Time-resolving the dynamics of plant autophagy molecular machinery.

PhD position in Biology. Plant Cell and Molecular Biology.

Department of Molecular Sciences, SLU, Sweden

Work environment
Swedish Agricultural University (SLU) is one of the highly-ranked universities world-wide. The department of Molecular Sciences belongs to the NJ-faculty and is located at the Uppsala BioCenter, Ultuna campus of SLU.  Our department is a vivid, multicultural workplace employing over a hundred researches with a very broad range of expertise including nanotechnology, inorganic and organic chemistry, structural biology, food science, microbiology, plant biochemistry and cell molecular biology. The department hosts or is responsible for outstanding facilities for protein crystallography, chromatography, bioreactor, NMR, mass spectrometry, advanced microscopy: AFM, SEM, confocal microscopy and contributes to the development and use of the Max IV synchrotron. The department provides a nourishing environment for establishing new transitional research. The doctoral student will be working in a young research group interested in plant autophagy. 

The project
We are looking for a highly motivated doctoral student to join us in investigating regulation mechanisms of plant autophagy.

Green, GFP-tagged autophagosomal marker in epidermal cells

 of Arabidopsis cotyledon under normal conditions. Red,

autofluorescence of chlorophyll.  Alyona Minina, unpublished.

3D reconstruction of autophagy marker detected in Arabidopsis
 root (the signal is color coded for depth).

Alyona Minina, unpublished.

Autophagy is the major catabolic process of eukatyotic cells, its molecular machinery is highly conserved and is controlled by the so called autophagy-related (ATG) genes. Autophagy is implicated in developmental processes and stress responses in all eukaryotes including plants. Plant autophagy is important for drought and salt stress tolerance, plant-pathogen interactions, fecundity and longevity of the plant (1, 2). In our previous studies we demonstrated that artificial up-regulation of autophagy has an invigorating effect on plant performance (3, 4). Despite the obvious importance of plant autophagy, little is known about the dynamics of this process. In this project the doctoral student will perform a detailed time-resolved in planta analysis of autophagic response to a short and prolonged stress, focusing on duration of the transcriptional and post-translational signaling. The PhD student will use forward and reverse genetics tools, build on the systems for in vivo autophagy detection developed in our group, analyse changes in the transcriptome dynamics, use advanced fluorescent microscopy and molecular biology tools to thoroughly characterize the chain of events activating and modulating plant autophagy response to various stress conditions. The knowledge obtained in this project will be an extremely important contribution to our understanding of plant autophagy.
Furthermore, the doctoral student will have a unique opportunity to  collaborate with the SweTree Technologies AB to test applicability of our proof of concept results on the crop tree species. 

Our selected publications most relevant to the project
Minina et al., 2018. JXB
Avin-Wittenberg et al., 2018. JXB
Minina et al., 2017. New Phyt
Minina et al., 2014. Trends in Plant Sci
Minina et al., 2013. JCB
Minina et al., 2013. Aging Cell




Education 
The department is an organizing participant of two graduate schools, providing access to a broad range of advanced courses on genetics, bioinformatics, cell and molecular biology, biochemistry, advanced microscopy, structural biology, statistics, teaching in higher education, career development, writing scientific publications etc.
As a part of the project, the doctorate student will receive an advanced personal training in the methods relevant for the project by the experts in our group and by our collaborators.

Qualifications

The successful candidate must have basic eligibility for third cycle education, i.e. she/he has taken a second cycle qualification or has completed course requirements of at least 240 higher education credits, including at least 60 higher education credits at the second cycle education and holds a Master's degree in biology or similar.

The candidate must be highly motivated, interested in working in a multicultural environment, be fluent in spoken and written English (upper secondary school grades equivalent to English B/English 6). Experience with molecular biology, basic knowledge of statistics and bioinformatics are required, experience with Arabidopsis thaliana model organism is a benefit.

Employment
Four years of full-time employment as a doctoral student at SLU. Additionally, the employment will be prolonged to compensate for the doctoral students' time spent on teaching at the department (up to 20% of the planned 4 years).

Supervision
Main supervisor:  Alyona Minina (E.A. Minina)

Co-supervisor:     Peter Bozhkov

Starting date

January 10th, 2019 or later (the date is negotiable)

SLU is an Equal Opportunity Employer
Read about the PhD education at the NJ faculty of SLU here
Selection among applicants meeting the requirements is made with reference to written application including curriculum vitae, copies of degrees and transcripts of academic records, one copy of the dissertation for masters or undergraduate degree, a list of at least two references familiar with the applicant's qualifications, certified knowledge of the English language and an interview.

How to apply
Please follow this link, scroll down to the bottom of the page and click on the button "Apply". Sign up using your email address and fill in the application form.
The application must be submitted no later than 2018.10.30. Incomplete applications or applications submitted after the deadline will not be considered.

Academic union representatives
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