This interview first appeared in Development.

The 2014 Society for Developmental Biology (SDB) Lifetime Achievement Award was jointly awarded to Christopher Wylie and Janet Heasman in recognition of their outstanding and sustained contributions to the field. At the 73rd Annual SDB meeting, where they were presented with the award, we asked Chris and Janet about their careers and their advice for young researchers.

You both started off in medical school and then switched to a career in basic research. What inspired you to make the switch?

C: Actually,much of it was due to one of my professors, J. Z.Young, who did several things that enhanced basic science in medicine. Because students enter medical school directly from high school in England, they do not get exposed to research. J. Z. introduced a BSc-level science degree into the medical school curriculum. This was offered to students who did well in their medical examinations, and also served as entry into the MD/PhD program. Both Janet and I went with this route and just fell in love with biomedical research. A major part of the BSc course was a research project. I did mine with Ruth Bellairs and became fascinated by embryo development. I tried to make a movie of one of the experiments that we were doing but, in those days, making movies of embryos was a very complicated business. The movie (of a chick embryo) I was making went on all night, so I had to sit in the hot room for hours (there were no heated slide chambers in those days). Because of the heat, the grease in the microscope would melt and the body of the microscope would slowly slip down the column, so it had to be refocused after each image. By about 3 o’clock in the morning I was virtually naked and dripping with sweat! But I couldn’t believe my eyes as more and more embryonic structures appeared, as if by magic. Of course I had seen diagrams of development in my lectures, but I had never actually seen it happening. I was absolutely gobsmacked! That was my epiphany. And so I finished my BSc and was lucky enough to get offered a PhD place. Of course, the original objective was to then return to clinical medicine but I never did. I was offered a lectureship at University College, London, and that was the end of my clinical career.
 
J: I even did a year of clinical training (in those days medical school was two years of preclinical training and then three years of clinical school) but I didn’t enjoy it. I had the chance to go to Dartmouth College and work as a teaching assistant with Chris in developmental biology. While I was there I gave three lectures and I remember thinking to myself, if I can do this – if I can teach developmental biology successfully – then I am going to go back to England, pull out of my medical career and register as a PhD student. And that is what I did.

You’ve both been involved in setting up developmental biology institutes – in Cambridge, Minnesota and Cincinnati – and these are all continuing to flourish. What do you think is the key to success in a good research department or institute?

C: I think you have to have the right people…and money! If you recruit scientists who are willing to interact with each other and not compete, then you’ll probably have a successful institute, especially if it is well funded. Another thing that might seem trivial but proved to be very important was the tea room! It offered a centre where principals, group leaders, graduate students, postdocs and technicians could all meet and talk informally. Every morning at 10.30 at the Wellcome/CRC Institute in Cambridge (now the Gurdon Institute) we would all go up to the tea room for tea/coffee and chat. The things that we chatted about were not just ‘do you have an antibody against x that we can borrow?’, it was also ‘how do you think the institute could work better?’, ‘how can we improve the vivarium?’, ‘how is our financial situation?’. This day-by-day interaction was amazingly helpful for all aspects of the institute’s activities, not just our own research. It certainly made faculty meetings shorter because we had already discussed pretty well everything that came up.

J: Yes, the tea room worked really well in England.We tried very hard to make it work in the USA, but it was hard to persuade people to go to the tea room. No one would allow themselves enough time off to interact over tea! I also agree that the success of an institute depends on having the right people and being very careful in the job searches. It is absolutely essential to hire people who are interactive and who are going to collaborate with each other. It’s also important to have freedom – the freedom to be able to do science the way you want.
 
C: Yes, in Cambridge, the institute was funded by the Wellcome Trust and the Cancer Research Campaign, and they gave us a free hand. So we were largely buffered against Cambridge University politics and departmental structure. Similarly, in Minnesota I was just given the money and told ‘we need a centre for developmental biology’.  And in Cincinnati I was given an even larger amount of money and told ‘build us a centre for developmental biology, Chris’. When you have such a financial advantage, it is not that difficult.

Chris, you have obviously been heavily involved with Development: you were Editor-in-Chief for a very long time and you made some pretty drastic changes to the journal when you started. How did you get involved with the journal and what prompted you to make those bold changes?

C: It all began when I was the Publications Officer of the British Society for Developmental Biology (BSDB). My job was to think up suitable symposium topics and identify people who could put a symposium together, edit the volume and to see it through to publication. At first, the papers presented at these symposia were published by Cambridge University Press as books, but the publication times were long and the costs were very high (and the profits to the society correspondingly small). So the BSDB moved to publishing their symposia as supplement volumes to The Journal of Embryology and Experimental Morphology (JEEM), which was owned and published by The Company of Biologists. The symposia attracted outstanding speakers (and therefore authors) from all over the world, and I couldn’t help noticing that the articles in the symposium supplements were generally more exciting than those in the parent journal. I thought, we are missing a lot of stuff in our journals in the UK. We need a journal that will capture the most recent advances in cellular, molecular and genetic approaches to developmental biology. So I went to several publishers and I said that I think there should be a journal (I had already called it Development in my mind) that captures all this stuff that the current British journals are missing. Lots of publishers took an interest in this. I was then approached by The Company of Biologists (who had heard about these discussions) and asked if I would take over the editorship of JEEM. I told them that I didn’t want to be the editor of JEEM but that I would consider being the editor of a different journal, one that had all the things that I thought should go into a topical developmental biology journal, and with a more modern format. Eventually they agreed. They said ‘Okay, do whatever you want.We will start a new journal, we will replace JEEM with this journal, and you can make whatever changes you want!’. And so I had a journal – Development – on my hands. It was absolute mayhem initially – it was probably June when we started and we had to have the issue out by January the following year – but, mercifully, the world’s developmental biologists reacted magnificently. I guess everyone else thought that there should be a journal like that, too.

That was over 25 years ago. How do you think the field has changed since then?
 
C: Well, I think the science – especially in terms of techniques and approaches – is changing all the time. In just one year, since I’ve retired, I can see by coming back to this meeting that there are techniques that we weren’t using just last year when I was in the lab.

J: Another big change is that everything is now online. The fact that no one uses libraries anymore has changed publishing, and it has changed interactions between people and groups.

C: It also means that, to some extent, it doesn’t really matter anymore where you publish, because people don’t go to libraries and open journals and go through them. They use searches and keywords so it doesn’t really matter whether your paper is published in what was formerly regarded as a ‘second tier’ journal or a premier journal; if your paper is good, it is going to be read.

J: And it is going to be reviewed in a very informal sense too – online. There are big pluses to that but there are also some minuses because sometimes only the people with the loudest ‘voices’ will be heard. Distinguishing gossip from good science is becoming more and more difficult these days.

C: Another thing that has changed a lot is the number of model organisms studied. When I was a student there were at least a dozen experimental model organisms being used to study development.We needed to learn their anatomy and embryogenesis to keep up with the genetic, molecular and cellular data coming out. However, as both the time and money required to set up the appropriate protocols and reagents became so great, the number of model organisms used contracted dramatically. So, during the time that I was an editor at Development,we ended up going from a dozen or so model organisms that made regular appearances in its pages to just four or five.

J: But now it has expanded again, which is really exciting. Techniques such as CRISPR have allowed us to go the other way. It was very noticeable at this meeting that there are again a variety of model organisms being used. Evolution is at the centre again.

Science seems to be quite competitive these days, and it is getting increasingly difficult to get an academic tenure track position. What is your advice to young people who are starting out?

J: To recognise that it is very important to develop your own ideas of what research you want to do, even as a graduate student; don’t wait until the postdoc stage. Actively think about where you want your career to go and look for the labs that will fit what you want to do, rather than looking for the lab that will take you. You will be impressive in an interview if you know what you want to do. Rather than thinking ‘how am I going to finish my graduate studies?’, ‘how am I going to get my first fellowship?’ and so on, think ‘what am I really interested in answering?’, ‘what biological question do I want to answer?’ and ‘which model system should I use?’.

C: I think you have to choose the right postdoc position. This is really, really important. Also, you need to find good mentorship. That applies at all levels. If you don’t have a good PhD mentor, who will look after your next stage by being honest about labs that you should or should not go to as a postdoc, you are at a serious disadvantage. Similarly, you need a good postdoc mentor whowill advise you about which places you should think about going to for getting a job (and where you should not think about going to!). And then, when you are an assistant professor, you need really good mentorship for all aspects of your research life, including: research approaches, collaborations that will help you, grant applications, recruitment of lab personnel, disputes that occur in your lab, where you should send your papers, what committees you should (and shouldn’t) sit on.Young faculty are not ready for that kind of stuff, and they need senior faculty to act as good mentors and who can offer them advice, read papers and grants, and provide honest feedback.

You’ve both had very successful careers working as a husband-and-wife team while raising a family. What is your advice to younger people who are starting off in terms of work-life balance?
 
J: I think my advice is just to do it. There is no easy way. And that is true whether you are a scientist or working in banking or business. It is a balancing act that requires constant communication. I think scientists in some ways have it easy if they work together. I can always say I know where Chris is – he is in the lab! I know how to contact him there. I actually think that science is a good career for husband and wife teams. And don’t take yourself, and science, too seriously; at the end of the day you are a small cog in a big wheel and your kids carry on after you.
 
C: And be prepared to work shifts. We used to do that a lot.
 
J: And my advice to young women is: don’t put off having kids until the time is right. Because the time is never right.

C: The problem with putting off kids until the ‘right time’ is that you have to set criteria for the right time, and it is hard to know when these have been met. It is easy to say ‘we will have children when…’. But of course you never reach the ‘when’.

And, finally, what would people be surprised to find out about you?
 
C: I don’t think there is much about me that would surprise people. I think the basis for my success in editorship and leadership has been that I’m not a particularly complicated or devious person. So nobody ever needed to try to second guess me! I suppose that, given the public persona required to teach, lead a research centre, or edit a major journal, people might be surprised to know that I’mnot a gregarious person. The best part of my career has been working quietly in the lab, trying to discover things, reading about the discoveries others have made (I really miss the library), and trying to integrate it all into new knowledge.

(6 votes)

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Here are the highlights from the new issue of Development:

Akt acts to reprogram germ cells

Primordial germ cells (PGCs) are unipotent – they go on to form germline stem cells and gametes. However, they are believed to possess latent pluripotency, allowing them to produce the next generation during the normal life-cycle, and to be reprogrammed to pluripotent embryonic germ cells (EGCs) upon experimental manipulation. Various protocols for EGC establishment have been reported, with varying efficiency. Yasuhisa Matsui and colleagues now report a highly efficient method for mouse PGC-to-EGC conversion, using Akt activation in concert with bFGF and LIF treatment (p. 4457). Using a relatively simple protocol starting from purified E10.5 PGCs in culture, the authors are able to achieve 60% reprogramming efficiency, which is significantly higher than any previous method. These reprogrammed EGCs readily contribute to mouse chimeras, including the germline. The authors suggest that Akt may act by inhibiting apoptosis of PGCs and/or by promoting signalling events (including via bFGF and LIF) that mediate PGC-to-EGC reprogramming, thus inducing the latent pluripotency of early PGCs.

Cerebral haemorrhage without leaky vessels

The vasculature of the central nervous system (CNS) is highly specialised, characterised by the formation of the blood-brain barrier that prevents leakage of vascular contents into the brain. Various molecules and pathways have been implicated in regulating angiogenesis in the CNS, including the αVβ8 integrin and members of the TGFβ pathway. It is thought that αVβ8 integrin expressed in the neuroepithelium regulates TGFβ signalling in the endothelium. On p.4489, Thomas Arnold, Louis Reichardt and colleagues set out to investigate this relationship and the effects of disrupting this signalling cascade on the CNS vasculature. The authors find that disruption of either the integrin or TGFβ pathway components leads to excess angiogenic sprouting, vascular dysplasia and cerebral haemorrhage. Importantly, however, these mutant mice display no signs of compromised blood-brain barrier formation and the vessels, although abnormal, are not leaky. Together, this work defines an important function for αVβ8 integrin-TGFβ signalling in limiting vascular sprouting in the CNS, and demonstrates that cerebral haemorrhage can result from abnormal angiogenesis rather than from blood-brain barrier breakdown.

Restricting liver progenitor potential

The liver possesses a remarkable capacity to regenerate, but what is the source of new cells during regeneration? The two epithelial cell populations – hepatocytes and cholangiocytes – can proliferate upon injury, but there is also evidence for the existence of an adult stem/progenitor cell, the liver progenitor cell (LPC), which resides in or near bile ducts and has both hepatocytic and cholangiocytic potential. Here (p.4448), Naoki Tanimizu and co-workers investigate the abundance and potential of LPCs from neonatal and adult mice. They find that the number of LPCs decreases during postnatal life, and also observe a change in their differentiation potential: adult LPCs are strongly biased towards the cholangiocyte fate and have very limited ability for hepatocytic differentiation, both in vitro and in vivo. Mechanistically, the authors show that the transcription factor grainyhead-like 2 (GRHL2), which is known to promote cholangiocyte differentiation, is more strongly expressed in adult LPCs than neonatal LPCs. GRHL2 in turn inhibits expression of miRNA122, which is important for the hepatocyte lineage. Thus, upregulation of GRHL2 in adult LPCs provides an explanation for their reduced hepatocytic potential, and its inhibition may help to produce functional hepatocytes in the adult liver.

The origin of the coronary vasculature

During heart development, the coronary vasculature forms by establishment of an endothelial plexus that expands around the heart. Current evidence suggests that the sinus venosus (SV), endocardium and proepicardium may all contribute to coronary development. However, the relative contributions of these sources and the molecular mechanisms regulating coronary angiogenesis are still unclear. In a detailed lineage-tracing analysis in mouse (p. 4500), Kristy Red-Horse and colleagues find that the SV and endocardium make spatially restricted and complementary contributions to the coronary vasculature, with dorsal and lateral vessels having primarily SV origin, while the endocardium contributes significantly to vessels of the ventral heart and ventricular septum. The proepicardium makes a minor, but non-spatially restricted, contribution. VEGFA has previously been shown to promote angiogenesis of a subpopulation of coronary vasculature, and the authors now find that VEGFC promotes growth of a complementary set of vessels – those derived from the SV. These data provide a comprehensive view of the sources of the coronary endothelium and help to unravel the mechanisms by which these vessels form.

PLUS:

An interview with Christopher Wylie and Janet Heasman

The 2014 Society for Developmental Biology (SDB) Lifetime Achievement Award was jointly awarded to Christopher Wylie and Janet Heasman in recognition of their outstanding and sustained contributions to the field. At the 73rd Annual SDB meeting, where they were presented with the award, we asked Chris and Janet about their careers and their advice for young researchers. See the Spotlight on p. 4415

How to make a cardiomyocyte

Kenneth Chien and colleagues discuss how insights into the molecular and cellular framework underlying cardiac development can be used to guide the in vitro specification of cardiomyocytes, whether by directed differentiation of pluripotent stem cells or via direct lineage conversion. See the Primer article on p. 4418

The cellular and molecular mechanisms of vertebrate lens development

Although lens induction has been studied for over 100 years, recent findings have revealed a myriad of signaling pathways and gene regulatory networks that are required for lens formation in vertebrates. Ales Cvekl and Ruth Ashery-Padan summarize recent progress in the field, emphasizing the interplay between the diverse regulatory mechanisms employed to form lens progenitor and precursor cells. See the Review on p. 4432

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The Minnesota Center for Philosophy of Science in the College of Liberal Arts at the University of Minnesota invites applications for a full-time postdoctoral position in conjunction with the project “Integrating Generic and Genetic Explanations of Biological Phenomena,” sponsored by the John Templeton Foundation. This project brings together scholars in philosophy and biology to address the problem of integrating different types of explanations from scientific approaches to bridge the divide between genetic and generic or physical explanatory approaches for three domains of biological phenomena: development, evolutionary novelty, and evolvability (for more details, see: http://genericgenetic.umn.edu/). Position duration: 03/01/2015 to 08/31/2017.

Applicants should have a Ph.D. or equivalent terminal degree in the biological sciences with a background in cellular and molecular development, demonstrated interest in theoretical issues in development and evolution, and evidence or promise of scholarly achievement. Familiarity with computational modeling methods is preferred. The successful candidate will: (a) work with the core team members (http://genericgenetic.umn.edu/people/core-team) on conceptual aspects of integrating genetic and generic or physical explanatory approaches, and (b) carry out an experimental program focusing on the relationship between the gene expression networks and physical dynamics involved in limb pattern formation with the aim of identifying integrated models that provide necessary conditions for the development and evolution of distinctive digit phenotypes in vertebrates.

Apply online: http://employment.umn.edu/applicants/Central?quickFind=125444

For questions regarding the position, please contact Alan Love at aclove@umn.edu.

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We recently demonstrated an improved method for homologous recombination (HR)-mediated genome editing using TALEN (Transcription activator-like effector nuclease) in zebrafish (Shin et al., 2014). In the study, we identified that a total of 3kb of homology in the targeting construct, 1kb of one arm and 2kb of the other arm, is sufficient to induce HR-mediated knock-in. Importantly, our results suggest that a specific targeting construct configuration (a double stranded break in the short homology arm) can enhance the efficiency of HR-mediated knock-in. I believe that the method is highly valuable due to its fundamental advantage, which is the ability to manipulate in vivo genome precisely. In this post, I discuss several potential applications using HR-dependent genome engineering.

Potential applications using HR-mediated genome engineering

1. Tagging fluorescent protein

HR-mediated gene targeting technology allows us to precisely deliver a relatively large DNA fragment encoding a fluorescent protein into a specific locus of the chromosome. For example, HR dependent GFP knock-in alleles will be useful to monitor the spatiotemporal localization of a target protein in vivo. Although there is a potential caveat such as altered protein functions due to tagging, this method allows visualization of tagged proteins in the physiologically relevant condition rather than overexpression context. Tagging a flouorescent protein along with biotinylation tag, such as avitag, will have an additional capacity to study protein-protein interactions. Because in vivo BirA-Avitag system (de Boer et al., 2003) can carry the advantage of mass spectrometry (MS) analysis, the resulting knock-in lines will be useful for tracing the tagged target gene product as well as screening for novel protein binding partners.

2. Mirroring gene expression

As shown in our paper, the expression of a target gene can be monitored by precisely inserted sequences encoding a fluorescent protein that is linked with ‘self-cleaving’ 2A peptides just in front of the a target gene’s stop codon. I believe this strategy will allow tracing of specific cells, which express both a target gene and a fluorescent reporter protein, without functional alterations of the gene products. In addition to this, the physical separation of a target gene product and a fluorescent reporter protein allows for independent protein behaviors, which is important for diversifying methodologies. For example, application of this method with Cre recombinase instead of a fluorescent reporter will result in Cre knock-in lines that can be used to generate tissue specific Cre driver lines for conditional knock-out mutants. Alternatively, specific cell types can be permanently labeled by crossing the ubi:Switch transgenic line (Mosimann et al., 2011) with Cre knock-in lines. Moreover, replacement of the bacterial biotin ligase BirA by a fluorescent reporter will serve as a biotinylation driver for tissue or cell specific gene expression profiling (Housley et al., 2014).

3. Generation of floxed alleles

To create conditional knock-out lines, a gene of interest must be modified by the insertion of two loxP sites to ecise the floxed exon(s) via Cre-mediated recombination. Although the insertion of a loxP site in the target locus can be accomplished by using loxP site containing single-stranded oligonucleotides (ssONs), insertion of two loxP sites can pose a challenge due to low efficiency of ssONs knock-in. Therefore, using a combination of two loxP site containing targeting constructs with TALEN is an useful and efficient strategy to obtain floxed alleles.

I believe that many other applications using HR-mediated genome engineering are already developed or will be invented for innovative research. Hence, our efficient HR-dependent knock-in method will allow many laboratories to generate multi-purpose knock-in lines and serve as a platform for development of more sophisticated genome manipulation methods.

Reference article:

de Boer, E., Rodriguez, P., Bonte, E., Krijgsveld, J., Katsantoni, E., Heck, A., Grosveld, F., & Strouboulis, J. (2003). Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice Proceedings of the National Academy of Sciences, 100 (13), 7480-7485 DOI: 10.1073/pnas.1332608100

Housley, M., Reischauer, S., Dieu, M., Raes, M., Stainier, D., & Vanhollebeke, B. (2014). Translational profiling through biotinylation of tagged ribosomes in zebrafish Development, 141 (20), 3988-3993 DOI: 10.1242/dev.111849

Mosimann, C., Kaufman, C., Li, P., Pugach, E., Tamplin, O., & Zon, L. (2010). Ubiquitous transgene expression and Cre-based recombination driven by the ubiquitin promoter in zebrafish Development, 138 (1), 169-177 DOI: 10.1242/dev.059345

Shin, J., Chen, J., & Solnica-Krezel, L. (2014). Efficient homologous recombination-mediated genome engineering in zebrafish using TALE nucleases Development, 141 (19), 3807-3818 DOI: 10.1242/dev.108019

I thank Nanbing Li-Villarreal for comments.

(2 votes)

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The morphological evolution of limbs and external genitalia were both essential adaptions to a life on land. While the former deals with the novel locomotory challenges facing an animal invading a terrestrial environment, the latter is concerned with something even more essential: reproduction! Living on land means that gametes can no longer be fertilized externally simply by releasing them in water, e.g. as frogs do. Male and female gametes need to be brought together as well as protected from dehydration. Internal fertilization, utilizing specialized external genitalia, solves this dilemma, delivering sperm to their target and hence providing protection inside the animal’s body.

In addition to the adaptive value of limbs and external genitalia in the context of the transition to land, there is also a striking similarity in the patterning genes expressed during the development of these two structures. For both these reasons, a potential co-evolution of limbs and genitals has been discussed in the past^1-4. In our recent Nature paper we have identified another, unexpected link between the limbs and external genitalia that may help to explain some of the molecular similarities between the two⁵.

 
From Limbs to Genitals

As might be expected for Cliff Tabin’s lab, this project also started out as a study focusing on limb development. At the time, Jérôme Gros (a former postdoc in the lab, now PI at Institut Pasteur, Paris) was investigating the earliest steps of limb initiation in vertebrate embryos. He found that in both mouse and chicken embryos the mesenchyme of the growing limb buds originates from the epithelial lateral plate mesoderm (LPM), through a process called epithelial-to-mesenchymal transition, or EMT⁶. Given the interest of our lab in evolutionary questions, former graduate student Jimmy Hu suggested looking for the presence or absence of the same process in the limb-less snake….of which he just happened to have a few embryos in his freezer – courtesy of Olivier Pourquié who had previously brought to our attention the presence of outgrowths at a hindlimb-like position. There was no evidence for such EMT at the level where forelimbs once were supposed to form. However, when looking at the hindlimb level, a clear EMT was visible – only in snakes the resulting mesenchymal cells of this “limb-like” bud contributed to their budding external genitalia, the so-called hemipenes (Figure 1). Such similarity in limb and genital bud initiation in squamates led us to question the developmental origin of external genitalia in other amniotes.

Figure 1. An epithelial-to-mesenchymal transition (EMT) underlies the developmental initiation of the house snake hemipenis and the mouse hindlimb bud. Breakdown of the basement membrane (laminin staining in red) is seen in both embryos (arrowheads).

 
Tracing the Origin of External Genitalia

Squamates (snakes and lizards) are interesting in this regard, as within their clade partial or complete loss of limbs occurred among several species, yet they all keep their hemipenes. Using micro-computed tomography in collaboration with Emma Sherratt (now at University of New England, Australia), we realized that all squamate embryos formed their hemipenis buds at the same level where hindlimbs would form, whereas the mouse genitalia were emerging more posteriorly, towards the tail (see video). Moreover, we were able to visualize the internal location of the cloaca, an endodermal signaling center known to be important for genital outgrowth. Intriguingly, the cloaca seems similarly shifted in all squamate embryos, into the presumptive hindlimb field. This prompted us to determine which cell populations actually give rise to the different species’ genitalia – a question that seemed far from settled, when consulting the available literature.

Using a lentiviral lineage tracing system we were able to demonstrate that, indeed, important differences exist in the developmental origin of external genitalia among different species: whereas the mouse genital tubercle is built mostly of tailbud-descendant cells, the Anolis lizard hemipenis consists of cells from the same embryonic lineage that gives rise to its hindlimbs. In both species the external genitalia thus seemed to “follow” the localized signaling of the cloaca. This suggested the possibility that the evolutionary change in cell populations forming the external genitalia could, at least in part, be attributable to a shift in the relative position of the cloaca.

 
A Deep Homology of Vertebrate Genitalia

An organ’s transcriptional signature is influenced by its developmental origin, yet can also give hints about evolutionary relations to other tissue types^7,8. We therefore performed comparative RNA-seq analyses on early and late budding stages of limbs and genitalia, in both lizard and mouse embryos. Working in distantly related species, while considering similar tissue types, comes with its own set of problems when performing comparative transcriptomic studies – however, after a somewhat rugged start, it soon became clear that the Anolis limb and genitalia transcriptomes show a much higher degree of overall similarity, than was the case for the mouse samples. Also, at early stages, the Anolis hemipenis transcriptome is virtually indistinguishable from a generic limb molecular signature, and only later differentiates into a genitalia-like state. This confirmed, at a molecular level, the relatedness of the cells building limbs and genitalia in the Anolis lizard. Moreover, by grafting the cloacal signaling center into chicken limb buds, we were able to partially induce transcriptional changes reminiscent of early genitalia development, demonstrating the conserved ability of limb cells to respond to these cloacal signals, and supporting the idea that change in the location of the cloaca would have induced a similar genetic program in a different target tissue.

This study offers a potential explanation for the still striking similarities in gene expression in species that develop limbs and genitalia from discrete cell populations⁴ – namely, that a limb-derived state could represent the ancestral condition for the emergence of external genitalia. As such, a limb-like gene regulatory network for genitalia growth might have become hardwired in a putative ancestral genome. The genitalia of mice and lizards, while not homologous to one another sensu stricto, might thus represent an example of Deep Homology⁹: with homology in the genetic programs being executed and induced by the same ancestral signaling source, the cloaca.

1. Kondo T, Zákány J, Innis JW, & Duboule D (1997). Of fingers, toes and penises. Nature, 390 (6655) PMID: 9363887

2. Yamada, G., Suzuki, K., Haraguchi, R., Miyagawa, S., Satoh, Y., Kamimura, M., Nakagata, N., Kataoka, H., Kuroiwa, A., & Chen, Y. (2006). Molecular genetic cascades for external genitalia formation: An emerging organogenesis program Developmental Dynamics, 235 (7), 1738-1752 DOI: 10.1002/dvdy.20807

3. Cohn, M. (2011). Development of the external genitalia: Conserved and divergent mechanisms of appendage patterning Developmental Dynamics, 240 (5), 1108-1115 DOI: 10.1002/dvdy.22631

4. Lin, C., Yin, Y., Bell, S., Veith, G., Chen, H., Huh, S., Ornitz, D., & Ma, L. (2013). Delineating a Conserved Genetic Cassette Promoting Outgrowth of Body Appendages PLoS Genetics, 9 (1) DOI: 10.1371/journal.pgen.1003231

5. Tschopp, P., Sherratt, E., Sanger, T., Groner, A., Aspiras, A., Hu, J., Pourquié, O., Gros, J., & Tabin, C. (2014). A relative shift in cloacal location repositions external genitalia in amniote evolution Nature DOI: 10.1038/nature13819

6. Gros, J., & Tabin, C. (2014). Vertebrate Limb Bud Formation Is Initiated by Localized Epithelial-to-Mesenchymal Transition Science, 343 (6176), 1253-1256 DOI: 10.1126/science.1248228

7. ARENDT, D. (2005). Genes and homology in nervous system evolution: Comparing gene functions, expression patterns, and cell type molecular fingerprints Theory in Biosciences, 124 (2), 185-197 DOI: 10.1016/j.thbio.2005.08.002

8. Wagner, G. (2007). The developmental genetics of homology Nature Reviews Genetics, 8 (6), 473-479 DOI: 10.1038/nrg2099

9. Shubin, N., Tabin, C., & Carroll, S. (2009). Deep homology and the origins of evolutionary novelty Nature, 457 (7231), 818-823 DOI: 10.1038/nature07891

(2 votes)

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In the early ‘90s, the discovery of neural stem cells in the adult brain aroused hope to exploit these cells to treat neurodegenerative diseases or even induce brain regeneration. Yet, the real potential of these cells is still unclear. In the last 15 years we have learned that during development neural stem cells are an heterogeneous population of progenitors whose neurogenic potential is restricted by spatial and temporal patterning mechanisms. Many of these cells at the end of development stop producing neurons but begin to generate a closely related related cell type: the astrocytes. Interestingly, some of these astrocytes, derived from all the main domains of embryonic progenitors, continue to produce neurons throughout life, fueling not only our brain but also our regeneration dreams. Unfortunately however, the neurogenic potential of these neuronal progenitors is restricted to few neuronal types destined to the olfactory bulb and dentate gyrus, a drop in the sea of neuronal types that characterize the CNS. Yet, given that astrocytes are widely distributed in the adult brain, understanding if besides those located in the neurogenic niches other astrocytic populations may retain a neurogenic potential is a highly relevant issue. In the early studies on adult neurogenesis, all brain regions beyond the olfactory bulb and dentate gyrus were stigmatized as “non-neurogenic”. This concept derived from the observation that in mice and rats these regions do not show active neurogenesis and when transplanted with neural stem cells these cells differentiate only into glia.

More recently, comparative studies have shown that in other mammalian species, including humans, a low level of neurogenesis occurs also in “non-neurogenic regions” such as the striatum and to a lesser extent the neocortex. Most importantly, brain lesions un-hide such neurogenic activities also in laboratory rodents. In some cases the newborn neurons were proposed to be generated by local progenitors, and recently it has been shown that in the mice striatum after stroke these local progenitors are astrocytes (Magnusson et al., 2014). We also obtained similar results in an excitotoxic model of Huntington disease (Luzzati et al. under revision). The main problem of these findings is that the fate of the newborn neurons generated in “non-neurogenic regions” remains largely unknown, and the hypotheses regarding their possible function/s range from an attempt to brain repair to an aberrant phenomena. Indeed, in all models of neurogenesis in “non-neurogenic regions” newborn cells have a short life span and fail to express typical markers of the neuronal types that populate the regions in which they are generated.

In the last few years our lab contributed to these studies showing that in rabbits newborn neurons generated in the SVZ also migrate toward the frontal cortex (Luzzati et al., 2003; Luzzati et al., 2006), and that local progenitors in the striatum are able to generate neurons (Luzzati et al. 2006). We also demonstrated that both the SVZ and local progenitors produce neurons in the striatum of a model of striatal progressive degeneration in mice (Luzzati et al., 2011)

Lateral view of a 3D model obtained from coronal sections stained with the marker of immature neuroblasts DCX. The location of the reconstructed region is outlined in the upper model. Chains of DCX+ neuroblasts (red) are mostly restricted to the vPSB and in close contact with blood vessels (violet)

In this issue of Development (Luzzati et al. 2014) , we describe a new model of adult neurogenesis in the lateral striatum (LS) of the Guinea Pig that adds some important pieces to the puzzle. First, we show that the LS of the Guinea Pig contains neuronal progenitors, likely of astrocytic nature, that are quiescent at birth but become transiently activated around weaning. This observation challenges the classic idea that the mature brain parenchyma is not permissive for the activity of neuronal progenitors, and it is thus of great interest for stem cell research. At the same time, the more significant feature of a neuronal progenitor it is its cell fate potential. We thus followed the fate of new LS neurons with BrdU and lentiviral vectors and clearly established that these cells have a short life-span, and do not differentiate into striatal neurons nor express markers involved in their specification. Nonetheless, these cells acquire complex morphologies and we propose that they represent a novel cell type. Interestingly, new LS neuroblasts share several features with neuroblasts generated during striatal degeneration in mice, such as expression of Sp8, a tropism for white matter tracts, and a short life span. At least in the guinea pig, the transient nature of neuroblasts may be related to their transient production and strongly support a transient role in circuit remodeling. Future studies should clarify if these cells actually represent a new player for brain plasticity. Moreover, it would be also interesting to understand if this form of plasticity is present also in other mammals, including humans, and if it plays any role after lesion. A comparative framework will be essential to answer these questions.

Luzzati, F., Peretto, P., Aimar, P., Ponti, G., Fasolo, A., & Bonfanti, L. (2003). Glia-independent chains of neuroblasts through the subcortical parenchyma of the adult rabbit brain Proceedings of the National Academy of Sciences, 100 (22), 13036-13041 DOI: 10.1073/pnas.1735482100

Luzzati F, De Marchis S, Fasolo A, & Peretto P (2006). Neurogenesis in the caudate nucleus of the adult rabbit. The Journal of Neuroscience, 26 (2), 609-621 PMID: 16407559

Luzzati, F., De Marchis, S., Parlato, R., Gribaudo, S., Schütz, G., Fasolo, A., & Peretto, P. (2011). New Striatal Neurons in a Mouse Model of Progressive Striatal Degeneration Are Generated in both the Subventricular Zone and the Striatal Parenchyma PLoS ONE, 6 (9) DOI: 10.1371/journal.pone.0025088

Magnusson, J., Goritz, C., Tatarishvili, J., Dias, D., Smith, E., Lindvall, O., Kokaia, Z., & Frisen, J. (2014). A latent neurogenic program in astrocytes regulated by Notch signaling in the mouse Science, 346 (6206), 237-241 DOI: 10.1126/science.346.6206.237

Luzzati, F., Nato, G., Oboti, L., Vigna, E., Rolando, C., Armentano, M., Bonfanti, L., Fasolo, A., & Peretto, P. (2014). Quiescent neuronal progenitors are activated in the juvenile guinea pig lateral striatum and give rise to transient neurons Development, 141 (21), 4065-4075 DOI: 10.1242/dev.107987

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The Institut Pasteur (Paris, France) announces an international call for group leader positions in the field of quantitative biology and modeling in developmental systems. Successful applicants will be integrated into the cutting edge interdisciplinary environment offered by an internationally renowned institute combining fundamental and translational research, in an attractive location in central Paris, in close proximity to other major research centers. Candidates with both an experimental and theoretical background, using quantitative approaches and willing to develop multidisciplinary projects related to developmental processes are encouraged to apply.

Successful junior candidates [1] will be appointed with a permanent position, and as head of a group of 6 people. These groups will be created for a period of 5 years and may thereafter compete for a full research group.
Successful mid-career and senior candidates will be appointed with a permanent position, and as head of a research group of 8 to 12 people. The groups will be created for 10 years (mid-term evaluation at 5 years) with the possibility of renewal.
Candidates should send their formal applications by E-mail to the Director of Scientific Evaluation, Prof. Alain Israël, at the Institut Pasteur (qubimo@pasteur.fr).

Application deadline: February 6, 2015

Short-listed candidates will be contacted for interview.

Applicants should provide the following (in order) in a single pdf file:
1. A brief introductory letter of motivation, including the name of the proposed group. Candidates are encouraged to contact the head of the Search Committee Francois Schweisguth (fschweis@pasteur.fr) or the head of the Department of Developmental & Stem Cell Biology Shahragim Tajbakhsh for queries (shaht@pasteur.fr).
2. A Curriculum Vitae and a full publication list.
3. A description of past and present research activities (up to 6 pages with 1.5 spacing; Times 11 or Arial 10 font size).
4. The proposed research project (up 6 pages with 1.5 spacing; Times 11 or Arial 10 font size).
Junior candidates [1] should also provide:
5. The names of 3 scientists from whom letters of recommendation can be sought, together with the names of scientists with a potential conflict of interest from whom evaluations should not be requested.

[1] Institut Pasteur is an equal opportunity employer. Junior group leaders should be less than 8 years after PhD at the time of submission (Dec 31, 2014). Women are eligible up to 11 years after their PhD if they have one child and up to 14 years after their PhD if they have two or more children.

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We have previously posted about the workshop that Development organised in September, titled ‘From Stem Cells to Human Development’. We provided a general summary of the meeting, as well as an overview of the stem cells ethics discussion that took place at the workshop. In addition, we have just published a video on this workshop on our YouTube channel, in which we interviewed both the organisers and some of the attendees. This short video gives a flavour of the aims, content and atmosphere of the meeting, and we would like to share it with you here.

As it is mentioned in the video, we can now announce that, following the success of this workshop we will be organising a follow-up meeting in early 2016! Look out for more information about it soon. Development will also be publishing in 2015 a special issue on Human Development, so check our previous Node post for more information on this.
 

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Post-Doc position in models of pattern formation and morphogenesis

1.Job/ project description:

The main objective is to:

a) Develop mathematical models of organ development (starting with but no restricted to teeth, hair and wings).  The mathematical models include intracellular gene networks, cell signalling and extra-cellular signal diffusion, bio-mechanical interactions between large
collectives of cells (all in 3D) (see above publications for orientative examples)

b) Develop models about the evolution of gene networks and embryonic development.

Our aims and research is devoted to understand how animal structure and morphology arises during the process of develpment by interactions between genes, cells and tissues. This is certainly a very complex process that involves many different kinds of interactions happening in complex spatio-temporal settings. Mathematical models are a good way to integrate this complexity to try to understand the biological logic of how animals transform from simple oocytes to animals that are functional and architecturally complex.

Our models take as inputs known or estimated gene networks and the initial distribution of cells in space (in a given stage in development) and provide as a result the final organ morphology and patterns of gene expression in a given organ (in a given, latter, stage of development). Each model is simply a mathematical implementation of a hypothesis about how an organ develops. We construct these hypotheses, based on experimental work from collaborating groups, and implement them in a computational model. The advantage of computational models in respect to merely verbal arguments is that the models provide precise quantitative predictions that are more easily to unambigously compare with experimental results (from new experiments aimed at testing the hypothesis). Merely verbal arguments are more difficult to be proven wrong or right and get even difficult to express when the process under study involves a large number of cells in complex movement and communication between them (as it is often the case in development). These easily lead to largely unintuitive dynamics that are hard to analyze without quantitative models.

In addition, computational models allow to explore not only the wild-type but also, by variaton in the underlying gene network, the range of possible morphological variants (and how they change through development). The capacity to play with the parameters of the model allows us to actually understand its dynamics.

Ultimately, a model is simply a summary of what we think we understand about a system but that allows us to see if the underlying hypothesis could work. That the model works does not imply that the hypothesis is right, further experiments are required, but if the model can not produce the right wild-type it means that the underlying hypothesis is wrong or incomplete. In other words, what we thought we understood, we did not actually understand.

The biotechnology institute includes a range of experimental biologitst working on several systems. The supervisor will be Dr. Salazar-Ciudad but the PhD would include close collaboration with Jukka Jernvall group and would include collaboration with other developmental biologists in the center. In addition, Jernvall’s group includes bioinformaticians, morphometricians, paleontologists and other evolutionary and
systems biologists (in addition to developmental biologists). The work may also include, optionally, collaboration, and spending some time, in Barcelona.
The modeling can focus on gene network regulation, cell-cell communication, cell mechanical interactions and developmental
mechanisms in general and, optionally, artifical in silico evolution.

2. Requirements:

The applicant should be a biologists, or similar, preferably with a strong background in either evolutionary biology, developmental biology or
theoretical biology. Some knowledge of ecology, zoology, cell and molecular biology are also desirable.

Bioinformaticians, systems biologists or computer biologists that do not have a degree in biology or similar similar would not be considered
(this excludes computer scientists, physicists and engineers).

Programming skills or a willingness to acquire them is required.

The most important requirement is a strong interest and motivation on science, gene networks and evolution. A capacity for creative and
critical thinking is also desirable.

3. Description of the position:

The fellowship will be for a period of 2 years (100% research work: no teaching involved) extendable to 2 more years.

Salary according to Finnish post-doc salaries.

4. The application must include:

-Application letter including a statement of interests
-CV (summarizing degrees obtained, subjects included in degree and
grades, average grade)

-Application should be send to Isaac Salazar-Ciudad by email:

isaac.salazar@helsinki.fi

Foreign applicants are advised to attach an explanation of their University’s grading system. Please remember that all documents should
be in English (no official translation is required)

5. Examples of recent publications by Isaac Salazar-Ciudad group.

-Salazar-Ciudad I1, Marín-Riera M. Adaptive dynamics under
development-based genotype-phenotype maps.
Nature. 2013 May 16;497(7449):361-4.

-Salazar-Ciudad I, Jernvall J. A computational model of teeth and
the developmental origins of morphological variation. Nature. 2010
Mar 25;464(7288):583-6.

6. Interested candidates should check our group webpage:

http://www.biocenter.helsinki.fi/salazar/index.html

The deadline is 15 of August (although candidates may be selected before).

Isaac Salazar-Ciudad: isaac.salazar@helsinki.fi

(1 votes)

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Graduate position for a PhD in gene networks, pattern formation and morphogenesis

1.Job/ project description:

The main objectives of the PhD project is to:

a) Develop mathematical models of organ development (starting with but no restricted to teeth, hair and wings).  The mathematical models include intracellular gene networks, cell signalling and extra-cellular signal diffusion, bio-mechanical interactions between large
collectives of cells (all in 3D) (see above publications for orientative examples)

b) Develop models about the evolution of gene networks and embryonic development.

Our aims and research is devoted to understand how animal structure and morphology arises during the process of develpment by interactions between genes, cells and tissues. This is certainly a very complex process that involves many different kinds of interactions happening in complex spatio-temporal settings. Mathematical models are a good way to integrate this complexity to try to understand the biological logic of how animals transform from simple oocytes to animals that are functional and architecturally complex.

Our models take as inputs known or estimated gene networks and the initial distribution of cells in space (in a given stage in development) and provide as a result the final organ morphology and patterns of gene expression in a given organ (in a given, latter, stage of development). Each model is simply a mathematical implementation of a hypothesis about how an organ develops. We construct these hypotheses, based on experimental work from collaborating groups, and implement them in a computational model. The advantage of computational models in respect to merely verbal arguments is that the models provide precise quantitative predictions that are more easily to unambigously compare with experimental results (from new experiments aimed at testing the hypothesis). Merely verbal arguments are more difficult to be proven wrong or right and get even difficult to express when the process under study involves a large number of cells in complex movement and communication between them (as it is often the case in development). These easily lead to largely unintuitive dynamics that are hard to analyze without quantitative models.

In addition, computational models allow to explore not only the wild-type but also, by variaton in the underlying gene network, the range of possible morphological variants (and how they change through development). The capacity to play with the parameters of the model allows us to actually understand its dynamics.

Ultimately, a model is simply a summary of what we think we understand about a system but that allows us to see if the underlying hypothesis could work. That the model works does not imply that the hypothesis is right, further experiments are required, but if the model can not produce the right wild-type it means that the underlying hypothesis is wrong or incomplete. In other words, what we thought we understood, we did not actually understand.

The biotechnology institute includes a range of experimental biologitst working on several systems. The supervisor will be Dr. Salazar-Ciudad but the PhD would include close collaboration with Jukka Jernvall group and would include collaboration with other developmental biologists in the center. In addition, Jernvall’s group includes bioinformaticians, morphometricians, paleontologists and other evolutionary and
systems biologists (in addition to developmental biologists). The work may also include, optionally, collaboration, and spending some time, in Barcelona.
The modeling can focus on gene network regulation, cell-cell communication, cell mechanical interactions and developmental
mechanisms in general and, optionally, artifical in silico evolution.

2. Requirements:

The applicant should be a biologists, or similar, preferably with a strong background in either evolutionary biology, developmental biology or
theoretical biology. Some knowledge of ecology, zoology, cell and molecular biology are also desirable.

Bioinformaticians, systems biologists or computer biologists that do not have a degree in biology or similar similar would not be considered
(this excludes computer scientists, physicists and engineers).

Programming skills or a willingness to acquire them is required.

The most important requirement is a strong interest and motivation on science, gene networks and evolution. A capacity for creative and
critical thinking is also desirable.

3. Description of the position:

The fellowship will be for a period of up to 4 years (100% research work: no teaching involved).

The purpose of the fellowship is research training leading to the successful completion of a PhD degree.

Salary according to Finnish PhD student salaries.

4. The application must include:

-Application letter including a statement of interests
-CV (summarizing degrees obtained, subjects included in degree and
grades, average grade)

-Application should be send to Isaac Salazar-Ciudad by email:

isaac.salazar@helsinki.fi

Foreign applicants are advised to attach an explanation of their University’s grading system. Please remember that all documents should
be in English (no official translation is required)

5. Examples of recent publications by Isaac Salazar-Ciudad group.

-Salazar-Ciudad I1, Marín-Riera M. Adaptive dynamics under
development-based genotype-phenotype maps.
Nature. 2013 May 16;497(7449):361-4.

-Salazar-Ciudad I, Jernvall J. A computational model of teeth and
the developmental origins of morphological variation. Nature. 2010
Mar 25;464(7288):583-6.

6. Interested candidates should check our group webpage:

http://www.biocenter.helsinki.fi/salazar/index.html

The deadline is 15 of August (although candidates may be selected before).

Isaac Salazar-Ciudad: isaac.salazar@helsinki.fi

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