Biology Education

Department of Biology | Lund University

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Nocturnal bird migration under the sun

Bird migration is to a large degree a nocturnal affair, as many passerines start their migratory flights soon after sunset and fly until early morning. It is however unclear how this pattern is affected by the large differences in night length that birds experience at different latitudes and with seasonal progression. When migrating at high latitudes the midnight sun means that there is no “night” at all for parts on the year, so what does this mean for the nocturnal schedule?

Using weather radar data we can identify the start and end of bird migratory movements at 14 different sites in Sweden, ranging from Kiruna to Ängelholm. Comparing the initiation and cessation of migration at different night lengths can give us clues to what cues birds use to initiate migration, and why so many birds migrate during night at all. I am looking for a motivated student analyze weather radar data of migratory activity in relation to night length at different sites and times.

Required knowledge: Comfortable with, or willing to learn, to analyse data in either excel or R.

Length of the project:  MSc or BSc, flexible depending on depth of analysis

Start date: Flexible

Contact info: Cecilia Nilsson, Cecilia.nilsson@biol.lu.se

http://cnilsson.science

https://portal.research.lu.se/sv/persons/cecilia-nilsson

 

 

February 3, 2025

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The crossing scheme to generate Drosophila melanogaster flies with brain tumor

Tumors are associated with elevated mutation rate. In Drosophila melanogaster flies, it is possible to use transgenic strains to tune the mutation rate in specific tissues, like the nervous system or intestine, so that the flies grow tumors in specific tissues. This is a valuable system to study the physiology and the impact of tumors.

The transgenic flies have phenotypic markers to indicate that they carry the transgene, such as white eyes (normal flies have red eyes) or apricot body (normal body color is brownish yellow). However, markers are located on different chromosomes (autosomes or sex chromosomes) and a carefully designed crossing scheme is required to generate flies with tissue-specific tumors.

In this project, we aim to generate flies with brain tumor. You will figure out the crossing scheme for two transgenic strains, 28590 and 8751, to achieve this goal. You will cross these two strains to produce offspring flies with various phenotypes, eliminating the impossible ones and keeping the suspects (just like what Thomas Morgan did; or Mendel).

Required knowledge

Strong interests in evolutionary biology. No specific experience required.

Length of the project

At least 8 weeks of hands-on lab work.

Start date 

Flexible

Contact info

Hwei-yen Chen hwei-yen.chen@biol.lu.se

https://portal.research.lu.se/en/persons/hwei-yen-chen

February 3, 2025

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Biology Short projects

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What makes a good learner: the evolution of cognition and memory in Caenorhabditis worms

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.

With as few as c.a. 300 neurons, Caenorhabditis worms show 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!).

Learning and memory inheritance have important implications in evolution, but their ecological relevance remains unclear – what is the variation across species? And how does the environment affect learning and memory? This project will investigate this variation across Caenorhabditis species and explore the interactions between the worms’ microbial environment and memory inheritance.

Required knowledge

Strong interests in evolutionary biology. No specific experience required.

Length of the project

Flexible. Worms are a convenient model animal with a life cycle of about 3 days, so data collection is fast once you get the hang of it.

We aim to include nine worm species in total. You may choose to focus on a subset of these species for a shorter project or study all nine for a full project.

Start date 

Flexible

Contact info

Hwei-yen Chen hwei-yen.chen@biol.lu.se

https://portal.research.lu.se/en/persons/hwei-yen-chen

February 3, 2025

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Biology Short projects

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Understanding work rate in breeding birds

One of the cornerstones of life history theory is that there exists a trade-off between current and future reproduction. What that really means is that if you invest a lot into one breeding attempt you will have less available energy for future reproductive attempts or for your own self-maintenance (thereby possibly reducing lifespan). Famous rocker Neil Young once sang, “It’s better to burn out than to fade away” and in a way the whole point of this area of research is to understand if he was right or not (perhaps not for rock stars, where other things than lifetime reproductive success might be of greater importance).

In birds, one of the most common ways to investigate this trade-off is to manipulate brood size, thereby either making it easier or harder for parents to feed all their young. The golden standard for such studies is to assume that work rate differs between parents with different brood sizes and even though there are studies that confirm this pattern the effects of such a manipulation seem to vary quite substantially between years and with other environmental factors.

Thus, we are missing one essential component in the puzzle, which is: how is feeding frequency (work rate) truly affected by brood size manipulations?

This question has been answered before, but only using short snapshots in time, counting feeding events over hours and possibly a few days. However, to understand the full effect of brood size manipulations on parental investment and work rate we need to know the energy spent throughout the full nestling period. Work rate is not a constant trait and varies over time as nestlings grow older and there could be differences in these patterns, according to brood size.

You will conduct the fieldwork in the period April-June in a population of nest-box breeding blue tits (Cyanistes caeruleus) in the scenic landscape surrounding Lake Krankesjön, circa 20 km east of Lund. You will get hands-on experience of capturing, handling, and ringing birds and the possibility to work with multiple techniques involved in measurement of feeding frequency and possibly also other areas of research. To get the most out of the project, it would be advantageous to have some prior experience of handling birds, and a driver’s license is required to be able to conduct the field-work. This is a project that can be modified and suited to your own interests – it would for example be easy to add other components into this framework (i.e. phenology, immunology, body temperature regulation etc.) – so please contact me, should you find this topic interesting.

fredrik.andreasson@biol.lu.se

https://portal.research.lu.se/en/persons/fredrik-andreasson

 

 

January 30, 2025

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Biology

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Immune response and inflammation in myocardial infarction and myocarditis: underlying mechanisms and novel treatments

We are inviting students interested in immunology and cardiovascular disease to perform their Master’s Degree project at the Cardiac Inflammation Research Group, CRC Malmö. Our group studies immune and inflammatory mechanisms involved in myocardial infarction, atherosclerosis and myocarditis. By using animal models and in-vitro studies we investigate the underlying disease mechanisms and aim to develop new treatments for translation into the clinic. In parallel, in our large cohorts of myocardial infarction patients, we are looking for new pathways and biomarkers that are important for the development of heart failure and other complications. You can read more about our research on our website and in our recent publications in the European Heart Journal (Marinkovic et al, 2019), Circulation Research (Marinkovic et al, 2020) and Critical Care (Jakobsson et al, 2023).
Our experienced post-docs are leading the work and provide hands-on supervision for master’s and PhD students. Our projects include in-vivo work with mouse models of myocardial infarction, atherosclerosis or myocarditis. We measure cardiac function by echocardiograpy, perform in-depth analyses of immune cell populations by flow cytometry, histology and immunohistochemistry. We have also developed an extensive database of single-cell sequencing data (CITEseq) for the detailed study of gene and surface protein expression in cells isolated from the heart, blood and immune organs of mice with myocardial infarction and myocarditis. In-vitro, we are using cell culture experiments (immune cells, cardiomyocytes, endothelial cells) to analyze cell function, gene expression, signaling pathways, and cellular metabolism (Seahorse). We use a wide range of methods such as microsurgery, immunohistochemistry, histology, light and fluorescent microscopy, ELISA, RT-PCR and Western Blot.
Our ongoing projects include:

  • Study the role of novel neutrophil sub-populations identified in our earlier research in the pathogenesis of myocardial infarction and myocarditis.
  • Study the impact of a treatment developed in our lab, based on blockade of the pro-inflammatory neutrophil mediator S100A8/A9, on the immune response in myocardial infarction and myocarditis.
  • Develop new immunomodulatory treatments against cardiac inflammation by using individual metabolites derived from the Krebs (tricyclic acid) cycle.
  • Identify immune cell populations responsible for increased vascular inflammation and atherosclerosis after a myocardial infarction.

If interested, please contact Dr. Alexandru Schiopu, group leader, at Alexandru.Schiopu@med.lu.se

January 30, 2025

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Molecular Biology

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Vision in Changing Waters – How do predatory zooplankton adapt to variable and changing light environments?

The water flea, Polyphemus, uses its large, highly-specialised eye to hunt for prey and navigate its habitat. They live in freshwater lakes that can vary tremendously in colour, clarity, and brightness. These habitats are also impacted by human activity that further changes their light conditions. This project aims to explore the capabilities of Polyphemus to adapt their visual system to these dynamic and challenging conditions.

Projects:
Projects of varying lengths are available and potential techniques may include behavioural experiments, molecular characterization of visual gene expression, environmental light measurement, and anatomical investigations. Both BSc and MSc projects are offered. 

Read more about this project here

Contact: Dr. Michael Bok, Biologihuset B320
michael.bok@biol.lu.se

January 29, 2025

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Biology

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How are bacteria coping with stress?

Just like us, bacteria often have to deal with stress. However, stress for bacteria is a bit different from the stress we are used to – it is something that causes damage to the cellular macromolecules: membranes, proteins, and nucleic acids. It can be chemical stress, caused by harmful compounds, or physical stress, such as heat. A limited supply of nutrients can also be regarded as stress. Bacteria have developed stress responses, which aim to temporarily increase tolerance limits. These stress responses are often specific; each specialized in a particular kind of stress. Some stress responses facilitate bacterial transition from a free-living organism to a host-invading pathogen.

The aim of this project is to investigate, at the molecular level, how the soil-living bacterium Bacillus subtilis deals with various types of stress. This bacterium can form structured multicellular communities called biofilms. Biofilms contain genetically identical cells that give rise to phenotypically distinct cell types, such as, for example, motile cells, surfactin producers, sporulating cells and matrix-producing cells. Biofilms provide a protective environment that enhances resistance to antibiotics and play an important role in the pathogenesis of many medically important bacterial pathogens. By studying how biofilms are affected by stress, we could develop strategies to disperse them.

30-60 cr MSc thesis project, flexible start date.

Qualifications needed: Good knowledge of molecular biology and microbiology.

If you are interested to get more information on current projects, please contact Claes von Wachenfeldt (claes.von_wachenfeldt@biol.lu.se)

January 29, 2025

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Molecular Biology

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Investigating the true nature of the Mitochondrial Calcium Uniporter Regulator (MCUR)

Mitochondria are essential cellular organelles involved in energy production via oxidative phosphorylation (OXPHOS), metabolite synthesis, calcium homeostasis, and stress responses. Despite their critical roles and extensive research on plant mitochondria, many aspects of their biology remain unclear. Advancing our understanding of these organelles will help address future challenges in food production posed by climate change and a growing global population.

Calcium is a key cellular component, acting as a second messenger in signaling pathways and playing key roles in ATP production and mitochondrial signaling processes. Calcium uptake into the mitochondrial matrix is regulated by the mitochondrial Ca²⁺ uniporter (MCU), a multimeric membrane channel complex. This complex includes regulatory proteins, one of which was reported to be the Mitochondrial Calcium Uniporter Regulator (MCUR). Although MCUR was identified in mammalian cells in 2015, its precise role and function are still debated. Conflicting studies suggest it regulates the MCU but that it is also is part of Complex IV in the Electron Transport Chain (ETC), or even functions as a proline transporter in yeast. While mammalian and yeast studies present discordant findings, MCUR proteins remain completely unstudied in plants.

This project aims to investigate the MCUR family in Arabidopsis thaliana to clarify their roles and the processes they are part of. Using genetic tools like CRISPR-Cas9 and insertional mutagenesis, knock-out mutants will be generated and analyzed through physiological and phenotypic studies. Protein-protein interaction assays and -omics analysis, such as transcriptomics and proteomics, will provide further insights into MCUR functions.

This research offers students the opportunity to contribute to a novel field while gaining experience in advanced physiological and molecular techniques. For more information, contact Olivier Van Aken (olivier.van_aken@biol.lu.se).

January 29, 2025

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Molecular Biology

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Understanding the impact of epigenetics on cell function and human health

DNA molecules in our cells are packaged around histone proteins to form a structure called chromatin, which preserves cell function. Chromatin contains so-called epigenetic information (for example, in the form of post-translational modifications of histones) that safeguards transcriptional programs and promotes genomic stability. Unsurprisingly, mutations in chromatin proteins and alterations of epigenetic information disrupt cellular processes and contribute to human disease.

How do epigenetic alterations cause human disease?

In our lab, we model disease-associated epigenetic aberrations in human cells, with the aim of understanding how these aberrations affect DNA repair, gene transcription, and cell division. The methods employed include human cell culture, advanced molecular biology and biochemistry, genomics, and high-content microscopy.

I am looking for a highly motivated master’s student to undertake a wet lab project. Interest in chromatin biology and epigenetics, transcription, and/or DNA repair is essential for the project.

You will be joining a newly formed lab, embedded in a stimulating research environment at BMC A11, and benefit from regular hands-on supervision from the group leader (Giulia Saredi). The project will ideally start in the autumn term, with a recommended length of 60 credits.

If you have any questions on the project, please contact me (g.saredi[at]dundee.ac.uk) and include a brief description of why you’re interested in joining the lab.

January 29, 2025

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Molecular Biology

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Strain-level profiling of antimicrobial-resistant bacteria in metagenomics data for tracking resistance to antibiotics

Abstract

Antimicrobial resistance (AMR) in bacteria—the ability to survive despite the presence of drugs (antimicrobials) designed to kill them or inhibit their growth—is a growing concern worldwide. This resistance makes standard treatments ineffective in humans and animals, leading to persistent infections and the increased spread of resistant pathogens. AMR results from complex interactions between humans, food, animals, and environmental systems. The unit of AMR resistance is the strain, a dynamic entity that can evolve or acquire resistance genes. Despite significant research efforts, gaps remain in understanding how strains acquire AMR, persist, and spread across these interconnected systems, which hampers our ability to model and control AMR effectively. It is also challenging to effectively trace AMR-carrying strains across diverse ecosystems, limiting our capacity to predict the emergence and spread of AMR. In this project, we propose to develop a computational tool to predict the emergence of AMR and trace the transmission and persistence of bacteria carrying AMR at the strain level in different systems using publicly available metagenomics and whole genome sequencing data. Building on the fast-expanding metagenomic databases, we will focus on a key system such as the human, food, animal, soil and water microbiomes. This research will provide much-needed capabilities in source-tracking of AMR-carrying strains and significantly improve the models used to predict and control their spread.

 

Background

Metagenomics, the study of genetic material recovered directly from any type of samples, has revolutionized our ability to study microbial communities, including those that harbour antimicrobial resistance genes (AMR). It allows for the comprehensive analysis of microbial diversity and function without the need for culturing individual organisms. Metagenomics can provide a complete picture of the microbial community structure and the presence of AMR, offering insights into the resistome (the collection of all resistance genes) of a given environment (De Abreu et al., 2021). It enables the discovery of novel resistance genes and mobile genetic elements such as plasmids that could contribute to the spread of AMR and contributed to elucidate the ecological interactions and environmental factors that influence the distribution and abundance of AMR. It also has the potential to reveal and track specific strains carrying AMR. Tracking AMR at the strain level is crucial for understanding the transmission dynamics and persistence of resistant bacteria. Previous traditional methods, such as multilocus sequence typing (MLST) and whole-genome sequencing (WGS), have been employed to track specific strains and for outbreak investigations. However, these methods often rely on the isolation and culturing of bacteria, which can be labour-intensive and limited to cultivable strains. Combined with WGS, metagenomics is a powerful tool to characterize AMR at the community level in a given system. However, metagenomics also has limits. Because it relies on short-read sequencing technologies, it is difficult to assign AMR to specific bacterial strains. Nonetheless, advances in bioinformatics have led to the development of strain-level metagenomics, where algorithms can differentiate between closely related strains within a metagenomics sample (Beghini et al., 2021; Olm et al., 2021). The development of long-reads sequencing, sometimes combined with short-reads sequencing, has also improved the resolution to trace AMR-carrying strains in metagenomics data.

Despite these advances, comprehensive strain-level tracking of AMR in diverse microbiomes (human, food, animal, environmental) remains challenging. Our project aims to address these limitations by developing novel bioinformatics methods and integrating high-quality WGS data with metagenomics to enhance the resolution of strain-level analysis.

 

Specific aims

The specific aims will be the following:

  1. Benchmark the existing tools used for strain-level profiling in metagenomics data
  2. Develop a computational tool to trace bacteria at the strain level from metagenomics and whole-genome sequencing
  3. Validate this tool on a set of metagenomics data and determine the bacteria strain transmission between (and persistence within) samples.

 

Contact

Dr. Ghjuvan Grimaud (Division of Biotechnology and Applied Microbiology)

ghjuvan_micaelu.grimaud@ple.lth.se

 

References

Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., … & Segata, N. (2021). Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. elife, 10, e65088.

De Abreu, V. A., Perdigão, J., & Almeida, S. (2021). Metagenomic approaches to analyze antimicrobial resistance: an overview. Frontiers in genetics, 11, 575592.

Olm, M. R., Crits-Christoph, A., Bouma-Gregson, K., Firek, B. A., Morowitz, M. J., & Banfield, J. F. (2021). inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nature Biotechnology, 39(6), 727-736.

January 29, 2025

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Bioinformatics Molecular Biology

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