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.
Project offers
Internship: Race for the Baltic
We are now looking for a Project Management Intern who wants to be part of our journey during spring 2025. Your role will be to work together with our project managers in international projects working for a healthier Baltic Sea. You like the idea of digging deep into environmental issues and supporting a fast-paced team. You are proactive and analytical, with a keen interest in cross-sector collaboration and results-oriented projects.
More information: https://www.raceforthebaltic.com/internship-spring-2025
Internship: Cyprus Wildlife Research Institute
We offer a variety of hands-on internship opportunities that allow students to develop practical skills in wildlife care, rehabilitation, ecological monitoring, and content creation. We would like to extend these opportunities to students from your university. A comprehensive list of programs, requirements, and further details is available at https://v.cwri.net/.
As of October 2024, we have proudly hosted 196 volunteers from 37 different countries, and we are eager to welcome more students who are passionate about working with wildlife and gaining international experience. Our placements are compatible with Erasmus+ programs, allowing students to use Erasmus+ scholarships to cover living expenses. Additionally, for a reasonable fee, we can arrange accommodation and airport transportation if needed.
Ing. Dominika Knazovicka
Cyprus Wildlife Research Institute
MSc Student Project: The Impact of Cellular Environment on IAPP Fibril Polymorphism - Cryo-EM Structural Analysis
This project explores how the intracellular environment affects hIAPP fibril polymorphism. Using the INS1-E cell line, a rat pancreatic β-cell model, we will induce hIAPP overexpression, extract cellular amyloid fibrils, and use these to seed in vitro aggregation. Structural analysis of these fibrils via cryo-electron microscopy (cryo-EM) will provide critical insights into the influence of the cellular milieu on fibril formation and morphology.
Project aims and description
1. Cell Culture and Transfection
The student will culture mammalian INS1-E cells under optimal conditions and induce hIAPP overexpression using plasmid transfection. Controls such as empty vectors will validate the experiments.
2. Amyloid Extraction and Validation
Amyloid fibrils will be extracted from lysed cells using detergent-based protocols and purified through ultracentrifugation, filtration or immunoprecipitation. Validation will be performed using Thioflavin T fluorescence or Congo red staining assays.
3. Seeding and Aggregation Assays
Cellularly derived fibrils will seed in vitro aggregation of monomeric hIAPP. Aggregation kinetics will be monitored using Thioflavin T fluorescence assays to evaluate the seeding ability and polymorphism of the fibrils.
4. Cryo-EM Analysis
Both cellularly derived and in vitro seeded fibrils will undergo cryo-EM for structural analysis. Samples will be vitrified, and high-resolution imaging will enable detailed 2D classification and 3D reconstruction to investigate polymorphic structures.
5. Biochemical and Biophysical Characterization
Techniques like SDS-PAGE, Western blotting, circular dichroism spectroscopy, and atomic force microscopy will complement structural findings, offering insights into fibril integrity and morphology.
6. Data Analysis
Structural data will be analyzed to compare cellular and in vitro fibrils. Aggregation kinetics will be statistically evaluated to correlate structural features with functional behavior.
Learning Outcomes
The student will gain hands-on experience in cell biology, biochemistry, biophysics, and structural biology. Skills include:
• Culturing and maintaining INS1-E cells.
• Extracting and purifying amyloid fibrils.
• Conducting Thioflavin T fluorescence measurements.
• Preparing and analyzing samples via cryo-EM.
• Interpreting structural and kinetic data to draw conclusions about fibril polymorphism.
Contact
If this project interests you, please contact:
• Dr. Michal Maj (michal.maj@kemi.uu.se)
• Dylan Valli (dylan.valli@kemi.uu.se)
Location: Department of Chemistry - Ångström, Uppsala University.
Root fusion in plants – establishing a model system using strangler figs
In nature, natural grafts can form when roots press against each other and create a functional fusion. Such root fusions can for example transfer carbohydrates to support shaded trees.
Plants of the genus Ficus is promising as a root fusion model system because a subset of Ficus species, the strangler fig trees, create abundant root grafts as they grow. Strangler fig trees start life in the canopy as epiphytes, and send roots down to the forest floor. The roots thicken and fuse with each other, producing a strong fused mesh surrounding the host tree; see for example here for some typical photos: https://maginams.ca/strangler-figs/ Strangler fig trees fuse their roots (presumably) to create sturdy support and to strangle their host tree to death so that they can take over that spot of sunlight in the canopy. We plan to use the exceptional root fusing ability of strangler figs to establish a root fusion model system in the lab, and study the fusion process in detail. Our pilot studies suggest it would work well in the lab.
The master project would be mostly lab based, and involve growing plants, setting up experiments, and a lot of histology and imaging. You would establish a model system for studying root fusion in the laboratory, and describe in detail how fusion occurs within a plant individual for one or two species. Imaging would be done initially by confocal microscopy or light microscopy, then you would prepare thin embedded sections using a microtome for detailed morphology analyses such as cell division patterns and vascular differentiation. Fluorescent dyes can be applied and movement of the dye followed. If time allows you could also set up experiments to test other questions, such as to what degree fusion between different individuals and species is affected by how closely related they are, or whether you could produce root fusion in the lab in other species such as Norway spruce or Scots pine.
Lab work will be in Charles Melnyk’s lab at SLU Uppsala. Supervision will be by Charles Melnyk (SLU Uppsala; https://melnyklab.com/) and Charlotte Jandér (UU; https://sites.google.com/view/charlottejander/home).
Project length: 30-60 hp.
Start date: Flexible; as soon as possible works well.
Contact: If interested, please contact charlotte.jander@ebc.uu.se
What makes a good learner?
The evolutionary ecology of cognition and memory in Caenorhabditis worms
We have two MSc projects (45-60 credits each) to investigate the evolution and ecology of cognition and transgenerational epigenetic memory in Caenorhabditis worms. With as few as c.a. 300 neurons, worms demonstrate a wide range of learning capabilities; they can associate olfactory cues with stress, learn to avoid pathogens, and can transmit their learned memory to their offspring (how convenient!). However, the regulation of their cognitive capacity remains unclear, and the ecology that facilitates the evolution of epigenetic memory inheritance is unknown.
Project 1: Being good at learning may seem universally beneficial. But is it? First, you can make mistakes. Second, there may be physiological costs associated with learning, forming memories, and keeping your nervous system in peak condition. Our recent results indicate that learning is regulated by the RNA interference (RNAi) pathway, but the capacity for RNAi-regulated learning may come with a potential fitness cost. This MSc project aims to investigate the costs of the active process of learning and memory inheritance using several RNAi mutants of Caenorhabditis elegans.
Project 2: C. elegans worms learn to avoid pathogenic food (Pseudomonas bacteria) and can transmit the learned avoidance through epigenetic mechanisms (in this case, non-coding RNAs) to naïve progeny that have never encountered the pathogen. Such epigenetic memory inheritance has important implications in evolution, but its ecological relevance remains unclear – can other Caenorhabditis species that occupy different ecological niches inherit pathogenic memories? And how does worms’ microbial environment affect their response to pathogenic learning? This MSc project is part of a larger study, where we aim to investigate learning and epigenetic memory inheritance across Caenorhabditis species, as well as explore the interactions between the worms' microbial environment and epigenetic memory inheritance.
Starting date: flexible
Required qualifications: Strong interests in evolutionary biology. No specific experience required.
Contact
Hwei-yen Chen, hwei-yen.chen@biol.lu.se
Martin Lind, martin.lind@hh.se
Martyna Zwoinska, martyna.zwoinska@ebc.uu.se
Investigating stability of enzymes and antibody-oligo conjugation
Project summary
The product development team at Navinci is currently seeking master thesis/degree students for spring 2025. During the time at Navinci, the candidate will work independently with a defined task and project goal. Navinci develops products to study protein interactions in tissues and cells. It is important that Navinci’s products are high quality, stable and robust in the hands of the customer. To meet this quality standard, all components must be stable during all stages of their cycle, from production to shipping and in the hands of the customer. In this project, the student will look at the stability of various components of the kits and propose improvements that can be made to enhance the product. The student will primarily work on the stability of enzymes and antibody-oligo conjugation.
The student will also learn what it is like to work at a life science company and will be a part of a larger team of scientists, engineers and product developers, taking part in meetings and the daily routines surrounding company activities. As Navinci is a smaller company where Research and Development, Production, and Sales and Marketing teams closely interact, it is a great chance for the student to learn about the inner workings of a biotech company. We are seeking candidates who are interested in working at a company, and who have an open attitude and are eager to learn new things.
All projects require experimental planning, lab work, analysis of data via microscopy and the possibility to run instruments for automation. The data from all projects is confidential.
Requirements:
- Basic knowledge and understanding of antibodies, proteins and molecular technologies
- Excellent written and oral English skills
- Strong capacity for organization and work
- Experience with lab work and pipetting
Willingness and ability to learn how to work with complex instrumentation and computerized systems such as microscopes and automated stainers.
During the selection process the following aspects will be considered:
- Recommendation letters certifying laboratory skills (Industry or academica)
- Degree grades
- Other relevant aspects of the candidate’s previous experiences
Submit your interest and CV to:
Benchmark the performance of benchmark classifiers
Background
Metagenomic methods have the potential to identify pathogens in case of suspected infection in an untargeted manner without prior knowledge. Metagenomics is rapidly moving from research applications to clinical diagnostics. The recent SARS-CoV-2 pandemic has illustrated the importance of preparedness for rapid identification of emerging pathogens. In an established collaboration between SciLifeLab and the Karolinska University Hospital, as part of Genomic Medicine Sweden (GMS) [1], we have developed a metagenomic assay for use in clinical infection diagnostics and we are presently working on transferring the assay to Oxford Nanopore for shorter turn-around time.
Project description
This master’s project will involve setting up simulated Oxford Nanopore data using Meta-NanoSim [2] or data available from the CAMI challenge [3], which will then be analyzed with various long reads taxonomic classifiers. The aim is to benchmark the performance of these classifiers, evaluating their accuracy in taxonomic profiling based on simulated nanopore data. This work will not only provide insights on classifier performance but also contribute to real-world clinical applications by validating these classifiers on clinical datasets.
In addition to evaluating classifiers, the student will have the opportunity to contribute to the open-source nf-core/taxprofiler pipeline [4] within the nf-core community [5], using the Nextflow workflow manager [6].
In this project, you will learn or improve skills in bioinformatics tool development, Nextflow pipeline development, and open-source collaboration. Additionally you will gain insights into the challenges associated with metagenomics analysis.
Contact
Supervisor: (lili.anderssonli@ki.se), Sofia Stamouli (sofia.Lili Andersson-Li stamouli@ki.se)
Group leader: Tobias Allander (tobias.allander@ki.se)
Read more in this PDF Pdf, 116 kB.
Interactions between dissolved organic matter and PFAS during drinking water treatment
Masters Project
Department of Ecology & Genetics, Limnology Department (Evolutionary Biology Center)
Supervisor: Dolly Kothawala (dolly.kothawala@ebc.uu.se; https://kothawala.weebly.com/)
Collaborations with Lutz Aherns (SLU, Ultuna), Philipp Wanner and Tabea Mumberg (Gothenburg University) and multiple drinking water suppliers.
Background
Per- and polyfluoroalky substances (PFAS) are human-made chemicals that have been used in industry and household products since the 1940’s. These chemicals are used in a wide range of applications including to make cooking materials non-stick, make fabrics stain resistant and are found in the foam used for firefighting. PFAS are now found everywhere in the environment, in water, air, soil and fish and long-lasting chemicals that persist in the environment. There are more and more studies linking PFAS exposure to harmful health effects in humans as well as other animals in the environment and thus there are efforts to reduce their concentrations in treated drinking water.
Project Description
This master’s project will involve setting up soil columns with the sand used for artificial infiltration. The lab study will attempt to mimic the same sand and environmental conditions found at infiltration sites at two drinking water treatment plants. The study will involve testing the removal efficiency of both PFAS and DOM under different conditions. This includes different levels of DOM and different sources of DOM as well as different temperatures typical of Swedish seasons. All the experiments will be developed in collaboration with partners at Gothenburg University, the Swedish University of Agricultural Sciences (SLU, Ultuna) and drinking water providers with similar set-ups.
Desired Qualifications
We are looking for an enthusiastic individual with a background in environmental studies, ecology and/or engineering who is interested in societally relevant issues such as drinking water quality. The master’s candidate will help design and build the experimental column set up and analyze water for DOM analysis, and help with preparing samples for PFAS analysis. The candidate would ideally have a drivers license (but not necessary) and be able to work collaboratively with as part of research team.
Start Time
We are looking for a Master’s student to start working on the project as soon as possible.
Contact Information
Please contact dolly.kothawala@ebc.uu.se for more information.
Leveraging AI and big data to build a state-of-the-art transcriptomics-based aging clock
Background
Big datasets are increasingly becoming available in biology, enabling the development of predictive models of unprecedented accuracy. In the field of aging, this has led to the emergence of “aging clocks” which can predict individuals’ ages using various types of omics data. Transcriptomics-based aging clocks hold great potential due to the large number of transcriptomic datasets. However, the lack of robust and accurate models has so far hindered their widespread applications. Our laboratory has developed a state-of-the-art transcriptomics-based aging clock, demonstrating its ability to predict cellular age across different datasets. Nonetheless, further improvements can be made by gathering more training data and testing additional modeling strategies.
Project aims and description
First the student will gather and preprocess relevant datasets to expand our existing transcriptomic database. Second, he will test and compare different modeling strategies, benchmarking them with published models. Third, and only if time permits, the student will apply his new state-of-the-art model to large scale Perturb-Seq datasets to map the genetic landscape of cellular age.
Contact
If this sounds of interest to you, don’t hesitate to contact:
Supervisor: Jérôme Salignon (Staff Scientist), jerome.salignon@ki.se
Group Leader: Christian Riedel, christian.riedel@su.se
Location of the internship: Dept. of Molecular Biosciences, The Wenner-Gren Institute | Stockholm University, Sweden
How do soil microbes acclimate – or adapt – to decades of altered agricultural practices
Excessive fertilization of agricultural lands leads to numerous undesired consequences such as nitrogen leaching and nitrous oxide emissions. Have you ever wondered how doing this for decades affects the ability of microbial communities to remove nitrogen from the soils? Do they do it better than expected, or do they do it worse? Is this due to shifts in microbial community composition, or do microbes evolve in response to fertilization? Much of the work to date has focused on reduced cooperation between legumes and their nitrogen-fixing bacteria, or on reduced decomposition by fungi in forest ecosystems, and indicates both changes in community composition and evolution of microbes can happen. This project will focus on denitrifier bacteria responsible for converting nitrite into nitrous oxide and dinitrogen using soils derived from long-term field experiments run by SLU. It could address questions including: How does chronic nitrogen addition affect the sensitivity of the resultant microbial community to further nitrogen fertilizer addition? Does it make them better at handling further large inputs of nitrogen? Or how many seasons of chronic nitrogen enrichment does it take for the denitrification metabolism of bacteria to change?
Depending on the interests of the student and their availability during the internship period, this project may involve isolation, identification and characterization of novel bacteria, assaying soil microbial activity, and working with anaerobic bacteria. This project could be made suitable for either a bachelor or masters project.
This project can begin in spring 2025.
Contact: If you are interested in this or a related topic, please contact Grace Pold, grace.pold@slu.se