The MRC Weatherall Institute of Molecular Medicine (WIMM) has fully funded 4-year Prize PhD (DPhil) Studentships available to start in October 2019. These Studentships are open to outstanding students of any nationality who wish to train in experimental and/or computational biology.
The Institute is a world leading molecular and cell biology centre that focuses on research with application to human disease. It includes the recently opened MRC WIMM Centre for Computational Biology and houses over 500 research and support staff in 50 research groups working on a range of fields in Haematology, Gene Regulation & Epigenetics, Stem Cell Biology, Computational Biology, Cancer Biology, Human Genetics, Infection & Immunity. The Institute is committed to training the next generation of scientists in these fields through its Prize PhD Studentship Programme.
The fully funded studentships include a stipend of £18,000 per annum and cover University and College fees.
Further information on the studentships, how to apply, and the projects available can be found at:
Studying limb regeneration in model organisms is important for the advancement of regenerative medicine in humans. We set out to study regeneration in the hind limbs of the African Clawed Frog Xenopus laevis – this animal is able to regenerate its hind limbs very early in development, but it loses this ability during metamorphosis. Additionally, there is a large and still growing body of evidence suggesting that charged particles called ions (for example, sodium, potassium, and chloride) are important for regulating pathways that control growth and regeneration. Though a relatively small number of biologists’ work is centered around this field, called bioelectricity, its implications thus far in the fields of developmental biology and regenerative medicine have been compelling. As an undergraduate, I had the privilege to be trained and to perform research in a lab that is at the forefront of this field, which had many unanswered and yet unresearched questions.
We – being myself and my team of mentors, Dr. Patrick McMillen and Professor Michael Levin, who were both Tufts undergraduates ten and twenty years before me, respectively – married the concept of bioelectrics and Xenopus hind limb regeneration to ask the question: what bioelectric changes do younger, regenerating froglets exhibit in response to amputation that older, non-regenerative tadpoles do not? This is part of the lab’s mission to discover regenerative therapies, based on manipulating bioelectric signaling, for various biomedical applications. We amputated the limbs of both regenerating tadpoles and non-regenerating tadpoles, and soaked them in a solution containing a molecule that glows in response to changing ion concentrations across cell membranes, also called membrane potential. By the time we were ready to analyze the results of this work, the product of observation and the scientific method led us to a bigger, more perplexing question to answer.
In performing these initial experiments, I did what I believed was my due diligence as a researcher: I needed controls! So I used the contralateral, uncut limbs of the froglets as controls, a common method used across many fields, to make sure the dye wasn’t being randomly soaked up by cells and to establish a baseline background for what the fluorescence would look like in un-injured, intact tissues. In fact, I quickly found that the dye was being taken up by cells in the contralateral limb, but only in the intact limbs of frogs that had the other limb amputated. Un-amputated froglets did not exhibit staining from the dye in either limb. I took this information to my mentors, sure that they would already have an explanation prepared, as professors and teachers before them always had when a question arose in lecture. For the first time in my academic career, nobody had an answer for me. This phenomenon had never been observed before, therefore nobody had asked the question; there was truly no one with an answer.
It is at this point in many young scientists’ careers that the potentially interesting project is swooped out from under them, their mentors realizing the value of the new findings, hungry for the credit. For others, their mentors do support intellectual curiosity and give them the freedom to pursue their own projects, but their projects do not see the light of day because there simply are not enough resources. For these reasons, the Tufts biology department, and more specifically, the Levin lab, are extremely unique. I could not have been more fortunate, because I was given both the freedom to head my own project and the resources to do so.
Ultimately, we found that the contralateral limbs of regenerating tadpoles glowed (in the presence of that molecule I mentioned earlier) in a region on the contralateral limb that very closely mirrors the plane of amputation. Our data revealed that the un-injured limb somehow knows the relative location (and even type) of injury, within about 30 seconds (Busse et al.Development 2018; doi:10.1242/dev.164210). This phenomenon has interesting implications for regenerative medicine. What we found is a distal region that not only recognizes, but also encodes information about an injury incurred by the body. If similar signaling phenomena can be found in mammalian systems, there is potential for the development of surrogate site diagnostics – looking at one site to decipher information about the health of another. This information is also evidence that contralateral limbs are not an appropriate control for experiments, and hopefully encourages everyone to think twice before using them as controls!
There are many more questions that we intend to answer in the future; for example, how does one part of the body sense that another part of the body has been injured? In the meantime, the context of this research is extremely important for anyone in any field of research to understand. I asked a question that nobody at the time could answer, and was given the opportunity to find an answer. The result was that I learned more collaborating with Dr. Patrick McMillen, Professor Michael Levin, and many others in the Levin lab than any biology course could have taught me. Many students are prompted to spend time answering questions throughout the duration of their degree, but I was encouraged to ask them, and it has fundamentally changed the way I think about learning. I had teachers who were not eager to prove what they knew, but rather who were eager to teach how they knew it.
The Turing Centre for Living Systems is seeking a highly motivated research engineer to fill the post of ‘leading data scientist/data analyst’, within CENTURI’s technology transfer platform. This position will be a central point of data analysis, data sharing and code sharing of our research community.
Three-year contract from the Aix-Marseille Université.
Deadline for Application: November 23
Applications should include:
a CV (including a list of publications)
a cover letter (describing past experience with data analysis)
Applications are open for the Wellcome Trust funded four year PhD programme in Developmental Mechanisms at the University of Cambridge. We are looking for talented, motivated graduates or final year undergraduates, and are keen to attract outstanding applicants in the biological sciences, who are committed to doing a PhD. We are able to fund both EU and *non-EU students.
Closing date: Thursday 3 January 2019 (by 12:00pm midday UK time)
For more details about the application process and the programme please see the website:
A postdoctoral position is available in the laboratory of Dr. Sophie Astrof at Rutgers University to study roles of cell-extracellular matrix (ECM) interactions in cardiovascular development and congenital heart disease. We have recently discovered that progenitors within the second heart field (SHF) give rise to endothelial cells composing pharyngeal arch arteries (Dev Biol 421:102–111, 2017). Projects in the lab focus on the role of ECM in regulating the development of SHF-derived progenitors into endothelial cells and their morphogenesis into blood vessels. The successful candidate will combine genetic manipulation, embryology, cell biology, and confocal imaging to study molecular mechanisms by which cell-ECM interactions and tissue microenvironment regulate cardiovascular development. Additional projects focus on the investigation of cell type-specific and cell-autonomous functions of fibronectin in development and signaling (Development 143:88-100, 2016). Interested candidates should send their CV and the names of three references to Sophie.astrof@rutgers.edu
Jeff Rasmussen tells the story behind his recent paper from the Sagasti Lab in Dev Cell.
This project began as an extension of my earlier postdoc work in Alvaro Sagasti’s lab investigating removal of axon debris following skin injuries in the larval zebrafish [1] and led me into scientific territory that I never anticipated. It is a story that would not have happened without open-mindedness, encouragement and—most importantly—help from colleagues in the fish community.
Sensory axon endings profusely innervate the skin, and skin injuries trigger axon degeneration. We previously discovered that keratinocytes are the primary phagocyte for degenerating axons in larval skin. But what cells eat axons that degenerate in the more complex adult skin?
In order to answer this question, I first needed a way to visualize sensory axons in adults. Most work in zebrafish has focused on the larval system, so markers for adults have lagged behind. Luckily, I came across a transgenic line made by a previous graduate student in Alvaro’s lab [2] that showed bright and specific expression of sensory axons in adults. The pattern of adult skin innervation revealed by this line caused this project (and my career) to take a twist.
A Striking Axon Pattern
Axons of Rohon-Beard neurons innervate most of the larval fish skin. Rohon-Beard axons in the skin rarely bundle (fasciculate). By contrast, this transgenic line revealed that axons of dorsal root ganglion (DRG) neurons, which innervate adult skin, were frequently bundled. More surprisingly, these bundles were evenly spaced across the surface of scales, which underlie the adult epidermis (Figure 1). Alvaro whole-heartedly encouraged me to dig deeper into what created these evenly spaced bundles, despite his lab having no experience working with post-embryonic stages.
Figure 1. Anatomy of adult zebrafish skin showing axons, vasculature and scale radii.
Thi’s Developmental Studies
Thi Vo, an undergraduate researcher in Alvaro’s lab, took on the challenge of analyzing post-embryonic development. Because many Rohon-Beard neurons die after only a few days of development, we expected that DRG axons would innervate the epidermis shortly thereafter. However, by staining isolated scales to visualize axons, Thi found that the axon bundles only appeared during late juvenile stages. So Thi next analyzed mutants lacking DRG neurons and found that the bundles never formed, proving that they were indeed DRG axons.
Thi also stained scales with phalloidin to visualize cell morphology and found that a set of elongated cells apparently presaged the path of the axon bundles. What could these cells be?
Lindsey’s Schwann cells
We initially hypothesized that the elongated cells were Schwann cells, the glia of the peripheral nervous system. Schwann cells are neural-crest derived, and Shannon Fisher’s group recently made a neural crest lineage reporter [3], which we learned was growing in Gage Crump’s lab at USC. To determine if the line labeled Schwann cells in adults, I made a trip across town to visit Lindsey Barske, a postdoc in the Crump lab, who was working with the neural crest reporters. One of Lindsey’s lines labeled Schwann cells coating the axon bundles, showing that they are nerves and giving us a key reagent to visualize their development. But when Thi and I analyzed the timing of Schwann cell migration, they appeared too late to pioneer the path of the DRG bundles, ruling out this hypothesis.
Michael’s Vessels
After hearing about our work at a Southern California Zebrafish Meeting, Michael Harrison, a postdoc in Ellen Lien’s lab working on heart and vascular development, suggested we analyze several of his chemokine mutants. Thi and I took a bus trip down Sunset Blvd to CHLA to collect scales from these mutants. Although this effort was ultimately fruitless, as luck would have it, Michael’s mutants expressed multiple transgenic reporters. One of these transgenes was fli1a:EGFP (a vascular reporter made by Brant Weinstein’s group) [4], which revealed that the axon bundles tightly associated with blood vessels (Figure 1). This was unexpected because we had initially ruled out a vascular contribution based on analysis of a vessel reporter not as broadly expressed as fli1a.
Intriguingly, axons and vessels also tightly associate in mammalian skin and axons promote vascular remodeling and arterial differentiation in mouse [5]. Were blood vessels the elongated cells that arose early in scale development? No, since we found that blood vessels only appeared along mature scales, once animals reached adulthood. What about the converse: did axons pattern the vessels? By again analyzing mutants lacking sensory neurons, we found that blood vessels appeared normal. Thus, in contrast to mammals, skin nerves and vasculature are independently patterned in fish. This was an important finding but, once again, the identity of the pioneering cells remained elusive.
Sandeep’s Osteoblasts
The scale surface is made from bone and contains a number of striking patterns. Remarkably, we noticed that the axon bundles and vessels aligned with scale radii, grooves in the bone that radiate from the scale center (Figure 1). Could osteoblasts, bone-forming cells, or osteoclasts, bone-degrading cells, guide axons and vessels? We first examined osteoclasts but found no evidence that they form the radii. Next, I made another crosstown trip to the Crump lab—this time with the help of Sandeep Paul—to look at osteoblast reporters. Sandeep’s lines showed that osteoblasts line mature radii, as suggested by pioneering ultrastructural studies [6, 7]. Imaging osteoblasts early in scale development revealed that they create the radial paths by polarized migration.
To test if osteoblasts promote skin innervation during regeneration, we used an inducible osteoblast ablation line made by Ken Poss’ group [8] and found that blocking scale regeneration by osteoblast ablation resulted in a reduction of axon density. To test if scale development similarly promoted innervation, we analyzed mutants that prevent scale development [9, 10]—provided as part of a “scale care package” by Matt Harris’ lab. These mutants had reduced skin innervation and vascularization, showing that scales are also required during ontogeny.
Figure 2. Intubation allows extended live-cell imaging of scale development and regeneration.
Full Scale Ahead
Although I never planned to work on scales as a model system, I am really excited about the potential for these mini-organs to reveal the cellular and molecular basis for cell type patterning during skin development and repair—questions that I will be pursuing in my newly formed research group at the University of Washington. Scales are evolutionarily related to other types of specialized skin appendages like feathers and hair. Thus, studies of fish scales may reveal general mechanisms for coupling organ maturation and growth to skin patterning. Scales may also yield insights into bone-nerve interactions that occur in diverse tissues, like antlers, teeth and long bones. An increasing number of genetic tools, together with advances in live-cell imaging of post-embryonic stages (Figure 2), suggest the future is bright for a resurgence of scales as a model system.
1 PhD Position : Characterization of Hedgehog morphogens in vitro and in vivo
Hedgehog (Hh) morphogens play important roles in development and cancer, but their mode of extracellular transport to target cells is only poorly understood. Thus, we aim at the characterization of various unusual posttranslational regulatory mechanisms in Hh biology, such as Hh multimerization on the surface of secreting cells via structural and biochemical analysis of Hh clusters, and the unusual mode of Hh transport and gradient formation.
We use a wide range of biochemical methods, such as recombinant protein production and chromatographic/functional characterization of proteins and Heparan sulfate-proteoglycans (HSPGs), determination of Shh/HSPG binding and in vivo testing of any obtained models of protein association and transport (In Drosophila melanogaster).
We invite applications from highly qualified and motivated students of any nationality. The applicant will hold a Masters degree (Biology, Chemistry, Biotechnology, Pharmacy or Biochemistry) and has gained first biochemical research experience. Experience in Drosophila experimentation is highly welcome, but not required. The successful applicant will find strong support within the excellent interdisciplinary environment of the SFB1348 of the University of Muenster.
CENTURI is recruiting up to 10 highly motivated postdoctoral fellows to work in an interdisciplinary life science environment. The available postdoctoral projects will be advertised online, with more projects being added to our website up until November 15.
CENTURI postdocs will have the opportunity to develop their project with more than one research group, bridging biology to other disciplines.
Candidates will have a background in any of the following fields: cell or developmental biology, immunology, neurobiology, biophysics, theoretical physics, computer science, bioinformatics, applied mathematics or engineering.
Candidates can either apply to one of the advertised CENTURI projects or submit their own project, providing that they meet the application criteria and that their application is supported by at least one host lab. These projects should be submitted to: postdocproject@centuri-livingsystems.org
Deadline for application and project submission: November 30, 2018
About CENTURI
Mainly located on the Luminy science campus (Marseille France), the Turing Centre for Living Systems is an interdisciplinary project federating a growing community of biologists, physicists, mathematicians, computer scientists and engineers in 15 research institutes.
The project focuses on 3 missions: Research, Education and Engineering
Stem cells are defined by the dual capacity to self-renew and to differentiate. These properties sustain homeostatic cell turnover in adult tissues and enable repair and regeneration throughout the lifetime of the organism. In contrast, pluripotent stem cells are generated in the laboratory from early embryos or by molecular reprogramming. They have the capacity to make any somatic cell type, including tissue stem cells.
Stem cell biology aims to identify and characterise which cells are true stem cells, and to elucidate the physiological, cellular and molecular mechanisms that govern self-renewal, fate specification and differentiation. This research should provide new foundations for biomedical discovery, biotechnological and biopharmaceutical exploitation, and clinical applications in regenerative medicine.
Cambridge Stem Cell Community
The University of Cambridge is exceptional in the depth and diversity of its research in Stem Cell Biology, and has a dynamic and interactive research community that is ranked amongst the foremost in the world. By bringing together members of both the Schools of Biology and Medicine, this four year PhD programme will enable you to take advantage of the strength and breadth of stem cell research available in Cambridge. Choose from over 50 participating host laboratories using a range of experimental approaches and organisms.
Programme Outline
During the first year students will:
Perform laboratory rotations in three different participating groups working on both basic and translational stem cell biology.
Study fundamental aspects of Stem Cell Biology through a series of teaching modules led by leaders in the field.
Learn a variety of techniques, such as advanced imaging, flow cytometry, and management of complex data sets.
Students are expected to choose a laboratory for their thesis research by June 2020, and will then write a research proposal to be assessed for the MRes Degree in Stem Cell Biology. This assessment will also be used to determine whether students continue on to a 3-year PhD.
Physical Biology of Stem Cells
Incorporated into the ‘Stem Cell Biology’ Programme, opportunities are available specifically for candidates with a Physical, Computational or Mathematical Sciences background, wanting to apply their training to aspects of Stem Cell Biology *.
Great inroads have been made towards understanding how stem cells generate tissue and sustain cell turnover, most of which have been made by studying the biochemistry of stem cells. Less is known of their function across scales – from molecules to tissue – or interaction with their physical environment. We aim to identify the importance of physical, chemical, mathematical and engineering considerations in stem cell functionality. This could include mathematical modelling, engineering controlled environments to control stem cell function, single molecule approaches to study molecular interactions, systems biology, or investigating stem cell’s response to forces in its environment.
Eligibility
We welcome applications from those who hold (or expect to receive) a relevant first degree at the highest level (minimum of a UK II.i Honours Degreeor equivalent). You must have a passion for scientific research.
Stem Cell Biology and Medicine Programme (funding by Wellcome)
We welcome applications from EU and non-EU candidates. The Wellcome Trust provide full funding at the ‘Home/EU’ rate. Funding does not include overseas fees, so non-EU applicants will need to find alternative funding sources to cover these.
‘Physical Biology of Stem Cells’ Programme (funding by the MRC)
We welcome applications from UK/EU candidates, with a Physical Sciences, Mathematical or Computational Sciences background. *The Medical Research Council provide full funding for UK applicants only. Applicants from EU countries other than the UK, are generally eligible for a fees-only award. Please check your eligibility status at https://www.mrc.ac.uk/skills-careers/studentships/studentship-guidance/student-eligibility-requirements/ before applying.
There is a vast amount of information known about how some animals pattern their bodies into repeated segments, especially in the fruit-fly Drosophila melanogaster. However, when compared to other arthropods, there are several characteristics that are derived in the fruit fly. It has a very short development time, a syncytium at the blastoderm stage allowing molecules free passage throughout the embryo and the segments are generated almost simultaneously. This is called the “long germ band” type of arthropod development.
While the fruit fly undergoes “long germ band” development, most arthropods belong to the “short germ band” type, in which the head and a small portion of the trunk are generated after gastrulation, but posterior segments are then added one by one from the so called segment addition zone (SAZ). An earlier article on the Node previously outlined the reasons the spider is an excellent study organism (https://thenode.biologists.com/day-life-spider-lab/lablife/) – but we want to highlight a recent discovery that builds to this earlier story: some chelicerates have undergone a whole genome duplication during their evolutionary history (Schwager et al., 2017; Leite et al., 2018). This genome duplication event has allowed some of the conserved sets of genes to retain duplicated copies, potentially having huge implications for the regulation and evolution of developmental processes in these animals – including segmentation.
What do we know about segmentation in the common house spider Parasteatoda tepidariorum? A remarkable discovery in this species was that the Delta-Notch and Wnt signaling pathways were involved in the differentiation of the cells of the SAZ. These findings shifted the view of canonical segmentation in arthropods, since these two pathways are not involved in long germ development of the fruit fly (for further information, see Oda et al., 2007 and Schonauer et al., 2016).
Strikingly, we found in 2017 that another conserved metazoan gene family has retained duplicated copies in Parasteatoda (Paese et al., 2017), the Sox genes (Sry-related HMG Box). In this study, we isolated 14 Sox genes, analysed their expression patterns at different stages of embryonic development (Paese et al., 2017) and studied their functional role with RNA interference (Paese et al., 2018). Interestingly, some of these genes have no detectable expression during embryonic development, and as noted in other studies, Sox genes have a high degree of redundancy (i.e. genes with conserved motifs that therefore can act in the place of the missing gene) and we only observed an obvious phenotype in one out of fourteen genes, a SoxB gene – Sox21b-1. (Expression pattern in Figure 1). This is an example of one of the genes that have undergone a duplication – in which each copy is dispersed in the genome of the spider.
Figure 1
Even though the gene’s name may not be the most memorable when compared to some genes in the fruit-fly, the phenotype when Sox21b-1 is knocked down is very unforgettable. Moreover, this gene has an expression pattern similar to what is seen with a related gene, Dichaete, in other arthropods – which has no detectable expression during spider embryogenesis (for more info, see Paese et al., 2017). For a quick spoiler: we first thought that Sox21b-1 had acquired Dichate function in this spider species. Wouldn’t that be amazing? And how would we be sure of that? Let’s do some functional analysis!
When we injected double-stranded RNA in the opisthosoma of a female spider, we obtained phenotypes of different penetrance. During one rainy night in Oxford, I was analyzing a dish with embryos that I removed from a cocoon that was deposited by a Sox21-b1 dsRNA injected female. Using a stereomicroscope, I was only able to identify the head region and a very strange single pair of appendages growing from where six pairs should be growing. At a first glance, I was very excited about finding a new phenotype, but kept searching for other embryos with the same pattern in different cocoons. Sadly, in this first injection round, only two injected females survived – however, a significant proportion of embryos displayed a phenotype.
I injected another seven spiders and the phenotypes matched the first round of injections (Figure 2 for the phenotypes). In class I phenotypes, most embryos displayed only the first three pairs of appendages (namely chelicerae, pedipalps and leg bearing segment 1 – L1) instead of six pairs, whereas class II lack the L1 segment and class III did not develop further after gastrulation. Much more interesting than lacking all the leg-bearing segments was that this anterior region was able to differentiate even in the absence of a developing SAZ! These findings are further evidence for the hypothesis that the short germ arthropods mechanism for anterior and posterior segmentation are decoupled.
Figure 2
Knowing this, we started analyzing which mechanisms were affected by the knockdown of this Sox gene. First, we assayed the expression of known cumulus formation and migration genes: decapentaplegic and Ets4. The expression of both genes was normal (Figure 3 of the paper – A to D). Then the next targets to be evaluated were genes involved with secondary layer formation (forkhead) and head patterning (hedgehog). Whereas the expression of the latter was normal, forkhead expression was completely lost. This information led us to analyse determinants of mesoderm and endoderm formation in older embryos and we indeed observed an effect on those two layers in the Sox21b-1 phenotype. However, we cannot be sure if this is a direct effect due to the lack of Sox21b-1 or caused by the overall lower number of cells, which has to be investigated further.
Figure 3
As mentioned before, the spider patterns its segments not following the Drosophila canonical mode, but instead through control by Delta-Notch and Wnt signaling, regulating pair-rule gene expression via caudal. Thus, we looked into the effect on expression of the known genes that are related to this mechanism in the spider. Interestingly, the expression of caudal, delta, hairy and wnt8 is lost in the SAZ, but we could still see the expression of the segment markers engrailed and hedgehog in the knockdown embryos. In summary, this means that this Sox gene is upstream of Wnt and Delta/Notch and this is additional evidence for the independence of anterior and posterior segmentation in the spider (Figure 4).
Figure 4
In conclusion, our study adds an important piece towards understanding segmentation in short germ arthropods and the effects of a whole genome duplication on developmental processes (Figure 5).
Figure 5
We might be far from a complete picture of how segmentation is regulated in spiders, but it is indeed exciting that there are many more pieces of the puzzle to be solved!
Supplementary References:
Leite, D. J., Baudouin-Gonzalez, L., Iwasaki-Yokozawa, S., Lozano-Fernandez, J., Turetzek, N., Akiyama-Oda, Y., Prpic, N. M., Pisani, D., Oda, H., Sharma, P. P., McGregor, A. P. (2018). Homeobox gene duplication and divergence in arachnids. Mol Biol Evol.
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