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silicoCROSS: a help in genetic crosses

Posted by , on 12 August 2013

I’m quite a lazy person, and as such I like to find solutions to boring and repetitive tasks.

One of those is the drawing of punnett squares in Drosophila genetics.

I wrote a little software (accessible here: silicocross.molecular.ch), that does basically that: drawing punnett squares.

When you access the software you are asked how many chromosomes you want to track:

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Let’s say we have a quite easy cross: on the second chromosome we have a mutant gene, that we want to have homozygous, and on the third we want to have a gal4 driver and a uas:GFP reporter.
So the number of chromosomes we want to track is two.

At this point you are asked for the model organism you are using, this is only relevant for the balancer chromosomes you are using. As at the moment I’m working only with flies, I suppose this will work better for basic tasks.

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After you choose your favorite pet, it’s time to add it’s genotype:

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There is just one thing left to do now: we have to specify the balancer chromosome in Optional settings:

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After pressing the submit button, the punnett square appears. At this point one could choose two genotypes for further crossing, this is not necessary in our case. Notice how death fly genotypes are highlighted in red. Sadly the gal4 system is not implemented yet, so in the phenotype you don’t see the GFP popping out (this is definitely in the to do list).

final

 

 

The system is still in heavy development (whenever I have some spare time and motivation), but I still use it in daily work when setting up crosses to have a nice graphic to glue in my fly-notebook or for teaching reasons. Hope it will be useful for the community as well.

At the moment I’m rewriting the core in python, as in my opinion this will give a less messed up code compared to the actual PHP core.

If you find bugs, have suggestions or else, don’t hesitate to contact me.

 

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PhD Positions at IRB Barcelona

Posted by , on 12 August 2013

Closing Date: 15 March 2021

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Description: One key objective of IRB Barcelona is to train future scientific leaders in a competitive international and multidisciplinary scientific environment. IRB Barcelona focuses its efforts on developing the scientific careers of more than 130 PhD students. The advanced research training programme includes specific scientific and technology courses and seminars, lab management workshops, media training and career development sessions.

Funded by the MINECO (Ministerio de Economía y Competitividad), the FPI Programme (Formación de Personal Investigador – Research Personnel Training) offers predoctoral positions covering a 48-month period. The PhD is performed in subjects associated with research projects (financed through the MINECO’s R+D+i National Plan call).

Candidates Eligibility:
Students who qualify to be admitted into a doctorate program in the 2013-2014 academic course or who are in a position to be enrolled or accepted on a doctoral program in Biology, Biochemistry, Pharmacy, Physics, Medicine, Chemistry or related areas at the time the formalization of the contract.

Some of the research projects that are expected to be granted a 2013 FPI Predoctoral position are:

  • Epigenetic Regulation of Chromatin Functions * PI: Dr. Ferran Azorín
  • Individual cell features and supracellular organisation in Drosophila morphogenesis * PI: Dr. Jordi Casanova
  • The Molecular Bases of Stem Cell Polarity and Malignant Transformation in Drosophila * PI: Dr. Cayetano Gonzalez
  • Spatio-temporal regulation of microtubule formation during cell division and cell differentiation * PI: Jens Lüders
  • Biomedical aspects of protein synthesis * PI: Dr. Lluis Ribas de Pouplana

To apply, please visit our vacancies webpage:
http://www.irbbarcelona.org/index.php/en/training-and-jobs/phd-fellowships/expression-of-interest

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Categories: Jobs

The Company of Biologists YouTube channel

Posted by , on 8 August 2013

COB2cAs you may know, the Node is run by the Company of Biologists, a UK-based charity and non-for-profit publisher funded in 1925. The Company of Biologists publishes 5 scientific journals: the well established Development, Journal of Cell Science (JCS) and The Journal of Experimental Biology, and the two open access journals Disease Models & Mechanisms (DMM) and Biology Open (BiO).

One of the main aims of the The Company is to promote research and study across all branches of Biology, and it does this by providing grants for scientific meetings, workshops and conferences. The Company also provides fellowships for students and postdocs to visit other laboratories and attend conferences and runs a series of trans-disciplinary workshops. The Node has featured many posts and reports from these activities.
 
 
This week, the Company of Biologists has launched its latest initiative- a company youtube channel. In this youtube channel you can find a variety of interesting movies:

 

– Movies on the history and activities of the Company:
 

 
 

– Interesting supplementary movies and animations featured in papers published by the journals of the company. Here is an example of a beautiful movie in the Development playlist:
 

 
 

The Node will obviously not be left out, and we have plans for some great content- so keep an eye out for Node movies on The Company of Biologists youtube channel!

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Categories: News, Resources, Video

Travelling Fellowships

Posted by , on 6 August 2013

Do you need to learn a new technique?  Are you planning a collaborative visit?  If so please have a look at The Company of Biologist’s Travelling Fellowships – http://www.biologists.com/fellowships.html. The next deadline is the 31st August 2013.

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Categories: Funding, News

PhD scholarship at UNSW, Sydney, Australia

Posted by , on 2 August 2013

Closing Date: 15 March 2021

 

UNSW logo

Developmental and Regenerative Dermatology Unit

School of Medical Sciences, University of New South Wales, Sydney Australia

 

PhD Scholarship

The Developmental and Regenerative Dermatology Unit is seeking a highly motivated and enthusiastic postgraduate student for a research project in skin (cancer) biology.

Recently, we made the pivotal discovery that Yes-associated protein (YAP) functions as a key molecular switch in epidermal stem/progenitor cell proliferation and differentiation (Beverdam et al., JID 2013). Currently, we are investigating the developmental genetic context in which YAP functions to control skin stem/progenitor cells in normal and in disrupted skin biology, and the PhD student will participate in this research.

We employ genetically manipulated mouse models, human skin samples, advanced imaging technology such as confocal microscopy and whole mouse in vivo imaging, gene and protein expression analyses and whole genome approaches to address our research questions.

Outcomes of our research will open up exciting new avenues for translational research and the development of treatments for human regenerative skin disease.

More information on the lab can be found here.

 

Award: Scholarships are valued at $24,653 per annum (tax exempt), and may be renewed for up to three years, subject to satisfactory progress.

Eligibility: All applicants must hold an Honours degree or equivalent in a related biological science (e.g. Developmental Biology, Genetics, Cell Biology, Pathology) and have a particular interest in the project on offer and have experience in histology, molecular biology techniques, cell culture, bioinformatics and mouse handling.

Application Process: Applicants should include the following documents

• Cover Letter

• Curriculum Vitae

• Copy of an academic transcript

• Names and contact details (email address and phone number) for at least 3 referees.

 

All applications should be emailed to Dr. Annemiek Beverdam: A.Beverdam@unsw.edu.au

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Categories: Careers, Jobs

This month on the Node- July 2013

Posted by , on 1 August 2013

Another busy month on the Node, with a particular focus on zebrafish. Plenty of meeting reports, research, interviews and more, as well as new job posts. Here are the highlights:

 

Meeting Reports

With conference season well underway, the Node saw several meeting reports this month:

Zebrafish node cropped– Leonardo and Joaquin posted several reports from the 8th european zebrafish meeting: an excellent summary of the talks on developmental biology topics, and 2 posts on the workshops preceeding the conference: the genome resources workshop and the morphogenesis workshop. Cat also posted on the lighter side of the conference, commenting on her first attendance of a fish meeting.

 

– Students from this year’s Woods Hole Embryology course wrote on their experience after 4 weeks and at the end of the course.

– And Alfonso shared his thoughts on the Morphogen Gradients meeting that took place in Oxford.

 

Research

image1– Keeping with the fish theme, we had several fish research posts on the Node this month: Neil wrote about his paper on a model of Fetal Alcohol Spectrum Disorder; while Megan wrote on a recent paper focusing on sex reversal in fish 

– Gary described a paper showing that waves of Cdk1 might be involved in the quick cell division of the early frog embryo

 and Mike Levin wrote about his recent paper showing that planaria can recall memories after decapitation, suggesting that memory storage can happen outside the brain

 

Interviews

Photo of Maria LeptinThis month also featured interesting interviews:

– The Node interviewed developmental biologist and EMBO director Maria Leptin

– Megan started her series of posts on developmental biology in New Zealand by interviewing clinical geneticist and developmental biology Stephen Robertson

– And the BSDB-SDB poster winner chain continues with an interview with the winner of the SDB poster prize at the ISDB meeting Kara Nordin

 

 

Also on the Node:

– Thomas gave his take on the new Crick institute in London and what it reveals about research in the UK

– Xujiang described his visit to a lab in Sydney to study honey bee behaviour, sponsored by a Travelling Fellowship from the Company of Biologists

– The Node followed the #sciconfessions discussion on twitter, and collated the best lab confessions (don’t tell Health & Safety!)

– and T.H.Morgan’s 1920s fly room was reconstructed for a new exhibition in New York

Reconstructed fly room

 Happy Reading!

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Categories: Highlights

Confess your lab sins

Posted by , on 31 July 2013

Remember the hashtag #overlyhonestmethods that was trending on Twitter a few months ago? Well, the new science hashtag to follow is #sciconfessions : a collection of the lab sins that you never told anyone (and definitely not to your Health & Safety officer!).

We storified our favourites, but why don’t join the discussion on Twitter and add your own confession? If you are not a Twitter user, why not leave a comment below and let us know your lab confession?

 
 
 

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Tags: ,
Categories: Lab Life, News

Beautiful stem cells on eurostemcell.org

Posted by , on 31 July 2013

Macrophages_Miron.previewHi everyone! I hope you’re enjoying the sun. We’ve just sent out our July newsletter over at EuroStemCell and we’ve got quite a bit of news that I thought my interest members of The Node:

 

 

 

 

  • Christele Gonneau joins us as a new image blogger and you can expect to see her popping up on The Node too. Meanwhile, we say farewell to Erin Campbell for a while as she anticipates the arrival of her second child.
  • We’ve also got a fab new 3-minute animation on disease modelling
  • There’s a new stem cell comic, Hope beyond Hype: Scottish Stem Cell Stories now available on eurostemcell.org
  • Plus two of our partners share updates on their research discoveries – the Centre for Genomic Research in Barcelona and the MRC Centre for Regenerative Medicine in Edinburgh
  • And if that’s not enough, we’ve got new translations of fact sheets and educational tools in Polish, Spanish and Italian for you to get your teeth into too.

So get your teeth into our latest exciting and beautiful stem cell materials by checking out our latest newsletter.

As ever, you can catch up with us between newsletters @eurostemcell on Twitter or by liking us on Facebook. Do also send us your comments or suggestions – via these channels or use our contact form to get in touch.

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Categories: Education, Images, News, Resources, Video

Remembrance of Brains Past

Posted by , on 30 July 2013

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What would happen to your memories and personality if, after decades of adult life, some portion of your brain was replaced with the progeny of fresh stem cells (as might happen in a treatment for degenerative brain disease)? Given the fascinating but poorly-understood examples of memory in aneural systems such as plants, ciliates, etc. (Eisenstein, 1975; Brugger et al., 2002; Volkov et al., 2008), is it possible that memories can be stored in tissues other than the brain? For that matter, how can arbitrary mental content (specific memories) be encoded and decoded within a physical medium such as a brain? What would be the dynamics of memories during brain regeneration?

It has been shown that memories survive the drastic reorganization of the nervous system during metamorphosis from larva to adult in insects (Sheiman and Tiras, 1996; Blackiston et al., 2008). However, there is only one model system in which true memory and complete brain regeneration can be studied in the same animal: planaria. Planaria are free-living flatworms with bilateral symmetry, a true centralized brain, and a very rich behavioral repertoire. They are thus a popular system for the study of addiction and withdrawal. They also have remarkable powers of regeneration: a resident population of adult stem cells (neoblasts) enable these worms to regenerate any bodypart after surgical removal (Gentile et al., 2011; Lobo et al., 2012). In the 1960’s, a visionary named James V. McConnell experimentally posed a bizarre question (McConnell, 1965): if planaria were trained to form a specific memory and then regenerated their entire brain after decapitation, would the memories still be accessible?

McConnell’s group performed a number of experiments that suggested that the answer was Yes (McConnell et al., 1959; McConnell, 1966) – animals regenerating their whole head seemed to show recall of memories formed via several different training paradigms and behavioral assays. Unfortunately, at the time, training and testing experiments had to be done by hand. Manual experiments with worms are very tedious – not only time-consuming (resulting in low N’s and weak memories in worms who can only be trained for a short time per day) but also open to subjectivity during scoring of behaviors and very hard to control (behavioral experiments are notoriously sensitive to the skill of the operator). These difficulties led to the results being confirmed in some labs but not reproduced in some others (Corning, 1967; Corning and Riccio, 1970; Travis, 1981), and the whole area was largely forgotten (Rilling, 1996; Smalheiser et al., 2001) as people moved on to genetically-tractable model systems and easier questions of neuroscience.

In our lab, we are interested in information processing in cells and tissues. We study how cells orchestrate their activity towards maintaining and repairing complex anatomies, and how behavioral programs interact with radically-altered bodyplans (Levin, 2011). Indeed, our work has shown that all cells, not just excitable nerve, can communicate via changes of resting potential during patterning in embryogenesis, regeneration, and cancer suppression (Levin, 2012). This led to the hypothesis that perhaps networks of non-neural cells might also support the memory and information-processing abilities of neural nets; perhaps the ability of organisms to detect deviations from their target morphology and effect repairs is a reflection of true memory of specific shapes implemented by non-neural bioelectrical networks (Tseng and Levin, 2013)? Our work blurs the line between cognitive science and developmental biology, and we wondered if there may be mechanistic similarities between memory of spatial pattern (morphogenesis) in somatic structures, and memory of temporal patterns (learning and inference) in the brain. Aside from understanding development and developing interventions to increase regenerative ability, we are also interested in the synthetic bioengineering of hybrid tissues with new information-processing capabilities (developing new distributed computational platforms).

In order to establish a new model for studying encoding of information in living tissues and probe the mechanisms that interface the mind to the body, we turned to the planarian. Our first step was to build a next-generation testing and training device for flatworms (it also works for Xenopus and zebrafish (Blackiston and Levin, 2012; Blackiston and Levin, 2013)). The goal was to overcome prior roadblocks for this work: our system not only tracks the movement of planaria, but uniquely provides individual feedback (rewards and punishments) to 12 worms at a time, consistently (24*7 training), thus enabling not only behavior analysis but automated training in learning paradigms (Hicks et al., 2006; Blackiston et al., 2010). The idea was to do away with variability in manual training procedures, overcome operator tedium, and produce quantitative, objective, computer-scored analysis of worm performance after training. Five years and many engineering problems later, we had a device and a successful training protocol for planaria.

Amazingly, the data showed that if worms were trained to remember a novel kind of chamber environment with a specifically rough (laser-etched) surface, they would recognize it again (as measured by their willingness to eat a piece of liver rather than spend time exploring a new environment as controls do) after complete head removal and regeneration (Shomrat and Levin, 2013). While there is still plenty of room for improving the training protocol to induce an even more robust memory, and the worms need a brief refresher after head regeneration in order to show good recall of the original training, the results clearly showed that a complex brain-derived behavior was driven by a memory that survived complete head regeneration.
Our data suggest that not only can memories be stored somewhere outside of the brain, but that they can be imprinted on a naïve regenerated brain. Our future efforts will be focused on molecular cell biology and biophysics approaches to understand 1) which tissues contain the memory (e.g., are neoblasts required? Is it everywhere, or in certain regions?), 2) what molecular pathways underlie the imprinting of this information onto the brain, and 3) how specific memories are encoded into, and decoded from, living tissues. These data establish the automated analysis of memory in regenerated planaria as a new, highly tractable, model system in which to probe new aspects of cognitive science and the intersection of neurobiology and regeneration.

At the moment, we do not know where and how the memory is encoded in the body, or how prevalent such pathways are throughout the tree of life. However, based on exciting recent work on bioelectricity in somatic cells (McCaig et al., 2005; Allen et al., 2011; Bissiere et al., 2011; Wu et al., 2011; Tseng and Levin, 2013), we suggest the fascinating possibility that memory could be globally distributed throughout the body: non-neural cells communicating bioelectrically through gap junctions (electrical synapses) form a neural-like network that could be a very rich medium for encoding information and directing cell activity during regeneration (Chakravarthy and Ghosh, 1997; Bose and Karmakar, 2003; Inoue, 2008). Future work in this system will shed light not only on fundamental issues of memory but also on the biomedically-relevant questions of how regenerative therapies interact with cognitive content in patients. There will also likely be interesting applications of hybrid or biologically-inspired technologies for computational tissues and new computer architectures (Costello et al., 2011; Holley et al., 2011; Adamatzky, 2012; Adamatzky et al., 2012) that we can yet only imagine in their vaguest form.

References Cited

    Adamatzky, A. (2012) ‘Slime mold solves maze in one pass, assisted by gradient of chemo-attractants’, IEEE transactions on nanobioscience 11(2): 131-4.
 
   Adamatzky, A., Holley, J., Dittrich, P., Gorecki, J., De Lacy Costello, B., Zauner, K. P. and Bull, L. (2012) ‘On architectures of circuits implemented in simulated Belousov-Zhabotinsky droplets’, Biosystems 109(1): 72-7.
 
   Allen, K., Fuchs, E. C., Jaschonek, H., Bannerman, D. M. and Monyer, H. (2011) ‘Gap Junctions between Interneurons Are Required for Normal Spatial Coding in the Hippocampus and Short-Term Spatial Memory’, J Neurosci 31(17): 6542-52.
 
   Bissiere, S., Zelikowsky, M., Ponnusamy, R., Jacobs, N. S., Blair, H. T. and Fanselow, M. S. (2011) ‘Electrical synapses control hippocampal contributions to fear learning and memory’, Science 331(6013): 87-91.
 
   Blackiston, D., Shomrat, T., Nicolas, C. L., Granata, C. and Levin, M. (2010) ‘A second-generation device for automated training and quantitative behavior analyses of molecularly-tractable model organisms’, PLoS ONE 5(12): e14370.
 
   Blackiston, D. J. and Levin, M. (2012) ‘Aversive training methods in Xenopus laevis: general principles’, Cold Spring Harbor Protocols 2012(5).
 
   Blackiston, D. J. and Levin, M. (2013) ‘Ectopic eyes outside the head in Xenopus tadpoles provide sensory data for light-mediated learning’, The Journal of experimental biology 216(Pt 6): 1031-40.
 
   Blackiston, D. J., Silva Casey, E. and Weiss, M. R. (2008) ‘Retention of memory through metamorphosis: can a moth remember what it learned as a caterpillar?’, PLoS ONE 3(3): e1736.
 
   Bose, I. and Karmakar, R. (2003) ‘Simple models of plant learning and memory’, Physica Scripta T106: 9-12.
 
   Brugger, P., Macas, E. and Ihlemann, J. (2002) ‘Do sperm cells remember?’, Behav Brain Res 136(1): 325-8.
 
   Chakravarthy, S. V. and Ghosh, J. (1997) ‘On Hebbian-like adaptation in heart muscle: a proposal for ‘cardiac memory”, Biol Cybern 76(3): 207-15.
 
   Corning, W. C. (1967) ‘Regeneration and retention of acquired information’, NASA.
 
   Corning, W. C. and Riccio, D. (1970) The planarian controversy, (ed. W. Byrne): New York: Academic Press.
 
   Costello, B., Adamatzky, A., Jahan, I. and Zhang, L. A. (2011) ‘Towards constructing one-bit binary adder in excitable chemical medium’, Chemical Physics 381(1-3): 88-99.
 
   Eisenstein, E. M. (1975) Aneural organisms in neurobiology, New York: Plenum Press.
 
   Gentile, L., Cebria, F. and Bartscherer, K. (2011) ‘The planarian flatworm: an in vivo model for stem cell biology and nervous system regeneration’, Dis Model Mech 4(1): 12-9.
 
   Hicks, C., Sorocco, D. and Levin, M. (2006) ‘Automated analysis of behavior: A computer-controlled system for drug screening and the investigation of learning’, J Neurobiol 66(9): 977-90.
 
   Holley, J., Jahan, I., Costello Bde, L., Bull, L. and Adamatzky, A. (2011) ‘Logical and arithmetic circuits in Belousov-Zhabotinsky encapsulated disks’, Phys Rev E Stat Nonlin Soft Matter Phys 84(5 Pt 2): 056110.
 
   Inoue, J. (2008) ‘A simple Hopfield-like cellular network model of plant intelligence’, Prog Brain Res 168: 169-74.
 
   Levin, M. (2011) ‘The wisdom of the body: future techniques and approaches to morphogenetic fields in regenerative medicine, developmental biology and cancer’, Regenerative medicine 6(6): 667-73.
 
   Levin, M. (2012) ‘Molecular bioelectricity in developmental biology: new tools and recent discoveries: control of cell behavior and pattern formation by transmembrane potential gradients’, Bioessays 34(3): 205-17.
 
   Lobo, D., Beane, W. S. and Levin, M. (2012) ‘Modeling planarian regeneration: a primer for reverse-engineering the worm’, PLoS Comput Biol 8(4): e1002481.
 
   McCaig, C. D., Rajnicek, A. M., Song, B. and Zhao, M. (2005) ‘Controlling cell behavior electrically: current views and future potential’, Physiol Rev 85(3): 943-78.
 
   McConnell, J. V. (1965) A Manual of Psychological Experimentation on Planarians. Ann Arbor, Michigan: The Worm Runner’s Digest.
 
   McConnell, J. V. (1966) ‘Comparative physiology: learning in invertebrates’, Annual Review of Physiology 28: 107-36.
 
   McConnell, J. V., Jacobson, A. L. and Kimble, D. P. (1959) ‘The effects of regeneration upon retention of a conditioned response in the planarian’, Journal of Comparative Physiology and Psychology 52: 1-5.
 
   Rilling, M. (1996) ‘The mystery of the vanished citations: James McConnell’s forgotten 1960s quest for planarian learning, a biochemical engram, and celebrity (vol 51, pg 589, 1996)’, American Psychologist 51(10): 1039-1039.
 
   Sheiman, I. M. and Tiras, K. L. (1996) Memory and morphogenesis in planaria and beetle. in C. I. Abramson Z. P. Shuranova and Y. M. Burmistrov (eds.) Russian contributions to invertebrate behavior. Westport, CT: Praeger.
 
   Shomrat, T. and Levin, M. (2013) ‘An automated training paradigm reveals long-term memory in planaria and its persistence through head regeneration’, J Exp Biol.
 
   Smalheiser, N. R., Manev, H. and Costa, E. (2001) ‘RNAi and brain function: was McConnell on the right track?’, Trends Neurosci 24(4): 216-8.
 
   Travis, G. D. L. (1981) ‘Aspects of the Social Construction of Learning in Planarian Worms’, Social Studies of Science 11: 11-32.
 
   Tseng, A. and Levin, M. (2013) ‘Cracking the bioelectric code: Probing endogenous ionic controls of pattern formation’, Communicative & Integrative Biology 6(1): 1-8.
 
   Volkov, A. G., Carrell, H., Adesina, T., Markin, V. S. and Jovanov, E. (2008) ‘Plant electrical memory’, Plant Signal Behav 3(7): 490-2.
 
   Wu, C. L., Shih, M. F., Lai, J. S., Yang, H. T., Turner, G. C., Chen, L. and Chiang, A. S. (2011) ‘Heterotypic Gap Junctions between Two Neurons in the Drosophila Brain Are Critical for Memory’, Curr Biol.
 

Michael Levin,
Tufts University
www.drmichaellevin.org/

Tal Shomrat,
Hebrew University

Training and testing workstation

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Categories: Research

In Development this week (Vol. 140, Issue 16)

Posted by , on 30 July 2013

Here are the highlights form the current issue of Development:

 

Nf2 regulates neural progenitor proliferation

F1.smallMutation of neurofibromatosis 2 (NF2) results in nervous system tumours. Molecularly, Nf2 has diverse functions, regulating cell-cell junction formation and various signalling pathways, including the Hippo-Yap pathway. However, the roles of Nf2 in the nervous system, and how its loss promotes tumorigenesis, are poorly understood. Here (p. 3323), Xinwei Cao and co-workers analyse the consequences of Nf2 deletion in the dorsal telencephalon. Although the mutant mice are viable, they display significant brain malformations associated with neural progenitor cell (NPC) hyperproliferation. To determine how Nf2 limits NPC expansion, the authors performed a microarray analysis and found many known targets of the transcriptional coactivator Yap upregulated upon Nf2 deletion, suggesting that Nf2 may inhibit Yap activity. Consistent with this, protein levels and nuclear localization of Yap and its paralog Taz are increased in Nf2 mutants. Moreover, Yap deletion rescues the Nf2 mutant phenotype – demonstrating the functional importance of this regulation. These data uncover a key role for Nf2 and Yap/Taz in regulating NPC proliferation in the developing brain.

 

Staying in sync through development

F1.small-1During embryogenesis, transcriptional regulation must be coordinated with growth and cell division, so that genes are turned on or off in the right cells at the right time. Arjun Raj and colleagues now investigate the coupling of gene expression and cell division in C. elegans (p. 3385). They find that global retardation of development by temperature change or gene mutation slows down the cell cycle, and this is accompanied by a similar delay in expression of particular developmental genes – so the synchrony between cell cycle and gene expression is retained. These findings suggest that transcription might be directly cell cycle dependent. However, mutations that cause cell cycle delays in specific lineages uncouple cell division and transcription, arguing against the onset of transcription being tied to a particular division cycle. Conversely, it is known that cell division in C. elegans embryos proceeds independently of zygotic transcription. Together, these data demonstrate that cell proliferation and gene expression are well synchronised, but raise the key question of how this synchrony is achieved.

 

How cilia know which way to point

F1.small-2Cells lining the lumen of various organs, such as the lung airway and the female reproductive tract, are multiciliated, and all the cilia are oriented in the same direction to generate flow. But how is cilia orientation coordinated within cells and across tissues? Chris Kintner and colleagues use the epithelial cells of Xenopus embryos as a model to study multicilate cell differentiation. On p. 3468, they identify a new regulator of cilia polarisation, the coiled-coil protein bbof1. Bbof1 is expressed in multicilate cells and localises to the axoneme and the basal body – the structure that determines cilia orientation. Upon bbof1 depletion, motile cilia still form, but are unable to generate significant flow because their orientation is disturbed. Notably, bbof1 is not required for the initial phase of cilia polarisation, but rather for the later refinement step, and for stabilising the alignment. Although the mechanism by which bbof1 acts remains unclear, this work identifies a key factor regulating cilia orientation and function.

 

Go with the flow: circulating BMP promotes endothelial quiescence

F1.small-3Blood flow through the developing vasculature regulates vessel formation – both via the distribution of endocrine factors, and via mechanical force-induced responses. Several signalling pathways are known to be involved in this process, including signalling via the TGFb receptor Alk1, whose activity promotes quiescence in newly formed arteries and whose expression is itself dependent upon blood flow. On p. 3403, Beth Roman and colleagues demonstrate that not only Alk1 expression but also its activity are dependent upon blood flow in developing zebrafish. They identify Bmp10 as the endogenous ligand for Alk1 in this context, and find that Bmp10 is exclusively expressed in the heart, and not in the vascular tissue. Through elegant experiments using embryos in which the heart has been stopped but alk1 expression restored, they show that Bmp10 injection can locally rescue Alk1 pathway activity and downstream transcriptional responses. Thus, their data suggest that blood flow is required to distribute cardiac-derived Bmp10 into the vasculature, where it activates Alk1 to promote quiescence in endothelial cells.

 

Histone methylation: not so dynamic after all

F1.small-4Polycomb group proteins are chromatin regulators with highly conserved functions. The Polycomb repressive complex 2 (PRC2) methylates H3K27 to stably silence target genes, including the HOX genes in Drosophila. More recently, Utx and Jmjd3 demethylases were found to reverse PRC2-mediated H3K27 methylation, and it has been suggested that a dynamic cycle of methylation and demethylation is required for appropriate regulation of gene expression. Now, Ömer Copur and Jürg Müller challenge this view (p. 3478), via the analysis of Drosophila Utx mutants. Lack of zygotic Utx function has no effect on Drosophila development, although mutant adults die shortly after hatching. Loss of both maternal and zygotic Utx, however, leads to larval death and to defects in HOX gene expression – in both the embryo and larval imaginal discs. Thus, it appears that Utx in Drosophila – and, by inference, H3K27 demethylation – is required only at early stages to set up the patterns of HOX expression; it is largely dispensable later in development, suggesting that H3K27 methylation may in fact be very stable.

 

An integral role for integrin β1 in the pancreas

F1.small-5Integrins mediate cell-matrix adhesion and are also capable of inducing intracellular signalling cascades to regulate cell proliferation, differentiation and other cell behaviours. In vitro, disruption of β1 integrin function has been shown to affect various aspects of pancreatic β-cell activity. On p. 3360, Vincenzo Cirulli and co-workers analyse the consequences of deleting β1 integrin in β-cells in vivo in mice. The mutant mice have smaller pancreatic islets that exhibit matrix adhesion defects when cultured in vitro. Notably, cell proliferation is severely impaired in the mutant β-cells, and the expression of cell cycle regulators is highly abnormal. However, these cells are able to differentiate properly and to express insulin, and are glucose responsive; in fact, they show increased levels of insulin and the mutant mice show no signs of diabetes. These results highlight differences between the ascribed functions of β1-integrin in vitro versus in vivo and define its key role in promoting proliferation during pancreatic islet development.

 

PLUS…

 

Adult neural stem cells: plastic or restricted neuronal fates?

F1.largeEduardo Sequerro and colleagues review studies of postnatal and adult neurogenesis, challenging the notion that fixed genetic programs restrict neuronal fate. They hypothesize that the adult brain maintains plastic neural stem cells that are capable of responding to changes in environmental cues and generating diverse neuronal types. See the Hypothesis article on p. 3303

 

Clustered protocadherins

F1cropposterWeisheng Chen and Tom Maniatis provide a concise overview of the molecular and cellular biology of clustered Pcdhs, highlighting how they generate single cell diversity in the vertebrate nervous system and how such diversity may be used in neural circuit assembly. See the Development at a Glance poster article on p. 3297

 

 

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Categories: Research