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The Node in Japan

Posted by , on 30 June 2012

Earlier this month, I attended the annual meeting of the International Society for Stem Cell Research, which was held in Yokohama this year. I won’t go into much detail about the meeting itself, because James and Dongjin wrote some great posts about it for the Node. If you haven’t yet read them, take a look:

Day 1 – Welcome to Yokohama
Day 2 – Translation begins here in Yokohama
Day 3 – The Emperor at ISSCR
Day 4 – A complete picture

The ISSCR always encourages tweeting at their conference, and I tried to livetweet some of the talks, where possible. Although there was wifi in all the hallways and lobbies of the conference centre, and in the rooms of at least one of the hotels, there was (almost) no wifi in the seminar rooms or the exhibit hall, which is where everything happened! That may have been one of the reasons that very few people took part in the Twitter conversation. Because we were in Japan, all of the non-Japanese attendees relied on wifi for their tweeting. I did keep track of everyone’s tweets, and collected many of them in a Storify, which you can find below.

One of the things I found on Twitter was a poll started by Paul Knoepfler. He could not attend ISSCR, but set up a poll to ask participants what they thought of the conference. From the percentage distribution of the answers it seems that only about twenty people have responded, but they overwhelmingly voted that the conference was “so so”. Unfortunately none of the respondents left a response, so it’s not clear what they didn’t like, or whether they had attended the conference before. It’s a big meeting, and takes some getting used to if you’ve only been to smaller events. I personally had the impression that there were more clinical and applied posters than in previous years, but the topics covered in the talks were very broad and included a lot of fundamental research.

Another online aspect of the ISSCR Meeting was the new ISSCR Connect, allowing ISSCR attendees to catch up after the conference and see some of the talks in the concurrent sessions that they missed. They’re offered by a staggered schedule. At the moment, people who attended the conference can log in and view the talks from the first group of concurrent sessions. (No link, because it’s only available to meeting attendees.) ISSCR Connect also has a networking section, and three groups – including the Node – used ISSCR Connect to announce a small get-together.

The Node’s meetup was during the Thursday afternoon coffee break, in the Exhibition Hall. The Hall was open to everyone for coffee and posters, and people interested in meeting other developmental biologists could drop by our little corner. Some people stayed for most of the break, while others came by briefly just to say hello or to grab some freebies. To the left is a picture of our little corner before people arrived. (Once they did, I didn’t have time to take photos!)

It was interesting to note that, even though the conference was in Japan, and there were many Japanese people there, I barely met any of them. A few came by the Node coffee break, but only to take some information from the table. It’s unfortunate, because I would have liked to meet more Japanese researchers!

On this same trip, before the conference started, I had a chance to interview Development‘s newest editor, Haruhiko Koseki. He observed that, in general, Japanese students and postdocs are not as likely to join in with social activities or be as assertive as scientists from other countries, and he believes that that might actually affect their success as scientists! The full interview will appear in Development and on the Node later this year, so keep an eye out for that.

Finally, below is the Storify from the conference. (My favourite part is the exchange about invisible mice between “Yogioner” and “R.J.” on Thursday afternoon.)

(more…)

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MBL course: Gene regulatory networks for Development

Posted by , on 28 June 2012

In October, the MBL in Woods Hole will host the 5th high level short course on developmental gene regulatory networks. Course directors are Eric Davidson and David McClay, with Isabelle Peter as Assistant Director.

From the course directors:

“This high level short course on developmental gene regulatory networks will be offered to graduate students, postdocs, and PI’s who wish to adapt or advance network approaches to their own research. The previous 4 editions of the course elicited extremely positive reviews from participants, and the 2012 Faculty includes some of the best scientists in this field in the world. For a description of the Course, the detailed Course Syllabus, and application materials, see http://hermes.mbl.edu/education/courses/special_topics/gern.html

The deadline for registration is August 6.

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CoB Workshop: Epigenetic Memory Day 3

Posted by , on 27 June 2012

Tuesday, third day of the workshop, brings up more arguments to the epigenetic memory debate. Alyson Ashe from Cambridge UK discussed the establishment and maintenance of silencing through generations in worms. Jonathan Chubb presented his work using Dictyostelium and live imaging to investigate pulses of expression and how it relates to epigenetic memory. Neil Brockdorff and Andy Bannister discussed histone modifications and their involvement in chromatin and transcriptional regulation (X inactivation and cancers respectively). Fantastic chunky chips for lunch and delicious Eton mess gave everyone the energy to carry on discussing the existence of early events in reprogramming (Amanda Fisher), X-inactivation in mouse embryos (Atsuo Ogura) and how cell type specificity is kept through mitosis. The workshop atmosphere resembles a chamber music session : epigenetic players take part in a very special session to write a new concerto. The interpretation of the music, however, can also generate few dissonances.

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CoB workshop: Epigenetic Memory, Day 2

Posted by , on 27 June 2012

The day starts with a sumptuous breakfast, and the promise of some great talks. Carl Wu talks about the assembly of histone variants at yeast centromeres. Edith Heard takes us through a journey of how X-inactivation occurs in mice. The talks by the students and postdocs are all very good as well. Helen Blau, then introduces Heterokaryons as a model to study the mechanisms of reprogramming.We break for lunch. The food at the workshop is top class.

The Wiston house is located in a typical English countryside, very green and expansive. After lunch we go on a long walk.  This is a great way to get people talking to each other, and unsurprisingly lengthy discussions  on Epigenetics carry on throughout the walk. Upon arrival to Wiston house, coffee and ice creams  are waiting for us, while Sir John Gurdon enthusiastically teaches and recruits people to play Croquet.

The afternoon session begins with an inspiring talk by Renato Paro on Hsp90, Polycomb and stalled polymerases in transcriptional regulation. We are then served Pimms and lemonade in the garden (a quintessentially English thing apparently!) after which a historian dressed quite appropriately for this setting, briefs us about the Wiston house and its various owners. This sprawling mansion was built in the sixteenth century and has quite a few stories to its credit.

Anna Philpott  gives us a task, we have to come up with the single biggest question in Epigenetic memory (!).  A lively discussion ensues after dinner, which comprises of defining Epigenetics (surprisingly more difficult than you might think!), and then leads to ideas related to Epigenetic inheritance during cell division, and finally Transgenerational epigenetic inheritance is discussed.  In a nutshell, according to John Gurdon, Renato Paro, Steve Henikoff and the others, “Epigenetic memory is to do with processes beyond the DNA sequence, that may be self-templating and result in the inheritance of transcription through the cell cycle”. This session is a real eye opener for me, I don’t know for sure if what I do qualifies as Epigenetics anymore! Will have to clarify that before the workshop ends….

This workshop is one of the best I have been to so far.  I am having a fantastic time listening to talks by those who have shaped our understanding of Epigenetics, through their seminal ideas. The workshop is in an amazing venue and has been organized to absolute perfection. All the talks have been very stimulating, I can’t wait to go back and tell my lab mates all that I have learnt here. The Company of Biologists, please hold a  workshop on germ cells next, so I can come back again!…

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@ICAR 2012: Introductory Workshop on the Mechanics of Plant Growth

Posted by , on 26 June 2012

Please join us on the first day of ICAR 2012  (Tuesday 2nd July 16.00-17.30) for a series of short topical introductions to the field and discussions. Find out how mechanics could enrich your everyday view of plants, and your research!

The mechanics of plant growth is a historically rich field, which has provided great insight into how plants grow. The field is undergoing a recent resurgence due to the development of new experimental methods, new modeling techniques, and the application of new technologies (e.g. micro- and nano-indentation, Fourier transform infrared spectroscopy, advanced imaging and quantification tools, Finite Element modeling).

This Workshop aims at two vital purposes:

  1. to (re)introduce the idea of growth mechanics to the plant community
  2. to provide a forum for imperative discussions regarding the application of a mechanical lens to the study of plant growth.

With short informative talks from:

Siobhan Braybrook (University of Bern, CH)
Arezki Boudaoud (ENS Lyon, FR)
Alexis Peaucelle (Universite de Paris VII, FR)
Daniel Kierzkowski (University of Bern, CH)     
 
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In Development this week (Vol. 139, Issue 14)

Posted by , on 26 June 2012

Here are the highlights from the current issue of Development:

BRAF signalling sets astrocyte numbers

Astrocytes are the most numerous cell type in the mammalian central nervous system but little is known about the regulation of astrocyte precursor proliferation during development. Using the astrocyte marker Aldh1L1-GFP, David Rowitch and co-workers now begin to fill this gap in our knowledge (see p. 2477). The researchers identify two morphologically distinct types of proliferative astrocyte precursor in the developing mouse spinal cord: radial glia (RG) in the ventricular zone and ‘intermediate astrocyte precursors’ (IAPs) in the mantle region. Astrogenic RG and IAPs proliferate in a progressive ventral-to-dorsal manner between embryonic day 13.5 and postnatal day 3, and signalling via BRAF (a RAF isoform that is expressed in the developing nervous system) is both necessary and sufficient to promote astrocyte proliferation. Notably, temporally regulated changes in signalling and cell-cycle regulatory mechanisms restrict the mitogenic activity of BRAF during spinal cord development, thereby regulating astrocyte numbers. Together, these results provide new insights into the temporal-spatial control of astrocyte precursor proliferation during mammalian spinal cord development.

PCP gives directional Notch signalling a leg up

Spatial regulation of signalling pathways during development is essential. In the Drosophila leg, a stripe of cells in each segment expresses the Notch ligand Serrate (Ser) and activates the Notch pathway, which is required to specify joints, in distal cells only. Now, on p. 2584, Sarah Bray, Máximo Ibo Galindo and co-workers reveal that the planar cell polarity (PCP) proteins Frizzled and Dishevelled control this spatial restriction of Notch activation. The researchers show that these PCP proteins are enriched at the distal side of cells in the developing leg and that elimination of PCP gene function in the cells proximal to the Ser-expressing cells alleviates Notch signalling repression, resulting in ectopic joint formation. Mutants that disrupt a direct interaction between Dishevelled and Notch also reduce the efficacy of repression, whereas increased levels of Rab5, an endocytic regulator, suppress ectopic joint formation. Thus, the researchers conclude, PCP controls directional Notch signalling in the Drosophila leg by regulating the endocytic trafficking of Notch.

PGCs hitchhike during gastrulation

During gastrulation, the cells that give rise to internal tissues and organs move into the interior of the embryo. The gastrulation movements of endodermal and mesodermal precursors are regulated by transcription factors that also control their cell fate. However, primordial germ cells (PGCs), which also internalise during gastrulation, are transcriptionally quiescent in many species, so they must use an alternative gastrulation strategy. On p. 2547, Daisuke Chihara and Jeremy Nance identify this strategy by showing that, in C. elegans, PGCs internalise by ‘hitchhiking’ on endodermal cells. PGC adhesion to endodermal cells, they report, is mediated by HMR-1/E-cadherin, which is post-transcriptionally upregulated in PGCs through a mechanism that involves the 3′ untranslated region of hmr-1. The researchers also show that expression of HMR-1 in PGCs is necessary and sufficient to promote their internalisation, which suggests that HMR-1 does not promote PGC-endoderm adhesion through homotypic interactions. Because embryonic endoderm and PGCs are closely associated in many species, this novel post-transcriptional gastrulation strategy might be widely used to promote PGC internalisation.

Foxp1/4 restrict secretory cell fates

The secretory epithelium protects the lungs from inhaled pathogens and other environmental insults that can lead to debilitating diseases, such as chronic obstructive pulmonary disease, by producing mucus. The epithelium contains several cell types, including secretory Clara cells and goblet cells, but the control of these cell fates during lung development and regeneration is poorly understood. Here (p. 2500), Edward Morrisey and colleagues report that the transcription factors Foxp1 and Foxp4 (Foxp1/4) control epithelial cell fate during both of these processes in mice. Loss of Foxp1/4 in the developing lung ectopically activates the goblet cell fate program, they show. Consistent with this finding, Foxp1/4 repress key factors in the goblet cell differentiation program, including anterior gradient 2 (Agr2), overexpression of which promotes the goblet cell fate in developing airway epithelium. Moreover, Foxp1/4 also restrict secretory and goblet cell differentiation during lung regeneration. Thus, by restricting cell fate choices during development and regeneration, Foxp1/4 generate the proper balance of functional epithelial lineages in the lung.

Limb induction Bmps along

The molecular pathways that control limb bud patterning and outgrowth are well understood but less is known about limb field initiation. The current model for this process proposes that retinoic acid sits at the top of a signalling cascade that induces the apical ectodermal ridge, the signalling centre for limb outgrowth. Bone morphogenetic protein (Bmp) signalling, which is involved in later limb development, plays no part in this model, but Juan Carlos Izpisua Belmonte and colleagues recently noticed that Xenopus tadpoles exposed to the Bmp inhibitor Noggin during tail regeneration sometimes develop extra hindlimbs. Here (p. 2557), the researchers show that temporary inhibition of Bmp signalling by overexpression of noggin or by using a synthetic Bmp inhibitor is sufficient to induce extra pectoral fins in zebrafish as well as extra limbs in Xenopus. Bmp signalling, they report, acts in parallel with retinoic acid signalling, possibly by inhibiting the known limb-inducing gene wnt2ba. Based on these results, the researchers propose an expansion of the existing limb induction model.

Out-Foxed: dopaminergic progenitor specification

During nervous system development, the transcription factors Foxa1 and Foxa2 regulate specification of the floor plate and of midbrain dopaminergic (mDA) neurons. However, whether Foxa1 and Foxa2 act directly or indirectly by regulating the expression of sonic hedgehog (Shh), which has similar roles, is unclear. Using chromatin immunoprecipitation followed by high-throughput sequencing, Siew-Lan Ang and colleagues now identify 9160 Foxa2 binding sites that are associated with 5409 genes in embryonic stem cell-derived mDA neuron progenitors (see p. 2625). Foxa2 directly and positively regulates key determinants of mDA neurons, the researchers report, and negatively inhibits transcription factors expressed in the ventrolateral midbrain. It also negatively regulates multiple components of the Shh signalling pathway and upregulates the expression of floor plate factors involved in controlling axon trajectories. These and other results represent the first comprehensive characterisation of Fox2a targets in mDA neuron progenitors and provide a framework for understanding the gene regulatory networks that control the development of this important progenitor population.

PLUS…

Somitogenesis

A segmented body plan is fundamental to all vertebrate species. Segmentation is initiated very early in the developing embryo during the process of somitogenesis. Here, Dale and colleagues provide an overview of somitogenesis and highlight the key events involved in each stage of segmentation. See the Development at a Glance poster on p. 2453.

Stem cell powwow in Squaw Valley

The Keystone Symposium entitled ‘The Life of a Stem Cell: from Birth to Death’ was held at Squaw Valley, CA, USA in March 2012. The meeting brought together researchers from across the world and showcased the most recent developments in stem cell research. Here, Chambers and Schroeder review the proceedings at this meeting and discuss the major advances in fundamental and applied stem cell biology that emerged. See the Meeting Review on p. 2457

Evolutionary crossroads in developmental biology: hemichordates

Hemichordates are a deuterostome phylum and closely related to chordates. They have thus been used to gain insights into the origins of deuterostome and chordate body plans. Rottinger and Lowe introduce representative hemichordate species with contrasting modes of development and summarize recent findings that are beginning to yield important insights into deuterostome developmental mechanisms. See the Primer on p. 2463

 

 

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CoB Workshop: Epigenetic Memory

Posted by , on 26 June 2012

After nearly 20 hours of traveling, I have arrived at the stately house Wiston in the English countryside county of West Sussex, England. Before even getting out of the car, I find it easy to shrug off the jet lag and fatigue; perhaps it has something to do with the serene landscape of green hills dotted with grazing sheep. Or, perhaps the Wiston House itself, which apparently dates back to 1573. I’m not exactly how to come to grips with that – I’m American after all; we think anything over 100 years old is historical.  Regardless, I’m quickly jolted back by the corporal reality of my own stench. I simply feel gross from my travels, so quickly, I head off to my room – a comfy little spot in an adjoining cottage next to a gothic styled church. I am relieved to discover that my room has all the modern amenities, but most importantly a shower.

Soon after returning, Nicky Le Blond announces that there will be an absolutely critical amendment to the meeting schedule. That instead of the allotted 1 hour, at 15 past 8 for a poster session, everyone is welcome to adjourn to the library for the European Cup match quarter final match between Italy and England.  After all, one must have their priorities. However, being American I can’t really say that is where my heart lays.

2 pm arrives quickly, bells ring and everyone quickly reconvenes in the converted Ballroom; the Epigenetics Meeting has begun.

Sir John Gurdon kicks off the meeting asking everyone, that in the spirit of this meeting/workshop to keep two themes in mind, both of which are centered on the concept of stability of the epigenetic mark. He suggests that after heritable marks are initiated one can consider two mechanisms that allow for their persistence or memory of these marks: one, a constant repeated reprogramming where the mark is constantly maintained and therefore readily perturbable, and/or, two, a stable mark that once initiated requires no maintenance. It’s unclear to me whether the two are mutually exclusive. Lastly, before handing over the microphone to Helen Blau, co-organizer of the meeting and first chair of the first session, he asks everyone to consider the cell cycle and memories that are cell cycle dependent.

After the first session, I am not only impressed with the lively discussion, and at time heated debates, amongst the participants, but the diverse representation from the participants — from the wide eyed graduate students to the seasoned meeting veterans and iconic figures.

Complete with a cast of provocateurs, amoungst the backdrop of the absolutely gorgeous setting of the Wiston House, I am certain that this meeting with make lasting memories that will persist throughout my scientific career, not however, requiring constant maintenance. However, jury is still out on issue of cell cycle dependency.

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Postdoctoral Research Associate position at UCL

Posted by , on 25 June 2012

Closing Date: 15 March 2021

Applications are invited to join a research group  investigating the developmental mechanisms, genetics and cell biology underlying neural tube closure and neural tube defects (NTDs). Recent research has identified key roles for Grainyhead-like transcription factors in regulating neural tube closure. The purpose of the current project is to further define the role of Grhl genes and their targets in neural tube closure. This project will complement ongoing studies that address the cell and developmental biology of neurulation, analysis of metabolic factors and testing of novel therapies.

This is an MRC-funded position in Nick Greene and Andy Copp’s lab and is available immediately (with some flexibility in start date). Applicants should have, or shortly expect to obtain, a PhD in developmental biology and/or molecular biology, preferably with some experience in mammalian systems.  Informal enquiries can be made to Dr Nick Greene (n.greene@ucl.ac.uk). Please apply at  http://www.ucl.ac.uk/hr/jobs/ Ref:1258912 (closing date 12th July).

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EuroStemCell: latest news and what next?

Posted by , on 25 June 2012

EuroStemCell is an EU-funded project focussed on public engagement with stem cell and regenerative medicine research. For the latest news on what we’re doing and major issues affecting the field, check out our June newsletter.

You’ve probably seen our posts on The Node before, so we thought you might like to have your say in what we do next. In April, just after our second birthday, we brought partners, funders and advisory board members together to take stock of the project. We explored 3 questions:

1. what have we achieved so far?
2. what have we learned?
3. what should our priorities be for the next two years, and beyond?

Discussion was lively and productive. We left the meeting abuzz with new ideas, excited about opportunities for collaboration and enthused about our re-established priorities. We’re busy translating that into a workable plan for the next two years, which we hope to share with you soon.

We’d love to get your thoughts to help us make the right decisions about what we do next. Visit eurostemcell.org to share your views on what we’ve done so far, and your ideas for improvements or new materials. Below are some things we’d especially like your input on.

Clinical trials and clinical research information

At our meeting, we identified clinical trials as an area where we’d like to provide more information and resources – both on what trials are happening, but also to help explain how clinical research really works. We’ve done a few things in this area so far:

  • Published two updates on clinical trials and stem cell treatments, in collaboration with our partner ECRIN
  • Published the online version of Hope Beyond Hype, a graphic story by our partner OptiStem. Look out for interactive and multilingual versions coming soon.
  • Updated our FAQ on clinical trials and stem cell treatments
  • Collated links to patient organizations and patient information websites throughout Europe
  • Collated all content on our site that relates to clinical trials and stem cell treatments in a one-stop topic page.

What else would YOU find useful? Use our Contact form at www.eurostemcell.org/contact to tell us.

How are we doing so far?

Here are some of visual reminders of EuroStemCell highlights that you might also like to comment on.

First, a summary of our first periodic report to the European Commission, our funders – a 10 page publication, with lots of pictures! View non-flash version

And a presentation of highlights from the first two years of the EuroStemCell project – also with lots of pictures!

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Meeting Report – The 4th Young Embryologist Meeting

Posted by , on 23 June 2012

The Young Embryologist Network (or YEN for short) held its fourth annual meeting this year on the 1st June. The conference began as a small afternoon gathering in a lecture room at UCL, but over the years it has now become a fully catered day-long event, this year filling a huge lecture theatre at the Institute for Child Health. Since the start, the ultimate aim of the meeting has been to promote interaction and collaborations between early career researchers working in developmental biology. The organisers themselves are also early career scientists, this year coming from UCL, the Institute of Child Health, NIMR and Kings College London.

Professor Liz Robertson was invited to present the keynote lecture this year, and she kicked off the day with a superb talk on cell fate decisions in the early embryo. She particularly focused on recent work from her laboratory relating to the many roles of Blimp1 in the development of the limbs, heart, gut and placenta. Liz stayed for the rest of the meeting to help judge the talks and posters, and was also the lucky winner of the YEM raffle!

The first session of the day covered the theme of early development. Yusuke Miyanari presented some interesting work on how the tight regulation of Nanog dose at the chromosome level is necessary for pluripotency during development. Wenchao Gu then addressed the role of Ldb2a as a novel regulator of the Nodal and MBP pathways in zebrafish embryos. Next, Daniel Grimes, presented work on the establishment of left-right symmetry in the early embryo. In a talk that stimulated lots of interesting questions, he demonstrated the requirement for Pkd1l1 in coupling the physical force of fluid flow at the node to the asymmetrical expression of downstream molecular targets. Jorge Beira closed the first session with a talk on apoptosis during tissue homeostasis. He suggested that specific cell death stimuli may activate distinct pro-apoptotic pathways, despite having the same outcome.

The YEM 2012 poster session

After the lunch break and poster session, a Q&A panel discussion was held on the theme of science publishing. Katherine Brown, the Executive Editor of Development, was joined by Katie Ridd, the Senior Editor of Nature Communications, and David Wilkinson, the Editor in Chief of Mechanisms of Development. Questions covered a wide range of topics including how a decision is made on whether a paper is sent out to reviewers, whether publishing reviewers comments is a good or bad idea, and how important impact factors really are. It was generally agreed that keeping authors anonymous for reviews doesn’t really work in practice, and that open access to journals will become more and more widespread in the future.

The second session of talks was focused on the theme of development and disease. Alex Palmer presented research using the Splotch mutant mouse to gain insights into how neural tube defects arise, and how folic acid supplementation is able to rescue these defects. Lara Brock then discussed how a cleft palate can form, and showed 3D modeling work to investigate the cellular mechanisms responsible for the directional growth of the palatal shelves. To conclude the second session, Iain Dykes spoke about the different mechanisms by which Hic2 acts in both pre- and post- transcriptional gene regulation during cardiac development.

The final session of the day was on the theme of migration and neural guidance, and Laura Ward started out by showing some amazing movies of the zebrafish neural tube to accompany her talk on tissue polarization during neural tube development. Antonio Schepis then discussed the role of alphaE-catenin in the regulation of cell-cell adhesion and membrane blebbing during epiboly. Fani Memi addressed GnRH neurons and their migration from the nasal placode to the hypothalamus. She demonstrated an important role for SDF-1 and its receptors in guiding this migration. Finally Christopher Clark gave the final talk of the meeting, presenting some elegant fate mapping work on the crucial role of alpha2 chimaerin in wiring the ocular motor system.

Liz Robertson presents the talk and poster prizes

The day concluded with a word of thanks to the kind sponsors of the YEM 2012. We rely upon sponsorship to keep our meetings ad membership free of charge so a big thanks to The Company of Biologists, Development, NIMR, UCL Faculty of Life Sciences, UCL Department of Cell and Developmental Biology, UCL Basic Life Sciences Domain, BSDB, Eurogentec, New England Biolabs, Eppendorf and Insight for contributing to this years meeting. Special thanks also go out to the whole YEM organizing committee, but particularly to Cynthia Andoniadou and Rachel Moore who helped the day run so smoothly!

The ever-popular wine reception after the meeting provided a great chance for everyone to network and continue the days discussions, as well as learning more about the Young Embryologist Network. Thanks to everyone who participated in YEM:2012. It was a great day! Congratulations to Christopher Clark and Daniel Grimes, who were awarded first and second prizes for talks, and to Scott Curran and Chiara Ragni, who won the first and second poster prizes.

For more information about the Young Embryologist Network, please visit the website (www.youngembryologist.org) or find us on Facebook.

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