The Department of Science and Environment, Roskilde University, invites applications for three positions as PhD fellows. The positions are limited to a period of 3 years (full-time studies) with expected starting dates 1 April 2022 or as soon as possible thereafter.
The PhD stipends are announced in open competition, by announcing six interdisciplinary PhD projects for which three successful candidates will be selected for different projects. The Department has a strategic focus on strengthening the interdisciplinary research collaboration between our main areas and the outlined projects are selected to support promising new interdisciplinary research topics at the Department.
Description of the PhD projects
The title of the prospective PhD projects are:
A. Glassy and physico-chemical properties of solutions of hyperactive antifreeze proteins: how do they influence aqueous solutions and what is their role in glass formation? Physics/Molecular Biology/Chemistry (Supervisors: Tina Hecksher/Hans Ramløv/Anders Malmendal)
Understanding the role of hyperactive antifreeze proteins (AFPs) in glass-formation will have an impact not only on our general knowledge about AFPs and glasses but can also be used in the context of cryo-preservation within medical fields and the food industry. The aim of the project is to investigate the dynamics of the protein interactions, the glass-forming ability, and the glassy properties of aqueous solutions of the AFPs and various low molecular weight solutes. The ideal candidate for the project has an MSc in physics, chemistry/physical chemistry or nanoscience, solid experimental experience, and a general curiosity towards the biological sciences.
B. Metal and plastic nanoparticle interaction with biological model systems studied using Atomic Force Microscopy and X-ray Scattering. Physics/Biology; (Supervisors: Dorthe Posselt/Amalie T. B. Jensen)
Pollution results in plastic- and metal nanoparticles (NPs) being ubiquitous in nature. Still little is known about uptake and toxicity in biological systems. The aim of the project is to obtain insight into the driving mechanisms behind NP uptake and toxicity by studying the interaction between different NPs and model cell systems. We seek a PhD candidate to conduct experiments with Atomic Force Microscopy, Small-Angle X-ray scattering, (single particle) Inductively Coupled Plasma Mass Spectrometry and Dynamic Light Scattering for this purpose. The ideal candidate has a background in Physics and/or Chemistry, or similar, and is motivated for performing interdisciplinary experimental work bridging physics and biology.
C. Understanding and regulating virulence and biofilm formation in bacterial pathogens: A chemical biology approach to reveal the molecular mechanisms of a novel intercellular signalling molecule.Chemistry/Molecular Biology; (Supervisors: William Goldring/Lotte Jelsbak).
Understanding and interfering with chemical signalling in bacterial pathogens is a novel and promising strategy for fighting infections. The aim of the project is to investigate the structure and molecular mechanisms of a novel bacterial signalling molecule with roles in virulence and biofilm formation, and how its activity is regulated. We seek a PhD student to synthesise a library of systematically designed signalling molecules, explore their biological effects on pathogen physiology, and conduct metabolite characterization and analysis. The ideal candidate will have successfully completed a Master’s degree or equivalent within chemistry or chemical biology prior to taking up the position. The ideal candidate has a strong foundation of experimental experience in both chemistry and biology, and research experience in these areas is an advantage.
D. How do planktonic marine invertebrates tackle salinity challenges? Chemistry/Molecular Biology/Environmental Science (Supervisors: Anders Malmendal/Hans Ramløv/Benni Winding Hansen)
Adaptation to varying salinity is essential for survival of marine copepods in certain environments and for optimization of copepods as live feed in the aquaculture industry. The project will apply an interdisciplinary approach to provide new genetic, biochemical, physiological and population-level understanding of this process. We seek a PhD student to study the response to abrupt as well as gradual changes in salinity in marine copepods at different timescales using physiological, molecular biological, proteomic, lipidomic and metabolomic measurements. The target organism(s) will be selected among species with known genomes, transcriptomes and where a certain knowledge of salinity tolerances has been obtained that are already isolated from relevant habitats and brought in culture. Both short-term responses in one generation of animals, and long-term population responses over several generations will be studied. The ideal candidate has experience/knowledge of chemistry and molecular physiology/environmental science.
E. Predicting the development of bacterial virulence by mathematical modelling. Mathematics/Medical Biology (Supervisors: Johnny T. Ottesen/ Fatima AlZahra’a Alatraktchi/Morten Andersen)
There are several biological theories predicting the development of bacterial virulence in a host. The ‘avirulence hypothesis’ postulates that as the death of the host means the end of the infection and consequently the end of further transmission, the bacteria will evolve toward symbiosis by reducing their virulence production when the infection is chronically established. Another theory is the ‘trade-off hypothesis’ which suggests that virulence is an unavoidable consequence of bacterial transmission, a mechanism that affects the host mortality rate. To date, it has not been possible to unravel the adaptive nature of virulence as it is necessary to capture the complex interactions of each infection. The project aims to develop and apply mechanism based mathematical modelling to predict bacterial virulence activity during infections and merge the fields of micro- and nano sensing of virulence molecules, microbiology and mathematical modelling to study the development of infections to design strategies for therapy or prevention that capitalize on the concepts of virulence evolution. The ideal candidate has experience/knowledge of computational modeling and has a natural science/engineering background in (pure or applied) mathematics, physics, chemistry, or biology. The candidate needs to be familiar with dynamical systems, analysis, linear algebra, statistics, and have experience with mathematical modelling preferable in biology or medicine or have the prerequisites to achieve such skills. An interest in interdisciplinary sciences is essential. Insight into parameter estimation, and programming (e.g., Python, Matlab, or R), cell culturing, metabolic activity, LC-MS and NMR is preferable, otherwise eagerness to learn about these themes is expected.
F. Antibiotic fingerprints: omics-profiling of antibiotic resistance and persister phenotypes in Pseudomonasaeruginosa (PA). Chemistry/Medical Biology/Molecular Biology (Supervisors: Biljana Mojsoska/Håvard Jenssen/Karen Angeliki Krogfelt/Anders Malmendal)
Antibiotic resistance and tolerance are phenotypes that bacteria use to survive destructive conditions. Most bacterial regulatory mechanisms behind these phenotypes are well studied, however, the current scientific challengeis to understand these mechanisms on a system level and apply this knowledge for the discovery of novel antibiotics.
The aim of the project is to understand how bacteria sense antibiotics and adapt to stress-induced environments. The focus is on using high-resolution “omics” approaches for investigating in-depth system-level responses in PA to novel drugs (e.g., peptoids), and known antibiotics while studying antibiotic resistance development and persister cells. The project is expected to develop a unique way of clustering multiple data for each antibiotic and novel drug candidate and making an antibiotic fingerprint model. The ideal candidate has a Master Degree or equivalent in Chemical Biology with emphasis on Microbiology and Biological Chemistry. Demonstrated knowledge of proteomic data analysis and laboratory skills in microbiology is an advantage.
The Doctoral School
The successful candidates will be enrolled in the Doctoral School of Science and Environment in accordance with the rules issued by the Ministry of Technology and Science and additional regulations issued by Roskilde University. The PhD students will be employed in accordance with the agreement between the Ministry of Finance and AC (the Danish confederation of Professional Associations. The Doctoral School of Science and Environment is an international graduate school that covers a broad range of research topics within the areas of science and environment.
Read more here https://ruc.dk/doctoral-school-science-and-environment
Department of Science and Environment is one of four departments at Roskilde University. The Department conducts basic and applied research within chemistry, physics, medical biology, molecular biology, environmental sciences and mathematics. Bachelor programs are offered within these areas, as are interdisciplinary Master programs. The Department’s laboratories are equipped with modern infra-structure and shared state-of-the art instrumentation. This includes recently acquired NMR, mass spectrometry (LC- and GC-MS, including high-resolution measurements and proteomics), and microscopy (AFM, confocal and fluorescence) instruments, microscope with cold stage, rate freezer and climate cabinets, GMO class 2 labs, flow cytometry, NGS, Q-PCR facilities together with calorimetry (ITC and DSC), chromatography (HPLC), and scattering (DLS, SAXS) instruments. For environmental science research is TOC, AAS
FTIR, ICP MS, GC MS, HPLC, CHNS elemental analyzer, Ion chromatograph, FIA and electronic particle counters i.e., Coulter counters available. As a PhD fellow, you will be associated with the research groups and get access to instrumentation of your main and co-supervisors. Read more here https://ruc.dk/en/department-science-and-environment
Responsibilities and tasks
The PhD position is an educational position and the main tasks are in accordance with chapter 3, Ministerial Order on the PhD Programme at the Universities and Certain Higher Artistic Educational Institutions (https://ufm.dk/en/legislation/prevailing-laws-and-regulations/education/files/engelsk-ph-d-bekendtgorelse.pdf)
Qualifications
You must hold a master’s degree or equivalent within the relevant fields as indicated above, and in addition fulfil the required qualifications indicated as part of the specific project.
You are required to have good communication skills and, to be a visible, involved participant in the Department’s daily activities, in addition to being willing to engage in disciplinary and interdisciplinary collaboration across the Department.
Assessment
In the assessment regarding employment consideration will be given to:
Relevant Master’s degree or equivalent (according to Danish Qualifications Framework for Higher Education: https://ufm.dk/en/education/recognition-and-transparency/transparency-tools/qualifications-frameworks/other-qualifications-frameworks/danish-qf-for-higher-education?set_language=en&cl=en).
Any additional academic requirements stated in the job advertisement.
In the assessment, regarding enrolment consideration will also be given to the following criteria:
Educational skills and any further professional qualifications
Grades at Master’s programme or equivalent
Your description of the Ph.D. project – Here you describe in which direction you would like to work and how your qualifications fit into the project (approximately one page).
Quality and relevance of the project description
Quality and relevance of the methodical and theoretical choices
Consistency and coherence between the problem and the choice of method and theory
If the PhD project seem realistic and feasible
Ability to complete the PhD project
Relevance of the project to the profile of the Doctoral School
Three PhD positions will be offered to the candidates fulfilling the requirements and expectations to the highest degree.
Questions
For further information about the positions, please contact Dean Susanne Sørensen on tel (+45) 4674 2111 or susa@ruc.dk.
The position will be filled according to the Agreement between the Danish Ministry of Finance and the Danish Confederation of Professional Associations (AC) and Job Structure for Academic Staff at Universities.
Application procedure
After the deadline for applications the Dean will shortlist applicants for assessment with assistance from the recruitment committee including the chairperson of the assessment committee.
Shortly after the application deadline all applicants will be notified whether or not their application has been selected for assessment.
The shortlisted applicants will be informed about the composition of the assessment committee, and each applicant will be given the opportunity to comment on the composition of the committee and – later on – their assessment.
Once the recruitment process is completed, all applicants will be informed of the outcome of their application.
Application
To apply for the position go to www.ruc.dk/en/job/
Only applications in English are accepted.
Applications must include:
1. Cover letter
2. CV
3. Documentation of education including grades from Master’s programme or equivalent
4. Your description of the PhD project – Here you describe in which direction you would like to work and how your qualifications fit into the project (approximately two pages at maximum).
5. Your time schedule of the PhD project
6. If applicable: Documentation for any research experience, work experience or publications.
Please submit your application no later than 4 March 2022.
Material received after this date will not be taken into consideration.
Roskilde University wishes to reflect the diversity of society and welcomes applications from all qualified candidates regardless of personal background.