Mobilomics - the study of molecular elements involved in rapid bacterial evolution

Applications are invited for a PhD fellowship/scholarship at Graduate School of Science and Technology, Aarhus University, Denmark, within the ‘Environmental Sciences’ programme located in Roskilde. The position is available from 1 May 2018 or later.


Title:
Mobilomics - the study of molecular elements involved in rapid bacterial evolution


Research area and project description:

The Department of Environmental Science in Roskilde is offering a PhD position in Mobilomics, the study of mobile genetic elements (MGEs) and molecular parasites such as IS elements, plasmids and bacteriophages.

We hereby offer a 3 year PhD position in molecular microbiology. The project will be focused on analyzing the role of mobile genetic elements in both laboratory experiments and the environmental setups by using state of the art methods e.g. DNA sequencing and proteomics techniques. This will involve the combined approach of cutting-edge molecular tools and bioinformatics analysis.

Mobile genetic elements are often neglected in metagenomic studies, mainly due to the difficulties of establishing their position and function in bacteria. But, these elements are key players in microbial evolution.

The PhD project will focus on developing new techniques to retrieve and sequence plasmids carrying genes of interest e.g. antibiotic resistance, bacteriophages and circular IS elements that shape bacterial evolution at fantastic rates. Work will be conducted partly in laboratory experiments and environmental explorations and will utilize the Oxford nanopore and Illumina sequencing facilities available in the department.

The PhD student will further establish and use bioinformatics pipelines for predicting mobile elements in large metagenomic datasets. The developed tools will then be used for studying mobile genetics elements such as plasmids, bacteriophages and IS elements in environmental samples.

Further work will include the elucidation of resistance pathway genes and other accessory genes carried on mobile genetic elements in contrasting environments, both pristine and those affected by various chemicals.

The research will be conducted individually and in collaboration with other researchers in the Environmental Microbial Genomics group (http://envs.au.dk/instituttet/sektioner/embi/emg/) amongst others mainly at Aarhus University in Roskilde.

Research questions/tasks include:

·         Developing methods for retrieving mobile genetic elements from various samples

·         Oxford nanopore and Illumina sequencing

·         Assembling and analyzing of MGEs. - Elucidation of mode of action of MGEs

·         Setting up in vitro evolutionary experiments to demonstrate how MGEs shape bacterial evolution

·         Collection and preparation of environmental samples containing relevant microbial communities

·         Investigate environmental impact of MGEs on community structures

·         Study of the activity and mechanisms of MGEs by transcriptomics and proteomics.

 

Qualifications and specific competences:

Applicants must have a Master’s degree (MSc) in biology, biochemistry, microbiology or similar from an internationally recognized University with a research thesis in one or more of the following areas: microbiology, genetics or biotechnology.

We expect the candidate to have the following qualifications:

·         Practical experience with molecular biology and microbial genetics

·         Knowledge about biotechnology and mobile genetic elements e.g. plasmids, IS elements and bacteriophages (preferred)

·         Experience with next-generation sequencing, qPCR and bioinformatics (preferred)

·         Good collaborator skills and team spirit

·         An excellent level of both spoken and written English to accommodate scientific communication and dissemination

 

Candidates will be evaluated on grades, publications of scientific articles in international peer-reviewed journals, motivation letter and refinement of project description. Please include in the application a project description proposal on ideas for planned research activities (½-4 pages).

 

Practicalities:

Application deadline 1 February 2018 at 11.59 PM MET (see more instructions below).

Please indicate in the application form: ‘2/3 financing is in place from supervisors projects, applying for 1/3 from GSST’.

Only candidates that are found qualified for this financing will be offered the position.

 

Place of Employment and Place of Work:

PhD will be enrolled in Graduate School of Science and Technology (GSST) at Aarhus University, and the place of work is Department of Environmental Science, Frederiksborgvej 399, 4000 Roskilde (near Copenhagen), Denmark.

 

Contacts:
Applicants seeking further information are invited to contact:

Professor Lars Hestbjerg Hansen, e-mail: lhha@envs.au.dk or Researcher Witold Kot, e-mail: wk@envs.au.dk

 

 

Application procedures

Before you apply

Information and attachments:

Please be aware that you must have all relevant appendices, attachments, addresses for referees, etc. ready when you apply, as the entire application must be uploaded to the system in one go.

Documentation of language skills:

The English language requirement at Graduates School of Science and Technology is comparable to an “English B level” in the Danish upper secondary school (“gymnasium”).

English language qualifications comparable to an “English B level” is documented by one of the following tests:

  • TOEFL test, minimum score: 560 (paper-based test) or 83 (internet-based test). The paper-based test must have a “total score”. From August call 2019, GSST no longer accepts the paper-based test.
    Aarhus University does not accept the TOEFL ITP test. Aarhus University’s TOEFL code is 8935. You must request that the test centre send your test results to Aarhus University, in order to enable verification of your test results.
  • IELTS (academic) test, minimum average score: 6.5 points
  • Cambridge English Language Assessment:
    Cambridge Certificate of Proficiency (CPE)
    Cambridge English: Certificate of Advanced English with grade A,B or C (CAE)
    Cambridge English: First Certificate  with grade A (FCE)

When to take the test and how to upload the documentation:
The test result must not be more than two years old at the time of application.

The English language test should be taken before applying for admission and uploaded under “language skills documentation” in the online application form.

It is possible to apply for admission before you have taken the test. In this case documentation stating that you have signed up for a test (please state expected submission date) must be uploaded. If the test result is not part of the original application the test result is to be sent to sphd@psys.au.dk no later than one month after the application deadline.

The following applicants are exempted from documenting their English qualifications/taking a test:

  • Applicants with citizenship from the following countries: Australia, Canada, Ireland, New Zealand, United Kingdom, United States, or one of the Nordic countries (Denmark, Finland, Iceland, Norway or Sweden).
  • Applicants with a Bachelor’s or Master’s programme completed in Australia, Canada, Ireland, New Zealand, United Kingdom, or United States. In this case, please upload your Bachelor’s or Master’s diploma under the section ”Language skills documentation”.
  • Applicants with a Bachelor’s or Master’s programme completed at Aarhus University for which the requirement was English B level at the time of admission. In this case, please upload your Bachelor’s or Master’s diploma under the section”Language skills documentation”.
  • Applicants able to document that English was the language of instruction during the whole period of their Bachelor’s and/or Master’s programme. This must be documented by uploading an official document from the institution stating this under “language skills documentation”. The onus is on the applicant to provide this information as GSST will not pursue information regarding language of instruction for any programmes or institutions.

 

The programme committee may request further information or invite the applicant to attend an interview.

How to apply:

1)      Find the application form:
Go to http://talent.au.dk/phd/scienceandtechnology/opencalls/
Choose February 2018 Call with deadline 1 February 2018 at 11.59 PM MET.
You will be directed to the call, and must choose the programme 'Environmental Sciences'  

2)      Fill in the following information:

  • Personal information
  • Academic background
  • Admission
  • Financing (if any)
  • Study: In the dropdown menu you must choose the project: "Mobilomics - the study of molecular elements involved in rapid bacterial evolution"
  • Source (how you found out about the call)

Next to some of the information fields you will find a number. Click on the number to get further directions on how to fill in the information field/what information is needed.

3)      Application attachments:
Please be aware that you cannot submit the application if one or several of these documents have not been uploaded.

If you wish to upload more than one document under each section, you must scan/merge all documents into one large PDF file and upload this. Please note that we reserve the right to remove scientific papers, large reports, theses and the like. Instead you can indicate a URL where the information is available.

Please note that all information in the application must be in Danish or English.

As a minimum all applications must include (pdf-files only, max. 20 MB, no zip):

  • One reference (template for references)
  • Curriculum vitae,
  • Motivation (max. 1 page)
  • Transcripts and diploma(s)
  • Project description (½-4 pages). This document should describe your ideas and research plans for this specific project. If you wish to, you can indicate an URL where further information can be found. Please note that we reserve the right to remove scientific papers, large reports, theses and the like.
  • Documentation of language skills if required.

After submission of the application, you will receive a confirmation e-mail with an application ID, you should use for reference if needed. The e-mail will also include a link to the application – GSST urges you to check that all mandatory data, marked with an asterisk (*), is registered correctly and all attached files are readable. In case of significant errors, you should reply to the confirmation e-mail with the correct details before the application deadline.

GSST reserves the right to verify the authenticity of your educational diploma and transcripts:

  • Request additional information to verify an application.
  • Reject the application if it is proven, or if the University has reasonable belief, that the information provided is false or if the applicant refuses to provide the requested information, whether or not an offer has already been made. 
  • For further information on applying, assessment procedures, etc. please see the GSST application guide here  

Please note:

  • The programme committee may request further information or invite the applicant to attend an interview.
  • The project will only be initiated if final funding (from GSST/the faculty) is secured.

All interested candidates are encouraged to apply, regardless of their personal background.