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Wellcome-Trust Funded Independent Senior Research Fellows in Quantitative Biomedicine at Warwick

Posted by , on 29 July 2015

Closing Date: 15 March 2021

Wellcome-Trust Funded Independent Senior Research Fellows in Quantitative Biomedicine.

A unique opportunity to launch an independent research career.

The University of Warwick has initiated a Wellcome-Trust funded research programme in “Quantitative Biomedicine” to bridge physical / mathematical sciences and biomedicine. The programme is of a cross-campus nature with strong participation from the Division of Biomedical Cell Biology and the Warwick Systems Biology Centre

We are seeking early career researchers who are no more than 4 years from obtaining a Doctoral degree with the potential to lead a strong independent research programme. The candidates will be selected based on their track record in innovative research and on the strength of the research proposal. Importantly, the proposal should make clear how the project benefits from quantitative methodologies. The proposed research programme should bring together physical and mathematical sciences (including but not restricted to computer science, physics, mathematics, statistics, chemistry, and engineering) and biomedical sciences (including, but not restricted to cell and developmental biology, neurobiology, immunology, microbiology and infection). Successful candidates will be provided salary, laboratory space, running costs and technical support for three years. The identified candidates will be expected to win externally funded fellowships within the contract period and will be mentored in preparing such applications.

Interested candidates should submit their CV, a two-page research proposal, and the names and addresses of three referees who are able to comment on the candidates past research work as well as the readiness of the candidate to embark on an independent career in research.

https://atsv7.wcn.co.uk/search_engine/jobs.cgi?owner=5062452&ownertype=fair&jcode=1475114&vt_template=1457&adminview=1

Informal enquires can be directed to

Mohan Balasubramanian, E-mail: m.k.balasubramanian@warwick.ac.uk

or Karuna Sampath (email: K.Sampath@warwick.ac.uk)

 

 

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Question of the month- interdisciplinary research

Posted by , on 29 July 2015

Developmental biology is becoming increasingly interdisciplinary, as biologists team up with physicists and mathematicians to address new and classical problems in the field from a new perspective. But should we all be pursuing such an approach or is there still room for ‘pure’ developmental biology approaches? Should we incorporate more physics/mathematics modules in the training of young scientists to facilitate interactions? And is it enough to collaborate with researchers outside your field on specific projects or should labs include mathematicians and physicists working alongside biologists? This month we are asking:

 

To what extent should we be interdisciplinary?

 

Share your thoughts by leaving a comment below! You can comment anonymously if you prefer. We are also collating answers on social media via this Storify. And if you have any ideas for future questions please drop us an email!

 

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From our sister journals- July 2015

Posted by , on 28 July 2015

Here is some developmental biology related content from other journals published by The Company of Biologists.

 

dmmlogo

 

 

 

Drosophila helps to elucidate the effects of radiation therapy

DMM019786.jpgChildren who are exposed to cranial radiation therapy (CRT) to treat brain tumours are at increased risk later in life for neurocognitive, motor and seizure disorders. Current radioprotective agents are difficult to administer and have severe side effects. Thus, Barry Ganetzky and colleagues used Drosophila to model and elucidate the toxic effects of CRT during juvenile development. First, they found that irradiating fly larvae with different doses of radiation reduces the percentage of animals that survive to adulthood and impairs motor activity of surviving adults, in a dose-dependent manner. These phenotypes are paralleled by an increased expression of activated death caspase-1, a cell death marker, in adult brains. Then, using flies at different developmental stages, they found that the toxic effects of radiation exposure become more severe with decreasing larval age at time of irradiation. Notably, flies with different genetic backgrounds show different sensitivity to radiation. Thus, Drosophila represents a useful system to model CRT-induced toxicity and to dissect key molecular and genetic pathways. These, in turn, might illuminate potential targets for radioprotective purposes. Read the paper here  (Open Access).

 

 

JCS

 

 

 

 

Of oocytes and PDKs

JCS167049F6Perturbations in energy metabolism cause meiotic defects in mammalian oocytes. It has been suggested that these may be exerted through pyruvate dehydrogenase kinases (PDKs) that act on the pyruvate dehydrogenase complex (PDH), which, in somatic cells, is inhibited by phosphorylation of its catalytic subunit PDHE1α at serine residues S232, S292 and S300; however, the role of particular PDKs in the maturation of meiotic oocytes is still unclear. Qiang Wang and colleagues, therefore, examined the individual contributions of known mammalian PDKs to the regulation of murine oocyte maturation. They found that oocytes that overexpress PDK3 have elevated levels of PDHE1α phosphorylated at S293, defects in polar body 1 (Pb1) extrusion, as well as a disorganised spindle and misaligned chromosomes. Moreover, in keeping with a central role of PDH in energy production, the authors also found decreased levels of ATP. These spindle and chromosome abnormalities, as well as metabolic defects could be rescued with a phosphorylation resistant PDH-S293A mutant. By contrast, knockdown of PDK1 or PDK2, both of which phosphorylate S232, caused defects in Pb1 extrusion, spindle assembly and chromosome alignment, but did not affect the level of total ATP. Taken together, these results reveal that PDK3-dependent phosphorylation of PDHE1α at S293 affects oocyte maturation through PDH inhibition and changes in metabolism, whereas PDK1/PDK2-mediated PDHE1α phosphorylation at S232 has effects on oocyte meiosis that may be independent of PDH’s role in energy production. Read the paper here .

 

 

Fly centrioles – different after all

JCS172627F3In contrast to vertebrate centriole pairs, where the mother and daughter centriole can easily be distinguished from each other by morphology, Drosophila centrioles lack structural differences and can only be recognised by identifying specific protein markers. Marco Gottardo, Giuliano Callaini and Maria Giovanna Riparbelli used electron microscopy to examine mother and daughter centrioles in a range of fly tissues. They found that mature centrioles of somatic cells comprised doublets with a distinct cartwheel structure, whereas differentiating male germ cells had centrioles that comprised triplets. However, no structural differences between the mother and daughter centrioles could be found in any of the tissues examined. By contrast, male germline stem cells (GSCs) contained centrioles that comprised doublets, triplets or a mix thereof. Upon careful examination of the GSC niche, the authors observed that the mother centriole comprised triplets and that the daughter centriole was made up of doublets that matured into triplets. In addition, the authors showed that the mother centriole extended projections to the apical plasma membrane, which could function as an anchor to keep the mother centriole stationary during centrosome separation. This study is the first demonstration of a structural asymmetry between mother and daughter centrioles in Drosophila, which might reflect an unequal distribution of centrosomal proteins, thereby providing important insights into centrosome biology in flies.  Read the paper here .

 

 

New roles for ROPs in plant growth

JCS172445F2Rho of plant (ROP) proteins belong to the sole family of Rho-like GTPases in plants and have been suggested to regulate the polarised growth of tip-growing cells by modulating interactions between the actin and microtubule cytoskeletons. However, most studies performed to date have relied on the overexpression of proteins, including constitutively active or dominant-negative isoforms, and therefore Magdalena Bezanilla and colleagues took advantage of the ease of reverse genetics and the low number of highly similar ROP proteins (ROP1–4) in the model moss Physcomitrella patens to analyse the role of ROPs using a loss-of-function approach. Knockdown of all four ROP genes by RNAi resulted in dwarf plants comprising small spherical cells that had a significantly smaller area, compared with control plants. The authors also observed that, surprisingly, ROP-knockdown plants had strongly reduced cell adhesion and an altered cell wall structure, suggesting that ROPs might have previously unappreciated roles. Importantly, the authors found that actin filaments were more dynamic and that actin arrays were more disordered in ROP-knockdown cells, but that there was no ROP-specific effect on the dynamics of the microtubule cytoskeleton. In summary, this extensive study provides important new insights into the functions of ROP proteins in cell adhesion, cell wall assembly and polarised cell growth – roles they possibly exert by suppressing actin dynamics.  Read the paper here .

 

 

JEB

 

 

 

 

Consequences of calcium decline on the embryogenesis and life history of Daphnia magna

Daphnia squareAmbient calcium is declining in thousands of soft-water lake habitats. Daphnia females provision their offspring with calcium and through that incur a potential allocation trade-off. Read the paper here.

 

 

Diverse dose–response effects of yolk androgens on embryo development and nestling growth in a wild passerine

/Passarine-squareYolk androgens in wild passerines show complex dose–response effects during early development, including both linear and non-linear responses for different traits. Read the paper here.

 

 

 

 

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PhD studentship/graduate teaching assistant position (x2)

Posted by , on 28 July 2015

Closing Date: 15 March 2021

School of Biological Sciences, Bangor University

Details on https://jobs.bangor.ac.uk/

 

The School of Biological Sciences seeks to recruit a Part-time Graduate Teaching Assistant/PhD Trainee. The successful candidate will assist with teaching across the range of disciplines in the School, but particularly in areas of Zoology, such as animal behaviour, conservation biology, evolutionary biology, systematics, comparative physiology and animal ecology. Candidates should expect to provide assistance with student research projects, practical classes, lectures, field trips, setting & marking assignments and in providing advice & pastoral care to students. Successful candidates will have the opportunity to register for a Postgraduate Certificate in Teaching in Higher Education (PGCertHE).

Successful applicants will also have the opportunity to undertake a PhD or MRes project under the supervision of one of the current academic staff of the School, and will be required to obtain agreement of a principal supervisor over the topic and logistical arrangements for a project. School and individual staff research interests can be seen on our website. Tuition fees for both research degree and teaching qualification will be waived during the period of employment.

Applicants should have a good first degree in a biological-related subject and ideally some previous experience of teaching or demonstrating. Good interpersonal skills and an interest in teaching and student welfare are essential.

Overall, it is expected that approximately 56% of the postholder’s time will be made available for PhD-study, whilst 44% of the time will be for teaching and associated duties. However, the majority of the teaching and related activities will be concentrated into two semesters between late September and Early June.

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Teaching & Scholarship Lectureship in Biology/Zoology – Bangor University

Posted by , on 28 July 2015

Closing Date: 15 March 2021

Developmental Biologists welcome!

 

Teaching & Scholarship Lectureship in Biology/Zoology

 

Details on https://jobs.bangor.ac.uk/

 

Job Number: BU00940
School/Department: School of Biological Sciences
Grade: 7
Salary Information: £31,342 – £37,394 p.a on Grade 7
Contract Duration: Permanent

Closing Date: 19-08-2015

 

The School of Biological Sciences wishes to appoint a Lecturer (Teaching and Scholarship), to assist in the development of our dynamic and growing school. Applications are particularly sought from outstanding individuals with teaching and scholarship strengths in the Biological sciences. In the last 4 years our undergraduate intake has increased we now recruit over 200 undergraduates onto our biology and zoology degrees per year and we have introduced new programmes at undergraduate and Masters level. To support this expansion, we have recently appointed nine academic staff, and we are currently seeking 3 more lecturers for mainly research-led posts. We are inviting applications for a new Teaching and Scholarship post to help enhance and develop the curriculum in our existing degree programmes, which are focussed around Zoology and Biology.

Bangor University is committed to excellence in teaching & scholarship and offers attractive career prospects for staff with such expertise.

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Lecturer in Biology/Zoology (3 posts) – Bangor University

Posted by , on 28 July 2015

Closing Date: 15 March 2021

Developmental Biologists welcome!

 

Details on https://jobs.bangor.ac.uk/

 

Lecturer in Biology/Zoology (3 posts)

 

Job Number: BU00844
School/Department: School of Biological Sciences
Grade: 7 or 8
Salary Information: £31,342-£37,394 (Grade 7); £38,511-£45,954 (Grade 8) p.a. depending upon experience

Contract Duration: Permanent

Closing Date: 10-08-2015

 

The School of Biological Sciences invites applications for three permanent Lectureships in the broad area of Biology encompassing the full spectrum of genes, organisms and ecosystems. As part of the College of Natural Sciences, we are a dynamic and growing School with a strong research record and successful recruitment onto our undergraduate and postgraduate degrees. Currently we are looking to expand our research base, and our teaching and outreach capabilities. Bangor University is committed to excellence in research, teaching & scholarship and offers attractive career prospects for staff with such expertise.

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Postdoctoral Fellowship in a state-of-the-art interdisciplinary institute in Toronto

Posted by , on 27 July 2015

Closing Date: 15 March 2021

What do you expect from a postdoc experience?

If you’d like to tackle big questions in biology in one of the top inter-disciplinary research institutes in the world, you should apply for the Charles H. Best Postdoctoral Fellowship at the Donnelly Centre in Toronto.

At the state-of-the-art Donnelly Centre, our researchers always seek new ways to study gene regulation, signal transduction, development, systems biology, proteomics, computational biology and functional genomics.

Our ideal candidate is a highly qualified graduate (2 years or less postgraduate) in the field of molecular, genetic and genomic research. Send your application to one or two primary faculty members in the Donnelly Center (Andrews, Bader, Blencowe, Boone, Caudy, Emili, Fraser, Greenblatt, Hughes, Kim, Krause, Moffat, Morris, Roth, Ryu, Sidhu, Taipale, Zhang), whose interests match your own (www.thedonnellycentre.utoronto.ca). Once you’ve agreed sponsorship with a faculty member, you must then send them a curriculum vitae, one page statement of research interests, transcripts, and three letters of reference. The deadline for applications is September 25, 2015. We will support the successful applicant for up to two years with a generous stipend. For additional information please visit www.charlesbestfoundation.ca .

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Embracing risk

Posted by , on 27 July 2015

This editorial by Ross Cagan was first published in Disease Models & Mechanisms.

 

I entered the science field because I imagined that scientists were society’s “professional risk takers”, that they like surfing out on the edge. I understood that a lot of science – perhaps even most science – has to be a solid exploration of partly understood phenomena. But any science that confronts a difficult problem has to start with risk. Most people are at least a bit suspicious of risk, and scientists such as myself are no exception. Recently, risk-taking has been under attack financially, but this Editorial is not about that. I am writing about the long view and the messages we send to our trainees. I am Senior Associate Dean of the graduate school at Mount Sinai and have had the privilege to discuss these issues with the next generation of scientists, for whom I care very deeply. Are we preparing you to embrace risk?

 

As a long-standing academic scientist, I like my tenure and my funding to arrive with minimum risk. Although this is a reasonable response to wanting a good life, it is not always the optimal approach for solving 21st-century biomedical problems. It discourages risk-taking and encourages playing to the grant agencies. Worst of all, my generation’s fear of risk bleeds down to you. We teach you how to design projects that are ‘bullet-proof’. You will build the Biomedicine Age, and you will need to take risks to do it.

A friend and serial entrepreneur once commented that “scientists can be quick to ‘go negative’…unusual ideas are met with ‘that won’t work’”. I would not go that far, but he does have a point. Most risky ideas don’t pan out and, if I just dismiss them, my batting average will be pretty high. But hard problems will never get solved, and some of the magic of science is lost. Try a lab meeting some time with a simple rule: no negative comments, only “yes, and…”. Perhaps the student’s idea is not exactly right but the really great idea is lurking nearby. Kill the first, and the great idea is also lost. This all feeds to a culture of innovation and risk.

 

Risk in the Biomedicine Age

Biomedical science today is in a similar position as the computer industry of the early 1980s. Then, computer research was dominated by government funding and made up mainly by academics, mostly physicists and mathematicians. The government decided that it was not going to increase funding and the computer industry was faced with a challenge. The next generation was all in: they believed they could make a difference, and they did. They opened their garages and built the Information Age. If you tell someone in Silicon Valley that a great project is risky, that’s considered a bonus.

We are now entering the Biomedicine Age. Our great challenge is to understand how our body works and bring that understanding to erasing disease. Cancer, heart disease, infection, neurodegenerative diseases and – perhaps our most profound health challenge – mental illness all represent hard problems that will transform who we are when they are solved. The key words here are ‘risk’ and ‘diversity’ (more on diversity in a future Editorial). Biomedical challenges will require biology PhD’s entering basic research as explorers, industrial research to create therapeutics, Wall Street to build its financial underpinnings, and professional communicators to explain it all to society. The brains-in-the-garage are…you.

This will require loving risk. Start a company. It will probably fail (mine did), but then start another (working on that). Worried that funding for startups is tight, that you will confront the ‘valley of death’? There is a much better financial structure now in biomedicine than there was for computers 30 years ago. We need your creativity. Apps, small devices, computational algorithms, blogs, new materials, innovative teaching etc. are all part of the Biomedicine Age. Create a new way of thinking about old problems and find a way to make your solution happen. Then find someone who will mentor you, encourage you that your idea is actually great. Succeeding will be sweet.

 

 

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Mole- So now you have your own lab! Part IV – The fit

Posted by , on 27 July 2015

This cartoon was first published in the Journal of Cell Science. Read other articles and cartoons of Mole & Friends here.

Mole part 4 Fig 1

Mole part 4 Fig 2

 

 

Part I- ‘The imposter’

Part II- ‘The teaching monster’

Part III- ‘The Pact’

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European Advanced School for Mouse Phenogenomics – pushing the boundaries of mouse genetics

Posted by , on 24 July 2015

The laboratory mouse has been a popular model in mammalian biology for obvious reasons and it has contributed to a number of landmark discoveries in biomedical research. Despite this, few courses and summer schools – which train future leaders in this field – focus on mouse genetics. Phenomin, a large-scale French national infrastructure for biology and health has organised the first European Advanced School for Mouse Phenogenomics. I was fortunate to be selected to participate in this school, which was held last month at a French château set atop a picturesque Alsacian landscape, some 30 miles from Strasbourg.

Chateau

The theme of the school was “good practices regarding the use of mouse models for biomedical research”. The four-day programme encompassed topics on mouse genetics, mutagenesis, functional tests using mouse models and international initiatives, databases and resources. Around 30 experts from these areas engaged the participants with their various talks and discussions.

Participants were mostly PhD students and some postdocs. The school began with a talk by Dr Yann Hérault of the Mouse Clinical Institute (ICS), Strasbourg. He introduced the structure and goals of Phenomin. Following this, Professor Emeritus Jean-Louis Guénet of Institut Pasteur gave an excellent lecture on the different populations of laboratory animals. He took us through the classical aspects of mouse genetics that reminded us of our university genetics lessons and refreshed our knowledge of this topic. This talk served as a prelude to the other sessions.

Many talks focused on recent advances in mutagenesis methods, especially the CRISPR/Cas9 technology. Although this method has been developed only recently, many labs around the world have picked it up quickly. One of the key advantages of this method is that it allows researchers to produce mouse mutants in a very short space of time, with fewer or no off-target effects when compared to other nuclease mediated mutagenesis methods. During the school, we discussed the limitations of this method, especially the ability to produce conditional/inducible mutants. As we speak, a paper published last week by the Zhang lab (MIT) shows inducible human stem cell lines (with the Flp/FRT and Cre/LoxP system) engineered by CRISPR/Cas9 method by dual guide RNA targeting. This method is becoming user-friendly, favourable and a key addition to the existing mouse genetics tool box. During my short early academic career, I have witnessed at least four different mutagenesis methods; some of them disappeared and some have become famous. Without doubt, mouse genetics will see more new technologies appearing in the future that will hugely influence our current understanding of many aspects of mouse biology. It is very exciting to be a researcher in this era of cutting-edge molecular technologies.

There was also a focus on the large-scale resources and data that are available for the mouse genetics community, especially on those generated for knockout mice via international efforts. My PhD work itself was carried out within a close collaboration with such a consortium. Although these resources have been available for many years, I often come across young researchers who weren’t aware of these valuable sources of mouse mutants. International efforts to build such resources allow researchers to save time on producing mutants and spend more time on the research question itself. The IKMC (International Knockout Consortium) is aimed at generating and distributing mouse mutants for each and every gene in the mouse genome. The IKMC has now spun out as IMPC (International Mouse Phenotyping Consortium), which phenotypes the mutants that are produced through IKMC and makes open access of the data. Gone are the days when a PhD student or a postdoc spent their entire time on generating a knockout mouse. Now they can just ‘stop-and-shop’ a desired mutant and start the experiment without spending much time on the generating the mutant itself. The open access data on primary phenotype from IMPC could be exploited to build hypotheses and test them. Also, there exists a resource database, CREATE (Coordination of resources for conditional expression of mutated mouse alleles) for Cre driver lines for those who are interested in conditionally ablating the genes in their desired cell types – the cherry on top of the cake!

The other topic I found very interesting was immunophenomics. Professors Bernard Malissen and Marie Malissen gave insights into pilot scale immune phenotyping studies to elucidate immune complexity through functional genomics. Professor Bernard Malissen runs an ambitious project at CIPHE, the centre for Immunophenomics at Marseille-Luminy where they aim to phenotype all the cellular components of the immune system under steady state and when challenged with pathogens. The outcome of their research holds great promise in the field of immunology and infection biology.

Ethics and animal welfare were discussed intensely during the school. The participants were reminded how to consider ethics and welfare of the animal throughout their research. Dr Jan-Bas Prins of LUMC, Netherlands gave an eye-opening lecture on ethics and humane animal research. He stressed how researchers should keep in mind the principles of 3-Rs (replacement, reduction, and refinement) throughout their animal experiments.

The highlight of the school’s programme was the workgroup sessions, where the participant groups were given topics (outside their own research) and relevant articles to discuss. They were also assigned to a supervisor/expert with whom they could discuss the topic and finally present it for a general discussion. This allowed the participants to critically go through the assigned topic and brainstorm the questions addressed and mouse techniques used in the studies. In my case at least, I gained ‘enlightenment’ on T-cell receptors – the topic which was assigned to my group and something which was totally new to me! The school also saw two poster sessions with PhD students and postdocs showcasing their excellent works involving various mouse mutants and their relevance to various diseases.

Kudos to the organisers of the school! They did a fantastic job of putting together a programme which perfectly fitted the needs of mouse genetics researchers and those who have begun their PhD studies. I hope the organisers will be able to secure funding to conduct the school in coming years. Although the sun decided not to shine during most of the days of the school, we were intensely soaked with science throughout the week!

Phenomin group pic

This post is also available from our lab blog – wattlab blog. Please visit for more interesting topics and discussions.

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