2021 has been an exciting year for both FocalPlane and the Node; both sites have new Community Managers, new series and new contributors. To celebrate the end of the year and to look forward into 2022, we bring you our Countdown to 2022. Each day we will feature an image from a scientist or illustrator that has contributed to our sites over the past year. We would like to thank all the participants for contributing to the calendar, particularly those that made original artwork/compositions.
We hope you enjoy viewing the calendar as much as we enjoyed making it!
I was introduced to the ideas of systems biology during my first year of Natural Sciences at Cambridge University. The interplay between modelling and data collection was very appealing to me. Thanks to one of my supervisors – Tim Fulton (also a PhD student in the Steventon Lab, University of Cambridge)- I was exposed to it in the context of developmental biology. He helped me get in touch with Dr Berta Verd whose interdisciplinary approach to research enticed me. We talked a lot and came up together with my project. Due to Covid we had to modify it to include modelling, but I found it more rewarding that way!
Studying bipotent posterior progenitors in Cichlids
I researched Neuromesodermal progenitor cells (NMps). They are a very interesting population of cells, persisting beyond gastrulation to generate both mesodermal and neural fates in the late embryo. This progenitor state is characterised by coexpression of two transcription factors – Brachyury (Tbxta) and Sox2 (Henrique et al. 2015). There are inter-specific differences in their proliferation dynamics – in chick and mouse embryos they proliferate, but in zebrafish they do not (Steventon and Martinez Arias 2017). This suggests they might be tuneable during the evolution of different axial elongation patterns (Sambasivan and Steventon 2021). My project was part of a larger effort in the Verd lab to see whether this might explain axial diversity observed in Lake Malawi cichlids.
I studied the NMps in Astatotilapia calliptera and Rhamphochromis chillingali – two species of cichlids from the Lake Malawi flock. They underwent a recent radial adaptation around a million years ago. Remarkably, the genetic differences between these species are very small (between 0.1-0.25% inter-specific divergence), while the morphological differences are immense (Malinsky et al. 2018). In particular, the vertebral count differs between those 2 species, making them a very suitable experimental system for studying the evolution of axial elongation.
I did in situ hybridisations of the fish embryos at various stages, with the help of Shannon Taylor – a PhD student in the Verd Lab. We used Hybridisation Chain Reaction v3.0 (Choi et al. 2018). Despite our best efforts we did not manage to get Sox2 to work in the tailbud. This meant I could not quantify NMps as one of the crucial markers was missing. This was a very humbling experience – experimental biology is much more capricious than I had thought. However, it also showed me what cooperation between labs can look like. Tim did a lot of HCR staining in zebrafish at the Steventon lab in Cambridge and so we asked him for advice. It turned out it took them a few months to get Sox2 working! This was very reassuring. Tim gave us some tips, but we only managed to try some of them. Figure 1. contains some of the best images we obtained.
Figure 1: Dorsal view of a mid somitogenesis stage Astatotilapia calliptera tailbud. Top – posterior, bottom – anterior. A – all genes visible, B – only Oct4, Tbxta and Tbx6 visible, C – only Sox2 visible. Note that all the genes except for Sox2 localise mostly to the nuclei, indicating that Sox2 staining did not work.
Modelling axial elongation
In parallel to the experimental work, I investigated the effect of blebbistatin – a myosin II inhibitor – on somitogenesis and axial elongation in zebrafish. In collaboration with the Steventon lab I analysed almost 100 timelapses of zebrafish embryos in order to determine if the rate of somitogenesis is influenced by blebbistatin. My analysis showed that it is not changed (Figure 2.). Other experiments with dye injection and cell tracking from the Steventon lab showed that the tail still elongates, but with limited cell mixing. This got us curious, how is that possible?
Figure 2: Violin plots of the rate of somitogenesis in minutes per somite in the control embryos (blue) and blebbistatin treated ones (red). Control n = 31, Blebbistatin n = 28.
In order to help address that problem I developed a conceptual model of the zebrafish Presomitic Mesoderm (PSM) elongation. I approximated the PSM as a uniform tissue in the form of a cut-off cone. To recreate the convergence-extension mechanism responsible for axial elongation in the zebrafish tail (Thomson et al 2021; Tada and Heisenberg 2012) I gave the cells two rules for movement: they have to stay a certain range of distances apart from each other, keeping the tissues continuous and preventing cells from occupying the same space; and the cells converge towards the x-axis, mimicking the convergence movements. I found that certain combinations of parameter values indeed lead to elongation without extensive mixing, which shows that – in agreement with our experimental observations – mixing itself seems to not be required for elongation but might rather be a side effect of a certain mode of elongation (Figure 3.).
Figure 3: Modelling results (here starting from a sphere). The coloured spheres highlight the cell mixing. A – the starting shape, B – shape after 100 iterations, C – shape after 500 iterations, 5 times slower movement than in B.
Summary
This was my first time being fully immersed in the lab. I actively took part in the lab meetings and journal clubs which were just as edifying as research itself! Overall, this was an incredible experience. It showed me that experimental biology is unpredictable and the relationship between results and time invested is non-linear. In contrast, computational biology has a much more linear relationship, almost always yielding something interesting! It also gives you the space to learn and think about underlying biological processes, how to recreate them in silico, consolidating your knowledge. This probably furthered my understanding of development the most! I am adamant I want to incorporate both experimental and computational approaches in my future research. I also gained much more understanding and appreciation of developmental biology and I want to specialise in it. I want to thank Berta, Tim, Shannon, Charlotte, Georgina, James, and Callum for welcoming me into their lab and helping me with the project, as well as BSDB for funding it.
References
Choi, Harry M.T., Maayan Schwarzkopf, Mark E. Fornace, Aneesh Acharya, Georgios Artavanis, Johannes Stegmaier, Alexandre Cunha, and Niles A. Pierce. 2018. “Third-Generation in Situ Hybridization Chain Reaction: Multiplexed, Quantitative, Sensitive, Versatile, Robust.” Development (Cambridge) 145 (12). https://doi.org/10.1242/dev.165753.
Henrique, Domingos, Elsa Abranches, Laure Verrier, and Kate G. Storey. 2015. “Neuromesodermal Progenitors and the Making of the Spinal Cord.” Development (Cambridge) 142 (17): 2864–75. https://doi.org/10.1242/dev.119768.
Malinsky, Milan, Hannes Svardal, Alexandra M. Tyers, Eric A. Miska, Martin J. Genner, George F. Turner, and Richard Durbin. 2018. “Whole-Genome Sequences of Malawi Cichlids Reveal Multiple Radiations Interconnected by Gene Flow.” Nature Ecology and Evolution 2 (12): 1940–55. https://doi.org/10.1038/s41559-018-0717-x.
Sambasivan, Ramkumar, and Benjamin Steventon. 2021. “Neuromesodermal Progenitors: A Basis for Robust Axial Patterning in Development and Evolution.” Frontiers in Cell and Developmental Biology. Frontiers Media S.A. https://doi.org/10.3389/fcell.2020.607516.
Steventon, Ben, and Alfonso Martinez Arias. 2017. “Evo-Engineering and the Cellular and Molecular Origins of the Vertebrate Spinal Cord.” Developmental Biology 432 (1): 3–13. https://doi.org/10.1016/J.YDBIO.2017.01.021.
Tada, Masazumi, and Carl-Philipp Heisenberg. 2012. “Convergent Extension: Using Collective Cell Migration and Cell Intercalation to Shape Embryos.” Development 139 (21): 3897–3904. https://doi.org/10.1242/DEV.073007.
Thomson, Lewis, Leila Muresan, and Benjamin Steventon. 2021. “The Zebrafish Presomitic Mesoderm Elongates through Compression-Extension.” BioRxiv, March, 2021.03.11.434927. https://doi.org/10.1101/2021.03.11.434927.
The IBDM is aninternationally renowned research center in developmental biology that studies fundamental mechanisms governing the organization and function of biological systems, using multiscale approaches in a range of animal and cellular models. Research activities at the IBDM synergistically connect developmental biology with molecular, cell and computational biology, as well as evolution, neurobiology, physiology, physiopathology, biophysics, and cancer. The IBDM uniquely fosters interdisciplinary approaches by its intimate connections with various research-training networks within the Aix-Marseille University (AMU) (CenTuri, NeuroMarseille, ICI (Cancer-Immuno), MarMaRa (Rare-Diseases), Marseille Imaging, Canceropôle-PACA).
The IBDM, affiliated with CNRS and AMU, strongly benefits from its collaborative and international scientific culture, English working language, and its fantastic environment on the Marseille Luminy campus, located in the heart of the Calanques National Park.
The IBDM is committed to promotingequality, diversity and inclusivity. The selected candidates will receive support to establish a group in a fully renovated building, have access to cutting-edge scientific core facilities,and will be assisted in obtaining a tenured position (CNRS or AMU), and in securing extramural funding (ATIP/Avenir, ERC, etc…).
To apply
Candidates should provide the following information in a single PDF file: a cover letter explaining their motivation to join the IBDM, a CV, a summary of their main research achievements (2 pages maximum), a future research project (5 pages maximum), and contacts of three references.
Applications and queries should be sent to the search committee (ibdm-call2022@univ-amu.fr) before March 1st 2022.
In person interviews will be scheduled from May 2022.
Frieda Leesch (PhD student, Pauli lab, Research Institute of Molecular Pathology) ‘A molecular network of conserved factors keeps ribosomes dormant in the egg’
Brad Cairns (Professor, Huntsman Cancer Institute) ‘Maternally-inherited anti-sense piRNAs antagonize transposon expression in zebrafish and medaka embryos’
The webinar will be held in Remo, our browser-based conferencing platform. After the talks you’ll have the chance to meet the speakers and other participants at virtual conference tables. If you can’t make it on the day, talks will be available to watch after the event on the Node. You can also sign up to our mailing list for email alerts.
Journal of Cell Science is pleased to invite submissions for the first JCS essay series. The theme is ‘Equity, diversity and inclusion in cell biology’, an important, relevant and timely issue that should be a guiding force in all that we do. We hear the terms being used more and more these days, but we’re all still early in the journey, and at JCS we want to create an opportunity to amplify voices that are not always heard in this space. Has equity, diversity and/or inclusion shaped your experience as a cell biologist in some way? We want to hear about and learn from your stories. We will publish a selection of submissions in the journal in an ongoing series and reward a stand-out essay from the initial call, chosen by a selection of our Editors and Editorial Advisory Board members, with a £500 prize.
All essays must be original pieces that have not been previously published. Any cell biologist at any career stage can submit an essay. Submissions must not be more than 2,000 words and can include figures and images. Please send your essay to jcs.essay@biologists.com.
The closing date has been extended to 15 January 2022.
On Wednesday 10 November, Development hosted three talks on stem cells and disease models.
Below you’ll find each of the talks, plus a Q&A chaired by Development Editor James Wells. The next #DevPres webinar will be a zebrafish special to celebrate the 25th anniversary of our Zebrafish Issue. It will be held on 8 December 2021 at 15:00 GMT, chaired by Alex Schier – subscribe to our mailing list for updates.
Dhruv Raina (formerly Max Planck Institute for Molecular Physiology, now Mosa Meat) ‘Cell-cell communication through FGF4 generates and maintains robust proportions of differentiated cell types in embryonic stem cells’
Marco Trizzino (Thomas Jefferson University) ‘Inability to switch from ARID1A-BAF to ARID1B-BAF impairs exit from pluripotency and commitment towards neural crest differentiation in ARID1B-related neurodevelopmental disorders’
Thanks to the #DevBio community for sharing their thoughts, especially on twitter. If you have some news that you think we should share on our blog, please get in touch at thenode@biologists.com. If you are interested in getting involved with writing preLights you can find out more here.
“You don’t need to be a professional ‘influencer’ to get your voice heard.”
This summer, I finished an unusual project in a neurobiology lab. Contrary to popular belief, internships in a science lab do not necessarily mean operating high-tech machines wearing a lab coat. My project, for example, is for science outreach.
Nowadays, science is no longer an exclusive domain for scientists, but more of public interest. More and more researchers are realising the importance of public outreach. My project is among the first few outreach projects that have successfully drawn funding. It is kindly sponsored by the BSDB Gurdon/The Company of Biologists Summer Studentships.
The Project
Like any hardcore scientist/science enthusiast, I enjoy gossiping about science. I just couldn’t help seeking out ways to spread my passion for it. So after finishing my BSc project in the Alicia Hidalgo Lab at the University of Birmingham, I stayed over the summer to help them with outreach. I designed a website for the lab, and produced 20 educational videos to show what neurobiologists do at the bench.
With Professor Alicia Hidalgo on Graduation Day
The videos were published on a YouTube channel Alicia set up, and got over 500 views in the first month. You can watch people in the lab explaining why study fruit flies, summarising what they’ve done in the latest research papers, and demonstrating how they work with DNA, proteins, cells, and lab animals. The lab website also has a strong emphasis on education ad science outreach. We have embedded videos, clickable 3D objects, and other interactive elements for interested people around the world to explore.
At first, I was as clueless as you probably are right now about how to make videos and websites. Over the two months, however, I taught myself the necessary skills. Now I can make animations, build a website with WordPress, film educational videos, and produce lay-people-friendly multimedia content.
Towards the end of the project, I had another idea. A friend of mine created a digital 3D object using 2D photos of a fossil, as an assignment in class. So I asked her for advice and started learning how to do it myself. A week later, I created a clickable digital 3D model of the fruit fly Drosophila, using 600 photos taken in the lab. I published it on a 3D-object sharing platform and soon forgot about it. But a few months later, I was approached by a scientist in the field of fluid mechanics asking aerodynamics questions! It’s nice to know what I made have resonated with scientists in other fields.
Working on the digital fruit fly model
What I’ve Learned
Having just graduated, I was reflecting on my uni experience throughout the summer. Doing the outreach project helped me figure it out. Despite getting a First Class Honours degree, I could barely recall 20% of my class notes. Apparently, this happens to virtually everyone. So detailed knowledge isn’t the most important thing one gains from uni. Then what is? While doing this project, I realised that I’ve gained three key transferable skills and insight.
1) Insight: life in the lab.
During my four-year degree, I worked on three research projects and peeked at the workings of research labs. I learned about collaborations, group dynamics, and stories of people at various stages of their academic careers. This leads me to my current position, an MRes student in Experimental Neuroscience, and I’m confident to move on to a PhD and beyond.
2) How to teach myself something from scratch.
The ability to learn anything with the internet is a crucial skill that got me through uni and this project. With information overflow versus a limited lifetime, modern scientists need to quickly locate what we need and master the necessary skills for their own research. Being able to teach ourselves anything unleashes a lot of potentials. You will be surprised at the opportunities it brings.
3) How to communicate with different audiences.
Communication, be it verbal or non-verbal, online or face-to-face, is a transferable skill across all careers. Learning how to present and promote one’s work online is arguably the most important skill in the modern age. By learning to promote the lab’s work online, I realised that you don’t need to be a professional “influencer” to get your voice heard.
So I started gossiping about things I’m passionate about – neuroscience, productivity hacks – to people around me. During my summer project, I started blogging, made a personal website, and even started making podcasts with friends! Instead of passively interacting with my phone when I’m bored, I now initiate deep conversations with people and share what I’ve learned with people around the world.
How can this help you, a fellow scientist?
Well, for starters, no matter which career stage you’re in, face this reality – if your work isn’t online, it doesn’t exist. Digital journals have made it easier to share our work, but that is not enough. Successful scientists actively share their work online, by social media, or interviews, which are published as articles, videos, or podcasts.
Never before have there been so many brilliant ways to promote our work, but never before has it been so difficult to compete with other voices to make sure that ours get heard. Creating a lab website, a YouTube channel, or a social media account will be a good start.
What Next?
The insights and skills I gained this summer are invaluable. As I’m starting my Master’s degree, I want to continue blogging and make more outreach stuff for future labs. I’m also considering a career in academia with teaching and public engagement elements. Maybe I’ll become a professor, or a science writer, to inspire curious minds around the world.
Finally, I want to thank all the amazing people in the Hidalgo Lab – Alicia, Marta, Guiyi, Jun, Maria, Lizzie, Naser, Deepanshu, Mike, and Anna. They have been such an enthusiastic and supportive team for my thesis and summer project. I also want to thank the BSDB studentship for their support throughout my project. I would strongly recommend future students to apply to the studentship, not only for wet-lab projects but outreach projects as well.
Here’s a short introduction to the Hidalgo lab if you are interested:
In the latest episode of Genetics Unzipped, Kat Arney takes a trip to the zoo, to find out how studying tumours across the animal kingdom, from naked mole rats to elephants, can reveal insights into cancer in our own species.
In 2014, geneticists at the University of Kiel in Germany published a paper describing tumours in two different species of tiny freshwater Hydra. Little more than a tube with tentacles, Hydra comprise three distinct groups of stem cells. One of these groups, known as interstitial stem cells, turned out to be the source of the cancers, which severely impacted growth and fertility.
But while Hydra may be the simplest organisms currently known to develop cancer, they are far from the only example outside our own species. Kat explores how cancer has been found on virtually every branch of the tree of multicellular life, from the simplest to the most complex. And she tells the story of how a family trip to the zoo led to the University of Utah’s Professor Josh Schiffman discovering the biological secret that explains why elephants hardly ever get cancer.
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
Mechanical regulation of cell division in developing tissues: Speed Vs Strength
During embryogenesis, dynamic mechanical forces act on developing tissues, inducing cellular mechano-responses. These changes in cellular behaviours such as cell division, adhesion, and motility are a vital aspect of tissue morphogenesis and homeostasis.
This summer, I was given the opportunity to work under Dr. Woolner at the University of Manchester’s Division of Cell Matrix Biology & Regenerative Medicine. Using a multidisciplinary approach, Dr. Woolner’s lab examines the cellular response of developing tissues to an applied mechanical force and seeks to identify the underlying molecular basis. This placement was an incredible and unique opportunity for me, as I was able to receive training and experience in a variety of new techniques used in biomechanics, mathematics, biomodelling and developmental biology.
Previous work by the Woolner lab demonstrated that the rate of cell division increases in epithelial cells following the application of a low-magnitude, uniaxial tensile force1. Work in other systems has shown that similar mechanically-induced increases in proliferation occur due to upregulation of the ERK1/2 pathway downstream of the stretch-activated calcium channel Piezo1, culminating in an upregulation of cyclin B2. Additionally, it is known that the orientation of cell division aligns with the axis of stretch1.
However, all current studies investigating the cellular response to tensile force involve rapid, instantaneous tissue stretching. Under physiological conditions, changes to mechanical tension in the developing embryo occur over a period of minutes to hours rather than seconds. In tumourigenesis, mechanical changes may take place over years. It is not currently known how cell division rate differs between fast and slow stretch regimes. Preliminary work suggests that slow-stretch regimes may not elicit the same division responses that are seen with instantaneous stretching.
My project aimed to help shed light on whether the speed or strength of an applied mechanical force is the major factor in altering cell division rate.
Using a tissue stretching apparatus, we applied an instantaneous, uniaxial stretch with reduced strength to tissues. For these experiments, Xenopus laevis embryonic tissue was used. Xenopus laevis embryos are a robust model organism for use in biomechanical research as they are large, develop externally and are easily visualised. I was very grateful for the opportunity to shadow members of the lab working with the Xenopus colony throughout the project. They are a unique model animal (I also have a few as pets!) and it was great to see how they are cared for and used responsibly in a research setting.
Fig 1. Selecting embryos at 2-cell stage for mRNA microinjection
In order to visualise the cell edge and nucleus, Xenopus embryos were injected at 2-cell stage with GFP-tubulin and Cherry-histone RNA. Straight away I was given the chance to jump in and get involved with the experiments, as I helped Gina (the Woolner Lab’s Research Assistant) with DNA miniprep and mRNA preparation. We proceeded with microinjection, which involved inserting a microscopic needle tip into each cell under an optical microscope. This was a very tricky procedure at first but by practicing alongside Gina, I was eventually able to go from struggling to inject 10 embryos in an hour to injecting over 50 in half the time!
Following overnight incubation, embryos were staged at early gastrula and the animal caps were dissected. Isolated animal cap explants are a versatile tissue able to survive and develop ex-vivo, making them ideal for live imaging. Dissecting the animal cap was done through an optical microscope using two sets of forceps. This was the most technically challenging aspect of my lab work, as it required a steady hand and patience but couldn’t be done too slowly or the embryos would become too developed. It was very rewarding to eventually get a perfect set of animal cap explants.
Following incubation on a fibronectin-coated silicone membrane, the animal caps were stretched and imaged. Shown in Figure 2 is a single frame from one of our live movies captured using confocal fluorescence microscopy. This was great experience, as imaging science was always of great interest to me but I had never previously had the chance to put my theoretical knowledge into practice. I also used image analysis software to calculate the mitotic index, as well as try cell population tracing. The Woolner lab uses tracing alongside vertex modelling3,4 to measure cell shape and infer mechanical stress across the tissue. The data collected during my project will be used to determine whether an increased cell division rate acts to relieve tensile stress across the tissue.
Fig 2. Fluorescent image of a Xenopus embryo animal cap explant experiencing a uniaxial stretch. Visualisation of the cell nucleus (magenta) and cell edge (green) allows image analysis techniques and cell population tracing to be performed. This was performed to calculate the mitotic index and biophysical properties of the tissue.
Alongside my core project work, I also successfully titrated the CDK-1 inhibitor RO-3306 to find the optimal concentration for cell division inhibition in Xenopus embryos. It is currently known that mechanical tension may increase cell division in fast-stretch regimes by promoting G1 to S phase transition5, which the Woolner lab will be investigating in slow-stretch regimes using a Fucci probe coupled with RO-3306 inhbition. Towards the end of my studentship, I was really grateful to have the opportunity to attend the 18th International Xenopus Conference. This was a great chance to discover the wide array of biomedical research using Xenopus currently being conducted worldwide and make valuable connections.
Fig 3. Xenopus laevis produce large, externally developing embryos which are easy to collect, visualise and manipulate. These properties make them particularly suitable for tissue stretch experiments.
I would like to thank everyone for all their support, guidance, patience and coffee & cake sessions throughout the internship. I am very grateful that I was able to receive the Gurdon/BSDB Summer Studentship and would recommend any student interested in developmental biology research to apply. Gaining first-hand lab experience in this field has given me invaluable skills and insight and has opened many doors for my future career.
References
Nestor-Bergmann A., Stooke-Vaughan G.A., Goddard G.K., Starborg T., Jensen O.E. and Woolner S. (2019) Decoupling the roles of cell shape and mechanical stress in orienting and cueing epithelial mitosis. Cell Reports26: 2088-2100
Gudipaty S.A., Lindblom J., Loftus P.D., Redd M.J., Edes K., Davey C.F., Krishnegowda V., Rosenblatt J. (2017) Mechanical stretch triggers rapid epithelial cell division through Piezo1. Nature543, 118-121.
Nestor-Bergmann A., Goddard G., Woolner S. and Jensen O.E. (2017) Relating cell shape and mechanical stress in a spatially disordered epithelium using a vertex-based model. Mathematical Medicine and Biology35 (Supplement 1): 1-27
Jensen O.E., Johns E. and Woolner S. (2020) Force networks, torque balance and Airy stress in the planar vertex model of a confluent epithelium. Proceedings of the Royal Society A476: 2237
Benham-Pyle B.W., Pruitt B.I and Nelson W.J. (2015) Mechanical strain induces E-cadherin-dependent Yap1 and β-catenin activation to drive cell cycle entry. Science 348(6238): 1024–1027.
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