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Islet Gene View 2.0 – Enhancing Pancreatic Islet Genomics for Diabetes Research

Are you passionate about bioinformatics, programming, and web development? Do you want to apply your skills to cutting-edge diabetes research? Join us in developing Islet Gene View (IGV) 2.0, an advanced interactive platform for exploring pancreatic islet genomics!

Why Study Pancreatic Islets?

Pancreatic islets are small clusters of cells in the pancreas. These cells play a crucial role in blood sugar regulation by producing islet hormones such as insulin and glucagon. Dysfunction in these cells leads to diabetes, a major global health challenge. Understanding islet biology is essential, but research is limited by the availability of samples that are typically sourced from deceased donors. That’s why it’s critical to maximize the accessibility and utility of existing data.

The Project: IGV 2.0

We are upgrading IGV to make pancreatic islet data more comprehensive and user-friendly for researchers. IGV 2.0 will integrate new donor datasets, enhance gene activity and genetic variation data, and introduce powerful new visualization tools for interactive analysis.

Who We’re Looking For

We are seeking a motivated Master’s student with:

  • Interest in bioinformatics, programming, and web development
  • Basicknowledge of R (with other programming languages is a plus)
  • Experience with R Shiny application development is a significant advantage
  • Curiosity and enthusiasm for analyzing biomedical data

You will be working within the Bioinformatics Unit at the Lund University Diabetes Centre (LUDC), based at CRC, Malmö. The project can begin as a research project in Spring 2025, with the option to transition into a Master’s thesis (2025-2026).

How to Apply

Send a brief statement of interest and your CV to Dmytro Kryvokhyzha (dmytro.kryvokhyzha@med.lu.se).

Current version of IGV:

Asplund O, et al. Islet Gene View – a tool to facilitate islet research. Life Sci Alliance. 2022. https://doi.org/10.26508/lsa.202201376

LUDC Bioinformatics Unit: https://www.ludc.lu.se/resources/ludc-bioinformatics-unit

Join us in advancing diabetes research through innovative bioinformatics!

March 5, 2025

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Bioinformatics

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Seaweed cultivation- food for the future

Are you interested in sustainable development and seafood of the future?
Souto Ocean Culture, Department of Process and Life Science Engineering at LTH, and Marint centrum are looking for an engaged student within the Tångkusten project.

About the project:
“Tångkusten” (Swedish for ’The seaweed coast’) is a regional development project dedicated to piloting seaweed cultivation in the Baltic Sea and assessing its market potential. A central element of the work in the project is the development of methods for reproduction and seeding of seaweed in a hatchery on land before they are deployed at sea. Hatchery methods have been developed in other countries for the seaweed species present in the southwestern Baltic Sea, but such methods require adapting and improving to better suit the specific conditions in the area we work in, which is the eastern coast of Skåne.
Currently no proven methods exist for cultivating seaweed in the Baltic Sea, which is precisely what the project is trying to address. We have been testing hatchery methods by adapting existing ones, which will constitute a valuable basis for the thesis work to build on. More recently, we have started developing methods for cultivation on land, based on the ‘germling clusters’ method developed for similar species in East Asia.

To improve the hatching, seeding and growth, we are interested in exploring the pulsed electric field (PEF) method. PEF involves the application of short, high-voltage electric pulses to cells, tissues, or other biological systems, leading to the increased permeability of cell membranes, a process known as electroporation. PEF has found widespread use in electrostimulation for various biological and industrial applications. A study on Nitzschia Closterium, a microalga, revealed that continuous and short-term direct current stimulation positively impacted growth and nutrient composition, suggesting promising applications for large-scale production.

Task description:
The aim of the master thesis (30-60 credits) work within the project is to explore the pulsed electric field method for reproduction, seeding and growth of two of our priority seaweed species, Ulva prolifera and U. intestinalis. The work will investigate whether PEF can affect any of the hatchery and/or land-based cultivation processes, including sporulation, settling and seeding of substrates, growth rates in free- and attached forms, among others.
The results of the work will be synthesized in a report, but the desired final product is one or several hatchery (draft) protocols that can be implemented in the company or at LU for subsequent commercial application.

What we offer:
The project has its base in Simrishamn, where we have a relatively simple indoors hatchery facility, which can be developed further if needed. We also have access to a small field lab at Marint centrum, with field equipment, scales, drying stove, freezers (-20º and -80º C), etc.
A smaller seaweed lab will be set up at Lund University.
But there will be office spaces, lunch-room, support and interaction with supervisors etc available at Marint centrum, which is located next door to the hatchery facility. It is therefore likely that the student working on this project will divide her/his time between Simrishamn and Lund.

Timeframe:
Starting in the spring of 2025.

Who are we looking for:
We are seeking a student with a strong interest in seaweed cultivation, the sustainable blue economy, and circular food systems. You are self-motivated, curious, and solution-oriented, with the ability to work both independently and collaboratively. Ideally, you have some experience in laboratory work and feel comfortable designing, assembling, and maintaining simple aquarium systems.

If you think you are the one we are looking for, please contact us for more information and for applying.

Contact
Federico Gómez Galindo, PhD
Professor of Food Engineering
Department of Process and Life Science Engineering
Division of food and Pharma
Lund University
federico.gomez@ple.lu.se
070 5805132

Josefine Larsson, PhD
Forskningskoordinator
Marint centrum Simrishamns kommun
Josefine.larsson@simrisham.se
Marintcentrum.se
0414-819190

February 24, 2025

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Biology

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Bees in space and time: Using historical samples to assess how bumblebees respond to land-use and climate change across Sweden

Over the last century, climate and land-use changes have altered ecosystems, shifted species distributions toward higher latitudes and altitudes, and led to changes in species’ phenology and morphology. In this project we focus on bumblebees, crucial to the pollination of wild plants and crops, and investigate the underlying mechanisms for why some species seem to cope with global changes, while others do not.

Background
Insect pollinators are integral to ecosystem functioning through pollination of wild plants and crops. In colder climates, bumblebees are particularly important due to their large body and facultative endothermy, which enables foraging in low temperatures and adverse weather conditions [1]. A large body size also enables foraging and dispersal over greater distances, which has become increasingly important due to loss and fragmentation of nesting and foraging resources driven by agricultural land-use changes. However, a larger body size also makes bumblebees sensitive to heat waves, which are predicted to increase due to climate change. Bumblebees are hence affected by two simultaneous environmental changes which seemingly push them to adapt in opposing directions: adapt to warming by decreasing in size, and to fragmentation by increasing in size. Long-term trends in body size have only been described for a few bumblebee species [2,3]. Not surprisingly, studies have struggled to draw conclusions about the contribution of individual environmental drivers because climate change and habitat loss have occurred simultaneously in temperate regions over the past centuries [4,5]. By assessing more species, with different ecological traits and niches, our understanding of how body size contributes to adaptation and persistence of species under global change can improve.

Aims and data collection
We will (i) study how body size of bumblebee species has shifted over time (>100 years) and across latitudes in Sweden and whether it is associated with species’ capacity to persist in changing landscapes and climate, and (ii) test whether such morphological shifts are plastic or due to genetic adaptation to new conditions, by exploring genetic changes across latitudes and elevation.
We will foremost make use of existing bumblebee collections in Swedish Natural History Museums (Lund, Gothenburg and Stockholm), possibly complemented by field sampling at around 6-10 sites across the country, from lowland to mountain areas. The body size of bees will be measured as the distance between the wing plates (Inter-Tegular Distance) and samples (a mid-leg) will be taken for further genetic analyses.

It is possible to do a shorter project (30 credits) that only uses museum material and focusses on the morphological shifts, but also to do a longer project (45-60 credits) and include fieldwork to obtain contemporary samples as a comparison. Depending on your interests and skills, it is also possibility to include assessment of genetic adaptation.

Contact: Anna Persson, anna.persson@cec.lu.se, Bengt Hansson, bengt.hansson@biol.lu.se

References

  1. Maebe, K., et al., Bumblebee resilience to climate change, through plastic and adaptive responses. Glob. Change Biol., 2021. 27(18): p. 4223-4237.
  2. Nooten, S.S. and S.M. Rehan, Historical changes in bumble bee body size and range shift of declining species. Biodiv. Conserv., 2020. 29(2): p. 451-467.
  3. Gérard, M., et al., Shift in size of bumblebee queens over the last century. Glob. Change Biol., 2020. 26(3): p. 1185-1195.
  4. Kelemen, E.P. and S.M. Rehan, Opposing pressures of climate and land-use change on a native bee. Glob. Change Biol, 2021. 27: p. 1017–1026.
  5. Gérard, M., et al., Impact of landscape fragmentation and climate change on body size variation of bumblebees during the last century. Ecography, 2021. 44(2): p. 255-264.
February 24, 2025

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Biology

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Genetic variants and alternative splicing in breast cancer

Modern genomics methods produce vast amounts of genetic data, but we have limited ability to interpret the effects of sequence variation on gene expression, protein function and the individual’s phenotype. This is a problem in clinical genetic testing, e.g. for diagnosis of hereditary breast cancer, where many variants are classified as ‘variant of unknown significance’ (VUS) for lack of functional information. Our aims are to understand how variants in regulatory motifs control alternative splicing and intron retention and to use this information to develop accurate methods for identification of functional variants. We are analysing alternative splicing and its association with germline variants and somatic mutations RNA and DNA sequencing data for thousands of women with sporadic or familial breast cancer.

 

Contact: Helena Persson, helena.persson@med.lu.se, http://research.med.lu.se/helena-persson

February 11, 2025

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Molecular Biology

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Characterization of bacterial virulence factors and their host-interactomes

During an infection, pathogens circumvent the host’s immune defenses via the expression of highly evolved virulence factors which hijack and re-wire the host’s molecular systems. At the same time, host proteins and cells of the innate and adaptive immune system bind to bacterial surfaces and virulence factors to neutralize the invading pathogens and prevent infection. An in-depth understanding of these molecular level events is not only essential for the understanding of disease on-set, progression, and host-immune evasion but also for the discovery of new targets for therapeutic intervention, and for the development of biotechnological applications.

 

Two tools have revolutionized structure-based discovery of novel proteins, AlphaFold and Foldseek. AlphaFold does very accurate predictions of 3D structures using AI, whereas Foldseek can be used to identify predicted or determined structural homologues with very low amino acid sequence identity. We have used AlphaFold and Foldseek to identify putative and novel virulence factors expressed by different human pathogens and are now looking for a motivated MSc student (45 of 60 hp) to characterize one of these.  

 

The project is centered around the characterization of the host interactomes of these virulence factors by quantitative affinity-purification mass spectrometry (MS) and structural proteomics (cross-linking and hydrogen-deuterium exchange (MS)). We are also interested in discovering whether the virulence factors contribute to further virulence mechanisms, such as host DNA degradation, which is a common trait to several of the enzymes we are currently studying. In addition to MS, the project will include methods in basic biochemistry, such as SDS-PAGE and western blot analysis, ELISA-based assays, nuclease activity assays etc…

 

We are looking for a student with experience in functional protein characterization and some of the biochemical methods listed above. No previous experience in MS or MS data analysis is required.

 

Our research group in Structural Infection Medicine is located at the Division of Infection Medicine at BMC in Lund. The group consists of a PhD student, who will be the co-supervisor of this MSc thesis and MSc students. The research group is working closely together with five other research groups, comprising of clinicians, preclinical researchers, PhD students, research engineers and technical laboratory personnel.

 

For more information, please contact the group leader Lotta Happonen, lotta.happonen@med.lu.se.

February 11, 2025

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Molecular Biology

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Goal direction behavior and its neuronal organization

To navigate effectively, an animal must align its body with its intended target and adjust its course as needed. In insects, this critical navigational process is governed by specific neurons located in a brain region known as the central complex (CX). However, the precise roles of CX subregions, such as the noduli, remain to be thoroughly explored. Interestingly, the development of noduli in termites seems to be associated with their transition from nymphs to reproductive forms, providing us with a unique opportunity to analyze how goal-oriented movements are generated by the neural circuits of the CX, both with and without noduli, which our project aims to investigate.

We will analyze the goal directed behavior of various termite castes and correlate the behavior with the presence or absence of CX noduli in a controlled laboratory setting. This research aims to uncover the evolutionary shift in termites from a primitive state (without noduli) to a more advanced CX, paralleling the significant evolutionary transition from wingless to winged insects.

 

Methods: The student will conduct behavioral analyses utilizing machine learning-based automatic tracking. These behavioral observations will be integrated with a quantitative 3D neuroanatomical analysis of termite brains through immunohistochemistry and confocal microscopy.

 

We are able to host two bachelor’s students.

 

If you are interested in termites, insects and the topic itself get in touch with:

 

Dr. Ayse Yilmaz-Heusinger, Lund Vision Group

Email: ayse.yilmaz-heusinger@biol.lu.se

February 7, 2025

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Biology Molecular Biology

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Use of synthetic biology tools for the production of therapeutic recombinant antibodies

We are looking for highly motivated students to be part of a project to optimize a cost-effective pipeline to produce recombinant humanized antibodies in mammalian cells as diagnosis tools for immune inflammatory responses and complement pathway related.

 

Brief project description

This master’s project is part of a larger PhD project for optimizing the affinity of recombinant antibodies and designing new antibody formats, such as nanobodies, ScFv, and full antibodies, with a higher half-life and better yield. This includes the discovery of new antibodies from immunized mouse and further high-throughput screening by the cloning antibody tool. The project involves the use of sequencing techniques from antibody-expressing cells, Golden-Gate-based molecular cloning, plasmid design, PCR amplifications, cell culture for expression in CHO cell lines and purification techniques. Once this pipeline is well established and optimized, the antibodies will be characterized and tested in ELISAs and functional assays for diagnostic, experimental and potentially therapeutic potential. We will investigate the complement system activation and inhibition related to these diseases, producing recombinant antibodies against complement proteins such as C1s, MASP-2, Factor D or C5aR1. The project also allows the student to be part of a publication to disseminate the results derived from this research.

 

Who are we looking for?

We seek an excellent student with a good understanding of biochemistry and molecular biology. Previous experience in a laboratory working with microbiology, cell culture and methods such as PCRs, ELISAs and Western blots will be valued, but it is not a requirement. We prioritize proactive students with teamwork skills and enthusiasm to learn with great interest and motivation in biomedical research.

 

Who are we?

We are a research group of around 15 people led by Professor Peter Garred and part of the Department of Clinical Immunology at Rigshospitalet and University of Copenhagen. Our focus is innate immunity, with a particular interest in the complement system’s role in health and disease. The group atmosphere is international, informal and friendly, and we are prepared to give you substantial supervision and support regarding your project.

 

Contact:

Group leader Professor Peter Garred

peter.garred@regionh.dk.

Please include your CV and transcripts in the email.

February 7, 2025

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Molecular Biology

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Developing Diagnostic Tools for Complement-Mediated Diseases

Are you passionate about immunology and biomedical research? This master’s project offers a hands-on opportunity to contribute to cutting-edge diagnostics for complement-mediated diseases.

The complement system (CS) is a key part of our innate immune defense, responsible for identifying and eliminating harmful pathogens and defective cells. However, the dysregulation of the CS and excessive inflammatory reaction have been linked to several diseases, such as IgA nephropathy, metabolic diseases and congenital disorders. Thus, there is a burgeoning need to develop new diagnostic tools. 

In this project, you will:

🔬 Develop and characterize monoclonal antibodies against complement factors.

🧪 Design and optimize immunoassays for detecting complement components as disease biomarkers.

🧬 Gain experience with techniques in molecular and cellular biology, such as cell culture, recombinant protein and antibody production, purification techniques, ELISA, and western immunoblotting, among others.

Your research will contribute to the development of novel diagnostic and therapeutic approaches, with the potential for publication in high-impact journals. This is an excellent opportunity to expand your scientific expertise, work in a collaborative research environment, and make a real impact in biomedical science.

If you are eager to develop innovative diagnostic tools and gain valuable lab experience, we will be very happy to hear from you! 

Who are we?

We are a research group of around 15 people led by Professor Peter Garred and part of the Department of Clinical Immunology at Rigshospitalet and University of Copenhagen. Our focus is innate immunity, with a particular interest in the complement system’s role in health and disease. The group atmosphere is international, informal and friendly, and we are prepared to give you substantial supervision and support regarding your project.

Contact:

Group leader Professor Peter Garred

peter.garred@regionh.dk.

Please include your CV and transcripts in the email

February 7, 2025

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Molecular Biology

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Plants in urban greenspaces

Urban vegetation is crucial to sustain urban biodiversity and ecosystem services to urban inhabitants (Gómez-Baggethun & Barton 2013), e.g. temperature and water regulation and space for recreation. Insect pollinators, such as bees, rely on flowering plants for foraging. Although in decline globally, they can sometimes find refuge in urban greenspaces, especially in brownfields and allotment gardens (Baldock 2020). Urban plant composition is therefore important to support pollinator populations. Species composition of urban greenspaces is, however, largely determined by aesthetic preferences and the availability in garden centres (Garbuzov, Alton & Ratnieks 2017; Avolio et al. 2018). This means that, although plants may be selected for their flowers, they do not necessarily provide pollen and nectar resources for insects (Garbuzov & Ratnieks 2014). Studies even show that spontaneous native vegetation can attract more pollinators than purposely planted species (Zaninotto, Fauviau & Dajoz 2023).

In this project, you will study the species composition of urban flowering plants in Malmö, using existing data on flowering plants in public and private urban greenspaces (private backyards/gardens, allotments, parks and green roofs), surveyed May-July/August. You will compile data on plant traits relating to, for example, pollen and nectar production and phenology (seasonality).

Potential research questions are:

  • How does greenspace type affect the value of the plant community for pollinators
  • How large is the contribution of spontaneous plant species to pollinator resources?
  • Are there differences across the season for the above?
  • What would a truly “pollinator friendly” planting look like?

This project can be adapted to 15-30 credits.

Contact: Anna Persson (anna.persson@cec.lu.se)

References
Avolio, M.L., Pataki, D.E., Trammell, T.L.E. & Endter-Wada, J. (2018) Biodiverse cities: the nursery industry, homeowners, and neighborhood differences drive urban tree composition. Ecological Monographs, 88, 259-276.
Baldock, K.C.R. (2020) Opportunities and threats for pollinator conservation in global towns and cities. Current Opinion in Insect Science, 38, 63-71.
Garbuzov, M., Alton, K. & Ratnieks, F.L.W. (2017) Most ornamental plants on sale in garden centres are unattractive to flower-visiting insects. PeerJ, 5, e3066.
Garbuzov, M. & Ratnieks, F.L.W. (2014) Listmania: The Strengths and Weaknesses of Lists of Garden Plants to Help Pollinators. BioScience, 64, 1019-1026.
Gómez-Baggethun, E. & Barton, D.N. (2013) Classifying and valuing ecosystem services for urban planning. Ecological Economics, 86, 235-245.
Zaninotto, V., Fauviau, A. & Dajoz, I. (2023) Diversity of greenspace design and management impacts pollinator communities in a densely urbanized landscape: the city of Paris, France. Urban Ecosystems, 26, 503-515.

February 6, 2025

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Biology Short projects

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The Wood White and the Cryptic Wood White butterflies: species differentiation through morphometrics and DNA barcoding

The Wood White – Leptidea sinapis (Linnaeus,1758) – and the Cryptic Wood White – Leptidea juvernica Williams,1946 – are two species of butterflies found in Sweden and distributed more broadly in Europe. Currently the only way to conclusively separate the two species morphologically is by comparing their genitalia, which is a time consuming process, and not something that can be done quickly in the field. Various butterfly collectors swear that they can separate the two species by their wing shape and/or wing markings, but this has not been rigorously tested. The species can be easily separated using the DNA barcoding.

The Biological Museum, Lund University, has an extensive collection of Leptidea from Sweden with over 800 specimens. The focus of the project will be on taking photographs of the wings for a morphometric examination as well as collecting new specimens for the morphometric analysis and for DNA barcoding.

Based on the results of the morphometric analysis, the different butterfly groupings will be DNA barcoded and the genitalia will be dissected from some selected specimens. That way we will test the hypothesis that it is possible to separate these two species based on their external morphology, and if this is indeed the case, many butterfly collectors will be grateful.

 

Required knowledge: We will teach the student how to carry out all the steps necessary to complete this project. The project will involve working with pinned insect specimens and their data, specimen photography and morphometric analysis, specimen collection in the field for DNA work, DNA extraction from the specimens, PCR, basic phylogenetic inference.

 

Bachelor’s or Master’s level: 30-60 cr (the project is scalable depending on the student’s needs)

 

Starting date: Flexible.

 

Supervision: Jadranka Rota, Biological Museum and Masahito Tsuboi, Division of Biodiversity and Evolution

https://portal.research.lu.se/en/persons/jadranka-rota

https://portal.research.lu.se/en/persons/masahito-tsuboi

 

Contact Jadranka Rota jadranka.rota@biol.lu.se for more information and planning

 

 

 

February 5, 2025

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Biology Short projects

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