Announcements
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Colorless and immunodeficient frogs - a valuable platform for tumor and developmental biology research - 2024-08-22
Ran et al. developed colorless and immunodeficient Xenopus tropicalis as a valuable platform for tumor and developmental biology research. Published in Communications Biology.
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Cerebellar granular neuron progenitors exit their germinative niche via BarH-like1 activity mediated partly by inhibition of T-cell factor - 2024-08-06
In amphibian, a pertinent model to study early cerebellar development, Barhl1 controls granular neuron progenitor exit from their germinative niche through T-Cell Factor inhibition and hes genes repression. Bou-Rouphael et al. in Development.
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1st Asian Xenopus Conference - 2024-07-29
November 24, 2024 (Sun) to November 26, 2024 (Tues).
Osaka University, Osaka, Japan.
Abstract Submission: September 30, 2024.
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The Spemann-Mangold organizer from egg to tailbud - 2024-07-24
Azbazdar & De Robertis publish in PNAS combined overexpression of hwa mRNA into a ventral cell with coinjection of known components of the Spemann-Mangold organizer to dissect the biochemical pathway of axial development.
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2024 Xenopus Researcher Survey - 2024-07-24
Open now!
We want to hear from you about how you use Xenbase and what we can do to make Xenbase even better.
Everyone is invited to opine! Just click here to take the survey!
...or scan the QR code if you'd rather do it on your mobile device.
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Discovering Frog Development in Unprecedented Detail - 2024-07-22
Laznovsky et al. utilized micro-computed tomography (micro-CT), a noninvasive 3-dimensional (3D) imaging technique with micrometer-scale resolution, to explore the developmental dynamics and morphological changes in Xenopus laevis. Published in GigaScience.
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Dr. Igor Dawid Memorial Symposium - 2024-05-05
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Competence for neural crest induction is controlled by hydrostatic pressure through Yap - 2024-04-30
Alasaadi et al. (Nature Cell Biology) show that neural crest competence decreases concomitantly with an increase in the hydrostatic pressure of the blastocoel.
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Noncanonical function of folate through folate receptor 1 during neural tube formation - 2024-04-30
Balashova et al. (Nature Communications) show that the interaction of folate with folate receptor 1, known as one of folate uptake systems, is necessary for neural tube formation by regulating cell-cell adhesion in human iPSC-derived neural organoids and in Xenopus laevis embryos independently of its canonical function of vitamin transport system for the participation of folate in metabolism.
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13th Structural Birth Defects Meeting - 2024-04-11
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Hoxc13 regulates claw formation in Xenopus - 2024-03-28
Carron et al. (Nature Communications) report that homologs of mammalian hair keratins are expressed in the claws of X. tropicalis, providing surprising evidence for a common evolutionary origin of mammalian, reptilian and amphibian claws and skin appendages.
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Sharing some videos about frogs published on YouTube - 2024-03-20
Some history on the development of Xenopus frogs as a model system in the laboratory as well as environmental impacts on the worldwide frog populations.
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Xenopus Meetings and Resources - 2024-03-14
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Developmental regulation of cellular metabolism is required for intestinal elongation and rotation - 2024-03-13
Grzymkowski et al. found atrazine, a widely-used herbicide, causes reversed intestinal rotation in tadpole stage Xenopus by elevating reactive oxygen species. Their research suggests benefits to antioxidant supplementation during pregnancy as intestinal malrotation is a common birth defect affecting 1 in 500 births.
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4th European Amphibian Conference - 2024-02-23
1-3 July, 2024
Bordeaux, France
Key datesAbstract deadline : 21st May 2024
Early bird registration : 30th April 2024
Registration deadline : 3rd June 2024
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In memoriam: Professor Igor Dawid (1935-2024) - 2024-02-21
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MC5 Plays Independent Roles in Congenital Heart Disease and Neurodevelopmental Disability - 2024-02-13
O'Brien et al. publish in the International Journal of Molecular Sciences that knockout models of smc5 reduces heart and brain size in Xenopus tropicalis phenocopying human disease.
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TBC1D32 variants disrupt retinal ciliogenesis and cause retinitis pigmentosa - 2024-02-13
Bocquet et al. publish in JCI Insight tbc1d32 knockdown in Xenopus causes elongated cilia, reduced pigmentation in the RPE and photoreceptor defects, copying inherited retinal disease identified from clinical patients.
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Happy Valentine's Day from Xenbase - 2024-02-13
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XRET 2024 - 2024-02-06
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From Stem Cells to Human Development, a Development/CoB meeting - 2024-01-31
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SDB Website Image Collection - 2024-01-29
The Society for Developmental Biology are seeking contributions of scientific images of development to showcase on their website.
Images of developing plants and animals, organs, tissues, and differentiating cells are welcomed.
All organisms are encouraged!
Image credit: Bob Goldstein and Adam Werts
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Dilute to Enrich for Deeper Proteomics - 2024-01-10
Pade et al. publish in the Journal of Proteome Research their analysis of yolk-depleted Xenopus laevis embryonic samples for enhanced frog proteome detection.
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Society for Developmental Biology 83rd Annual Meeting - 2024-01-08
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Neural Crest development and disorders: from patient to model system and back again - 2023-11-15
March 3-6, 2024
Giens Peninsula, FranceRegistration now open!
*Note – the first 30 PhD students that register will only pay 300 euros for registration
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Self-Organization in Biology Freiburg Spemann-Mangold Centennial Symposium - 2023-10-31
September 16-29, 2024 | University of Freiburg, Germany
Abstract Submission Deadline: May 3, 2024.
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Cell & Developmental Biology of Xenopus: Gene Discovery & Disease - 2023-10-31
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The Allied Genetics Conference - TAGC24 - 2023-10-17
Gaylord National Resort &. Convention Center
Metro Washington, DC
March 6-10, 2024Registration & Abstract Submisssion Open: September 29, 2023
Abstract Submisstion Deadline: November 9, 2023
Early Registration: December 13, 2023
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Xenbase Survey - 2023-09-21
Please take the Xenbase survey.
Your input is valuable!
Feedback from the Xenopus community helps us prioritize feature development.
Let us know what you like, don't like, and want in the future to help us facilitate achieving your research and educational goals.
Survey closes October 31, 2023.
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Mitochondrial Metabolism and Hif1a induce the Organizer - 2023-09-20
MacColl-Garfinkel and colleagues discover that mitochondrial metabolism can instruct cell fate. The Spemann-Mangold Organizer consumes more oxygen than other regions of the embryo due to an inner mitochondrial membrane leak activating Hif1a. Hif1a cooperates with Wnt signaling inducing the Organizer.
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3D Printed Molds for Microinection and Microscopy - 2023-09-20
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Bidirectional multiciliated cell extrusion is controlled by Notch-driven basal extrusion and Piezo1-driven apical extrusion - 2023-09-12
Ventrella et al. publish in Development that multiciliataed cells are extruded from the epithelium basally and apically using two distinct means. This bidirectional mechanism represents a novel form of cell extrusion.
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19th International Xenopus Conference - 2023-09-03
The 19th International Xenopus Conference August 20-24, 2023, Cambridge, Maryland, USA.
Thank you!
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The Allied Genetics Conference 2024 - 2023-08-08
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In Memoriam: Dr. Donald D. Brown (1931-2023) - 2023-08-08
Professor Don Brown, highly regarded developmental biologist at Carnegie Institution for Science, Baltimore MD, passsed away 31st of May, 2023. He was 91.
News release from Carnegie Science.
In Memoriam by Halpern & Harland, Dev. Biol. (2023)
Donald Brown: Pioneer of embryo development and advocate for early career funding - Thoru Pederson
Nature | Vol 620 | 10 August 2023 | p271
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Critical histone modifier for multiciliated cell differentiation identified - 2023-08-08
Multiciliated cells of Xenopus larval skin carry hundreds of motile cilia. Angerilli, Tait and colleagues show cilia tuft formation is blocked on the level of ciliogenic gene expression if the prospective larval skin lacks SUV4-20H1/KMT5B, the histone methyltransferase that converts H4K20me1 to H4K20me2.
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Nineteen distinguished scientists recognized as 2023 ASCB Fellows - 2023-08-08
Congratulations to Bill Bement!
Professor at University of Wisconsin, Madison.
Elected as a Fellow of the American Society for Cell Biology 2023.
Dr. Bement gave a rather entertaining (not his fault) Keynote talk at the 19th International Xenopus Conference.
Check out his lab's website.
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Xenopus Developmental Biology 1-week practical course - 2023-07-31
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Call for papers: Translating Multiscale Research in Rare Disease - 2023-06-22
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CRISPR/Cas9-based simple transgenesis in Xenopus laevis - 2023-05-23
Shibata et al. established a simple transgenesis method for X. laevis based on CRISPR/Cas9 technology - NEXTrans (New and Easy Xenopus Transgenesis) using common single guide RNA (sgRNA) and a preset donor vector for more efficient target integration into a putative harbor site.
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RAF1 deficiency causes a lethal syndrome that underscores RTK signaling during embryogenesis - 2023-05-22
Wong et al. document the first human phenotype resulting from the germline loss-of-function of the proto-oncogene RAF1 (a.k.a. CRAF). In cultured cells and in vivo using Xenopus assays RAF1 p.Thr543Met mutation acted as a loss-of-function allele abolishing downstream ERK pathway signaling.
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Pleiotropic role of TRAF7 in skull-base meningiomas and congenital heart disease - 2023-05-19
Mishra-Gorur et al. publish in PNAS inherited mutations of TRAF7 cause congenital heart disease while somatic mutations cause brain tumors. Shared genetics of the disparate pathologies can be traced to the common developmental origin of the tissues from the neural crest.
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Prof Christine Holt awarded the Brain Prize - 2023-05-08
Dr. Christine Holt with Dr. Erin Shuman and Dr. Michael Greenberg awarded the Lundbeck Foundation 2023 Brain Prize for their major contributions to modern neurobiology.
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Open job positions at Xenbase - 2023-05-03
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Single-cell profiling of Xenopus mucociliary epithelium - 2023-04-25
Lee et al. profile the developing Xenopus mucociliary epithelium from pluripotent to mature stages by single-cell transcriptomics. This work sheds light on normal mucociliary development and provides avenues to study dysregulated epithelium in diseases like asthma or COPD. Science Advances.
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Call for papers: Cell and Tissue Polarity - 2023-04-18
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The H2A.Z and NuRD associated protein HMG20A controls early head and heart developmental transcription programs - 2023-04-11
HMG20A is part of the H2A.Z/PWWP2A/NuRD-axis protein chromatin complex regulating differentiation in neural crest and cardiomyocytes linages. Herchenröther et al. in Nature Communications.
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Production and characterization of monoclonal antibodies to Xenopus proteins - 2023-04-05
Horr et al. refined existing protocols to produce mouse monoclonal antibodies directed against Xenopus proteins of interest. All antibodies from this project submitted to the Developmental Study Hybridoma Bank (DSHB) will be curated on Xenbase as soon as they are made public. Published in Development.
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Call for papers: Special Issue of "Cells": Molecular and Clinical Advances in Understanding Early Embryo Development - 2023-03-30
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19th International Xenopus Conference - 2023-03-08
Registration is now open.
Deadlines:
General Registration and Abstract Submission: June 15, 2023.
Trainee Travel Award application: May 15, 2023.
Housing: July 30, 2023.Visit the conference website.
Conference poster: please post and share
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Xenopus Bioinformatics Workshop (MBL Course) - 2023-01-27
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Cold Spring Harbor Laboratory Course - 2023-01-27
Cell & Developmental Biology of Xenopus: Gene Discovery & Disease
April 12 - 25, 2023
Key Dates:Application Deadline: January 31, 2023
Arrival: April 11th by 6pm EST
Departure: April 25th around 12pm EST
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Development Special Issue: Modelling Development in vitro - 2022-12-01
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Cytoplasmic organization promotes protein diffusion in Xenopus extracts - 2022-12-01
Huang et al. use Xenopus laevis egg extracts as a model system to study diffusion dynamics in organized versus disorganized cytoplasm. Nature Communications.
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Membrane potential affects pluripotency - 2022-11-30
Sempou et al. demonstrate the electrical properties of embryonic stem cells can play a critical role in the transition from pluripotency to a differentiated state. Nature Communications.
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Multiciliated cells probe mechanical environment during epithelial integration - 2022-11-29
Ventura and Amiri et al. in Nature Communications reveal how migrating cells in the Xenopus embryo join a tissue by using finger-like extensions (filopodia) to read mechanical information from neighboring cells. Adding new cells into tissue is a key process in sculpting organs during normal development, but it is subverted during the metastatic spread of cancer cells.
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Development Special Issue: Metabolic and Nutritional Control of Development and Regeneration - 2022-11-29
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Cell clusters softening triggers collective cell migration in vivo - 2022-11-02
Marchant et al. demonstrate in Nature Materials cells within clusters from embryonic tissue dynamically decrease their stiffness in response to temporal stiffening of the native substrate initiating collective cell migration.
They further show decreasing microtubule acetylation and consequent cluster stiffness is sufficient to trigger collective cell migration in soft non-permissive substrates.
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Xenbase joins the Alliance of Genome Resources - 2022-10-14
A big leap forward for Alliance of Genome Resources (AGR) with the inclusion of Xenopus data from Xenbase
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Cell landscape of larval and adult Xenopus laevis at single-cell resolution - 2022-09-21
Liao et al. published in Nature Communications their construction of the first Xenopus cell landscape to date, including larval and adult organs. They identify common cell lineage-specific transcription factors in vertebrates, including fish, amphibians and mammals. They provide a large-scale resource for research on Xenopus metamorphosis and adult organs.
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Nascent transcriptome reveals orchestration of zygotic genome activation in early embryogenesis - 2022-09-07
Nascent transcriptome profiling during zygotic genome activation (ZGA) from whole Xenopus blastula and dissected subregions, Chen and Good (in Current Biology) unveil predominant transcription from maternal-zygotic genes and distinct spatial patterns, reconcile regulatory mechanisms of ZGA, and discover a link to sequential activation of germ-layer-specific genes.
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Focal Impact Model of Traumatic Brain Injury in Xenopus - 2022-08-24
Spruiell Eldridge et al. published in the International Journal Of Molecular Sciences modeling traumatic brain injury using Xenopus tadpoles.
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Oocytes maintain ROS-free mitochondrial metabolism by suppressing complex I - 2022-08-17
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Vertebrate Cranial Placodes - 2022-07-20
Dr. Gerhard Schlosser published a two-volume book set through CRC Press detailing the development and evolution of vertebrate cranial placodes.
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Normal Table of Xenopus development: a new graphical resource - 2022-07-14
Zahn et al. published in Develoment a new normal table resource of images chronicling the development of Xenopus frogs.
View the Zahn drawings and landmarks table on Xenbase.
View the accompanying poster.
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Xenopus laevis v10.1 and Xenopus tropicalis v10 genomes - 2022-07-14
- both genomes fully integrated into Xenbase
- BLAST mRNA, protein, and CDS
- viewable on JBrowse
- morpholino tracks aligned
- relevant files available on Xenbase FTP and downloads page
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Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex - 2022-07-13
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SDB Science Communication Internship - 2022-07-12
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ARVCF catenin controls force production during vertebrate convergent extension - 2022-05-04
Huebner and Weng et al. identify a poorly characterized catenin, Arvcf, as a regulator of force production during vertebrate head-to-tail axis extension. Published in Developmental Cell.
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Microridge-like structures anchor motile cilia - 2022-04-25
The actin cytoskeleton is highly dynamic during early development of multiciliated cells (MCCs). Yasunaga et al. published in Nature Communications that anchoring subapical actin filaments requires the presence of microridge-like structures formed during MCC development.
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Uncovering the mesendoderm gene regulatory network through multi-omic data integration - 2022-04-25
Jansen et al. built a pipeline to create GRNs using highly dimensional multi-omic datasets to predict new TF-DNA/TF-TF interactions during mesendoderm development. Published in Cell Reports.
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Nutritional control of thyroid morphogenesis through gastrointestinal hormones - 2022-04-25
Takagishi et al. publish in Current Biology studying nutritional control of Xenopus thyroid morphology requiring external nutrients. GIP induces thryoid folicle formation.
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3rd European Amphibian Club - 2022-04-07
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Green oxygen power plants in the brain rescue neuronal activity - 2021-12-20
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Cold Spring Harbor Laboratory Course - 2021-12-20
Cell & Developmental Biology of Xenopus:
Gene Discovery & Disease
March 30 - April 12, 2022
Application & Materials Deadline: January 31, 2022
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Development, Growth & Differentiation (DGD) Special Issue - 2021-11-16
Call for Papers!
Submit a manuscript to Development, Growth & Differentiation (Wiley),the official journal of the Japanese Society of Developmental Biologists
For the special issue “Versatile utilities of amphibians: from molecular, cellular, and developmental biology to physiology”
Special issue flyer (pdf).
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A systemic cell cycle block impacts stage-specific histone modification profiles during Xenopus embryogenesis - 2021-11-09
Pokrovsky et al. publish in PLoS Biology their study investigating the relationship between the propagation of epigenetic information (histone modification profiles) and the developmental cell proliferation during Xenopus embryogenesis.
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Ttc30a affects tubulin modifications in a model for ciliary chondrodysplasia with polycystic kidney disease - 2021-10-27
Getwan et al. publish in PNAS their work studying skeletal ciliopathies. A data mining-based in silico screen found ttc30a to be related to known skeletal ciliopathy genes. CRISPR/Cas9 targeting replicated limb malformations and renal cysts identical to the models of established disease genes.
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Bicc1 and Dicer regulate left-right patterning through post-transcriptional control of the Nodal inhibitor Dand5 - 2021-09-23
Maerker et al. published in Nature Communications show that pkd2-mediated post-transcriptional repression dand5 through bicc1 and dicer is a central process in symmetry breaking. Ciliary activity of the calcium channel Pkd2 is crucial for asymmetric leftward flow sensing at the vertebrate left-right organizer.
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If you use Xenbase and other online resources respond to this RFI to ensure continued funding - 2021-09-13
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18th International Xenopus Conference - 2021-09-10
The 18th International Xenopus Conference wias held virtually August 15-19, 2021.
Content for registrants will be available until Friday, September 17, 2021.
Official conference website.
Registrants click here to log in.
Congratulations to Helen Willsey and Alice Godden named John Gurdon outstanding speaker award winners!
Many thanks to the organizers, speakers, presenters, and participants.
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Howard Hughes Hanna Gray Fellowship - 2021-08-06
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Xenopus 1: student travel grants, frogs, and husbandry - 2021-07-28
Xenopus 1 welcomes Nasco frogs.
Visit https://xenopus1.com/ for details.
Travel grants for students interested in attending training courses available.
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Xenopus, from basic biology to disease models in the genomic era - 2021-07-19
Edited by Abraham Fainsood and Sally A. Moody.
Available for Download, Read Online, or purchase.
Click here to view a PDF flier containing the table of contents.
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The Wnt/PCP formin Daam1 drives cell-cell adhesion during nephron development - 2021-07-19
Krneta-Stankic et al. show that the Wnt/PCP formin Daam1 regulates cytoskeletal membrane dynamics and E-cadherin localization within developing nephrons.
Published in Cell Reports.
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Designing CRISPR guide RNAs - sample workflow - 2021-06-22
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Three-dimensional folding dynamics of the Xenopus tropicalis genome - 2021-06-14
Animal interphase chromosomes are organized into topologically associating domains (TADs). Niu et al. show that X. tropicalis is a powerful model for chromosome architecture analysis suggesting that chromatin remodeling plays an essential role in de novo TAD establishment. Published in Nature Genetics.
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ModelMatcher - 2021-04-14
a new registry connecting Scientists and Clinicians
• Use your Xenopus expertise to help patients and clinicians
• Boost the clinical significance of your Xenopus research
• Share your genes of interest
• Xenopus research is supported by ModelMatcher
Visit ModelMatcher to register
Click the link: https://www.modelmatcher.net
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SDB 80th Annual Meeting - 2021-03-31
Society for Developmental Biology
80th Annual Meeting
Virtual, July 12-16, 2021Registration Deadline is June 14, 2021, 11:59 PM ET
Eddy De Robertis to receive SDB Lifetime Achievement Award
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The Scf/Kit pathway implements self-organised epithelial patterning - 2021-03-23
Social distancing is no mystery to Xenopus cells! Chuyen et al. report how thousands of multiciliated cells distribute into a regular pattern in the developing epidermis, through homotypic repulsion and homing at intercalation sites. Published in Developmental Cell.
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The skin microbiome of Xenopus laevis and the effects of husbandry conditions - 2021-03-10
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Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly - 2021-03-10
CRISPR/Cas9-mediated mutation of Coat protein complex 1 (COPI) subunit COPB1 in X. tropicalis recapitulates features of the human "coatopathy" syndrome including microcephaly and cataracts. Published in Genome Medicine.
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Genesis Special Issue: Aquatic Models of Developmental Disorders - 2021-03-04
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Chromatin accessibility and transcription factor activity (during gastrulation) - 2021-02-22
Single‐cell chromatin‐accessibility and transcriptomic analyses identify the contribution and cooperation of key transcription factors in zygotic gene expression. Transcriptional heterogeneity at the gastrula stage of vertebrate embryogenesis is involved in mesoderm induction, dorsal‐ventral patterning, and establishment of the dorsal axis. Bright et al. published in EMBO J.
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Kids First Funding Opportunity - 2021-02-19
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Office of Research Infrastructure Programs (ORIP) Strategic Plan - 2021-02-17
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Lrp2-mediated endocytosis is essential for neural tube closure - 2021-02-17
Kowalczyk et al. identify a conserved role for Lrp2 in anterior neural tube closure and forebrain development. Loss of Lrp2 affects both apical constriction as well as planar cell polarity. Published in Development.
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Nasco will stop selling Xenopus - 2021-02-08
The number of suppliers of Xenopus animals is changing.
Click below to read about optons to purchase live animals.
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Eddy De Robertis conferred SDB lifetime achievement award - 2021-01-26
Dr. Edward (Eddy) M. De Robertis, Distinguished Professor, Biological Chemistry, Norman F. Sprague Chair of Molecular Oncology Investigator, University of California Los Angeles and Howard Hughes Medical Institute investigator, has been awarded the 2021 Society of Developmental Biology Lifetime Achievement Award.
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Notch signaling induces cell death or cell fate change of multiciliated cells - 2021-01-25
Tasca et al. describe how multiciliated cells are removed from airway-like mucociliary epithelia during developmental tissue remodeling. In addition to cell death, these highly specialized cells can also change their identity toward another cell type, which was considered impossible, challenging the concept of terminal differentiation. Published in Developmental Cell.
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Development Special Issue: Imaging Development, Stem Cells and Regeneration - 2021-01-07
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In Memoriam - 2020-12-17
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hps4 gene responsible for periodic albino in Xenopus - 2020-12-07
Hermansky-Pudlak syndrome type 4 is a human hypopigmentaion and bleeding disorder. Mutations in the hsp4 gene in Xenopus results in lower pigmentation in the eyes and skin. Periodic albino mutant X. laevis may be a useful model in studying this human syndrome.
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Xenbase Winter Newsletter 2020 - 2020-12-01
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Xenbase v5.0 - 2020-11-23
Release v5.0 of Xenbase is now available.
Among the latest improvements are:
- Phenotypes
- X. tropicalis genome v10.0 integration
- Redesigned homepageStay safe!
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Phenotypes on Xenbase - 2020-11-20
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IJMS Special Issue: Molecular Aspects in Fish and Amphibian Reproduction and Development - 2020-10-22
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Epigenetic sperm programming - 2020-09-15
Sperm contribute genetic and epigenetic information to the embryo. Oikawa et al. published in Nature Communications show homogeneously methylated histone H3 at the same genomic locations in most sperm cells.
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A regeneration-permissive environment requires myeloid cells following tail amputation - 2020-09-10
Aztekin et al. interrogated natural tail regeneration during regeneration-competent and -incompetent developmental stages finding the myeloid lineage is essential for regeneration. Find their study at Development.
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Zoom through the time of COVID with Xenbase - 2020-08-20
Xenbase is committed to advancing your research program in these trying times of remote online working.
Stay healthy, social distance, wear a mask and explore Xenbase.
Sincerely,
The Xenbase Team
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GSK3 Inhibits Macropinocytosis and Lysosomal Activity through the Wnt Destruction Complex Machinery - 2020-08-19
Albrecht et al. publish in Cell Reports Wnt-induced macropinocytosis is regulated through glycogen synthase kinase 3 (GSK3) and the β-catenin destruction complex.
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Roles of NMDARs in Visual Circuit Development - 2020-08-18
Kesner et al. publish in Cell Reports that N-methyl-D-aspartate receptors (NMDARs) on post- and presynaptic neurons regulate neuronal morphology in opposing manners.
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Predation threats over 24 hours activate extension of axons in tadpole brains - 2020-08-13
Mori et al. investigated the induced gene expression and axon morphology changes in the brains of tadpoles under the threat of predation. Published in Scientific Reports.
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IXB Young Investigator Award Update - 2020-08-05
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Professor Anna Philpott elected member of EMBO - 2020-07-21
Dr. Anna Philpott of the University of Cambridge elected to membership of the European Molecular Biology Organization (EMBO) for 2020.
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Xenopus Models of Organogenesis and Disease - 2020-07-13
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MBL Virtual Programs - 2020-06-26
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Long-term transcription factor binding stabilizes gene expression - 2020-06-23
Gurdon et al., published in PNAS, show that long-term (hours to days as opposed to seconds) non-competitive binding of transcription factors such as neurogenic Ascl1 stabilizes gene expression.
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SDB 79th Annual Meeting - 2020-06-11
Society for Developmental Biology 79th Annual Meeting
ONLINE
July 9-16, 2020
Abstract submission deadline: May 6, 2020
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Autism risk gene dyrk1a is required for ciliogenesis and brain size - 2020-06-01
Willsey & Xu et al., using X. tropicalis, show that mutations in the neurodevelopmental disorder risk gene, dyrk1a, disrupts cell cycle progression and ciliogenesis causing brain defects. Published in Development.
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Southeast Regional SDB Meeting 2020 - 2020-04-23
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ATAC-seq in Xenopus - 2020-04-14
Esmaeili et al. published in Developmental Biology their ATAC-seq study assessing chromatin accessibility during Xenopus gastrulation.
Processed ATAC-seq data viewable on JBrowse coming soon.
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Xenopus, from basic biology to disease models in the genomic era - 2020-04-13
Abraham Fainsod and Sally Moody are seeking contributions for a book to be published by Taylor and Francis CRC Press.
Please communicate your interest to them by May 15, 2020 and prepare to submit your contributions by January 2021.
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The Allied Genetics Conference 2020 Online - 2020-04-09
TAGC is going virtual.
April 22-25, 2020. Registration is now open. Attend via Zoom.
Click here to view the announcement.
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GBrowse on Xenbase - 2020-04-09
Archived genomes viewable on GBrowse.
As well as...
X. laevis v9.2
X. tropicalis v9.1 and v10.0
Click "read more" on how to access archived genomes on Xenbase GBrowse:
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18th International Xenopus Conference - 2020-04-07
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Uncovering selective cooperation between the retinoblastoma and p53 cancer pathways in X. tropicalis - 2020-02-28
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2020 Xenopus White Paper - 2020-02-05
The 2020 Xenopus Community White Paper is now available!
PIs: Please reference the White Paper in your NIH grant proposals and contact your program officers.
Download the 2020 Xenopus White Paper:
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Cell & Developmental Biology of Xenopus: Gene Discovery & Disease 2020 Course at Cold Spring Harbor - 2020-02-04
March 25 - April 7, 2020
This course is designed for those new to the Xenopus field, as well as for more advanced students who are interested in emerging technologies.
Application & Materials Deadline: extended to February 11, 2020. Last chance to apply!
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Ray Keller Awarded the 2020 SDB Lifetime Achievement Award - 2020-01-31
Congratulations to Dr. Ray Keller on receiving the 2020 Society of Development Biology (SDB) Lifetime Achievement Award.
Ray is a pioneer in the biomechanics of morphogenesis introducing conversion extension in gastrulation to generations of Xenopus researchers.
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2020 Xenopus Bioinformatics Workshop - 2020-01-24
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Xenopus stem cells used to build living programmable organisms - 2020-01-16
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Trachea-esophageal Disease Studies Using Xenopus - 2019-12-19
Back to back papers published in Developmental Cell from Nasr et al. and Kim et al. recapitulate human congenital trachea-esophageal birth defects using Xenopus.
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Xenopus tropicalis v10 genome - 2019-11-22
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Xenbase v4.12.1 Release - 2019-11-21
Included in the latest Xenbase release:
- Xenopus tropicalis genome v10 sequence and assembly
- GEO GSE visualization (view our tutorial video)
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Xenbase Survey 2019 - 2019-10-23
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Xenbase Newsletters - 2019-10-22
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Basal cells in Xenopus mucociliary epithelium - 2019-09-24
Haas et al. using Xenopus mucociliary epidermis, the mouse airway, and human airway basal cells demonstrate that wnt is necessary for cilia formation during differentiaion. In basal cells, wnt prevents specification of epithelial cell types by activating the master transcription factor, ΔN-Tp63 which is required to retain basal cell stemness during development. Published in Cell Reports.
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The Epigenetic Control of Pluripotent Signal Competence - 2019-09-19
Gentsch et al. demonstrate that maternal pluripotency factors initiate epigeneic remodelling of thousands of regulatory elements on which signal mediators act to regionalise zygotic genome activity, specifying the three germ layers. Their discovery is a first step in understanding how proteins permit a cell type-specific signal response. Published in Nature Communications.
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Single Amino Acid Change Underlies Distinct Roles of H2A.Z Subtypes in Human Syndrome - 2019-09-12
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Defining the vertebrate cardiac proteome - 2019-09-11
Federspiel et al. published in PLoS Biology their study identifying the core protein composition, complexes, and pathways in vertebrates from Xenopus to human heart. They reveal that each species shares a unique set of proteins with humans but not the other vertebrates studied.
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Roberto Mayor elected new member by EMBO - 2019-09-09
Dr. Roberto Mayor, Professor of Developmental and Cellular Neurobiology at University College London’s Division of Biosciences, was elected by The European Molecular Biology Organization (EMBO) as a new member.
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XenHead: cranial development - 2019-09-01
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***atlas test page*** - 2019-09-01
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Xenopus Anatomy and Histology Atlas - 2019-09-01
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Heart development - 2019-09-01
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Pronephric kidney anatomy - 2019-09-01
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Early development: X. laevis histology - 2019-09-01
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High-resolution Images and Movies of Xenopus Frogs - 2019-09-01
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Zahn Drawings of Xenopus laevis Development - 2019-09-01
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Inner ear histology - 2019-09-01
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Xenopus Staging Landmarks Table - 2019-09-01
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Color Atlas of Xenopus laevis Histology - 2019-09-01
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Cranial placodes in Xenopus development - 2019-09-01
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Digital dissection of X. laevis - 2019-09-01
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In vivo microtomography of gastrulation - 2019-09-01
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Xenopus Resources and Emerging Technologies Meeting 2019 - 2019-08-19
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How to get NGS data from EMBL-EBI in to the GEO-Xenbase pipeline - 2019-08-08
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IXB: The International Xenopus Board - 2019-07-05
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IXB Young Investigator Award - 2019-07-05
Outstanding junior faculty awardees will be recognized at the International Xenopus Conference in Portsmouth, UK (August 23-27, 2020) where they will present an award lecture.
Nominations must be received by June 30th, 2020.
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Xenbase Tutorials: GEO Data Simple and Advanced Search - 2019-07-01
Please view the Xenbase tutorial videos for the simple and advanced search interface for Xenopus GEO datasets.
Added tutorial: Navigating a GSE page.
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Morpholino Side Effects, cont. - 2019-06-21
Paraiso et al. published in Developmental Cell their meta-analysis of available transcriptomic datasets collected during embryogenesis showing induction of an immune response is not a general side effect of morpholinos.
Contrasting study to Gentsch et al.
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10th Course Developmental Biology Institut Curie - 2019-06-21
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Spatiotemporal Patterning of Zygotic Genome Activation - 2019-06-19
Chen et al. published in Developmental Cell imaging nascent transripts (dependent on cell size) at the single-cell level in Xenopus during zygotic genome activation (ZGA).
Click here to view their press release.
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Rebecca Heald Elected to the National Academy of Sciences - 2019-05-10
Congratulations to Dr. Rebecca Heald for being elected as a member of the National Academy of Sciences.
She is a pioneer in cell biology studying cell spindle assembly and biological size control using Xenopus laevis and Xenopus tropicalis.
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Richard Harland Elected as Fellow of the Royal Society - 2019-04-22
Congratulations to Richard Harland, a newly elected Fellow of The Royal Society of London. Professor Harland is a pioneer in the field of developmental biology whose major contributions include understanding dorsal ventral patterning and neural plate induction and patterning.
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Xenbase v4.11 Release - 2019-03-22
Xenopus expression data from GEO available. Viewable on JBrowse.
View our tutorial video.
X. laevis protein expression profiles on gene pages.
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Genome Editing Workshop 2019 - 2019-02-19
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SDB 78th Annual Meeting - 2019-02-08
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Xenopus ORFeome v2 - 2019-01-31
Updated Xenopus ORFeome clones include:
~10,250 genes, ~7,700 with human orthologues in X. laevis
~3,970 genes, ~3,800 with human orthologues in X. tropicalis
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Request for Information (RFI): NICHD Strategic Plan Fiscal Years 2020-2024 - 2019-01-09
PLEASE take the time to respond by Feb. 15 and convey your opinions on how your research interests are represented at the NICHD.
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Evolutionarily conserved Tbx5-Wnt2/2b pathway orchestrates cardiopulmonary development - 2018-11-15
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Xenopus animal cap transcriptome - 2018-10-08
Building a mucociliary epithelium.
Angerilli et al.published in Nucleic Acids Research the dynamic transcriptional landscape in X. tropicalis Animal Cap explants during differentiation into mucociliary epithelium.
Providing an online Web Tool, they detail global changes in mRNA expression, an unanticipated diversity of mRNA splicing isoforms, expression of repetitive DNA elements, and the complexity of circular RNAs.
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Development Special Issue: - 2018-09-14
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Phenotype Survey - 2018-08-13
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2018 Genome Editing Workshop - 2018-07-31
Xenopus Genome Editing Workshop
Marine Biological Laboratory
Woods Hole, MA
Next Workshop: October 18-27, 2018.
Register Here
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9th international Curie/SU Developmental Biology Course - 2018-06-20
Institut Curie and Sorbonne Université (SU) organize their 9th International Developmental Biology course.
Practicals : September 17-October 6,2018 (3 weeks)
Lectures: October 8-19, 2018 (2 weeks)
Organizers: A. Bardin, Y. Bellaïche, C. Fournier-Thibault, J.L. Maître, M. Umbhauer
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RSPO2 inhibition of RNF43 and ZNRF3 governs limb development independently of LGR4/5/6 - 2018-06-14
Four R-spondin secreted ligands (RSPO1-RSPO4) act through their LGR4, LGR5 and LGR6 receptors amplifying WNT signalling. An allelic series of recessive RSPO2 mutations in humans causes tetra-amelia syndrome, characterized by lung aplasia and a total absence of the four limbs. Szenker-Ravi et al. published in Nature that RSPO2, without the LGR4/5/6 receptors, serves as a direct antagonistic ligand to RNF43 and ZNRF3, constituting a master switch that governs limb specification.
Photo credit: Amelie Fossul
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Gene expression during Xenopus embryogenesis measured at single-cell resolution - 2018-05-08
Briggs et al. performed single-cell RNA sequencing at 10 embryonic stages 5 to 22 hours post fertilization. Gene activity data read from the mRNA of 137,000 cells show that while the frog embryo appears to be in an undifferentiated state, cells begin to take on their eventual identities. Their findings are published in Science.
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9th Aquatic Models of Human Disease Conference - 2018-04-27
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Quantitative Proteomics After Spinal Cord Injury - 2018-04-09
Lee-Liu et al. published in Molecular & Cellular Proteomics their study measuring the proteomic response in X. laevis after spinal cord injury (SCI).
SCI was induced at regerative and non-regenerative stages. They quantified a total of 6,384 proteins, with 172 showing significant differential expression in the regenerative stage and 240 in the nonregenerative stage, with an overlap of only 14 proteins.
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17th International Xenopus Conference - 2018-03-22
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Morpholino Side Effects - 2018-03-14
Gentsch et al. published in Developmental Cell highlight:
Brachyury KO and KD in frog equally affect phenotype-causing downstream genes.
Other transcriptional anomalies are unique to morpholino-based KDs and controls.
Morpholinos can trigger an innate immune response and off-target mis-splicing.
Optimization of KD conditions mitigates but does not eliminate these side effects.
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Asymmetric cell division breaks pluripotency in vivo - 2018-03-08
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Tissue stiffening coordinates morphogenesis by triggering collective cell migration in vivo - 2018-02-28
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Eye Regrowth in Xenopus Embryos - 2018-02-23
Kha et al. published in Exp Eye Res. st. 27 tailbud embryos can readily regrow functional eyes after removal of specified eye tissues with a rapid process that happens faster than normal eye development.
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Society for Developmental Biology 77th Annual Meeting - 2018-01-26
Portland, OR USA
July 20-24, 2018
Registration now open.
Visit: https://www.sdbonline.org/2018mtg
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2018 Xenopus Bioinformatics Workshop - 2018-01-24
Registration now open.
May 13-19, 2018
at the NXR at the MBL in Woods Hole, Massachusetts.
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Cell and Developmental Biology of Xenopus: 2018 Course at Cold Spring Harbor - 2018-01-10
April 4-17, 2018
This course is designed for those new to the Xenopus field, as well as for more advanced students who are interested in emerging technologies.
Application Deadline: January 31, 2018
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Xenbase v4.7 - 2017-12-27
Gene co-expression and co-regulation graphs
Perron Lab retinal screen images
BLAST search results point to JBrowse
Other amphibians: Rana catesbeiana, Nanorana parkeri, and Ambystoma mexicanum genomes added to JBrowse and BLAST
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Xenbase-NXR RRID Initiative - 2017-12-13
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Phosphorylation Dynamics Dominate the Regulated Proteome during Early Xenopus Development - 2017-12-13
Peuchen et al. published in Scientific Reports their study making quantitative measurements of the Xenopus phosphoproteome beginning with stage VI oocytes, oocyte maturation to a fertilizable egg, and three time points following fertilization.
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Regulatory remodeling in the allo-tetraploid frog Xenopus laevis - 2017-12-12
In this study, published in Genome Biology, Elurbe et al. identify non-allelic homologous recombination between old repeats as the likely source of deletions that happen much more frequently on the S subgenome in X.laevis.
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Proteomics of fertilization in the Xenopus egg - 2017-11-29
Presler et al. present comprehensive measurements of the biochemical events governing the cell cycle and blocks to polyspermy after fertilization. Published in PNAS, the study introduces new methods to systematically calculate phosphosite occupancy.
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Xenbase v4.6 - 2017-10-27
Check out the latest changes to Xenbase:
Added experimental regulation visualization
Reworked stock center lines and strains
Added XLRRI (US) and CRB (Europe) stock centres to the list of vendors
Added links to laevis 9.2 and tropicalis 9.1 genome assemblies and gene models. Both are BLAST'able
Replaced GBrowse gene snapshots with Xenbase images
Increased support for JBrowse
Added counts for mutant lines and available jobs to the landing page
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EctoMap - 2017-10-26
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The brain is required for normal muscle and nerve patterning during early Xenopus development - 2017-10-19
Herrera-Rincon et al. published in Naure Communications their use of an amputation assay in Xenopus laevis to show that absence of brain alters subsequent muscle and peripheral nerve patterning during early development. This phenotype can be rescued by modulating bioelectric signals.
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Comprehensive analyses of hox gene expression in Xenopus laevis embryos and adult tissues - 2017-10-16
Kondo et al. published in Developement, Growth, and Differentiation their analysis of two homeologous sets (L and S) of four hox gene clusters A through D and 13 paralogous groups. Read the article to see the expression of 76 genes during developement and in adult tissues.
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Xenopus Lab Survey - 2017-09-29
Do you work with Xenopus?
If your answer is YES, then we need to hear from you!!!
We want to know 3 basic things about Xenopus research.
* How many Xenopus labs and researchers are there in the world?
* How many Xenopus frogs are used in research?
* How frequently do you ovulate your frogs?
The survey will take less than 3 minutes.
Survey closes October 31st, so don't delay, fill it in today!
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Xenopus Resources and Emerging Technologies Meeting - 2017-09-26
Read/download the meeting summary.
Held August 26th – 29th, 2017 at the National Xenopus Resource (NXR) at the Marine Biological Laboratory (MLB) at Wood's Hole, MA.
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Digital dissection of Xenopus laevis using contrast-enhanced computed tomography - 2017-09-08
Porro and Richards published in the Journal of Anatomy their detailed views of adult Xenopus laevis anatomy. View their visualizations of skeletal and muscular anatomy; the nervous, respiratory, digestive, excretory and reproductive systems; and the major sense organs.
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Sorting at embryonic boundaries requires high heterotypic interfacial tension - 2017-08-30
Canty et al. published in Nature Communications their study investigating the underlying mechanisms of cell sorting of ectoderm-mesoderm separation during early embryonic development.
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New X. laevis 9.2 and X. tropicalis 9.1 GFFs - 2017-08-25
Xenbase GFF tracks for X. laevis 9.2 and X. tropicalis 9.1 official genomes are now available on Xenbase FTP and GitLab account!
View on JBrowse: trop and laevis.
GFFs were created by merging NCBI and JGI GFF files.
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The Zahn Drawings - 2017-08-04
A new developmental series for Xenopus, ‘the Zahn drawings’ and a complementary set of bright field photographs have been published in Development. These drawings provide researchers with views of the tadpole stages during cranial development, NF stage 22-50.
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Mitotic chromosome assembly despite nucleosome depletion in Xenopus egg extracts - 2017-07-25
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In Situ Microprobe Single-Cell Capillary Electrophoresis Mass Spectrometry - 2017-07-07
Metabolic Reorganization in Single Differentiating Cells in the Live Vertebrate (Xenopus laevis) Embryo.
Onjiko et al. published in Analytical Chemistry their study peering, for the first time, into the formation of metabolic single-cell heterogeneity during early development of a vertebrate embryo.
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Congratulations to the 2017 SDB Awardees - 2017-06-30
Society of Developmental Biology awards
Edwin G. Conklin Medal:
Philippe M. Soriano (Icahn School of Medicine at Mount Sinai)
Elizabeth D. Hay New Investigator Award:
Maria Barna (Stanford University)
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Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes - 2017-06-29
Drew et al. integrate the largest-scale mass spectrometry protein interaction datasets from a variety of human and animal cells and tissues. The machine-learning framework generates the most comprehensive and accurate human protein complex map to date. Published in Molecular Systems Biology.
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Xenbase v4.4 - 2017-06-27
Xenbase launched 4 new features (June 2017, Xenbase v 4.4).
1. NEW Interactive RNA-seq temporal expression graphs for trop and laevis.
2. View the latest ‘Xenopus Research Articles’
3. NEW Interactive gene-interaction visualization.
4. Xenopus Article Page, now includes a list of references cited in the paper.
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8th International Course on Developmental Biology - 2017-06-15
This course is to provides participants with comprehensive coverage of paradigms, problems and technologies of modern Developmental Biology with a particular attention to stem cells.
Workshop: September 18-October 7, 2017/ Seminars: October 9-20, 2017.
Paris, France
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miR-182 Regulates Slit2-Mediated Axon Guidance by Modulating the Local Translation of a Specific mRNA - 2017-04-05
Bellon et al. published in Cell Reports the role of microRNAs in mRNA-specific translation during axonal pathfinding of Xenopus laevis retinal ganglion cells (RGCs). They found that miR-182 targets cofilin-1 mRNA, silencing its translation. Slit2 rapidly relieves this repression without causing miR-182 degradation. Their data support a model where miR-182 reversibly gates the selection of certain mRNAs for fast translation depending on extrinsic cues.
we investigate the local role of miRNAs in mRNA-specific translation during pathfinding of Xenopus laevis retinal ganglion cell (RGC) axons.
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Leftward Flow Determines Laterality in Conjoined Twins - 2017-04-04
Tisler et al. published in Current Biology their study of an enigmatic left-right defect in conjoined twins. Twins fused at the thorax: left twins are normal, laterality is disturbed in one-half of right twins due to insufficient suppression of the Nodal inhibitor, dand5.
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GO: Gene Ontology terms on Xenbase - 2017-02-16
Expanded representation of Gene Ontology (GO) terms associated with gene product function added to Xenopus gene pages.
Look for the tab on gene summary pages...
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High variability of expression profiles of homeologous genes for Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus laevis - 2017-02-10
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Genesis Special Issue - Xenopus: Advances and Emerging Technologies - 2017-02-07
Check out the January 2017 issue of Genesis highlighting current advances using Xenopus as a biomedical research model.
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De novo mutations in SMCHD1 cause Bosma arhinia microphthalmia syndrome (BAMS) and abrogate nasal development - 2017-01-26
Gordon et al. report in Nature Genetics that missense mutations in the epigenetic regulator SMCHD1 mapping to the extended ATPase domain of the encoded protein cause BAMS in all 14 cases studied.
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Spinal cord regeneration in Xenopus laevis - 2017-01-24
Edwards-Faret et al. describe in Nature Protols their methods for the husbandry of Xenopus laevis tadpoles and froglets and procedures to study spinal cord regeneration.
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Call for Papers: Development Special Issue - 2017-01-10
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Congratulations to Professor Sir James Cuthbert Smith, FRS - 2017-01-09
Professor Sir Jim Smith of The Francis Crick Institute was knighted in the Queen's New Year's Honours (2017) for services to medical research and science education.
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Cell and Developmental Biology of Xenopus: 2017 Course at Cold Spring Harbor - 2016-12-22
March 29 - April 11, 2017
This course is designed for those new to the Xenopus field, as well as for more advanced students who are interested in emerging technologies.
Application Deadline: January 6, 2017
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European Amphibian Club 2017 - 2016-12-06
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Mechanosensing is critical for axon growth in the developing brain - 2016-11-16
Koser et al. identify mechanical signals as important regulators of axon pathfinding. In vitro, substrate stiffness determined growth patterns of Xenopus retinal ganglion cell axons. In vivo atomic force microscopy revealed a noticeable pattern of stiffness gradients in the embryonic brain.
Published in Nature Neuroscience.
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Direct reprogramming of fibroblasts into renal tubular epithelial cells by defined transcription factors - 2016-11-14
Kaminski et al. identified 4 factors that are able to directly reprogram fibroblasts into renal tubule cells.
Induced renal tubule epithelial cells (iRECs) are similar to their native counterparts with respect to their transcriptional profile and morphological features, and can integrate into kidney organoids and decellularized kidneys.
Their research is published in Nature Cell Biology.
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A simple and efficient method to visualize and quantify the efficiency of chromosomal mutations from genome editing - 2016-11-14
Fu et al. published in Science Reports a simple and efficient method to visualize and quantify the efficiency of genomic mutations induced by genome-editing. Their approach is based on the expression of a two-color fusion protein in a vector that allows the insertion of the edited region in the genome in between the two color moieties.
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Gene Regulatory Networks White Paper 2016 - 2016-11-07
A “final” draft of the GRN white paper is in the works, but several people request that the current working white paper draft be made publicly available.
This would allow everyone to refer to the white paper in grants or manuscripts. The GRN White Paper draft will be hosted on Xenbase.
This current draft will eventually be replaced with the final 2016 version.
Click here to download the draft of the GRN White Paper.
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Genome evolution in the allotetraploid frog Xenopus laevis - 2016-10-20
Session et al. published in Nature describe the analysis of the subgenomes of the allotetraploid Xenopus laevis. The L subgenome more consistenly resembles the ancestral condition and the S subgenome is more disrupted by deletion and rearrangment.
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CRISPR/Cas9 mediated knockout of rb1 and rbl1 leads to rapid and penetrant retinoblastoma development in Xenopus tropicalis - 2016-10-19
Naert et al. published in Science Reports CRISPr/Cas9-mediated deletion of the retinoblastoma (rb1) and retinoblastoma-like 1 (rbl1) genes. Biallelic inactivation of these genes results in tumor formation. This is the first CRISPR/Cas derived cancer model in the frog and it is the first non-mammalian genetic retinoblastoma cancer model.
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2016 John Gurdon Prize Winner - 2016-10-10
This year's recipient is Rachel Stephenson. She is pursuing her graduate studies in laboratory of Ann Miller at the University of Michigan.
Please click below to learn more about her work and the other award recipients and their research.
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Metrics to Assess Value of Biomedical Digital Repositories - 2016-10-03
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Identification of Genetic and Genomic Variants by Next-Gen Sequencing in Non-human Animal Models (U01) - 2016-09-29
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Gene Regulatory Systems in Development - 2016-09-29
March 27-30, 2017
Parador de Carmona, Carmona, Spain
Registration: January 31, 2017
Abstracts: extended to January 31, 2017The European Marie-Curie consortia DevCom and ZENCODE-ITN are jointly organising this conference. The topics of the conference will be single-cell profiling, chromatin dynamics, regulatory networks and evolutionary plasticity, with a profound role for Xenopus and zebrafish as model organisms.
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DeLill Nasser Award for Professional Development in Genetics - 2016-09-29
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Xenopus Workshops and Meetings at the NXR - 2016-09-21
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2016 Xenopus Research Resource Survey - 2016-08-28
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8th Aquatic Animal Models of Human Disease Conference - 2016-08-08
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Single-cell mass spectrometry comparing metabolites in left and right cells in the 8-cell Xenopus laevis embryo - 2016-07-22
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Gene Regulatory Networks for Development Course at MBL - 2016-07-21
Special Topics Course: Gene Regulatory Networks for Development
October, 9-22, 2016
Marine Biological Laboratory, Woods Hole, MA
Deadline to apply: July 29, 2016
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7th international Curie/UPMC Developmental Biology Course - 2016-07-20
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GSA Seeks Support Regarding MOD Funding - 2016-06-30
The Genetics Society of America (GSA) is seeking support for revision of plans to consolidate and reduce the funding of MODs funded by the National Human Genome Research Institute (NHGRI/NIH).
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Updated Xenopus laevis genome annotation - 2016-06-03
Gene Model Annotation 1.8.3 of the X. laevis 9.1 Genome Build
The latest annotation of the X. laevis 9.1 genome is ready!
This release only includes updating the gene symbol of existing gene models.
The files for this annotation release, GFFs and FASTA, can be downloaded from the Xenbase FTP page, under the X. laevis genome assemblies and gene models category.
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NIGMS Seeks Input on Resource Needs and Team Science - 2016-05-19
The National Institute of General Medical Sciences (NIGMS) released requests for information (RFI) in April asking for input on resource needs and “team science.”
Please advocate for Xenopus biomedical research!
Comments due by June 3, 2016.
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2016 National Academy of Sciences - 2016-05-16
Xenbase, and on behalf of the world wide Xenopus research community, congratulates the newly appointed members to the National Academy of Sciences who both currently and in earlier times in their careers, use Xenopus in their research.
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2016 Xenopus White Paper - 2016-05-09
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American Academy of Arts and Sciences 2016 Newly Elected Members - 2016-05-02
Congratulations to Christof Niehrs and Nancy Ip for being elected to the American Academy of Arts and Sciences.
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Noggin4 is a long-range inhibitor of Wnt8 (not BMP) signalling that regulates head development in Xenopus laevis - 2016-04-13
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Xenbase Release 3.11.0 - 2016-04-12
- Transgene links added to gene pages
- RRID field added for antibodies
- Proper name display for lines, transgenes, and strains
- Reformatted the "Cite Xenbase" page; added Xenbase publications
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2016 Weinstein Cardiovascular Development and Regeneration Conference - 2016-03-16
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Searchable Databases of Xenopus RNA-Seq Expression Profiles - 2016-02-22
Update: Owens et al. published in Cell Reports high-resolution, absolute number mRNA transcript data during X. tropicalis development from fertilization to tadpole stages, a developmental period approximating the first 8 weeks of human gestation.
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2016 Xenopus Bioinformatics and Genome Editing Workshops - 2016-02-12
Registration now open.
Bioinformatics workshop: May 1-7, 2016
Genome Editing workshop: May 6-14, 2016
at the NXR at the MBL in Woods Hole, Massachusetts.
Discounted costs if you attend both workshops!
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Epigenome reference map track hub - 2016-02-10
Update:
Track hubs now include trop v9.1 assebly. A collection of over 70 epigenome reference maps of Xenopus tropicalis early development has been released with the publication of “Embryonic transcription is controlled by maternally defined chromatin state” in Nature Communications.
For instructions click here.
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RNA whole-mount in situ hybridization proximity ligation assay (rISH-PLA) - 2016-02-10
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Xenopus phylogeny revised: six new species - 2016-01-26
Six new polyploid speciies added, plus one species is reinstated.
The new classifications are made by using multiple sources of information, including DNA, recordings of vocalizations, CT scanning of internal anatomy, and chromosome analysis.
Evans et al., PLoS One. 2015 Dec 16;10(12).
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Cell and Developmental Biology of Xenopus: 2016 Course at Cold Spring Harbor - 2016-01-04
Gene Discovery & Disease
April 5-18, 2016
Instructors:
Mustafa Khokha, Yale University
Karen Liu, King's College London, UK
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Xenbase Release 3.8 - 2015-12-07
- Added IMPC mouse phenotype gene page links
- Added PANTHER GO search links on gene pages
- Added XenMine links on gene pages (Data Mining section)
- Reformatted stock centre search and display
- Bug fixes and enhancements
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Whitman Center Fellowship Program at the MBL - 2015-12-01
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On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development - 2015-11-10
Peshkin et al. published in Developmental Cell
- A genome-scale resource of mRNA and protein expression for vertebrate embryogenesis
- Temporal patterns of change in mRNA and protein abundance are poorly correlated
- A simple kinetic model explains protein expression as a function of mRNA levels
- Embryogenesis is driven by maternal protein dowry and tissue-specific transcription
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16th International Xenopus Conference - 2015-10-27
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Advanced Imaging Workshop at the MBL - 2015-09-29
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Xenopus laevis genome v9.1 released - 2015-09-17
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NSF Funding Opportunities - 2015-09-17
Small Buisiness Innovation Research (SBIR) and Small Business Technology Transfer (STTR) projects on Advanced Technologies for Functional Genomics in Organismal Systems
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Genesis: Special Issue - 2015-09-16
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Developmental Biology: Genomics Special Issue - 2015-08-31
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NIH launches new initiative to study the basis of human birth defects - 2015-08-04
There are some important funding opportunities at the NIH in which the utility of Xenopus for research in human congenital disorders is ideal.
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6th Course on Developmental Biology - 2015-06-29
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Congratulations to the 2015 Society of Developmental Biology award winners - 2015-06-24
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Xenopus models for Human eye diseases - 2015-06-22
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Xenopus laevis genome v8.0 released - 2015-06-18
The Xenopus laevis genome v8.0 is available at chromosome scale.
It can be accessed via BLAST or by selecting the 8.0 version within GBrowse.
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The BSDB introduces the Cheryll Tickle Award - 2015-06-16
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Xenbase Release 3.5 - 2015-06-03
- Updated FTP landing page for data downloads
- Release of new feature ORFeome v1.0
- Migration of NCBI E-utilities from SOAP to REST
- laevis-only genes now display on gene pages
- Latest XAO update added
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Xenbase Spring Newsletter 2015 - 2015-05-15
- Xenopus ORFeome v1.0
- Outbred X. laevis Genome
- Updated Genome Browser Tracks
- Data Downloads
- X. laevis Chromosome Nomenclature
- Newly Nominated National Academy Members
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2015 Xenopus PI Meeting - 2015-05-11
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Portuguese Society for Developmental Biology, 3rd Meeting - 2015-04-08
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2015 Gordon Research Conference on Neural Crest & Cranial Placodes - 2015-03-24
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BSCB/BSDB Joint Spring Meeting 2015 - 2015-03-24
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Xenopus oocytes used to characterize rare disease caused by potassium channel mutations - 2015-03-04
Simons et al. report in Nature Genetics analyzing the activity of mutations in human KCNH1 voltage-gated potassium channels related to Temple-Baraitser syndrome in Xenopus oocytes.
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Size matters: the bigger the nucleus, the sooner transcription begins - 2015-03-04
Jevtic and Levy report in Current Biology nuclear size scaling in Xenopus early development contributes to midblastula transition timing.
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2015 Gordon Research Conference on Developmental Biology - 2015-03-03
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UK Xenopus Meeting - 2015-02-06
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Highly efficient gene knockout by injection of TALEN mRNAs into oocytes and host transfer in X. laevis - 2015-01-22
Nakajima & Yaoita describe in the journal, Biology Open, a combination of oocyte injection of TALEN mRNA injection with oocyte host transfer enhances effectiveness of gene modification.
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Protege Short Course - 2015-01-15
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Symposium: Systems Biology of Development and Differentiation - 2015-01-05
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Recent genome-wide analyses in Xenopus - 2014-12-10
We highlight a collection of recent articles detailing genome-wide analysis in Xenopus using high-throughput ChIP-seq and RNA-seq methods.
Check them out!
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48th Annual Meeting of the Japanese Society of Developmental Biologists - 2014-12-02
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Cell and Developmental Biology of Xenopus: 2015 Course at Cold Spring Harbor - 2014-12-02
Gene Discovery and Disease
April 9-21, 2015
Scholarships available! Application deadline February 23, 2015
Instructors:
Mustafa Khokha, Yale University
Karen Liu, King's College London, UK
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A Tribute to Sir John Gurdon - 2014-11-25
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Cytokinesis signaling visualized in vitro, using Xenopus cell-free system - 2014-11-07
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Xenbase Release v3.3 - 2014-10-30
· New morpholino feature added
· New genome builds and gene models
· Transgenic nomenclature guidelines
· New genome editing links added
· GEISHA (chicken) orthology imported into database and added to gene pages
· 10,000+ PubMed Central (PMC) article images added to Xenbase
· OMIM disorders associated with Xenopus genes added to gene pagesCheck out the Xenopus antibody database and improved genome browser.
Please send us comments and feedback.
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DevCom Workshop - 2014-10-14
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National Xenopus Resource at the MBL - 2014-09-25
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Congenital heart disease protein 5 associates with CASZ1 to maintain myocardial tissue integrity - 2014-09-18
Sojka et al. published in the journal Development their findings that the cardiac transcription factor CASTOR (CASZ1) directly interacts with contenital heart disease 5 protein (CHD5).
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15th International Xenopus Meeting - 2014-09-04
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Xenopus genome editing workshop - 2014-09-04
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A celebration of the life and genius of Yoshiki Sasai (1962-2014): An obituary - 2014-08-25
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52nd Annual Midwest Society for Developmental Biology Meeting - 2014-08-22
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Gene Regulatory Networks for Development - 2014-08-15
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Firing and wiring: Hebbian axonal remodelling in Xenopus - 2014-08-12
Munz et al. report in the journal Science their examination of axon remodelling of ipsilaterally projected retinal ganglion cells (RGCs) in response to synchronous or asynchronous firing.
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Smells Like Development - 2014-08-11
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The 7th Aquatic Animal Models of Human Disease Conference - 2014-08-11
December 13-18, 2014, Austin, Texas
$500 Travel Award sponosored by Genesis, the Journal of Genetics and Development for junior Xenopus investigators
Keynote Speaker: Monte Westerfield
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Sp8 regulates inner ear development - 2014-05-12
Chung et al. published in The Proceedings of the National Academy of Sciences that the eclipse mutant of Xenopus tropicalis has alterations in the sp8 gene locus. These tadpoles had decreased startle reflexes and altered swimming balance resulting from faulty embryonic inner ear development.
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A new Xenopus model for Urofacial Syndrome - 2014-05-08
Roberts et al. identified and knocked down the Xenopus orthologue of human HPSE2: establishing for the first time an in vivo vertebrate model for urofacial syndrome (UFS). This is the first study to shed light on the mechanisms underpinning the clinical features of UFS.
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Timothy Mitchison and Andrew Murray elected to membership of the National Academy of Sciences - 2014-05-02
Dr. Mitchison and Dr. Murray's seminal research using Xenopus egg cell extracts greatly contributes to our understanding of the cell cycle progression and cell division.
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Developmental Biology: Xenopus Issue - 2014-05-01
Submissions to a special issue of the journal Developmental Biology entitled: Modeling Human Development and Disease in Xenopus will open on August 1, 2014. Manuscripts can be submitted until November 1 2014, although earlier is better. Peer review must be completed and manuscript disposition determined no later than March 15th 2015, for publication in late spring.
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Richard Harland elected to membership of the National Academy of Sciences; awarded the SDB 2014 Conklin Medal - 2014-04-30
Dr. Harland found that BMP antagonists are fundamental for the patterning of germ layers. His research expands our knowledge of neural induction/patterning, FGF signaling, planar cell polarity, and developmental control of RNA splicing.
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Quantitative proteomics of Xenopus laevis embryos - 2014-04-24
Expression kinetics of nearly 4000 proteins during early development.
Sun et al. report the largest developmental proteomic dataset for any animal.
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PCP and Septins Compartmentalize Cortical Actomyosin to Direct Collective Cell Movement - 2014-04-23
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SDB 73rd Annual Meeting - 2014-04-15
Dr. Richard Harland will be honored with the The Society for Developmental Biology’s E.G. Conklin Medal.
Dr. Janet Heasman and Dr. Christopher Wylie will recognized for their lifetime achievements in developmental biology.
For meeting information please visit: sdbonline.org/2014mtg
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CRISPr/Cas9-mediated targeted mutagenesis in Xenopus - 2014-03-18
In back-to-back articles published in genesis, Blitz et al. and Nakayama et al. each report CRISPr/Cas targeted transgenesis works well in Xenopus tropicalis.
For additional information on genome editing techonologies, click here.
(shown: targeted silencing of six6 and tyrosinase genes)
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2014 Xenopus White Paper - 2014-03-14
Representatives of the research community have released the 2014 Xenopus White Paper summarizing strategic resource development.
Download 2014 Xenopus White Paper
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2014 Xenbase Survey - 2014-02-27
Please take our survey!
Your feedback is essential for guiding us to better serve your research needs.
Your opinion matters to us!
Click here to launch the survey
Thank you for the responses so far!
Please keep them coming.
We will be closing the survey on Friday March 11, 2014.
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Par3 controls neural crest migration by promoting microtubule catastrophe during contact inhibition by locomotion - 2014-02-04
Moore et al. report the requirement for par3 to regulate cellular microtuble breakdown as neural crest cells migrate.
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Cell & Developmental Biology of Xenopus at CSHL - 2014-02-03
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3rd Annual Xenopus Bioinformatics Workshop - 2014-01-31
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Christopher Wylie and Janet Heasman Honored with SDB Lifetime Achievement Award - 2014-01-29
Wylie and Heasman are being honored for their outstanding and sustained research and mentoring contributions to the field of developmental biology.
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2014 Xenopus White Paper (edit requests) - 2014-01-28
Representatives of the research community have drafted a 2014 Xenopus White Paper summarizing strategic resource development.
Please review, make comments on, and sign the Xenopus White Paper.
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UK Xenopus Meeting - 2014-01-03
February 28, 2014
King's College, London
Deadline for registration (Free) is 15 January 2014.
UK researchers gather for their annual meeting in London.
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Eddy De Robertis and Nick Spitzer elected members of the National Academy of Science - 2013-12-17
Dr. De Robertis and Dr. Spitzer recognized for their work in dorsal-ventral embryonic patterning and mechanisms of neural differentiation
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New Xenopus Genome Assemblies - 2013-12-11
The Xenopus Genome Consortium has released the newest laevis v7.1 and tropicalis v8.0 assemblies.
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Insights into autism and epilepsy using Xenopus - 2013-11-19
The Xenopus tadpole model offers many advantages for studying the molecular, cellular and network mechanisms underlying neurodevelopmental disorders.
Modified image from Chris Ciarlegilio detecting GABA (green) in the CNS from a stage 49 tadpole.
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Xenopus as a disease model for heterotaxy in humans - 2013-11-11
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Xenopus advances regeneration studies - 2013-11-01
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In vivo Microtomography of Xenopus Gastrulation - 2013-10-17
Moosmann et al. in a multi-center collaboration, captured amazing 4D images of coordinated cell movements in gastrulating embryos. Published in the May 15th issue of Nature.
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Jim Smith Awarded 2013 Waddington Medal - 2013-10-16
His current research investigates how cells of the very early vertebrate embryo form specialised tissues such as muscle, skin, blood and bone.
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Marianne Bronner Receives 2013 Conklin Medal - 2013-10-16
Her fundamental research using animal models including Xenopus contributes tremendously to our understanding of neural crest development and biology.
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2013 Xenopus PI Meeting Summary - 2013-09-06
Meeting held August 23-25, 2013 at the MBL in Woods Hole, MA USA
Researchers from around the world came together to discuss the Xenopus White Paper and community resources.
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Genesis: Xenopus Special Issue - 2013-09-05
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Developmental Neurobiology: Xenopus Issue - 2013-09-05
April 2012
Volume 72, Issue 4
Pages 463–675
Issue edited by Hollis T. Cline and Darcy B. Kelley
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John Gurdon Wins 2012 Nobel Prize - 2013-08-10
John B Gurdon (Cambridge, UK) and Shinya Yamanaka (Tokyo, Japan) share the 2012 Nobel prize for medicine or physiology.
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Welcome to the new Xenbase - 2013-08-01
In addition to our new look, check out the new Xenopus antibody database and improved genome browser.
Please send us comments and feedback.
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image strip: nkx3-1a - 2013-07-05
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image strip: helen willsey 04 - 2013-07-05
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image strip: helen willsey 01 - 2013-07-05
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image strip: helen willsey 05 - 2013-07-05
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image strip: Myers & Krieg 2013 - 2013-07-05
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image strip: tadpoletumor - 2013-07-05
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image strip: TUNEL assay - 2013-07-05
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image strip: brachyury - 2013-07-05
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image strip: hex-GFP - 2013-07-05
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image strip: helen willsey 06 - 2013-07-05
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image strip: helen willsey 07 - 2013-07-05
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image strip: Barriga et al 01 - 2013-07-05
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image strip: FCIS - 2013-07-05
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image strip: Barriga et al 02 - 2013-07-05
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image strip: chordin - 2013-07-05
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image strip: helen willsey 03 - 2013-07-05
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image strip: Xla.Tg(CMV:mGFP;cryga:mCherry)NXR - 2013-07-05
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image strip: Xla.Tg(eef1a1:GFP;cryga:GFP)Krieg - 2013-07-05
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image strip: helen willsey 02 - 2013-07-05
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image strip: Xla.Tg(CMV:Hsa.B4GALT1-eGFP)Ueno - 2013-07-05
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image strip: eye field transcription factors - 2013-07-05
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image strip: cranial placodes - 2013-07-05
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image strip: e-cadherin - 2013-07-05
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