This week, #SciTwitter has been focussed on discussions around publishing, starting with prestige-signalling, followed by a big announcement from eLife, which received mixed reactions on Twitter. Going forward, eLife will no longer be accept or reject papers after review, but will publish a version of record (VOR) alongside public peer reviews. Check out their announcement for more details. We’ve picked out some tweets on both topics, and as always, click on the tweet for the full discussion and the opportunity to fall into a Twitter rabbit hole!
Prestige-signalling
We're doing a thing! Speakers @HHMINEWS Science Meetings will no longer put journal names on their talk slides. Instead display first author, year, PMID (or DOI) like @ardemp Why? -end prestige-signaling -people can actually find reference#nojournalnamesontalkslidespic.twitter.com/POe1M45pf6
I’m sympathetic to this idea, but it really makes most sense if the slides are available for download. Otherwise not so productive for me. Taking note of a DOI or PMID would detract from talk (Authors, year and journal name I can just about cope with). https://t.co/Hqt5i9zSgF
Today, we’re introducing a new model that eliminates accept/reject decisions.
By publishing every paper with eLife reviews as a Reviewed Preprint, we plan to restore autonomy to authors, ensuring that they will be judged by what, not where, they publish. https://t.co/OAsiOVFStIpic.twitter.com/lhnNElQp7y
Now that I've had a chance to see peoples' questions about @eLife's new publishing model, time for a thread for a thread with some details and answers. https://t.co/tD1BovOzLd
The 2nd Crick-Beddington Developmental Biology Symposium took place at The Francis Crick Institute between 9-10 October 2022. The hybrid symposium was generously funded by the MRC Rosa Beddington fund, which was established to uphold her memory and support curiosity-led science. Although a little later than originally planned, the conference maintained a similar ethos to the 1st symposium in 2019 (see an overview of that meeting from Alex Gould and Vicki Metzis and my previous Meeting Summary); many of the plenary speakers had direct links to Rosa and the talk topics reflected Rosa Beddington’s love of embryos and microscopy, as well as her meticulous description of morphogenesis. Shankar Srivivas, a former postdoc with Rosa and co-organiser of the meeting, opened the symposium with memories and photos of Rosa, mentioning her work on transplanting the mouse node (Beddington, 1994), how she believed in unity between all model organisms and how she often felt more comfortable behind the camera than in front of it.
Shankar Srinivas (organiser) begins the symposium by sharing some memories and photos of Rosa Beddington.
Patrick Tam (University of Sydney) began the meeting by discussing how he and Rosa had a common interest in mouse gastrulation and were each other’s first collaborators in the late 1970s. Patrick presented a spatial transcriptomic atlas of the gastrula mouse embryo that provides insights into the molecular activity underpinning lineage trajectory during gastrulation. Matthew Stower (Srinivas lab, University of Oxford) also discussed mouse gastrulation, using light-sheet imaging to reveal coordinated, collective migratory behaviours in the dorsal visceral endoderm. In their first talk as an independent group leader, Diana Pinheiro (Research Institute of Molecular Pathology) employs computational modelling to understand the collective internalisation of the mesendoderm in response to morphogen signalling during zebrafish gastrulation. Yanlan Mao (University College London) also uses computational modelling to understand how mechanics generates the three major folds in the Drosophila wing disc and how structures are maintained under stress, such as when larvae are constricted. On this theme of mechanics and morphogenesis, Caren Norden (Gulbenkian Science) discussed optic cup development, revealing the importance of the extracellular matrix for the migration of a population of ‘rim cells’ into the retinal neuroepithelium and Toby Andrews (Priya lab, Crick) zebrafish heart morphogenesis and the role of mechanical stretching for trabecular development. Similarly, Golnar Kolahgar (University of Cambridge) explained how vinculin-dependent mechanosensory activity in Drosophila enterocyte progenitors maintains homeostasis of the intestine. Irene Miguel-Aliaga (MRC London Institute of Medical Sciences) presented a different perspective on the Drosophila gut, discussing how inter-organ communication creates sex differences in intestine geometry and function, revealed using microCT. Simon Bullock (MRC Laboratory of Molecular Cell Biology), a former graduate student with Rosa Beddington, uses Drosophila as a model to understand how dynactin-dynein complexes asymmetrically localise RNA transcripts, including Gap genes. Drosophila segmentation was the focus of Jacques Bothma‘s talk (Hubrecht Institute) as well. Jacques has developed ‘LlamaTags’ for rapid imaging of transcriptional dynamics to reveal how the genome encodes and interprets time. Alain Chédotal (Vision Institute) similarly works on the leading edge of technology, employing virtual reality for the characterisation and 3D analysis of cleared human embryos. Jan Huisken (University of Göttingen) concluded the imaging theme by presenting Flamingo, a low-cost, customisable, modular light-sheet imaging microscopy set-up that can be shipped around the world and operated remotely.
The outside of The Francis Crick Institute.
Several of the talks reflected on metabolism. Josh Brickman (reNEW), a former postdoc with Rosa, looked back at their time together with humour, reflecting how Rosa had insisted he work on transcription factors, to which he now credits his career. Josh explained how transcription factor residence on enhancers supports plasticity in foregut stem cells and lipid metabolism alters gene expression via sirtuin-dependent acetylation. Aydan Bulut-Karslioglu (Max Planck Institute for Molecular Genetics) uses mTOR-inhibited embryonic stem cells as a model to show that fatty acid degradation sustains mammalian diapause. Moving from development to cancer, Salvador Aznar-Benitah (Institute for Research in Biomedicine) discussed how metastasis-initiating cells have high fatty acid metabolism and are sensitive to dietary fats, such as palmitic acid. Meritxell Huch also showed how lipid metabolism can reprogram differentiated liver tumour cells and discussed the importance of TET1-mediated demethylation for de-differentiation during liver regeneration. Selin Jessa (Kleinman lab, McGill University) presented the developmental origins of paediatric gliomas, focusing on the links between histone 3 lysine 27 methylation mutations and 3′ Hox genes.
Another emergent theme from the meeting was developmental principles across scales. At the population level, Hugh Ford (Chubb lab, Laboratory for Molecular Cell Biology) uses Dictyostelium to study cAMP signal propagation and cell migration. In tissues, Danelle Davenport (Princeton University) explained how the periodic pattern of skin appendages is established via polarising morphogenesis and Jakub Sumbal (Koledová lab, Masaryk University) presented insights from single-cell RNA-sequencing data of terminal end buds during mammary gland epithelial branching. Val Wilson (University of Edinburgh), a former postdoc in Rosa’s lab, presented research on two populations of axial progenitors in mice (neuromesodermal progenitors and lateral-paraxial mesodermal progenitors) and how signalling controls fate decisions within these populations. At the cellular level, Tamara Caspary (Emory School of Medicine) began her talk by explaining how Kathryn Anderson and Rosa Beddington catalysed her research in mouse ‘hat’ gene mutations, which were later mapped to ciliogenesis and Hedgehog signalling. Tamara showed how these two processes could be uncoupled through the activity of ARL13B in the cilia versus the cytoplasm. Rita Sousa-Nunes (King’s College London), a graduate student with Rosa, similarly aims to uncouple the proteome and transcriptome. Rita began her talk by sharing how Rosa once said to her “if she did it all again she’d [work on] flies and she’d [work with] with Daniel St Johnston”. Using Drosophila neural stem cells as a model, Rita explained how quiescent cells retain untranslated transcripts in their nuclei. Finally, Alex Schier (University of Basal) reminisced about how he once sat next to Rosa before she gave a talk, remarking to him, “I hope I don’t faint”. Alex presented on how the cell develops a specialised form and function by expressing gene ‘modules’, using the differentiation of zebrafish notochord and hatching gland as a model system.
Tamara Caspary told the story about her work was catalysed by the motivation of Rosa Beddington and Kathryn Anderson (1952-2020).
A new addition to this year’s programme was two sessions of flash talks by a selection of the poster presenters. Equipped with just three minutes each, the flash presenters covered a wide range of different topics within developmental biology. They did a fantastic job of enticing the audience to visit their poster during the breaks and poster sessions. Several speakers use live cell imaging to answer their development questions: Sunandan Dhar (Saunders lab, National University of Singapore) studies cell fusion in skeletal muscle; Jean-Francois Derrigand (Spagnoli lab, King’s College London) is exploring exocrine pancreas morphogenesis; Michael Smutny (University of Warwick) is investigating global tissue reshaping zebrafish gastrulation; Markus Schliffka (Maitre lab, Curie Institute) studies the fluid dynamics of microlumens that form in the mammalian blastocyst; and Cerys Manning (University of Manchester) follows dynamic decisions in the development of the eye. Also studying eye development, Jana Sipkova (Franze lab, University of Cambridge) investigates the role of Eph/Ephrin signalling and mechanics in neuronal migration between the eye and the optic tectum. Making the link between mechanics and development, Eirin Maniou (Galea lab, University College London) uses 3D printing to measure mechanical forces during chick neural tube closure in vivo and Sera Weevers (Tsiairis lab, Friedrich Miescher Institute for Biomedical Research) studies how osmosis-driven mechanical stretching underlies the establishment of the Wnt organiser in Hydra. Further understanding the connections between signalling, transcriptional regulation and cell fate, Sergio Menchero (Tuner lab, Crick) aims to uncouple transcriptional and morphological changes by comparing opossum and mouse organogenesis. Similarly, Joaquina Delas (Briscoe lab, Crick) studies how cell fate decisions in the neural tube are regulated at the chromatin level by differential binding and differential element availability and Vicki Metzis (Imperial Collge London) investigates how the posterior neural fate is acquired via CDX2. Furthermore, Lisa Thomann (Lemaire lab, CRBM) uncovers the role of PI3K signalling in ascidian notochord development. Finally, at the subcellular level, Azelle Hawdon (Zenker lab, Australian Regenerative Medicine Institute) studies sub-cellular mRNA asymmetry in mammalian embryogenesis and Chantal Roubinet (Baum lab, University College London) spoke on the asymmetric inheritance of nuclei during Drosophila neuroblast divisions.
As well as the plenaries, selected talks and flash talks, there were also presentations from ThermoFisher and 10X Genomics. For ThermoFisher, Sarawuth Wantha presented the Amira software, suitable for large lattice light-sheet microscopy data, transmission electron microscopy, AI-based segmentation and high-content screening. On behalf of 10X Genomics, Nicola Cahill introduced the Chromium, Visium and Xenium platforms for single-cell sequencing, spatial transcriptome and in situ applications, respectively.
A final variation from the first meeting was the hybrid aspect. I was fortunate to attend most of the meeting in person; however, I didn’t miss out by having to duck out a little early to catch my train. I was able to quickly log in to the live stream on Zoom to watch the concluding remarks. I hope those of attended virtually also found the hybrid format helped accessibility. The switching, too, between in-person and video presenters was seamless and it was great that those who could not attend in person were still able to share their work with us.
Concluding remarks from Nic Tapon (organiser) sharing some of Rosa’s paintings of Mendel, appropriate because this year marked the 200th anniversary of his birth.
Nic Tapon concluded the symposium by thanking the speakers, the Crick Events team, sponsors and co-organisers; Shankar Srinivas, Alex Gould and Caroline Hill. Nic explained how two of Rosa’s paintings of Mendel that hang in the Crick were especially appropriate this year because it’s the 200th anniversary of Mendel’s birth.
Thank you to the organisers for their effort in assembling the symposium together, chairing sessions and for the smooth execution of the programme. I also thank all the speakers for sharing their stories, both of their science and their memories of Rosa Beddington.
Where did we come from? And how are we related to the ancient species that came before us? Asking questions like these is part of what makes us human. But, genetically speaking, what really does make us human?
Dr Kat Arney
In the latest episode of the Genetics Unzipped podcast, we’re exploring what we can discover about our evolution from our DNA, and what evolutionary secrets might be contained in the ancient DNA of our ancestors. Dr Kat Arney looks at why this year’s Nobel Prize awarded for the genomics of ancient humans, how genetic mutations allow Tibetans and their dogs to survive in high altitudes, and dispelling the myth about why many adults can drink milk.
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
On Monday 12 September, we livestreamed a session from our meeting ‘From Stem Cells to Human Development’, as part of our Development presents… webinar series.
Below you can find the recordings of the talks from Sarah Teichmann and Sergiu Pasca, as well the panel discussion featuring Amander Clark, Robin Lovell-Badge, Sergiu Pasca, Sarah Teichmann and Magdalena Zernicka-Goetz, chaired by Patrick Tam.
Sarah Teichmann (Wellcome Sanger Institute, UK) ‘Human development: one cell at a time’
Sergiu Pasca (Stanford University, USA) ‘From stem cells to assembloids: constructing and deconstructing human nervous system development and disease’
Panel discussion with Amander Clark, Robin Lovell-Badge, Sergiu Pasca, Sarah Teichmann and Magdalena Zernicka-Goetz ‘Technical, ethical and legal challenges of studying early human development’
Applications are invited for a Postdoctoral Research Scientist to join A/Prof Duncan Sparrow’s laboratory at the University of Oxford to work on a project using mouse models to investigate environmental influences on embryonic heart development that may lead to congenital heart disease in humans. This is a 5 year position fully funded by the British Heart Foundation. Applications are particularly welcome from women, black and minority ethnic candidates who are under-represented in academic posts in Oxford. https://tinyurl.com/bdd5raa7
Twitter has felt a little quieter on the #devbio front these past two weeks, perhaps in anticipation of the long awaited #ISDB2021, which kicked off this Sunday. If you have not made it to the meeting this time, you can still follow along using the hashtag #ISDB2021. We have also pick a few other tweets with interesting discussions that caught our eyes, as well as bringing you the preLights related to developmental and stem cell biology.
— International Society of Developmental Biology (@IntSocDevBiol) October 16, 2022
In vitro, in vivo or both, and does it matter?
As someone happily spending an entire career applying knowledge from in vitro & cell culture experiments to the context of the whole animal it's always puzzling how little many fields care about testing their hypotheses in the complex setting of a living breathing organism.
Sometimes, when I’m feeling like my research doesn’t matter, I read my spam emails. In my spam emails, I am “prominent” and “eminent.” My submissions are urgently needed. I am invited to serve as a keynote speaker at conferences in fields like plant ecology and marine biology.
Dr David A. Menassa and Professor Diego Gomez-Nicola at the University of Southampton, UK recently published an article in Developmental Cell where they reveal how the microglial population colonises the human frontal cortex. Dr Menassa gave us a behind the scenes look at how the story came together.
How did you get started on this project?
I joined the Gomez-Nicola lab in October 2017 as a research fellow. The funding had been granted by the Leverhulme Trust prior to my arrival, and all was in place to set the human lifespan study in motion.
The task of securing healthy human tissues from whole embryos to advanced ageing was a challenging one. It took several years to establish the tissue collection and 12 tissue resources within the UK and abroad were consulted. There was a substantial administrative load. Human tissue work in general is fraught with challenges: even when one acquires the tissues, there are no guarantees that the antigenic targets will have been preserved. The assumption is that they should be, but there are many factors that come into play making work with human tissues a good exercise in patience, focus and resilience. Once the frustrations were out of the way, the project kicked off at full speed. I was lucky to be part of a very supportive laboratory environment, working alongside a team of intramural and extramural collaborators. This paper is evidence of great teamwork and we are delighted to be able to share our findings with the scientific community.
What was already known about the developmental dynamics of microglia in the human brain prior to your work?
Two studies on adult human tissues (including one from the Gomez-Nicola lab) were published in 2017 showing that microglial turnover in humans is much faster than previously thought and that the entire population is renewed several times during a lifetime [2, 3]. Additionally, microglial proliferative dynamics increase during pathology and have been the target of therapies to limit proliferation in neurodegenerative disease particularly Alzheimer’s disease models [4]. Very little was known about microglial dynamics during the critical stages of human brain development and the early postnatal age, and this was largely due to the limited availability of tissues for research.
In the latter half of 2020, two papers profiled microglial developmental states during early embryonic and early fetal lives in humans [5, 6]. These studies showed that ontogenic pathways were conserved between mice and humans and that microglia became immunocompetent from as early as the 11th week of gestation. In 2022, the regional microglial transcriptome was described in humans between 8-23 weeks of gestation: this was the first study to look at specific anatomical regions such as the cortex and the cerebellum [7]. Altogether, these studies offered an important view of specific temporal windows during development. In our study, we covered the entire human lifespan, detailing the spatiotemporal dynamics of microglia from the moment these cells arrive to the human developing brain at 4 pcw up until they turnover very slowly in adult life. We profiled these cells in all layers of the cortex in the frontal lobe, the brain region responsible for higher order cognitive and executive function in humans.
Can you summarise your findings?
There are four important temporal windows during human brain development when we see microglial changes: the first one is when microglia arrive to the brain with the onset of circulation at 4 pcw; the second is at the transition between embryonic to fetal life at 9-10 pcw; the third is at 13-14 pcw and the fourth is during early childhood between 0.5-1 year of age. Microglial expansion in the brain is via a wave-like pattern of cycles of migration and proliferation, increasing cell number, which is further refined by selective cell-death. The changes in microglial dynamics are aligned with co-occurring neurodevelopmental processes. We found no sex differences during these developmental stages. In adult life, the population self-renews at a relatively steady rate until advanced ageing. This pattern of colonisation is unique to humans and is strikingly different than what we see in mouse.
Figure 1 Microglial dynamics across the human lifespan. This graphical abstract was modified from [1] and shows the proliferation, cell number and cell death changes of microglia between 3 postconceptional weeks and 75 years of life. The arrows represent ongoing processes.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
Seeing the first fully labelled embryo for microglia, other tissue-resident macrophages and proliferative cells in the brain matter, liver, spleen, spinal cord, and heart all visible in one slide was a special moment. I remember sending Dr Gomez-Nicola the first image and we were both excited and thrilled that it was all worth the wait; the signal was very clear and from that point onwards, we were confident that the project was heading in the right direction. The second moment was when we had all the data unblinded and plotted across the lifespan for all tissues: it was a roadmap, and we could see the exact pattern that microglia followed prenatally and postnatally.
And what about the flipside? Any moment of frustration or despair?
Human tissue research is challenging, but the end-result is very rewarding. In this paper, we could not obtain samples with consent for research use from late childhood and adolescence. Therefore, we are missing part of the whole picture. As the pattern of growth and myelination of the frontal lobe is unique in humans during these stages, it will be interesting to see what happens to microglial dynamics.
Where will this story take you next?
Now that we know the temporal windows of relevance in microglial dynamics, the next step is to begin dissecting how microglial cells interact with the neurodevelopmental environment. This could be by elucidating the cues that these cells get from the brain at each step and in this way, we can start identifying why the population behaves the way it does. This is important as microglia are part of the neuropathology of neurodevelopmental disorders. To find out how these cells contribute to normal and altered neurodevelopment, we need to dissect the signalling pathways between them and developing neurons.
What is next for you after this paper?
I am currently stipendiary lecturer of neurophysiology and neuroscience at the Queen’s College, University of Oxford and visiting researcher in neurodevelopment at the Croatian Institute for Brain Research, University of Zagreb. I am continuing my research on microglial development and how this relates to neurodevelopmental disorders. I am applying for tenured positions in the UK and Europe to set up my own research group.
Bibliography
1. Menassa, D.A., et al., The spatiotemporal dynamics of microglia across the human lifespan. Dev Cell, 2022.
2. Askew, K., et al., Coupled Proliferation and Apoptosis Maintain the Rapid Turnover of Microglia in the Adult Brain. Cell Rep, 2017. 18(2): p. 391-405.
3. Réu, P., et al., The Lifespan and Turnover of Microglia in the Human Brain. Cell Rep, 2017. 20(4): p. 779-784.
4. Olmos-Alonso, A., et al., Pharmacological targeting of CSF1R inhibits microglial proliferation and prevents the progression of Alzheimer’s-like pathology. Brain, 2016. 139(Pt 3): p. 891-907.
5. Bian, Z., et al., Deciphering human macrophage development at single-cell resolution. Nature, 2020. 582(7813): p. 571-576.
6. Kracht, L., et al., Human fetal microglia acquire homeostatic immune-sensing properties early in development. Science, 2020. 369(6503): p. 530-537.
7. Li, Y., et al., Decoding the temporal and regional specification of microglia in the developing human brain. Cell Stem Cell, 2022. 29(4): p. 620-634.e6.
by Haneen Alsehli, Shrinidhi Madhusudan, Marie-Christin Leitner and Katherina Tavernini
For most of us, this was the first in-person conference since starting our PhDs, or since the COVID-19 pandemic hit. All of us were very excited to get inspired, network and talk about our work by presenting our projects, either with a poster or giving a selected talk.
First day, first lunch and we had already met new people, we started chatting and had a good time. Despite being at different stages of our PhDs, we shared the same thoughts and fun stories – we laughed a lot! From that moment on, we had a great conference group, where the friendships will last beyond the meeting.
This conference was located in a beautiful setting just a one hour train ride south of London. At Wotton House,we could explore the beautiful natural surroundings during breaks, but also study, work and listen to talks in a historic setting. Overall, we were exceptionally well taken care of during this meeting.
During the talks and poster sessions, we had the chance to listen to outstanding talks from experts in the field. We all appreciated the amount of unpublished data, and for Haneen, who is writing up at the moment, this kind of literature review was very useful. For others, hearing about new methods in talks that were outside our areas of expertise were beneficial, as we began to think about translating them to our own work.Furthermore, the industry sponsors at the event were also very accommodating and we look forward to taking their expertise and methodology back to our institutes.
Since we were all presenting our work, we all experienced the great atmosphere of this meeting. We had fruitful discussions at our posters that not only allowed us to gather ideas for future experiments, but to get feedback on our work from an international audience. We discussed our work with group leaders, representatives from industry, postdocs and of course, fellow students, which we appreciated and found very rewarding.
This meeting was highly interactive and we all acknowledge the effort that was made to foster interactions among the participants. The ‘speed-networking’ event forced some of us outside of our comfort zones, to interact with PIs and senior scientists. Each dinner, we were randomly assigned to tables and had a dedicated seat. Although being apprehensive initially about the place cards, we soon came to appreciate it, especially after having interesting conversations with participants that we might not have otherwise met. With this setting, we had the opportunity to talk to different group leaders, students, editors; to discuss science, ask questions and spin ideas about future developments.
We all really appreciated the effort the organisers took to make this conference as safe as possible. We felt that Covid measures were taken seriously, which allowed for great and almost carefree networking.
If you ever have the chance to participate in this conference, go for it! You will hear about the latest amazing research, make new friends, interact and network with experts in the field from all over the world. We would definitely recommend attending and meeting great people and potential future collaborators along the way.
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 Tanya Z. Berardini, Ph.D (TAIR Director) and Leonore Reiser, Ph.D (Senior Scientific Curator)] who describe the work of TAIR.
The Arabidopsis Information Resource (TAIR) was established in 1999 with US National Science Foundation funding and the goal of creating a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Arabidopsis was the first plant genome to be sequenced (1). Since then, over twenty years of research have continually improved the sequence and functional annotation of a genome that serves as a reference for an ever-increasing number of newly sequenced plant genomes (2). TAIR integrates, interconnects, and consolidates information from peer-reviewed published literature with sequence and stock information (3) so that researchers can spend less time searching for information and more time developing and testing hypotheses guided by work that has already been done.
Who runs the resource?
TAIR was created at the Department of Plant Biology of the Carnegie Institute for Science and the National Center for Genome Resources (NCGR) and supported by the NSF from 1999 to 2013. Since 2014, it has been administered and maintained by the non-profit organization, Phoenix Bioinformatics (4). Phoenix has a small team of dedicated data curation scientists, who meticulously curate and update TAIR data, and software engineers, who maintain and update TAIR’s database and tools. Newly curated information from the literature is added weekly.
Where does funding come from?
Since 2014, TAIR’s operations have been funded by subscriptions from academic and other non-profit institutions, individual researchers, corporations and countries (e.g., China through its National Science and Technology Library). Institutional subscriptions are priced based on past year usage, so that institutions that use the resource more contribute more to its maintenance and growth. TAIR’s subscription support is as global as its user base. Phoenix Bioinformatics has additional funding from the NSF and the Sloan Foundation for other aspects of its work.
Can one access TAIR without a subscription?
Unlimited access to TAIR’s data and tools almost always requires a subscription. However, TAIR provides a limited number of free page views for occasional users each month. This is similar to the monthly allotment of complimentary articles often offered by online newspapers and magazines. After the monthly limit is reached a subscription is encouraged. Upon request, TAIR grants full access for teachers and students at non-subscribing institutions for classes that use TAIR in their curriculum. US Historically Black Colleges and Universities (HBCUs) are granted free access. Finally, we grant country-wide access to those countries that fall into the ‘low-income economies’ categorization of the World Bank.
What tools and resources are available for researchers?
The TAIR locus page is a treasure trove that consolidates in-house data, data pulled from other resources by APIs, and links to external resources with complementary information. New articles, gene symbols and full names, gene summaries, Gene Ontology (GO) and Plant Ontology (PO) annotations, germplasms and phenotypes based on those articles are added by data curation scientists to a subset of loci on a weekly basis.
Researchers can find information for single genes or they can download data (sequences, descriptions, GO annotations) for sets of genes or even the whole genome.
There are two types of quarterly data releases: (A) Public data releases are a year old and are released for public reuse with a CC-BY reuse license. (B) Subscriber data releases reflect the most recent year’s data.
TAIR provides data search and browsing services, data analysis tools, and data visualization tools, such as genome browsers (e.g., JBrowse) and a BLAST service that includes unique datasets.
JBrowse at TAIR, 3 out of 250+ tracks shown
How can the community contribute?
Make data FAIR (5).
Use AGI identifiers for the Arabidopsis genes in papers!
Use stock identifiers from NASC and ABRC for seed and DNA stocks. They allow us to link these stocks unambiguously to locus records at TAIR.
Register gene symbols, use the symbols for genes that already exist and check that symbols you want to use are not already in use.
Beta site (in progress): New look of the TAIR Locus Page
Any hidden gems, features that are new, or that researchers might be less aware of?
The biggest hidden gem is that if you email us, we will respond within 24 hrs during a regularly scheduled work week.
Not only can one view information for one gene at a time, one can also upload a list of genes and retrieve gene descriptions, sequences, and GO annotations (and other types of data) in bulk.
The TAIR YouTube channel has tutorials and webinars of different lengths explaining various features of the resource. Watch a video and learn something new.
Access to PhyloGenes (www.phylogenes.org) is integrated into the TAIR Locus page. You can link to the Panther-based gene family, explore experimental and phylogenetically-inferred functional information for gene family members in Arabidopsis and 29 other plants, and take advantage of experimental annotations made in Arabidopsis and other model organisms.
Plant Homolog Section of TAIR Locus Page
The TAIR Job listings page is very active with about three new listings posted a week. Some labs recruit almost exclusively by posting their grad student and post-doc openings at https://www.arabidopsis.org/news/jobs.jsp. All openings are also shared through our Twitter account (@tair_news).
References:
The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 408, 796–815 (2000). doi.org/10.1038/35048692
Nicholas J Provart, Siobhan M Brady, Geraint Parry, Robert J Schmitz, Christine Queitsch, Dario Bonetta, Jamie Waese, Korbinian Schneeberger, Ann E Loraine. Anno genominis XX: 20 years of Arabidopsis genomics, The Plant Cell. 33(4):832–845 (2021). doi.org/10.1093/plcell/koaa038
Tanya Z. Berardini, Leonore Reiser, Donghui Li, Yarik Mezheritsky, Robert Muller, Emily Strait, Eva Huala. The Arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome. Genesis. 53(8):474-85 (2015). doi.org/10.1002/dvg.22877
Leonore Reiser, Tanya Z. Berardini, Donghui Li, Robert Muller, Emily M. Strait, Qian Li, Yarik Mezheritsky, Andrey Vetushko, Eva Huala. Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model, Database. Volume 2016, (2016). doi.org/10.1093/database/baw018
Leonore Reiser, Lisa Harper, Michael Freeling, Bin Han, Sheng Luan. FAIR: A Call to Make Published Data More Findable, Accessible, Interoperable, and Reusable, Molecular Plant 11(9):1105-1108 (2018). doi.org/10.1016/j.molp.2018.07.005
Contributed by Tanya Z. Berardini, Ph.D (TAIR Director) and Leonore Reiser, Ph.D (Senior Scientific Curator)
Rnf20 shapes the endothelial control of heart morphogenesis and function Linda Kessler, Rui Gao, Nalan Tetik-Elsherbiny, Olga Lityagina, Azhar Zhailauova, Yonggang Ren, Felix A. Trogisch, Julio Cordero, Yanliang Dou, Yinuo Wang, Evgeny Chichelnitskiy, Joscha Alexander Kraske, Patricia Laura Schäfer, Chi-Chung Wu, Guillermo Barreto, Michael Potente, Thomas Wieland, Roxana Ola, Joerg Heineke, Gergana Dobreva
Universal DNA methylation age across mammalian tissues A.T. Lu, Z. Fei, A. Haghani, T.R. Robeck, J.A. Zoller, C.Z. Li, R. Lowe, Q. Yan, J. Zhang, H. Vu, J. Ablaeva, V.A. Acosta-Rodriguez, D.M. Adams, J. Almunia, A. Aloysius, R. Ardehali, A. Arneson, C.S. Baker, G. Banks, K. Belov, N.C. Bennett, P. Black, D.T. Blumstein, E.K. Bors, C.E. Breeze, R.T. Brooke, J.L. Brown, G. Carter, A. Caulton, J.M. Cavin, L. Chakrabarti, I. Chatzistamou, H. Chen, K. Cheng, P. Chiavellini, O.W. Choi, S. Clarke, L.N. Cooper, M.L. Cossette, J. Day, J. DeYoung, S. DiRocco, C. Dold, E.E. Ehmke, C.K. Emmons, S. Emmrich, E. Erbay, C. Erlacher-Reid, C.G. Faulkes, S.H. Ferguson, C.J. Finno, J.E. Flower, J.M. Gaillard, E. Garde, L. Gerber, V.N. Gladyshev, V. Gorbunova, R.G. Goya, M.J. Grant, C.B. Green, E.N. Hales, M.B. Hanson, D.W. Hart, M. Haulena, K. Herrick, A.N. Hogan, C.J. Hogg, T.A. Hore, T. Huang, J.C. Izpisua Belmonte, A.J. Jasinska, G. Jones, E. Jourdain, O. Kashpur, H. Katcher, E. Katsumata, V. Kaza, H. Kiaris, M.S. Kobor, P. Kordowitzki, W.R. Koski, M. Kruetzen, S.B. Kwon, B. Larison, S.G. Lee, M. Lehmann, J.F. Lemaitre, A.J. Levine, C. Li, X. Li, A.R. Lim, D.T.S. Lin, D.M. Lindemann, T.J. Little, N. Macoretta, D. Maddox, C.O. Matkin, J.A. Mattison, M. McClure, J. Mergl, J.J. Meudt, G.A. Montano, K. Mozhui, J. Munshi-South, A. Naderi, M. Nagy, P. Narayan, P.W. Nathanielsz, N.B. Nguyen, C. Niehrs, J.K. O’Brien, P. O’Tierney Ginn, D.T. Odom, A.G. Ophir, S. Osborn, E.A. Ostrander, K.M. Parsons, K.C. Paul, M. Pellegrini, K.J. Peters, A.B. Pedersen, J.L. Petersen, D.W. Pietersen, G.M. Pinho, J. Plassais, J.R. Poganik, N.A. Prado, P. Reddy, B. Rey, B.R. Ritz, J. Robbins, M. Rodriguez, J. Russell, E. Rydkina, L.L. Sailer, A.B. Salmon, A. Sanghavi, K.M. Schachtschneider, D. Schmitt, T. Schmitt, L. Schomacher, L.B. Schook, K.E. Sears, A.W. Seifert, A. Seluanov, A.B.A. Shafer, D. Shanmuganayagam, A.V. Shindyapina, M. Simmons, K. Singh, I. Sinha, J. Slone, R.G. Snell, E. Soltanmaohammadi, M.L. Spangler, M.C. Spriggs, L. Staggs, N. Stedman, K.J. Steinman, D.T. Stewart, V.J. Sugrue, B. Szladovits, J.S. Takahashi, M. Takasugi, E.C. Teeling, M.J. Thompson, B. Van Bonn, S.C. Vernes, D. Villar, H.V. Vinters, M.C. Wallingford, N. Wang, R.K. Wayne, G.S. Wilkinson, C.K. Williams, R.W. Williams, X.W. Yang, M. Yao, B.G. Young, B. Zhang, Z. Zhang, P. Zhao, Y. Zhao, W. Zhou, J. Zimmermann, J. Ernst, K. Raj, S. Horvath
Discovery and characterization of LNCSOX17 as an essential regulator in human endoderm formation Alexandro Landshammer, Adriano Bolondi, Helene Kretzmer, Christian Much, René Buschow, Alina Rose, Hua-Jun Wu, Sebastian Mackowiak, Bjoern Braendl, Pay Giesselmann, Rosaria Tornisiello, Krishna Mohan Parsi, Jack Huey, Thorsten Mielke, David Meierhofer, René Maehr, Denes Hnisz, Franziska Michor, John L. Rinn, Alexander Meissner
The Neuroscience Multi-Omic Archive: A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain Seth A. Ament, Ricky S. Adkins, Robert Carter, Elena Chrysostomou, Carlo Colantuoni, Jonathan Crabtree, Heather H. Creasy, Kylee Degatano, Victor Felix, Peter Gandt, Gwenn A. Garden, Michelle Giglio, Brian R. Herb, Farzaneh Khajouei, Elizabeth Kiernan, Carrie McCracken, Kennedy McDaniel, Suvarna Nadendla, Lance Nickel, Dustin Olley, Joshua Orvis, Joseph P. Receveur, Mike Schor, Timothy L. Tickle, Jessica Way, Ronna Hertzano, Anup A. Mahurkar, Owen R White
Transient Polycomb activity represses developmental genes in growing oocytes Ellen G. Jarred, Zhipeng Qu, Tesha Tsai, Ruby Oberin, Sigrid Petautschnig, Heidi Bildsoe, Stephen Pederson, Qing-hua Zhang, Jessica M. Stringer, John Carroll, David K. Gardner, Maarten van den Buuse, Natalie A. Sims, William T. Gibson, David L. Adelson, Patrick S. Western
The imprinted Mir483 is a growth suppressor and metabolic regulator functioning through IGF1 Ionel Sandovici, Denise S. Fernandez-Twinn, Niamh Campbell, Wendy N. Cooper, Yoichi Sekita, Ilona Zvetkova, David Ferland-McCollough, Haydn M. Prosser, Lila M. Oyama, Danilo Cimadomo, Karina Barbosa de Queiroz, Cecilia S.K. Cheuk, Nicola M. Smith, Richard G. Kay, Katharina Hoelle, Noel H. Smith, Stefan H. Geyer, Lukas F. Reissig, Wolfgang J. Weninger, Kenneth Siddle, Anne E. Willis, Martin Bushell, Susan E. Ozanne, Miguel Constância
Cellular senescence modulates progenitor cell expansion during axolotl limb regeneration Qinghao Yu, Hannah E. Walters, Giovanni Pasquini, Sumeet Pal Singh, Daniel León-Periñán, Andreas Petzold, Preethi Kesavan, Cristina Subiran, Ines Garteizgogeascoa, Dunja Knapp, Anne Wagner, Andrea Bernardos, María Alfonso, Gayathri Nadar, Andreas Dahl, Volker Busskamp, Ramón Martínez-Máñez, Maximina H. Yun
Effects of α-crystallin gene knockout on zebrafish lens development Mason Posner, Kelly L. Murray, Brandon Andrew, Stuart Brdicka, Alexis Roberts, Kirstan Franklin, Adil Hussen, Taylor Kaye, Emmaline Kepp, Mathew S. McDonald, Tyler Snodgrass, Keith Zientek, Larry L. David
Machine-learning dissection of Human Accelerated Regions in primate neurodevelopment Sean Whalen, Fumitaka Inoue, Hane Ryu, Tyler Fairr, Eirene Markenscoff-Papadimitriou, Kathleen Keough, Martin Kircher, Beth Martin, Beatriz Alvarado, Orry Elor, Dianne Laboy Cintron, Alex Williams, Md. Abul Hassan Samee, Sean Thomas, Robert Krencik, Erik M. Ullian, Arnold Kriegstein, John L. Rubenstein, Jay Shendure, Alex A. Pollen, Nadav Ahituv, Katherine S. Pollard
A single cell atlas of the cycling murine ovary ME Morris, MC Meinsohn, M Chauvin, HD Saatcioglu, A. Kashiwagi, NA. Sicher, NMP Nguyen, S Yuan, Rhian Stavely, M Hyun, PK Donahoe, B Sabatini, D Pépin
A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics Amitabh C. Pandey, Jon Bezney, Dante DeAscanis, Ethan Kirsch, Farin Ahmed, Austin Crinklaw, Kumari Sonal Choudhary, Tony Mandala, Jeffrey Deason, Jasmin Hamdi, Azeem Siddique, Sridhar Ranganathan, Phillip Ordoukhanian, Keith Brown, Jon Armstrong, Steven Head, Eric J. Topol
hPGCLCs in 2D culture using BME overlay method from Overeem, et al.
A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates Peng He, Kyungtae Lim, Dawei Sun, Jan Patrick Pett, Quitz Jeng, Krzysztof Polanski, Ziqi Dong, Liam Bolt, Laura Richardson, Lira Mamanova, Monika Dabrowska, Anna Wilbrey-Clark, Elo Madissoon, Zewen Kelvin Tuong, Emma Dann, Chenqu Suo, Isaac Goh, Masahiro Yoshida, Marko Z Nikolić, Sam M Janes, Xiaoling He, Roger A Barker, Sarah A Teichmann, John C. Marioni, Kerstin B Meyer, Emma L Rawlins
Bat pluripotent stem cells reveal unique entanglement between host and viruses Marion Déjosez, Arturo Marin, Graham M. Hughes, Ariadna E. Morales, Carlos Godoy-Parejo, Jonathan Gray, Yiren Qin, Arun A. Singh, Hui Xu, Javier Juste, Carlos Ibáñez, Kris M. White, Romel Rosales, Nancy J. Francoeur, Robert P. Sebra, Dominic Alcock, Sébastien J. Puechmaille, Andrzej Pastusiak, Simon D.W. Frost, Michael Hiller, Richard A. Young, Emma C. Teeling, Adolfo García-Sastre, Thomas P. Zwaka
Transplantable human thyroid organoids generated from embryonic stem cells to rescue hypothyroidism Mírian Romitti, Adrien Tourneur, Barbara de Faria da Fonseca, Gilles Doumont, Pierre Gillotay, Xiao-Hui Liao, Sema Elif Eski, Gaetan Van Simaeys, Laura Chomette, Helene Lasolle, Olivier Monestier, Dominika Figini Kasprzyk, Vincent Detours, Sumeet Pal Singh, Serge Goldman, Samuel Refetoff, Sabine Costagliola
A single cell atlas of the cycling murine ovary ME Morris, MC Meinsohn, M Chauvin, HD Saatcioglu, A. Kashiwagi, NA. Sicher, NMP Nguyen, S Yuan, Rhian Stavely, M Hyun, PK Donahoe, B Sabatini, D Pépin
Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments Laurent Gatto, Ruedi Aebersold, Juergen Cox, Vadim Demichev, Jason Derks, Edward Emmott, Alexander M. Franks, Alexander R. Ivanov, Ryan T. Kelly, Luke Khoury, Andrew Leduc, Michael J. MacCoss, Peter Nemes, David H. Perlman, Aleksandra A. Petelski, Christopher M. Rose, Erwin M. Schoof, Jennifer Van Eyk, Christophe Vanderaa, John R. Yates III, Nikolai Slavov
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