This rather lengthy summary describes a fascinating progress in the field of GRN modeling; it is a review of the article “Predictive computation of genomic logic processing functions in embryonic development”, which appeared few days ago in PNAS.

Gene regulatory networks (GRNs) are complex systems of interacting genes that deploy in both space and time and are the main regulatory logic behind the specification of cell fates during embryogenesis (Li et Davidson, 2009). Gene networks can be derived for any developmental process or structure and, in simple terms, consist of nodes (the genes themselves) connected by lines, which represent the causal relationships between the different genes. More or less, the GRNs unfold in time in a hierarchical mode where the products of earlier genes serve as regulatory factors (inputs), controlling the expression (output) of downstream targets. Provided that sufficiently detailed knowledge about the gene expression pattern and interactions for a given process is available, a computational model of the respective GRN can be constructed. The main objective of constructing a GRN model is to be able to causally explain each regulatory event in the system and, most importantly, to be able to predict the outcomes of experimental perturbations.

One of the the most complete, if not the best for any developmental process to date, is the GRN behind endomesoderm specification in the embryo of a sea urchin with the lovely name Strongylocentrotus purpuratus, famous for being the favorite model organism in Eric H. Davidson’s lab. Eric’s lab has been instrumental in establishing the endomesoderm network, which currenty contains some 50 genes, and their recent article describes the generation of a Boolean computational model, which beautifully and correctly reconstructs the spatiotemporal expression pattern of the interacting genes and allows for predictions to be made about the effects of changes in the system (Peter et al, 2012).

The computational model has been created by the incorporation of several sources of data: observations on the expression patterns of regulatory genes in space and time and results from trans and cis perturbation experiments. There are four spatial domains in the sea urchin embryo, based on differential gene expression, concerned with the endomesoderm specification -skeletogenic and non-skeletogenic mesoderm, and anterior and the future posterior endoderm. The data was used to construct an abstract representation of the interactions using Boolean logic. At the core of the model are the vector equations – one for every gene in the model. Each equation captures all inputs that sum at a respective node and give its output in Boolean terms, 1 – “on” or 0 – “off”. Understandably, the inputs are the outputs of other genes in the system and the relevant maternal inputs provide the initial triggers – the starting regulatory state.

A strong feature of the model is the incorporation of several other characteristics of the developing embryo, like the notion of intercellular signalling, embryonic geometry (which is the relative position of the four spatial domains in the embryo) and real-time kinetics of gene expression. Including such parametres in the model is important for the configuration of the spatial domains relative to each other changes with time and the kinetics of target gene transcription is a function of the temporal expression features of its regulators (like kinetics of RNA and protein synthesis and turnover). As for the latter, an earlier investigation by the same group has revealed a rather surprising phenomenon, that the step time (this is the “interval between activation of a given regulatory gene and the activation of an immediate downstream target…”) is rather uniform for most genes operating during early sea urchin development, and is approximately 3 hours. This characteristic was included in the model.

The usefulness of the computational model was first revealed by testing its ability to reproduce the regulatory state (the sum of all known regulatory genes expressed at a particular time interval) for each domain. Remarkably, there was a perfect match between the experimentally observed and computed patterns of expression of 33 genes, with only two exceptions – the bm1/2/4 and wnt8 genes. For these genes, the model resulted into a novel expression domain or prolonged expression, respectively, which is most likely due to the lack of knowledge about additional inputs operating in the embryo. Second, the incorporation of a uniform time step in the model successfully reproduced the observed dynamics of spatial gene expression, which is rather surprising, and further supports the idea that the regulatory genes of the S. purpuratus embryo operate with similar kinetics. Curiously, when the model was run with a different step time ( of 4 hours instead) the result was a catastrophic discrepancy in the expression kinetics of many genes.

The next task, and a most daunting one, was to challenge the model’s explanatory power by manually changing selected initial parameters (“removing” or “expressing ectopically” selected genes) and comparing the computational results with data derived from previous experimental perturbations of those same genes. For instance, in one of the settings the authors extinguished delta expression from the skeletogenic mesoderm, which in the model resulted in the loss of gatae and gcm  expression in the non-skeletogenic mesoderm and the ectopic expression of V2 endoderm genes, like blimpb1, foxa and hox11/13b. So far so good – this was exactly in agreement with the experimental observations. However, the real predictive power of the model was revealed when the expression of additional genes appeared perturbed, genes that have not yet been tested experimentally! For example, the GRN model predicted that the absence of delta affects not only gatae and gcm, but also genex and j(suh). It would be interesting to experimentally investigate the expression profile of the latter two genes in embryos injected with delta morpholinos, to check whether their patterns conform to the model’s predictions. If they do, then “Hail The Model!”; if they do not, it would simply mean that there exist regulatory inputs beyond our current knowledge.

In a final and rather challenging test, the authors computationally mimicked an experiment from the classic days of transplantation studies by Hoerstadius, when donor skeletogenic micromeres were transplanted on the animal pole of a host embryo, which resulted in a complete second gut and associated mesodermal tissues. In modern terms, this implies that the donor micromeres were sufficient to induce the downstream GRN required for endomesoderm development. However, in their model the authors computationally endowed the animal pole cells (which normally do not form skeletogenic micromeres) with maternal factors sufficient to induce the micromere cell fate. Then, remarkably, the surrounding cells formed three successive spatial domains – ring 1, 2 and 3, which expressed the regulatory states of the mesoderm, veg1 and veg2 endoderm, respectively, precisely mimicking the experimental results.

In conclusion, this study demonstrates the great predictive importance of GRN modeling but also its usefulness for further in silico evaluation of current GRNs structure and discovery of knowledge gaps, or lacunae, as described by the authors. One type of lacunae appear as discrepancies between what is observed and what is computationally generated but, as this study reveals, their frequency is low. In fact, what seems as a rare “failure” of the model could potentially guide future investigations.

References:

Peter IS, Faure E and Davidson EH, Predictive computation of genomic logic processing functions in embryonic development, PNAS Early Edition, Aug 27^th 2012

Li E and Davidson EH, Building developmental gene regulatory networks, Birth Defects Research (Part C) 87:123–130, 2009

(1 votes)

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When you click on an author’s name on a Node post, you are currently shown a page with all of the posts by that author. You can try it on this post.

In a few weeks, this is going to change! We will soon have profile pages for everyone who has written (or will write) on the Node. The profile page will list biography information that you can edit yourself. We’ve created a page that describes how to do that.

If you currently have a post anywhere on the Node, whether it’s a job ad or a two-year-old conference report, I recommend checking what you have filled out in your profile, because it will soon be public!

We have a few other changes in the works for the Node, and we hope to have the redesign up in the third week of September. If you can find a minute to update your profile before September 13, that would be very helpful.

You can always edit your profile later, but please just be aware that in a few weeks the biography section from your profile will become public.

The information page clearly describes what part of your profile will become public, and how to edit it.

If you have any questions, let us know via email, or leave a comment below.

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To celebrate our 25th Anniversary (see here for some memories of the last quarter century of the journal), and to look forward to the next 25 years, Development is hosting a one day symposium in Cambridge on October 25th 2012. We’ve got a great line-up of speakers, and we’ll also be holding a panel discussion on the future of the field. We hope some of you will be able to join us for this exciting event!

Here are the details:

Development: Past, Present and Future

One-day Symposium

October 25th 2012

Magdelene College, Cambridge, UK

Join us for a special one-day symposium featuring talks from members of Development’s editorial board past and present, and concluding with a panel discussion on the future of developmental biology.

Speakers:

Kenneth Chien     Magdalena Götz     Peter Lawrence

Thomas Lecuit     Mike Levine     Olivier Pourquié     Jim Smith

To register, please go to

http://www.biologists.com/dev_symposium_2012.html

Here’s the poster for the meeting

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The Wellcome Trust-Medical Research Council Stem Cell Institute provides outstanding scientists with the opportunity to undertake ground-breaking research into the fundamental properties of mammalian stem cells.

The Institute offers a comprehensive flow cytometry service to its members. The facility comprises MoFlo and FACSAria l cell sorters, Cyan and LSR-Fortessa analysers, and associated flow cytometry equipment.

The role will encompass:

Heading a team of two people providing high quality cell sorting and analysis services for various research projects.
Future proofing the flow facility in the Stem Cell Institute, and manage the operation, upkeep and development of equipment.
Recruitment, training and line management of second member core facility staff.
Provide training, advice and guidance to researchers in the theory and practice of flow cytometry.

The ideal candidate will have all of the following:

A proven ability to design flow experiments and to analyse and interpret data.
Be computer literate and technically innovative.
Excellent communication and interpersonal skills in this service-focused environment
Excellent organisational and interpersonal skills.
Extensive expertise in multiparameter flow cytometry.
Experience in a multi-user flow cytometry service will be an advantage.

The successful applicant will be able to demonstrate leadership qualities and the ability to work well within an academic research setting.

This appointment is subject to a health assessment.

Whether an outcome is satisfactory will be determined by the University.

The University values diversity and is committed to equality of opportunity.

The University has a responsibility to ensure that all employees are eligible to live and work in the UK. CLOSING DATE: 21st September 2012 at 12.00pm INTERVIEW DATE: Week beginning 8th October 2012

If you have not been invited for interview by the 1st October 2012, you have not been successful on this occasion.

Applications must be made via our online applications site on:

http://www.stemcells.cam.ac.uk/careers-study/vacancies/

We do not accept applications by post or email except in exceptional circumstances.

Please note that you cannot amend your application once you have submitted it, so please ensure that you upload all the correct documents the first time.

Application Forms:

All applications MUST include the following:

-Cover letter
-CV
-The relevant CHRIS form (Parts 1 & 2 ONLY).

If you do not wish to submit the Equal Opportunities data, please upload a blank form to the applications site.

Contact:

If you have any questions, please email cscrjobs@cscr.cam.ac.uk

This appointment is subject to a health assessment.

Whether an outcome is satisfactory will be determined by the University.

The University values diversity and is committed to equality of opportunity.

The University has a responsibility to ensure that all employees are eligible to live and work in the UK.

Quote reference: PS00519

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The purpose of this summary is to present to “The Node” readers a recent update to the story which, in my opinion, is a quite interesting example of the phenomenon of programmed genome rearrangement (PGR) that occurs in the lamprey Petromyzon marinus.

Programmed genome rearrangement describes the regulated structural changes in the genome, which result in the generation of new coding sequences, changes in the control of genome functions and gene expression etc, within ontogeny (not to be confused with similar structural changes on the phylogenetic level). Although on a smaller scale, a form of PGR also occurs during the formation of the T- and B-cell progenitors in mammals, the V(D)J somatic recombination system, which generates the diversity of forms of the Ig- and T-cell receptors.

The PGR in P. marinus occurs during embryonic development and results in the differential deletion of hundreds of millions of base pairs specifically in the genomes of the somatic lineages, as contrasted to the germline. In effect, the germline retains sequences that are deleted in the soma. Of course, this is not the first known case in the Metazoan clade (it has been previously described in sciarid dipterans, nematodes, copepods, etc (see references in the articles cited below)) but according to the authors, it is the first known example of a genome rearrangement of such scale in vertebrates, which makes it especially important for better understanding the evolution and mechanisms of vertebrate gene regulation. Speculatively, lampreys eliminate particular sequences from the somatic tissues’ genomes, which are otherwise important for the complex meiotic rearrangements and pluripotency regulation in the germline, because misregulation of such sequences in the soma may lead to disruptions in genome integrity and defects in cell commitment/differentiation (e.g., tumorigenesis). However, DNA breaks are also visible at later stages of development, which suggests that further rearrangements probably do occur, possibly in a tissue-specific mode (as suggested by variation in the DNA content measured by flow cytometry), which may potentially lead not only to loss of function, but also to the assembly of new sequences (regulatory, coding, etc), that facilitate the differential development of the somatic lineages.

In the newer of the studies, the authors used a customized oligonucleotide microarray that targeted all available germline sequences and a small fraction of the somatic sequences. This revealed that nearly 13% of the screened germline sequences were deleted in the soma and that five of the promising candidate sequences were expressed in the juvenile and adult testes. A large fraction of the somatically deleted sequences are single-copy and protein-coding DNA, which argues against a predominant deletion of repeats. Intriguingly, the authors do not rule out the possibility that whole chromosome elimination may also contribute. Genes presented in the deleted regions include: APOBEC-1, cancer/testis antigen 68, WNT7A/B, SPOPL etc, which in other vertebrates have known roles in cell fate maintenance, proliferation and oncogenesis. Interestingly, some of the genes indentified in the germ-line specific fraction have homologs in other vertebrates where they are not known to function in germline development. I could easily hypothesize that those genes were recruited for germline functions during lamprey evolution or, alternatively, they were germline-specific in ancestral vertebrates but they were later deployed in somatic functions with concomitant loss of germline function. Or it simply means that our knowledge about vertebrate germline function genes is imperfect!

Despite this important differences in genome biology between lampreys and gnathostomes (as we know them), there are many fundamental similarities in embryonic development and gene content. It is expected that some of the factors involved in the lamprey’s PGR will have homologs in gnathostomes. I am curious whether these homologs perform similar functions in jawed vertebrates? Do such PGR mechanisms of a similar scale (excluding the V(D)J system) occur in gnathostomes as well?

From a broader view, these observations suggest that lampreys use an additional strategy for gene regulation as compared to the rest of vertebrates. However, it is important to note that similar PGRs also occur in hagfish (Myxini (please, see the references)). One is prompted to ask: “What is the extent of this process in Myxini? Do their PGRs specifically occur in the soma versus the germline, as in lampreys?” Considering the fact that both lampreys and hagfish use PGRs, it is legitimate to suggest that this strategy of gene regulation was an ancestral system for the early vertebrates, and that the evolution of a gene regulation system predominantly based on epigenetic modification of chromatin was a later invention. However, this is a pure speculation.

Whatever the case is, I imagine that there exist specific DNA sequences that recruit the recombineering machinery (RM) to those regions destined for deletion. Then, it should be of importance that these sequences are occupied by the RM in the particular somatic lineages only and not in the germline. This could be achieved by any of the mechanisms that regulate the function of other regulatory sequences, like enhancers for instance, and may include control of sequence accessibility via epigenetic modification on the chromatin. In addition, tissue-specific expression of the RM components could also be a factor.

Future exploration of the PGR phenomenon will surely provide better understanding of the mechanisms that regulate genome stability, with important implications for cancer biology as well.

References:

Genetic consequences of programmed genome rearrangement, Current Biology, August 21 2012

http://www.cell.com/current-biology/retrieve/pii/S0960982212006732

Programmed loss of millions of base pairs from a vertebrate genome, PNAS, July 7 2009

http://www.pnas.org/content/106/27/11212.long

(5 votes)

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Here are the highlights from the current issue of Development:

Retinoic acid’s developmental role illuminated

The role of all-trans retinoic acid (RA) in hindbrain development and other developmental processes is usually studied by blocking endogenous RA synthesis and then continuously supplying exogenous RA by soaking embryos in all-trans RA or by implanting RA-soaked beads. Now, on p. 3355, David Bensimon and colleagues use photo-isomerisation of 13-cis RA to all-trans RA and vice versa to manipulate RA activity spatiotemporally in zebrafish embryos. In embryos in which all-trans RA synthesis is impaired, they report, brief incubation in all-trans RA or in 13-cis RA followed by UV illumination before the bud stage rescues hindbrain development. By contrast, rescue is impaired in embryos treated with all-trans RA and then exposed to UV light. Notably, activation of all-trans RA via photo-isomerisation of 13-cis RA at the end of gastrulation in head, but not tail, precursor cells rescues hindbrain development. These results suggest that all-trans RA is sequestered in embryos during normal development. Furthermore, they illustrate how RA activity can be spatiotemporally controlled in developing zebrafish embryos.

Branching out studies of dendritic patterning

The dendritic arbours of neurons in the central nervous system have highly diverse morphologies that determine neuronal connectivity and, consequently, brain function. But how is dendritic architecture sculpted during development? On p. 3442, Kazuto Fujishima, Mineko Kengaku and co-workers investigate this question by combining computer simulations and time-lapse imaging of cultured mouse cerebellar Purkinje cells. The researchers show that the characteristic Purkinje cell space-filling dendritic arbour of non-overlapping branchlets is shaped by several reproducible dynamic processes, including constant tip elongation, stochastic terminal branching and retraction triggered by contacts between growing dendrites. This last process, they report, is regulated by protein kinase D signalling. Their computer simulation of dendrite branch dynamics, which incorporates their experimental measurements, reproduces dendritic development in live Purkinje cells and confirms the important contribution that dendritic retraction makes to the formation of the Purkinje cell dendritic arbour. Further development of this two-pronged approach, suggest the researchers, will help to clarify the fundamental mechanisms of dendrite patterning in the developing brain.

Pancreatic development keeps its Sox on

All mature pancreatic cell types arise from a pool of organ-specific multipotent progenitor cells. Cell-intrinsic and cell-extrinsic cues promote the proliferation and cell fate commitment of these progenitor cells but what integrates these cues during pancreatic morphogenesis? Maike Sander and co-workers now report that the transcription factor Sox9 forms the centrepiece of a gene regulatory network that controls pancreatic development (see p. 3363). Pancreatic progenitor-specific ablation of Sox9 during early mouse pancreatic development, they report, leads to cell-autonomous loss of fibroblast growth factor receptor 2b (Fgfr2b), which is required to transduce mesenchymal Fgf10 signals. In turn, Fgf10 is required to maintain progenitor expression of Sox9 and Fgfr2b. Perturbation of this Sox9/Fgfr2b/Fgf10 feed-forward expression loop results in pancreas-to-liver fate conversion. Given that Fgf signalling is necessary for pancreatic progenitor cell proliferation, the researchers propose that a Sox9/Fgf feed-forward loop coordinately controls organ fate commitment and progenitor cell expansion in the developing pancreas, a finding that may advance efforts to generate insulin-producing cells for therapeutic use.

COP1 sheds light on root development

Although the roots of most plant species are not directly exposed to light, root growth is controlled by light and integrated with the growth of above-ground organs. Here (p. 3402), Teva Vernoux, Jian Xu and colleagues uncover a novel long-distance mechanism by which light signals through the master photomorphogenesis repressor COP1 to coordinate root and shoot development in Arabidopsis. The authors show that, in the shoot, COP1 regulates shoot-to-root transport of auxin by controlling transcription of the auxin efflux carrier gene PIN-FORMED1 (PIN1). In addition, they report, COP1 regulates auxin transport and cell proliferation in the root apical meristem by modulating the intracellular distribution of PIN1 and PIN2 in the root, thereby ensuring rapid and precise tuning of root growth to the light environment. Together, these results identify auxin as a long-distance signal in light-regulated plant development and show how spatially separated control mechanisms can converge on a single signalling system to coordinate development at the whole plant level.

Pten-less neuroblasts stop en route

Neuronal precursors in the subventricular zone (SVZ) of the adult rodent brain differentiate into neuroblasts and migrate through the rostral migratory stream (RMS) to the olfactory bulb, where they differentiate into interneurons. Diverse extracellular cues control neuroblast migration but what are the intracellular pathways that respond to these cues? On p. 3422, Suzanne Baker and colleagues identify a role for Pten, a negative regulator of phosphoinositide 3-kinase (PI3K) signalling, in mouse neuroblast development. The PI3K-Akt-mTorc1 pathway is inactivated in migrating neuroblasts in the SVZ and RMS, they report, but activated when the cells reach the olfactory bulb. Postnatal deletion of Pten, they show, causes aberrant activation of PI3K-Akt-mTorc1 signalling, premature termination of neuroblast migration, neuroblast differentiation and enlargement of the SVZ and RMS. Notably, live imaging of slice cultures shows that, although some Pten-null neuroblasts lack directional migration and have a non-polarised morphology, others migrate normally towards the olfactory bulb. Thus, the researchers suggest, the neuroblast migration defect associated with Pten loss is secondary to precocious neuroblast differentiation.

Haploid ESCs: a future in the germline

Parthenogenetic haploid embryonic stems cells (ESCs), which have recently been established through chemical activation of unfertilised mouse cells, give rise to a wide range of differentiated cell types in embryos and in vitro. But can they contribute to the germline, which is the defining hallmark of mouse diploid ESCs? Here (p. 3301), Martin Leeb, Anton Wutz and co-workers show that parthenogenetic haploid mouse ESCs have a robust germline potential and that transgenic mouse strains can be produced from genetically modified haploid ESCs. Differentiation of haploid ESCs in chimeric embryos, they report, correlates with the acquisition of a diploid karyotype by the ESCs through endoreduplication. By contrast, haploid ESCs induced to differentiate to an extra-embryonic fate by expression of the transcription factor Gata6 retain their haploid content. Parthenogenetic haploid mouse ESCs, the researchers conclude, are authentic pluripotent ESCs that can, potentially, be used to elucidate new details about developmental pathways through extension of genetic screens and manipulations directly into mouse models.

Plus…

Left-right patterning: conserved and divergent mechanisms

This Development At a Glance poster by Nakamura and Hamada summarizes the common and divergent mechanisms by which LR asymmetry is established in vertebrates.

Review: Principles and roles of mRNA localization in animal development

Intracellular targeting of mRNAs, which has long been recognised as a means to produce proteins locally, has recently emerged as a mechanism used to polarise various cell types. Here, Florence Besse and colleagues review the regulation and functions of RNA localisation during animal development. See Review on p. 3263

Review: Partitioning the heart: mechanisms of cardiac septation and valve development

On p. 3277, Zhou, Chang, and colleagues review the morphogenetic events and genetic networks that regulate spatiotemporal interactions between the cells that partition the heart.

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Let’s take a very close look at the inside of a fish!

A recent paper in the Journal of Cell Biology describes a technique for generating large, composite, images from electron microscopy data. Frank Faas, Raimond Ravelli, and colleagues at the Leiden University Medical Center developed a method to computationally collect and align EM images. In the data viewer accompanying the paper, they show a large section of a zebrafish embryo, 5 days post-fertilisation, which is comprised of 26,434 individual images! The total size of the composite image is 921,600 pixels by 380,928 pixels. (For reference, the screenshots below are 500 pixels wide.)

In these screenshots you can see the overall fish in the bottom right, with the red area indicating where the larger, detailed, view is located. These are two different magnifications of the (edge of the) eye. In the bottom image you can also see the edge of the composite image, and appreciate how many individual images there are, and how well they connect.

To find out more about the method, and its practical applications, read the full paper and editorial at JCB.

Faas FG, Avramut MC, M van den Berg B, Mommaas AM, Koster AJ, & Ravelli RB (2012). Virtual nanoscopy: Generation of ultra-large high resolution electron microscopy maps. The Journal of cell biology, 198 (3), 457-69 PMID: 22869601

(2 votes)

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A few months ago, we published an interview with Stephen Fleenor, who won the poster award at the BSDB meeting. He won attendance to the SDB meeting in Montreal, where he passed on the baton and interviewed the winner of the SDB poster prize, John Young:

Stephen Fleenor: In which lab do you work?

John Young: I work in Richard Harland’s lab, at UC Berkeley.

SF: How long have you been there?

JY: I’ve been in his lab for four years, but I’ve been a student for five, because we do rotations the first year.

SF: I see. Well, congratulations on winning the poster prize. What was the crux of the poster?

JY: I’m interested in morphogens. I took a class from Mike Levine when I was a first-year student, and I was totally taken by the dorsal gradient and eve stripe enhancers, and I wanted to do something similar in vertebrates. So I chose to look at the neural plate. The neural plate is first induced to become neural tissue, and then it’s patterned by factors like Wnt, Fgf and retinoic acid. I chose to study Wnt and have been looking at Wnt-responsive genes in neuralized ectoderm. I first looked for direct transcriptional targets of Wnt signalling, and once I found those, I looked for the regulatory regions that mediated Wnt responses in these targets.

SF: And have you found regulatory regions?

JY: Using ChIP-qPCR with beta-catenin I found one regulatory region for one of my candidates that looks really good. Based on that I’m now doing ChIp-Seq with the beta-catenin antibody. I found a lot of direct targets of Wnt signalling, and a number of them showed specific expression in the posterior neural tissue. The two that I followed up with suggest that they modulate AP patterning.

The targets that I followed up after the screen were sall1 and sall4. I chose to work on these two because sall4 is a stem cell factor, and Sall1 has a human mutation associated with it. No one had yet looked at their roles in neural patterning in frogs, though, so I thought they’d be good ones to follow up on.

SF: Sounds like a pretty solid story

JY: It’s coming along!

SF: Have you ever won a poster prize before?

JY: Just at a retreat, and that was second place. This is real!

SF: Was it for the same work?

JY: Yes, it was, but it was a while ago, before things had been fleshed out.

SF: What was the element of your poster that now made it prize-worthy on an international scale?

JY: I think it was that I had knocked down the second Sall gene as well. At first I only had sall1, but now I’m working on both sall1 and 4. And at that time I didn’t have any of the ChIP data either. My project was first to find direct targets, and then I decided to look for the regulatory regions. Finding direct targets was really cool in itself, but it was only half the story.

SF: You’re four years into your PhD research. What are your plans?

JY: I’m going to do a postdoc in Cliff Tabin’s lab. I’m so excited about that, but it’s not until next summer. Now I have a year to finish up this story, and I also need to finish this completely separate project, looking at noggin mutants that I induced in Xenopus tropicalis.

SF: Do you think you’re close to closing the door on the Wnt project?

JY: I think so. I think once we get the beta-catenin ChIP-Seq data back that we can make a nice story out of that. The noggin stuff is not too far off either, so I can get it done in a year.

SF: Are you going to go to the BSDB meeting in Warwick?

JY: Absolutely! I’ve only been to Europe twice – once when I was 15, and in Oslo a number of years ago. I haven’t been to Europe much at all, so I’m looking forward to this opportunity.

At the BSDB meeting in 2013, John will, in turn, interview the winner of the BSDB poster prize.

(3 votes)

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I’ve just returned from this year’s Santa Cruz Developmental Biology meeting. Some of you may have seen the tweets I was sending out from there (see Storify for the collected set), but a combination of limited ability to multitask and limited laptop battery life meant I didn’t cover all the talks. So to add to what I missed, and for those who prefer more than 140 characters of coverage, here’s a summary of some of the highlights.

SCDB is a bi-annual broad developmental biology meeting, held at the beautiful wooded campus of UC Santa Cruz. With only around 180 participants, it’s a fairly small and very friendly event, with plenty of opportunity for informal discussions. This year, it was organised by Bob Goldstein, Amander Clark and John Tamkun, and topics discussed at the meeting ranged from the evolution of segmentation in arthropods (Mike Akam, University of Cambridge) to ligand/receptor interactions in axon guidance (Elke Stein, Yale University), with pretty much every model organism, tissue and process in between.

Despite covering the whole breadth of the field, there were some definite themes running through the meeting – aside those defined by the program. Multiple talks dealt with the germline: how you make it, put it in the right place and maintain it. Both Diana Laird (UCSF) and Jeremy Nance (NYU Skirball Institute) focussed on the earliest stages of gonad formation in the mouse and the worm respectively. Diana’s work looks at the interactions between migrating primordial germ cells and the various niches they encounter during migration through the embryo, while Jeremy presented data on the mechanisms by which C. elegans germ cells are internalised during gastrulation. Moving to later stages of the nematode, Jane Hubbard (NYU Skirball) demonstrated that nutrient status is a key determinant in regulating germ cell proliferation. The importance of environmental signals was echoed by Timothy Kelliher (Walbot lab, Stanford), who showed that hypoxia triggers germ cell formation in maize (where there is no pre-defined germline as in animals). Perhaps most spectacularly, Bruce Draper (UC Davis) presented his latest work on how mature germ cells influence sex determination in zebrafish: look out for his upcoming paper on sex-changing fish!

As is becoming standard in developmental biology meetings these days, talks were filled with beautiful movies of everything from early stage Drosophila embryos (Dan Kiehart, Duke University and Jen Zallen, Sloan Kettering) to regenerating axolotl (Saori Haigo, Center for Regenerative Therapies Dresden and UCSF) and mouse neural tube closure (Lee Niswander, University of Colorado Denver). But all were (or at least claimed to be!) put in the shade by Eric Betzig’s keynote lecture on super-resolution in vivo imaging: for unprecedented intracellular resolution in developing tissues, the future apparently lies with the Bessel beam.

In a third recurring theme, several speakers discussed the regulation of cell division and its impact on cell fate. Asako Sugimoto (Tohoku University) showed beautiful work on spindle assembly in C. elegans, directly comparing oocyte meiotic division, where the spindle is small and acentrosomic, with the following first zygotic mitosis, in which both centrosomes and chromatin direct microtubule assembly and spindle formation. Laurie Smith (UCSD) uses stomatal development in maize as a model to study asymmetric division, and shared her latest insights into the pathways regulating this process in plants. Finally, Roel Nusse (Stanford University) presented a tour-de-force study on the regulation of embryonic stem cell division by Wnt signalling – another paper to keep an eye out for in the future.

Away from the lecture theatre, the poster sessions were very lively and interactive – congratulations to poster prize winners Shawn Chavez (human blastocyst development), Harshani Peiris (planarian stem cells) and Jacqueline Tabler (ciliopathy models in mouse), although I’m sure there could have been many more winners among the great posters I saw. The Friday evening wine tasting and social session was also enlivened by the surprise entertainment: I’m not sure how many companies get called up and asked if they would sponsor a Mariachi band, but Nikon stepped up to the plate and delivered.

All of this means that the next set of organisers for this meeting – Jeremy Nance, Diana Laird and Amy Ralston – have a lot to live up to: not just in topping the Mexican minstrels, but mainly in putting together a fantastic and diverse set of speakers and fostering a welcoming and collaborative atmosphere. Look out for SCDB2014: I’m sure it’ll be a good’un!

(9 votes)

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Decisions, decisions.  Stem cells face the task to self-renew or differentiate, a decision made out of the combination and coordination of numerous regulators.  With the activation or suppression of transcriptional activators and the activation or suppression of repressors, it’s easy to see how understanding this process is anything BUT easy.  Today’s images are from a Development paper that describes the importance REST in neural stem/progenitor self-renewal and differentiation.

Neural development begins with neural stem cells and progenitor cells, and follows a specific time-line of differentiation involving neurons and glial cells.  The orderly progression through cell fates requires a complex network of regulators, but the specifics are unclear.  A recent paper in Development describes the importance of REST, a transcriptional repressor of neuronal genes, in the development of the nervous system.  REST, along with its co-repressor CoREST, suppresses neural fates in cells outside of the nervous system.  In this paper, Covey and colleagues found that REST maintains neural stem/progenitor (NS/P) cell self-renewal, and limits maturation into neural and glial cell fates.  In addition, a high level of REST in embryonic stem (ES) cells is important in suppressing transcription of neuronal genes, but is not required for ES pluripotency.  NS/P cells lacking REST have reduced self-renewal capacity and precocious neuronal differentiation.  As seen in the images above, REST heterozygote (middle) and homozygote knockout (right) ES cell-derived neurospheres have increased numbers of neurons (red, TUJ1) compared with control neurospheres (left).  REST null neurospheres also produced fewer astrocytes (green, GFAP).

For a more general description of this image, see my imaging blog within EuroStemCell, the European stem cell portal.

Covey MV, Streb JW, Spektor R, & Ballas N (2012). REST regulates the pool size of the different neural lineages by restricting the generation of neurons and oligodendrocytes from neural stem/progenitor cells. Development (Cambridge, England), 139 (16), 2878-90 PMID: 22791895

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