The Faculty of Science and the Mathematical Institute invites applications for a
four-year

PhD Student on Mathematical Modeling of Cell-ECM Interactions During Angiogenesis (1.0 fte)
Project description
The opening is for a research position, within the field of mathematical or theoretical biology, computational physics, applied mathematics or computational science.

The outgrowth of new blood vessels from pre-existing vessels, called angiogenesis, is a crucial step in wound healing and tumor growth. Cell-based simulation models help to analyze how cells assemble into blood vessels and other tissue structures. Recently our group has developed novel techniques for modeling one of the key controlling factors of angiogenesis, the extracellular matrix (ECM). The ECM is a diverse class of jelly or hard materials providing structural support to the tissue and that acts as a medium for cell-cell communication.

The work will be embedded in the Multiscale Mathematical Biology team at the Mathematical Institute and the Institute of Biology Leiden. The team carries out mathematical biology research in close collaboration with experimental researchers. The team focuses on modelling pattern formation and morphogenesis in multicellular organisms and bacterial ecosystems. More information about the group can be found on biomodel.project.cwi.nl.

Key responsibilities
The project will be part of an NWO-funded Vici-project that will unravel how the extracellular matrix (ECM) coordinates the interactions between endothelial cells and other cells contributing to angiogenesis, and how modifications of the ECM, as they can occur for example near tumors, can modify the structure of new blood vessel networks. In this project you will work closely together with experimental researchers, that will test the mathematical models in the wetlab by imaging of cell cultures and zebrafish experiments.  Your task will be to develop novel mathematical models, which will be informed by literature data and the insights coming from the wetlab. Your models will be experimentally validated by your direct colleagues in the wetlab, based on which you will correct and update your models. Based on cycles of iterative model refinement and experimental validation, you will unravel aspects of angiogenic sprouting, and prepare your insights for publication in the biological, biophysical, and/or biomathematical literature.

The mathematical models will be based on hybrid cellular Potts model, in which stochastic models of cell motility interact with continuum and discrete models of the ECM.  You will contribute to the development of novel and efficient numerical methods for simulating the biomechanics of the ECM, that will interface naturally with pre-existing, stochastic models of endothelial cell behavior. You will integrate the novel methodology into our lab’s modeling framework Tissue Simulation Toolkit, and prepare the new developments for public release alongside our scientific publications.

Selection criteria

• Master’s degree in applied mathematics, computational/theoretical physics, theoretical biology, computer science or a related discipline;
• Excellent written and oral proficiency in English;
• Ability to work independently in a multidisciplinary environment;
• Fluent interdisciplinary communication skills with scientists in cell biology and mathematics;
• Keen interest in cell and developmental biology;
• Experience in (numerical) mathematical modeling (e.g., Cellular Potts modeling, particle-based simulations, PDEs, FBA);
• Excellent programming skills in C++.

Research at our faculty
The Faculty of Science is a world-class faculty where staff and students work together in a dynamic international environment. It is a faculty where personal and academic development are top priorities. Our people are driven by curiosity to expand fundamental knowledge and to look beyond the borders of their own discipline; their aim is to benefit science, and to make a contribution to addressing the major societal challenges of the future.

The research carried out at the Faculty of Science is very diverse, ranging from mathematics, information science, astronomy, physics, chemistry and bio-pharmaceutical sciences to biology and environmental sciences. The research activities are organized in eight institutes. These institutes offer eight bachelor’s and twelve master’s programmes. The faculty has grown strongly in recent years and now has more than 2,200 staff and almost 4,200 students. We are located at the heart of Leiden’s Bio Science Park, one of Europe’s biggest science parks, where university and business life come together. For more information, see http://www.science.leidenuniv.nl.

The Mathematical Institute (MI) is responsible for the research and education in mathematics and statistics at Leiden University. The institute has a strong international orientation. Its mission is to perform high quality research at the frontiers of mathematical knowledge, and to educate future generations of mathematicians and statisticians in a friendly but challenging environment. For more information see https://www.universiteitleiden.nl/en/science/mathematics.

The Institute of Biology Leiden (IBL) is an internationally oriented institute for research and education in biology. IBL performs top quality innovative fundamental and strategic research that will lead to scientific progress, contribute to solutions for societal challenges, and generate industrial opportunities, reflected in the general theme ‘Healthy Lives in a Changing World’. The Institute is organized in three multidisciplinary clusters: Animal Sciences & Health, Plant Sciences & Natural Products and Microbial Biotechnology & Health. For more information see: https://www.universiteitleiden.nl/en/science/biology. There is a large research community in The Netherlands (in particular, in Leiden), including many PhD students. There is close collaborating nationwide.

Terms and conditions  
We offer a full-time position for initially one year. After a positive evaluation of the progress of the thesis, personal capabilities and compatibility the appointment will be extended by a further three years. Salary range from € 2,325.- to € 2,972.- gross per month (pay scale P, in accordance with the Collective Labour Agreement for Dutch Universities).

Leiden University offers an attractive benefits package with additional holiday (8%) and end-of-year bonuses(8.3 %), training and career development and sabbatical leave. Our individual choices model gives you some freedom to assemble your own set of terms and conditions. Candidates from outside the Netherlands may be eligible for a substantial tax break.  Additional budget allows for research visits abroad and attendance of international conferences. More at http://www.workingat.leiden.edu/.

All our PhD students are embedded in the Leiden University Graduate School of Science www.graduateschools.leidenuniv.nl. Our graduate school offers several PhD training courses at three levels: professional courses, skills training and personal effectiveness. In addition, advanced courses to deepen scientific knowledge are offered by the research school.

Diversity
Leiden University is strongly committed to diversity within its community and especially welcomes applications from members of underrepresented groups.

Information
Enquiries about the position can be made to Prof. dr. Roeland Merks, merksrmh (on server:) math.leidenuniv.nl. Also see the group website at http://biomodel.project.cwi.nl.

Applications
To apply for this vacancy, please send an email to merksrmh (on server: ) math.leidenuniv.nl. Please ensure that you join to your application the vacancy number and the following additional documents:

•              A letter of motivation

•              An updated CV

•              The letters of recommendation by 1 or 2 former supervisors

•              The transcripts of your MSc studies

•              Examples of previously written code

Only applications received before April 15th, 2019 will be considered.

Enquiries from agencies are not appreciated.

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The Faculty of Science and Institute of Biology are looking for a

Senior Research Technician in Cell and Developmental Biology and Imaging

Key responsibilities
The opening is for a research technician position within the field of cell and developmental biology and imaging. The position is in an interdisciplinary team of mathematical and experimental biologists. Our team specializes in the mathematical and computational modeling of angiogenesis. We are currently setting up an experimental research line, which will directly test the mathematical models in the lab. Discrepancies between the lab observations and the mathematical models identify the gaps in our understanding, based on which the mathematical models will be updated or rejected.   Our team focuses in particular on the coordination of collective endothelial cell behavior by the extracellular matrix (ECM). We will use cell cultures, followed by in vivo studies in the zebrafish.

As senior technician you will actively participate in the interdisciplinary research of our group. You will be responsible for setting up and running experimental work to test our mathematical models in collaboration with an experimental PhD student and with a number of PhD students in mathematical modeling.

Your key tasks include:

• Setting up and maintaining experimental systems such as cell cultures, lab-on-a-chip, zebrafish, in vitro and in vivo imaging using time-lapse microscopy, quantitative reflection microscopy, TIRF, and 4D imaging using a VAST system;
• Fluorescent imaging of dynamic cell behavior, cell morphology and ECM characteristics in vitro and in vivo under the influence of a range of pharmacological and genetic experimental interventions, including ECM characteristics such as stiffness, matrix orientation and acidity using imaging techniques, which will lead to insight in conjunction with the model;
• Active participation in image analysis and digital annotation of the results;
• Practical assistance of the PhD student, including teaching of experimental skills;
• Active participation in the research projects, including interpretation and reporting.

Selection criteria

• Master’s or Bachelor’s degree in cell biology, biophysics, imaging or a related discipline, with minimally 2 years of relevant work experience. Applications from postdocs will also be considered;
• Outstanding experimental skills in cell and developmental biology and imaging;
• Keen interest or experience with image analysis and/or mathematical modeling approaches;
• Fluent interdisciplinary communication skills with scientists in cell biology and mathematics;
• Excellent written and oral proficiency in English;
• Ability and enthusiasm for working in a multidisciplinary environment;
• You are a team player, but also able to work independently;
• You take initiative and have a strong interest in academic research.

Research at our Faculty
The Faculty of Science is a world-class faculty where staff and students work together in a dynamic international environment. It is a faculty where personal and academic development are top priorities. Our people are driven by curiosity to expand fundamental knowledge and to look beyond the borders of their own discipline; their aim is to benefit science, and to make a contribution to addressing the major societal challenges of the future.

The research carried out at the Faculty is very diverse, ranging from mathematics, information science, astronomy, physics, chemistry and bio-pharmaceutical sciences to biology and environmental sciences. The research activities are organised in eight institutes. These institutes offer eight bachelor’s and twelve master’s programmes. The faculty has grown strongly in recent years and now has more than 1,300 staff and almost 4,000 students. We are located at the heart of Leiden’s Bio Science Park, one of Europe’s biggest science parks, where university and business life come together.

The Institute of Biology (IBL) is positioned in the Faculty of Sciences. The core business of IBL is to perform top quality innovative fundamental and strategic research that will lead to scientific progress, contribute to solutions for societal challenges, and generate industrial opportunities. The Institute is organised in three multidisciplinary clusters: Animal Sciences & Health, Plant Sciences & Natural Products and Microbial Biotechnology & Health. Presently, over 120 fte (including postdocs and PhDs) are employed at IBL.

The Mathematical Institute (MI) is responsible for the research and education in mathematics and statistics at Leiden University. The institute has a strong international orientation. Its mission is to perform high quality research at the frontiers of mathematical knowledge, and to educate future generations of mathematicians and statisticians in a friendly but challenging environment.

Terms and conditions
We offer a one year term position with the possibility of renewal based on need, funding and performance. The salary range is from €2.835 to €3.895 gross per month (pay scale 9 in accordance with the Collective Labour Agreement for Dutch Universities).

Leiden University offers an attractive benefits package with additional holiday (8%) and end-of-year bonuses (8.3 %), training and career development and sabbatical leave. Our individual choices model gives you some freedom to assemble your own set of terms and conditions. For international spouses we have set up a dual career programme. Candidates from outside the Netherlands may be eligible for a substantial tax break. More at: https://www.universiteitleiden.nl/en/working-at/job-application-procedure-and-employment-conditions.

Diversity
Leiden University is strongly committed to diversity within its community and especially welcomes applications from members of underrepresented groups.

Information
For more information about the IBL, please visit https://www.universiteitleiden.nl/en/science/biology.

Enquiries can be made to Prof. dr. Roeland Merks,  telephone 071-5277106, email r.m.h.merks  (on server)  biology.leidenuniv.nl. More information about the research group is at http://biomodel.project.cwi.nl.

Applications
To apply for this vacancy, please send an email to sylvius  (on server) biology.leidenuniv.nl with a motivation letter, cv and the names and phone numbers of two referees, no later than April 26. Interviews will take place in week 19. You are kindly requested to be available during this time

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The Giraldez laboratory at Yale University is seeking to recruit a highly qualified Associate Research Scientist as a long-term scientist in the laboratory (www.giraldezlab.org). Prerequisites for appointment on the research scientist track include a doctoral degree and relevant postdoctoral experience. 

The successful candidate will be a highly-motived scientist with excellent organizational, mentoring and leadership skills. They will be responsible for coordinating the overall scientific operations of the Giraldez lab and will provide critical training and mentoring to individual lab members. In addition, the successful candidate will have the opportunity to participate in multiple research projects and drive a scientific project aligned with the major interests of the laboratory. The successful candidate will have the following attributes:

This appointment can be renewed indefinitely provided the need for the position continues, the funding for the position is available, and the expectations for performance are met.

To apply to this position please submit the following using the Interfolio Link: https://apply.interfolio.com/50482:

1) A one-page cover letter describing your motivation for the position, research experience, and relevant mentoring/organizational experience, 

2) biosketch or CV, 

3) three letters of references

4) PDFs of three publications .

 

For inquiries please contact hiba.codore@yale.edu. Please include “Associate Research Scientist” in the subject of the email.

 

Applications are now open and will be considered on a rolling basis. Salary will be commensurate with experience and the appointment includes an attractive benefits package in line with an appointment in the research track within the Yale School of Medicine

 

Yale University is an Affirmative Action/Equal Opportunity employer. Yale values diversity among its students, staff, and faculty and strongly welcomes applications from women, persons with disabilities, protected veterans, and underrepresented minorities.

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The story behind our recent paper “Heat Oscillations Driven by the Embryonic Cell Cycle Reveal the Energetic Costs of Signaling” Developmental Cell, 48(5), pp.646–658.e6.

At the end of 2014, a friend asked me “What is your story”? I had just started my postdoc in the laboratory of Karla Neugebauer and was a bit perplexed by the direct question. I started talking about some loose project ideas of mine involving words like development, metabolism, and RNA – after all, I joined an RNA lab after doing my PhD on fly development, growth control, and lipid metabolism. But the story behind our paper did not start for another few months.

Historically, metabolism and developmental biology are deeply connected. This was emphasized in Joseph Needham’s mammoth three-volume work “Chemical Embryology” published in 1931 on the subject of physico-chemical embryology. This research faded away since the molecularization of experimental embryology, but over the last few years has reemerged as a quantitative field of study in developmental biology. Two consecutive meetings, the 2016 Company of Biologist Workshop ‘Metabolism in Development and Disease’ and the 2017 EMBO Symposium ‘Metabolism in Time and Space’ (Krejci & Tennessen 2017), highlighted that developmental biologists are once again investigating the role of cellular metabolism in growth, differentiation, and maturation during development. This resurgence of metabolisms role in development sets the stage for our story.

Developing embryos, like all living systems, are open systems exchanging energy and matter with their environment. They function out of equilibrium and require a continuous supply of energy to remain alive. From a thermodynamic perspective, metabolism can be regarded as an energy converter that directs energy from nutrients through an interconnected web of chemical reactions to meet the energetic and biosynthetic demands of growth, proliferation, and development. An emerging view is that this bioenergetic function of metabolism is tightly regulated in time and space in order to fulfill the changing energetic and biosynthetic demands of animal development (See Miyazawa & Aulehla 2018 and Gándara & Wappner 2018 for reviews). One particular example is that highly proliferative cells exploit increased glycolytic activity even in the presence of oxygen – a metabolic state known as aerobic glycolysis or the Warburg effect (Ward & Thompson 2012). How and why cells adopt this metabolic state has been the focus of intense research in the last decade and is not entirely understood. It has been recognized that this metabolic wiring supports the increased energetic and biosynthetic demands necessary for rapid cell growth and proliferation during development and disease. Indeed, implanted mammalian embryos seem to utilize Warburg metabolism with high levels of glucose uptake, glycolytic activity, and lactate production. Interestingly, early embryos undergoing rapid reductive cleavage divisions do not rely on glucose but rather use pyruvate, lactate and amino acids as energy sources (Gardner 1998). This indicates that early embryos rely on respiration to proliferate and switch their metabolic state during the transition from the cleavage to the blastocyst stage. This metabolic switch seems to coincide with the transition from maternal to zygotic instructions of developmental control known as maternal-to-zygotic transition (MZT) when maternally deposited RNA is degraded and zygotic gene expression is initiated.

Karla Neugebauer’s laboratory at Yale University focuses on the regulation of transcription and splicing in a variety of biological contexts, including MZT. When I joined the lab, RNA-interactome studies had just identified many ‘classical’ metabolic enzymes of intermediary metabolism as RNA-binding proteins and I was intrigued by the idea of combining expertise with the Neugebauer lab to study the dynamic interplay between transcription, RNA-binding proteins and metabolism during early zebrafish embryogenesis, particularly during MZT. Although this was the original idea for my project in her lab if you’ve read our paper you know that we ended up elsewhere… using calorimetry to measure the heat flow between a developing embryo and its surroundings. How did the project change so drastically? Stay with me, as I will explain in the next few paragraphs.

The change in a metabolic state is usually associated with a change in the energetic and biosynthetic requirements of the system under investigation. In the case of embryonic cleavage stage development, cells lack growth phases and thus become smaller as they divide. One could hypothesize that they use oxidative phosphorylation because of the absence of volumetric growth. However, increasing embryonic cell number demands precursors (e.g. nucleotides, fatty acids, and amino acids) for DNA replication, an increase in plasma membranes, and protein synthesis. Thus, the embryo must produce and/or polymerize the precursors necessary for cleavage stage development. Each cell of the embryo must also expend energy to assemble and disassemble cellular machinery (e.g. chromatin, mitotic spindles), generate forces needed to segregate the chromosomes and divide the cell, and change the activity of signaling pathways that enforce cell cycle phasing, even in the absence of volumetric growth. As development proceeds and the embryonic cell cycle gains G1 and G2 phases, the embryo faces the additional energetic demands of volumetric growth and might switch to aerobic glycolysis as a metabolic strategy to fulfill those. But what are those energetic demands? I realized that we lack a quantitative understanding of how the metabolic energy converted by different metabolic states is partitioned among the complex array of cellular processes that take place during cell growth, proliferation, and development. What if we could put numbers on energetic requirements of making a new cell or an embryo? Maybe then we will be able to understand why metabolism functions the way it does. I became fascinated by the thought of studying the energy budget of early embryogenesis and my focus shifted away from the regulation and interplay of RNA biology and metabolism during MZT. This is where our story truly started – with the question of how to measure the energy required for embryonic development.

The amount of energy dissipated by an animal per unit of time is defined as metabolic rate and is reported in energy units per unit time in Watt (joule/second) or Watt per kg body mass (W/kg).  An average human at rest consumes ~2000 kcal per day and dissipates energy in the form of heat at a rate of about 100 W or 1 W/kg (Joules/s*kg). These estimates are conceptually based on the first law of thermodynamics. The change in energy (2000 kcal /day) equals heat dissipated (100W) minus work. The average human is at rest – not growing or conserving any energy – and does not perform any net chemical synthesis or anabolic reactions. All the 2000 kcal/day is converted by catabolic reactions and immediately used by various cellular processes defined as maintenance reactions to keep the individual alive or away from thermodynamic equilibrium. Now let’s consider a growing organism which must perform anabolic reactions and invests energy into chemical synthesis of new biomass in order to grow. In this case, the organism conserves energy and performs net chemical synthesis. Measurements of heat dissipation now reflect the difference between energy consumption in the form of nutrients and energy conservation by biosynthesis, which is equal to the net change in enthalpy of all the reactions taking place in the system. This is how heat dissipation differs from respiratory metabolic rate measurements such as O₂ consumption or CO₂ production. They reflect rates of catabolic reactions and are inherently blind towards energy conservation in the system by anabolic reactions.

Heat dissipation is directly connected to the laws of thermodynamics. When approaching this question, I thought, “maybe we can measure the heat flow between developing embryos and their environment using calorimetry.” It’s also possible that I always wanted to stick a developing organism in a calorimeter to see what I could measure… Isothermal titration calorimetry (ITC) is traditionally used to measure the heat transfer associated with a biomolecular interaction to determine the binding constant, stoichiometry, enthalpy and entropy of the binding event in solution, without the need of labels.  After spending a few weeks of optimizing a 17 years old ITC machine housed in the biophysical core facility into measuring heat flow for prolonged periods of time without titrations, we were ready to try to measure the heat flow associated with early development. It worked incredibly well – and I was thrilled when I saw the first heat flow data from early zebrafish embryos undergoing cleavage stage development (see picture).

 

The initial finding was that the heat flow between embryo’s undergoing cleavage stage development and their environment increased over time. Surprisingly, however, I discovered that there was a small (~2% of the mean) but reproducible heat flow oscillation superimposed on the steady increase. The period and number of oscillations matched the division cycles taking place during this phase of embryogenesis. The oscillations suggested the presence of cyclic energetic events associated with embryonic cell proliferation, leading us to wonder if the oscillations are associated with the embryonic cell cycle.

After the initial discovery, I started a collaboration with Joe Howard, a biophysicist, to tackle the theory and thermodynamic aspects of heat flow during embryonic development. In the summer of 2015, Joe was invited faculty for the physiology course at the Marine Biology Laboratory (MBL) in Woods Hole, Massachusetts. We decided to take the project to the MBL for two weeks and I had the pleasure to work with two amazing students on the energetic costs of embryonic development. Manuel Razo was interested in the temperature scaling of the heat flow and Mathijs Vleugel started to investigate the underlying metabolic state and mitochondrial biology of embryos undergoing cleavage stage development. The two weeks at the physiology course and the MBL deeply influenced my thinking about the energetics of development and science in general. The course brings together scientists from diverse backgrounds and provides a truly collaborative and open environment. We started to throw ideas around and discussed what these heat flow oscillations could be? As the early embryonic cell cycle is solely composed of DNA replication, mitosis and cytokinesis, a prediction was that these heat flow oscillations could represent the energy used by either of those processes.  My personal bet was on mitosis – but it turned out we were all wrong.

The experiment which pointed us in a new direction was when I blocked both DNA replication and mitosis by inhibitors. To our surprise, the heat flow oscillations persisted with a similar period and amplitude as control treated embryos. What followed was a series of quantitative heat flow measurements combined with perturbation experiments, theoretical modeling, and order of magnitude estimates for energetic costs of oscillatory cellular processes to investigate the underlying principle of the heat flow oscillations. We were able to show that they were driven by the phosphorylation and dephosphorylation reactions catalyzed by the cell cycle oscillator, the biochemical network controlling mitotic entry and exit, and thus revealed the energetic costs of cell cycle signaling.

In summary, the story started with an unconventional idea and a discovery.  It evolved to show that quantitative heat flow measurements combined with perturbation experiments, theoretical modeling, and order-of-magnitude estimates can be a powerful approach to dissect the energetic costs of various cellular processes driving embryogenesis. In our work, we postulated that the energetic cost of cell cycle signaling likely reflects the thermodynamic burden of imposing accurate and robust timing on cell proliferation during development, as predicted by a theoretical tradeoff between energy dissipation and precision of biomolecular oscillators. I am currently working on establishing systems to measure the accuracy of the embryonic cell cycle and modulate the oscillatory heat flow amplitude and phase to test these in-silico predictions in-vivo and in-vitro. Furthermore, we have been able to allocate the oscillatory component to the energetic cost of the cell cycle signaling representing 2% of embryos total energy expenditure. What about the other 98%? Why does it increase during cleavage stage development – even absence of volumetric growth?

Bibliography

Gardner, D.K., 1998. Changes in requirements and utilization of nutrients during mammalian preimplantation embryo development and their significance in embryo culture. Theriogenology, 49(1), pp.83–102.

Gándara, L. & Wappner, P., 2018. Metabo-Devo: A metabolic perspective of development. Mechanisms of development, 154, pp.12–23.

Krejci, A. & Tennessen, J.M., 2017. Metabolism in time and space – exploring the frontier of developmental biology. Development (Cambridge, England), 144(18), pp.3193–3198.

Miyazawa, H. & Aulehla, A., 2018. Revisiting the role of metabolism during development. Development (Cambridge, England), 145(19), pp.dev131110–11.

Ward, P.S. & Thompson, C.B., 2012. Metabolic Reprogramming: A Cancer Hallmark Even Warburg Did Not Anticipate. Cancer cell, 21(3), pp.297–308.

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Searching for a post-doc who is passionate about both teaching and research. We are studying the interplay between division and inductive signaling. In particular, we are exploring how signaling receptors are trafficked in dividing cells to generate asymmetric induction of a cardiac progenitor lineage. We are also using comparative genomics to explore the evolutionary constraints that shape gene regulatory networks. We study these questions in the invertebrate chordate, Ciona robusta. Ciona embryos consists of extremely low cell numbers allowing high resolution analysis of intra-cellular dynamics in intact embryos. The ease of generating transgenic Ciona embryos make this an excellent model organism for undergraduate research. We have recently initiated a collaboration with Danelle Devenport at Princeton focused on similar processes in cultured mouse epithelial cells. This is a great opportunity for a post-doc with an interest in undergraduate teaching and research. My former post-doc is moving on to a tenure-track position at a small liberal arts college and it was clear that the combination of a strong research record along with a demonstrated commitment to undergraduate mentoring and teaching made her a strong candidate for these very competitive positions.

​Applicants should have a PhD (or be close to completing one) in a relevant subject area. Excellent communication skills and a commitment to undergraduate mentoring are essential.

To apply or if you have questions about the position – please send your CV and a cover letter describing your interest to Bradley Davidson at bdavids1@swarthmore.edu. I will be in touch with instructions for submitting a formal application.  

Proposed start date: June 1st, 2019 (Flexible).

(1 votes)
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The Young Embryologist Network (YEN), is an academic body aiming to bring together early career scientists within the wide field of developmental biology, in order to provide opportunities to present talks and posters, network and collaborate, and gain research or career advice.

YEN was set up in 2008 by graduate students in the prestigious Department of Cell and Developmental Biology at University College London.  Every year, the YEN hosts an annual conference at a UK research institution with great success. The conference is entirely organised by graduate students and junior post-doctoral scientists, and has remained free to attend since 2008, due to the generosity of sponsors and grants.

The 2019 conference is being held on the 13th of May 2019 at the Francis Crick Institute in London.

 

 

The deadline for Registration is the 19th April. Register here:

youngembryologists.org/yen-2019/conference-registration

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Jim Smith introduced the Beddington medal with heartfelt memories of Rosa Beddington and her time at the NIMR. Please read more of his thoughts here. Some complicated selfies were taken as the medal was passed over before David went on to present the work that has deserved him this award.   In the words of his PhD supervisor: “The really impressive thing about David’s work is that he did not come to my lab to fit in with an existing line of research but created one of his own”.  Jamie Davies, University of Edinburgh. David received his undergraduate degree in Sport and Exercise Science at the University of Stirling (2010-2014). With this, he achieved a first-class honours degree and the prize for the best overall performance throughout a physiology related degree (British Physiological Society Undergraduate Prize). His dissertation project investigated associations between ADRB2 mutations (an adrenaline receptor gene in humans) and athlete status/athletic ability measurements. Subsequently, he was awarded a University of Stirling Head of School Summer Bursary Award to remain in Stirling during the summer of 2014 and investigate the relationship between transcribed ultra-conserved regions of RNA (T-UCRs) and the development of diet-induced insulin resistance in humans (Summer 2014). He then moved to the University of Edinburgh for his MSc by Research in Biomedical Sciences (2014-2015). Again, he received a distinction and was awarded the Class Prize for best student. During this time, he studied the physiology of S-acylation the regulation of skeletal muscle energy expenditure by an obesity-associated phospholipase as part of two research placements. David has been awarded the Beddington medal for his exceptional work performed during his 3-year MRC-funded PhD at the University of Edinburgh with Prof Jamie Davies and Dr Peter Hohenstein (2015-2018): The thesis is titled ‘Mechanisms of kidney vascularisation and the roles of macrophages in renal organogenesis’. During his PhD, he gave several oral and poster presentations at national and international conferences, supervised students (including a Gurdon Summer Studentship Awardee), established numerous international collaborations, was awarded travel grants (including a BSDB Conference Grant), and reviewed manuscripts for leading journals (including Cell Reports, Angiogenesis, and Scientific Reports). He is now a post-doctoral fellow at the UK Dementia Research Institute (University of Edinburgh; 2019- present), continuing research in macrophage biology under the supervision of Prof Josef Priller. His current focus in on brain macrophages (microglia) in development, neurodegeneration, and aging. Thesis description Kidneys are specialised organs that clean the blood, removing waste while retaining what is useful. This requires a complex vasculature, and its formation as a foetus develops is poorly understood. I started my PhD research by using advanced microscopy techniques to visualise how blood vessels form in three-dimensions in the mouse kidney. In doing so, I identified when and from where the first blood vessels enter the kidney, and how blood vessels pattern at the edge of the kidney throughout development. Blood vessels can form through angiogenesis (branching of new vessels from pre-existing ones) and/or vasculogenesis (assembly of new vessels from the coalescence of endothelial precursor cells). It has long been thought that a combination of both processes occurs during kidney vascularisation; however, my thesis work indicates that this concept may not be correct. My data instead suggest that kidney vascularization relies on growth and remodelling of pre-existing vessels (angiogenesis) and does not depend on vasculogenesis at any point (Publications 1 and 5 in CV). When assessing the entire 3D vascular tree of the kidney, isolated endothelial cells were never observed at any developmental age. Instead, all vessels, including the newly forming ones, were connected to pre-existing vessels that could be traced to the major circulatory vessels. I then focused on the blood vessels at the edge of the kidney, which I found to consistently and accurately pattern around a special collection of cells – the cap mesenchyme. The cap mesenchyme contains cells that eventually become the cleaning tubes of the kidney, the nephrons. This cell population undergoes rounds of splitting at the kidney’s periphery. As this happens, I demonstrated that blood vessels migrate through the newly opened regions between the separating cap mesenchymal populations (Publication 1 in CV). This occurs in cycles throughout development and is likely to be vital for the oxygenation of the kidney’s outer region, the site where important processes such as nephron formation take place. I determined that a signalling molecule, semaphorin-3f, and its receptor, neuropilin-2, were expressed in a pattern consistent with them having roles in this cyclical patterning of blood vessels; however, using mouse models where the genes for these molecules were deleted, I established that they were not vital for this process (Publication 2 in CV). I next shifted my research focus towards a specialised cell type known as the macrophage (macro = big; phage = eater) in the developing kidney (Publication 3 in CV). Macrophages are immune cells best known for clearing foreign and damaged cells. These cells have vital roles during animal development, but little is known about their specific functions during kidney development. Macrophages arrived in the mouse kidney early during its development, where they were required to clear away misplaced cells to ‘set-the-stage’ for early kidney development (Publication 6 in CV, under review). Throughout later development, most macrophages wrapped around blood vessels and I demonstrated their ability to eat endothelial cells (which usually line the blood vessels) and red blood cells (which are carried within them) within the kidney. I also established that kidney macrophages produced many molecules linked to blood vessel development, and so I examined the consequences of macrophage-loss on blood vessel formation. Blood vessels normally form continuous networks in the kidney; however, when macrophages were depleted (by blocking a macrophage-survival signalling pathway), connections between renal blood vessels were reduced (Publication 6 in CV). Publications

1. Munro DAD, Hohenstein P, Davies JA. 2017. Cycles of vascular plexus formation within the nephrogenic zone of the developing kidney. Scientific Reports. 7: 3273.
2. Munro DAD, Hohenstein P, Coate TM, Davies JA. 2017. Refuting the hypothesis that semaphorin-3f/neuropilin-2 guide endothelial patterning around the cap mesenchyme in the developing kidney. Developmental Dynamics. 246:1047-1056.
3. Munro DAD, Hughes J. 2017. The Origins and Functions of Tissue-Resident Macrophages in Kidney Development. Frontiers in Physiology. 8:837. (Review)
4. Mills CG, Lawrence ML, Munro DAD, El-Hendawi M, Mullins JJ, Davies JA. 2017. Asymmetric BMP4 signalling improves the realism of kidney organoids. Scientific Reports. 7:14824.
5. Munro DAD, Davies JA. 2018. Vascularizing the kidney in the embryo and organoid: questioning assumptions about renal vasculogenesis. Journal of the American Society of Nephrology. (Perspectives article).
6. Munro DAD, et al. Macrophages restrict the nephrogenic field and promote endothelial connections during kidney development. eLife 2019;8:e43271 DOI: 10.7554/eLife.43271

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A postdoctoral position is available in the laboratory of Dr. Jessica Mark Welch in the Bay Paul Center to study the spatial organization of microbial communities in the human mouth. The successful candidate will use fluorescence in situ hybridization, spectral imaging microscopy, and computational image analysis to investigate microbial community structure and will interact closely with collaborators at other institutions as well as with the vibrant and collegial MBL scientific community.

The position is for 2 years, and may be extended beyond this period contingent on securing additional funding.

Physical requirements: This position requires fine motor skills and willingness to work with potentially biohazardous materials and standard laboratory chemicals including fixatives and solvents.

Basic qualifications: A Ph.D. in biological sciences or a related field is required.  

Preferred qualifications: Experience with confocal microscopy, computational image analysis, bioinformatics, and/or microbiology is desirable.

Instructions: To apply, please visit the MBL Employment Opportunities website: https://www.mbl.edu/hr/employment/. The following documents are required: (1) a cover letter describing your interests, skills, and prior research experience, including any specific experience with the job responsibilities listed above; (2) a curriculum vitae/resume; and (3) the names and contact numbers of three persons who can be contacted for letters of reference, at least one of whom must have acted as your supervisor in a previous research position.

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The Rohner Lab at the Stowers Institute for Medical Research has an opening for a Postdoctoral Researcher to develop an independent project investigating the molecular, genetic, and developmental mechanisms of how cavefish maintain health under diabetes-like phenotypes. The lab has previously found that the cavefish Astyanax mexicanus develop high-blood sugar and insulin resistance as part of their natural strategy to survive in the caves but without the usually associated health problems (Riddle et al. Nature. 2018 Mar 29;555(7698):647-651). Visit http://research.stowers.org/rohnerlab/ for more information.

The selected candidate will investigate the molecular mechanism underlying these impressive adaptations. The candidate will closely work with the core facilities at the institute to perform single-cell RNA sequencing, proteomics, and functional validation in vitro and in vivo. The candidate will receive strong support from the core facilities that provide advice, training and service to enhance the Institute’s interdisciplinary and collaborative research programs. Current core facilities are staffed by over 100 scientists with expertise in bioinformatics, cytometry, histology, imaging, microarray, next generation sequencing, transgenic and ES cell technologies, proteomics and molecular biology. The Stowers Institute offers a highly competitive compensation and benefits package.

The position is funded for two years through a grant by the Juvenile Diabetes Research Foundation and can be renewed for up to five years in order to allow enough time to develop a research program/publication record that makes the postdoc a strong candidate for an independent position. The Rohner Lab has a strong commitment for mutual success and is dedicated to providing support for all lab members.

Minimum requirements include a doctoral degree in the life sciences, chemistry, or biomedical engineering. Experience in one or more of the following areas is desirable: molecular biology, developmental biology, genetics, genomics, evodevo, physiology.

In addition to excellent verbal and written communication skills, successful candidates must be dynamic and highly motivated, work independently and creatively, able to work in a team-oriented environment, and proficient at problem solving.

Application Instructions: To apply, please submit (1) a brief cover letter, (2) a current CV, and (3) contact information for two professional references to Dr. Nicolas Rohner at nro@stowers.org cc: careers@stowers.org.

 

About the Stowers Institute for Medical Research

The Stowers Institute for Medical Research is a world-class basic biomedical research organization focused on improving our understanding of fundamental mechanisms of biology and using this knowledge to guide the development of innovative treatments to improve human health.

Our dedicated scientists collaborate across a variety of disciplines, studying many different aspects of health and disease. A primary goal of our research is to understand the principles that guide the function and behavior of living organisms and individual cells. Discoveries resulting from this kind of research often prove to be major milestones along the path toward novel therapies and cures (visit www.stowers.org). Jim Stowers, founder of American Century Investments, and his wife, Virginia, opened the Institute in 2000. Since then, the Institute has spent over 900 million dollars in pursuit of its mission.

Currently, the Institute is home to almost 550 researchers and support personnel; over 20 independent research programs; and more than a dozen technology-development and core facilities. The Institute has been ranked 3^rd place by the Scientist for best places to work in the world: https://www.the-scientist.com/features/best-places-to-work-academia-2012-40676

Kansas City is an emerging metropolitan city in the Midwest with a high quality of living and affordability. Visit https://www.visitkc.com for information about living and working in Kansas City.

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We are looking for an intellectually curious and motivated postdoctoral fellow to join in the fun exploring how glia regulate neurogenesis and neuronal fate-specification. Our approaches are interdisciplinary and involve genetics, live imaging, computational modelling, single cell RNA sequencing, etc. Available projects include: (1) Understanding how signals from glia impart unique neuronal identities (a follow up to Fernandes et al., Science, 2017). (2) Characterising glial diversity in the visual system. (3) Exploring glial involvement in neuroepithelial proliferation.

​Applicants should have a PhD in a relevant subject area (or be close to completing their degree), excellent communication skills, a collaborative spirit and a kind heart. The ideal candidate will have a strong background in molecular biology, cell and/or developmental biology as well as experience with imaging. Knowledge of signal transduction, Drosophila genetics and bioinformatics are a plus but not essential.

Formal applications will be accepted online through UCL’s job portal till May 3rd, 2019. If you cannot meet this deadline but would like to apply, please contact Dr. Fernandes as soon as possible.

Proposed start date: August 1st, 2019 (Flexible).

For more details please contact Dr. Fernandes at vilaiwan.fernandes@ucl.ac.uk (along with a CV and cover letter describing research interests).

Note: Our lab and UCL value and support diversity. Funding is guaranteed beyond Brexit.

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