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

(6 votes)

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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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4th – 7th February 2015

The major goal of this Fusion Conference is to bring together in a single forum the diverse group of researchers who study fibroblast growth factor (FGF) signaling. This will provide a unique opportunity to discuss new results and to target future research areas. Among the topics to be covered in this FGF signaling in adult tissue homeostasis, repair, regeneration and angiogenesis; 3)  aberrant FGF signaling in developmental/hereditary diseases meeting are: 1) the mechanisms by which FGF signaling governs organogenesis and tissue patterning during embryonic development; 2) the role of including skeletal syndromes, hearing loss and hypogonadism.

Target Audience

Reflecting the pleiotropic functions of FGF signaling in human biology, FGF researchers encompass a wide range of scientific disciplines, including structural biologists, biochemists, cell biologists, endocrinologists, developmental biologists, geneticists, pharmacologists and clinicians.

Important Deadlines

Early bird and Talk Submission deadline– 30 Nov 14

Poster Submission – 21 Nov 14

Last Chance – 28 Nov 14

Register at: https://www.fusion-conferences.com/registration28.php

(1 votes)

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Hello! We’ve got lots of new things to share, including a film and fact sheet combo that looks at cell fate, cell identity and reprogramming, a closer look at an unusual model organism, and an interview with stem cell scientist and Parkinson’s disease specialist Malin Parmar.

Also featured in this news update: schools outreach in Scotland and Spain, and six new Spanish translations.

As ever, we’re keen to hear from readers of The Node – on Twitter, Facebook, or via our website. You can get involved as a writer or translator, tell us about the stem cell events you’re involved in, make comments or suggestions, or just say hello! And for regular stem cell news, why not subscribe to our monthly newsletter?

Cell Fate: Journeys to Specialisation

EuroStemCell’s latest film looks at how specialized cells develop from stem cells.

Cell Fate: Journeys to Specialisation premiered in Heidelberg earlier this month, followed by a lively Q&A session with Andreas Trumpp, featured scientist Thomas Graf, and great questions from the audience.

Read more about the launch and the making of the film.

New fact sheet: Cell identity and reprogramming

Our body contains several hundred different types of specialised cells. Each cell has very specific features that enable it to do its job. Yet every cell in your body contains the same genes – the same biological ‘instruction book’. So what makes each type of cell different? And can we control or change cell identities? How might this help us develop new approaches to medicine? 

Read more

Snail fur: an alternative model organism for stem cell research

In this guest blog post Hakima Flici, a postdoctoral researcher at NUIG’s Regenerative Medicine Institute (REMEDI), tells us a bit more about her particular area of stem cell research…the model organism hydractinia echinata.

Read more

The work of this REMEDI lab also featured recently in a BBC Future news story, The animal that regrows its head (and in Spanish: El animal que regenera su propia cabeza)

Interview with Malin Parmar: cell therapy for Parkinson’s disease

Malin Parmar heads a research group focused on developmental and regenerative neurobiology at Lund University in Sweden. The ultimate goal of her research is to develop cell therapy for Parkinson’s disease.

At this year’s Hydra summer school we spoke to Malin about how she got started in stem cell research, what she’s working on at the moment, and her view of the prospects for treating Parkinson’s disease with stem cells.

Read more

Amazing stem cell questions at Inverkeithing High School

This Stem Cell Awareness Day PhD student Jamie Gillies joined Richard Axton and Cathy Southworth at Inverkeithing High School in Scotland to share with students the exciting world of stem cell biology and the work of being scientists. Here’s his account of the day, and the intriguing questions the students asked.

Read more

Transdifferentiation workshops for secondary students at CRG

The Centre for Genomic Regulation (CRG) in Barcelona has started the school year with a new workshop for high school students. The workshop is taking place every Thursday in the CRG Teaching and Training Lab facilities, a space specifically designed for the training of new researchers and for outreach activities.

Read more

Six new Spanish fact sheet translations

Muchas gracias to our translators!

• Reprogramación celular: como convertir cualquie célula del cuerpo en una célula madre pluripotente
• Investigación y terapia con células madre: tipos de células madre y sus aplicaciones actuales
• Ética y reprogramación celular: cuestiones éticas después del descubrimiento de las células iPS
• Nuevas herramientas para la investigación de enfermedades: células reprogramadas en modelaje de enfermedades
• Enfermedad hepática crónica: Como puede ayudar la medicina regenerativa?
• Infarto: Cómo pueden ayudar las células madre?

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Here are the highlights from the current issue of Development:

Meristem maintenance is KNOX so simple

Class I KNOX transcription factors, such as SHOOT MERISTEMLESS (STM) and KNAT1, are known to play a role in the plant shoot apical meristem (SAM), where they are thought to prevent differentiation and hence promote stem cell maintenance. Now, on p. 4311, Urs Fischer and colleagues uncover a role for STM and KNAT1 in another Arabidopsis meristem – the vascular cambium, which is a lateral meristem that gives rise to xylem and phloem cells. They first show that STM and KNAT1 are expressed in undifferentiated cambial cells but also in differentiated phloem and xylem cells. The researchers further demonstrate that xylem fibre formation is reduced in stm and knat1 mutants, suggesting that STM and KNAT1 promote the differentiation of cambial derivatives. In addition, they report that STM and KNAT1 regulate xylem differentiation via transcriptional repression of BLADE-ON-PETIOLE 1 (BOP1) and BOP2, which are not expressed in the SAM. Together, these findings demonstrate that, in contrast to their function in the SAM, STM and KNAT1 promote cell differentiation in the cambium, suggesting that the exact role of these transcription factors in other meristems needs re-examination.

TBX1: at the heart of epithelial properties

During its development, the heart tube undergoes rapid elongation, fuelled by the addition of cardiac progenitors from the second heart field (SHF). The gene regulatory networks governing SHF formation have been studied extensively, but little is known about the basic cellular features of SHF cells. Now, Robert Kelly and co-workers show that the transcription factor TBX1, which is implicated in both normal SHF development and congenital heart defects, regulates the epithelial properties of mouse SHF cells (p. 4320). Using immunofluorescence microscopy, they first show that SHF cells in the dorsal pericardial wall constitute an apicobasally polarised epithelium. Transmission and scanning electron microscopy reveal the presence of monocilia on the apical surface of SHF cells and of actin-rich filopodia on their basal surface. Using live-imaging of thick-slice cultures, the researchers demonstrate that these filopodia are dynamic, extending towards and making contact with surrounding tissues. Importantly, they report that TBX1 plays a crucial role in regulating these epithelial cell features; cell shape, cell polarity and filopodia dynamics are perturbed in Tbx1-/- mutants. These exciting findings suggest that TBX1-mediated control of epithelial state is crucial for heart development.

Mesogenin 1 masters the presomitic mesoderm

During development, neuromesodermal (NM) stem cells give rise to both neural cells and paraxial presomitic mesoderm (PSM) cells, but what dictates PSM fate? Here, Terry Yamaguchi and colleagues show that a single transcription factor – mesogenin 1 (Msgn1) – acts as a master regulator of PSM development (p. 4285). They show that the overexpression of Msgn1 in mouse ESCs cultured as embryoid bodies (EBs) is sufficient to drive PSM differentiation. Microarray and ChIP-seq analyses of Msgn1-overexpressing EBs confirm that Msgn1 controls the expression of key regulators of PSM development, including those involved in epithelial-mesenchymal transition and segmentation. Importantly, the researchers demonstrate that Msgn1 overexpression in NM stem cells in vivo biases fate towards the PSM; the contribution of these cells to the neural tube is reduced while the number of PSM cells is dramatically increased. Finally, the authors show that Msgn1 overexpression can partly rescue the PSM differentiation defects observed in Wnt3a−/− embryos, suggesting that Msgn1 functions downstream of Wnt3a as master regulator of PSM fate. Given the role of the PSM as a precursor for a multitude of cell types, this finding has important implications for the fields of cellular reprogramming and regenerative medicine.

Basonuclin 2: a regulator of spermatogenesis

Embryonic germ cells display strikingly different fates with regard to mitosis and meiosis, depending on their sex. In female mice, germ cells switch from mitosis to meiosis shortly after reaching the foetal gonad where they generate the lifelong pool of oocytes. However, in males, meiosis and mitosis are actively repressed, and germ cells remain quiescent in the gonad until birth, when they resume mitosis and start generating spermatocytes. Here (p. 4298), Philippe Djian and colleagues demonstrate that Basonuclin 2, an extremely conserved transcription factor specifically expressed in male germ cells, suppresses meiosis. More surprisingly, they also show that Basonuclin 2 is required for mitosis repression and, later in life, for meiosis progression during spermatogenesis and maintenance of the spermatogonial stem cells that ensure spermatocyte production during life. Furthermore, Basonuclin 2 is necessary for the expression of DNMT3L, a key protein that is involved in spermatogenesis, and for the repression of meiotic genes (Stra8, Msx1 and Msx2) that are normally expressed in female germ cells. These findings, which uncover a new regulator of male gametogenesis, are likely to further our understanding of spermatogenesis in humans.

From embryonic stem cells to gastruloids: early development in a dish

One of the first patterning events of embryogenesis occurs during gastrulation: three-dimensional (3D) cell movements reorganise the embryo, a mass of morphologically similar cells, into an axially organised structure with three germinal layers (endoderm, mesoderm and ectoderm). To date, two-dimensional (2D) culture models have failed to recapitulate such complex cell behaviours linking cell movement to cell fate. Here (p. 4231), Alfonso Martinez Arias and colleagues show that 3D aggregates of mouse embryonic stem cells cultured in mesendoderm-promoting medium undergo cell movements, axial organisation and germ layer specification, features reminiscent of gastrulation. They demonstrate that the expression of endoderm (Sox17, Fox2A) and early mesoderm (Brachyury) markers becomes polarised in these aggregates. Later, cells originating from the Brachyury-expressing ‘territory’ are extruded from the aggregate. These ‘gastruloids’ thus present a powerful tool that can be used to study early embryonic tissue specification in a dish, an unprecedented feat in vitro.

PLUS…

Reactive oxygen species and stem cells

Recent work suggests that reactive oxygen species (ROS) can influence stem cell homeostasis and lineage commitment. In this Primer, Ghaffari and colleagues provide an overview of ROS signalling and its impact on stem cells, reprogramming and ageing. See the Primer on p. 4206

Chemokines in development and disease:

In our latest poster and companion article, Wang and Knaut provide an overview of chemokine signalling and some the chemokine-dependent strategies used to guide migrating cells. See the poster on p. 4199

Leaf development and morphogenesis

The development of plant leaves follows a common basic program, which can be modulated to generate a diverse range of leaf forms. Bar and Ori review recent work examining how plant hormones, transcription factors and tissue mechanics influence leaf development. See the Review on p. 4219

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