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  • PhD

Edinburgh, Scotland
20. November 2019
 

20 November 2019

PhD Position in Edinburgh

4-year PhD-Project in UK as part of a competition                                              


Deanery of Biomedical Sciences                                                  

Regulation of breathing is critical to our capacity to accommodate deficits in oxygen availability and demand during, for example, sleep and ascent to altitude. It is generally accepted that a fall in arterial oxygen increases afferent discharge from the carotid bodies to the brainstem and thus delivers increased ventilatory drive, which restores oxygen supply and protects against hypoventilation and apnoea. However, the precise molecular mechanisms involved remain unclear. We recently identified as critical to this process the AMP-activated protein kinase (AMPK), which is key to the cell-autonomous regulation of metabolic homoeostasis. This observation is significant for many reasons, not least because recent studies suggest that the gene encoding the AMPK-α1 catalytic subunit has been subjected to natural selection in high-altitude populations. It would appear, therefore, that evolutionary pressures have led to AMPK being utilized to regulate oxygen delivery and thus energy supply to the body in the short, medium and longer term. Contrary to current consensus, however, our findings suggest that AMPK regulates ventilation at the level of the caudal brainstem, even when afferent input responses from the carotid body are normal. We therefore hypothesized that AMPK integrates local hypoxic stress at defined loci within the brainstem respiratory network with an index of peripheral hypoxic status, namely afferent chemosensory inputs. More significantly still, AMPK deficiency led to marked hypoventilation, rather than hyperventilation, and frequent prolonged apneas during hypoxia. Therefore, further investigations will not only extend our understanding of the hypoxia-responsive neural networks that regulate breathing and oxygen supply, but reveal as yet undiscovered, brainstem nuclei that are critical to this process, where AMPK deficiency and consequent dysfunction may precipitate sleep-disordered breathing and hypertension associated with either ascent to altitude or metabolic syndrome-related disorders. The present project will utilize confocal imaging and electrophysiology, to explore further the neuronal mechanisms and brainstem circuits through which AMPK deficiency precipitates respiratory dysfunction.

References
Evans AM, Mahmoud AD, Moral-Sanz J, Hartmann S. (2016). The emerging role of AMPK in the regulation of breathing and oxygen supply. Biochem J, 473, 2561–2572.
Mahmoud, A.D., Lewis, S., Juricic, L., Udoh, U.A., Hartmann, S., Jansen, M.A., Ogunbayo, O.A., Puggioni, P., Holmes, A.P., Kumar, P., Navarro-Dorado, J., Foretz, M., Viollet, B., Dutia, M.B., Marshall, I., Evans, A.M. (2016). AMP-activated Protein Kinase Deficiency Blocks the Hypoxic Ventilatory Response and Thus Precipitates Hypoventilation and Apnea. AJRCCM, 193, 1032-1043.
Ikematsu, N., Dallas, M. L., Ross, F.A., Lewis, R.W., Rafferty, J.N., David, J.A., Suman, R., Peers, C., Hardie, D.G., Evans, A.M. (2011). Phosphorylation of the voltage-gated potassium channel Kv2.1 by AMP-activated protein kinase regulates membrane excitability. PNAS, 108, 18132-18137.
Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership.
"We strongly encourage applicants from a wide variety of backgrounds because we believe diversity is an essential driver of good science. We are committed to providing an inclusive and supportive training environment" (EASTBIO BBSRC).

This opportunity is only open to UK nationals (or EU students who have been resident in the UK for 3+ years immediately prior to the programme start date) due to restrictions imposed by the funding body. EU applicants without a history of residency in the UK are eligible to apply, but would only be awarded the fees (not the stipend). All candidates should have or expect to have a minimum of an upper 2nd class degree in an appropriate discipline.
 

Download application and reference forms via:  http://www.eastscotbiodtp.ac.uk/how-apply-0

 

Completed application form along with your supporting documents should be sent to our PGR student team at sbms-postgraduate@ed.ac.uk by 5th January 2020.

References:

Please send the reference request form to two referees. Completed references for this project should also be returned to sbms-postgraduate@ed.ac.uk by the closing date: 5th January 2020. It is your responsibility to ensure that references are provided by the specified deadline.

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  • PhD

University of Technology, Graz
13. November 2019
 

13 November 2019

Interdisciplinary PhD positions at TU Graz

PhD positions at the Institute of Biochemistry

The Institute of Biochemistry at the Graz University of Technology is looking for three highly motivated PhD candidates with a genuine interest in understanding molecular mechanisms of biochemical processes.

One PhD position is available as a university assistant position involving teaching and research activities in the group of Peter Macheroux. The research project will have a focus on developing highly specific inhibitors of chorismate synthase, the last enzyme of the common shikimate pathway toward the biosynthesis of aromatic compounds, such as phenylalanine, tyrosine and tryptophan. Toward this goal, we will attempt to determine the structure of the enzyme in complex with lead structures to gain insight into the interaction with amino acid residues in the active site in order to improve the affinity of potential inhibitors. This project will be carried out in collaboration with Andreas Winkler (structural biology) and Rolf Breinbauer at the Institute of Organic Chemistry (organic synthesis of inhibitors). The ultimate aim of the project is the development of therapeutically useful drugs targetting chorismate synthase (1,2).

A FWF-funded PhD position is available in the research group of Gustav Oberdorfer. The groups primary research interests are designing and engineering of biomolecular structures and their function - a multi-facetted effort that combines computational biology, structural biology, biochemistry and biophysics (3, 4). The PhD project will be part of a small local research consortium combining three different disciplines of modern life sciences. In an effort to integrate protein design with optogenetics (group of Andreas Winkler) and tumor immunology (group of Julia Kargl) the successful candidate will employ light responsive dimerization modules to design, engineer and test modern anti-cancer drugs. More specifically, the goal will be to design light-regulated heterodimerization modules that can be linked to different single chain antibodies that would enable T-cell mediated tumor killing with high temporal and spatial precision.

The third PhD position is available in the research group of Andreas Winkler. Objectives in this group revolve around an integrative structural biology approach addressing mechanisms of signal transduction in natural light-regulated enzymes. Understanding principles of sensor-effector modularity and how nature adapts them for diverse requirements, is key to improve success rates of artificial designs for the generation of novel optogenetic tools. In this project, the focus will be set on combining biochemistry and various tools of structural biology (crystallography and hydrogen-deuterium exchange coupled to mass spectrometry) including local collaborations in NMR (Tobias Madl) and cryo-EM (Tea Pavkov-Keller) to address the functional role of structural asymmetry in bacterial red-light photoreceptors (5, 6). Eventually, appreciation of molecular details of structural asymmetry will be helpful for a more rational approach to the design of artificial light regulated functionalities.

All projects provide in-depth, interdisciplinary training in biomedical and biotechnological research in an international and stimulating environment. The thesis projects follow an integrative approach and combine structural biology, enzymology, computational protein design and biophysics to decipher biosynthetic pathways, molecular mechanisms of catalysis and development of biomedical tools, employing a wide range of cutting-edge techniques.

Applicants must hold (or be close to obtaining) an undergraduate degree equivalent to a Master in any discipline of natural, life sciences or computer sciences. The ability to work in a team, initiative, flexibility as well as good organizational and learning skills are required. The selection procedure, all training activities and communications will be in English. Thus, excellent written and spoken English skills are required. Successful applicants will get employed for up to four years (initial contract for one year with the option of prolongation upon successful performance) with a contract that includes social benefits.

Interested applicants should send a motivation letter, CV, one-page summary of their research experience and contact details of two potential referees until the 9th of December 2019 to 

office.ibc@tugraz.at

Prospective starting dates throughout 2020 can be discussed upon acceptance.

References: 1 – Rodrigues-Vendramini F A V, Marschalk C, Toplak M, Macheroux P, Bonfim-Mendonca P, Svidzinski T I E, Seixas F A V, Kioshima E S. (2019) Promising new antifungal treatment targeting chorismate synthase from Paracoccidioides brasiliensis. Antimicrobial Agents & Chemotherapy 63:1-14. 2 – Bueno P S A, Rodrigues-Vendramini F A V, Toplak M, Macheroux P, Kioshima E S, Seixas F A V. (2019) New inhibitors of chorismate synthase present antifungal activity against Paracoccidioides brasiliensis. Future Microbiology 14:969-980. 3 - Oberdorfer G, Huang P-S, Xu C, Pei X Y, Nannenga B L, Rogers J M, DiMaio F, Gonen T, Luisi B, Baker D. (2014) High thermodynamic stability of parametrically designed helical bundles. Science 346 (6208): 481-485. 4 - Boyken S E, Chen Z, Groves B, Langan R A, Oberdorfer G, Ford A, Gilmore J M, Xu C, DiMaio F, Pereira J H, Sankaran B, Seelig G, Zwart P H, Baker D. (2016) De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity. Science 352 (6286): 680-687. 5 - Gourinchas G, Etzl S, Göbl C, Vide U, Madl T, Winkler A. (2017) Long-range allosteric signaling in red light–regulated diguanylyl cyclases. Sci Adv 3 (3), e1602498. 6 - Gourinchas G, Heintz U, Winkler A. (2018) Asymmetric activation mechanism of a homodimeric red light regulated photoreceptor. eLife 7, e34815.

 

 

 

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  • PhD

King's College, London
11. November 2019
 

11 November 2019

Research Associate at King's College London

The group of Prof. Sergi Garcia-Manyes in the Department of Physics at King’s College London is seeking a highly motivated individual with a PhD in Physics, Biophysics, Physical Chemistry or related disciplines with an interest in working on mechanobiology from the single molecule perspective.

The candidate will work on the development and application of two force spectroscopy single molecule techniques (atomic force microscopy and magnetic tweezers) to unravel the dynamics under force of several proteins that are physiologically exposed to mechanical forces.

See here for full details: https://www.jobs.ac.uk/job/BWJ360/research-associate

Closing Date: 1st December 2019

Contact: sergi.garcia-manyes@kcl.ac.uk

 

 

 

 

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  • PhD

Bristol and Bath, England

06 November 2019

PhD Opportunity in Enzyme Simulation and Coding

A PhD project in competition for funding from the  South West Biosciences Doctoral Training Partnership (SWBio DTP) is available for high-quality applicants (1 or high 2:1 first degree and/or MSc experience).
The student will be based at the University of Bath (supervised by Alison Walker & Stephen Wells) and it involves significant code development. The project will also involve (enhanced sampling) molecular dynamics simulations through collaboration with my group in Bristol, and students will benefit from the excellent environment for computational (bio)chemistry there.
Extremophilic enzymes: investigating structural adaptation through rapid physics-based geometric simulation
Enzyme dynamics and flexibility are key to its function: many enzymes undergo substantial, reversible conformational changes during operation. For extremophilic life-forms and biocatalysts for industrial biotechnology, enzyme flexibility is crucial for activity and durability. The project will examine structural adaptations that can change the rigidity which is finely balanced to allow sufficient stability. Geometric simulations of intrinsic flexible motion and enhanced sampling molecular dynamics will be used to explore the motion of different enzyme structures. Motions ranging from small local rearrangements to large domain motions such as hinge motion, will be explored in a highly efficient manner. The student will acquire an in-depth knowledge and training in enzyme structure and function, interpretation of experimental measurements, and programming skills and techniques using C++ and Python.
See further details and how to apply.
 
For further information please contact:
Dr. Marc W. van der Kamp
BBSRC David Phillips Research Fellow
School of Biochemistry
Faculty of Biomedical Sciences
& Centre for Computational Chemistry, School of Chemistry
University of Bristol
Biomedical Sciences building
University Walk
Bristol BS8 1TD
Tel: +44 117 3312147 (office)
Marc.vanderKamp@bristol.ac.uk

Website:https://vanderkampgroup.wordpress.com/
Twitter: @marcvanderkamp

A top 10 UK university (QS Rankings 2019)
A top 2 UK university with leading employers (High Fliers 2018)
A top 5 UK university for research (THE analysis of REF 2014)
A top 6 European university for teaching (THE 2018)
 

 

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  • PostDoc

Strasbourg University
6. November 2019

 

06 November 2019

Postdoctoral Position in Strasbourg

Postdoctoral Position: Biophysics of Membrane Polypeptides or Fibers
 
The laboratory Membrane Biophysics and NMR at the University of Strasbourg has an opening for a postdoctoral position with experience in using biophysical techniques for the analysis of peptides and proteins associated with membranes or with fibers. The aim of the project is to reveal the structural determinants that define lipid recognition in membranes and to characterize changes in structure, dynamics, oligomerization and topology of the protein as well as the lipids during recognition. Another ongoing project is the structural investigation of peptide fibers with strong nucleic acid and lentiviral transfection potential.

Candidates should have good experience in biophysical methods used during the investigation of membranes.
Techniques of the laboratory include biomolecular solid-state NMR, solution NMR approaches, optical methods, light scattering, ITC, peptide synthesis and/or the biochemical production of proteins. The candidate should have good knowledge of some of these techniques, particularly searched after a experts in MAS solid-state NMR of polypeptides. S/he should have an interest in working in a highly interdisciplinary, international and collaborative environment. The project and position are funded by a three-year grant from the French National Agency for Research (ANR). The University of Strasbourg chemistry, life sciences and structural biology departments have excellent scientific records, with a multitude of collaborations world-wide.

Strasbourg is a very nice city on the French side of the Rhine river, at the border to Germany, with easy access to nearby mountains (Vosges, Black Forrest, Alps). Being in the heart of Europe it takes only short train rides to multiple destinations of scientific and/or touristic interest.
 
Candidates should send their CV, publication list and contact info for three references to:
 
Prof. Burkhard Bechinger,
bechinger@unistra.fr
Web Sites:
http://www-chimie.u-strasbg.fr/~rmnmc/
https://icfrc.fr/en/

 

 

 

 

 

 

 

 

 

 

 

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  • PhD

Bath and Bristol, England
6. November 2019
 

05 November 2019

PhD Studentships in Bristol

There are two PhD opportunities the competitively awarded SWBio DTP studentship programme (see swbio.ac.uk).
Please notify any high-quality students that are interested in a PhD using biomolecular simulation. The University of Bristol has a strong environment for computational (bio)chemistry and ample computational resources.
 
Details:
1. SWBio DTP funded CASE PhD studentship, in collaboration with Immunocore
Developing better biopharmaceuticals using biomolecular simulation and design.
Using affinity-matured designed CD8+ T-cell receptors, bi-specific biologics can designed to target a range of diseases, including cancer. A better understanding of the molecular determinants that govern CD8+ T-cell mediated immunity is key to improve the activity and specificity novel therapeutic interventions that can enhance (immunotherapy, vaccines, etc). With (enhanced sampling) molecular dynamics simulations and data from Immunocore, detailed insight will be obtained and protocols developed to predict variants with improved affinity and selectivity. See the full project details.
 
2. SWBio DTP funded project
Simulation-led redesign to generate enantioselective biocatalysts
This project will focus on understanding and manipulating type II polyketide synthase systems, such as the multi-enzyme system producing the antibiotic actinorhodin. Molecular dynamics and QM/MM reaction simulations will be used to obtain insights and suggest mutations that change the stereoselectivity of key enzymes. Mutations will then be tested experimentally, in collaboration with Prof. Matt Crump. We will also pursue the use of structural biology (protein NMR, X-ray crystallography) to support and confirm modelling studies. See the full project details.


Deadline for application for both: Dec 2nd 2019.


See the details for how to apply and the application process on the SWBio DTP website.
 
Please do contact :
Dr. Marc W. van der Kamp
BBSRC David Phillips Research Fellow
School of Biochemistry
Faculty of Biomedical Sciences
& Centre for Computational Chemistry, School of Chemistry
University of Bristol
Biomedical Sciences building
University Walk
Bristol BS8 1TD
Tel: +44 117 3312147 (office)
Marc.vanderKamp@bristol.ac.uk

Website: https://vanderkampgroup.wordpress.com/

Twitter: @marcvanderkamp

 

A top 10 UK university (QS Rankings 2019)

A top 2 UK university with leading employers (High Fliers 2018)
A top 5 UK university for research (THE analysis of REF 2014)
A top 6 European university for teaching (THE 2018)
 

 

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  • Professorship

Utrecht University, Netherlands
03 September 2019

03 September 2019

Open Positions in Chemistry

at a world class center of research and education in Utrecht, Netherlands           

 

The Department of Chemistry (https://www.uu.nl/en/organisation/department-of-chemistry) at Utrecht University in the Netherlands is renowned as a world class center of excellence and innovation in both research
and education, fully resourced and equipped with state-of-the-art technological platforms.
Our approach is characterized by a connected, open and can-do spirit that stimulates personal initiative and curiosity. You are encouraged to take ownership and create value while sharing your knowledge both internally and across the wider (global) research community. We strive every day to enable this mission because we know it is the only way to make the breakthroughs that will help to solve the challenges facing the world.
Meaningful opportunities in life sciences and sustainability. The Department is growing and actively recruiting new staff members for our two core areas of fundamental research – molecular level life science research and nanomaterials research for sustainability. This research takes place within two advanced and future-focused facilities:


• The Bijvoet Center https://www.uu.nl/en/research/bijvoet-center-for-biomolecular-research advances our understanding of life at the most detailed molecular level by using cuttingedge structural and analytical methods in combination with state-of-the-art molecular biology, biochemistry as well as biophysical methods. This has the potential to help us understand the cause of diseases in a fundamental way.
• The Debye Institute https://www.uu.nl/en/research/debye-institute-for-nanomaterials-science for Nanomaterials Science tackles sustainability through research into catalysis, nanostructures and colloids, and nanophotonics.
This has the potential to yield valuable sustainability benefits for opto-electronic applications such as LEDs and miniaturized lasers, and advanced catalytic applications such as biomass valorization and small molecule activation.

Interested in joining us?
We’d love to hear from you if you have a broad research background in either of these areas and would like to be part of this stimulating and diverse environment. We are particularly interested in hearing from female scientists worldwide who contribute their skills and curiosity to our inclusive approach to life and work.

Utrecht University: Enjoy a great work-life balance in
a wonderful city

Utrecht is an attractive city located in the heart of the Netherlands, one of the world’s most open and connected countries. Utrecht University reflects this philosophy by offering a flexible work/life balance that prioritizes your well-being within an understanding and supportive, international environment.

Open positions in Chemistry:
Associate/ Full professor: Mapping the in-vivo molecular landscape
Developing a research program that studies the impact of the overall organization and function of molecules on spatio-temporal processes in cells and tissue.

Assistant/ Associate professor: Dynamic organization in native membranes
Developing a research program that studies and manipulates interactions between membrane components and proteins under physiological conditions.

Assistant/ Associate professor: Conformational switches in regulation
Developing genetic, chemical, and computational tools to probe and manipulate protein dynamics relevant for function on a cellular level.

Associate/ Full professor: Quantum chemical modelling
Contribute to a sustainability research program that models hybrid organic/inorganic interfaces on the nanoscale

Assistant/ Associate professor: Quantum chemical simulation
Contribute to a sustainability research program that simulates (charged) catalytic interfaces in batteries.

Assistant/Associate professor: Electron microscopy related to materials and catalysis
Contribute to a catalysis and materials science-oriented research program through an expertise in (in situ) electron microscopy.

 

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  • PostDoc

University of Würzburg
27 August 2019

 

27 August 2019

Post-doctoral Researcher (m/f/d)

in crystallographic methods and software development at the University of Würzburg   

Scope and your role

You will undertake research in the group of Dr. Andrea Thorn to improve the quality of measurements and processing of XFEL, neutron and conventional X-ray diffraction data, to establish major error sources and to define new best practices for macromolecular diffraction experiments. We aim to create new automatic and visual diagnostics by expanding the AUSPEX software (www.auspex.de) using statistical analysis, machine learning and visual data representation. In order to do so, collaboration was set up with four major diffraction facilities in Europe: the BESSY synchrotron in Berlin, the European Spallation Source (ESS) in Lund, the ESRF in Grenoble as well as the European XFEL in Hamburg. You will visit these facilities regularly to develop and implement new diagnostics in close collaboration and publish your results in peer-reviewed journals. Furthermore, you will be expected to contribute to teaching, training, public outreach and to present your work at in-house and international meetings.

What we offer
We offer a 30-month full- or part-time position at the Rudolf-Virchow Center (RVZ) of the University Würzburg, the birthplace of X-rays, with a competitive salary commensurate with your training and experience according to salary agreement TV-L. Your position is funded by the German Federal Ministry of Education and Research (BMBF) as part of the AUSPEX project (press release). This exciting project will allow you to define new quality standards in macromolecular structure determination and to establish a European network in the crystallographic community. Our group is well-connected and AUSPEX is part of the CCP4 suite for macromolecular crystallography. We maintain close ties with other method developers worldwide.


The  RVZ is an excellent place to develop yourself further and a range of training & development opportunities will be available to you, including:

  • Research, leadership and management courses
  • Advice, coaching and career support at the JMU Research Academy
  • Courses in teaching within a certified educational training program
  • Career Support at the JMU Academic Staff Development Office
  • Assistance for grant applications from the JMU Research Advancement Centre and the JMU Service Center for Research and Technology Transfer You will have access to both national and the public-service pension schemes (VBL), health care, and 30 days of holiday  entitlement (if working full-time) in addition to 13 annual public holidays in Bavaria. The University also offers access to employee shopping/travel discounts, and there might be cake on occasion. The JMU Welcome Center  supports international candidates with finding accommodation, general information regarding taxes, insurance, healthcare and other administrative matters. The University also offers support for candidates with children, including the University kindergarten, advice regarding school placement, holiday programs and flexible work hours.

Qualification profile
You should have a doctoral degree in a chemical, biological, physical, computational or other relevant subject or be due to complete your doctoral studies within 3 months of applying. You should be able to develop your own ideas, and have the necessary skills to successfully drive and complete a research project, both working independently and as part of a team. We are looking for someone with a good working knowledge of Linux, Python and C++, ideally including common crystallographic libraries such as gemmi, cctbx or clipper. You should be good at statistical data analysis, ideally including experience with the statistical package R. Web-based programming skills (e.g. JavaScript, html5, css), previous experience with machine learning and neural networks are also a bonus. You should have previous experience in crystallography or be willing to learn both its theoretical basis as well as how to conduct crystallographic experiments on the job.
You should be a good communicator, willing to convey complex problems to lay audiences, as well as to instruct and supervise students. An excellent command of English is a prerequisite; German language skills will also be required, but if you do not speak German, we will offer training. Due to the collaborative nature of this project, you should be willing to travel. Female scientists are particularly encouraged to apply! Disabled applicants will be preferentially considered in case of equivalent qualification.

Application
The position will start on 1st October 2019 or later. Applications should be sent by e-mail as one single pdf-document including: cover letter, curriculum vitae (including software projects you contributed to, teaching experience and academic track-record), diplomas/certificates and 3 addresses of referees by 8th September 2019 to

mailto:andrea.thorn@uni-wuerzburg.de

https://www.uni-wuerzburg.de/en/home/

https://www.uni-wuerzburg.de/en/welcomecentre/start-page/

https://www.uni-wuerzburg.de/en/rvz/home/

support for candidates

 

If you have any further questions, please do not hesitate to contact us!

Rudolf-Virchow-Zentrum für Experimentelle Biomedizin der
Universität Würzburg
Dr. Andrea Thorn
Josef-Schneider-Str. 2 / Haus D15
D-97080 Würzburg

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