The Metazoa, our corner of the great assemblage of life, is a curious and fascinating topic, but one that is relatively obscure in these days when a great many of the scientists studying animals are concerned with them as biomedical model systems. ‘The Animal Kingdom: A Very Short Introduction’ goes a long way to illuminating this relative obscurity, and is likely to become an excellent first point of call for undergraduate and graduate students of evolutionary-developmental biology (‘evo-devo’). It will also make for a fascinating read for biomedical scientists who are fed up of their evolutionarily-minded colleagues lecturing them about how fascinating velvet worms (Phylum: Onycophora) are.

Animals come in a huge variety of sizes and forms and their interrelationships have been the subject of often very heated debate since the 19^th century. The coming of the age of molecular biology has revolutionised these debates by enabling zoologists to infer evolutionary relationships by comparing DNA and protein sequences; they no longer have to rely on the vagaries of morphological comparisons. This has lead to a number of significant revisions. Previously well-established groups such as ‘Articulata’, which united segmented invertebrates such as insects and earthworms, have been shown to be artefacts of convergent evolution or widespread character loss. As with all revolutions, there have been dissenting voices (tales of warring academics who wouldn’t set foot in the same lecture theatre as one another are not unknown). However, as the sophistication of molecular phylogenetic techniques has advanced, and datasets have grown exponentially owing to the power of next-generation sequencing (people talk only of phylogenomics these days), a consensus of the animal phylogeny has been arrived at. Of course, the arrangement of many groups is still unresolved and problems remain, but the broad brush strokes of animal evolution are agreed upon: the family tree of the 30-odd animal phyla (Prof. Holland recognises 33 in his book) is largely established. As a guide not only to the diversity of animals, but also to their evolution ‘The Animal Kingdom: A Very Short Introduction’ thus comes at a very timely juncture.

Prof. Holland’s book takes readers on a tour of the Metazoa using an evolutionary framework. After discussing the issue of what an animal is, and then addressing the much thornier one of how to organise our thinking about them phylogenetically, the book discusses each of the prominent groups. Firstly dealing with the basal animals that do not possess bilateral symmetry (sponges, jellyfish and the like), and then taking each major group of Bilateria in turn, the book provides a lucidly written guide to the diversity of animal form and how it is generated during development. As such, it is an excellent introductory evo-devo text.

For old hands, the description of the molecular revolution of the 1980s and the discovery of the ‘developmental toolkit’ is particularly entertaining. Capturing the excitement at the discovery of the homeobox sequence is a difficult thing to do in 2012, when it is possible to sequence a human genome in 15 minutes. But it’s worth the money on its own. I heartily recommend it.

(8 votes)

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Progress in understanding how cells interpret their genome has gathered significant momentum in recent years. Of course, the (now historical) catalyst to this was the entry into the genomic age, marked most obviously by the sequencing of the human genome. However, it is the genome-wide application of novel techniques for understanding how this genome is interpreted that has begun to unlock its secrets. In 2007, the international ENCODE consortium reported its initial attempts to annotate, in exhaustive detail, the best understood 1% of the human genome (ENCODE Project Consortium, 2007). The application of such genome-wide efforts to the leading invertebrate model species, Caenorhabditis elegans and Drosophila melanogaster, was published earlier this year (modENCODE Consortium, 2010a, b).

Much has come out of these gargantuan efforts, but one of the most prominent conclusions has been that general speaking, the genome is pervasively transcribed. A whole universe of RNA molecules exist inside cells, and while the extent to which they are functional remains a subject of much debate, it is clear that understanding this universe will yield fundamental insights into cellular, and developmental biology. Against this backdrop, recent work outlining the positive gene regulatory roles of particular populations of non-coding RNAs (ncRNAs) constitute hugely important discoveries. They build upon a landmark study, published in 2009 (Guttman et al. 2009), that for the first time systematically identified a population (~1600) of long multi-exonic ncRNAs in four murine cell lines. Correlative analysis with existing and novel expression datasets suggested putative functions for numerous distinct sets of lincRNAs. At the other end of the size scale, short (<2kb) RNAs, termed enhancer RNAs (eRNAs) have recently been shown to be transcribed from active enhancers in a neuronal cell culture system (Kim et al. 2010). Both of these findings give meaning to the pervasive transcription observed in the ENCODE and MODENCODE studies, but they don’t address the function of such RNA species. Do the RNAs themselves act to govern transcription or cell behaviour, or is it merely the act of transcribing them that is important, perhaps to re-model the local chromatin environment?

This conundrum has begun to be resolved, at least for longer species of ncRNAs, in the last two years. Two papers, one using differentiated cell lines (Ørom et al. 2010), and one in reference to ES cell biology, again from Eric Lander’s group (Guttman et al. 2011), have unequivocally demonstrated the functional importance of ncRNA species themselves. In the first, after using the ENCODE annotations to identify a population of 3019 putative long ncRNAs, a combination of reporter siRNA-mediated knockdown and expression analysis was able to show that the knockdown of particular ncRNAs were in seven cases able to decrease the expression of neighbouring genes, implicating the RNAs as positive regulators of a diversity of developmental processes. In the second study, building on their data set of lincRNAs (Guttman et al. 2009), the authors have demonstrated using short hairpin RNAs that dozens of lincRNAs are fundamental players in promoting and controlling the gene regulatory networks that govern both pluripotency, and differentiation into a range of different lineages. Further, they show that many lincRNAs specifically interact with chromatin regulatory proteins, and present a model that fully integrates ncRNAs into gene regulatory programmes that control cell fate.

Thus, extensive evidence now exists that implicates ncRNAs both in cis and in trans as fundamental controllers of all aspects of cell biology. The implications of such work will be felt across cell and developmental biology. As important as the findings themselves though, has been the illustration that integrating a diversity of epigenetic, comparative genomic and next generation sequencing approaches is capable of revolutionizing our understanding of how phenotype derives from genotype. The stage is set for application of these approaches over the coming years to develop from cell lines to developmental contexts. ncRNAs of all flavours are likely to be of fundamental, and as yet underappreciated, importance.

References

ENCODE Project Consortium (2007) Nature 447: 799-816.

Guttman M et al. (2009) Nature 458: 223 – 227.

Guttman M et al. (2011) Nature 477: 295 – 300.

Kim TK et al. (2010) Nature 465: 182 – 187.

modENCODE Consortium (2010a) Science 330: 1775-1787.

modENCODE Consortium (2010b) Science 330: 1787-1797.

Ørom UA et al. (2010) Cell 143: 46-58.

(5 votes)

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Book Info:  Developmental Biology: A Very Short Introduction by Lewis Wolpert. Aug 2011. 152 pages. ISBN: 9780199601196 (Paperback) Price: $11.95 /£7.99

The very first sentence Lewis Wolpert writes in Developmental Biology: A Very Short Introduction communicates the sense of wonder that seeps amongst developmental biologists: “that we develop from a single cell, the fertilized egg, just one tenth of a millimeter in diameter—smaller than full stop—is amazing. That egg has all the information to develop into a human being.”

And with this sentence begins a marvelous journey into the world of life. Wolpert navigates effortlessly in the complexities of the flowering of life to eloquently synthesise the process of development. From the cell to the embryo to the fetus, Wolpert fabulously explains the process through which life sprouts and develops into a mature organism. Make no mistake though, this book is no popular science. It is very much an academic look into the field of developmental biology.

But what makes this book so different from the developmental biology volumes on library shelves is obviously its size. At 152 pages, it makes up for a quick read and is a good book to carry around if you are new to the field. Major concepts are concisely explained and the illustrations are sometimes all you need to understand what’s going on (I mean what better way to understand the development of genitalia in humans than a diagram).

For an academic book, Developmental Biology: A Very Short Introduction is refreshingly refreshing! Why? Because Wolpert is not only interested in explaining concepts here and there. Instead, he wants to provide readers with an overall and complete view of developmental biology. He wants us to see how the different concepts, mechanisms, processes intertwine with one another to culminate into incredibly sophisticated vertebrates, invertebrates and plants. He explains, synthesises and ultimately frames everything into the bigger picture. Not only is this style exciting and makes for a better read but it also makes for better understanding because Wolpert always tells you where he is going. Wolpert even asks some atypical questions. For example, can an embryo be considered a human? Or is DNA really the blueprint of life?

However the book does not come without its headaches—literally. I got headaches while reading the book for two very different reasons. Firstly, the book does not shy away from jargons (it is after all an academic book) and it’s hard to keep up. Although jargons are dutifully explained, they keep cropping up again and again until eventually my brain became impermeable to them new rather complicated words. Secondly and perhaps more disappointingly: the book has a pungent ammonia smell which gives those old tabloid newspapers a run for their money. Oxford University Press (the publisher) really does a disservice to this wonderful text which is a big shame.

Nonetheless this book remains a must-read for anyone who wants to understand the development of life. Just make sure that you have a couple of aspirins by your side when you read this book.

(5 votes)

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The Society for Developmental Biology (SDB) has partnered with Wiley-Blackwell to publish a new web-based encyclopedic resource for developmental biologists—WIREs Developmental Biology­.  This collection of invited peer-reviewed review articles encompasses the vast field of developmental biology with content chosen by an expert team of editors.  It is an online-only publication open to all for its first two years of publication and thereafter to subscribers and SDB members.

The Editors-in-Chief are three outstanding developmental biologists: John C. Gerhart (University of California, Berkeley), Gail R. Martin (University of California, San Francisco), and Eric F. Wieschaus (Princeton University).

In an announcement in the Winter 2012 issue of SDB e-news, Gerhart said, “WIREs Developmental Biology offers a dynamic and integrated approach to its encyclopedic coverage of the field exposing the interconnectivity of developmental processes.”  Describing the projects origins he said, “This venture grew from conversations held in the Society [SDB] well over a decade ago regarding the need for an authoritative discipline-encompassing publication” that was “updateable and interactive.”

WIREs articles can be browsed either by topic or issue. The WIREs model takes advantage of the web platform with embedded links within articles out to scientific databases and other relevant sites.  Additionally, under the “Resources” tab readers can find further reading, videos, and links to our companion learning resources at SDB CoRe (see Node article here).  As the field grows, content will continue to be expanded and existing articles updated.  There are also opportunities for community interaction through article comments.

Go ahead and dive into the content at WIREs Developmental Biology. Patterning, organogenesis, stem cells, and evolution are just a few of the topics.   A range of organisms are represented including plants, worms, frogs, flies, and even humans.  Take advantage of this new encyclopedic resource for your teaching needs and your own enrichment in the field of developmental biology.

(6 votes)

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Building on the success of last year’s event, ECD 2012, which will take palce on 12-15 October 2012, will bring together scientists from the fields of epigenomics, genetics and bioinformatics to discuss the latest developments in this fast-moving field. The meeting will discuss recent advances focusing on genome-wide approaches that are revolutionizing the field.

Scientific organising committee:
Stephan Beck, University College London, UK
Susan Clark, The Garvan Institute of Medical Research, Australia
Andy Feinberg, Johns Hopkins University School of Medicine, USA
Anne Ferguson-Smith, University of Cambridge, UK

Venue: Johns Hopkins University Baltimore, MD, USA

Date: 12-15 October 2012

https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=298

Further information on this Wellcome Trust Scientific Conference, and a list of invited speakers, will be available soon. To be kept updated, please contact us at scientificconferences@hinxton.wellcome.ac.uk.

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Even with an extra day, February is always over before you know it. Nevertheless, a lot of interesting content appeared on the Node in this short month. Have a look at some of these highlights:

Resources

Michael Barresi shared an educational approach he’s been using in the undergraduate developmental biology course he teaches:

“My students have been interacting with leading scientists in the field of developmental biology holding organized Q&A video conferences focused on current and seminal research articles. I am posting this to the Node as since I started using this pedagogical approach I have been recording these discussions, and with full consent provided, I have established an online repository of these recordings via my lab website.”

The videos are all on his site, and you can find out more in his post on the Node.

Earlier this month, Nishal Patel posted a list of freeware for scientists, highlighting several free tools that can be very useful in the lab, such as Dropbox for accessing files from different computers, Doodle for scheduling meeting, or OMERO for managing microscope images. See his full list here.

Research

Tracy Chong described her work on the hermaphroditic reproductive system of planarians, and the long journey the animals made from Sardinia to her final published BMC Developmental Biology paper.

Victoria Hatch discussed an interesting Nature paper that suggests a correlation between blood-borne factors and neurogenic decline in mice.

Erin Campbell’s monthly image feature this time focused on neuron precursor cell divisions and cerebral cortex development, from a recent Development paper.

Jobs and careers

Natascha Bushati interviewed Andrea Hutterer about her career in science management. She shares how it can be difficult to move from research to a career away from the bench:

“My scientific CV was good, but I had virtually no other relevant experience. Many employers appreciate even the smallest amount of experience more than a fantastic scientific CV, so what you really need when coming out of a PhD or postdoc is to get a foot in the door.”

If you’d rather stay in research, you’re in luck: a new postdoc position at Thomas Jefferson University was posted on the Node a few days ago. Remember, if you’re looking for a developmental biologist to join your lab, you can easily add your own job posting if you have a Node account. And if you’re looking for a job, you can subscribe to the job-specific RSS feed.

Meetings and courses

Some meetings and courses were announced on the Node front page (including the chick meeting that was rescheduled after last year’s earthquake in Japan), but as usual, keep an eye on the events calendar and see what’s coming up.

Once you’ve registered to attend a conference, take a look at these tips from the GSA to make sure you get the most out of it. And when you come back, you write about the meeting on the Node, like Katherine Brown did at the EuroSyStem conference in Slovenia.

Finally, at the end of last month, Ger Sabio wrote a detailed post about the International Course on Developmental Biology in Chile:

“For me, all of the faculty of the course were extremely good professors: Their lectures were very clear and they were all very open to questions or doubts and were very watchful and helpful in the lab. Eric [Wieschaus], however, was something else. I can’t actually explain how or why, but, as an example, he took it upon himself to single handedly sharpen most of our pincers to ease embryo peeling and larval dissection!”

(1 votes)

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4^th Young Embryologist Meeting

Friday 1^st June 2012

UCL Institute of Child Health, London

Registration and Abstract Submission NOW OPEN (until March 31st)

The 4^th Young Embryologist Meeting (YEM:2012) will take place on the 1^st of June 2012 in the Kennedy Lecture Theatre at UCL’s Institute of Child Health, London. It will be a full day event from 10am to 5pm.

At the annual YEM, we aim to facilitate the discussion of various topics of developmental biology in a relaxed and cordial atmosphere. YEM:2012 is free and open to everyone, though preference is given to PhD students and post-docs for talks and posters. This year, we are pleased to welcome Professor Liz Robertson (Sir William Dunn School of Pathology, University of Oxford) as our keynote speaker. We will also have a Q&A Session about publishing, with Katherine Brown (Executive Editor of Development), Katie Ridd (Senior Editor of Nature Communications), and David Wilkinson (Editor in Chief of Mechanisms of Development) as panel members.

Registration and abstract submission close on 31^st March 2012. To find out more about the meeting, to register, or to submit an abstract for a talk or poster, please visit the Young Embryologist Network website:

www.youngembryologist.org

If you would like to get more out of your research and meet your fellow researchers, join the YEN! Sign up to our mailing list for updates on future events by emailing: youngembryologistnetwork@gmail.com

Join the YEN Facebook group or follow YEN on Twitter @YEN_Tweets

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(1 votes)

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In these times of financial instability and prudence, researchers across the globe seem to be finding things tough. Here in Japan fiscal worries are abundant, particularly following the disastrous earthquake and tsunami of 2011. Government debt is spiralling and tax rises seem imminent, but what consequence will this all have on research funding?
It seems the axe may be about to fall; in what amounts to a cost-cutting exercise, government advisors have recommended the amalgamation of the 5 main science-funding bodies. These include the prestigious RIKEN organisation, which has a diverse portfolio of research institutes, including several covering the life-sciences, such the Center for Developmental Biology (CDB) in Kobe. RIKEN president Ryoji Noyori has informed research staff that the organisation would continue in its attempts to develop into a world-class research institution, but hinted at a new focus on “needs-based” science. It seems likely that basic science research may take a hit, although the plans won’t come into effect until 2014.
In a related development, public sector workers across Japan may soon see pay cuts of up to 7.8% for the next 2 years; money directly earmarked for tsunami-related reconstruction projects. These cuts could also affect researchers working in publicly funded institutions.

It all sounds a bit bleak, but there are still excellent opportunities for researchers to work in Japan:

RIKEN CDB is on the lookout for aspiring PIs.

For Postdocs interested in joining a lab at a RIKEN institute, the Foreign Postdoctoral Fellowship is a great source of funding.

JSPS also offers attractive (tax free) fellowships for long and short-term stays.

(3 votes)

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Summary
This popular course is a collaboration between MRC Harwell, the Leeds Institute of Molecular Medicine, the RSPCA Transgenic Training Working Group (TTWG) and the Wellcome Trust Sanger Institute. It aims to introduce experienced technicians and scientific staff involved with the management of GM mouse colonies to best practice with respect to the 3Rs and animal welfare. The programme covers historical and current best practice in the maintenance of GM mouse colonies for scientific research and the differing disciplines involved in production, phenotyping and archiving.

Please Note: To optimise discussion and interaction between participants and trainers, places on this course are limited and selection will be based upon information provided. An application form must be included as part of the registration process. Please see below for full details.

Programme
Topics covered will include:
– Nomenclature
– Basic colony management
– Maintaining transgenic and gene-targeted lines
– Breeding for experimental purposes
– Maintenance of high health status colonies

All of these will be presented with particular attention to the 3Rs and animal welfare.

The course will start at 10:30 on Wednesday 6 June and finish at 16:30 on Friday 8 June 2012.

Scientific organisers
James Bussell Wellcome Trust Sanger Institute, UK
Neil Dear Leeds Institute of Molecular Medicine, UK
Nikki Osborne RSPCA, UK
Sara Wells Medical Research Council, Harwell, UK

Keynote speakers
Karen Steel Wellcome Trust Sanger Institute, UK
Ian Jackson Medical Research Council Human Genetics Unit, UK

Confirmed tutors
James Bussell Wellcome Trust Sanger Institute, UK
Neil Dear Leeds Institute of Molecular Medicine, UK
Adrian Deeny University College London, UK
Martin Fray Medical Research Council, Harwell, UK
Richard Houghton Wellcome Trust Sanger Institute, UK
Nikki Osborne RSPCA, UK
Ian Rosewell, Cancer Research UK
Sara Wells Medical Research Council, Harwell, UK
Jacqui White Wellcome Trust Sanger Institute, UK
Ben Woodman Leeds Institute of Molecular Medicine, UK

For more information, see https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=287

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The Genetics Society of America has published a very useful list of tips for first time conference attendees, called “How to Get the Most Out of a Conference“. It’s written with GSA conferences in mind, but it’s applicable to most big meetings, and useful for returning attendees as well! Reposted with permission. Original list on the GSA site.

How to Get the Most Out of a Conference:
Tips for First-Time Attendees

Before the Meeting

Plan ahead: Look through the Program Book or the schedule of events online to determine which sessions you are interested in based on the topic, speaker, and format. If the conference has an online itinerary planner, take advantage of it to search abstracts, save sessions you are interested in, and print out an agenda for yourself. If full abstracts are only available online, think about printing those that you might want a hard copy of while at the conference.

Set your goals: Many conferences can seem overwhelmingly busy. If you’re wondering how to navigate the many sessions, consider focusing on a few topics that interest you instead of trying to hear everything. Remember to schedule some time in between sessions for talking to speakers or even just the person sitting next to you. If you are seeking a postdoctoral position or other employment, be sure to bring a few copies of your CV with you.

Networking: Ask your advisor which researchers you should meet and who might be interested in your work.

Prepare short introductions of yourself, your research, and your plans for the future. It’s helpful to have both a 10-second and a 30-second introduction, so you’ll be prepared when you bump into the right person on the elevator or at a reception.

Business cards: Bring a big stack of business cards. You never want to have to scribble your name on a scrap at paper for your next collaborator or mentor. If you don’t already have then, you can order from an office supply store or print them yourself with card stock designed for this purpose. Be sure to include at least your name, contact information, and school/institution—and possibly a one-line description of your research topic or professional interest.

At the Meeting

Attend sessions and trainee events: Use your planned agenda as a guide, but don’t be afraid to try something new. Attend a talk that is in not your own field or check out posters you may know nothing about. You may discover new ideas or collaborators where you least expect them.

Networking: When you are not attending sessions, don’t miss the opportunity to catch up with your colleagues and meet new people. Don’t be afraid to talk to strangers. Arrive a little early at sessions and sit next to someone you don’t know and introduce yourself. People love to talk about their work, so asking them what they do is a great conversation starter. If you’d like to know this person better, give him/her your business card. Also, collect cards from those you meet and follow up with them later in the meeting or after you’re home. A good place to keep business cards is in your badge holder. If you have promised to send them something after the meeting, make a note of it on their card and remember to do so.

After the Meeting

Take time to reflect: Did you meet your goals? It is helpful to write a summary of your experience for your personal records. You can include descriptions of sessions that interested you, ideas that came up, and who you met.

Complete the Survey: Most meeting planners will email an end-of-conference survey; your feedback is the best tool that conference organizers have to make improvements for the future. If there’s something you especially liked or wish had been different, let them know. If you get an e-mail with a link to a post-conference survey, please respond promptly.

Follow up: Send a follow-up email as soon as possible after the conference to anyone with whom you would like to stay in contact. If there were sessions that interested you and that you missed, contact the speakers by e-mail and request copies of their slides.

(3 votes)

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