About the Cluster of Excellence CMFI

The surfaces of the human body host colonies of microorganisms, known as microbiomes. Along with bacteria which have a positive effect on human health, microbiomes contain potentially life-threatening pathogens. In the past, broad-spectrum antibiotics have often been used to tackle them. Nowadays it is known that this not only promotes resistance to antibiotics – in many cases it also damages the microbiome as a whole. Researchers in the Cluster of Excellence "Controlling Microbes to Fight Infections" aim to develop a new strategy to control infections.

Their goal is to find new, targeted agents which will have a positive effect on the microbiome. We know that useful bacteria help to keep down the harmful ones. In order to understand and exploit the underlying mechanisms, the Cluster of Excellence will bring together researchers from the fields of molecular, bioinformatics and clinical disciplines. The speakers of the Cluster are professor Andreas Peschel and professor Heike Brötz-Oesterhelt of the Interfaculty Institute of Microbiology and Infection Medicine at the University of Tübingen, along with professor Ruth Ley, Director of the Max Planck Institute for Developmental Biology. The University Hospital Tübingen and the German Center for Infection Research (DZIF) are also partners in the Cluster.

News

03/30/2021

New bioreporter approach

New bioreporter approach increases chances of discovering unknown bioactive compounds

Read more

03/17/2021

New CMFI Junior Research Group

Bastounis Lab launched

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02/09/2021

New rapid test to detect coronavirus antibodies developed

CMFI involved in development of new rapid test to detect coronavirus antibodies

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Events

04/15/2021

Jan Löwe, Molecular mechanisms in bacterial cell division

Joint Microbiological Colloquium, 15.04.2021 | 12:30 pm

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04/22/2021

Rolf Müller, tba

Joint Microbiological Colloquium, 22.04.2021 | 12:30 pm

Read more

Open Positions

PhD Position
Host-pathogen Interactions & Biomechanics

PhD position (E13 TV-L, 65%) – Host-pathogen interactions and cell biomechanics

to be filled as soon as possible. The position is initially limited to three years.

 

The Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI) in the Interfaculty Institute of Microbiology & Infection Medicine (IMIT) at the University of Tübingen is looking to fill one PhD position (E13 TV-L, 65%) as part of Junior Group Leader Dr. Effie Bastounis’ research group.

The earliest starting date for this position will be on 20.05.2021. The position is funded for a period of 3 years at least.

The available position focuses on using and further developing an organotypic device for applying shear stresses onto host endothelial cells during infection with intracellular bacterial pathogens. The goal is to understand the mechanism whereby fluid shear stresses impact: (i) pathogen adhesion onto host cells; (ii) pathogen internalization into host cells; and (iii) the ability of the intracellular pathogens to spread from cell to cell.

 

Specific research project

Endothelial cells that line the inner lumen of our vessels are constantly exposed to shear stresses due to blood flow and are experiencing alterations in the stiffness of the extracellular matrix (ECM) on which they reside (Bastounis et al., 2019). Changes in both these mechanical cues contribute to multiple pathologies including atherosclerosis, and often correlate with increased susceptibility to bacterial infection (Bastounis et al., 2018). However, most clinical studies on these correlations lack causality and are rather observational in nature. Using a multi-well impinging flow jet to impart varying shear stresses and gradients into endothelial cells in culture residing on varying stiffness ECMs we will investigate how those alone and in synergy impact direct adhesion and uptake of pathogenic intracellular bacteria, as well as their ability to spread from cell to cell. The goal of the project is to discover how shear flows impact host cell mechanotransduction and tension, thus facilitating or obstructing intracellular bacterial pathogen dissemination through endothelia.

 

Candidate profile

The ideal candidate preferably brings along a degree that demonstrates an interdisciplinary background in both life and engineering sciences. While a background in host-pathogen interactions, cell biology, microscopy is a plus, a solid background in basic computer programming (e.g. MATLAB, python etc.) and/or image processing is also important to carry out the planned studies and analysis. We are looking for a highly motivated candidate with excellent communication and initiative skills, who is excited to conduct interdisciplinary studies and can team up with the various scientists with whom we are collaborating. We offer work environment that is strongly stimulating with state-of-the-art infrastructure and various facilities (check the IMIT and CMFI websites) which will provide the successful applicant with unique opportunities to develop a strong interdisciplinary portfolio in microbiology, microscopy, cell biology and biomechanics.

 

For further information about the position, please contact Effie Bastounis by email (ebastounspam prevention@stanford.edu) and visit our website https://www.bastounislab.org.

Applications with a short cover/motivation letter, CV/biosketch, diploma(s) and two contacts for references should be sent via email to ebastounspam prevention@stanford.edu or officespam prevention@cmfi.uni-tuebingen.de.

Deadline: April 23, 2021

The University aims to increase the proportion of women in research and teaching and urges suitably qualified women scientists to apply. Qualified international researchers are expressly invited to apply. Disabled persons with equal aptitude will be given preferential consideration.

Postdoctoral Position
Host-pathogen Interactions & Biomechanics

Postdoctoral position (E13 TV-L, 100%) – Host-pathogen interactions & biomechanics

to be filled as soon as possible.

 

The Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI) in the Interfaculty Institute of Microbiology & Infection Medicine (IMIT) at the University of Tübingen is looking to fill one postdoctoral position (E13 TV-L, 100%) as part of Junior Group Leader Dr. Effie Bastounis’ research group.

The earliest starting date for this position will be on 20.05.2021. The position is funded for a period of three years at least.

The available position focuses on using and further developing an organotypic device for applying shear stresses onto host endothelial cells during infection with intracellular bacterial pathogens. The goal is to understand the mechanism whereby fluid shear stresses impact: (i) pathogen adhesion onto host cells; (ii) pathogen internalization into host cells; and (iii) the ability of the intracellular pathogens to spread from cell to cell.

 

Specific research project

During infection with the food-borne intracellular bacterial pathogen L. monocytogenes, large infected domains in epithelial cell monolayers are forced to extrude to form 3D mounds due to the collective and cooperative onslaught triggered by their uninfected neighbors. This mechanical competition between uninfected and bacterially-infected cells is driven by innate immunity signals and appears to limit pathogen dissemination through the epithelium (Bastounis et al 2021). The project seeks to investigate how signaling and cytoskeletal dynamics correlate with changes in host cell mechanics during intracellular bacterial spread through epithelial monolayers. We also want to understand the contribution of extracellular mechanical cues (extracellular matrix stiffness, shear flow and mechanical strains) in promoting or obstructing this biomechanical battle in favor of the host.

 

Requirements

  • PhD in biomedical engineering/bioengineering or related life sciences or engineering field
  • Experience with microscopy, image processing and programming (e.g. MATLAB, python)
  • Experience with in vitro mammalian cell cultures systems
  • Excellent communication and initiative skills
  • Ability to team up with others to conduct interdisciplinary studies

 

Responsibilities

  • Participate in and execute research projects (e.g. setting up lab equipment, collecting and analysing data, writing papers, and presenting at conferences)
  • Participate in routine laboratory tasks (e.g. planning/preparations for experiments, lab maintenance and procedures)
  • Work with the PI on strategy and project planning development and assist on mentoring of students
  • Assist on organization and management of (inter)national collaborations

 

We offer work environment that is strongly stimulating with state-of-the-art infrastructure and various facilities (check the IMIT and CMFI websites) which will provide the successful applicant with unique opportunities to develop a strong interdisciplinary portfolio in microbiology, microscopy, cell biology, and biomechanics.

For further information about the position, please contact Effie Bastounis by email (ebastounspam prevention@stanford.edu) and visit our website https://www.bastounislab.org.

Applications with a short cover/motivation letter, CV/biosketch, diploma(s) and at least two contacts for references should be sent via email to ebastounspam prevention@stanford.edu or officespam prevention@cmfi.uni-tuebingen.de.

Deadline: April 23, 2021

The University aims to increase the proportion of women in research and teaching and urges suitably qualified women scientists to apply. Qualified international researchers are expressly invited to apply. Disabled persons with equal aptitude will be given preferential consideration.

PhD Position in Synthetic Organic Chemistry/Natural Products Chemistry

PhD Position (E13 TV-L, 50%) in Synthetic Organic Chemistry/Natural Products Chemistry

The research group NatResource at the Eberhard Karls University Tübingen is looking for a PhD student (m/f/d) to discover new bacterial natural products using techniques in analytical chemistry and chemical synthesis. We are a young and highly motivated research team at the interface of natural products isolation and synthetic organic chemistry with special interest in finding new antibiotics.

As part of a grant from the German Center for Infection Research (DZIF), we seek an enthusiastic scientist with a Master’s degree in Synthetic Organic Chemistry, Natural Products Chemistry, Microbiology, Biochemistry, or closely related disciplines. The project is focused on finding new lead compounds for the treatment of bacterial infections. Candidates are expected to be highly interested in organic chemistry and natural products.

The position is initially funded for 3 years.

Interested scientists should submit their application documents (CV, motivation letter, two references, grade transcripts) as a single PDF-file via email to: chambers.hughesspam prevention@uni-tuebingen.de by May 31st 2021.

The website of the PI can be found at https://www.hughesresearchgroup.de/.

Equal opportunities are an integral part of our personnel policy; we therefore particularly encourage qualified women to apply. Disabled persons with otherwise equal qualifications are given priority.

BTA/CTA/MTA or Laborant as Technician

As part of Cluster of Excellence: CMFI – Controlling Microbes to Fight Infections, we seek an enthusiastic

BTA/CTA//MTA or “Laborant” (m/f/d; E9 TV-L, 50%)

 

The research group NatResource at the Eberhard Karls University Tübingen is looking for a technician to cultivate and extract bacteria as well as organize a bacterial extract library. We are a young and highly motivated research team at the interface of natural products isolation and synthetic organic chemistry with a special interest in finding new antibiotics. 

The project is focused on finding new lead compounds for the treatment of bacterial infections. Candidates should have experience/training in microbiology and, ideally, some English proficiency.

The position is initially funded for 2 years.

Interested candidates should submit their application documents (CV, motivation letter, two references) as a single .pdf-file via email to: chambers.hughesspam prevention@uni-tuebingen.de by May 1, 2021

The website of the PI can be found at https://www.hughesresearchgroup.de/.

Equal opportunities are an integral part of our personnel policy; we therefore particularly encourage qualified women to apply. Disabled persons with otherwise equal qualifications are given priority.

CMFI Early Career Research Program
Grant

 

CMFI Early Career Research Program

The Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)” at the University of Tübingen aims to support outstanding scientists early in their careers and to stimulate research in the areas of interest of the Cluster. Towards this goal we are offering:

Postdoctoral Fellowships

Eligible Applicants

  • PhD obtained within the last 4 years but not in Tübingen
  • a good knowledge of English
  • peer reviewed publications in academic journals with at least one first authorship
  • currently not working in Tübingen *

 

Applicants must present a mentoring agreement by an academic host within the Cluster of Excellence CMFI.

 

Funding

  • 24 months with a salary according to TV-L E13 
  • 10.000 € consumables per year
  • extension up to 12 months possible

 

How to apply

Interested Applicants can get in touch with principal investigators within the Cluster of Excellence CMFI (https://uni-tuebingen.de/de/173847) and find an academic host. Subsequently, they have to develop a research project in agreement with their academic host and send the proposal to lisa.bleulspam prevention@med.uni-tuebingen.de.

 

Documents to be submitted

  1. Planned research project (max. 5 pages including references)
  2. CV with list of publications
  3. Motivation letter including career planning (max. 1 page)
  4. Mentoring agreement by the CMFI host, including a statement on the qualification of the applicant and the proposed research project

 

Downloads:

Questionnaire for the statement of the CMFI host

Hosting agreement

 

* or current research stay in Tübingen no longer than 6 months (this time will be deducted from the total duration of funding)

Postdoctoral researchers in Mathematical and Computational Population Genetics

The newly founded independent junior research group Mathematical and Computational Population Genetics headed by Franz Baumdicker at the University of Tuebingen has an opening for

Postdoctoral researchers (f/m/d)

The group develops and applies mathematical models and bioinformatic tools with a special focus on microbial evolution. We are interested in a variety of evolutionary scenarios including CRISPR Cas Evolution, Pan-Genome Evolution, Horizontal Gene Transfer, Fluctuation Selection, and Cooperation in Bacteria. The postdoc will work at the intersection of Mathematical Population Genetics / Computational Biology / Bioinformatics using mathematical population genetics, phylogenetics, statistical analysis, machine learning algorithms, and large scale simulations to derive new theoretical results, develop open source software and apply them to (microbial) genome data.
For scientific questions please contact fbaumdicker@gmx.de.
Candidate profiles we would love to see:
– PhD degree in (Bio-)Mathematics, Statistics, Bioinformatics, Computational Biology or a related field
– Interest in interdisciplinary research
– Strong mathematical preparation and interest
– Good computational skills (e.g. in Python, R)
– Independent, responsible and committed work
– Fluency in (scientific) English
What we offer:
– Salary according to TV-L, E13 (100%)
– The group is part of two Excellence Clusters (Controlling Microbes to Fight Infections & Machine Learning) in Tuebingen, which offers an excellent research environment with plenty of potential collaboration partners.
– Flexible starting date and possibility to start the project remotely in the initial phase
– Focus on research (no formal teaching duties)
– Responsibility to conduct your own research projects with a high amount of autonomy
Researchers from outside Germany are particularly encouraged to apply.
Applications and inquiries should be sent to office@cmfi.uni-tuebingen.de.
Please send your application as a single PDF file and include a brief statement on your interests and experience, CV (including a possible list of publications and the contact info of two academic references), and university transcripts. Severely disabled persons are given preferential consideration if they are equally suitable.
The review of applications will begin in October 2020 and continues until the positions are filled.

job offer as PDF

PhD students in Mathematical and Computational Population Genetics

The newly founded independent junior research group Mathematical and Computational Population Genetics headed by Franz Baumdicker at the University of Tuebingen has an opening for

PhD students (f/m/d)

The group develops and applies mathematical models and bioinformatic tools with a special focus on microbial evolution. We are interested in a variety of evolutionary scenarios including CRISPR-Cas Evolution and Dynamics, Pan-Genome Evolution, Horizontal Gene Transfer, Fluctuation Selection, and Cooperation in Bacteria. The PhD students will work at the intersection of Mathematical Population Genetics / Computational Biology / Bioinformatics using mathematical population genetics, phylogenetics, statistical analysis, machine learning algorithms, and large scale simulations to derive new results, develop open source software and apply them to (microbial) genome data.
For scientific questions contact fbaumdicker@gmx.de.
Candidate profiles we would love to see:
– Master’s degree in (Bio-)Mathematics, Statistics, Bioinformatics, Computational Biology or a related field
– Interest in interdisciplinary research
– Strong mathematical preparation and interest
– Good computational skills (e.g. in Python, R)
– Independent, responsible and committed work
– Fluency in (scientific) English
What we offer:
– Salary according to TV-L, E13 (65%)
– Dissertation at the Faculty of Natural Sciences working with two advisors
– The group is part of two Excellence Clusters (Controlling Microbes to Fight Infections & Machine Learning) in Tuebingen, which offers an excellent research environment with plenty of potential collaboration partners.
– Integration into the DFG priority programme SPP2141, where appropriate
– Focus on research (no formal teaching duties)
– Responsibility to conduct your own research projects with a high amount of autonomy
Researchers from outside Germany are particularly encouraged to apply.
Applications and inquiries should be sent to office@cmfi.uni-tuebingen.de.
Please send your application as a single PDF file and include a brief statement on your interests and experience, CV (including a possible list of publications and the contact info of two academic references), and university transcripts. Severely disabled persons are given preferential consideration if they are equally suitable.
The review of applications will begin in October 2020 and continues until the positions are filled.

job offer as PDF