Please find out more about the Special Issue on our call for papers page on the Development website. The deadline for submission is 15 May 2023.
Natalia López Anguita (PhD student in the Stem Cell Chromatin Groupat the Max Planck Institute for Molecular Genetics) ‘Role of hypoxia in pluripotent cells and during differentiation via gastruloid formation’
Hannah Brunsdon (Postdoctoral Research Fellowin Liz Patton’s group at theIGC, University of Edinburgh) ‘Aldh2 is a metabolic gatekeeper in melanocyte stem cells’
Benjamin Jackson (MD-PhD Candidate in Lydia Finley‘s group at Memorial Sloan Kettering Cancer Center) ‘A non-canonical tricarboxylic acid cycle underlies cellular identity’
“Whatever the species – whether insects, birds, mammals or fish – and however far the distance, somehow these animals know when to leave and where to go. So is this behaviour hardwired into their genetic code?”
Dr Kat Arney
In the latest episode of the Genetics Unzipped podcast, we’re taking a look at the birds and the bees – not like that! – from the unusual migratory habits of European blackcaps and the ‘greatest shoal on earth’ to the division of labour in a beehive, we’ll be exploring the role that genetics plays in shaping animal behaviours.
In their recent manuscript, published in Developmental Cell, Vijina Varapparambath, Mabel Maria Mathew, Anju Pallipurath Shanmukhan, and colleagues explore the mechanism underlying de novo shoot regeneration. They discover that mechanical feedback between two populations of juxtaposed cells – one which will eventually become the shoot and the other its neighbors – is what propels fate changes and sculpts the regenerating shoot meristem. Now, one of the co-first authors and the co-corresponding author, Mabel, gives us some insights into the story behind the paper.
What was already known about the topic?
Tissue culture-induced de novo shoot regeneration is one of the many remarkable regenerative abilities of plants. It relies on the right balance of phytohormones, auxin and cytokinin, to exploit the totipotency of plant cells and generate entire shoot and/root systems from any tissue. High auxin promotes the formation of undifferentiated callus from which shoots arise. Notably, only a few cells of the callus could reprogram and develop into a complete shoot system (Gordon et al., 2007; Kareem et al., 2015).
How did you get started on this project?
We called the sub-population of callus cells that have the potential to make the shoot ‘progenitors’. These cells were marked with the expression of polar auxin efflux carrier, PINFORMED1 (PIN1). We were curious about the stochastic selection of certain cells to become progenitors and how they progress into the shoot (Fig 1A). To understand this, we followed hundreds of progenitors in real-time by confocal-based live imaging and found that around one fourth of these progenitors did not make shoot meristem. Why some sub-populations succeeded in making shoot meristem while others failed intrigued us. This was where the project started.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
Contrary to popular expectation, our investigations revealed that the reason why some progenitors aborted was not the lack of the shoot stem cell regulator, WUSCHEL. The observation was striking; even though WUS is necessary (Zhang et al., 2017), its abundance alone does not guarantee successful shoot regeneration. Rather it was the localization pattern of cell polarity markers such as PIN1, that predicted successful shoot regeneration. The next goal was to identify the mechanism by which these progenitors achieved shoot regeneration. We performed a comparative transcriptome analysis using several genetically engineered backgrounds; some of which could regenerate shoot and others that could not. While profiling the changes in gene expression during the onset of progenitor formation, we identified an over-representation of XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 9(XTH9) in the backgrounds that could regenerate shoot. XTH9 encodes an enzyme for cell wall loosening and had an unexpected spatial expression. We found it to be expressed solely in a shell of cells (which we refer to as the non-progenitor cells) encapsulating the progenitor, that underwent stretching. As opposed to the commonly held notion that stretching cells often divide, these surrounding cells hardly divided. This was a hypothesis-generating result and turned out to be a key milestone for the story.
What was the key experiment?
We were curious about what causes the specific local expression of XTH9. Through extensive follow-up genetic and biochemical approaches including ChIP seq, we discovered that a transcription factor and shoot-promoting factor, CUP-SHAPED COTYLEDON 2 (CUC2), activated XTH9 expression solely in non-progenitor cells. We further established that the CUC2-XTH9 regulatory axis promoted cell polarity in the progenitor non-cell autonomously. In parallel, Anju modulated the components of the regulatory axis with the challenging inducible system, which allowed us to capture even their temporal necessity and their transient behavior. Thus, we were able to identify the biochemical component that conferred productive fate to the regenerating progenitors. This exciting result made us even more intrigued to investigate how the coordination between the progenitor and its neighbors is able to generate the precise biochemical output for shoot regeneration. We asked what is the nature of this coordinated interaction between the progenitor and neighboring non-progenitor cells? What happens if you disrupt it? To answer this, we undertook a series of approaches. We tracked the growth of the progenitor cells and the neighboring non-progenitor cells at single-cell resolution. Then, we analyzed their differential growth rate using MorphoGraphX. We studied the differential stress patterns between the progenitor cells and their neighbors by visualizing their microtubule orientation. And finally, we disrupted the coordination by targeted laser ablation of either the progenitor or their neighboring cells. These key experiments led us to the following two conclusions: First, there is a mechanical conflict between the progenitor cells and their neighbors. Second, feedback between mechanical and biochemical properties of the cells is crucial to self-organize the cells of shoot progenitors in the absence of any tissue patterning cues. By this time, it was clear that we needed a model to interpret these conclusions. We proposed four models and eliminated three of them. It was most exciting as we steered closer to that one model that all our experimental evidence aligned with. Through this model, we proposed that the expanding non-progenitor cells act as a ‘constriction shell’ similar to a rubber band serving a dual role. First, to facilitate the enclosed progenitor cells to grow and divide, and second to provide a mechanical constriction causing the progenitor cells to bulge out. Meanwhile, the growth of the progenitor cells likely feeds back on the non-progenitor and further triggers its expansion (Fig. 1B-1C) (Varapparambath et al., 2022).
Figure 1: shoot progenitors arise stochastically from undifferentiated callus (A), and abide by the model of “mechanical-conflict” (B) to eventually become a shoot (C).
And what about the flipside: any moments of frustration or despair?
The progenitors, during their early stages, will be buried beneath 2-3 layers of callus cells which makes the progenitor detection and their real-time tracking challenging. This, in addition to the irregular topology of the callus, makes it easy to miss the progenitors. But unfortunately, that was not all. We all could uniformly agree that after performing a whole genome transcriptome approach, you will always end up with more than what you need. This happened to us as well. After much struggle and a marathon of efforts by one of the co-first authors, Vijina, to lead several follow-up genetic experiments and ChIP seq, we landed on a single target, XTH9.
Where will this story take the lab?
This is the first study to integrate the feedback between tissue mechanics and biochemical pathways for specifying cell identity during plant regeneration. But that is just the tip of the iceberg. The lab’s long-term goal will be to seek answers to some of the fundamental questions such as the link between cell division and cell polarity during de novo organogenesis. The lab is also in the process of branching out into exploring cellular heterogeneity using de novo shoot regeneration as a model.
What is next for you after this paper?
After working on this story, I developed an inclination toward the relationship between mechanics, cell polarity, and cell fate. I look forward to exploring it further through theory and modelling-based approaches. Co-first author Vijina aspires to step into the field of evolutionary development. The other co-first author, Anju has her mind fixed on delving deeper into the cell biology of fundamental life processes not just in plants, but also in other organisms.
References
Gordon, S. P., Heisler, M. G., Reddy, G. V, Ohno, C., Das, P. and Meyerowitz, E. M. (2007). Pattern formation during de novo assembly of the Arabidopsis shoot meristem. Development134, 3539–3548.
Kareem, A., Durgaprasad, K., Sugimoto, K., Du, Y., Pulianmackal, A. J., Trivedi, Z. B., Abhayadev, P. V, Pinon, V., Meyerowitz, E. M., Scheres, B., et al. (2015). PLETHORA Genes Control Regeneration by a Two-Step Mechanism. Curr Biol25, 1017–1030.
Varapparambath, V., Mathew, M. M., Shanmukhan, A. P., Radhakrishnan, D., Kareem, A., Verma, S., Ramalho, J. J., Manoj, B., Vellandath, A. R. and Aiyaz, M. (2022). Mechanical conflict caused by a cell-wall-loosening enzyme activates de novo shoot regeneration. Dev. Cell57, 2063–2080.
Zhang, T.-Q., Lian, H., Zhou, C.-M., Xu, L., Jiao, Y. and Wang, J.-W. (2017). A Two-Step Model for de Novo Activation of <em>WUSCHEL</em> during Plant Shoot Regeneration. Plant Cell29, 1073 LP – 1087.
The big news on #ScienceTwitter (and indeed Twitter more broadly) surrounds the flock becoming a herd as the community hedges with more and more users opening accounts on Mastodon.
There is plenty of great advice out there if you are considering moving, or would like to open your first account. We found the top thread useful, and you’ll find us on Mastodon soon. However, while we are learning to toot and boost, it’ll be important to see how moderation works in the herd.
People saying it doesn’t matter which Mastodon instance you join are being misleading: 1. Each one has different moderation policies 2. Not every one allows you to formally “move” there 3. Who is on that instance and who they follow determines your federated timeline content
Our latest SciArt profile features Arpan Parichha, a PhD student in Shubha Tole’s lab in Mumbai. Arpan told us about his passion for using art to address important issues in science, such as gender equity, as well as communicating science to the general public.
Where are you originally from and what do you work on now?
I was born in Kolkata, India, and I now work at Tata Institute of Fundamental Research, Mumbai as a grad student in the lab of Prof. Shubha Tole. My thesis work involves understanding the role of canonical Wnt signaling in the developing telencephalic midline. I am examining how Wnt signaling dynamics are essential for several dorsal midline brain structures like choroid plexus, Cajal Retzius cells (CR cells), and fimbrial scaffold.
Women in STEM An abstract art aiming to depict the importance of women in STEM. Hybrid digital drawing using pencil sketch + dot art + line art
Were you always going to be a scientist?
Not at all. I always wanted to become a doctor and had zero clue about the life of a scientist. The society where I grew up imposed two choices for my career: becoming a doctor or an engineer. During my college days, I had an opportunity to live the life of a grad student for two months (when I was a summer research fellow), and it was when I decided to explore the world of academia. I found the life of a researcher to be cool and much more interesting than the conventional 9-to-5 job.
Daffodils Inspired by the poem of Willam Wordsworth
And what about art – have you always enjoyed it?
I have been passionate about art since childhood and joined an art school when I was eight years old. I am formally trained in landscape art and abstract oil painting. Now, I want to fuse abstract art with science to create something insightful.
What or who are your most important artistic influences?
I was deeply influenced by the scientifically precise artworks of David Goodsell. These paintings are mesmerizing and capture the intricate details of molecular and cellular processes inside the cell.
Gender in STEM Abstract artwork depicts that science depends on the brain and not gender. Hybrid digital drawing using pencil sketch + dot art + line art
How do you make your art?
I use all kinds of media (digital, pencil sketch, oil, and watercolor) to create my artwork. These days I use an iPad to create my digital drawings. Sometimes I combine these two styles to create a hybrid approach. I try to make my abstract artwork in a way that it remains open to interpretation. Many of my paintings voice the importance of gender equality in science and the importance of women in STEM education.
I post my paintings and artwork on Instagram, YouTube, and Twitter. Besides abstract art, I make animated videos (using vector graphics) on PowerPoint, which explain a biology concept or increase public awareness of research.
Video thumbnail depicting some of the faces behind the approach of studying brain development in a dish i.e. brain organoids. This video was selected as a winner for the People’s choice video contest organized by SFN and Brain facts.org.
Does your art influence your science at all, or are they separate worlds?
During my college time, I was fascinated by microscopy. Notably, I perceive confocal microscopy images as artworks. Art is really an integral part of my science. The artistic mindset helps me conceptualize biological questions and design new experiments for my research. As a grad student, I always scribble in my notebook when I’m designing experiments or have exciting results. Putting down my thoughts as drawings really helps me to think like a scientist. I always find it easy to communicate my science by drawing models, cartoons, and flowcharts.
The struggle of women in STEM Abstract artwork depicts the struggle of women in STEM. Hybrid digital drawing using pencil sketch + dot art + line art
What are you thinking of working on next?
I want to promote science and concepts of biology using Instagram, YouTube, and Twitter.
I have realized students and the young generation should be exposed to the fascinating life of scientists. Hence in many of my YouTube videos, I wish to highlight the person behind the science. Getting to know the scientists, along with their science, always gives that personal touch. After all, science is done by people for people. Unfortunately, the young generation is not as influenced by the life of a scientist compared to a Hollywood film star. Hence I strongly feel that science needs to be popularized in a creative way that attracts young minds.
I have started posting a 1-minute video summary on YouTube of papers I read or hear in a journal club. These one-minute videos give the audience a flavor of exciting discoveries by scientists worldwide. For example, I explained how a scientist could study the neanderthal brain in a dish in a “YouTube Short” video. Moreover, I aim to spread awareness about public health by using animated YouTube videos. For example, in a recent video, I explained how alcohol can affect our brain and why we should say no to alcohol
In the future, I wish to make podcasts on my youtube channel where I can ask scientists about their life and how they got interested in science.
Thanks to Arpan and all the other SciArtists we have featured so far.We’re looking for new people to feature in this series – whatever kind of art you do, from sculpture to embroidery to music to drawing, if you want to share it with the community just email thenode@biologists.com (nominations are also welcome!)
Girish Kale, Lemke lab, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg. Germany
I guess I am speaking for everyone when I say that the ISDB 2021 conference was a much-needed source of serendipity. Although postponed by a year, the conference brought together an excellent line-up of speakers with four keynote lectures, a Harrison medal lecture, a closing plenary lecture, along with 10 scientific symposia; all centered on developmental biology. It was a feast!! Oh, did I mention the nearly 400 posters? This is where we test the limits of how much knowledge one can acquire in a short amount of time.
In my view, this meeting was a great amalgamation of what we are doing, as a scientific community, to get a global understanding of the journey of life, starting from a single cell to the formation of the entire organism. Speaking of single cells; it became abundantly clear that single cell -omics techniques, like ‘single cell RNAseq’, are becoming mainstream bread-and-butter for understanding developmental processes. Each of the symposia I managed to attend had at least one talk where the technique was used to test and/or construct scientific hypotheses. We were joking that anyone playing a drinking-game, having to drink every time ‘single cell RNAseq’ was mentioned, would be, at the very least, unsafe for driving.
In the past, I have been skeptical about the utility of in vitro experiments in developmental systems: I mean, why would you use an in vitro cell/tissue culture system to understand what’s happening in vivo? in vivo systems are so beautiful to begin with!! I would say, this meeting changed my mind. For one, that’s probably the only way we can experiment with rhinoceros; but more importantly, I got the impression that we, as a scientific community, are reaching a critical mass of research and researchers who know the in-and-out of modelling in vivo processes in vitro. With organoids, gastruloids, axioloids, segmentoids, intestinoids, etc. leading the way, the era of -oids is upon us, and one can only imagine the endless possibilities it presents.
Here I have to mention a couple of personal highlights. The location: it was my first time at the Atlantic Ocean (I know I am a bit lazy that way), and this was one thing I am sure everyone at the meeting enjoyed thoroughly. A short walk from the beaches was a nature reserve that hosted flamingos, along with plenty of other interesting fauna. Also, meeting the speakers was a great opportunity to learn how one can shape their thinking to be a great scientist, as well as become an interesting human being. Exchanging ideas, while sitting on the lawn by the pool, made this one of the best meet-the-speakers session I have experienced.
Of course, the most natural thing that happens at conferences happened here as well, meeting old colleagues and friends, and making new connection with peers, despite all the corona-worries. Also, I hope every foodie got the opportunity to try out the amazing fish food in restaurants around the conference venue. I guess the conference organizers had realized the importance of networking, and pushed us to arrange for dinner on three out of five conference evenings, giving us additional social and informal bonding opportunities.
If you are curious about the study involving rhinoceros, and many other unpublished data, we have also compiled a list of various preprints discussed during the ISDB2021 meeting. So, feel free to check our preList for the meeting as well.
Niveda Udaykumar, Indian Institute of Technology Kanpur (IITK), Kanpur. India
This year’s ISDB meeting was one filled with exciting opportunities to dive into the fascinating field of developmental biology. I was looking forward to this conference from the moment I submitted my abstract!
My experience at this conference was very fulfilling with scientific and personal realizations. I have very fond memories and experiences of this conference, which was my first solo international trip!
I liked several aspects of this conference, the first being the diverse speaker line-up, from the Harrison Medal lecture, the Keystone lectures, symposium speakers, and the oral presentations. The line-up of speakers catered to the scientific interests of most of the attendees, if not all! The talks ranged from trying to recapitulate human somitogenesis in vitro to evo-devo and metabolism. I was impressed with the poster session, with about 400 posters that showcased exciting ideas and hypotheses from all around the world.
Another great aspect was the ample time for the participants to interact with each other. This time was particularly useful as I got to discuss my research with several people, get feedback and talk about potential future positions with PIs. On some days, this time was spent catching up with old colleagues and friends. I appreciated the organizers’ efforts in the networking sessions, ‘Meet the Speakers’, where the participants could interact with any speaker of their choice. The parallel session of ‘Meet the Editors’ too well-received, where the Editors of prominent journals such as ‘Development’ and ‘Cells and Development’ interacted with the participants and familiarized them with their potential manuscript submissions.
Finally, I felt that the choice of location for the conference was perfect. We were privileged to have clear beautiful blue skies with sunny weather on most days, and the serene beaches of the Algarve were breathtaking. As an attendee of the conference, I know that I came back home refreshed and motivated, caught up with old friends, and made new friends, and I thank the organizers for their efforts in organizing such a fantastic conference.
Girish and I (read mostly Girish) have prepared a preList of the preprints that were mentioned in the ISDB conference. Please take a look at it, and if we have missed any, please don’t hesitate to contact either of us.
Meet the speakers session during ISDB2021. Photo credits: Euclides Fernandes Póvoa (4 votes) Loading...
There have been long-standing debates around the risk of selective serotonin uptake inhibitor (SSRI) use during pregnancy due to the potential effects on fetal brain development. Our studies, which have been recently published in Development, identify an essential role of transient serotonin uptake transporter (SERT) expression in non-serotonergic neurons during neural circuit development in the hippocampus, and disrupting this SERT function leads to sex-biased deficits in hippocampal electrophysiology and behaviors. This suggests that cataloguing the risks of SSRI exposure during particular timing of human fetal brain development could be critical to enhance the sensitivity of the investigations. Differences in cognitive behaviors in the male versus female mice imply that certain neural circuit dysfunctions, particularly in females, resulting from early life SSRI exposure may not manifest until later life and under certain environmental conditions. An outstanding question is how the findings in mouse models may help refine SSRI uses, to safeguard the mother and the offspring. We would appreciate comments and suggestions on our work.
SERT is specifically expressed in a subset of CA3 pyramidal neurons during hippocampal circuit establishment. Figure extracted from De Gregorio, et al. (No Ratings Yet) Loading...
Over the last few months, I’ve been involved in a project coordinated by ASAPbio looking at the potential benefits of, and challenges with using, public preprint peer review – for researchers, funders and publishers. A meeting next month at the Janelia Campus (sponsored by HHMI, ASAPbio and EMBO) will bring together these diverse perspectives, with the aim of promoting community consensus and support for preprint peer review.
This meeting will be live-streamed and is open to anyone from the scientific community to engage with the meeting virtually. If you’re interested in finding out more, or want to sign up to attend, take a look at the meeting website.
Importantly, we really want to hear your experience of and thoughts on preprint feedback and review, through this survey. Responses to the survey will help shape the discussion at the meeting. It should only take 5 minutes to complete, so please do give us your input!
“One of the things that we’re really interested in is whether or not we can take these genes that are used in carnivory and pop them into crop plants”
Dr Tanya Renner
In the latest episode of the Genetics Unzipped podcast, we’re looking at the gruesome world of plants eating animals. There’s something unnatural about carnivorous plants. We’re so used to plants being at the bottom of the food chain, that to see them trapping, killing and eating animals seems to go against the laws of nature. But of course, carnivory in plants is very real and has evolved multiple times in response to a lack of nutrients. We speak with Dr Ulrike Bauer about the biomechanics of how pitcher plants make their surfaces so slippery, Dr Kadeem Gilbert tells us about what is able to survive inside a pitcher plant’s death trap, and Dr Tanya Renner talks about how she’s trying to put sundew genes into crops.
If you enjoy the show, please do rate and review on Apple podcasts and help to spread the word on social media. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com Follow us on Twitter – @geneticsunzip
Royal Society Publishing has recently published a special issue of Philosophical Transactions B: Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom
Compiled and edited by Guojun Sheng, Thorsten E Boroviak, Urs Schmidt-Ott and Shankar Srinivas, the articles can be accessed directly at www.bit.ly/PTB1865
A print version is also available at the special price of £35.00 per issue from sales@royalsociety.org
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