PhD offers: modelling the effect of noise in gene regulatory network governing early mammalian development, starting from 1 October 2020 or later – (1 +3 years )
We are seeking two PhD students to work in the Unit of Theoretical Chronobiology (Brussels, Belgium) on a project related to the modelling of cell differentiation. This interdisciplinary project will focus on the relation between the structure of the gene regulatory network (GRN) governing cell differentiation and its sensitivity to noise.
For more information, see: https://www2.ulb.ac.be/sciences/utc/home.html
The Tissue Regeneration Laboratory within the Biology Department at Wake Forest University is seeking a qualified and highly motivated individual for the position of Lab Manager / Research Assistant to support our work uncovering mechanisms of tissue regeneration in axolotl salamanders. The primary tasks will include managing lab resources, caring for the lab’s axolotl colony, and undertaking research. The candidate will be involved in setting up our lab as it launches at Wake Downtown. Wake Downtown is located in Winston-Salem’s Innovation Quarter, adjacent to the Wake Forest School of Medicine and the Wake Forest Institute for Regenerative Medicine (WFIRM). Winston-Salem boasts a phenomenal cost of living, a thriving arts scene as the home to the North Carolina School of the Arts, and is only a few hours’ drive to either the Outer Banks or the Blue Ridge Parkway/Smoky Mountains.
The candidate will be responsible for managing lab inventories, implementing safety protocols, maintaining and caring for axolotls and their facility, and conducting lab work such as PCR genotyping, RNA and DNA extractions, molecular cloning, creating transgenic axolotls, and fluorescence microscopy. The candidate should be motivated to gain proficiency at troubleshooting experiments, analyzing data, and communicating results. Opportunities exist for independent research and mentorship toward next professional steps (e.g. postbac to grad/med school). The candidate should minimally have a Bachelor’s degree and a fundamental understanding of molecular biology, including hands-on research experience in cell and molecular biology or a related field. Experience working with animals, especially aquatic organisms, is appreciated but not required. Excellent organizational, record-keeping and collaborative interpersonal skills are essential.
This position has full benefits and is funded for two years, with the possibility of extension dependent upon lab funding. Salary will be commensurate with prior experience. We are intentional about building a diverse, inclusive, and supportive team of colleagues. More information about our lab values can be found here.
To apply, please send a CV, a cover letter expressing interest and highlighting relevant experience, and contact information for 3 references to Dr. Josh Currie (currie.regenerationlab@gmail.com). Please reference “Tissue Regeneration Lab Manager / Research Assistant” in the subject line. Starting dates are flexible beginning from September 1st, 2020.
The N-Glycome regulates the endothelial-to-hematopoietic transition
Dionna M. Kasper, Jared Hintzen, Yinyu Wu, Joey J. Ghersi, Hanna K. Mandl, Kevin E. Salinas, William Armero, Zhiheng He, Ying Sheng, Yixuan Xie, Daniel W. Heindel, Eon Joo Park, William C. Sessa, Lara K. Mahal, Carlito Lebrilla, Karen K. Hirschi, Stefania Nicoli
Maternal iron deficiency perturbs embryonic cardiovascular development
Jacinta I. Kalisch-Smith, Nikita Ved, Dorota Szumska, Jacob Munro, Michael Troup, Shelley E. Harris, Aimée Jacquemot, Jack J. Miller, Eleanor M. Stuart, Magda Wolna, Emily Hardman, Fabrice Prin, Eva Lana-Elola, Rifdat Aoidi, Elizabeth M. C. Fisher, Victor L. J. Tybulewicz, Timothy J. Mohun, Samira Lakhal-Littleton, Eleni Giannoulatou, Duncan B. Sparrow
Cell surface fluctuations regulate early embryonic lineage sorting
Ayaka Yanagida, Christopher Revell, Giuliano G. Stirparo, Elena Corujo-Simon, Irene M. Aspalter, Ruby Peters, Henry De Belly, Davide A. D. Cassani, Sarra Achouri, Raphael Blumenfeld, Kristian Franze, Ewa K. Paluch, Jennifer Nichols, Kevin J. Chalut
Epithelial layer unjamming shifts energy metabolism toward glycolysis
Stephen J. DeCamp, Victor M.K. Tsuda, Jacopo Ferruzzi, Stephan A. Koehler, John T. Giblin, Darren Roblyer, Muhammad H. Zaman, Scott T. Weiss, Margherita DeMarzio, Chan Young Park, Nicolas Chiu Ogassavara, Jennifer Mitchel, James P. Butler, Jeffrey J. Fredberg
Cytoplasmic polyadenylation by TENT5A is required for proper bone formation
Olga Gewartowska, Goretti Aranaz Novaliches, Paweł S Krawczyk, Seweryn Mroczek, Monika Kusio-Kobiałka, Bartosz Tarkowski, Frantisek Spoutil, Oldrich Benada, Olga Kofroňová, Piotr Szwedziak, Dominik Cysewski, Jakub Gruchota, Marcin Szpila, Aleksander Chlebowski, Radislav Sedlacek, Jan Prochazka, Andrzej Dziembowski
Paranode stability requires UNC5B expression by oligodendrocytes
Omar de Faria Jr., Diane S. Nakamura, Samuel Clemot, Doyeun Kim, Mihai Victor Mocanu, Roland Pilgram, Jenea M. Bin, Edwin W. Wong, Amir Shmuel, Abbas Sadikot, Susan L. Ackerman, Timothy E. Kennedy
Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development
Anoushka Joglekar, Andrey Prjibelski, Ahmed Mahfouz, Paul Collier, Susan Lin, Anna Katharina Schlusche, Jordan Marrocco, Stephen R. Williams, Bettina Haase, Ashley Hayes, Jennifer G. Chew, Neil I Weisenfeld, Man Ying Wong, Alexander N. Stein, Simon Hardwick, Toby Hunt, Zachary Bent, Olivier Fedrigo, Steven A. Sloan, Davide Risso, Erich D. Jarvis, Paul Flicek, Wenjie Luo, Geoffrey S. Pitt, Adam Frankish, August B. Smit, M. Elizabeth Ross, Hagen U. Tilgner
Wnt/PCP-primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells
Anika Böttcher, Maren Büttner, Sophie Tritschler, Michael Sterr, Alexandra Aliluev, Lena Oppenländer, Ingo Burtscher, Steffen Sass, Martin Irmler, Johannes Beckers, Christoph Ziegenhain, Wolfgang Enard, Andrea C. Schamberger, Fien M. Verhamme, Oliver Eickelberg, Fabian J. Theis, Heiko Lickert
Human muscle stem cells are refractory to aging
James S. Novak, Davi A.G. Mázala, Marie Nearing, Nayab F. Habib, Tessa Dickson, Olga B. Ioffe, Brent T. Harris, Marie N. Fidelia-Lambert, Christopher T. Rossi, D. Ashely Hill, Kathryn R. Wagner, Eric P. Hoffman, Terence A. Partridge
Macrophages provide a transient muscle stem cell niche via NAMPT secretion
Dhanushika Ratnayake, Phong D. Nguyen, Fernando J. Rossello, Verena C. Wimmer, Abdulsalam I. Isiaku, Laura A. Galvis, Alasdair J. Wood, Ziad Julier, Thomas Boudier, Viola Oorschot, Kelly L. Rogers, Mikaël M. Martino, Christophe Marcelle, Graham J. Lieschke, Jeroen Bakkers, Peter D. Currie
Hematopoietic stem cells fail to regenerate following inflammatory challenge
Ruzhica Bogeska, Paul Kaschutnig, Malak Fawaz, Ana-Matea Mikecin, Marleen Büchler-Schäff, Stella Paffenholz, Noboru Asada, Felix Frauhammer, Florian Buettner, Melanie Ball, Julia Knoch, Sina Stäble, Dagmar Walter, Amelie Petri, Martha J. Carreño-Gonzalez, Vinona Wagner, Benedikt Brors, Simon Haas, Daniel B. Lipka, Marieke A.G. Essers, Tim Holland-Letz, Jan-Philipp Mallm, Karsten Rippe, Paul S. Frenette, Michael A. Rieger, Michael D. Milsom
A Wnt-specific astacin proteinase controls head formation in Hydra
Berenice Ziegler, Irene Yiallouros, Benjamin Trageser, Sumit Kumar, Moritz Mercker, Svenja Kling, Maike Fath, Uwe Warnken, Martina Schnölzer, Thomas W. Holstein, Markus Hartl, Anna Marciniak-Czochra, Jörg Stetefeld, Walter Stöcker, Suat Özbek
The Echeverri lab at the MBL seeks a highly motivated individual to join the Eugene Bell Center for Regenerative Biology and Tissue Engineering as a Postdoctoral Researcher. The successful candidate will work on the molecular mechanisms of scar free skin regeneration in axolotls.
The specific goal of the project is to examine the role of different cell types in responding to the injury cues and in later remodeling collagen. The position will initially be offered for two years with the possibility of extension.
Basic Qualifications:
Applicants should have a Ph.D. in a biology related field. Must have prior experience working in the field of cell and developmental biology, as well as experience with molecular biology, cell culture and research animals. Must be independent, enthusiastic, self-motivated, productive, and enjoy working in a collaborative environment.
Preferred Qualifications:
The ideal candidate will have direct experience with working in vivo in an animal model. Previous experience with cell culture, molecular biology and imaging would be a plus.
Required documents:
1. Cover letter explaining specifically why you are interested in joining our lab to work on this project and what positive qualities you would bring to our team.
2. Curriculum vitae.
3. Apply online : https://recruiting.ultipro.com/MAR1033MBL/JobBoard/4c3007c3-6354-41de-a13f-d95be60d91e9/?q=&o=postedDateDesc
4.
A Postdoctoral Fellow position is immediately available (08/21/20) in the NSF-Simons Center for Quantitative Biology and in the Department of Molecular Biosciences at Northwestern University.
The successful candidate will employ high throughput genomics (e.g. CRISPR and next-generation sequencing) and computational tools to study dynamic gene regulatory networks in mammalian stem cells.
Examples of our representative publications include: https://biorxiv.org/cgi/content/short/2020.04.20.050559v1, Cell 167 (1555-1570), Journal of American Statistical Association 109 (48-62), Molecular Cell 55 (758-770), Nature 486 (496–501).
Applicants should have a Ph.D. or equivalent in relevant fields. The background in genomics or computational biology or stem cell biology is a plus. The candidate will work with a group of developmental and computational biologists in a highly interdisciplinary environment.
Interested applicants should email their curriculum vitae and contact information for three references to Professor Alec Wang awang@northwestern.edu.
In the latest episode of Genetics Unzipped, Dr Kat Arney takes a look at the progress that’s been made in tackling rare genetic disorders (and the challenges that remain) and we hear from a prenatal genetic counsellor about how new tests are helping people carrying genetic variations make decisions about starting a family.
With Dr Ron Jortner (founder and CEO of Masthead Biosciences and trustee of the Cambridge Rare Disease Network) and Genetic counsellor Kira Dineen.
A postdoctoral Research Associate position is currently available for an individual to work in the laboratory of Prof. Anna Philpott within the Cambridge Stem Cell Institute (https://www.stemcells.cam.ac.uk/research/pis/philpott). The Philpott lab has broad interests in understanding the fundamental mechanisms that determine cell fate choice and differentiation during embryonic development and in cancers, as well as how these processes are co-ordinated with cell cycle progression.
The successful candidate will undertake a project focused around transcriptional regulation of lineage fidelity during fate specification and differentiation of mouse embryonic stem cells, focusing on uncovering epigenetic and co-factor-dependent mechanisms underlying these processes. There is also an opportunity to work on parallel mechanisms of fate specification and differentiation in Xenopus frog embryos.
The successful candidate will have a PhD, considerable experience in stem cell biology, epigenetics, molecular biology, developmental biology, or a similar field, and a proven track record in scientific publication. Prior experience in mammalian cell culture is essential. Experience of epigenetics and/or transcriptional regulation are essential, while experience of genome-wide transcriptional analysis, and in particular analysis at the single cell level, and/or CRISPR technology would also be an advantage. Applicants must display an ability to undertake project management, work within a multi-disciplinary team environment, have good presentation and communication skills and the ability to contribute to an environment supporting researchers at all stages of their careers.
The Wellcome – MRC Cambridge Stem Cell Institute (CSCI) is a world-leading centre for stem cell research with the mission to transform human health through a deep understanding of stem cell biology. https://www.stemcells.cam.ac.uk/ .
Apply online at http://www.jobs.cam.ac.uk/job/26715/
Fixed-term: The funds for this post are available for 3 years in the first instance. Once an offer of employment has been accepted, the successful candidate will be required to undergo a health assessment and a security check.
Closing date for applications is 21/09/2020 with interviews date to be confirmed.
Informal enquiries should be directed to Prof. Anna Philpott, ap113@cam.ac.uk
Please quote reference PS23867 on your application and in any correspondence about this vacancy.
The University actively supports equality, diversity and inclusion and encourages applications from all sections of society. The University has a responsibility to ensure that all employees are eligible to live and work in the UK.
Transitions between cellular identities are fundamental to metazoan biology, from development to disease. Yet how cells navigate accurately between distinct identities remains poorly understood. A primary challenge is that transition is intrinsically dynamic, an outcome of time and stimulation. The methodology and the theory necessary to capture and decode these molecular and cellular dynamics are underdeveloped.
This Workshop aims to highlight innovative interdisciplinary approaches to the question of how biological transitions occur. We bring together practitioners in stem cell and developmental biology with theorists and experimentalists from physics, mathematics and engineering. The goal is to explore avenues for examining cell state transitions across multiple scales. We will consider concepts, tools and technologies, and model systems.
The Workshop will be run in virtual format using bespoke software to facilitate break out discussions. Early-career researchers will be offered a 1 to 1 mentoring opportunity with a senior investigator. The Workshop will be free for those selected to attend.
We offer 10 places for early-career researchers (PhD, postdocs and PIs in the first 3 years of their first appointment) to attend our virtual Workshops along with the our invited speakers.
The deadline date for applications is 28 August 2020.
During development, the establishment of directional left-right (L-R) asymmetry is crucial for the correct positioning of organs within the body. How symmetry is broken in the embryo is still incompletely understood at the molecular level, as is its evolutionary history. A new paper in Developmenttackles this problem with an analysis of L-R asymmetry in the basal chordate amphioxus. We caught up with first author Xin Zhu and supervisors Yiquan Wang and Guang Li of Xiamen University in Fujian, China, to find out more about the work.
Xin, Yiquan and Guang (L to R)
Yiquan and Guang, can you give us your scientific biography and the questions your lab is trying to answer?
YW I did my undergraduate study at Anhui Normal University, China, between 1978 and 1982, and then postgraduate training at Shanxi Normal University between 1984 and 1985. I was a teaching assistant at Anhui Normal University in 1983 and became a lecturer there in 1986. My major job during this period was teaching, but I also joined several research programs including developing methods to preserve and breed Chinese alligators in captivity. I then moved on to do my Ph.D. at Nanjing Normal University between 1992 and 1995, followed by postdoctoral training at China Pharmaceutical University in 1997. I went to Hong Kong University of Science & Technology as a visiting scholar in 1998. During this time, I learned many molecular skills, with which I studied the phylogenetic relationship of several groups of animals and developed DNA markers to distinguish Chinese herbs. I became a Professor at Nanjing Normal University in 1999, a visiting professor at Texas University (Houston), USA, in 2000, and a visiting scientist at the University of Cincinnati, USA, in 2001. Several different topics were studied during these years, varying from geography and phylogenetic relationships of reptiles, isolation of genes encoding snake venom, and human population genetics. In 2002, I came back to China, settled down at Xiamen University, and began my work with amphioxus. I retired in January 2018 and Guang inherited my laboratory.
GL Both my Master’s (2003-2006) and Ph.D. (2006-2010) training were supervised by Yiquan, although I also spent nearly one and a half years (2008-2010) in Peter Holland’s laboratory at the University of Oxford as a visiting student. My major interest in this period was gene family evolution among chordates and their potential relationships to certain morphological and physiological features. In 2010, I became an Assistant Professor at Xiamen University and carried on my study on amphioxus in Yiquan’s laboratory. However, I turned my research focus to evolutionary and development biology. To do this, we first established methods for acquiring amphioxus gametes and embryos all year round in 2013, and then methods for generating amphioxus mutant and transgenic lines in 2014 and 2018, respectively. With these methods, we are now able to do in-depth gene function studies in amphioxus. In 2017, I was promoted to be an Associate Professor at Xiamen University and took all responsibilities for the ‘amphioxus lab’ initially set up by Yiquan.
Xin, how did you come to work with Yiquan and Guang and what drives your research today?
I worked on muscle development in fish during my Master’s training. I enjoyed it very much and gained a lot of knowledge and skills in this field. Because of this, I decided to continue my research on developmental biology for my Ph.D. At that time, Yiquan and Guang’s team was working on amphioxus embryonic development with their newly developed methods. Their research topic attracted me very much. In addition, Xiamen University is one of the best and most beautiful universities in China. For these reasons, I sent my CV and expressed my interest to join the team, and luckily, Yiquan and Guang approved my application – I guess they were probably taken by my interests and background in developmental biology. Before I joined the team in 2015, the lab had almost finished their analysis on Cer, Nodal, Lefty and Pitx functions in amphioxus asymmetry development, and had also acquired some evidence indicating that cilia and Hedgehog (Hh) signalling probably act upstream of these genes. I was fascinated by how cilia and Hh signalling regulate amphioxus asymmetry and therefore took this for my Ph.D. study.
What makes amphioxus a good model for studying the development and evolution of L-R asymmetries?
XZ, YW, GL There are several reasons. First, amphioxus occupies a key phylogenetic position among chordates. Second, amphioxus has orthologues (but fewer family members) of most, if not all, genes involved in vertebrate L-R development. It did not undergo extensive genome duplications like vertebrates, and thus retained many features of ancestral chordates. This makes studying the functions of these genes with genetic tools in amphioxus much easier than in vertebrates. Third, in terms of structures, amphioxus embryos are much simpler than those of vertebrates. For example, at the early neurula stage when L-R asymmetry begins to be established, amphioxus embryos are composed of only two layers of cells. Fourth, most morphological features of L-R asymmetry are formed within 24 h after fertilization, and are easy to detect under a stereoscope. Lastly, we have developed a series of methods in recent years which enable us to conduct in-depth functional analysis of genes in amphioxus embryos.
Early neurula stage amphioxus embryos in which Smo or Hh mRNA has been injected, showing Dand5 expression.
Can you give us the key results of the paper in a paragraph?
XZ, YW, GL We think the key results show that Hh signalling is asymmetrical in amphioxus embryos, and this asymmetric signal is required for and acts upstream of asymmetric Dand5 expression. In addition, we also provide evidence suggesting that asymmetric Hh signalling is achieved through a cilia movement-dependent asymmetric distribution of extracellular Hh protein.
Do Hh signalling and motile cilia play a conserved role in asymmetry in other animals?
XZ, YW, GL Motile cilia appear to play a conserved role in all major lineages of deuterostomes, although their function in asymmetry formation in other bilaterians has not been reported. However, Hh signalling in asymmetry has been demonstrated only in mice, chickens, amphioxus and sea urchins, up to date. Notably, the signalling regulates asymmetry in these animals through different L-R genes: Dand5 in amphioxus and Nodal in mice, chicks and sea urchins. It is currently unclear whether the signalling regulates Dand5 expression in mice (or other vertebrates) as in amphioxus, but it is clear that the signalling is not essential for Nodal expression in amphioxus. Interestingly, most Hh signalling genes are expressed in the site at which asymmetry first occurs in sea urchin and vertebrate embryos. This suggests that the Hh signalling might have an earlier role in the asymmetry development of these animals – future studies are needed to clarify this hypothesis.
The effect of nodal flow on L-R patterning is currently explained by two competing models (two-cilia versus morphogen) – which model does your data best support?
XZ, YW, GL If we must choose one, we would go for the morphogen model, because our data indicate that Hh protein (a kind of morphogen) is asymmetrically distributed in a cilia movement-dependent manner as the morphogen model suggests. However, if the target sensed by the second cilia in the two-cilia model is a morphogen, our results also fit the two-cilia model, as we showed that Hh signalling transduction also requires cilia in amphioxus embryos.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
XZ I got really excited when I found that the Hh fusion protein was asymmetrically distributed in Hh-myc mRNA-injected embryos. This not only told us why Hh signalling is asymmetrically activated in amphioxus embryos, but also explained why caSmo mRNA injection could induce more right isomerism phenotype than Hh mRNA injection.
I got really excited when I found that the Hh fusion protein was asymmetrically distributed
And what about the flipside: any moments of frustration or despair?
XZ There were many moments of frustration during my research on the project. One of them concerns cilia. We have been trying to obtain an amphioxus mutant with cilia defects for many years. For this, we tried to knockdown Kif3a or knockout Kif3a and Foxj1 genes. However, none of these treatments could stop ciliogenesis in the early stages of amphioxus embryos. I was really sad when I saw these negative results.
So what next for you after this paper?
XZ I graduated and left Xiamen in July, and am now working at Changsha University in China. Fish muscle regeneration could be my research area for the next few years.
Where will this work take your lab?
YW, GL Several interesting questions were raised from this work. Why is Hh protein able to be transferred by cilia movement? Is Hh protein enveloped before being transported? Why do Ptch mutants show no L-R defects? Is there a nodal flow in amphioxus embryos and where is it? We have already begun to conduct experiments to address these questions, and hope we can get more exciting results in the near future.
Finally, let’s move outside the lab – what do you like to do in your spare time?
YW I like to meet friends to have some tea or play cards with them.
GL I like to stay at home with family, or have a walk with friends or family within the campus or along the beach.
XZ I like to do some sports in my spare time, such as tennis, golf or swimming. Sometimes I also like going for walks along the beach with my friends and thinking about my research project.
In the NordenLab, we aim to untangle the events that lead to the development of organs. In this context, we study the formation of the vertebrate retina and span different developmental stages from optic cup formation to neuroepithelial growth and neural lamination. Our investigations span the cellular to the tissue level and we combine cell and developmental biology approaches with advanced quantitative imaging, image analysis, mechanobiology and, in collaboration, theoretical modeling.
Our current main model system is the zebrafish, due to its fast ex utero development, unmatched possibilities for in vivo imaging and ease of genetic, pharmacological and mechanical perturbations. Currently we set up additional systems in the lab with the establishment of retinal 3D cultures and organoids using mouse and human iPS cells.
We are looking for a postdoctoral researcher with strong interest in these topics, excited about cross-disciplinary research with a biology, physics or computer science background. The applicant would always have experimental aspects in any project. Prior knowledge of the zebrafish system is not a prerequisite.
The working language at the institute is English.
Applicants should email a description of research interests, a CV and the names of two to three potential references to Caren Norden (cnorden@igc.gulbenkian.pt).
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In the latest episode of Genetics Unzipped, Dr Kat Arney takes a look at the progress that’s been made in tackling rare genetic disorders (and the challenges that remain) and we hear from a prenatal genetic counsellor about how new tests are helping people carrying genetic variations make decisions about starting a family.
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