Project offers

IBG works in several ways to stimulate students themselves to create, develop and maintain relevant contacts with work-life. One part of this effort is to help you as a student to find suitable projects for research internships, degree projects, etc. In the project database, we publish project offers from academia, corporations and government agencies. We sometimes also announce different career-promoting events of a more general nature.

Some projects are described in English; others in Swedish. The current offers are listed below.

Offer a project

More information about projects

Project offers

Master thesis project: Investigating SAMD9/9L activity in cellular defense and growth control

Background:
SAMD9 and SAMD9L are evolutionary-conserved, interferon-stimulated genes, broadly expressed in human tissues. Variants in SAMD9/9L can potently disrupt protein translation and affect cell proliferation and have been associated to predisposition to myeloid malignancies.

Project description and aims:
In this project, we will use molecular and cell biology techniques to investigate the role of SAMD9/9L proteins in stress responses and address the following questions:
- What are the molecular mechanisms involved in SAMD9/9L activation and regulation?
- How are SAMD9/9L activation and regulation affected when mutant variants are expressed?

Desired skills:
Proficiency in English is essential and experience in cell culture or molecular cell biology techniques is advantageous for the position.

Duration:
The position is expected to last 6 to 12 months, starting in autumn 2024. The exact start date can be agreed upon based on the candidate's availability.

Location:
The research work will be conducted at Dept of Medicine, Karolinska Institute – Stockholm (see contacts below).

Contacts information:
Interested candidates should submit a complete CV and a motivation letter to:
Elisa Saccon (elisa.saccon@ki.se), Postdoctoral Researcher - Bryceson Lab,
Center for Hematology and Regenerative Medicine (HERM)/Neo, Dept. of Medicine, Huddinge - Karolinska Institutet

For any questions regarding the position, do not hesitate to contact us!
We look forward to your application!

Master thesis project: ‘Determining chemical stress effects in single phytoplankton cells’

Master-thesis background
Phytoplankton, oceanic photosynthetic unicells, contribute approximately 50% of the world’s primary production and form the basis of all aquatic food webs. The survival and growth of these vital ecosystem members is easily disturbed by external stress such as exposure to chemical pollutants (e.g. herbicides or oil spills).

Master-thesis project description and aims
In this master thesis, you will to make use of available hydrogel microfluidic devices to immobilize single cells of phytoplankton. You will learn how to make these devices and subsequently expose individual cells to defined gradients of chemicals. After training in automated microscopy, you will measure the effects of chemical exposure via imaging and analyze the resulting (image) data.

Methods
In this project, you will learn the following methods:
• Basic microbiology
• Microfluidic device construction and operation
• High-throughput automated fluorescence microscopy
• Analyzing single-cell growth and fluorescence in large image datasets

You should be a master-level student with some experience in e.g. image analysis, microscopy and/or phytoplankton and a keen interest for interdisciplinary science.

Students from all walks of life and backgrounds are welcome to apply!

Have a look at what we are up to: https://behrendtlab.com/

Interested? Please contact Lars Behrendt, lars.behrendt@scilifelab.uu.se. The scope of the project is a 45-60 hp master thesis

Master thesis project: ‘The effects of hypoxia on single phytoplankton cells’

Background
Phytoplankton, oceanic photosynthetic unicells, contribute approximately 50% of the world’s primary production and form the basis of all aquatic food webs. In the ocean phytoplankton are periodically exposed to oxygen (O2) at levels below their biological O2 demand (‘hypoxia’), which can negatively affect their photosynthesis, productivity and overall ability to cope with additional stressors (e.g. pollution, temperature).

Master-thesis project description and aims
In this master thesis, you will create hypoxic environments within (available) microfluidic devices and be responsible to establish gas mixing procedures and measure O2 levels. You will categorize the response of single phytoplankton cells to these hypoxic environments via advanced microscopic fluorometry imaging.

Methods
In this project, you will employ the following methods/equipment:
• Microbiological cultivation
• Automated gas mixing using high-precision mass flow controllers
• Oxygen sensing using optical O2 sensors
• Microfluidic devices for the creation of gaseous environments
• Advanced chlorophyll fluorometry imaging

You should be a master-level student with a strong background in (ideally) microfluidics, microbiology, finite-element modeling, O2 sensing and/or numerical methods.

Students from all walks of life and backgrounds are welcome to apply!

Have a look at what else we are up to: https://behrendtlab.com/

Interested? Please contact Lars Behrendt, lars.behrendt@scilifelab.uu.se. The scope of the project is a 45-60 hp master thesis.

Master thesis project: ‘The phenotyping of single microalgae for industry applications’

Background
Photosynthetic microalgae have strong potential as bioproducers of food, chemicals and fuels. Yet, despite their importance for industry applications, the systematic selection of single microalgae for improved productivity or stress resilience (‘phenotyping’) has remained largely inaccessible.

Master-thesis project description and aims
In this master thesis, you will (i) construct small-scale photobioreactors (‘Phenobottles’) and (ii) use PhenoChip to expose single microalgae of industrial relevance to varying levels of flue gas and categorize their response using advanced microscopic fluorometry imaging. Following single-cell selection, and if time permits, you will categorize the photophysiology of the resulting microalgae cultures in Phenobottles.

Methods
In this project, you will use the following methods/equipment:
• Microbiological cultivation
• Hardware engineering using Arduino, 3D printing and software scripting
• Microfluidic devices for the creation of flue-gas environments
• Advanced chlorophyll fluorometry imaging

You should be a master-level student with an engineering- or physics- background and (ideally) already possess basic knowledge in the 3D printing, arduino, microfluidics, finite-element modeling, and/or numerical modeling. Students from all walks of life and backgrounds are welcome to apply!

Have a look at what else we are up to: https://behrendtlab.com/

Interested? Please contact Lars Behrendt, lars.behrendt@scilifelab.uu.se. The scope of the project is a 45-60 hp master thesis.

Master thesis project: ‘Does light mediate bacteria-phytoplankton interactions?’

Master-thesis background
Phytoplankton, oceanic photosynthetic unicells, contribute approximately 50% of the world’s primary production and form the basis of all aquatic food webs. Phytoplankton blooms threaten ecosystems and support bacterial growth; dead phytoplankton sink and sequester CO2 in the ocean. The growth, death, and interactions of phytoplankton thus play a huge role in global biology and climate, but their basic biology remains surprisingly poorly understood.

Methods
In this project, you will learn the following methods:
• Basic microbiology
• High-throughput automated fluorescence microscopy
• Tracking single-cell movements in large image datasets
• Transferrable statistical and data science approaches

You should be a master-level student with some experience in e.g. image analysis, microscopy and/or phytoplankton and a keen interest for interdisciplinary science.
Students from all walks of life and backgrounds are welcome to apply!

Have a look at what else we are up to: https://behrendtlab.com/

Interested? Please contact Lars Behrendt, lars.behrendt@scilifelab.uu.se. The scope of the project is a 45-60 hp master thesis.

Master thesis project: ‘From environment to evolution: why retain genes in organelles?’

Master-thesis background
New evolutionary theory has proposed a link between an organism’s environment and the set of organelle genes that it retains – more dynamic environments favor more gene retention. We have an exciting and unique experimental setup with which to explore this “universal” theory. We can constrain individual cells in place and subject them to changing environments while simultaneously measuring their survival and performance with detailed microscopy. Using a selection of algal species, this project will test evolutionary predictions with single-cell measurements, both revealing new aspects of phytoplankton behavior and testing this grand-scale evolutionary theory.

Master-thesis project description and aims
In this master thesis, you will use our unique, cutting-edge automated microscopy in combination with advanced cell tracking to measure the effects of dynamic light exposure to different phytoplankton. The hypothesis is that organisms retaining more organelle genes will be relatively less challenged by dynamic environments.

Methods
In this project, you will learn the following methods:
• Basic microbiology
• High-throughput automated fluorescence microscopy
• Tracking single-cell movements in large image datasets
• Transferrable statistical and data science approaches

You should be a master-level student with some experience in e.g. image analysis, microscopy and/or phytoplankton and a keen interest for interdisciplinary science.
Students from all walks of life and backgrounds are welcome to apply!

Have a look at what else we are up to: https://behrendtlab.com/ and https://org.uib.no/stochasticbiology/

Interested? Please contact Lars Behrendt, lars.behrendt@scilifelab.uu.se. The scope of the project is a 45-60 hp master thesis

Immunoprofiling of different subtypes of lymphoma using multiplexed immunofluorescence (mIF)

The lymphoma tumor microenvironment (TME) which consist of fibroblasts, eosinophils, mast cells, macrophages, T-cells and other types of immune cells play an important role in tumor initiation, progression and resistance to therapy.

The aims of this study are:
-to investigate the expression of six biomarkers in different subtypes of lymphoma using mIF.
-to characterize the interaction between immune cells and tumor cells in microenvironment and correlate with clinical data.
-to map the distance between immune cells and tumor cells and investigate any correlation with clinical parameters.
We are looking for a motivated Masters student to join and continue our project which intends to (i) Further image analysis in QuPath software (https://qupath.github.io/) for cell segmentation, classification, scoring and distance analysis.
(ii) Subsequent data analysis and statistical analysis with R software

Duration
20-30 weeks (30-45hp).

Start
June-July or Autumn 2024.
For more information, please contact Jamileh Hashemi at Dept of Immunology, Genetics & Pathology (IGP) Uppsala University
jamileh.hashemi@igp.uu.se

Assistant needed for Experiment on Evolution at Range Margins

We are looking for an assistant to help taking care of a plant experiment on the evolution of range margins (see abstract below). This experiment is part of an international collaboration across 11 universities, led by John Pannell at the University of Lausanne, Switzerland.

Our site is near the Botanical Garden (near EBC) and the work can start as soon as possible to be continued until the end of September. Working on this project for part of the time is also possible, but preferably for longer periods or with only shorter interruptions. You will share the work with another person so both of you can do some travel during the summer.

We are looking for a well- organized and responsible person who has some experience with growing plants or with gardening. Botanical knowledge or a degree in biology are not required —detailed instructions will be provided.

The tasks include watering when needed (yes, especially when it is nice outside…), weeding and taking data once a week during June and July.

Watering will need to be done up to 3 times a week and takes up to 2-3 hours each time. In exceptionally hot weather, watering 4 times a week could be needed. During rainy weather, on the other hand, there may be no need to water but the experiment should be checked twice a week anyway. Weeding and the weekly measurement campaigns will take 1 to 4 hours per week, depending on how the experiment develops.

If desired, there is also the possibility work a with another project and to join a week-long measuring campaign at the experiment in mid-August.

Watering in intense sun should be avoided (best to water mornings or end of afternoon/evening), but else you are free to do this work during hours that suit you.

This work can be easily be combined with, for example, writing up a thesis, taking courses, or with other work at EBC or in the vicinity.

Please get in touch if you are interested!

Contact person: Sophie Karrenberg, sophie.karrenberg@ebc.uu.se

Student’s projects on acquired structure-functions of viruses

In the projects, students will learn following multidisciplinary techniques according to their expectations and interests. Molecular and Cellular biology: Cloning and mutagenesis, Fluorescent imaging, qPCR, Protein purification, and Cell culture. Virology: Virus detection and titration, Virus purification. Infectious cloning. In situ viral RNA hybridization. Endocytosis assays. Structural biology: Cryo-electron microscope imaging. Atomic modeling and the refinement of virus proteins. Structural analysis and rendering. Biophysics: DSF (Differential Scanning Fluorimetry), MST (MicroScale Thermophoresis)

We offer the studies on structural acquisitions in artiviruses such as mosquito Omono River virus (OmRV) and shrimp infectious myonecrosis virus (IMNV), and in human flaviviruses such as Dengue virus (DENV) that have originated from invertebrate flaviviruses such as Culex flavivirus (CxFV). To attest our hypothesis using mutagenesis and functional assays, we have generated the first infectious DNA clone of the OmRV (Wang et al., Virology 2022), IMNV (Hernandez et al., unpublished 2024) and CxFV (provided by NIID, Japan). Artiviruses pose tremendous economic losses in fishery industry due to their high-mortality to shrimps and fishes, while flaviviruses pose diverse health issues in domestic animals and humans, and therefore, the offered projects will lead to find new precautions of controlling these problematic viruses.

Degree Project Topic 1: Elucidating structure-functions of acquired surface crown protein in shrimp IMNV.
Degree Project Topic 2: Cryo-EM structural studies on CxFV and DENV single-round infectious particle (SRIP).
Research Training Topics: Depends on the students’ interests, we will offer studies on following topics.
• Cellular assays for testing in situ nascent single-stranded RNA transcription
• Cellular and molecular assays for testing virus transmission
• In vitro biophysical assays for testing particle stability and protein-protein interactions
• Structural studies on the virus transcription/replication in the atomistic levels

For further information, please contact Kenta Okamoto
Homepage: https://www.uu.se/en/department/cell-and-molecular-biology/research/molecular-biophysics/okamoto-lab
Email: kenta.okamoto@icm.uu.se (Kenta Okamoto, Research PI/Docent)

Master thesis projects fall 2024 at Gyros Protein Technologies

Background
Gyrolab technology offers fully automated miniaturized immunoassays simplifying the workflow with increased performance. Immunoassay techniques are widely used for determination of the concentration of biomolecules in wide range of applications in life science. It has been used in established areas like drug and vaccine development and in vitro diagnostics for decades, but also it is also used in new emerging fields including cell and gene therapy. The ELISA technique has been the
gold-standard but new more efficient techniques with improved performance are replacing this methodology.

Master thesis projects

Development and optimization of solid phases for microfluidic flow-through immunoassays

The Gyrolab platform is based nanoliter sized affinity columns for flow-through immunoassays. One critical component are the functionalized particles forming the affinity column. To further improve the performance of the immunoassay system particles with different characteristics will be produced. The work will include both surface functionalization of particles and evaluation of them in immunoassay applications.

Contact information
Contact person: Johan Engström
Email: johan.engstrom@gyrosproteintech.com

Assessing TBE risk in outdoor occupations

2024-05-13

Background: Tick-borne encephalitis (TBE) is a significant public health threat in regions with prevalent tick populations. In Europe, the number of TBE cases increased from 2012 to 2020, and there was a spread towards the northwest in continental Europe. TBE is a viral infection transmitted to humans through the bite of infected ticks, primarily in forested areas. Outdoor workers, e.g. forest workers, hunters, berry pickers and farmers, due to their occupation, under high risk of TBE infection. This project aims to synthesize existing research findings and insights related to TBE risks in these specific occupational groups.

Aim and Method:

Identify gaps in the existing literature concerning TBE vaccination rates, factors influencing coverage, and successful intervention strategies among these occupations.
Analyses the data that collected from surveys targeted at specific outdoor occupational groups to assess their coverage of TBE vaccinations and the policies implemented by their employers regarding vaccination.

Expected starting time: The work will be carried out at the earliest convenience or during the autumn semester 2024 with supervisors from Umeå University and the National Veterinary Institute (SVA) in Uppsala.

Requirements: We are seeking a student in the field of public health, occupational health, or a related medical program who possesses academic interests. The orientation of the work can be partially adapted to your educational background and interests. Literature assessment and data extraction will be included so you should master Excel or a statistical language. The student can either do a degree thesis (15 hp) or individual project-based work (15 hp). The student need to have some knowledge of Swedish since the survey data we collected is in Swedish.

Contact person:
Junwen Guo, junwen.guo@umu.se
Anna Omazic, anna.omazic@sva.se

Structure and function of proteins from an algal bloom-regulating virus

2024-05-07

This project focuses on studying the bloom-regulating virus Chaetoceros tenuissimus DNA virus type II (CtenDNAV-II), a ssDNA virus of the family Bacilladnaviridae. This virus encodes for three viral proteins (VPs): VP1, VP2 and VP3. Based on sequence and structural analysis, VP1 appears to function as a lipase, potentially involved in disrupting endosomal membranes during replication. VP2 is the capsid protein, and VP3 is the replication initiation protein (Rep) (2). We have previously determined an atomic structure of the capsid and a low-resolution model of the capsid interior. Our current objective is to deepen our understanding of the virus's replication cycle, including viral genome release, replication and virion assembly. To achieve this, we aim to conduct functional and structural studies of the individual viral proteins VP1-3. The student project can be adapted to the student's interests. It may involve cloning, expression, and purification of one or a few viral proteins, cryo-EM, crystallography, bioinformatic analysis and biochemical/biophysical characterisation.

Interested? Contact: Anna Munke, anna.munke@icm.uu.se
Lab of Molecular Biophysics, Department of Cell and Molecular Biology

Master thesis - Optimization of the production process of viral vectors in HEK293 cells

2024-05-06

Working at Cytiva in the Life Sciences industry means being at the forefront of providing new solutions to transform human health. Our incredible customers undertake life-saving activities ranging from fundamental biological research to developing innovative vaccines, new medicines, and cell and gene therapies.

We are looking for a Master Thesis student that will be working from the site in Uppsala and is available to start HT 2024

What you’ll do:

The project will focus on improvement of transient production of viral vectors in HEK293 cells. The overall aim of the project is to investigate if the current industry-standard and established procedures for viral vector production can be improved.
Independently solve problems of "trouble shooting character" in project work.
Maintain laboratory notebooks in accordance with company policy and legal requirements.
Present scientific and technical results internally, through oral and written communication in Swedish and English.
The master thesis work is expected to be performed onsite at Cytiva Uppsala.

Who you are:

To succeed in this position, you need to be result-oriented, flexible, and creative with a strong collaborative attitude.
We are looking for someone with the drive and capability to initiate, individually or in co-operation with others, plan, perform, analyze, document and present results to progress the project forward.
Available to take on a 20 week Master thesis project work during the autumn of 2024.

Interview and selection will happen continuously and the opening can be filled before last day of application. For further information about project, please contact hiring manager Henrik Johannesson, henrik.johannesson@cytiva.com We look forward to hearing from you!

Population genetic structure of the rare pine wood-living longhorn beetle Tragosoma depsarium in Sweden

2024-04-22

Population genetic structure of the rare pine wood-living longhorn beetle Tragosoma depsarium in Sweden – relations to forest composition and management history?

Would you like to contribute to our understanding of the effects of human activities on species genetic diversity? Why not join our team to study the impact of forest management on an endangered saproxylic beetle?

We seek motivated Masters students to join our project which intends to (i) describe the genetic diversity and population structure of T. depsarium in Sweden and (ii) determine if populations have suffered loss of genetic diversity due to forest management and isolation. During the summer 2021, the geographic distribution of the beetle in Sweden was assessed at a large scale through extensive pheromone trapping, and several populations were sampled along its distribution range. DNA was extracted for each individual and sent for RAD sequencing. The student will have the opportunity to analyse RADseq data from raw data to more advanced analyses, including population genetics. The study could be performed as a standalone bioinformatics study based on existing RADseq data, but also include hands-on experience with field sampling and DNA extraction techniques based on additional studies that will be performed in 2024. The results will be useful for implementing more efficient conservation management strategies for this beetle in Sweden.

Required qualifications and learning goals

You have a keen interest in evolutionary ecology, genetics and conservation biology. Through this project you have the opportunity to develop your skills and experience in practical entomology and field sampling, hands-on genetic techniques, bioinformatics, biological conservation, population genetics and other statistical analyses. You don’t need prior experience from bioinformatics. The work environment will be in English. The project has already started but you will have the opportunity to suggest studies and approaches of your own interest!

Contact Audrey Bras, Research Centre for Ecological Changes, University of Helsinki, Finland (audrey.bras@helsinki.fi) https://www.helsinki.fi/en/researchgroups/life-history-evolution/people or Mattias Larsson (mattias.larsson@slu.se) for more information.

Seasonal effects in the Przewalski's horse gut microbiome

2024-04-10

Tasks include:

Analyse microbiome DNA sequence data, interpret results, reading scientific papers, and write a thesis about the findings. The results will be published in a scientific journal.

Requirements:

An interest in learning about wildlife microbiomes and coding in R.

Duration:

20-30 weeks (30-45hp).

Start:

Flexible, June or Autumn 2024.

For more information, please contact Elin Videvall at Animal Ecology, EBC, Uppsala University (elin.videvall@ebc.uu.se).

Capercaillie and effects of predation on reproduction: an experimental test.

2024-04-08

Capercaille (Tetrao urogallus), a lek breeding species, is also considered to be an umbrella species. It has been declining over much of its range, where fragmentation and/or nest predation seems to be the main causes of this decline.

The aim of this project is to investigate potential predators, both mammals and birds’ effects on nests of the Capercaille. We will use an experimental approach and put out chicken eggs filled with plaster and painted with small dots to mimic the natural eggs of Capercaillie. We will put out the eggs in the field where we know there are Capercaillies leks. We will then go back to the experimental nests to observe if there have been any predation events on the eggs. If it is a mammal, we can observe tooth marks on the eggs which species that has been the predator (see photo below from an event from an earlier study).