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Postdoc positions in developmental neurobiology

Posted by , on 27 October 2010

Closing Date: 15 March 2021

POSTDOC POSITIONS IN DEVELOPMENTAL NEUROBIOLOGY

The MRC Centre for Developmental Neurobiology in London (UK) is opening two 3-5 years post-doctoral fellowships to work in Prof. Corinne Houart’s team, investigating the cellular and molecular mechanisms controlling telencephalon regionalisation and regulation of forebrain complexity in zebrafish and mouse. The comparative studies will use molecular and cell biology, high-resolution imaging, in vivo cell manipulation and genetics.

The candidates need a PhD. degree and research experience in molecular biology, developmental neurobiology and genetics.

The salary starts at approximately £30.000 per annum exclusive of London Allowance.

For enquiries regarding the posts offered, please contact Corinne Houart – MRC Centre for Developmental Neurobiology, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 1UL – corinne.houart@kcl.ac.uk.



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PhD studentship available: Chemical systems biology in zebrafish

Posted by , on 27 October 2010

Closing Date: 15 March 2021

We are seeking applications from highly motivated candidates, with a physical sciences background, and an interest in biology, to carry out a PhD to establish zebrafish as a model organism for chemical systems biology with which to carry out high-throughput chemical biology screens.

The zebrafish is a well-established vertebrate model organism due to its amenability for genetic screens, and its fantastic qualities for live imaging. Embryonic zebrafish also represent an almost ideal system for the study of small molecule function in vivo, due to their small size, aquatic existence, availability in large numbers, and molecular, cellular and system level similarities to higher vertebrates including humans. As with genetic screens, it is possible to employ different small molecule screening strategies using zebrafish. One can perform phenotypic screens, whereby one first identifies an interesting phenotype caused by a small molecule, and subsequently identifies the biological target(s) of effective compounds. In so doing one can discover new mechanisms of small molecule function, and, importantly, also identify new roles for known and novel proteins during biological processes. One can also carry out reverse pathway engineering whereby one selects a known target protein (possibly a drugable target), rationally designs a chemical library likely to affect this target, finds high affinity binders or inhibitors in-vitro and then tests the ability of candidate chemicals to affect the target in vivo, after which its biological effects can be studied.

This PhD project would be part of an ongoing collaboration between Dr. David Lyons (CNR) and Prof. Manfred Auer (CMVM, DPM, CIR) and would benefit from a unique combination of expertise in model organism biology, screening methodologies, chemistry and biophysics. Dr. Lyons’s lab focuses on the genetic and cellular basis of nervous system formation in zebrafish, with extensive experience in zebrafish biology and screening regimes. Prof. Auer is a biophysical chemist, who has 20 years of experience in the development of drug discovery technologies.  Prof. Auer’s lab designed, established and runs a unique chemical biophysics platform for lead compound discovery and chemical target validation. They can produce large scale tagged or untagged one-bead one-compound libraries, which they test against drug targets in bead based, chip based, cellular and now model organism assays. Small molecule compound function will be investigated in the PhD project in zebrafish using a systems aporoach. The molecular basis of biological systems will be studied using optical and phenotypic zebrafish models screened against fluorescently labelled small molecule and peptidomimetic libraries. Combined with top of the line mass spectrometry and single molecule microspectroscopy we hope to identify and validate new target compound pairs in a systematic approach. The successful applicant will therefore join a unique interdisciplinary environment, with ambitious long-term goals to carry out rapid cost effective high throughput screening of small molecule function at a whole organism systems level.

The ideal candidate will have a first class honours undergraduate degree, or an MSc with distinction in a relevant subject. Due to the ambitious and broad ranging challenges of this project significant laboratory expertise (> 1year) in a relevant area such as chemistry, biochemistry, or biophysics is required.

Interested candidates should first send a Curriculum Vitae and statement of specific interest to Dr. Lyons (david.lyons@ed.ac.uk) and Prof. Auer (manfred.auer@ed.ac.uk) by December 1st to discuss their potential suitability for the position. Short listed candidates will then be invited to apply formally through the Centre for Neuroregeneration website before panel interview.

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ReplicationDomain

Posted by , on 26 October 2010

ReplicationDomain is an online database resource for storing, sharing and visualizing DNA replication timing and transcription data, as well as other numerical epigenetic data types. Data is typically obtained from DNA microarrays or DNA sequencing. Our site has a user registration system that allows registered users to upload their own data sets. While non-registered users may freely view and download public data sets, registered users may upload their own data sets and view them privately, share them with other registered users, or make published data sets publicly available. In addition we have implemented additional mechanisms that allow users to restrict sharing of data sets to a user designated group of registered users. Further details on the database usage are in the User Guide Page, while data set details are in the Documentation Page.

Mus musculus_MM8_D3_ESC_Chr5_60200463-75644002

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In Development this week (Vol. 137, Issue 22)

Posted by , on 26 October 2010

Research highlights from the current issue of Development:

Novel Hh targets fly in

Hedgehog (Hh), a secreted morphogen, acts in a paracrine fashion to regulate tissue patterning during embryogenesis. Its tissue-specific effects are mediated by the transcription factor Cubitus interruptus (Ci), but how it exerts such effects is unclear. On p. 3887, Thomas Kornberg and colleagues address this question by identifying novel Drosophila Hh targets. Using chromatin-binding experiments to identify genes that are bound by Ci during Drosophila organogenesis, and by using expression data from wild-type embryos and Hh pathway mutants, they identified a set of Hhresponsive genes, many of which represent novel targets. Their validation of these targets in developing tissues, such as the dorsal ectoderm, showed that they are expressed in a tissue-specific manner, but, unexpectedly, that some targets are induced in an autocrine fashion. The authors also show that, in the tracheal primordium, some Hh target expression is subject to combinatorial control by Ci and an Hh-independent transcription factor. These unexpected features of Hh signalling provide new insights into our understanding of this pathway.

Modelling to get a head(fold)

Formation of the head fold (HF), the first three-dimensional structure to form in the embryo, is a crucial event that initiates heart, foregut and brain development. Although the molecular factors involved in HF development are becoming known, the biophysical mechanisms governing this transformation have yet to be investigated. Now, on p. 3801, Larry Taber and colleagues combine experimental and modelling approaches to determine the forces that drive HF formation in chick embryos. They generated a computational model for HF formation, and by inducing three distinct morphogenetic mechanisms – convergent extension in the neural plate (NP), cell wedging along the anterior NP border, and cell shaping outside the NP – they were able to simulate HF formation in this model. By comparing the changes in tissue morphology, mechanical strains and regional tissue stresses observed in the model with those measured experimentally in ex ovo embryos, the authors confirm that these three modelled morphogenetic mechanisms can alone provide the forces that drive HF formation.

Embryonic variations on a histone theme

Numerous histone variants exist in eukaryotes, and the replacement of canonical histones with such variants probably contributes to chromatin remodelling. Chromatin remodelling occurs during fertilisation, as germ cells become totipotent zygotes, but the role of histone variants during this process is unknown. On p. 3785, Fugaku Aoki and colleagues assess the dynamics of histone H2A and its variants, H2A.X, H2A.Z and macroH2A, during mouse oogenesis and pre-implantation development. They report that all variants are present in oocytes; by contrast, only H2A.X is abundant in one-cell embryos. The authors confirmed this postfertilisation reduction in H2A, H2A.Z and macroH2A using transgenic mice that express tagged H2 variants, and by microinjecting embryos with mRNA for these variants. Domain-swapping experiments showed that the C-terminal 23 amino acids of H2A.X enable its incorporation into chromatin after fertilisation, and that the concomitant reduction of H2A.Z and macroH2A is required for normal development. The authors suggest that altered histone composition might therefore contribute to the genome remodelling, and hence reprogramming, that occurs postfertilisation.

Meristem homeostasis: it takes three

In plants, the shoot apical meristem (SAM) provides all the cells that are needed for post-embryonic growth and development of the leaves, stems and flowers. In Arabidopsis, a peptide ligand derived from CLAVATA3 (CLV3) regulates the SAM stem cell pool by signalling through two receptor complexes – a homodimer of the receptor-like kinase CLV1 and a heterodimer consisting of the receptor-like protein CLV2 and the protein kinase CRN/SOL2. Now, Shinichiro Sawa and colleagues report that the receptor-like kinase RPK2 also has a vital role in SAM maintenance (see p. 3911). They show that loss-of-function mutations in RPK2 result in SAM stem cell expansion and increased numbers of floral organs, as seen in clv1 and clv2 mutants. Notably, the RPK2 mutant phenotypes are additive with those of clv1 and clv2 mutations. Moreover, biochemical analyses in Nicotiana benthamiana reveal that RPK2 forms homodimers but does not associate with CLV1 or CLV2. The researchers propose, therefore, that three, rather than two, CLV3 signalling pathways regulate meristem homeostasis.

Lymphangiogenesis: macrophages show restraint

Lymphatic vessels play crucial roles during embryogenesis and in adult animals but the origin of their progenitor cells is controversial. Recent studies have suggested that during neo-lymphangiogenesis in inflammatory settings, macrophages transdifferentiate into lymphatic endothelial cells and/or release prolymphangiogenic growth factors, but are these mechanisms involved in the development of the normal lymphatic vasculature? On p. 3899, Natasha Harvey and co-workers suggest that the answer to this question is no. Using lineage tracing, the researchers show that lymphatic endothelial cells arise independently of the myeloid lineage during both embryogenesis and tumourstimulated lymphangiogenesis in the mouse. Thus, they suggest, macrophages are not the source of lymphatic endothelial progenitor cells in these settings. Furthermore, the dermal lymphatic vasculature in macrophage-deficient mice is hyperplastic because of increased lymphatic endothelial cell proliferation. So, rather than providing pro-lymphangiogenic growth factors, macrophages provide signals that restrain lymphatic endothelial cell proliferation. Given these results, any attempt to treat disease-stimulated lymphangiogenesis by targeting macrophages needs careful consideration, conclude the researchers.

Grainyhead heads up apical junction formation

Epithelial cell differentiation requires the formation of the apical junctional complex, a membrane-associated structure that includes adherens junctions (which mediate stable adhesion between epithelial cells) and tight junctions (which regulate the movement of water and solutes between epithelial cells). Now, on p. 3835, Kai Schmidt-Ott and colleagues report that the mammalian transcription factor grainyhead-like 2 (Grhl2), an epithelium-specific homologue of Drosophila Grainyhead, regulates the molecular composition of the apical junctional complex. Grhl2, they report, determines the expression levels of E-cadherin and claudin 4 (Cldn4) – key components of adherens junctions and tight junctions, respectively – in several types of epithelia. Other experiments reveal that Grhl2 regulates epithelial differentiation in vitro and in vivo, that Grhl2 deficiency in mice results in defective neural tube closure, and that Grhl2 associates with conserved cisregulatory elements in the Cldn4 and E-cadherin genes. Together, these data suggest that Grhl2 is a transcriptional activator of apical junctional complex components and is, therefore, a crucial participant in epithelial differentiation.

Also…


Since its discovery, FGF signalling has been implicated in numerous developmental processes and in disease. Now Karel Dorey and Enrique Amaya provide an update of the main developmental processes for which FGF signalling is vital during early vertebrate embryogenesis.

For more details, see the Primer article on p. 3731.

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Hello from Nairobi

Posted by , on 24 October 2010

My apologies for the lag in updates from field collections in China.  I got a little distracted with submitting a paper and writing a K99/R00 that seem to have consumed the last month of my life.  But what better reward than a 3 week trip to Kenya!

Yes, I am a roving postdoc.  Boston is starting to grow on me, but as one of my travel companions/colleagues said yesterday “the best thing to do in Boston is leave.” The current trip is an “ambassadorship” sponsored by the department of Genetics at HMS to represent and work for a non-profit organization called “Seeding Labs”.  Seeding Labs was started by a former HMS graduate student, Nina Dudnik, and aims to distribute research resources to developing countries to better equalize opportunities.  I got involved because in all the travels I’ve done, for work and for play, I’ve met people with that spark in the eye, the passion and drive, but not the essential things they need to do something with all of that energy.  By way of example, I met a graduate student at Xinjiang University who saved from her own salary for months to buy an antibody for the protein she was studying because the lab didn’t have the money.

The primary mission of Seeding Labs so far has been to collect surplus (working) laboratory equipment to distribute to universities all over the world, and a particularly close relationship has formed with Kenyatta University in Nairobi.  Phase 2 of the project is a personnel exchange.  Four fellows from KU spent 2 months this summer working at Novartis in Boston, and now the three of us from Harvard are spending two weeks at KU running workshops on teaching, grant writing, statistics, career development and graduate school applications, presentations skills, etc.  We’re also touring labs, meeting faculty and students, and doing everything we can to encourage growth and research development.  The first 48 hours has been invigorating and a lot of fun, and we’re squeezing in some trips to see wild animals amongst the work.

I’ll continue posting updates while I’m here, because I would love to bring awareness of this fabulous program to the Node community.  If any of you would like to learn more or get involved, check it out at www.seedinglabs.org

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Postdoctoral position in Cell and Developmental Biology

Posted by , on 22 October 2010

Closing Date: 15 March 2021

St. Jude Children’s Research Hospital, Dept. of Genetics

POSTDOCTORAL POSITION in Cell and Developmental Biology is available to study the cellular and molecular mechanisms controlling the development of the lymphatic vasculature using available mouse models and its functional roles in health and disease. Highly motivated individuals who recently obtained a PhD. or MD degree and have a strong background in molecular and developmental biology are encouraged to apply. Interested individuals should send their curriculum vitae, a brief description of their research interests, and the names of three references to:

Guillermo Oliver, Ph.D (guillermo.oliver@stjude.org)

Department of Genetics

St. Jude Children’s Research Hospital

332 N. Lauderdale, Memphis, TN 38105

http://www.stjude.org/oliver

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Biology lecture posters

Posted by , on 21 October 2010

One of my (many) geeky passions is the overlap between art and science: Science as art (think of the Nikon image competition) or art inspired by science. That last category includes these lecture announcement posters from UNC Chapel Hill.

Poster for a recent lecture by Peter Wilf

The posters are designed by developmental biologist Bob Goldstein, and printed by The Merch in Carrboro, who normally print posters for dance parties rather than biology lectures!

If you’ve seen the posters online before, I may have been responsible for that as well… I wrote about them on my old blog in early 2009, and the link got picked up by BoingBoing and subsequently by The Scientist, who interviewed Bob by phone about his posters (see video below).

In an additional small world connection, Bob’s former graduate student Erin started writing for the Node, featuring pretty images from papers. That brings us full circle from “art inspired by science” to “science as art”.

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Building blocks

Posted by , on 19 October 2010

Somites are the building blocks of the vertebrae, skeletal muscle and dermis…literally and figuratively.  Somites define the segmented features of vertebrate embryos, and are repeated blocks of epithelial cells formed sequentially, from anterior to posterior, and at regular intervals on either side of the neural tube.  A paper in the November 1 issue of Development helps our understanding of the signaling cascade that acts during somitogenesis.

Integrins are transmembrane proteins that function in cell adhesion, migration, signaling and proliferation, which are all important processes during development.  Previous research had demonstrated a role for integrins in the formation of somites in certain organisms, but the exact requirement or mechanism was not clear.  This month in Development, Rallis and colleagues show that β1-integrin is important for formation of all somites in chick embryos.  They also found that β1-integrin functions in “outside-inside” signaling, meaning that signals from the extracellular matrix bind to integrins and result in the activation of signaling within the cell.  Specifically, β1-integrin functions cell-autonomously to activate Wnt and Notch signaling, via ILK, which leads to compartmentalization and boundary formation of somites.

Images above show a schematic of a chick embryo (A) and β1-integrin (red) localization during somite formation (TOPRO3, in blue, stains nuclei and shows somite organization).  β1-integrin was found at the borders of both older, anterior somites (B) and newly formed somites (C).  There was also an anterior-posterior gradient of β1-integrin in the presomitic mesoderm prior to somite formation (white versus yellow arrow in D, and zoomed image in E).  Interestingly, β1-integrin was found in the core of somites (F, arrowhead), and showed a continued segmented pattern in much later embryos (G).

Reference:  Charalampos Rallis, Sheena M. Pinchin and David Ish-Horowicz (2010).  Cell-autonomous integrin control of Wnt and Notch signalling during somitogenesis.  Development 137, 3591-3601.  Paper can be found here.

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Tree of Life – biodiversity linked

Posted by , on 18 October 2010

From Arabidopsis to zebrafish, every species –living and extinct – is linked to every other species. Not just metaphorically, but also literally on the Tree of Life website, which ambitiously aims to create a linked database with information on every species and group of organisms.


(Image from Tree of Life, used under Attribution-NoDerivs 3.0 Unported license)

Launched in 1995 the site was originally developed for biologists who might need to find phylogenetic information, but got so many requests from students and educators that they expanded their reach and now Tree of Life also provide “treehouse” pages, featuring accessible information for a wider audience.

Incidentally, the educational aspect of Tree of Life reminded me of another project I recently heard about: Phylo is a trading card game of which the cards are produced online by volunteers. The cards can then be used to teach children about biodiversity, much like the treehouse pages on Tree of Life

Like Phylo, content on Tree of Life is also contributed by volunteers. Scientific content is peer reviewed, and contributed by scientists and science educators, but anyone can submit media (such as images) to the site.

There’s a lot to be discovered on the site, so have a look around. It’s a work in progress, as it will be a long time until they’ve filled it with complete pages for every organism!

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Axon guidance, synaptic plasticity and regeneration meeting report

Posted by , on 13 October 2010

For anyone who has never been, Cold Spring Harbor Laboratories organize some really great conferences. The axon guidance, synaptic plasticity and regeneration conference, formerly the axon guidance synaptogenesis and plasticity conference, is biannually held in September and other than occasional heavy showers you can expect some fabulous weather. The campus, with the harbor that runs alongside it, is very beautiful especially with the first hint of autumn colour.

This year axon guidance and regeneration seemed to predominate over synaptic plasticity. The first day started with an evening session and whilst the jetlag can be a problem one of the other great things about these conferences is ‘The Leading Strand’, a password protected website that allows meeting participants to re-watch talks for a limited period of time after the conference. Sadly, but perhaps understandably, this appears to be becoming less and not more popular. Perhaps people feel that it’s unnecessary since there are no parallel sessions that force you to miss something.

The first session opened with some of our favourite axon guidance molecules Slit, Robo, Ephs and Ephrins. Adam Guy from the Neuronal Growth Mechanisms Lab, RIKEN Brain Science Institute, got the dubious honour of closing the session with a late night talk showing chemorepulsion of sensory axons in the chick spinal cord by a phospholipid, suggesting a specific axon guidance role and possibly a novel group of guidance molecules.

Wednesday opened with one of the few sessions that focused on synapses and circuits. This included a very interesting talk by Nicola Allen on an astrocyte secreted factor that can induce synapse formation in vitro. Nicola went on to describe the biochemical identification of the molecule and to show that hippocampal slice cultures from the knockout mouse do have an electrophysiological phenotype. The day finished with a plenary lecture which by Peter Devreotes on chemotaxis in which he sort to bring together the many different strands of research and show how they might fit together. It was a fascinating but rapid overview of the topic and there is clearly still much left to understand.

Thursday was easily the busiest day of the conference with talks until 3.30pm, a poster session until 5.30pm and then an evening session of talks from 7.30pm. You certainly get your money’s worth of science at Cold Spring Harbor!

Friday began with the second session on stem cells, regeneration and disease. In vivo laser axotomy appears to be the tool of choice for investigating regeneration at the moment and in combination with zebrafish and C.elegans, models which are so amenable to manipulation and live imaging, will certainly yield much useful and interesting data. After lunch we were treated to two more plenary lectures, the first given by Tom Jessell on ‘The nerves and networks of spinal motor control’ and the second by Eva Marder on ‘Compensation in robust network performance’, both were truly captivating and quite humbling.

The conference dinner on Friday evening was preceded by a very impressive performance by the up and coming violinist Hahn-Bin. After such a cultured beginning it was all downhill from then on…the less said about the drunken dancing the better!

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