We are looking for a PhD student in Medical Science with an orientation towards Molecular Biology and a special interest in bioinformatics and bacterial stress response. The position at the Department of Molecular Biology at Umeå University is temporary for four years to start immediately or as agreed.
When bacteria encounter stressful conditions they rewire their intracellular physiology to increase their chances of survival until the environment becomes favourable again. One of the ways they do this is by producing the “alarmone” nucleotides ppGpp and pppGpp that alter the gene expression profile of the cell through interactions with multiple targets. (p)ppGpp is produced by enzymes of the RelA-SpoT Homologue (RSH) superfamily, which can be single- or multi-domain in structure. The current project concerns the part of the RSH superfamily comprised of Small Alarmone Synthetases (SASs) carrying a single (p)ppGpp synthesis domain. There are at least 12 different classes of SASs, which have evolved through gene duplication, horizontal gene transfer and differential loss, and multiple classes can be present in the same bacterium. It is not known why bacteria carry multiple SASs, and what their functions are in the cell. Only recently have details come to light about SAS regulation, when it was shown that the SAS RelQ from pathogen Entercoccus faecalis is regulated in vitro both by single stranded RNA, and its product pppGpp. This raises questions of how general this regulation is among SASs, what sequence and structural regions are involved, and what are the RNA targets in living cells. We will address these questions through bioinformatic methods including comparative molecular evolutionary analyses and analyses of next generation sequencing (NGS) data of SAS-bound RNA fragments.
Applicants must hold a University degree equivalent to a European University Master degree of at least 240 credits (ECTS) in Biological and Health Sciences at the time of the recruitment, or equivalent levels of education otherwise acquired in Sweden or abroad.
The successful candidate should be able to design and carry out analyses of genomic (NGS), RNA and protein sequences, and present the findings. You must have experience in bioinformatics and computer programming (e.g. Python, Perl), as well as phylogenetic analysis of protein sequences. You need to be fluent in spoken and written English which will be evaluated by the postgraduate studies board of the department.
You should be highly motivated and able to work productively in a team as well as independently. Excellent communication skills for interacting effectively with senior colleagues and peers are required.
Basis of assessment
The evaluation of the ability and potential to perform well is based primarily on:
Good collaborative skills, drive and independent work ability are considered as positive merits.
A selection will be made among qualified applicants on the basis of their qualifications and their ability to benefit from studies at the doctoral level. After the selection of the suitable candidate, the process for the admission to doctoral studies will commence. An admission decision will not be taken by the faculty’s director of studies until an individual study plan has been approved by the departmental admission board.
How to apply
You apply through our recruitment system. Your application must contain the following documents written in English or Swedish:
Union information is available from SACO, +46-(0)90-786 53 65, SEKO, +46-(0)90-786 52 96 and ST, +46-(0)90-786 54 31.
For questions regarding the position contact Gemma Atkinson, email@example.com
More about us
The Atkinson lab is part of the Umeå Centre for Microbial Research (UCMR), an interdisciplinary research centre devoted to top quality research and novel applications in the field of microbiology.
You can find more information about us at www.ucmr.umu.se and www.molbiol.umu.se/english.
090-786 53 65
090-786 52 96
090-786 54 31