Doing great science depends on teamwork, whether this is within the lab or in collaboration with other labs. However, sometimes the resources that support our work can be overlooked. Our ‘Featured resource’ series aims to shine a light on these unsung heroes of the science world. In our latest article, we hear from Steve Lisgo and Janet Kerwin, who describe the work of the Human Developmental Biology Resource (HDBR) Atlas.

When was the HDBR Atlas established and what are its aims?

The HDBR Atlas was established in 2020 and was developed from the Human Developmental Studies Network (HuDSeN) and Electronic Atlas of the Developing Human Brain (EADHB) projects, which began in 2002. The HDBR Atlas brings together 3D models, high resolution histology sections and gene expression data, and aims to facilitate the learning and understanding of human embryonic and fetal development.

Who runs the HDBR Atlas?

The Human Developmental Biology Resource (HDBR; www.hdbr.org) is an MRC/Wellcome funded human embryonic and fetal tissue bank, managed across two centres: Newcastle University and UCL. The samples collected by the resource are used in registered research projects in the UK and overseas. Data generated both by HDBR users and produced in house at London and Newcastle HDBR centres are disseminated through the HDBR Atlas. The Newcastle HDBR group lead on curating and developing the website.

What can researchers find in the HDBR Atlas? 

The HDBR Atlas is a freely available website comprising four sections: 1) 3D models of normal embryos (Carnegie stages (CS)12 to CS23) and fetuses (8-11-post conception weeks), plus a series of karyotypically abnormal embryos. 2) Annotated histology sections of whole CS12-23 embryos at low and high resolution. 3) Organ systems, including gastrointestinal, nervous, urogenital and visual systems, and with a new feature on the developing cardiovascular system. The latter includes movies and interactive 3D models (CS12-16), annotated H&E sections (CS14-22), and fetal heart dissections (8-17 post conception weeks (pcw)). 4) Gene expression data for 129 genes from CS11 to 19 pcw. All the HDBR Atlas resources are available to download on request.

How can the community contribute?

We encourage users of HDBR material to return data images (or physical slides, if this is easier) so that the data can be made publicly available via the HDBR Atlas. Anyone who has human embryonic or fetal protein or gene expression data generated from microscope slides can submit data to us using the submission form available on our website (https://hdbratlas.org/data-submission.html). Expertise in different organ systems is always welcome to define anatomy in the 3D models and annotate 2D histology sections.

Any hidden gems, features that are new, or that researchers might be less aware of?

Previously, we have shown 2D images and movies of 3D models on the Atlas. Recently, we have added interactive 3D reconstructions of early heart development (https://hdbratlas.org/interactive/heart.html) which can be manipulated and zoomed in/out by the user.

If money was no object, what would you like to add to the HDBR Atlas?

Generate 3D models for all stages of development from 3 to 20pcw; create more detailed/comprehensive labelling of the histology sections; further develop the high resolution eHistology viewer to include transverse, sagittal and frontal section planes at each Carnegie Stage, and expand this into fetal stages; produce a fully searchable gene expression database with sets of marker genes for key structures e.g. cardiac markers and distinct brain regions; and create a section on comparisons between human and mouse development for different organ systems.

Feedback from users of the Atlas

‘Many thanks for a wonderful resource!’

‘I would like to take this opportunity to reiterate how useful the HDBR is. It is an amazing resource, unequal in its ability to support developmental biology research. My sincere gratitude to all the dedicated staff involved.’

‘I have used the 3D images in lectures (thanks!) and would really like to see these accompany any further additions/stages. 2D histology sections are also extremely useful to help lab members understand what they should be looking for in our own experiments.’ 

‘This is a great project! We linked to certain images for our graduate embryology workshops last semester. The students really liked it!’

‘Again, thank you for putting together this incredible resource.’

Thanks to everyone who has contributed to our ‘Featured resource’ series so far. You can read the whole series here. Let us know which resource(s) is essential for your research and we’ll add them to our list. Get in touch at thenode@biologists.com.

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For our latest SciArt profile, we continue our adventure into 3D artwork and showcase the the neuro-woodwork sculptures from Louis-Jan Pilaz. LJ is an Assistant Professor at the University of South Dakota, Sanford School of Medicine, where his lab works on early cortical development.

Where are you originally from and what do you work on now?

I was born in France. This is where I got my PhD, related to neural stem cell biology. During my master’s, I worked in Colette Dehay’s lab and I completely fell in love with radial glia. I think they are the most amazing cells in the universe, so full of mysteries. Flash-forward 13 years, after a couple postdocs in Nick Gaiano’s lab and Debby Silver’s, I am now working on them in my own lab. We are interested in many aspects of early cortical development and our daily bread is working with microscopes.

Were you always going to be a scientist?

Science has always been a huge part of my life. Going to college, I wanted to be an ethologist. Then I ran across a pamphlet on cognitive sciences and majored in that. Afterwards, I wanted to go back to heavy-duty biology, so I started working in the Dehay lab and so on.

And what about art – have you always enjoyed it?

While I was born in France, my mom is Dutch. This meant that every summer we would travel to the Netherlands, where we would spend a lot of time in museums. I am a huge fan of Vermeer and Rembrandt. I can also get really moved by contemporary art. Also, my grandfather was a painter and my great-grandfather was a carpenter. Those sets of genes probably gave me this irresistible need to tinker, to try artsy things. 

What or who are your most important artistic influences?

I don’t feel I am consciously influenced by any artist in particular. All the pieces of art I was exposed to as a kid are probably doing their job subconsciously. There are so many talented neuroscientists turned artists! I love the works of Greg Dunn, Needles and neurons, Laura Bundesen, Maria Zanfir…

How do you make your art?

I have to admit that I use a lot of power tools. And I keep learning how to use new ones to shape the wood the way I want to. The most critical tool in my workshop is the scroll saw, it allows me to give the wood the intricate shape of a neural cell, and then I have a whole arsenal for the final touches. Importantly, most of my creations start on my computer.

Does your art influence your science at all, or are they separate worlds?

They are quite separate for now, but I get to interact with a lot of amazing scientists who are interested in my work, that I may not have met if it weren’t to talk about my creations. While I love creating cells in wood, my priorities are my lab and my family. 

What are you thinking of working on next?

I want to scale up. I want to make 6-foot neurons, astrocytes, microglia and of course radial glia. I also want to combine several cells together to create big installations.

You can follow LJ on twitter: @NeuroWoodworks – artwork and @ljpilaz – science.

Thanks to LJ and all the other SciArtists we have featured so far. You can find the full list here. We’re always on the lookout 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!)

(5 votes)

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We offer one fully funded postdoctoral position up to five years in the Laboratory of Genome Integrity located at the National Institutes of Health (NIH, Bethesda, MD). NIH is the largest biomedical research agency in the world, fosters world-renowned researchers and provides access to state-of-the art innovative technologies and scientific resources.

Our laboratory uses human and mouse embryonic stem cells (ESCs) as well as mouse embryos to understand the molecular mechanisms underlying cell fate decisions. The applicant should have or about to have a PhD in Developmental Biology, Genetics, Molecular Biology or similar, and must have demonstrated expertise on molecular biology/mammalian cell culture (preferably in embryonic stem cells). Knowledge in mouse embryology, single-cell RNAseq, chromatin architecture and/or next generation sequencing technologies will be considered as an advantage.

The applicant will be involved in a variety of exciting projects ranging from studying the relation between cell plasticity/totipotency and chromatin architecture to exploring the underlying mechanisms of new regulators of Zygotic Genome Activation. We seek a highly motivated, creative individual, eager to learn and develop new technologies and complex cell systems based on live cell/embryo imaging, single-cell technologies and CRISPR-based editing interested in understanding how a single cell can develop into a complex multicellular organism in vitro and in vivo.

Please send a brief cover letter and CV via e-mail to:
Email: sergio.ruizmacias@nih.gov
Laboratory web: https://ccr.cancer.gov/Laboratory-of-Genome-Integrity/sergio-ruiz-macias

Applications will be accepted until the position is filled.

Recent publications:
• Vega-Sendino, et al (2021) The ETS Transcription Factor ERF controls the exit from the naïve
pluripotent state. Sciences Advances, 7(40): eabg8306.
• Olbrich, T., et al (2021) CTCF is a barrier for 2C-like reprogramming. Nature Communications
12, article number: 4856.
• Markiewicz-Potoczny, M., et al (2020) TRF2-independent protection of telomeres in pluripotent
stem cells. Nature, 589: 103-109.

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Debate on the status of the field of developmental biology continue to rumble on, including an open letter to Claudio Stern from Peter Lawrence published on the Node. You can read the letter here, as well as a reply from Alfonso Martinez Arias. Remember, the Node is your site and if you would like to share your hope and fears for the future of developmental biology all you need to do is register and then you are free to post. Please get it contact if you need any support doing this, or if you would like to collaborate with others on a post.

preLights in #devbio

Wonder how rigidity sensing contributes to mechanical failure in epithelial tissues? Go check this preprint.

Plakoglobin to the rescue: how the vertebrate homologue of β-catenin senses mechanics during early embryogenesis to maintain naïve pluripotency.

Hox has got the nerves. Hox genes maintain neurotransmitter identity from development to adulthood.

Playing tug-of-war with chromosomes to generate specific aneuploidies

If you would like to write for the Node, check out our recent list of writing ideas. If you would like to contribute to our ‘Developing news’ blog, please get in touch at thenode@biologists.com

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At the end of 2021 and beginning of 2022, Journal of Cell Science (JCS) put out a call for essays on ‘Equity, diversity and inclusion in cell biology’. JCS introduced the series to amplify voices that are not always heard in this space. After receiving some fantastic essays on a range of different topics, they selected three winners and have now published these essays, as well as those from the runners-up.

You can read all the essays here: https://journals.biologists.com/jcs/pages/essay-series-edi

Editorial: https://journals.biologists.com/jcs/article/135/7/jcs259967/275017/Essay-series-on-equity-diversity-and-inclusion-in

If you have a story about equity, diversity and inclusion that you’d like to share, we’d love for you to post it on the Node. Get in contact (thenode@biologists.com) if you have any questions or would like help posting your article.

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Birds do it. Bees do it. We even have evidence that fleas do it, although whether or not those fleas are educated remains to be determined. And by ‘it’, I of course mean cannibalism.

In the latest Genetics Unzipped podcast, Dr Sally Le Page explores the gruesome side of family life in the natural world, getting stuck into a spot of cannibalism and asking: “When exactly should you eat your relatives?”

Sally takes a look at different examples of cannibalism across the animal kingdom, from offspring eating their mothers to males giving up their lives for sex and siblings devouring each other in the womb.

We meet the Taita Hills caecilian, an amphibian species where mothers produce extra thick skin that is eaten by their young, and spiders who digest their own internal organs to feed their spiderlings. We discover how male spiders give up everything, including their lives, for a chance at mating, why barn owls employ a ‘lifeboat’ strategy to eat their siblings, and why you might not want to put your hand inside a sand tiger shark’s uterus…

Genetics Unzipped is the podcast from The Genetics Society. Full transcript, links and references available online at GeneticsUnzipped.com.

Subscribe from Apple podcasts,Spotify, or wherever you get your podcasts.

Head over to GeneticsUnzipped.com to catch up on our extensive back catalogue.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

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The first LMCB retreat in 10 years provided a much-needed rejuvenation of scientific connections and discussions after two years of Covid restrictions. 

Hinxton Hall, on the Wellcome Genome Campus near Cambridge, was a perfect scenic location for what the next two days had in store for us. The retreat began with a talk from the LMCB director, Alison Lloyd, who reminded us about the importance and wonders of tissue biology from the angle of peripheral nerve homeostasis and repair. This introduction set the stage for a range of exciting talks throughout the next two days, presented by LMCB PhD students, postdocs, and group leaders, as well as invited external speakers.

The internal talks provided an opportunity to sample the range of cutting-edge research from across the institute. The topics went across scales from identifying enhancers in neurons to collective cell dynamics and mechanobiology and understanding how morphogenesis shapes an organ through development. 

One of the many highlights of the retreat was the flash talk session where selected PhD students and postdocs explained their research in three minutes. This was a friendly competition with the winning prize going to Giulia Paci from the Mao lab, who presented her work on microfabricated tools to apply mechanical forces in developing tissues. This session highlighted the range of techniques and approaches used across the institute including mathematical modelling, electron microscopy, and state of the art light microscopy.

If you didn’t think the flash talks were challenging enough, every student had the chance to draw their own research posters at the poster sessions. This saw a range of artistic attempts to explain research projects with pen and paper. I personally found the poster session to be so much fun, and I could now put names to faces and faces to exciting research projects. It was also a good opportunity to identify converging interests and to think about future collaborations and discussions.

In addition to talks from researchers within the LMCB, we were lucky to have excellent talks from three external scientists. The first of these was Soyon Hong from the UK Dementia Research Institute at UCL, who talked about the role of microglia in Alzheimer’s disease. We also had an entertaining talk from Mark Miodownik on the use and potential of animate materials to create a more sustainable planet for the future. The final external speaker was Rachel McKendry, who spoke about using quantum materials for early disease diagnosis. This was particularly relevant in the context of the Covid pandemic, as she highlighted technology that enabled the detection of low vial loads.

Now onto the social events, which lived up to their high expectations. The retreat started with a speed-dating session where we moved around small groups and gave a 30 second introduction. It was a great way to hear about the range of interests from colleagues and to get a hint of their hobbies away from science. 

One general aspect I have noticed about scientists is their humour, perhaps because research requires a creative quirk. This was certainly confirmed in the pantomimes. Students and postdocs had filmed a pantomime prior to the retreat which was shown as a short film after dinner. Our pantomime was scripted and filmed by the very talented Jimmy Van Hear, a PhD student in the Mao lab, and it was called the Cephalopod Contest, taking inspiration from the popular Netflix series ‘Squid Game’. As you can imagine, this was great light-hearted fun about the institute, the life of a scientist, and of course we also mocked our group leaders. Don’t worry…. the group leaders got their revenge on our pantomime with a LIVE performance of their own! After the endless laughs, the first night ended with a Ceilidh. Yes, that’s a bunch of energetic scientists being taught Scottish dance moves to fast paced music. This was a great chance to chill out and have fun outside of the scientific activities.

It wouldn’t have been a complete scientific retreat without a biology-themed Dragons’ Den competition! Over the two days, we got together into designated groups and brainstormed pitches and project names for the Dragons (LMCB group leaders). Group members then presented to the Dragons, who were willing to invest their own chocolate coins for the most promising projects. The projects were humorous, creative, and often inspired by our external speakers. We heard about a proposal to grow meat from your own cells and therefore bypassing any issues around animal consent (although as one Dragon pointed out, you could call this cannibalism). Another project pitched to speed up wound healing with a bioactive spray. But the winner of the audience vote, perhaps inspired by Mark Miodownik’s talk on animate materials, was the project ‘FungalFind’ which aimed to identify pollutants with genetically engineered fungi.

An exciting aspect of scientific training involves interacting with the community – gaining the social skills to spark collaboration, start new conversations, ask relevant questions and communicate with scientists from a range of different disciplines. Starting my PhD journey in a pandemic and joining a new research institute meant that the community aspect of science had faded, and my social skills felt rusty. During the retreat, I have met the faces I pass in the corridor, and I feel well connected to different research groups across my institute. I also feel much more confident about approaching colleagues and getting my ideas across. This experience has stressed the importance of in-person interactions and highlighted how ideas and creativity are much more fruitful in real life. 

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Following our Development presents… webinar earlier this month, which celebrated Development’s Special Issue on The Immune System in Development and Regeneration, we are currently asking for feedback on the webinar series and invite you to complete a short survey using the button below.

The survey should take around 6 minutes to complete and we encourage everyone to participate – even if you have not attended a Development presents… webinar before. Your feedback will help to determine the future direction of the series. Please complete the survey before Wednesday 6 July.

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The Centre for Trophoblast Research will again run its popular course in placental biology, online, from Monday 11th to Friday 15th July 2022.

This online course is aimed at students, post-docs, established researchers, medical & veterinary healthcare professionals and industry colleagues interested in cutting-edge placental biology and research.

Most content will be pre-recorded lectures and practical sessions given by investigators at the forefront of the placental biology field. There will be daily live Q&A sessions with the speakers, and opportunities to give talks and network.

Lectures and practical topics include:

Human & mouse placental development
Organoids, explant and trophoblast cultures
Materno-fetal interactions
Immunology
Placental transport
Angiogenesis
Clinical study design
Placental metabolism
Stem cell embryo models
Genome editing
Grant/fellowship writing
History of human embryos

We hope you will join us!

Limited places. Register here : https://www.trophoblast.cam.ac.uk/placentalbiologycourse/registration

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The Fossils, Phylogenies, Genomes, Embryos & the Evolution of the Deuterostomes symposium took place at the Natural History Museum in London to honour the work and contributions of the late palaeontologist R.P.S. ‘Dick’ Jefferies. In a field that is often looking to the future, it can be easy to take for granted the work that has come before or to overlook the early iterations of hypotheses we investigate today. This brilliant symposium, featuring speakers working across the scope of deuterostome evolution, was a fitting celebration of the pioneering work carried out by Dick Jefferies.

Joining the British Museum in the 1960s, Dick’s research focused on deuterostome fossils. Although many of his predictions have subsequently been disproved, some of his then-radical ideas have in fact been confirmed by more modern techniques. For example, his perhaps unexpected hypothesis of a clade comprising the tunicates and vertebrates (the Olfactores), has been subsequently supported by molecular data. Modern imaging approaches have also been key to confirming the validity of some of his ideas. A brilliant talk by Imran Rahman showed beautiful high-resolution X-ray scans supporting Jefferies’ idea of gill slits in early echinoderm fossils called the Stylophora. A particularly entertaining talk by Bertrand Lefebvre to round out the day detailed the painstakingly slow fossil sectioning-and-tracing technique employed by Jefferies’ to draw the same hypotheses now reached with very rapid microscopy approaches.

A particular highlight of the symposium was the breadth of research represented in the talks. Trends in developmental biology might sometimes lean towards developmental genetics and -omics, but the ‘evo’ side of evo-devo holds valuable contributions for the field. An excellent talk by Elizabeth Clark detailed the modelling of locomotion from fossil traces, and several talks (Paschalia Kapli, Graham Budd, Rachel Warnock) discussed persistent problems in phylogenetics. It was great to see the representation of such diverse research, and clear that there are still many open questions in the field – some of them pondered by Jefferies himself – remaining to be answered.

The Fossils, Phylogenies, Embryos & the Evolution of the Deuterostomes meeting was held on 12 May. It was supported by The Company of Biologists and The Palaeontological Association and organised by Max Telford, Jeffrey Thompson, Tim Ewin, Tim Littlewood, Greg Edgecombe, and Paul Barrett.

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