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In Development this week (Vol. 142, Issue 1)

Posted by , on 16 December 2014

Here are the highlights from the current issue of Development:

 

Planar cell polarity squeezes in on the action

FigureThe planar cell polarity (PCP) pathway regulates the polarization of epithelial tissues in various contexts, but recent studies suggest that the PCP pathway also influences other aspects of morphogenesis. Here, Sergei Sokol and colleagues uncover a role for PCP signalling during apical constriction in Xenopus embryos (p. 99). They show that the core PCP protein Vangl2 accumulates at the apical surface of blastopore bottle cells, which undergo apical constriction during gastrulation. The depletion of Vangl2 perturbs apical constriction and hence blastopore formation. The authors further demonstrate that Rab11, a marker of the recycling endosome, localizes to the apical surface of constricting cells in a Vangl2-dependent manner; apical staining of Rab11 is absent in Vangl2-depleted embryos, suggesting that PCP signalling modulates endocytic trafficking. Finally, the authors show that Rab11 in turn modulates Vangl2 distribution and that it cooperates with Myosin V to regulate apical constriction. Together, these studies highlight a novel role for the PCP pathway during apical constriction and support a positive-feedback model in which both PCP signalling and endocytic trafficking function to regulate apical constriction.

 

Epiblast development: getting up to speed

FigureThe epiblast of mammalian embryos undergoes a period of rapid growth shortly after implantation, thereby establishing a population of cells that will give rise to the embryo proper. Here, Miguel Ramalho-Santos and co-workers show that chromodomain helicase DNA-binding protein 1 (Chd1) is required for the transcriptional output that drives this rapid growth (p. 118). They first show that Chd1–/– mouse embryos display post-implantation defects; analyses of lineage and patterning markers indicate that Chd1–/–embryos arrest in the transition between E5.5 and E6.5, prior to anterior-posterior patterning and the onset of gastrulation. The researchers further show that transcriptional output per cell is reduced inChd1–/– mouse embryonic stem cells (ESCs) compared with control ESCs. In line with this, the amount of RNA polymerase II present at gene bodies and transcriptional start sites is decreased in mutant ESCs. Finally, the authors document that Chd1 also directly regulates the output of ribosomal RNA in both ESCs and the epiblast. In summary, the authors propose that Chd1 promotes a global increase in transcriptional output by both RNA polymerase I and II that, in turn, sustains the rapid growth of the epiblast.

 

Ezh2: balancing cell differentiation in the lung

FigureDuring development, the lung endoderm is patterned along its anterior-posterior axis, giving rise to distinct epithelial lineages, such as the alveolar cells that mediate gas exchange, and the basal and secretory cells that line the airways. In this issue (p. 108), Edward Morrisey and colleagues show that the polycomb repressive complex 2 component Ezh2 restricts the basal cell lineage during lung development, thereby allowing correct patterning of the lung. The researchers report that Ezh2 is broadly expressed in the lung during early development but then gradually becomes downregulated as development progresses. Importantly, they demonstrate that the endoderm-specific deletion of Ezh2 impairs secretory cell differentiation while inducing the ectopic and premature development of basal cells that express the transcription factor Trp63 and other basal cell markers. Furthermore, they report that Ezh2 deletion gives rise to a cell population that might represent an intermediate state between basal and secretory states. These and other findings indicate that Ezh2 controls the phenotypic switch between basal cells and secretory cells, and regulates both the temporal and spatial patterning of the lung.

 

MRTFs at the heart of epicardial motility

FigureThe epicardium – the single-cell layer of mesothelium that surrounds the heart – harbours a population of progenitor cells that modulates heart development and contributes to various cardiac lineages. During heart development, these epicardium-derived progenitor cells (EPDCs) undergo epithelial-to-mesenchymal transition and migrate into the sub-epicardial space, but the mechanisms regulating their mobilization remain unclear. On p. 21, Eric Small and colleagues show that myocardin-related transcription factors (MRTFs) regulate the motility of mouse EPDCs as well as the maturation of coronary vessels. They demonstrate that MRTF-A and MRTF-B are enriched within the epicardium, where they localize to the perinuclear space. The researchers further demonstrate that, in epicardial-mesothelial cells cultured in vitro, TGFβ signalling leads to the nuclear accumulation of MRTFs and the activation of a cell motility gene expression program. Importantly, the epicardial-specific ablation of Mrtfa and Mrtfb causes sub-epicardial haemorrhage; mutant hearts display a disorganised epicardial layer. In addition, lineage-tracing studies reveal a novel epicardial-derived coronary pericyte population that contributes to coronary vessel integrity and that is depleted in mutant embryos. Together, these findings, which link EPDC motility to cell differentiation in the heart, highlight novel approaches that could be used to manipulate EPDCs for cardiac repair.

 

Mga fuels pluripotent cells

FigureThe dual specificity T-box/bHLH-zipper transcription factor Mga is expressed in pluripotent cells of the mouse embryo and in embryonic stem cells (ESCs), but its function in these cells is unclear. Here, Virginia Papaioannou and colleagues examine the role of Mga in early development and show that it is essential for the survival of pluripotent cells (p. 31). They first show that Mga depletion in early mouse embryos and ESCs causes growth defects; increased cell death is observed in the inner cell mass (ICM) of mutant embryos in vivoand in vitro, and in Mga mutant ESCs cells in vitro. Lineage specification, in contrast, is unaffected by Mgadepletion. The researchers further identify the enzyme ornithine decarboxylase (ODC), which converts ornithine to putrescine in the polyamine synthesis pathway, as a candidate downstream target of Mga. Accordingly, they demonstrate that exogenous putrescine can rescue the ICM in Mga mutant embryos and the survival of Mga mutant ESCs. These findings highlight a role for polyamines in pluripotent cells and suggest that Mga controls cell survival in early embryos and ESCs by regulating polyamine pools.

 

Plus…

In recognition of recent breakthroughs and in line with Development’s recent expansion into the stem cell field, we recently organized a workshop – ‘From Stem Cells to Human Development’ – that was held in September 2014. In this issue, you will find a report from this meeting as well as an Editorial and several Spotlight articles that address key issues in this field.

Looking inwards: opening a window onto human development

Development Editors announce a new focus on human developmental biology and discuss how they hope to support this expanding field. See the Editorial on p. 1

Ethical considerations in chimera research

The use of human tissue, particularly in the generation of chimeric animals, throws up important ethical considerations that scientists and policy-makers must consider. See the Spotlight article by Göran Hermerén on p. 3

 

From naïve pluripotency to chimeras: a new ethical challenge?

The ability to create chimeric animal models using naïve human pluripotent stem cells is now on the horizon. Should we be concerned about using such chimeric animals? Insoo Hyun discusses these concerns on p. 6

Mouse and human blastocyst-derived stem cells: vive les differences

Early human and mouse embryos exhibit significant differences in their development and, as discussed by Janet Rossant, these are reflected in the properties of stem cell lines derived from these embryos. See the Spotlight on p. 9

 

Modeling human lung development and disease using pluripotent stem cells

Successful disease therapy often requires an in-depth knowledge of basic developmental biology, not only through study of model organisms but crucially also of human tissue. Hans-Willem Snoeck discusses the importance of using human stem cell models for understanding human lung development and disease. See the Spotlight on p. 13

 

On human development: lessons from stem cell systems

In September 2014, over 100 scientists from around the globe gathered at Wotton House near London for the Company of Biologists’ workshop ‘From Stem Cells to Human Development’. The workshop covered diverse aspects of human development, from the earliest stages of embryogenesis to differentiation of mature cell types of all three germ layers from pluripotent cells. , Here, Alexander Medvinsky and Frederick Livesey summarise some of the exciting data presented at the workshop and draw together the main themes that emerged. See the Meeting Review on p. 17

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Why Not Publish Your Antibody Validation Data

Posted by , on 15 December 2014

Antibodies are frequently used in developmental biology labs, but their validation is crucial to provide the information needed in order to reliably interpret the results of experiments. Antibody validation is also important to help scientists chose antibodies that will be suitable for their experiments, yet the results of these validations rarely get published.

To try and help F1000Research recently launched the Antibody Validation collection. Myself, along with my colleague Matt Helsby from Citeab and Mei Yeung from PeproTech EC Ltd are the guest editors of the collection which aims to provide a platform where researchers and companies can both publish their antibody validation studies regardless of the outcome, and look up existing validation articles for antibodies or experimental setups of their interest. Our goal is to enhance the reliability and reproducibility of antibodies in scientific research. Referees reviewing the validation studies will not focus on novelty and impact, but rather on whether the study is scientifically sound and provides all the relevant information. This allows us to publish validations which might otherwise be lost and include detailed methods and complete data (for example entire western blots).

Formal publication allows scientists doing these validations (which can be onerous and time consuming) to get some tangible credit for their efforts through a recognised citation which once peer reviewed, is indexed in PubMed. So, if you are using antibodies and you are regularly validating them, why not write up this data and publish it? By sharing your information you can help others receive valuable information about antibodies giving them more confidence in which ones they should use in their studies.

We want to be as inclusive as possible in this initiative and encourage participation from everyone involved in using, validating and manufacturing antibodies. So, if you have any thoughts on the collection or would like to be involved please let us know (research@f1000.com), as your suggestions/help will be most welcome.

Andy Chalmers (CiteAb/University of Bath)

 

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PhD position in developmental neurobiology- 2

Posted by , on 12 December 2014

Closing Date: 15 March 2021

How do carbohydrates instruct brain development?

APPLICATION DEADLINE 16th January 2015

Project Code:

2015-EastBio-001

The emergence of a brain at the front-end of a growing embryo requires very precise orchestration to make sure that the right structures form in the right place at the right times. Central to this process is not only the giving of instructions but also their proper transmission and reception.  Over the past few years scientists have made considerable strides  in identifying the protein signals, or ‘signalling proteins’, which transmit instructions between cells. Signalling proteins are produced by a source and move to their target where they are sensed by receptors on the surface of the target cell. The target cell then changes its behaviour in response to the signal.  A puzzling conundrum is that, despite intense efforts, only a relatively small number of signalling proteins have been identified compared to the complexity of instructions needed to produce the brain. We have focused our attention on the role played by a completely different class of molecules, the carbohydrates, in cell signalling. We are particularly interested in the idea that interactions between carbohydrates and proteins expand the diversity of instructions.

This project  will employ state-of-the-art confocal microscopy in combination with live cell imaging to look in detail at the interaction between biologically powerful signalling proteins called ‘morphogens’ and a structurally diverse type of carbohydrate called ‘Heparan sulphate’ (HS), a linear polysaccharide which is modified by differential sulphation. Morphogens are a class of signalling protein important for brain development as cells are very sensitive to the amount they encounter such that even small changes in level can have a dramatic effect on brain development including developmental defects. We have discovered that the pattern of HS sulphation regulates morphogen gradient emergence and signalling in the developing brain and that mouse mutants with abnormal HS structure have brain malformations (Conway et al., 2011; Clegg et al., 2014). In order to investigate the molecular mechanism in more detail, we are developing a novel culture system, which allows us to apply a source of morphogen labelled with green fluorescent protein (morphogen-GFP) to developing brain tissue and then track its movement over time. By comparing the behaviour of morphogen-GFP when presented with normal and abnormal HS we can build up a picture of how HS normally functions and how the process can go awry. The overarching goal of the project is a deeper understanding of how carbohydrates and proteins coordinate to instruct biological processes.

This project will provide training in advanced confocal microscopy and image analysis as well as more standard molecular biology techniques involved in building GFP expression constructs, gene expression analysis, and working with transgenic mice. Live cell imaging is an area of rapidly-growing importance in both academia and commercial environments, because only this technology delivers results with high temporal and spatial resolution of molecular events such as the in vivo distribution of morphogens etc. The skills acquired will be of great value and transferrable to many other research areas, either in academia or the biotechnology / pharmaceutical sector.

This project is part of the BBRSC EASTBIO Doctoral Training Partnership. For information on this scheme please see http://www.eastscotbiodtp.ac.uk/

References
Clegg, J. M., Conway, C. D., Howe, K. M., Price, D. J., Mason, J. O., Turnbull, J. E., Basson, M. A. and Pratt, T. (2014) ‘Heparan sulfotransferases hs6st1 and hs2st keep erk in check for mouse corpus callosum development’, The Journal of neuroscience 34(6): 2389-401.

Conway, C. D., Howe, K. M., Nettleton, N. K., Price, D. J., Mason, J. O. and Pratt, T. (2011) ‘Heparan sulfate sugar modifications mediate the functions of slits and other factors needed for mouse forebrain commissure development’, The Journal of neuroscience 31(6): 1955-70.

 

Additional Project Info:

This project is part of the BBSRC EASTBIO Doctoral Training Partnership and applications will be directed to this programme.
To apply for this PhD  position please visit the Edinburgh Neuroscience PhD Gateway
http://www.edneurophd.ed.ac.uk/development-neurones-and-networks/how-do-carbohydrates-instruct-brain-development%232015-eastbio-001
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PhD position in developmental neurobiology- 1

Posted by , on 12 December 2014

Closing Date: 15 March 2021

Functional importance of HS carbohydrates in brain development.

APPLICATION DEADLINE 5th January 2015

Project Code:

2015-CIP-012

Understanding the developmental mechanisms which create the CNS of healthy individuals is important for understanding neurological and psychiatric disorders with neurodevelopmental components. Although great strides have been made in identifying key regulators of this process our understanding is still rudimentary. Improving our knowledge base in this area is likely to impact on future attempts to understand disease and regenerate damaged circuitry.

While the roles played in signalling by proteins, secreted ligands and their receptors as well as transcription factors, has been intensively studied the roles played by carbohydates, while generally acknowledged as important, have been under-explored. Our research focuses on a class of membrane-associated and extracellular molecules called heparan sulphate proteoglycans (HSPGs) and more specifically on their carbohydrate component heparan sulphate (HS). HS interacts with signalling molecules critical for development so is well placed to coordinate developmental programs.  The permutations of HS structural modification, largely as a result of differential sulphation, are so numerous that HS has the potential to be the most information-rich biopolymer known, making it an excellent candidate for regulating complex events involved in brain development and an important molecular system to understand.

The corpus callosum is a well studied model system for the development of complex neural structures and connectivity so is ideal for investigating the function of novel signalling molecules such as HS. We have identified HS modifying enzymes which are essential for normal callosal development proving the functional importance of differential HS sulphation in this sysyem (Conway et al., 2011; Clegg et al., 2014). We are now well placed to take this work to the next level and investigate the underlying cellular and molecular functions of the hitherto relatively unexplored HS molecule.

This project will explore how the controlled regulation of differential HS sulphation by HS modifying enzymes is an essential component of brain development. The project will use transgenic mouse, ex vivo culture, and/or imaging approaches to obtain a deeper understanding of the normal cellular and molecular functions of HS in the developing mammalian brain.

 

References:

Clegg, J. M., Conway, C. D., Howe, K. M., Price, D. J., Mason, J. O., Turnbull, J. E., Basson, M. A.and Pratt, T. (2014) Heparan sulfotransferases Hs6st1 and Hs2st keep erk in check for mouse corpus callosum development, J Neurosci 34: 2389-401.

 

Conway CD, Howe KM, Nettleton NK, Price DJ, Mason JO, Pratt T. (2011) Heparan sulfate sugar modifications mediate the functions of slits and other factors needed for mouse forebrain commissure development. J Neurosci. 31:1955-70.

 

Pratt lab page

http://www.ed.ac.uk/schools-departments/integrative-physiology/staff-profiles/tom-pratt

 

To apply for this PhD position please go to the Edinburgh Neuroscience PhD gateway page

http://www.edneurophd.ed.ac.uk/development-genetics/functional-importance-hs-carbohydrates-brain-development%232015-cip-012

 

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Two Postdoc scholarships in Cancer Biology

Posted by , on 11 December 2014

Closing Date: 15 March 2021

Two Postdoc scholarships in Cancer Biology

with focus on the EMT process

at Umeå Centre for Molecular Medicine

http://www.umu.se/english/about-umu/news-events/grants/12-1803-14

 

Umeå Centre for Molecular Medicine (UCMM) (www.ucmm.umu.se) is an interdisciplinary research centre with several research groups that study areas of biological and medical relevance. Localized in a tight environment of diverse biomedical laboratories, UCMM forms a creative and interactive unit for cutting edge biomedical research.

 

The scholarships are for 1 year with the possibility for 1 year extension.

Starting date: As soon as possible

Project description

The main focus is to understand the molecular mechanisms that control the epithelial-to-mesenchymal-transition (EMT) process. The project will initially use developmental biology processes as model systems to study EMT, with the possibility to validate our results in established in vitro and in vivo cancer models. The applicants will use functional experiments such as cell and tissue cultures, as well as chick in ovo electroporations and analysing relevant mice mutants. The studies involve common developmental and molecular biology methods like; immunohistochemistry, in situ hybridization, and statistical analyses and image preparations.

Qualifications

The ideal candidates should be PhDs with a background in cancer, molecular or developmental biology, and passed an animal research course. A thorough theoretical and practical grounding in molecular and cell biology is a prerequisite. Practical experience with functional cancer (EMT) models, vertebrate embryonic model systems, molecular and cell biology methods and live imaging is an advantage. The applicants should be proficient in written and spoken English, and have good computer skills (Word, Photoshop, Excel). Of importance are also good organizational, independence, cooperation and problem solving skills.

Other qualifications

An international postdoctoral training in the field of Cancer Biology, Molecular Biology or Developmental Biology is a merit.

 

For further information please contact: Professor Lena Gunhaga, 090-785 44 35, lena.gunhaga@umu.se

 

Applications that are submitted electronically should consist of a single document in Word or PDF format and include the following information; 1) The applicants research interest, experience and suitability for the scholarship

(max 1 page).

2) Methods that the applicant master (max 1 page).

3) Curriculum Vitae of the applicant including publication list.

4) Names and contact information of 2 referees, and stated professional

relationship with the applicant (max 1 page).

 

Your complete application marked with reference numberFS 2.1.12-1803-14, should be sent to medel@diarie.umu.se to be received by 8 of February, 2015, at the latest.

We look forward to receiving your application!

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Fully funded Healing Foundation PhD Studentship available to UK/EU or international students 2

Posted by , on 11 December 2014

Closing Date: 15 March 2021

Title: The role of reactive oxygen species (ROS) during tissue repair and regeneration

Supervisors: Professors Enrique Amaya and Ralf Paus, University of Manchester

Application deadline: January 30, 2015

Description:

There has been a resurgent interest in identifying the mechanisms by which various organisms are able to regenerate fully functional appendages and organs, as this information may help pave the way towards treatments in humans that better facilitate a regenerative response following injury. We recently found that appendage regeneration induces a sustained production of reactive oxygen species (ROS), and this production is necessary for appendage regeneration [1]. The overall aim of this project is to investigate the regulation and role of ROS during tissue repair and regeneration, using a variety of model organisms, including Xenopus embryos and tadpoles, zebrafish larvae and human skin organ culture [2]. Importantly, this project aims to determine the extent to which sustained ROS production is necessary for tissue repair and regeneration across different organisms, and whether an inability to produce a controlled and sustained increase in ROS levels may be associated with loss of regenerative capacity in mammals, including humans. A key question that needs to be addressed in pursuing this work will be to determine the mechanisms responsible for the production of ROS following injury.

The main questions this PhD project will aim to answer are:

1. What are the mechanisms that lead to the production of ROS following injury in various model organisms?
2. Is a role for sustained ROS production essential in tissue repair and regeneration across different model organisms?
3. What is the role of ROS production in adult human skin wound healing?

Related Publications

1 Love, N.R., Chen, Y., Ishibashi, S., Kritsiligkou, P., Lea, R., Gallop, J.L., Dorey, K. and Amaya, E. (2013) Amputation-induced reactive oxygen species (ROS) are required for successful Xenopus tadpole tail regeneration. Nature Cell Biology, 15:222-228.

2 Meier NT, Haslam IS, Pattwell DM, Zhang GY, Emelianov V, Paredes R, Debus S, Augustin M, Funk W, Amaya E, Kloepper JE, Hardman MJ, Paus R. Thyrotropin-releasing hormone (TRH) promotes wound re-epithelialisation in frog and human skin. PLoS One. 2013 Sep 2;8(9):e73596.

Further information: http://www.ls.manchester.ac.uk/phdprogrammes/projectsavailable/project/?id=1917

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Fully funded Healing Foundation PhD Studentship available to UK/EU or international students 1

Posted by , on 11 December 2014

Closing Date: 15 March 2021

Title: The role and regulation of metabolic reprogramming during successful appendage regeneration

Supervisors: Professors Enrique Amaya and Royston Goodacre, University of Manchester

Application deadline: January 30, 2015

Description:

Many vertebrate species, including fish, amphibians and reptiles, have the ability to regenerate their appendages following amputation [1,2]. The regeneration process coordinates a variety of biological processes, all of which rely on molecules and energetic equivalents produced during cellular metabolism. Yet despite its intuitive importance, very little is known about how cellular metabolism is regulated during vertebrate tissue regeneration.

We recently found that the expression of a substantial number of genes governing glucose metabolism was greatly altered during Xenopus tadpole tail regeneration [3]. These data and others have led us to hypothesize that glucose metabolism and its regulation plays an essential role during vertebrate appendage regeneration [4]. Furthermore, we found that appendage regeneration induces a sustained production of reactive oxygen species (ROS), and this production is necessary for appendage regeneration [5]. The overall aim of this project is to investigate the regulation and role of carbohydrate metabolism during appendage regeneration, using Xenopus embryos and tadpoles as the model organism. More specifically we plan to explore the link between ROS production and metabolic reprogramming, in the context of tissue regeneration and embryogenesis. The main questions we wish to answer are:

1. Do embryos and regenerating tissues exhibit the Warburg effect, such that anabolic pathways are promoted?
2. What is the effect of ROS production on cellular metabolism in regenerating tissues?
3. What are the critical molecular targets of ROS that facilitate anabolic pathways during tissue regeneration?

This project will combine advanced in vivo studies with advanced metabolomic and proteomic analyses.

References

1 Brockes, J.P. and Kumar, A. (2008) Comparative aspects of animal regeneration. Annu Rev Cell Dev Biol 24: 525-49.

2 Sanchez Alvarado, A. and Tsonis, P.A. (2006) Bridging the regeneration gap: genetic insights from diverse animal models. Nature reviews 7: 873-84.

3 Love, N.R., Chen, Y., Bonev, B., Gilchrist, M.J., Fairclough, L., Lea, R., Mohun, T.J., Parades, R., Zeef, L. and Amaya, E. (2011) Genome-wide analysis of gene expression during Xenopus tropicalis tadpole tail regeneration. BMC Dev Biol 11: 70.

4 Love, N.R., Ziegler, M., Chen, Y. and Amaya, E. (2013) Carbohydrate metabolism during vertebrate appendage regeneration: What is its role? How is it regulated? BioEssays, in press.

5 Love, N.R., Chen, Y., Ishibashi, S., Kritsiligkou, P., Lea, R., Gallop, J.L., Dorey, K. and Amaya, E. (2013) Amputation-induced reactive oxygen species (ROS) are required for successful Xenopus tadpole tail regeneration. Nature Cell Biology, 15:222-228.

Further information: http://www.ls.manchester.ac.uk/phdprogrammes/projectsavailable/project/?id=1918

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Travelling Fellowship deadline approaching!

Posted by , on 10 December 2014

Are you a postdoc or student planning to visit a collaborator’s lab?

Then apply for a Development travelling fellowship! You can be awarded up to £2,500 (or currency equivalent) to offset travel costs and expenses, and there are no restrictions on nationality.

 

The deadline for application is the 31st of December.

Find out more on the Travelling Fellowships website and by reading the posts by previous successful applicants.

 

Travelling Fellowships image

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A Day in the Life of a Turtle lab

Posted by , on 9 December 2014

We are Juan Pascual-Anaya and Tatsuya Hirasawa, two postdoctoral fellows at RIKEN (Kobe, Japan), in the laboratory of Shigeru Kuratani. We both have been working for the last 4-5 years using turtles as a model organism in the laboratory, studying different aspects of the carapace development.

 

Turtles

Three different turtles used in our lab.

 

The turtle shell, composed of dorsal and ventral moieties, the so-called carapace and plastron, respectively, is an outstanding example of what in evolutionary biology is called a morphological novelty. If you think of the body plan of a general tetrapod, you’ll realize that the turtle is the only one with such a display of the ribs in the dorsal part of the animal, disposition in which during development the shoulder girdle eventually ends up below the ribs (when generally it is outside the ribcage –we know everyone would be touching his or her shoulder blade at this moment–). The turtle shell is a genuine evolutionary innovation, as it has no counterpart in other animals. We are interested in uncovering the developmental mechanisms underlying this morphological novelty.

Using the turtle as a model in the laboratory is not so different from using for example the chicken, but with one big disadvantage: turtles only lay eggs seasonally, meaning that we need to concentrate all of our efforts to perform in vivo experiments during the summer. We mostly work with the Chinese soft-shell turtle, Pelodiscus sinensis (picture above, on the right). And why is that? Well, the Chinese soft-shell turtle is a delicacy found in the Asian market. Here in Japan, where it is called suppon (スッポン), it is used for the preparation of an exquisite dish, the suppon-nabe in which the turtle is cooked in a soup with rice. This fact makes it possible to directly order eggs to a local farm. And that is exactly what we usually do. During the reproductive season, we order around 100 eggs weekly. Then, depending on the availability, we’ll get that or less… or nothing. For example, when the weather worsens, the turtles do not lay eggs.

This is what we usually do in a day, or more strictly, along the whole season:

When the eggs arrive, they do it slightly burrowed in a wet sand or mud, with no so much water, just enough to keep the humidity within the box. We then need to dig them out, clean the excess of sand and put them on a clean and wet litter. We then culture them at 30 degrees. Fortunately, the development of P. sinensis is quite synchronous, more than in chicken, and we can know exactly in which stage the embryos will be everyday. There are several staging tables available for many turtles. For P. sinensis, our supervisor Shigeru Kuratani reported such standard table back in 2001 (Tokita and Kuratani, 2001).

 

Eggs of Pelodiscus sinensis just after arriving to the lab.

 

So, we then will use most of the eggs to get embryos at given stages in which we would like to study the expression pattern of a gene, that is to do in situ hybridizations. The eggs of P. sinensis are quite small, so we need to manage them with care to avoid just smashing them and losing embryos. We use fine forceps and dissecting scissors to open them, and if the embryo is old enough, we peel the egg’s shell little by little, until the embryo is fully visible. When the embryos are way too young, for instance until stage 11 or so (like stage HH16 of chicken), the embryo can be dragged completely in a piece of egg’s shell, put this upside-down, and then extracted from the egg shell. It’s like using a holed piece of paper to extract young embryos of chicken, but using the shell itself. Then, the embryos are just fixed in paraformaldehyde as in standard protocols.

The eggs, on the other hand, can be windowed as the chicken ones, but with a very small hole. Then, we can assay the embryos with a number of techniques. This includes electroporation, DiI labellings, embryological operations, and so on. In one experiment that I have been involved recently, I was introducing morphogen-soaked beads into the lateral trunk of the turtle embryo. This is just as it has been done in chicken, but in miniaturized egg! You can see in the picture below a windowed egg and the embryo inside.

Psinensis_TK14-11-08-08-005OLYMPUS DIGITAL CAMERA

Windowed egg of P. sinensis showing an embryo at stage TK13-14

 

Last, we sometimes need just hatched juveniles. P. sinensis juveniles usually hatch around a month and a half after they arrive to the lab, and here you can see the birth moment in the following video:

 

 

I hope you liked what can be done using turtles in the lab.

Thanks!

Juan and Tatsuya.

 

 

Node day in the life new doodle squareThis post is part of a series on a day in the life of developmental biology labs working on different model organisms. You can read the introduction to the series here and read other posts in this series here.

 

 

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Seeing cells from a different angle

Posted by , on 7 December 2014

Brunskill et al, 2014

Thanks to microscopy, scientists can compete with the most talented photographers and take the most astonishing pictures! Although I have been focusing on microscopy pictures in this blog, microscopy is not the only way to make pretty pictures of cells.

In recent years, the rapid progress in sequencing technology has propelled this technique to the front stage and it is now widely used to study gene expression in single cells. Whereas with microscopy, we can observe only a limited number of parameters per cell, sequencing allows us to observe the expression of thousands of genes per cell.

DNA sequencing is the technology that determines the nucleotide order of a given DNA fragment (for example: ATTTCGAGCCGT). Sequencing can be used to screen for genetic mutations or for paternity testing for example. In the case of gene expression studies, the RNA rather than the DNA is sequenced. Gene expression is the process by which information from a gene (DNA) is used in the synthesis of a protein (gene product). The intermediate molecule between the DNA gene and the protein is RNA. RNA is encoded from DNA and used to synthesize the protein it is coding for. Thus in order to define gene expression in a single cell, we isolate the RNA from the cell, sequence it to identify it and quantify it. The more RNA molecules there are coding for a specific protein, the higher the expression for the corresponding gene is.

In a recent study published in Development, Brunskill and colleagues used this RNA-seq technology in order to create an atlas of gene expression patterns in the developing kidney. For example, this picture is a “heatmap” showing the gene expression pattern in the renal vesicle (a region within the kidney). Each horizontal line corresponds to the expression level of one gene, with red for high expression, yellow for intermediate expression and blue for low expression. Each vertical column corresponds to a single cell. From this heatmap, Brunskill and colleagues observed that the gene expression pattern in the renal vesicle is highly polarized with very distinct gene expression profile in the proximal cells (left portion of the heatmap) versus the distal cells (right portion of the heatmap).

Unsurprisingly, this high-throughput technology is becoming increasingly popular as it provides very detailed information about single cells, highlights unforeseen patterns among tissues, beautifully captures the uniqueness of each cell and, one must admits, generates fascinating graphical displays!

 

Picture credit:

Brunskill E. W, Park, J-S, Chung E. Chen F., Magella, B., and Potter S. S. (2014). Single cell dissection of early kidney development: multilineage priming. Development 141, 3093-101.

doi: 10.1242/dev.110601.

 

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Categories: Research