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This month on the Node – December 2011

Posted by , on 30 December 2011

Many of you may have a few days off from work at the moment. If you want to catch up on what you missed on the Node this month, read on:

BenchFly bingo game

Benchfly, a site with free video protocols and other resources for researchers, has created “Group Meeting Bingo”. The site generates bingo cards with the particular phrases common to various fields of research. They have cards for biochemistry, cell biology, and various other fields, but no developmental biology…yet!

So, let’s make a developmental biology bingo game!

Add suggestions for words to include to the post. We already have quite a few, but I’m sure you’ll find something that hasn’t been mentioned yet. You still have this weekend to add words.

Rejuvenating old cells

With the new year approaching, you may have been pondering the passage of time lately. Another year gone, another year older. But there’s hope still! Sasha wrote about a recent paper that shows that your cells are never too old for pluripotency!

“(…) Researchers began to wonder whether cellular aging was a barrier to iPS cell conversion. In a recent paper published the November issue of Genes in Development, entitled “Rejuvenating senescent and centenarian human cells by reprogramming through the pluripotent state,” Lapasset and colleagues from the Institute of Functional Genomics in France report that they have overcome this barrier and generated iPS cells from human donors as old as 101 years.”

Book reviews

Continuing from last month, we’ve republished more book reviews from Development. Click on a cover to read the review.

  

     

Also on the Node:
Dates and deadlines, including an extended early registration deadline for the LASDB meeting
-“Pigs that Fly” – Jonathan’s third rotation lab for the Wellcome Trust PhD programme.
– For more, see the full December archive.

 

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Book review: Epigenetics in all its glory

Posted by , on 29 December 2011

This book review originally appeared in Development. Melissa Mann reviews “Epigenetics: Linking Genotype and Phenotype in Development and Evolution” (Edited by Benedikt Hallgrímsson and Brian K. Hall).

Book info:
Epigenetics: Linking Genotype and Phenotype in Development and Evolution Edited by Benedikt Hallgrímsson, Brian K. Hall University of California Press (2011) 472 pages ISBN 978-0520267091 (hardback), 978-0520948822 (eBook) £59/$68 (hardback), $85 (eBook)

Ask ten scientists their definition of epigenetics and you may get ten answers. In its simplest form, epigenetics can be defined as above (epi) the level of genes (genetics), and in the book entitled Epigenetics: Linking Genotype and Phenotype in Development and Evolution, the editors, Benedikt Hallgrímsson and Brian K. Hall, have assembled 23 chapters that collectively embody epigenetics as described by this broad definition. Although the book is organized into four parts, it can be distilled into three themes that each discusses a more detailed interpretation of the field: molecular epigenetics, classical epigenetics/epigenetic interactions, and epigenetic interactions and evolution.

In its modern molecular reiteration, epigenetics is defined as a change in gene activity without a change in DNA sequence. Most molecular definitions of epigenetics also include the idea of heritability, or memory of gene activity, through cell division. Here, epigenetic modifications modulate gene expression through DNA methylation, histone modifications, changes in chromatin structure, and effects of non-coding RNAs. This book includes five chapters on molecular epigenetics, covering various organisms and topics from asexual organisms in the study of epigenetic variation to epigenetics and human disease. One chapter highlights neural development in which cell-fate switches are intimately linked with epigenetic changes. For example, transition from a neural stem cell to a progenitor cell involves a switch in co-factor associations. In response to Notch effector molecules, the HES1 repressor complex is transformed into a HES1 activator complex, thereby inducing a progenitor cell fate. A different mechanism may be utilized in neuronal fate specification in the neocortex. Changes in DNA looping and nuclear matrix binding may specify an upper layer neocortical fate. This chapter describes the current understanding of various epigenetic mechanisms involved in neural cell fate decisions.

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Celestial or Cellular?

Posted by , on 26 December 2011

The Cell: An Image Library™ offers you a little fun this week. Please enjoy our quiz, Celestial or Cellular?
Take a look at the images and see if you can tell whether they are of cellular or celestial origin.
Take your best shot, and enter your answers at http://asterisk.apod.com/viewtopic.php?f=29&t=26228. Visit again each day this week for a new quiz and the correct answers to the previous day’s quiz.
Enjoy, and please share this with your friends.
Visit The Cell: An Image Library and learn how to submit your images.
Reuse of quiz images may be subject to licensing restrictions, which will be revealed with the identity of the image on the day following the quiz.

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Modeling stem cell population dynamics

Posted by , on 23 December 2011

Many tissues and organs contain self-renewing stem cell populations that are crucial for their maintenance. Synthesizing the relative effects of anatomical constraints, cell proliferation dynamics and cell fate specification on the overall stem cell population dynamics is challenging, and so we reasoned that dynamic computational models that have the potential to systematically manipulate different influences might facilitate an understanding of experimental studies on self-renewing cell populations.

In our study published in Development [1] we have built a computational model of germline development in C. elegans. In this model, germ cells move, divide, respond to signals, progress through mitosis and meiosis, and differentiate according to a developmental program specified for a “cell”. This developmental program incorporates cellular decision-making that influences germ cell behavior, as defined by a subset of cell components and their dynamic interactions. Simulations driven by the model recapitulate C. elegans germline development and the effects of various genetic manipulations, as shown in supplementary movies, also available at [2].

Our analyses of model simulations and laboratory studies suggest that: (1) when the ligand interaction occurs over a short distance (that is, reaching only the distal-most germ cells), small differences in this distance destabilize the system and introduce unexpected variability; (2) inherent differences between progenitor cell types need not necessarily be invoked to explain complex differentiation dynamics upon reduction of receptor activity; (3) population dynamics and anatomical constraints influence niche residence; and (4) the germ cell proliferation rate during larval stages influences the differentiation pattern in the adult.

The computational modeling in this project has been carried out in the computational science laboratory at Microsoft Research in Cambridge, in close collaboration with the Hubbard lab. We are applying and developing modeling methods that were originally introduced for building and understanding engineering and software systems. Since biological systems are far more complex and robust than man-made engineering systems, a long term goal of this research is to challenge the ways engineering and software systems are currently constructed and understood.

[1] Y. Setty, D. Dalfo, D.Z. Korta, E.J. Albert Hubbard, and H. Kugler, A model of stem cell population dynamics: in-silico analysis and in-vivo validation, in Development, vol. 139, 47-56, 2012.

[2] http://research.microsoft.com/celegans

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PhD Programme in Human Biology, University of Tsukuba, Japan

Posted by , on 23 December 2011

Closing Date: 15 March 2021

The University of Tsukuba, Japan is offering fully-funded PhD studentships to do research in Japan. They have close ties with many international universities, including the University of Edinburgh. Joint projects between Edinburgh and Tsukuba will be available. The University of Tsukuba, located 1 hour from Tokyo, is one of the top universities in Japan, and does outstanding biological research. All courses and research will be in English.

Please visit this site for further details and for application forms: http://hbp.tsukuba.ac.jp/en/

The deadline is 4th January, 2012, and interviews will be held in Edinburgh on 22nd and 23rd January.

Send informal enquires to both Tilo Kunath (tilo.kunath@ed.ac.uk) and Prof Satoru Takahashi (satoruta@md.tsukuba.ac.jp)

 

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Stem cells, cellules souches, Stammzellen: taking research to Europe’s public

Posted by , on 22 December 2011

It’s been a busy year for EuroStemCell: Europe’s stem cell hub – see www.eurostemcell.org for more information on who we are. We’d like to wish The Node community a happy festive season and a great start to 2012. But before we say goodbye to 2011, we thought you might be interested to know about some of the things we’ve been doing recently…

EuroStemCell goes multilingual

eurostemcell.org is multilingual! Or tri-lingual, at least.

The EuroStemCell website is now available in 2 additional languages, German and French, with Italian and Spanish coming soon. Just click on the flag icons to the right of any page on the website to give the newly translated interface a whirl.

Read more about our translation project, or go straight to the French or German homepage.

Research updates from EU-funded stem cell projects

Our research updates keep you informed about progress in public-funded European stem cell research. Here’s a recent example from our partner, NeuroStemcell.

Using stem cells to develop new therapies for Parkinson’s and Huntington’s diseases

NeuroStemcell brings stem cell biology and clinical science together to develop and test new approaches to stem-cell-based therapy. We study Parkinson’s (PD) and Huntington’s (HD) diseases, which are degenerative diseases of the brain.

Read more about NeuroStemcell

 

Italy meets the UK to discuss the future of stem cells in the clinic

Over 100 Italian and UK scientists and politicians came together on 12 December for a Summit on Regenerative Medicine organized by the Italian Embassy in London and the School of Science Technology and Health, University Campus Suffolk. Their aim: to bring the collective expertise of academics, industry and the political world to bear on the question of how to take basic stem cell research towards the clinic.

We went along to the meeting – read our report on the discussions

Inside the lab

We’ve got two new guest bloggers on our site: Anestis Tsakiridis is sharing his insider’s view of stem cell research in his blogs, Behind the Bench: A series about researchers and their rituals; and we’re delighted to welcome Alzheimer’s researcher Selina Wray, who posted her first blog, A fish out of water, on our site just last week.

Meet the stem cell scientists

We’ve also been busy talking to experts across the stem cell field. Read our interviews with Cedric Blanpain, Yann Barrandon, Christine Mummery, Doug Sipp, Karen English and Nick Barker on the site now and keep your eye out for our chats with Jane Visvader, Connie Eaves and others in the New Year.

Stem cell factsheets

We’ve got an ever-growing set of fact sheets giving quick access to the key facts about different areas of stem cell and regenerative medicine research. The content is written by researchers and  reviewed by senior scientists.  The fact sheets are designed for non-specialists but why not check them out next time for a quick overview next time someone asks you about something a little outside your own field? Take a look at the whole collection (13 published so far, some in French & German too), but here’s one of our latest…

Type 1 Diabetes: How could stem cells help?

Diabetes is a common life-long condition and the number of children being diagnosed with type 1 diabetes is increasing. The symptoms can be controlled but there is no cure. For many, diabetes means living with daily insulin injections and the possibility of long-term damage to their health. How might stem cells help?Read our factsheet about stem cells and diabetes

 

Keep up with Europe’s stem cell news

Sign up to our newsletter to stay in touch with all the latest news from the EuroStemCell project. From February 2012 we’ll be sending out a  monthly newsletter. For more regular updates, you can follow us on Twitter, check out our Facebook page or subscribe to our RSS feeds.  And if you haven’t visited the site for a while, do take a look and get in touch with your feedback and ideas.

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Book review: A practical guide to human stem cell biology

Posted by , on 22 December 2011

This book review originally appeared in Development. Neil Singh and Ludovic Vallier review “Human Stem Cell Technology and Biology” (Edited by Gary S. Stein, Maria Borowski, Mai X. Luong, Meng-Jiao Shi, Kelly P. Smith and Priscilla Vasquez).

Book info:
Human Stem Cell Technology and Biology: A Research Guide and Laboratory Manual Edited by Gary S. Stein, Maria Borowski, Mai X. Luong, Meng-Jiao Shi, Kelly P. Smith, Priscilla Vasquez Wiley-Blackwell (2011) 419 pages ISBN 978-0-470-59545-9 £93.50/€112.20 (hardback)

Do we need another book on human stem cell biology? The field is fairly long in the tooth now, thirteen years after Thomson first derived human embryonic stem (ES) cells (Thomson et al., 1998). There are many books that cover the theoretical aspects of the discipline (Oderico et al., 2004) and others that attempt to collate protocols useful to human stem cell biologists (Sullivan et al., 2007). Nevertheless, the new book Human Stem Cell Technology and Biology succeeds in combining both of these characteristics, providing not only a clear account of the scientific discoveries underpinning human stem cell biology, but also a useful range of laboratory protocols. The end product may be less comprehensive than Lanza’s classic text (Lanza et al., 2009), but it is perhaps more manageable and appropriate for a newcomer to the field or for an early career scientist working with human pluripotent cell lines for the first time.

The editors are all based at the Center for Stem Cell Biology & Regenerative Medicine at the University of Massachusetts Medical School. The individual chapters are written predominantly by scientists from institutes on the East coast of the United States, although some contributors are based in Australia, Canada and China. The book is divided broadly into five sections: an introduction; two sections on the culture and characterisation of human pluripotent stem cells; and two sections covering more recent technologies and applications relevant to human ES cells.

In the introduction, the authors have managed to distill over 50 years of stem cell advances in just a few pages of text. Although this may be too short for experienced scientists hoping for a colourful narrative history of each breakthrough, we think it does well to bring even novice readers up to speed with current thinking in stem cell biology, from the bottom up.

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Eye-ing the body electric

Posted by , on 20 December 2011

How do you make an eye? One early trigger for eye formation in Xenopus, as a new Development paper from Michael Levin’s lab shows, is a small change in bioelectric signals. In fact, that trigger alone is enough to induce eye development in other parts of the body.

In an experiment that measured regions of hyperpolerization in the developing Xenopus embryo, the researchers found two small hyperpolarized spots in the anterior neural field – exactly where the eyes are later formed. Was this change in transmembrane potential (Vmem) related to eye development? To find out, the group carried out a series of experiments to show that the hyperpolarized cells were indeed the same cells that later formed the eye. Not only that, but depolarizing these cells disrupted eye development, suggesting that the transmembrane potential is part of a required signalling mechanism for eye formation.

Eye development involves the formation of an “eye field” from a region of the anterior neural field. This is regulated by eye field transcription factors (EFTFs) such as Pax6 and Rx1. Levin and his colleagues demonstrated that the transmembrane potential in the eye field regulates expression of these EFTFs. When they depolarized the hyperpolarized cells in the eye field, expression levels of Pax6 and Rx1 went down, which explains why eye development was affected upon depolarization.

But what happens if you alter the Vmem not just in the region where eyes are normally formed, but in other parts of the body? To test this, the researchers globally disrupted the Vmem by introducing dominant negative potassium channel subunits into all four blastomeres of four-cell embryos. Within the eye region, the results were as before: many of the embryos did not form functional eyes in the eye region when the Vmem was disrupted. And outside of the eye region? After just changing the transmembrane potential, eyes started to pop up in different parts of the body! Several of the embryos now developed eye tissue in the gut area, and these ectopic eyes have morphological characteristics very similar to regular, functional, eyes.

Ectopic eye, with lens, formed on a tadpole’s gut.

Eye formation caused by a change in transmembrane potential outside of the eye region was also associated with an upregulation of the expression of eye field transcription factors Pax6 and Rx1, suggesting that a bioelectric signal alone is sufficient to initiate the molecular mechanisms required for eye development.

So why don’t we have eyes everywhere? In the discussion section of the paper, the authors hypothesize that a narrow, specific, range of Vmem is associated with the development of particular tissues. This suggests that the eye region is the only area where the Vmem is at the optimal level to upregulate the required transcription factors at the right moment in development to form an eye.

Bioelectric signals also control other physiological processes, such as cell migration and wound healing, but this is the first study that shows a role of bioelectric parameters in eye development.

Development is more than gene regulation alone, and we’re slowly starting to find out all the mechanisms and processes that work together to form organs and organisms.

ResearchBlogging.orgPai, V., Aw, S., Shomrat, T., Lemire, J., & Levin, M. (2011). Transmembrane voltage potential controls embryonic eye patterning in Xenopus laevis Development DOI: 10.1242/dev.073759

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In Development this week (Vol. 139, Issue 2)

Posted by , on 20 December 2011

Here are the highlights from the current issue of Development:

 

Balanced ephrin/Eph signals drive topographic mapping

During development of the retinotectal axonal projection, which connects the retina to the optic tectum in the midbrain, the axons of neighbouring retinal ganglion cells project to neighbouring positions in the optic tectum (topographical mapping). However, although retinal fibres rigidly target their destinations in some experimental circumstances, in others they adapt to grossly diverse targets. Here (see p. 335), Franco Weth and colleagues present a surprisingly simple model that explains these hitherto puzzling discrepancies. In this model, topographical axonal mapping relies solely on the balance of forward and reverse signalling by the ephrin/Eph family of guidance molecules. To test their model, the researchers develop a novel ephrin/Eph (double-cue) stripe assay and show experimentally that the simultaneous presence of forward and reverse ephrin/Eph signalling is indeed sufficient for appropriate topographic growth decisions in chick embryonic nerve fibres. Moreover, using computer simulations, they show that their new model is capable of reproducing the discrepant data collected over the years on topographic mapping by the retinotectal axonal projection.

Complex dance of eye morphogenesis unveiled

Optic cup morphogenesis (OCM), which generates the basic structure of the vertebrate eye, is usually depicted as a series of epithelial sheet folding events but experimental evidence to support this stepwise model is lacking. Now, Kristen Kwan, Chi-Bin Chien and colleagues investigate the cellular dynamics of OCM in zebrafish by combining four-dimensional time-lapse imaging and cell tracking (see p. 359). The researchers show that OCM depends on a complex set of sometimes unanticipated cell movements that are coordinated between the prospective neural retina, retinal pigmented epithelium and lens, the tissues that comprise the mature optic cup. Using their cell tracking data, the researchers construct subdomain fate maps for these three tissues that might provide clues to developmental signalling events. Finally, they show that similar movements occur during chick eye morphogenesis, which suggests that the complex choreography of cell movements that shape the vertebrate eye is conserved. These new insights into eye development could, therefore, help to improve our understanding of human eye defects.

Shedding light on Rho kinase signalling

Small-molecule inhibitors can be used as loss-of-function tools to investigate the molecular mechanisms of development but, although exposure to these inhibitors can be temporally controlled, their effects are not spatially restricted. Now, Nanette Nascone-Yoder and colleagues have generated a pharmacological agent that allows for photoactivatable, and hence spatiotemporally limited, inhibition of Rho kinase (see p. 437). Rho signalling is involved in many morphogenetic events, including primitive gut elongation in Xenopus embryos. The researchers install a photolabile ‘caging’ group on Rockout, a small-molecule inhibitor of Rho kinase, and show that caged Rockout (cRO) can permeate Xenopus embryonic tissues. When cultured in the dark, cRO-treated embryos develop normally, but UV irradiation of the right side of these embryos produces animals with a unilaterally shortened gut. Finally, the use of cRO reveals a differential requirement for Rho signalling on the left and right sides of the gut during intestinal rotation. Photocaging pharmacological inhibitors, the researchers conclude, might be a generalisable technique for producing loss-of-function reagents for use in multiple developmental contexts.

The eyes have it: bioelectric induction

Endogenous steady-state ion currents, voltage gradients and electric fields produced by ion channels and pumps regulate patterning and have been implicated in adult eye wound healing. So might they play a role in eye development? On p. 313 Michael Levin and co-workers report that transmembrane voltage potential (Vmem) is an important component of the eye induction cascade in Xenopus. The researchers identify a hyperpolarised cluster of cells in the anterior neural field of Xenopus embryos and show that depolarisation of the lineages from which these cells are derived results in malformed eyes. Remarkably, given our understanding of lineage restrictions and plasticity, manipulation of Vmem in non-eye cells induces ectopic eye formation far outside the anterior neural field. Other experiments show that a Ca2+ channel-dependent pathway transduces the Vmem signal and regulates the pattern of eye field transcription factor expression. This new information on the roles of voltage gradients as mediators of patterning during embryogenesis might have implications for the development of regenerative approaches to ocular diseases. (See also this post on the Node.)

Heads up for neural specification

During mouse embryogenesis, the anterior ectoderm develops into neural derivatives (the forebrain) and non-neural derivatives (the cephalic non-neural ectoderm). On p. 423, Kirstie Lawson, Anne Camus and co-workers use single-cell labelling and gene expression analysis to provide new insights into this cell fate choice. At late gastrulation, they report, the expression patterns of anterior ectoderm genes overlap significantly and correlate with areas of prospective fate but do not define lineages. They show that the rostral limit to forebrain contribution is more distal than previously reported. Finally, they report that some precursors of the anterior neural ridge, a signalling centre that is involved in forebrain development and patterning, are clonally related to neural ectoderm and are dispersed over a broad area of the anterior ectoderm where neural precursors also reside. Together, these results suggest that, although the segregation of neural and non-neural cells in the anterior ectoderm is incomplete at the gastrulation stage, there are elements of regionalisation in this tissue that preconfigure the organisation of the head.

ROCK solid epithelial organisation

The basement membrane is essential for epithelial tissue organisation and function but what restricts the basement membrane to the basal periphery of epithelial tissues and what are the basement membrane-mediated signals that regulate coordinated tissue organisation? On p. 411, Melinda Larsen and colleagues use cultures of embryonic mouse submandibular salivary glands to investigate these questions. They show that inhibition of the Rho kinase ROCK in these cultures results in basement membrane accumulation throughout the epithelial compartment. ROCK-mediated control of Par-1b localisation in the outer basal epithelial cell layer (which produces basement membrane) is responsible for normal basal basement membrane positioning, they report. Moreover, inhibition of Par-1b kinase activity prevents basement membrane deposition and disrupts tissue organisation. Conversely, overexpression of Par-1b drives ectopic basement membrane production. These and other results suggest that Par-1b is a master regulator of basement membrane deposition in developing salivary glands and that ROCK control of Par-1b function is essential for normal epithelial integrity and organisation.

PLUS…

When cell cycle meets development

The recent Company of Biologists workshop ‘Growth, Division and Differentiation: Understanding Developmental Control’, which was held in September 2011 at Wiston House, West Sussex, UK. Kaldis and Richardson   review the common themes that emerged from the meeting, highlighting novel insights into the interplay between regulators of cell proliferation and differentiation during development.

See the Meeting Review on p. 225

Palatogenesis: morphogenetic and molecular mechanisms of secondary palate development

Mammalian palatogenesis is a highly regulated morphogenetic process, the complexity of which is reflected by the common occurrence of cleft palate in humans. Here, Bush and Jiang review major advances in our understanding of the mechanisms that control secondary palate development.

 See the Review Article on p. 231

Shaping sound in space: the regulation of inner ear patterning

Groves and Fekete review recent studies of inner ear development and patterning, which reveal that multiple stages of ear development are orchestrated by gradients of signaling molecules.

See the Review Article on p. 245

 

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