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Literary Paper Openings

the Node — Fri, 24 May 2013 09:40:45 +0000

What would a paper be like if it started with the opening line of a famous book? Since yesterday Twitter has been buzzing with answers to that question! We have storified some of the tweets below, but the discussion is still up and running, so why not follow the hashtag #LiteraryPaperOpenings?

Woods Hole Images Round 2- the winner

the Node — Tue, 21 May 2013 15:12:32 +0000

The polls have closed for the second round of beautiful images from last year’s Woods Hole course. Making an unexpected dash to victory in the last hours of voting, the two-headed regenerated planaria is the winner of this round!

This picture was taken by Chang Liu of the Shanghai Institute of Biochemistry and Cell Biology. It shows a regenerated Dugesia sanchezi planarian immunostained for acetylated tubulin (green) and phospho-histone-H3 (dividing cells, purple).

The runners-up to this competition were an image of a slipper limpet larva by Joyce Pieretti (University of Chicago), Manuela Truebano (Plymouth University), Saori Tani (Kobe University) and Daniela Di Bella (Fundacion Instituto Leloir); the embryo of a dwarf cuttlefish by Maggie Rigney (University of Texas, Austin) and Nipam Patel (University of California); and a Longfin inshore squid by Wang Chi Lau (Chinese University of Hong Kong).

Look out for this winning image in the cover of a coming issue of Development, and stay tuned for round 3 of the Woods Hole image competition!

San Francisco Declaration on Research Assessment

Katherine Brown — Fri, 17 May 2013 10:43:11 +0000

In December last year, a group of editors and publishers, including editors from our sister journal Journal of Cell Science, got together at the annual ASCB meeting to discuss ways in which we could improve the way in which scientific output is evaluated. There is much discontent in the community with the all-pervasive importance of the Impact Factor, and this meeting looked at how we might find a more balanced way to assess individual researchers and their work.

Today, the results of this discussion are being made public, with the release of the “San Francisco Declaration on Research Assessment” website, and accompanying editorials in Science, eLife and other journals. As initial signatories to the Declaration, The Company of Biologists and its journals fully support, and comply with, the proposals for Publishers stated in the Declaration - look out for more information on this in an upcoming editorial in Development.

I’d encourage you to read the Declaration, and - if you agree with its principles - to sign it. In my personal opinion, reflected in what I frequently hear from members of the community, the prevalent use of the Impact Factor as a mechanism to judge a scientist’s worth (and hence future job prospects) isn’t healthy. I also think that developmental biologists may suffer more than some in other fields: the very nature of our work often makes for long-term projects, and so the two-year window of the Impact Factor does not reflect the speed of our field. So I hope that this Declaration will help to change the culture of research assessment, and to ensure that research and the researchers behind it are assessed on their individual merits and not on the number associated with the journal in which they happen to have published.

We’d love to hear your thoughts on this Declaration, so please comment below if you’ve got anything you’d like to discuss with the journal and with the developmental biology community at large.

From Sequence to Function

CMDooley — Fri, 17 May 2013 09:38:35 +0000

It took longer than the human genome, if by only a few years, but it has finally arrived. The sequencing of the zebrafish (Danio rerio) genome reported in Howe et al. is one of two zebrafish publications to recently appear in the journal Nature. The second article, Kettleborough et al., makes use of this high quality genome sequence and not only creates the tools required for the functional annotation of all zebrafish protein coding genes, but describes the active pursuit of this goal.

About a decade ago, when the human genome was first published, there was a lot of hope and expectations that this would lead to an immediate advance in the treatment of many diseases and the understanding of ourselves. As these things often are, it turned out there is a lot more to understanding our genomes than just the decoding of a reference sequence. Now with the zebrafish genome in hand it is possible to see that 70% of human protein coding genes have a direct zebrafish ortholog. This at the same time represents 84% of all human genes with a disease association in OMIM. Although both vertebrate organisms it still remains striking, almost humbling at just how close we as humans are to our aquatic relatives. It will be the continuation of detailed investigations involving model organisms which will play a fundamental role in connecting genotype to phenotype.

It is exactly this similarity which forms the basis of Kettleborough et al.’s approach in actively knocking out all 26,000 zebrafish protein coding genes. We still do not understand the function of a large proportion of our own genes but by providing loss of function alleles as a resource to the greater community and also functionally annotating these alleles we will hopefully gain greater insight into our own genomes.

Investigating the phenotypic outcomes of these alleles is now well under way at the Wellcome Trust Sanger Institute. The phenotypic consequences within the first 5 days of development are evaluated and annotated as part of a multi-allelic phenotyping approach explained in detail in Dooley CM et al.

All alleles, availability, phenotyping information and much more is available at: http://www.sanger.ac.uk/Projects/D_rerio/zmp/ so stop by and have a look!

A Taste of Stem Cells

Kif Liakath-Ali — Thu, 16 May 2013 16:09:00 +0000

Continuous supply of mature differentiated cells by adult stem cells is required in most of adult tissues especially those with rapid turnover rates. In recent years, using advanced cell biological methods, many studies have uncovered homeostatic mechanisms that are driven by specific tissue resident stem cells. Mammalian lingual epithelium (tongue) always had been a focus for identifying diverse taste receptors, cells and their mechanism of action. However, stem cells for this high turnover tissue remained largely uncharacterized. In a recent study published in Nature Cell Biology, Tanaka et al., show how homeostasis and regeneration of lingual epithelium are maintained by distinct stem cell population.

Mammalian tongue is composed of taste buds and keratinized epithelial cells, the later providing rigidity for the organ. The authors of this study attempted to identify stem cells that generate these differentiated epithelial cells. They combine the knowledge of classical thymidine labeling studies and state-of-the-art multicolour cell lineage techniques. It has been proposed previously that the keratin 5/14 positive lingual epithelial cell population possesses characteristics of stem cells. Authors of this work proved that these cells were not a distinct population of cells that gives rise to differentiated cells, however the stem cells they have identified do express these markers. To identify the individual population origin of differentiated cells, they labeled cells with CreERT2-inducible multicolour fluorescent reporters (green, blue, orange, red). They identified few label retaining cells after 28 days at the interpapillary pit (IPP) of the lingual epithelium. To identify a specific marker within this small population of cells, they have crossed various stem cell marker-CreERT2 knock-in mice with the multicolour expressing rainbow mice and confirmed Bmi1 (Bmi1 polycomb ring finger oncogene) as a lingual stem cell marker! Previously, Bmi1 has been reported as intestinal stem cell marker. There is no obvious explanation on how they chose Bmi1 as a likely candidate (cherry pick?!). However, further experiments with RNA in-situ hybridization proved the highest expression of this gene in lingual epithelial stem cells. Taste bud cells were not labeled long-term in Bmi1^CreER/+/Rosa26^rbw/+ mice confirming that the Bmi1-positive cells identified are unipotent stem cells giving rise to keratinized epithelial cells.

Furthermore, to examine the regenerative capacity of Bmi1-positive stem cells, the authors injured the lingual epithelial cells with different doses of irradiation. Progeny of Bmi1-positive cells were detected on the surface of keratinized epithelial cells at day 7 after irradiation and regenerated the injured tissue. To analyze the regenerative ability in the absence of Bmi1-positive cells, they have effectively deleted Bmi1-positive cells by crossing Bmi1^CreER/+ mice with Rosa26^{loxp–stop–loxp–dta/+} mice. In this system, Tamoxifen induction of CreERT2 trigger the expression of Diphtheria toxin (DTA) which kills the cells. Removal of Bmi1-positive cells leads to decreased proliferation of basal cells, proving the hypothesis that the Bmi1-positive cells play a role in tissue regeneration.

The authors conclude that the Bmi1-positive cells are slow cycling long-term stem cells, giving a hint to hunt for rapid proliferating stem cell population in lingual epithelium, which is not identified yet. Also, further investigations on the role of Bmi1-positive cells in lingual origin of squamous cell carcinoma would allow targeting this gene for therapeutic interventions.

Tanaka T, et al., Identification of stem cells that maintain and regenerate lingual keratinized epithelial cells. Nature Cell Biology. 2013 May;15(5):511-8.

Enter the EuroStemCell non-fiction writing competition!

Emma Kemp — Wed, 15 May 2013 13:56:56 +0000

Spring has sprung! The sun is out at last (sort of), but that’s not the only great news we’ve got from EuroStemCell: we’ve launched our first ever stem cell non-fiction writing competition.

This is your chance tell a stem cell story with your imaginative science writing, by creating a comic or by writing a poem. And you could win 300 Euros and see your work live on eurostemcell.org.

Judges for the competition include CellStemCell Editor Debbie Sweet and well-known science fiction author Ken McLeod, amongst others.

Go on, give it a go! Full details at http://www.eurostemcell.org/stem-cell-competition

In other news from EuroStemCell, there’s lots of new material on our website:

an article from scientist Roger Barker on the truth about stem cell therapies for neurological disorders

a new fact sheet on stem cells and leukaemia

a commentary from social scientist Emma King on her experience of following the development of a regenerative medicine research project.

Our latest newsletter fills you in on this and more.

Sign up to receive our monthly e-newsletter at http://www.eurostemcell.org/newsletter. You can also keep in touch by following @eurostemcell on Twitter or liking us on Facebook. Your feedback is always very welcome - via these channels or use our website contact form to get in touch.

The Node new community manager!

Cat Vicente — Tue, 14 May 2013 12:44:49 +0000

Hi! My name is Cat and I am the new Community Manager here at The Node. I am originally from Portugal, but moved to the UK to study a long time ago (almost a decade!). Until very recently I was a PhD student at Jordan Raff’s lab in Oxford, using fruit flies to study how centrosomes are formed- so I like to think of myself as a cell biologist with a developmental twist! Although I had a great time in the lab, I eventually realized that I enjoyed much more interacting with scientists and hearing about their science than doing my own…

This is why I am so excited about my new position as The Node Community Manager- in its essence, The Node is a place to bring scientists (you!) together, to share ideas and opinions and the latest research. I want to play my part in facilitating that! Eva did an excellent job in setting up and developing The Node in the last three years, and that is a hard act to follow. Going forwards, I will do my best to continue making The Node the vibrant and dynamic community website that it is, and you’ll be hearing a lot more from me in the coming months. Meanwhile, please continue to contribute content and comments to The Node, and do not hesitate to contact me if you have any suggestions, questions or comments. You can drop me an email at thenode [at] biologists.com (or by clicking here) and please do say hello if you see me at a conference. I look forward to meeting you!

Disease Models & Mechanisms (DMM) announces new Editor-in-Chief and Senior Editors

Paraminder Dhillon — Thu, 25 Apr 2013 12:40:44 +0000

This week, Disease Models & Mechanisms (DMM) formally announced the appointment of a new team of academic editors to lead the journal. Ross Cagan, Associate Dean of the Graduate School for Biological Sciences at Mount Sinai Medical Center, succeeds Vivian Siegel as the Editor-in-Chief, and he is joined by Senior Editors Monica Justice, Professor of Molecular and Human Genetics at Baylor College of Medicine, and George Tidmarsh, Chief Executive Officer at La Jolla Pharmaceutical Company.

Ross, Monica and George describe their interest in and vision for DMM in an inaugural editorial published in the latest issue of the journal. “This is a challenging but also an exciting time for science”, they write. “Our tools are not only more powerful, their level of improvement itself is accelerating. Not surprisingly, we are now trying to imagine how these tools can be applied to disease. What we find remarkable is that the founders of DMM understood these trends years ago.”

Describing some of the obstacles to the translation of biological findings to clinical benefit, they continue: “Many of the failures we have seen in translating novel basic biological discoveries to useful medicines are a result of the inadequacies of the animal models we use at the critical juncture between bench and bedside”. To address these inadequacies and promote future drug development, the team aims to introduce new standards for the rigorous preclinical assessment of animal models of disease.

Another issue raised is the lack of reproducibility of scientific findings, which has been reported in several journals. The new editors argue that negative data can be as informative as positive data when exploring therapeutics, so aim to encourage the publication of useful negative results: “….we will help promote –through our publications – a change in the scientific culture responsible for the asymmetric publication of positive results”.

Vivian Siegel, Broad Institute of MIT and Harvard, has stepped down after four years as Editor-in-Chief. In her farewell editorial, she reflects on the changes that DMM has undergone since launch, including the move to become open-access and, recently, a change in Creative Commons license to further promote access and sharing.

“About a year and a half ago, I agreed to become the Director of Scientific Education and Public Communications at the Broad Institute of MIT and Harvard, and realized I would have limited time to devote to DMM, too little to give it what it needs to continue to grow” Vivian writes, explaining her decision to leave DMM. “I encouraged The Company of Biologists to identify academic editors instead of another professional editor to succeed me, as I felt that the journal had now reached an age where its lead editors should be researchers actively engaged in the work covered by the journal.”

DMM is an open-access biomedical journal that publishes research and reviews focusing on the use of model organisms to provide insight into disease mechanisms, diagnostics and therapeutics. Founded in 2008, the journal was the fourth to be launched by the Company of Biologists.

To find out more and access the latest issue of the journal, go to http://dmm.biologists.org/

Towards a staging series for dinosaur embryos?

Rachael Inglis — Fri, 19 Apr 2013 10:37:45 +0000

Last week, I was distracted somewhat by a palaeontology article in Nature: Reisz and colleagues reported their discovery of some fossilised dinosaur embryos. Not exactly relevant to my research, but very cool nonetheless…

The remains that they unearthed in southern China are from the early Jurassic period, almost 200 million years old, and are thought to belong to a Lufengosaurus species. This was a sauropodomorph dinosaur: a group distinguished by their large size, with a very long neck and tail and a small head. The most famous of the sauropodomorphs were probably the Diplodocus species.

These fossils are so unusual, and so informative, because they include embryos at a range of developmental stages. The majority of fossilised dinosaur embryos discovered to date have been single clutches of eggs, all synchronised in their development, which provides only a snapshot of development in that particular species. Finding a whole collection of samples from the same species, but at different stages, gives a rare insight into the dynamics of development in an extinct animal.

The authors focused on the growth of the thigh bone, analysing 24 femurs that ranged in length from 12 to 22 mm. Using sectioning and histological techniques, they showed that these bones were highly vascularised at all stages, so they think that these giant dinosaurs began life with rapid embryonic growth.

They also observed that the dinosaur femurs became thicker on one side as they grew larger, and developed a prominent fourth trochanter (an outgrowth to which the main thigh muscle attaches). In living tetrapods, asymmetrical bone thickening and the growth of skeletal features at muscle attachment sites depends on the muscles being active during embryonic development. This suggests that these ancient embryos also used their muscles to move around inside their eggs, and that these movements were an important part of their development too.

I was really amazed by how much information could be gleaned from these tiny fossilised remains. Geology rocks! In evo-devo, we use observations from extant species to make inferences about their common ancestors, but if palaeontology can provide insights into the embryonic development of extinct animals, it might help us to think about the evolution of some developmental processes from a different, and very interesting perspective.

Reisz, R.R. et al (2013) Embryology of Early Jurassic dinosaur from China with evidence of preserved organic remains, Nature 496: 210-214.

New Reviews Editor at Development!

Caroline Hendry — Fri, 22 Mar 2013 14:45:50 +0000

Dear readers of the Node,

Hi there! My name is Caroline and I am the new Reviews Editor covering all things stem cells at Development. I come to you from the land down under, namely Australia, where I did my PhD on kidney development and stem cells in the lab of Prof Melissa Little at the University of Queensland. Shortly thereafter, I landed myself what I considered to be “the dream postdoc” studying lineage reprogramming and iPSC disease modelling in the lab of Prof Ihor Lemischka at Mount Sinai School of Medicine, New York. USA. But fate was not finished with me yet, and now I find myself in Cambridge, UK, in the hallowed halls of the Development offices. Having moved continents three times in less than two years, I am definitely ready to settle!

I am really looking forward to bringing you the latest and greatest in all things stem cells and development. The stem cell field grows larger by the month but no matter how big it gets, its foundations will always be in development. The two are inextricably linked. In one sense, the stem cell field can be thought of as applied developmental biology, and this is certainly the case for stem cell therapies. But understanding the fundamental mechanism of how stem cells can give rise to an entire tissue or organism is as much an integral part of developmental biology as any other, and so deserves to be studied in its own right.

I can’t wait to hear more from everyone as my time here goes on. I’m really looking forward to meeting you at all at various conferences and getting your thoughts on stem cells in development! There are big things planned for stem cells in the journal this year so stay tuned!