The recent joint meeting of the British Societies for Developmental Biology (BSDB) and Cell Biology (BSCB) in Warwick provided an exciting opportunity to catch a glimpse of the future of these two fields. “Old” questions of how cell fates are allocated during development are now being tackled with new technologies and new knowledge of how gene expression can be regulated.

Since I made the decision to write this report after the conference was over, I’m outlining only a few talks which I have attended and found interesting. I’ve written this in three parts. Part one covers some of the presentations on transcriptional regulation, the second part will be about transcription factor networks, and part number three covers several topics which do not fit into the first two categories: Stem cells, limb development and evo-devo.

Part 1: Transcriptional Regulation

Mike Levine (University of California, USA) opened the conference by presenting his lab’s work on the suppression of transcriptional noise during dorsal-ventral patterning of the early Drosophila embryo. One mechanism they have found to underly such robustness is the deployment of multiple enhancers for the same expression patterns, so-called “shadow enhancers”. Levine also reported that rapid transcriptional responses to signals can involve a mechanism in which RNA polymerase II is kept in a paused state near the promoter, ready to receive a ‘go’ signal. It remains to be seen if these mechanisms are utilized in other systems to confer robustness and responsiveness.

To map the location, density and orientation of paused RNA polymerase II (Pol II), John Lis (Cornell University, USA) introduced a recently developed method called “GRO (Genome-wide nuclear Run-On) -seq”, which uses nuclear run-on followed by large-scale parallel sequencing. The analysis of these parameters in mouse embryonic stem (ES) cells and isogenic embryonic fibroblasts (MEFs) uncovered peaks of paused Pol II on both the sense and antisense strands close to the transcription start site in CpG-associated promoters. Lis pointed out that the function of the antisense polymerase remains unclear, but it presumably acts by regulating transcription orientation and efficiency. He also explained why the presence of paused polymerase is interesting for us developmental biologists: The comparison of the Pol II profiles in ES cells and MEFs revealed that many genes differ in their Pol II state in the two cell types.

Bob Kingston (Harvard Medical School, USA) discussed how Polycomb Group (PcG) genes are involved in regulating the changes in Hox gene expression during differentiation of human ES cells. They identified a region between HOXD11 and HOXD12 (“D11.12”), which is H3K27 methylated, occupied by PcG proteins, and shows changes in nucleosome occupancy upon differentiation. Such an arrangement is characteristic of Drosophila Polycomb response elements (PREs), cis-regulatory sequences required for PcG mediated repression. In a series of experiments they could show that specific sequences in this region are required for PcG-mediated repressive activity of a D11.12 reporter, and that this repression was maintained during differention, thereby identifying the first PRE-like element in a mammalian system. Furthermore, the endogenous D11.12 locus is dynamically occupied by PcG proteins in differentiating hESCs. Whether or not this region is required for embryonic development remains to be determined.

Peter Fraser (The Babraham Institute, Cambridge, UK) showed us what transcriptional regulation looks like in the nucleus: He presented his team’s work on intra- and interchromosomal interactions during transcription. In mouse erythroid cells, they encountered sub-nuclear foci highly enriched in active RNA Pol II, so-called “Pol II factories”. Transcriptionally active genes up-regulated by the transcription factor Klf1 in the definitive erythroid lineage, were predominantly present in the same foci, together with large amounts of Klf1 protein. They found that Klf1 is required for this clustering of co-regulated genes. Fraser’s work encourages us to refrain from thinking of transcriptional regulation as a linear phenomenon, but we should rather start imagining the process in its 3-dimensional spatial, nuclear context, in which specific transcription factories cluster regulatory proteins and their co-regulated targets, to optimize the coordination of transcriptional control. These factories preferentially transcribe a specific network of genes and might be a major factor underlying tissue-specific chromosome organization.

More about the discussion of transcription factor networks as it took place in this meeting will follow in part two.

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There are many ways to write a collaborative research article, review, grant or conference proposal. One of the most comfortable frameworks when there are more than two of you actually doing the writing, and especially if you’re scattered on different continents, is Google Docs.

Documents in progress such as your article text, abstract, cover letter to the editor and your figure legends, are uploaded in a confidential manner. One single, centralized version can then be modified in real time by anyone you invite, confidentially, to edit it. The online editor greatly resembles Microsoft Word or OpenOffice, and like the latter, is completely free of charge. Unlike OpenOffice, it doesn’t reside in your own computer, though. The major advantage is not having to merge versions, when your slowest collaborator gets back to you with revisions to version 6 and you are already on versions 10 and 11 with your more responsive team members.

The instigator of the article or grant application would do best to set up a Google account, if they do not already have one because they use Gmail, or Google Reader for their RSS feeds. (If you don’t know what an RSS feed is, never fear, watch this space in the future. RSS feeds are not immediately necessary for writing an article, except when you want to be sure that you are including the absolutely latest relevant primary source articles. We’ll show you how.)

A similar mechanism exists for multiple people working on spreadsheets (for your phenotype tables or five-year budgets), and it is now also possible to make drawings in this centralized, updated-in-real-time way. I have yet to try this possibility. However, Google Docs also accepts as an upload any sort of document – presentations, PDFs, images – that can subsequently be downloaded and examined by all your collaborators from this one centralized source. It’s already an advantage, and I’m certain it will get better and better.

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(Originally published in Development)

In February 2010, in the beautiful setting of Wiston House, nestled at the foot of the hilly South Downs in Sussex, UK, The Company of Biologists, the not-for-profit organisation that publishes Development, held the inaugural meeting of their new workshop series dedicated to biological research. The meeting was titled ‘Neural Stem Cells in Development and Disease’, and was organised by Kate Storey, Professor of Neural Development at the College of Life Sciences of the University of Dundee, and Silvia Marino, Professor of Neuropathology at Barts and The London School of Medicine and Dentistry. They were also assisted by the workshop chairman, François Guillemot, Programme Leader of the Division of Molecular Neurobiology at the National Institute for Medical Research in London. The scientific scope and themes of this workshop are covered in more detail in a meeting review published in Development but, to get a glimpse behind the scenes, we talked to Kate Storey and Silvia Marino and asked them about the organisation of the ‘Neural Stem Cells in Development and Disease’ workshop.

Silvia Marino (left) and Kate Storey (right) with workshop chair François Guillemot.

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When we did a survey among attendees of the British Society for Development Biology meeting in April, we asked what topics you would like to discuss on the Node. One of the top answers was careers, so we’ll be sure to include posts about opportunities in developmental biology, and we hope you’ll join us to share some of your stories and tips, or let us know if your lab is hiring.

To start you off, here is an uplifting story about an unconventional entry into a developmental biology career.

Earlier this month, the Carnegie Institution for Science in Baltimore awarded one of their staff members, Dianne Williams, with the Carnegie Service to Science Award. Dianne joined the institute in 1983, not as a research student, but as a lab dishwasher as part of a work program for inner city youth. She then started preparing fly food for Allan Spradling’s lab, and learned about Drosophila maintenance and molecular biology. While working during the day, she attended Johns Hopkins University at night and eventually earned her MSc degree, publishing her graduate work in a first-author paper in PNAS. After that, she continued to work as a technician in the Spradling lab, and produced an antibody against the germline protein Vasa that is currently used by researchers around the world.

It’s certainly not the most straightforward route to a career in the lab, and Dianne must have put a lot of effort and energy into studying biology at night after already working in a lab all day. But it does show that there is more than one way to the bench.

How did you end up in biology? And what do you hope to do next?

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Earlier this month, Shinya Yamanaka, of the Gladstone Institute of Cardiovascular Disease in San Francisco, won the March of Dimes Prize in Developmental Biology for his groundbreaking work on induced pluripotent stem cells (iPS cells). Yamanaka was the first to generate iPS cells from somatic cells – first from mouse fibroblasts and later from human fibroblasts – showing that it was possible to create pluripotent cells without relying solely on embryonic stem cells. He received his award on May 3 at the Fairmont Pacific Rim Hotel in Vancouver.

The March of Dimes Prize, worth $250,000, has been awarded since 1996 to developmental biologists whose work contributes to the prevention and treatment of birth defects and other diseases. Five of the past recipients have gone on to win Nobel Prizes.

Here is a video about the award, showing past winners (until 2007)

(image from Wikimedia commons)

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At the Node we welcome reports from scientific meetings, but only if the meeting organizers and speakers allow it. I’m currently writing the Node’s guidelines for meeting reports, and then realized I could fill an entire post with additional information and links. Unlike the guidelines, anything in this post is very general advice and not Node-specific.

First, find out if the meeting organizers have outlined a specific media or reporting policy. It varies a lot between meetings, and what is fine for one type of conference is absolutely not okay for another. For example, you are not allowed to report on any of the presentations at a Gordon Research Conference. They’re very explicit about this policy, and you should respect that. At the the other end of the spectrum is the Society for Neuroscience, who encouraged bloggers to write about their 2009 conference, and even selected a group of official “Neurobloggers”.
Most meetings will have a reporting policy in between these two extremes, and if they put their policy on their website, it usually tells you to ask for permission. CSHL updated their reporting policy in 2009 to include bloggers, and requires you to ask permission from the presenters before you write about them or their research. They also ask you to let them know whenever you intend to blog from or about one of their meetings. Keystone Symposia’s policy is very similar, and also asks you to ask permission from the speaker before blogging about their presentations.

What if there are no guidelines published? To avoid catching speakers and organizers by surprise, e-mail the meeting organizers to let them know you want to write about the meeting, and suggest that you will ask permission from each speaker individually before mentioning any scientific content. If the meeting organizer says that you’re not allowed to blog anything from the meeting, don’t do it. If they give you permission, save that correspondence in case you get into an unexpected conflict later. (This is why e-mail is better than asking in person!) The speakers’ e-mail addresses will usually be in the program booklet. Once you have decided that you liked a talk so much that you want to write about it, drop them a line. They might want to see your blog post before you upload it, or want to know where to find it.

If you haven’t asked for permission, or haven’t received it, you can still write a little bit about the meeting, but only as much as is already publicly available. This means that if a meeting organizer only publishes the name of the conference and the location, you can’t even mention the names of people who were there without their consent. If the entire program and all the poster abstracts are publicly available, you can include the names of speakers and the general topic of their talk or poster.

So why are conference organizers so strict about blogging? Aren’t the talks public knowledge now that the audience heard them? No!
The purpose of scientific conferences is not to tell the whole world about new research, but to update a group of other scientists about current projects. This means that a lot of unpublished data are shown; data that still need to be published in a journal. Most journals will not publish data that have previously been published elsewhere, and that includes results mentioned on a blog. To put it very bluntly: A blog post that contains unpublished data has the potential to ruin someone’s career.

A lot of journals do publish official meeting reports, but these are sent to the speakers before it’s published. When speakers see a draft of the meeting report that includes a little too much detail about their work, they ask the author to remove it. If you write about a talk on your blog, speakers have no such control over it. Organizers and speakers may still contact you after you publish the blog post, and ask for it to be removed. Please do so if they ask.

To summarize: if you want to blog about a meeting, make sure you have permission from the organizers and speakers, or only mention as much as is already publicly available.

(Photo by Eva Amsen. Taken at Science Online London 2009 – a conference that explicitly encouraged participants to blog about the talks.)

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Earlier this year, Cold Spring Harbor Asia opened a new conference centre in Suzhou, China. Located near Shanghai, the conference centre gives the research community in Asia an international conference centre close to home.

The Cold Spring Harbor Asia conference centre lobby reflects Chinese design. (Image used with permission)

After the opening ceremony on April 6, the new conference centre was host to two back-to-back meetings: the “James Watson Symposium on Cancer” and the ‘Francis Crick Symposium on Neuroscience”.

The September schedule looks especially appealing for developmental biologists, with “Human Genetics and Genomics” from September 6 to 10, and “Molecular Switches and Genome Function in Stem Cells & Development” from September 21 to 25.

I’m curious to see how the presence of the conference centre will affect research in Asia in the long term. If you’re attending one of the conferences at the new location, why not drop by the Node to tell us what you think!

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(Interview by Kathryn Senior. Originally published in Development)

Stephen Wilson is Professor of Developmental Genetics at University College, London, UK. He was recently awarded the Remedios Caro Almela Prize for Research in Developmental Neurobiology. We interviewed Steve to find out about how he started on the road to developmental biology research, how he got interested in the brain, his achievements and future challenges.

What originally set you on the road towards a career in science?

I dropped biology at school and was all set to study metallurgy at University for no good reason at all. Luckily I realized this just before starting. The fact that the course was entirely populated by male students helped my decision-making… I took a year off, worked in a school lab and realized that I loved biology – that was the start.

You have chosen to focus on the most complex organ – the brain – what prompted that choice?

I went to Steve Easter’s lab as a post-doc to work on the developing eye and retino-tectal projection. You might say it was serendipity but the first time I tried to label retinal axons, I stuck the needle through the back of the eye and into the brain. I labelled lots of neurons that were not supposed to be there. My time as a post-doc was spent trying to find out more about these very early forebrain neurons – I’m still on the same mission.

What is the most frustrating challenge that you have had in your research and how did you tackle it?

Perhaps ‘frustrating’ is not the right adjective but a challenge that taught me a lot arose during my time as a post-doc. My closest friend at the time (with whom I shared an apartment) was working on essentially the same project as me but in a competing, neighbouring lab. This was quite a challenge for us to cope with. We both learned that friendship is far more important than the transient troubles one faces in the lab – most of which resolve and fade from memory in a few months.

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From April 12 to 15, the British Societies for Cell Biology and Developmental Biology are holding a joint meeting in Warwick. The program is full of interesting talks: Always two at the same time, making it hard to choose what to listen to.

Personally, I’m excited about this event because it is the first time I get to show people the Node! We’re projecting the Node on screen at our booth, and I’ll be walking around in between the talks to show people how to use the site. I hope we get lots of feedback and enthusiastic contributors!

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In February 2010, The Company of Biologists (which publishes Development and hosts the Node) organized the first of a series of workshops. The theme of the workshop was “Neural Stem Cells in Development and Disease”, and was attended by a variety of researchers: some work on the role of neural stem cells in development, while others studied disease models. The workshop was unique in bringing together scientists from these different areas.
In a few weeks, we’ll post an interview with the organizers of this workshop, so you’ll hear more about it. For now, here’s a group shot of all the participants

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