(This interview previously appeared in Development)

This August, the Society for Developmental Biology (SDB) held their annual meeting in Albuquerque, New Mexico, USA, jointly with the Japanese Society of Developmental Biologists (JSDB). The JSDB has recently increased their international profile under the presidency of Dr Shinichi Aizawa from the RIKEN Center for Developmental Biology (CDB). We caught up with him at the SDB/JSDB joint meeting to discuss the projects that the JSDB has been undertaking under his leadership to expand the activities of the society beyond the borders of Japan.

What are you working on at the moment?

I’m interested in head development, specifically focussing on questions ranging from anterior-posterior axis formation to the early regionalisation of the brain. I have generally used a mouse genetics approach in this work, but I have also become interested in phylogenetic aspects, and am working with non-model animals such as Suncus, pig, gecko, soft-shelled turtle and the lobe-finned fish Polypterus.

How long have you been President of the Japanese Society of Developmental Biologists?

I’ve been president for four years. At our society, the president of the society and chairman of each annual meeting are two separate positions. The president and board (14 members) are elected by the members of the society, and their terms last for up to four years. The president nominates the chairman of the annual meeting with the agreement of the board members. I understand that this is different from the structure at the SDB, where the society president is also the head of the annual meeting.

How old is the JSDB?

The society was founded in 1968, and we currently have approximately 1400 members. More information can be found on the JSDB web site.
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WormBase — wormbase.org — is the central data repository for Caenorhabditis elegans and related nematodes.

C. elegans is a well-known system for studying problems in developmental biology, the benefits of which I will quickly rehash here. Its rapid generation time from fertilized egg to gravid adult (3.5 days) and small size (1mM) permit 1000’s of animals to be grown on a single plate in short order. As a self-fertilizing hermaphrodite, isogenic populations can be generated from a single animal. And the presence of occasional males permits standard crosses to create different genetic backgrounds. Moreover, the complete (and invariant from worm to worm) developmental lineage and neuronal connectivity are known. Thus C. elegans is an ideal system in which to conduct genetic screens looking for mutations that specifically disrupt developmental processes. Comparison to the baseline lineage and neuronal connectivity can provide quick insight into gene function, and standard genetic techniques can be used to identify interacting or regulatory genes.

WormBase supports the use of C. elegans as a model system by collecting and annotating experimental data from the published literature. By placing these data in a rich intellectual framework, WormBase facilitates further discovery that may not be readily apparent from studying the data in isolation. For example, WormBase gene summary pages contain manually curated, concise descriptions of the gene, which report gene function (summarized from null phenotype analysis when available), expression patterns, ortholog assignments,  and link to OMIM (Online Mendelian Inheritance of Man) if predicted orthologs are associated with genes involved in human disease. These pages also display phenotype data based on both mutant analysis and RNAi knockdown experiments. Further, these gene pages display the results of in-house homolog analysis using a number of different analysis tools: BLASTP, Inparanoid 7, Compara and TreeFam. Finally, WormBase is an active member of the GO Consortium and has placed a consistent effort on annotating genes with GO biological process and molecular function terms, as well as placing gene function in the context of a cell component when warranted.  These GO assignments together with the rest of the curation efforts and services WormBase provides, put C. elegans research in a larger biological scope for the understanding of biological processes and create a ready means for our community to access it.

Cross species analysis is also supported by WormBase. Currently, WormBase contains the completed genomic sequence of C. elegans and has recently added  five genomes of related sister species, bringing the total to ten nematode genomes (five sister Caenorhabditis and five distantly related nematode genomes).  The C. elegans genome can be viewed and navigated using the latest GBrowse genome viewer developed by Lincoln Stein.  This genome viewer allows direct comparisons between C. elegans predicted gene structures to  some of these different species in its synteny viewer.

What if your model system of choice isn’t C. elegans? First, don’t despair; it’s never too late to switch organisms. We jest. Still, WormBase has great utility for users working in other model systems. First, you can bring the extensive experimental evidence available in C. elegans to bear on research problems outside of the system. For example, you can search WormBase using Uniprot identifiers to quickly identify orthologs. You can also navigate through the complete cell pedigree using an Anatomy Ontology browser, or explore neuronal connectivity of C. elegans through the direct links to NeuralNet.  Ontology browsers are also provided for GO terms and phenotypes, which should provide you with a wealth of information and context for your gene of interest.

Recently, WormBase celebrated its 10th anniversary, a heady milestone and veritable eternity in internet time. WormBase has come a long way from our initial days of housing mainly genomic data for a single nematode to now hosting pages upon pages of extracted biological descriptions of various aspects of those genes sequenced so long ago.  And now that we have many more genomes to deal with, the fun continues in a new direction to build a richer repository for scientists to use to uncover the mechanisms of development.

I’d also like to take this opportunity to point out related projects that may be of interest. As mentioned above, the Caenorhabditis Genetics Center houses, catalogs, and provides strains to the worm community.  Many knockout and allele generating consortiums are willing suppliers of strains with a lesion in your favorite worm gene. These include the C. elegans Gene Knockout Consortium,  the National Bioresource Project of Japan, and  NemaGENETAG. WormAtlas along with  NeuralNet is another very important web resource that we link to for our community to get an  in-depth view of the anatomy and wiring of the worm.  And finally, WormBook,  a companion website to WormBase, is a peer-reviewed reference guide to the genetical analysis and experimental methods used for studying C. elegans, as well as providing copious chapters reviewing all aspects of the biology of C. elegans and related species.

(6 votes)

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I always travel with my suitcase packed with genes. Airports, planes and trains offer me the only instances where I find two hours solid of work, and they (genes) are then my best companions. However, in my discipline – developmental biology – it seems lately that, by simply analysing more genes, we are not getting closer to understanding how the information in the genome flows within cells as these multiply and form wonderfully complex organs and organisms. That is why this time I arrived in Cumberland Lodge with little luggage, but with plenty of room in the suitcase to be filled.

The workshop “Stochasticity in cell and developmental processes”, sponsored by The Company of Biologists, and organized and chaired by James Briscoe (NIMR, London) and Alfonso Martínez-Arias (University of Cambridge), revolved around an unsettling question: if the molecular mechanisms that underlie the function of cells (and thereby life) are intrinsically disordered and noisy, how then does development proceed in such a predictable and robust manner -i.e. it looks totally deterministic? The intense scientific sessions distilled two main messages to be taken home. First, at a cellular level, heterogeneity rules. Sometimes cells and organisms coach this heterogeneity through interactions to reduce noise and to generate coordinated patterns of activity or gene expression, for example, oscillatory behaviors. Some other times, though, it seems that this heterogeneity is actually used by the system, and therefore is built-in within the cells – either individually or collectively.

Second, we need to quantify. Not that cell and developmental biology have been totally disconnected from maths, but qualitative descriptions, often open for interpretation, have abounded. Numbers will take us from classical cellular and developmental biology to a frontier located at the intercept between biology and physics – a frontier that will rapidly blur. The intelligent combination of quantification, modeling and experimentation (the latter more powerful than ever) is already demystifying some of the biology concerning stem cell biology and organ growth. The science and the discussions that followed at this workshop gave the strong feeling that this new frontier in cell and developmental biology is within reach.

The organizers brought together a very interesting sampler of scientists along a (morphogenetic?) gradient of expertise – from the mostly experimental to the mostly theoretical – all of whom were already engaged in research at this frontier or, at least, thinking to move into it. A great mix.

In addition, the cocktail shaker could not have been better chosen. Cumberland Lodge is an elegant, old manor house surrounded by meadows, tall oak and chestnut tress and randomly passing pheasants, and it’s located in the middle of the Great Park of Windsor. Meals and coffee/tea breaks were held in wonderful rooms, with comfy couches, and decorated with old portraits, black and white photographs, and modern paintings. Just perfect for informal and productive chats. Dinner, and after dinner drinks, were especially productive (and who has ever doubted the exquisiteness of the English cuisine?!). The organizational support prior to and during the meeting, provided by Nicky Le Blond (The Company of Biologists), ensured that the meeting ran smoothly.

Now back to the lab. Genes, numbers, cells, functions, all wandering stochastically in my head. What a pleasure.

(10 votes)

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Today I gave a grant writing seminar for about 25 participants and went through the general structure and preparation as well as the expectations of reviewers and granting agencies.  The whole presentation went really well, and I clearly had an interested audience actively taking notes and asking really insightful questions.  A good conversation followed about international collaborations and preliminary data. (How are you supposed to present preliminary data when you don’t have the resources or equipment to do some of the the first fundamental experiments?) One junior faculty member even gave me a grant he was about to submit to ask me for feedback and suggestions, and I think I can expect several more to follow.  So I felt overall quite useful in expressing that this is a learned skill that takes years to acquire, that it’s worth the investment, and that individuals shouldn’t get frustrated by failure and give up.  They seemed surprised by the rejection rate in the US.

Two things came out of these conversations that were particularly striking. One was a question – “Are there mechanisms built in that recognize when you have difficulty with an approach and spend too much of your money troubleshooting before things start to work?”  That’s something none of us really have to worry about.  Grants in the US are *huge* by comparison, and we can spend time trying different things without worrying about the funds running out too quickly. We can be at least a little bit innovative and risky day to day. Here, a grant that is $20,000 is quite good. But that money has to be wisely and carefully spent, and there isn’t much wiggle room for trial and error if things don’t go precisely according to plan. And science is hard – sometimes things that “should” work just don’t work. It was a really good question and one I wasn’t sure how to answer other than “lean on the experience of others to work out technical issues more quickly so you can move forward more efficiently” and I strongly advised them to implement multiple experimental approaches to a given question – something is bound to work.

The most animated conversation that came of the day was surprisingly focused on the budget.  I hadn’t planned to talk much about administrative specifics until I was in a conversation with a faculty member this morning who said that the university “takes” from the research money they receive.  She really didn’t like this. It’s something I had already heard a few times since I was here, and it suddenly occurred to me what they were talking about.  So I used a slide in my seminar to explain the way it works in the US and probably most other places – there are “direct costs” like salaries, equipment, supplies, etc and “indirect costs” that are the institutional overhead (space, administration, electricity, water, etc). The indirect costs at KU are about 15% of the total grant, but the communication between the administration and the researchers hasn’t clearly stated what that money is for and how researchers should budget accordingly.  One of the grants administrators (also a research faculty) was present, which was fabulous because the two of use seemed to work well together to clear up a lot of misconception and mistrust.  Win.

On a less serious note – it’s Culture Week!  This is fascinating.  One week each year, the campus of KU becomes a festive environment of multiculturalism.  They have performances each night from all over Africa, so we’re getting to feel like we’re traveling the whole continent in our very short stay. There were dancers, musicians, and martial artists from Nigeria, Tanzania, and more in addition to the students at KU.  Even salsa dancers! Here I was captivated by the students from the school for the blind dancing a traditional African dance in grass skirts when the announcer enthusiastically introduced the KU salsa dancers as “probably the only students on the campus who know how to do this dance.” Exotic is clearly a matter of perspective!

Speaking of exotic.  The editing of this blog post was interrupted by one of those spectacular “wow” moments that come fewer and fewer as one gets more and more traveled.  I was sitting in the balcony area at the university guest house when a young man came to introduce himself.  He’s from Rwanda and visiting with his  dance troupe for culture week.  After a long chat, the whole group of about 20 young folks invited me to join them and burst out in traditional songs and dances.  He explained to me that these are not what they did for the performance – those were costumed and choreographed.  These were part of the long history of Rwandan culture, as one called it their “pastoral poetry”.  I can’t even begin to describe the scene.  It was one of marvel and mystery that this is such a rich culture I was getting a fleeting peek into.  Something I’ve never experienced before and may never have the blessing again.

(1 votes)

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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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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 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.

(3 votes)

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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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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

(3 votes)

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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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