Postdoctoral researcher in CIS Engineering for Antimicrobials and Biocontrol

Description of the workplace

The position is based at Lund University’s Faculty of Medicine, within the Department of Experimental Medical Sciences, specifically the Medical Structural Biology research unit. The division focuses on uncovering molecular mechanisms of health and disease through advanced imaging and biophysical approaches.

The research group hosting this position studies Contractile Injection Systems (CIS) — natural protein machines used by bacteria to deliver molecular cargo. The group's mission is to understand the structure, function, and application of CIS for use in both biopesticide development and targeted antimicrobial delivery. The team is interdisciplinary, with expertise in molecular microbiology, structural biology, bioinformatics, and protein engineering, and currently includes the PI, a PhD student, and a research expert in bioinformatics.

The workplace fosters strong international collaboration, with close integration with the Halberg Group at Copenhagen University (Insect neuroendocrinology and physiology) and the Collin Group (immune-relevant enzymology and translational infection research) at Lund University. The postdoctoral researcher will work primarily in Lund but is expected to engage in frequent collaborative work across the Öresund region, including regular experimental coordination with Copenhagen-based researchers and data collection at national facilities such as MAX IV (Lund), SciLifeLab (Stockholm), and CFIM (Copenhagen), where cryo-electron microscopy (cryo-EM) and tomography (cryo-ET) are performed.

The group values a collegial and supportive research environment, with open communication, structured mentoring, and a strong emphasis on work-life balance. Lund University provides an excellent infrastructure for interdisciplinary and early-career research development.

Description of the AMBER project context 

This post-doctoral position is part of the EU cofund research project AMBER, Advanced Multiscale Biological imaging using European Research infrastructures, will address scientific and sectoral gaps in biological imaging ranging from molecular, through cellular, to tissue, organ and organism levels of organisation, and is coordinated by LINXS Institute of advanced Neutron and X-ray Science.

AMBER is funded by the EU Marie Skłodowska-Curie (MSCA) COFUND scheme.

Around 20 postdocs will be recruited in the fourth call 2025, with each fellowship lasting 36 months.

AMBER has six core partners: Lund University/MAX IV, Sweden, the European Spallation Source (ESS), Sweden, the European Molecular Biology Laboratory (EMBL), Institut Laue-Langevin (ILL), France, the International Institute of Molecular Mechanisms and Machines, (IMOL), Poland, and the Leicester Institute of Structural and Chemical Biology, United Kingdom.

Your work may include clinical and biomedical projects. It may also include technique development work aimed at combining imaging techniques and data analysis to provide a more integrated picture of life processes in the context of health and disease. To be a postdoc fellow at the AMBER programme you will get unprecedented medical, biological, and methodological capabilities, with a profound potential impact for Europe’s next generation of research and researchers. When you have completed the AMBER programme you will be extraordinarily well equipped to further your career in academia, at infrastructures, in the health and MedTech sectors, and beyond.

For more information about the total announced post-doctoral positions within in the AMBER co-fund project please visit https://www.euraxess.se/jobs/341970.

The interviews will start in November 2025. For more information about AMBER, application and evaluation process etc please visit: ambercofund.eu.

Description of the project

This interdisciplinary project explores the discovery, structural analysis, and rational redesign of bacterial Contractile Injection Systems (CIS) — evolutionarily conserved protein complexes that function as nano-syringes to inject molecular effectors into target cells. CIS hold exceptional promise as modular and programmable tools for precision delivery of biomolecules, with transformative applications in infection biology, biomedicine, and sustainable agriculture.

The project addresses two primary application areas:

1. In biomedicine: the aim is to selectively target and neutralize antibiotic-resistant pathogens (e.g., Staphylococcus aureus) by delivering customized antimicrobial payloads such as enzymes, CRISPR-Cas constructs, or peptides via engineered CIS. This work emphasizes specificity, minimizing disruption to the commensal microbiota.

2. In insect pest management: reprogrammed CIS are designed to deliver neuropeptides or RNA interference (RNAi) molecules to key osmoregulatory targets in pest species (e.g., beetles), reducing chemical pesticide usage while sparing beneficial insects.

The research involves:

• Microbiome sequencing and metagenomic mining to identify novel CIS candidates from diverse ecological niches (skin, gut, insect microbiomes)
• Recombinant expression and purification of CIS variants
• High-resolution cryo-EM and cryo-ET imaging to resolve molecular structure and guide engineering
• Protein design and molecular modeling, supported by AI tools such as AlphaFold2
• Development of functional assays in insect and bacterial systems to evaluate targeting, delivery, and physiological effects

This project is hosted at the Faculty of Medicine, Lund University in the Department of Experimental Medical Science and involves close collaboration with:

• The Halberg Group (University of Copenhagen) – experts in insect physiology and osmoregulatory control
• The Collin Lab (Lund University) – leaders in bacterial pathogenesis and enzymatic immune modulation

Cryo-EM and cryo-ET data collection will be carried out at national facilities including MAX IV (Lund) and partner platforms in Stockholm and Copenhagen. This postdoctoral fellowship offers a unique opportunity to work at the interface of structural biology, microbiome research, and applied biotechnology, contributing to the development of next-generation therapeutic and biocontrol strategies.

Work duties and responsibilities

At Lund University, a postdoctoral position should provide opportunities for scientific and pedagogical qualifications. Primarily, there is scope for qualifications in research, but also for some higher education pedagogy training. Teaching may also be part of the job duties.

As a postdoctoral researcher in this interdisciplinary project, you will play a key role in the development of programmable CIS/BIS, combining structural biology, microbiome analysis, and protein engineering to create novel precision delivery tools.

Your main responsibilities will include:

• Identifying and characterizing new CIS candidates through microbiome sequencing, metagenomic mining, and comparative genomics
• Cloning, expressing, and purifying CIS proteins or complexes using advanced molecular biology techniques
• Performing cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) for high-resolution structural analysis of CIS
• Redesigning CIS components and engineering new variants for delivery of specific effectors (e.g., antimicrobial peptides, RNAi, CRISPR-based constructs)
• Conducting functional in vitro and in vivo assays to evaluate target specificity, delivery efficiency, and phenotypic effects in bacterial and/or insect systems
• Analysing and interpreting structural, functional, and bioinformatic data, and contributing to collaborative publication efforts
• Engaging with an interdisciplinary research team, including microbiologists, structural biologists, and host-pathogen experts
• Presenting your work at national and international conferences, and contributing to funding applications and dissemination activities

You will be based at Lund University (Lund, Sweden), with frequent interaction with collaborators at University of Copenhagen and regular visits to national imaging facilities, such as MAX IV in Lund, and partner cryo-EM centres in Stockholm and Copenhagen.

Short research stays or secondments may also be arranged, depending on your career development plan.

While the position follows standard full-time working hours, flexibility may be required during data collection periods, especially when using high-demand infrastructure facilities (e.g., synchrotron/cryo-EM sessions). Travel within Europe for conferences, collaboration meetings, or training is expected.

This role offers a high degree of autonomy and creativity and is ideal for a researcher eager to contribute to next-generation bioengineering solutions while building strong interdisciplinary expertise.

Qualifications

Minimum requirements are:

• Candidate needs to have a maximum 8 years after a doctoral degree (PhD), as required by the project Grant Agreement signed with the European Commission,
• At least one original publication in a peer-reviewed journal,
• A background in the relevant methods,
• A complete application package submitted through the AMBER portal (including CV and detailed research plan), and finally,
• Strict compliance with the MSCA mobility rule that the researcher must not have resided or carried out his/her main activity (work, studies, etc.) in the host organisation'scountry for more than twelve months in the three years immediately prior to the call deadline.

Each project will have additional specific requirements that candidates have to fulfill, be sure to check what these are before you apply.

Specific requirements for the position are:

• You have a PhD (or equivalent foreign degree) in molecular biology, microbiology, biochemistry, structural biology, biotechnology, or a related field. The degree must be completed no later than the time of employment decision.
• You have experience of conducting independent research of high quality, demonstrated through peer-reviewed publications.
• You have experience of standard molecular biology techniques, such as molecular cloning and protein expression.
• You have experience of cryo-EM, cryo-ET, or other structural biology techniques.
• You have good oral and written communication skills in English.
• You can work both independently and collaboratively within interdisciplinary teams

Meritorious for the position are:

• You have experience of structure-based protein design or engineering.
• You have experience with protein structure prediction tools, such as AlphaFold2 or Rosetta, including multimeric complex prediction.
• You have experience of microbiome sequencing, genome mining, or metagenomic data analysis.
• You have worked with host-pathogen interaction models, antimicrobial peptides, or CRISPR-based systems.
• You have experience of insect models or RNAi-based screening.
• You have experience of functional delivery assays (e.g., in bacterial or insect systems).
• You have been involved in interdisciplinary or collaborative research environments.

Personal suitability, enthusiasm for interdisciplinary research, and motivation to work at the interface of structural biology and applied biotechnology will be considered in the overall evaluation.

The assessment of applicants will be based primarily on their scientific merit and potential as researchers. Emphasis will be placed on scientific ability within the subject area.

We offer

Lund University is a governmental authority, which means you get special benefits, generous holidays and a favorable occupational pension. We also have a flexible time agreement that creates good conditions for a balance between work and leisure.

Read more on the university's website about being employed at Lund University, Work with us.

About the employment

The position is a fixed-term position of three years, 100% with start date on 2026-01-01 or as agreed. Employment at Lund University is conducted in Sweden, you are therefore expected to be able to perform your work on site in Lund.

The employment is limited to a maximum three years, according to the collective agreement on fixed-term employment as a postdoctoral researcher (the Swedish Employers' Association). A postdoctoral position is intended as an initial step in a career and as an opportunity to further deepen and broaden research expertise.

Additional information

We offer a collaborative and supportive research environment that values teamwork, open communication, and shared scientific goals. You will be encouraged to take an active role in mentoring Master's and PhD students, contributing to group activities, and fostering a positive team spirit.

We also support the development of independent research profiles, and you will be encouraged to engage in grant writing and career development activities as part of your postdoctoral training.

You do not need to be an expert in both infection biology and insect physiology from the beginning — but you must be willing and able to learn quickly within a collaborative and interdisciplinary team.

Instructions on how to apply

For more information and documents/templates/europass link, please visit https://www.ambercofund.eu/for-applicants.

Incomplete applications will not be considered. Please make sure that you upload all the required documents specified below i-ix.

If you are interested in applying for more than one position (maximum 3) you must be prepared to make a full application for each individual position.

Applications shall be written in English and all documents shall be in pdf format.

i) A Curriculum Vitae (europass format). Your CV shall be exported to a PDF file that you use in your application.

ii) A detailed research plan including any foreseen secondments (candidates can suggest more than the mandated one, they can also suggest their own secondments), schools and conferences as well as a templated budget plan. The research plan should be as concise as possible, 3 pages, including one-third page of summary/abstract.

Additional texts to include in the PDF are:

iii) Letter of Commitment from any additional secondment partners the candidate wishes to bring

onboard.

iv) Evidence of English proficiency (minimum CEFR B22, also checked at interview).

v) A draft Individual Career Development Plan (ICDP).

vi) Two reference letters.

vii) Any additional documents to support the application.

viii) Ethical questionnaire (HE ethics checklist + research ethics commitment)

In addition, the application will require:

ix) Any candidate can apply for maximum of 3 positions. You must apply for each individual position. A list with order of preference of positions should be sent to the AMBER management. amber@linxs.se

More information about the Faculty of Medicine