We are reproducing Escondido, Arroyo, Tigre, Chica, and Pichijumo. Sabinos is common, but it’s less common than others. So far, we are trying to characterise some developmental features.
One of my students is working on the Rad-seq, and we are starting to work with RNA-seq, and we are a trying to compare the genetic convergences across different cavefish lineages, particularly including some less studied populations such as Escondido, which is from the [second] linage in the Guatemala region. We are trying to compare the differences during early development because we have realised that they have a very particular mutant in some visual pigments, so we are trying to match that variation with the phenotype. We are also exploring the phenotypic convergence with other cavefish in Mexico, like Prietella phreatophila, a catfish in the northern part of Mexico, and also with other families of cavefishes from the southern part of Mexico. We are trying to investigate them for convergences in phenotype, particularly in some processes related with asymmetry that has been reported in Astyanax and in P. phreatophila, and we are trying to check out if it’s consistent across cavefish living in Mexico or only in these two cavefish.
What kinds of asymmetry is this?
Astyanax is very interesting because in Pachón there has been described a directional asymmetry, as well as in Ictalurids [such as Prietella], and actually it’s in the same side, left turn of the head. Particularly in a cave called Chica there is one very well characterised Astyanax hybrid population (between the surface [fish] and the cavefish). In that population there is fluctuation asymmetry, [toward the] left or right, [similar to] chiclids, [that have] fluctuating asymmetry in the mouth of a scales-eating species. It’s interesting that when you analyse it in the hybrid population, the asymmetry is different in comparison to the other caves.
I understand that there are a lot more resources for you to study these types of species now. But obviously, it is generally a group of species that is not studied by an enormous number of people around the world. Are there particular challenges associated with that?
Yeah, I think one of the challenges is that there are a very restricted number of people working with these [species]. And in a way, it’s fascinating, because you will find something new for sure. But [from another point of view], in research groups [studying established organisms] it is easier.
We were trying to characterise the microbiome of the fish, we have a paper on that. And it was a little challenging, because there was not a lot of information already published on protocols or how to treat the data. Or when we are trying to set up [experiments], for example, for physiology or for another kind of ecological analysis, it’s sometimes difficult. But in a way, I think it’s very, very interesting. During my Bachelor’s, I was working with mice, the typical model in the lab, and somehow I think that the number of questions sometimes can be very restricted because there’s already so many studies in these animals, that it’s difficult to come up with something new.
You did touch upon this when you’re describing your work, but was there a specific thing that convinced you that these fish are what you want to work on?
I think the main reason was a because I have always been interested in mechanisms driving the evolution of morphology. When I started working on the lacustrine forms, it was like “Why do they have these different teeth, or different heads, or different body shapes?” and in the caves it’s dramatic, the change is impressive. Are these important morphological changes? When I started investigating the environment, it’s fascinating that they can survive under those conditions. That was one of the reasons.
Another important thing to highlight in Astyanax is that we have the Annual Meeting. It is very interesting because there are a lot of young people, together with senior researchers, and the community is very open. Because it’s not a model organism, [everyone is] really [willing] to talk about the system in a very open way, and include new researchers. Particularly for me, when I was finishing my PhD, this was a very dramatic point, because I saw a potential in the system that I can be included. And I have a lot of things in my favour, I am from Mexico, I can work in the field, I can do a lot of in situ experiments. Even nowadays, there are very few Mexicans working with Astyanax. It just happened that there were a lot of things that made me realise that there was a lot of potential in the [Astyanax] system for me.
Would you say there’s a particular question in your field that you find really fascinating? Or a finding or a result that you really weren’t expecting?
Yeah, as a systematic biologist, I have a very, very important question for me, which is how many species [the cavefish are]. This is an important question from two different perspectives. One is conservation. The other is from an evolutionary point of view, because for sure, they can hybridise, even lineages between the two branches can hybridise. So in a way, it’s very difficult to test for the biological concept of a species. Sometimes it’s difficult even for the developmental biologists, because they are really trying to understand the link between the gene and the morphology. We are trying to understand the mechanisms giving rise to this kind of systems, and how easy it is to speciate in this context. So the implicit question regarding these ecomorphs or ecotypes is, are they different species? And how significant is this for the evolutionary history of the model?
So in a way, it was very interesting for me at the beginning, because when I started going to these conferences on Astyanax, it was very easy for me to always think about the systematics, about the phylogeny. And sometimes [other groups] were interpreting some variation in the morphology through local adaptation. But actually, it’s related to the [evolutionary] history of the system, like the number of vertebrae, or various characteristics, actually, they were shared by ancestry, not by local adaptation. So I think that’s very, very important in these kinds of studies, trying to link between the genetics and the morphology. That’s one of the reasons I want to have a very good notion of how many times this [cave dwelling] model has evolved, because if it [evolved] only once, the interpretation of repeated evolution, or whatever we are asking, is different. The other question that is very fascinating for me is how their morphology can be so divergent, even under gene flow circumstances. How is this possible without any barriers [between the putative species]? That’s the reason we work with Astyanax.
How does data analysis and sharing between labs that use Astyanax and related species differ, in your opinion, compared to studies that use more established model organisms? You said, it’s a fairly open community. But you know, are there any major differences?
I must admit that I don’t know if I have enough experience on this question. All of my experience is with Astyanax. Even though during my Bachelor’s I was working with mice, I’m not familiar with other groups. In the lab where I was working, they were very specific in the questions that they were [asking], and it was not very easy to share information with other labs.
In my opinion, one of the things that the Astyanax model has is that [researchers working on it] are very open. For example, when we were trying to reproduce a fish, we were obtaining a lot of information [from other groups].
From what I know about Astyanax, that there are labs that work on it in the context of heart regeneration, because some have a non-regenerative heart, in contrast to the regenerative zebrafish heart. How large is the community that works on the more phylogenetic aspect of the species compared to those working on developmental or regenerative questions and is there any crosstalk?
Nowadays, a lot of people are trying to [investigate] this model [from] the eco-evo-devo perspective. They have realised [that it is important to distinguish between the different Astyanax lineages], because some of the results that they get are related with the lineage, and not with particularly with the environment. In these terms, there is a growing number of labs wanting to work in the field, know more about the ecology in situ, learn more about the behaviour, the physiological adaptations. Some are is trying to [replicate] experiments in the field, check if the same thing happens in the lab versus in natural conditions. In my opinion, the species gives a very particular opportunity, because it’s not like in other places where it’s very difficult to get access to the cave systems in the in the field. So nowadays, even though regulations are increasing, they are attainable. [Researchers] can [request] permits and get them in a year, which a reasonable time. So it’s more a question of what the interests of the researchers are, because they can really put their questions in different contexts, and navigate between eco, evo, and devo.
Is there anything else that you would like to add?
The problem with non-model organisms is the conservation situation. For sure, nobody will catch Mus musculus from the field, they already have so many reproductive lines in captivity that they don’t have to. The non-model organisms are in the opposite situation. Most of the labs [working on them] want to have more wild lines, more related with what is really happening in the field. And if you have 200 labs working [on cavefish], imagine the impact that we can have on the natural population. These cavefish are not really large [populations]. We published, just at the beginning of 2023, a paper [on] size estimation of the fish population in the caves, and it’s maybe around 1000 fish, or [a few thousands] of fish. It’s not really that large [a] number. And imagine, in the last 10 years, more or less, there have been around 200 fish extracted from the caves. So if you imagine a system that has to recover from 20% of the population being lost only because of scientific sampling, it’s a problematic situation.
When you try to make researchers aware of the situation, [they] really believe that the main extinction drivers of this kind of population are not related with our sampling. Most of us really believe that it’s all global warming, or local people extracting water for drink. I’m very surprised, because normally you have to fight this kind of attitude outside the scientific [world]. So in my position, I’m trying to make people aware of this, but it’s not easy. But none of the above is false. Global warming, and people extracting water for drink, are part of the problem. Thus, it’s important to be part of the solution, and maybe we should consider what we can do to solve the conservation situation.
Some of the most iconic populations, like Pachón, you can find thousands of papers published on it. And it’s in a little bit of a critical conservation situation right now. Many labs have been able to reproduce it. And most [subpopulations] can be easily [obtained] from [other] labs. But even nowadays, to avoid inbreeding, some labs could require to collect wild fish. The Guatemala region has conservation issues, because although they are not easily-accessible caves, most populations are very small, and not well-connected between them, because of the phreatic level of the water, which can lead to extinction more due to their demography than to other causes. So its conservation situation is very different. But in a way, we have the same situation in other places.
And it’s not only in Astyanax, it could happen in other non-model organisms too. For example, Axolotl is also an amazing model system. If 50 labs in the world start working with one particular population, there can really be an impact in the local population. That is why I think we need to be more aware of the impact and do our best to guarantee the prevalence of this model for future generations. [Because] what makes these organisms amazing also makes them vulnerable, in a way.
Understanding the effects of the environment on animal physiology and biomechanics is at the core of Journal of Experimental Biology. Environmental factors such as temperature, food availability, sound or the presence of predators can profoundly shape how an animal grows and matures into an adult. In this Special Issue, we take a close look at developmental plasticity, which is the influence of conditions experienced during early development on an animal’s phenotype. In her classic book of 20 years ago, ‘Developmental Plasticity and Evolution’, Mary Jane West-Eberhard proposed that ‘alternative phenotypes’ that arise in organisms under different early life conditions play a critical role in moulding animal evolution and diversification (West-Eberhard, 2003). The ensuing years have seen increasing attention on how developmental plasticity may contribute to evolution. Given this, coupled with the explosion of new information on the epigenetic mechanisms underlying developmental plasticity, the growing number of submissions to JEB in this area, and the fact that an earlier special issue on ‘Phenotypic Plasticity’ (Hoppeler et al., 2006) is now 18 years old, the time seemed right for a special issue on developmental plasticity. In the current issue, we have capitalized on the diversity of animal models under study, from worms to dung beetles and lizards to mice, to assemble a strong comparative approach to the topic. We also aimed to bring together researchers considering developmental plasticity from diverse angles, from molecular and cellular biology to whole animal physiology, ecology and evolution, to more fully understand and integrate new approaches and research findings.
Developmental plasticity is defined by the rearing environment, from nutrition to social conditions, which provides critical information that developing animals use to shape the maturation process and resultant adult behaviour and physiology. Such context-dependent plasticity during development is often considered to be both widespread and adaptive, although the extent to which this is the case remains unclear (Sánchez-Tójar et al., 2020). It is also important to recognize that conditions such as resource limitations or exposure to environmental contaminants can result in damaged phenotypes that are clearly not adaptive. In this Special Issue, Metcalfe (2024) discusses a third possibility – that variation in early conditions need not always result in obvious adult changes, but may alter developmental trajectories in ways that have more nuanced consequences over longer periods of time. Other articles in this Special Issue focus on identifying critical environmental factors that serve as cues for developmental adjustments, and how these, in turn, are transduced within the developing animal. For example, information transmission may be mediated by parental behaviour (e.g. Mariette, 2024) or indirectly via provisioning of the egg. Hotter temperatures, food scarcity or stress (e.g. from predators) experienced by a parent provide anticipatory cues to developing animals that may prepare them for similar stressors in later life. Food availability or nutrition, in particular, appears to be of fundamental importance in an animal’s developmental trajectory, to the point where we may ask whether it is a ‘master’ regulator of development. Understanding the mechanisms involved in nutritional effects on development is a critically important area for future research.
Cover: The male gazelle dung beetle (Digitonthophagus gazella) develops nutritionally plastic head horns. Males with access to low-quality nutrition during their larval stage develop into hornless adults (left). By contrast, males with access to a high-quality diet develop into large adults with exaggerated head horns (right; both images are on the same scale). Rohner et al. (jeb245976) review the many ways in which plasticity, symbionts and niche construction interact in shaping dung beetle development and evolution. Photo credit: Patrick Rohner. (No Ratings Yet) Loading...
Exceptional students from anywhere in the world are invited to apply!
Who can apply? We’re excited to welcome outstanding young scientists who have completed their BSc or MSc studies or are in their final year, in the fields of biological/medical sciences, and are considering conducting a Ph.D. Applicants are expected to possess outstanding academic records and substantial research experience.
What will you get? A two-month immersive research experience in an outstanding world-class university. Undertaking your own research project with amazing mentors in a stimulating environment. Interacting with students and principal investigators in the Faculty in informal settings. Full flight ticket reimbursement as well as housing and living allowance of up to $2000.
Why Choose Us? As the largest and most diverse Faculty of Medical & Health Sciences in Israel, we pride ourselves on fostering cutting-edge research led by globally renowned scientists and a diverse cohort of local and international students. Our state-of-the-art facilities boast the latest scientific equipment, with access to clinical samples sourced from Israel’s premier hospitals. Moreover, Tel Aviv, an international metropolis, offers picturesque beaches, a bustling nightlife, and a progressive atmosphere.
How to Apply? Two steps: 1. Identify a lab aligned with your research interests and contact the principal investigator directly by email to secure a sponsor. 2. Upload the following documents to this Online Form: i. CV, ii. BSc diploma and transcripts, iii. MSc diploma and transcripts (including partial records,if applicable), iv. A 1-page cover letter outlining your research interests and motivation for joining the program, and a Letter of support from a principal investigator in the Faculty.
Our lab is located at the Instituto de Fisiología, Biología Molecular y Neurociencias from CONICET and University of Buenos Aires within the main campus of the Facultad de Ciencias Exactas y Naturales in Buenos Aires, Argentina. We are embedded in a large and beautiful green area of Buenos Aires facing the giant Rio de la Plata.
Research summary
We are interested in how early postnatal maladaptive development and miswiring of cortico-limbic circuits could enhance our predisposition to develop psychiatric disorders such as anxiety, stress vulnerability and depression in adult life.
Group photo of the lab (Photo credit: Fernando Vázquez-Rovere)
Lab roll call
Mariano Soiza-Reilly: I have the huge responsibility (and pleasure) of leading this young team of researchers.
Tamara S. Adjimann: PhD student – I am finishing my PhD thesis on the effects of pharmacologically increased levels of serotonin, induced by postnatal fluoxetine, on the brain morphology and function.
Carla V. Argañaraz: PhD student – I´ve been part of the lab since its early stages, first as an intern and now as a PhD student working on the effects of early adversity on the serotonergic system.
Rocío B. Foltran: Postdoc – I joined the lab to study how hyposerotonergy and stress in early life can have consequences in emotional behavior in adult life.
Grace Wu: Master student – I investigate how a specific serotonin receptor is implicated in the morphological changes in a cortico-limbic circuit produced in an early postnatal stress model.
Melina Maidana: Master student – I’m working on my degree’s thesis, which consists of studying adult mice behavior after treating them with a serotonin receptor antagonist in early stages of their life.
Favourite technique, and why?
Mariano Soiza-Reilly: I’m particularly attached to an immunofluorescent technique called array tomography that is extremely useful to quantitatively explore molecular and fine anatomical features of synaptic circuits. I learned this technique during my first postdoc in Boston more than 10 years ago and since then it has been accompanying me throughout my scientific career.
Apart from your own research, what are you most excited about in developmental and stem cell biology?
Mariano Soiza-Reilly: There are so many great advances in these fields. For instance, current investigations in cortical development combining the use of organoids (or even assembloids!) and transcriptomics are certainly stunning. I´m always fascinated by current advances in the technologies available to obtain hiPSCs from patients and to differentiate them to better understand (and perhaps to treat) many neurological and psychiatric disorders with developmental origins.
How do you approach managing your group and all the different tasks required in your job?
Mariano Soiza-Reilly: I guess a fundamental factor for me is to try to enjoy every aspect of the academic career. I try to transmit this philosophy to students and young collaborators. Of course everyone is different (and this is great in a team!) but it is important to reach a balance of the different tasks to avoid the burnout. I like to think that I’m open and available to all the people in the lab, not only regarding lab life, but also for career advice. In general, we establish clear goals and objectives and then we help each other to reach them timely. We work very much as a family and this is key to maintain a nurturing and relaxing environment that facilitates career development. Having the right scientific collaborators also contributes to keep this atmosphere.
What is the most complicated issue in your job?
Mariano Soiza-Reilly: One of the most demanding tasks for labs like ours, based in peripheral countries, is to obtain international visibility from colleagues based in central countries. Sadly, our countries devote quite small budgets to science and often we have to apply to international calls to try to have access to more realistic budgets for science. This is extremely hard to achieve and only can happen with international visibility and successful collaborative work.
What is the best thing about where you work?
Mariano Soiza-Reilly: Our lab is placed in a new building with a great community of colleagues and students, and surrounded by trees and the waters of the Rio de la Plata. We are immersed in a large scientific community where many young researchers start their scientific careers. It is a huge privilege to be part of that process.
Tamara S. Adjimann: PhD student – The institute is placed in a new building with many facilities that make doing science more comfortable. Our lab is quite spacious and luminous, which makes going to work more pleasurable. Also, we are surrounded by a lovely community that is always looking to make improvements and keep pushing forward for the benefit of all.
Carla V. Argañaraz: PhD student – I think the best thing about our workplace is that we get to be in a pretty quiet place, near an ecological reserve and next to the river, so coming here you get the kind of peace that big cities rarely allow. Of course this would mean nothing without the awesome group of people that always receives you with a smile, they are truly the heart of the community here.
Rocío B. Foltran: Postdoc – I think that it’s the atmosphere, not only because it’s surrounded by nature away from the craziness of the city, but because it’s next to several other scientific institutes and the natural sciences faculty, filled with people who love science as much as we do.
Grace Wu: Master student – The people! The institute has a collaborative environment where everybody is so nice, respectful, patient and always willing to help each other out. Also the building is well maintained and comfortable to work in, and the view from the lab is peaceful and calming, perfect to look at while having a little break.
Melina Maidana: Master student – The comfortable work environment is a remarkable quality of the lab.
What’s there to do outside of the lab?
Mariano Soiza-Reilly: I enjoy doing sports and spending time with my family. Buenos Aires is a beautiful city with many corners to be discovered.
Tamara S. Adjimann: PhD student – There is a lot to do around here. Buenos Aires is one of the most active cities in the world, with many diverse activities to enjoy both during the day and night. There are lots of restaurants and cafés, many parks and museums and lots of places to discover in its surroundings. The people here are very warm and friendly, and will make everything even more enjoyable.
Carla V. Argañaraz: PhD student – Our city is so big and diverse that it offers something to fit every taste. You can find great art museums, usually next to lovely parks where you can take a stroll after. Buenos Aires is filled with cultural activities, from clubs playing local music to jazz clubs all over the city, you can find any genre you want and have a nice drink while listening to some music. There’s also lots of green spaces if chilling and reading there is your thing, and of course, lots of beautiful libraries to find your book companion.
Rocío B. Foltran: Postdoc – Buenos Aires is a very culturally rich city, and I enjoy going to the theater, to the cinema, to eat some delicious meals or to rest in some of the green parks.
Grace Wu: Master student – Buenos Aires is a city that never sleeps, so for the night owls this means open bars, restaurants and clubs till late night! If not, there are many green areas to practice sports or have a little walk, museums, concerts, theaters, markets, cute cafes… you name it! Also, the gastronomy is diverse and great, especially the meat and wine ;)
Melina Maidana: Master student – near Ciudad Universitaria you can go for a walk and visit the “Parque de la memoria”.
Group photo of the lab (Photo credit: Fernando Vázquez-Rovere)
Browse through other ‘Lab meeting’ posts featuring developmental and stem cell biology labs around the world.
Transportation is one of the main environmental issues of a scientific conference, usually accounting for around half of the event’s total CO2 emissions.
But innovative ideas can help mitigate this impact, without compromising the benefits of bringing people together. Sally Lowell and her colleagues recently ran a multi-hub conference across three different regional locations for the European Society for Developmental Biology meeting which ran in September 2023.
Shreyasi Mukherjee is a postdoc at Massachusetts General Hospital and Harvard Medical School, using stem cell-derived embryo models to study how epigenetic complexes regulate tissue organization and cell fate decisions during very early embryonic development. Shreyasi is keen to write about the fast-evolving field of stem cell-based embryo models. Having experienced working in India, the UK and the US, she also plans to highlight the scientists and research from the Global South countries on the Node. We chatted to Shreyasi to find out more about her background and her plans as a Node Correspondent.
Congratulations on being selected as one of our new correspondents! What made you decide to apply to become a Node correspondent?
I follow many of The Company of Biologists journals like Development, Journal of Cell Science and Disease Models and Mechanisms. I had recently transitioned from PhD to postdoc and veered into a slightly new field. There is so much literature and it is overwhelming. I was looking for opportunities to write for preLights because I thought that would help me hold myself accountable and stay current in the field. But I also enjoyed the different kind of articles the Node puts out. When I saw the opportunity to become a correspondent, it was a no brainer for me to try and see what happens.
Have you done much science communication/ writing before?
I’ve written my PhD thesis and papers in the last couple of years, but I haven’t really done much other types of science writing. When I was working as research assistant, I would help organise an event where students from high school and undergrads come to the lab and we talked to them about our research. I’ve tried to do similar outreach things throughout my PhD and even now, I still talk to high school and college students back in India. I’m trying to show them what the career trajectory in research looks like. I’m also involved with the Genetics Society of America and doing some science outreach with them. We’re organising Capitol Hill Day, as a part of the upcoming TAGC conference.
Over the past few years, I’ve become more cognizant of the necessity to do science communication, not just for the scientific community, but to get the public and even our families to understand the importance of basic biological research. I really enjoy the science TikToks and podcasts out there, which I think are great ways to give people snapshots of how science actually happens.
What is your background and what is your current research focus?
I grew up and did my undergrad in India, where the education system is very different. You don’t really get a chance to do hands on research as an undergrad. This is true for most places except a few of the more elite institutions. You learn a lot of the concepts but at that point you don’t really know what research looks like as a career.
I wanted to see what research was all about, so I got a scholarship to do my master’s at the University of Edinburgh in neuroscience. That was a valuable experience because I got to do my dissertation in a lab setting. After that, I wanted to get more research experience, so I came back to India and worked as a research assistant for a few years. I worked with flies, looking at chromatin dynamics in early fly development and how perturbations in the environment can cause transgenerational or intergenerational effects in flies. That was my first experience thinking about research questions and executing a research hypothesis.
I did my PhD in developmental biology at the Cincinnati Children’s Hospital. It was a great experience. I mainly worked with human embryonic stem cell-based differentiation systems, trying to understand the mechanisms that provide transcriptional specificity to the Wnt pathway.
While I was doing my PhD, I knew that I wanted to look more into the interplay of developmental signalling and other processes during early development, like epigenetic regulation and transcription factor activity. I wanted to integrate and study all of that in a 3D model that has more spatial context. I decided to be more invested in the epigenetic field when I transitioned to my postdoc. I’m now using stem cell derived embryo models and studying how epigenetic complexes, especially the Polycomb complexes, regulate tissue organisation and cell fate decisions during very early embryonic events like gastrulation. Even though it wasn’t too much of a field switch, it’s still very intimidating because there is so much literature on chromatin function between the many epigenetic complexes and so much interplay. But there are still many outstanding questions in chromatin regulation that I think are very interesting, especially during the cell fate transitions in development.
You’ve worked in quite a few different countries. How has that experience shaped you?
There’re a lot of immigrants who have gone to other countries for their PhDs. I think their journeys are all a bit unconventional and unique. I think my experience has helped me become a better scientist. The structure in which science works, the funding for science, the resources that are allocated — all these things are so different back in India. The way you’re viewed on the global level is also different. When I was working in India, I would reach out to people and rarely get a response. When I started applying to PhD programmes, I got rejected several times because they said that I needed to have research experience in Western countries. That made me very discouraged because I didn’t know how I could change this. Now that I’m in the US, people reply very quickly and nicely when I email. I think there are a lot of perception issues based on where people come from.
Do you have any ideas about what kind of content you will contribute to the Node?
I would like to highlight the research being done in Global south countries. Most research being talked about, even if they’re from countries in the Global South, are normally from elite institutions or projects with a lot of international collaborations. There are a lot of disparities in terms of funding and allocation of resources, even simple things like buying cell culture equipment. Scientists often end up spending a disproportionate amount of funding on publishing and buying consumables due to currency conversions. By writing about the research going on in the Global South, I hope to explore the researchers’ career trajectories and highlight any unique challenges they face in research. There’s also another interesting perspective there because many of those scientists left their country to do a postdoc in a Western country, but then went back home to set up their own labs, which I think is extremely necessary. It will be interesting to get their perspective about how they adjusted to the transition. I hope that writing more about the research in the Global South can create a change in perception when people are judging job applications from candidates.
We look forward to seeing more research from the Global South being highlighted! Is there anything else you want to write for the Node?
I would like to get more up to date on the literature around modelling development with stem cells. There are now so many in vitro embryo models that recapitulate different processes. These models are not all-encompassing, but they’re good in studying many aspects of morphogenesis, tissue organisation, and species-specific developmental processes. This is very exciting because I think in developmental biology, we are at the point where technologies like single cell and spatial transcriptomics allow us to get very high-resolution information into early developmental processes.
I’m also interested in comparing the models derived from conventional versus unconventional organisms. I was recently reading a preprint about spheroids derived from cavefish which was fascinating. I love the idea of a bottom-up approach in making an embryo.
What do you hope to gain from the experience of being a Node correspondent?
I would love to get to know other correspondents and gain a sense of community within the science writing field. I really look forward to learning from other correspondents and from The Company of Biologists team and expand my professional network. It would be really cool to see what happens behind the scenes in publishing.
The Node is such an international community. I’m hoping to learn how to write in a way that’s more globally accessible to reach an international audience.
Finally, is there anything about you that people find surprising? What do you like to do in your spare time?
Something that really helped me through grad school was getting into comedy. I started taking improv classes, because during the pandemic, I wanted to be involved in something that was the complete opposite of academia.
It was such a great experience for me. I found a community of really funny people. It has helped me develop my public speaking skills and have more perspective on things. It’s also gotten me interested in other forms of comedy. Since then, I’ve also been dabbling in doing sketch writing, stand-up and long-form comedy!
That sounds fun! Do you mix science with comedy or are they separate?
For me, they are completely separate. Although for stand up, I do have a little bit of material about how ridiculous it is to go to grad school. Comedy has really helped me in the past few years because I always know that no matter how bad my day is, in the evenings I get to laugh with a group of people I enjoy spending time with. It also helps put things in perspective — when you have a bad day because your Western blot didn’t work, but your scene partner is a physician, and they had a really bad day but they’re still there being so funny. It’s important to think beyond just being in the lab. I think most beginner improv classes are free so everybody should just go take one. You can be silly and not think about anything else!
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Royal Society Publishing has recently published a special issue from Philosophical Transactions B entitled – Causes and consequences of stochastic processes in development and disease.
The issue is organised and edited by Dagan Jenkins, Jonathan Chubb and Gabriel Galea.
About this issue Biology is inherently variable. Some differences between individuals are controlled by genetics and predictable: all Chihuahuas are smaller than Great Danes even though they are members of the same species. This issue presents studies of biological variability which is not predictable, emphasising ‘random’ differences between cells or organisms. Sources of random variability are identified using both statistical methods and cellular analyses, in controlled cultures and growing tissues. Some studies show that consequences of variability can be positive, for example by allowing a population to resist external stresses, like plants resisting unpredictable weather. In other situations, it can be detrimental, such as by allowing some cancer cells to resist treatment or resulting in error-prone embryo development which causes malformations at birth. This issue arises from a Royal Society discussion meeting held in April 2023.
Purchase the print issue at the reduced price of £40 by contacting sales@royalsociety.org
In a new study, Joshua Gendron and colleagues find that plants can measure two different photoperiods to independently control seasonal flowering and growth, and the vegetative growth is partially dependent on the production of myo-inositol, a precursor required in many processes that control growth (1). First author Qingqing Wang takes us through the story behind the paper.
After earning my PhD in fish reproductive physiology from a laboratory in China, I ventured to the US and secured a postdoctoral position in the Gendron lab, initiating my journey into the field of botany. While transitioning from zoology to botany presented significant hurdles, my background in biology, which encompassed genes, molecules, and proteins, eased the process of assimilating knowledge into the botanical sphere. Fortunately, the steadfast support of my lab colleagues, along with Josh Gendron’s encouragement, fostered within me the belief that creativity and problem-solving acumen are indispensable in scientific research, igniting a fervent passion for botanical pursuits.
In our laboratory, we have elucidated a metabolic daylength measurement (MDLM) system that is crucial for regulating plant growth under short winter photoperiod conditions. Notably, the post-dusk induction of one gene, PHLOEM PROTEIN 2-A13 (PP2-A13), in short days is pivotal for sustaining plant growth in winter but not summer photoperiod (2). This led me to speculate about the existence of a contrasting pathway that is regulated by MDLM system controlling plant summer growth. My exploration of photoperiod-related literature primarily uncovered research focused on the CONSTANS- FLOWERING LOCUS T (CO-FT) module’s role in regulating flowering, leaving much unknown about other pathways controlling plants’ summer growth.
MIPS1 as a model to study photoperiod-controlled growth.
Delving into the RNA-seq database curated by Gendron lab (3), I meticulously examined gene expression profiles from RNA-seq, seeking candidates exhibiting heightened expression under summer long day conditions. Amidst the constraints of Covid-induced isolation, devoid of laboratory benchwork, I seized the opportunity to immerse myself in extensive literature reviews pertaining to each intriguing gene. I came across a gene called MYOINOSITOL-1-PHOSPHATE SYNTHASE 1 (MIPS1), which plays a pivotal role in myo-inositol biosynthesis. Myo-inositol is an essential sugar that governs various cellular processes crucial for growth regulation. Notably, MIPS1 displayed elevated expression under summer long-day photoperiods, and we discovered that its mutant counterpart, mips1, exhibited specific growth defects under summer long-day conditions but not winter short-day conditions, contrasting with the pp2-a13 mutant. We observed that MIPS1 has a long-day-specific growth effect, prompting us to investigate whether growth is photoperiod-controlled and how MIPS1 responds. To address this, I cultivated both wild type and mips1 mutant plants under critical photoperiod conditions and monitored their growth. As the daytime lengthened, wild type growth was minimal in photoperiods less than 12 hours light to 12 hours dark (12L:12D). However, in photoperiods of 12L:12D or longer, wild type growth accelerated significantly, while the mips1 mutant exhibited clear growth defects. Upon seeing these results, I was excited to share the findings with everyone. The two years of effort dedicated to growing plants under various conditions in the same growth chamber proved worthwhile. These results indicate that growth is indeed controlled by photoperiod and requires MIPS1.
Those findings prompted us to investigate the potential involvement of the CO-FT mechanism in regulating MIPS1 expression. Interestingly, genetic data indicated that MIPS1 expression is not controlled by the CO-FTpathway, which led us to wonder a pivotal question: What regulatory network governs MIPS1 expression, thereby determining plant summer growth rate?
Parallel control by MDLM for MIPS1 required for long day rapid growth, and CO-FT for photoperiod flowering.
We employed a starch-less pgm mutant with a dysfunctional MDLM system to examine the regulatory effect of MDLM on MIPS1 expression. As expected, the photoperiodic expression of MIPS1 was absent in the pgm mutant, confirming our hypothesis that MDLM system regulates MIPS1 expression. Then I think about how to design an experiment to decouple photoperiodic growth and photoperiodic flowering. Exposing the plant to low light intensity, nearing the compensation point where photosynthesis equals respiration, could exhaust starch and sucrose reserves and therefore impeding MDLM but not CO-FT system. I grew plants in low light intensity condition and found that the mips1 mutant phenotype disappeared, while flowering time remained consistent with long-day conditions, which is making us exciting. This sustained our model that MDLM regulates plant growth in parallel to CO-FT regulated flowering. To further test this model, I propose a classic experiment akin to the “night break” experiments used to test photoperiodic flowering. In “night break” flowering experiments, long day plant flowers in long day but not short day photoperiod. However, introducing short pulses of light during the night in short-day conditions promotes flowering. Similarly, to assess whether photoperiod regulates rapid growth, we propose dividing the daytime in long-day conditions into two segments: one exposed to high light intensity and the other to low intensity. We found that the mips1 mutant phenotype would manifest in the segment under intense light, while the wild-type size would exceed that of the segment under light exposure during the initial portion. Moreover, flowering timing in both scenarios would mirror that of long-day conditions. This suggests that plants can discern an absolute photoperiod using low light-sensing photoreceptor mechanisms to regulate flowering time. Concurrently, they can gauge the photosynthetic duration as a metabolic day length to govern growth.
Plants detect two different daylengths to control seasonal flowering and growth (Adjusted from previous papers (4, 5)). Photoperiodic flowering detects an “absolute” photoperiod that is sensed by photoreceptors that control CO stability,activated at low light intensities. Photoperiodic growth detects the photosynthetic period measured by the metabolic daylength measurement system, which is defined as the duration of time that light is above the photosynthetic compensation point.
In the end…
This journey has taught me that in scientific research, one must be passionate, diligent, possess problem-solving skills, embrace teamwork, and be willing to challenge and follow classic principles. This model has filled and expanded our understanding of plant regulation by photoperiod, which extends beyond just flowering time; there are many other processes for photoperiodic regulation. Moreover, by utilizing different durations and intensities of light exposure, we can achieve separate regulation of flowering and growth in crops, leading to conservation of energy resources for crops in the future.
References
Q. Wang, W. Liu, C. C. Leung, D. A. Tarté, J. M. Gendron, Plants distinguish different photoperiods to independently control seasonal flowering and growth. Science 383, eadg9196 (2024). https://doi.org/10.1126/science.adg9196; PMID: 38330117
W. Liu, A Feke, C. C. Leung, D. A. Tarte´, W Yuan, M. Vanderwall, G. Sager, X. Wu, A. Schear, D. A. Clark, B. C. Thines, and J. M. Gendron, Ametabolic daylength measurement system mediates winter photoperiodism in plants. Dev. Cell 56, 2501–2515.e5(2021). doi: 10.1016/j.devcel.2021.07.016; pmid: 34407427
C. C. Leung, D. A. Tarté, L. S. Oliver, Q. Wang, J. M. Gendron, Systematic characterization of photoperiodic gene expression patterns reveals diverse seasonal transcriptional systems in Arabidopsis. PLOS Biol. 21, e3002283 (2023). doi: 10.1371/journal.pbio.3002283; pmid: 376990558. T. C. Mockler et al., The DIURNAL project: DIURNAL
J. M. Gendron, D. Staiger, New Horizons in Plant Photoperiodism. Annu. Rev. Plant Biol. 74, 481–509 (2023). doi: 10.1146/annurev-arplant-070522-055628; pmid: 36854481
J. M. Gendron, C. C. Leung, W. Liu, Energy as a seasonal signal for growth and reproduction. Curr. Opin. Plant Biol. 63, 102092(2021). doi: 10.1016/j.pbi.2021.102092; pmid: 34461431
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