Important dates
The call opens: 22 September 2023
Application deadline: 29 October 2023
Final interview: 5-6 December 2023
Umeå University is one of Sweden’s largest institutions of higher education with over 35,000 students and 4,200 faculty and staff. We are characterised by world-leading research in several scientific fields and a multitude of educations ranked highly in international comparison. Recent breakthroughs include deciphering the molecular mechanisms of the bacterial CRISPR-Cas9 system and its repurposing into a tool for genome editing, a method that was awarded the 2020 Nobel Prize in Chemistry.
The call opens: 22 September 2023
Application deadline: 29 October 2023
Final interview: 5-6 December 2023
The two Swedish Centres of Excellence – Umeå Centre for Microbial Research (UCMR) and Umeå Plant Science Centre (UPSC) – at Umeå University are currently running the ‘Excellence by Choice’ Postdoctoral Programme in Life Science offering a highly interactive and multidisciplinary research environment.
The programme aims to encourage new synergies in life science with a focus on molecular and translational research, train outstanding young researchers, and stimulate cutting-edge research in Umeå. Patron for the programme is Nobel laureate Emmanuelle Charpentier, who discovered the CRISPR-Cas9 gene editing technology during her time as a scientist and group leader in Umeå.
In this third call, seven postdoctoral fellowships are open to all nationalities.
Read a feature article at Nature website:
Big ideas welcome: postdoc call in Sweden seeks original thinkers
Read interviews with current ‘EC’ postdocs in Umeå at the Umeå University website:
Gabriel Torrens, Joram Kiriga Waititu, Samuel Agyei Nyantakyi, Jagadish Mangu, and Aicha Kriia.
1. Vaccine-induced immune responses and protection from infection mortality in old adults
Background: Increased vulnerability to infectious diseases is described from the age of 65, which accounts for approximately 20 percent of Sweden’s population. Purpose: The successful applicant will assess immunity and protection to respiratory infectious agents in a cohort of >2000 older individuals that have been longitudinally sampled for capillary blood since Sep 2021. The goal is to reveal factors that correlate with infection- or vaccination-induced induction of robust and protective immunological memory to clinically relevant respiratory pathogens.
Aims/planned research activities: You will further develop our current research strategy (Vikström Lancet RHE 2023, Blom Lancet ID, 2023) and (1) develop a multiplex-based assay for detection of pathogen specific antibodies (2) characterize immune memory to several respiratory pathogens in the oldest old and (3) combine immunological and registry-based data to reveal correlates of protection against infection or severe/fatal disease.
Significance: This project will improve basic understanding of immune responses in older adults and generate data that can be used to implement more efficient protective measures against clinically relevant respiratory pathogens.
The project is joint between Dr Mattias Forsell and Anders Johansson, that provides complimentary expertise in molecular and cellular immunology, vaccinology, virology, epidemiology, and clinical infectious diseases.
Contact:
Mattias Forsell, Dept of Cinical Microbiology
Anders Johansson, Dept of Clinical Microbiology
2. Interactions between bacterial membrane vesicles and enteric viruses
This research explores the relationship between enteric viruses and the gut microbiome, focusing on species F adenovirus and bacterial membrane vesicles (BMVs). Understanding these interactions is vital for disease prevention and treatment.
Specific aims:
1. Create a BMV library from bacteria and study their impact on enteric virus infection using advanced methods.
2. Identify BMV-associated factors affecting viral infection.
3. Examine BMV-associated factors' structural and functional properties in modulating viral infection.
Our project utilizes advanced techniques: electron microscopy for BMV ultrastructural analysis, microbial genetic methods, in-vitro tissue culture models, and proteomic, lipidomic, and metabolic studies for host-microbe interactions. We aim to produce and test BMVs in virus infection models.
Prof. Sun Nyunt Wai has more than 25 years of experience in BMV research, whereas Associate Prof. Annasara Lenman is an expert in virus-host interactions. Using genetically modified BMV-producing bacterial strains, we will investigate how BMVs interact with viruses. This research addresses a gap in the understanding of bacterial and viral interactions in the human gastrointestinal (GI) tract, providing novel insights into the molecular mechanisms underlying GI tract illnesses and potential therapeutic targets. This collaboration leverages the distinct expertise and tools of both researchers, making this project essential for advancing our knowledge in this field.
Contact:
Sun Nyunt Wai, Dept of Molecular Biology
Annasara Lenman, Dept of Clinical Microbiology
3. New targets for treatment and prevention of saprolegniasis in salmonid fish
Swedish aquaculture is a small but well-developed industry with high standards regarding animal health and welfare. Still, pathogens are a serious threat to the welfare of captive fish. Oomycetes of the genus Saprolegnia are widespread problems in fish hatcheries and current therapies are solely based on hazardous chemicals. Therefore, we aim to establish a laboratory assay for hyphal growth of Saprolegnia spp. and determine essential genetic queues governing filamentation. Based on this, we aim to identify and test anti-germinating and hyphal-blocking compounds against Saprolegnia to prevent growth of the pathogenic form. Proof-of-concept tests will be performed at Vattenbrukscentrum Norr AB on infected fish eggs. We will use established omics techniques to investigate gene circuits which govern filamentation of Saprolegnia parasitica and other species. Based on these findings, we will test chemical and natural compounds which inhibit Saprolegnia filamentation, boost infection resistance of fish or both.
C. Urban has long standing experience with human fungal pathogens serving as fundament to identify essential genes. L. Persson and H. Jeuthe will provide extensive knowledge in fish biology and aquaculture needed to perform proof of concept evaluations in natural environments. The study will inspire new anti-Saprolegnia compounds which are urgently needed to improve environmental conditions in Swedish fish hatcheries.
Contact:
Constantin Urban, Dept of Clinical Microbiology
Henrik Jeuthe, Vattenbrukscentrum Norr AB
4. Role of mitochondrial dysfunction in host cell-autonomous immunity against Chlamydia
Chlamydia trachomatis is the most prevalent bacterial agent of sexually transmitted diseases and a common cause of blinding eye infections. Given its obligate intracellular lifestyle, it is imperative for the pathogen to preserve the functional intactness of its host cell. In this context, the host cell’s mitochondria likely play a central role, not only because they are the powerhouses of the cell, but also because their dysfunction could alarm the host cell of the invader.
In this collaborative project, we, the Sixt lab and the Wanrooij lab, strive to combine our complementary expertise in host-pathogen interactions and mitochondria, respectively, to explore the possible role of mitochondrial distress in cell-autonomous immunity against Chlamydia.
Specifically, we aim to determine if C. trachomatis itself impairs mitochondrial function, or if it can protect mitochondria from known stressors. Moreover, we will determine the consequences of mitochondrial dysfunction on bacterial growth, host cell viability, and innate immune signalling. To address these questions, we have at hand a rich set of cell biological, biochemical, and microscopic assays specialized to the study of infection and mitochondria. Overall, this work will illuminate the interplay between Chlamydia and mitochondria, potentially revealing novel opportunities for therapeutic intervention, and can deepen our understanding of the molecular processes that mediate the signalling of mitochondrial stress.
Contact:
Barbara Susanne Sixt, Dept of Molecular Biology
Paulina Wanrooij, Dept of Medical Biochemistry and Biophysics
5. The effects of horizontal gene transfer on cell decision making
Horizontal gene transfer plays an important role in how bacteria adapt to stressful environments. It has also been highlighted as a significant vehicle by which bacteria gain new functions and repair broken genes. Yet, the random swapping of genetic information may also interfere with the regulation of key molecular pathways. In particular horizontal gene transfer may disrupt certain genetic architectures and impose selection for robustness. To investigate the effects of horizontal gene transfer on adaptation and genetic architecture, this project will use mathematical models of microbial communities exposed to stress, such as antibiotics.
Drawing upon Eric Libby's expertise on evolutionary modeling and Peter Lind's expertise on the genetic regulation of stress responses, the postdoc will use theoretical modeling to explore how different genetic networks that confer stress resistance evolve in the presence of horizontal gene transfer. Specifically the models will test the hypothesis that the resulting genetic architectures strike a balance between fitness and robustness to horizontal gene transfer, and that these architectures have few hierarchical interactions. The postdoc will benefit from being based at the interdisciplinary center IceLab where research groups use a variety of quantitative modeling tools to study evolution and there are many opportunities for support and academic career development.
Contact:
Eric Libby, Dept of Mathematics
Peter Lind, Dept of Molecular Biology
6. Linking molecular structure and function with ultrafast multidimensional spectroscopy
In this project, we will use two-dimensional time domain spectroscopy to identify the structural determinants of binding and catalysis of chitin by a novel lytic chitin monooxygenase with the aim to identify the link between molecular structural changes and optical features. These enzymes are responsible for the metabolism of complex carbohydrates (chitin) by gut microbial species. The successful implementation of this project will unveil unknown mechanisms of binding and reaction, as well as allow the development of new protocols for the detection of correlations in complex molecular systems. This interdisciplinary project combines biology, physics, and computational biochemistry.
The proposed approach can be applied to other biological systems and will provide the first steps for researchers to develop drugs tailored to manipulate gut microbiome composition and find new cures for diseases.
We will combine the advanced optical pump-probe techniques available in Dr. Maccaferri’s lab to study electronic properties in materials and biochemical entities with the expertise of Dr. Mateus’ in systems biology approaches to identify new proteins involved in polysaccharide utilization pathways. The experimental work will be strongly supported with molecular dynamics simulations, area of expertise of Dr. Lizana’s lab.
Contact:
Nicolò Maccaferri, Dept of Physics
André Mateus, Dept of Chemistry
Ludvig Lizana, Dept of Physics
7. Dissection of Zika virus maturation at molecular resolution
The genus Flavivirus harbours important arthropod-borne human pathogens, such as dengue viruses (DENV), tick-borne encephalitis virus (TBEV) and Zika virus (ZIKV). Within infected cells, virus particles assemble at the endoplasmic reticulum (ER) and mature in the course of their transit through the Golgi and Trans-Golgi Networks (TGN). A postulated critical step in the maturation process is a low-pH induced rearrangement of the viral surface proteins within the TGN. The proposed conformational change yields an arrangement of surface glycoproteins resembling the mature virus, but bound to an unprocessed precursor-membrane protein (prM) which is consecutively cleaved by host furin protease. Currently, our understanding of this maturation intermediate is limited to low resolution studies or extrapolated from isolated domains. Specifically, we do not understand how the furin site is exposed at the virion surface, a critical feature necessary to generate infectious virus. In the course of the project, the fellowship recipient will structurally dissect the steps of flavivirus maturation, thereby producing a more complete picture of the viral life cycle.
The recipient will benefit from the flavivirology expertise of the Anna Wernstedt lab and the structural virology expertise of the Max Renner lab. We also benefit from the Umeå Centre for Electron Microscopy (UCEM) which enables us to collect cryogenic electron microscopy (cryo-EM) data locally on state-of-art instruments.
Contact:
Anna Överby Wernstedt, Dept of Clinical Microbiology
8. Microbial chemical production via synthetic biology
Compared with other renewable energies, biofuel is storable and compatible with the current fossil fuel infrastructures, and it is therefore considered to play a major role in replacement of fossil fuels and mitigation of climate change. The project aims to develop programmable tools using novel chemo-optogenetic systems to rewire metabolic pathways in suitable microorganisms for efficient production of valuable chemicals as well as biofuels from renewable feedstocks. The engineering of metabolic pathways requires precise control over the levels and timing of metabolic enzyme expression. The project aims to establish new synthetic biology tools to rewire metabolic pathways based on chemo-optogenetic systems that can switch on/off genes with light. We plan to use these tools to increase production of value-added chemical compounds and biofuels as a sustainable energy source.
The Wu lab has developed a set of novel chemogenetic and chemo-optogenetic tools and used them in cell biology research (Angew Chem 2014, 2017, 2018, Nat Chem Biol 2019, Nat Meth 2023).
The Sellstedt lab is focusing on energy production mediated by microorganisms, such as hydrogen from actinobacteria, bioethanol from fungi and biodiesel from algae (Genome announc 2015, Nature 2002, Bioenerg Res 2012, Biotech Biofuel 2020).
The project will combine expertise from both labs using a combination of techniques such as molecular cloning, genetic engineering, biochemistry, microbial fermentation, cell imaging and analytical techniques.
Contact:
Anita Sellstedt, Dept of Plant Physiology
9. The effect of altered dNTP pools on genome stability and physiology
Maintaining proper levels of deoxyribonucleoside triphosphates (dNTPs) is crucial for genome stability. Dysregulation of dNTP pools is linked to a variety of diseases, but the precise pathological mechanisms remain unclear. This project aims to establish a new animal model that has the potential to transform our approach in studying dNTP metabolism. Our initial focus will be on developing the methodology of dNTP measurements in C. elegans, and thoroughly dissecting the physiological consequences of altered dNTP levels in C. elegans. Following this, we will extrapolate observations from C. elegans to the mouse model, thereby deriving conserved principles that underlie the effect of aberrant dNTP pools on genome instability and pathogenesis. Our ultimate goal is to elucidate the fundamental mechanisms underlying altered dNTP pools in human health and disease, thereby informing therapeutic innovations for treating these disorders.
The proposed research combines the distinct expertise of two labs, pioneering an innovative system for the analyses of dNTP metabolism. The Chabes lab possesses unique expertise in the field of dNTP metabolism, enabling them to perform sophisticated dNTP pool analyses. The Chen lab has extensive knowledge in genetics, behavioural analysis, and physiology in C. elegans.
Contact:
Changchun Chen, Dept of Molecular Biology
Andrei Chabes, Dept of Medical Biochemistry and Biophysics
10. Developing data-driven structural refinement of neutron reflectometry data to understand processes at biological membranes
Neutron reflectometry is a powerful tool in structural biology that can provide unique insight into processes at biological membranes. Because such processes are involved in e. g. infection, protein homeostasis, and cancer, structural characterization will be key in any medical advances. A major challenge and bottleneck in the field today is structural
interpretation of the data. Therefore, this project aims to develop computational tools to unveil the 3D architecture of key proteins during action in their membrane environment, and hence contribute to next-generation methodologies developed for the upcoming European Spallation Source (ESS).
The project will be supervised in the Andersson lab with focus on developing data-driven simulation approaches. A computationally efficient way to generate in-simulation calculated scattering profiles will be developed to bias simulations by a maximized-entropy approach towards a molecular-level structural solution. Preference will be given to candidates with experience in Python programming and/or MD simulation. The biological question to be studied is the molecular mechanism of how the Bcl-2 (B-cell lymphoma 2) protein family regulates cell survival by controlling mitochondrial membrane permeability, a regulation process believed to induce cancer growth as well as treatment resistance. The co-supervising Gröbner lab will provide NMR and neutron reflectometry data as basis for development of data-driven computer simulations.
Contact:
Magnus Andersson, Dept of Chemistry
Gerhard Gröbner, Dept of Chemistry
11. Adaptation and virulence-associated traits in bacteria interacting with Acanthamoeba castellanii
This project aims to enhance our understanding of how the amoeba Acanthamoeba castellanii interacts with Gram-negative and Gram-positive bacteria. Very little is known about the interactions between A. castellanii and the “ESKAPE” pathogens, a group of six highly virulent and antibiotic resistant bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). A. castellanii shares a habitat with many ESKAPE pathogens and thus acts as a putative source of emerging pathogenic features (e.g., antibiotic resistance), which pose a threat to human health. The main aims of the study are i) to explore the impact of the amoebic environment on bacterial lifestyle in ESKAPE pathogens using high-throughput imaging (HTI) screening, and ii) to understand the phenotypic and genomic changes associated with bacterial pathogens during long-term intra-amoebal host adaptation. The successful candidate will have access to state-of-the-art methods, including i) the SparkCyto imaging system, ii) Confocal microscopy, iii) Transmission electron microscopy (TEM), iv) Flow cytometry, and v) (Meta)genomic sequencing.
A. castellanii-ESKAPE interaction experiments will be carried out in Aftab Nadeem’s lab, while Laura Carroll's lab will utilize bioinformatic approaches to identify microbial genomic determinants associated with long-term intra-amoebal host adaptation and antimicrobial resistance phenotypes.
Contact:
Aftab Nadeem, Dept of Molecular Biology
Laura Carroll, Dept of Clinical Microbiology
12. Mode-of-action of a novel anti-Cryptosporidium compound family
Since 2009, we have been working on chemotherapy targeting C. parvum. In collaboration with Fabrice Laurent (INRAE, France), we have developed a highly effective chemotherapy. We have performed studies in infected cell culture, mice, as well in neonatal lambs, with very good results. The proposed project is to establish the mode-of-action on molecular level in C. parvum. This goes via following aims: 1) identify / ideate the target(s) of our candidate compounds by chemo-proteomic methods. 2) verify the target(s) by recombinant expression in heterologous host. 3) solve the structure (crystallography / EM) of the target with the molecule bound.
The postdoc will work in close collaboration with C. Hedberg’s current medicinal chemistry effort together with Fabrice Laurent, but will focus on biochemistry and structural biology, thus supported by L-A. Carlson and his group. The methods include chemical proteomics, cloning and expression of targets, and structure elucidation (crystallography / EM). F.L. supports the project with C. parvum expertise and preparative isolation of parasites. Over last five years, we have moved from medicinal chemistry, all the way to extensive in vivo studies in neonatal lambs. However, we need to sort out the mode of action of our compounds at a molecular level, which is the last piece of the puzzle. Further, our compounds are having the potential to reach market as a chemotherapy in commodity animals, as well as in man, suggesting importance of the work.
Contact:
Christian Hedberg. Dept of Chemistry
Lars-Anders Carlson, Dept of Medical Biochemistry and Biophysics
To qualify as a postdoctoral fellowship holder, the candidate is required to have completed a doctoral degree or a foreign degree deemed equivalent to a doctoral degree in the relevant field. This requirement is usually fulfilled after successfully completing all the requirements of the doctoral programme, including passing their dissertation defense. This qualification requirement must be fulfilled no later than at the time of the application closing date.
Candidates should have completed their doctoral degree, no more than three years before the application closing date. If there are special reasons, candidates who completed their doctoral degree prior to that may also be eligible. Special reasons include absence due to illness, parental leave, appointments of trust in trade union organizations, military service, or similar circumstances, as well as clinical practice or other forms of appointment/assignment relevant to the subject area.
The application should include:
1. A Curriculum Vitae
2. A motivation letter including research interests, qualifications, and motivation for applying for the position with the particular project idea selected from the list (max 2,000 characters with space)
3. A publication list including both published papers and preprints with web/DOI
4. A description of up to a total three (3) of your publications and/or preprints that you consider at present to represent your scientifically most valuable work, answering the following questions (max 3,000 characters with space):
a. Why you consider a particular publication to be the scientifically most
valuable?
b. What was your specific contribution(s) to this published research work?
c. What was your role in the manuscript writing and publishing of the
work?
5. Names and contact details of at least two references
6. A verified copy of doctoral degree certificate or documentation that attests completing all the requirements of the doctoral programme, including passing the dissertation defense.
The application must be submitted electronically.
Online application deadline: 29 october 2023
A short list of candidates will be invited to submit a short research proposal based on the project idea and to participate in the final interview. The interviews are performed by a panel of UCMR/UPSC researchers.
Date of final interview: 5 - 6 December 2023
Questions can be addressed to UCMR research coordinator Ingrid.soderbergh@umu.se
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