Biology Education

Department of Biology | Lund University

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Population genomics and colour morphology

Bombus sylvarum is a small bumblebee species which has a melanistic morph in southern Sweden. However, further north in Sweden it can be found as both a melanistic and light morph within the same population. This is in contrast to other parts of Europe such as the UK where it only exists as a light morph. Due to the morph’s discrete nature, we hypothesis that these are controlled by a single or a few loci, which we would like to identify. The student would work with whole genome sequences of individuals from the same population to infer candidate loci. The work can further be complemented with field work in lake Kvismaren were both morphs exist, either to estimate frequency of the two morphs or collect individuals for DNA lab work.

We are looking for a master student to join us in exploring the population genomics of bumblebees and hoverflies. However, we can also offer 15-credit projects involving field and/or DNA-lab work.

About our lab

We are interested in the evolution of sex chromosomes, as well as questions about local adaptation and conservation genomics. We can offer projects giving both experience in the DNA lab, as well as skills in analysing next generation sequencing data. For projects including lab work and population genetic questions we would prefer the student to have taken the course Molecular Ecology and Evolution, or equivalent course. We are also open to students taking an integrative approach, combining genetic methods with other analyses, such as niche modelling and morphometrics.

Interested?

If you are interested in this project in particular, similar projects on morph variation in Volucella bombylans, or projects involving population genomics and sex chromosomes in bumblebees and birds, please do not hesitate to contact us! We would love to set up a meeting to discuss any project in more detail and answer any questions you might have. Please contact both of us in an email:

Simon Jacobsen Ellerstrand: simon.jacobsen_ellerstrand@biol.lu.se

Bengt Hansson: bengt.hansson@biol.lu.se

March 19, 2024

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Biology

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Flower variation in Digitalis purpurea

Flower color is one of the most striking traits to attract pollinators and it varies between species and populations.

Pollinators may have preferences for certain flower colors (but antagonists like florivores as well).

At the same time, environmental factors like soil nutrients, pH, water availability, and tissue structure can influence color.

Aim: Disentangle the biotic and abiotic agents affecting color in native populations of D. purpurea

 

We look for a highly motivated student interested in plant-pollinator interactions and/or flower evolution.

Join our international research group passionate about flowers!

Have a look at twitter for more information:

https://x.com/SLozadaGobilard/status/1768757303379972377?s=20

 

CONTACT:

Sissi Lozada Gobilard

sissi.lozada_gobilard@biol.lu.se

March 18, 2024

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Biology

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GeoMx-EcoTyper Cell deconvolution/cell states

The tumor microenvironment (TME) is a complex and dynamic landscape that plays a pivotal role in the progression and behavior of cancer. Comprising various non-cancerous cells such as immune cells, fibroblasts, and endothelial cells, the TME interacts intimately with tumor cells, influencing growth, metastasis, and response to therapy. Understanding these interactions is crucial for the development of targeted therapies that can more effectively combat cancer by disrupting the supportive network tumors rely on.

However, this requires knowledge of the cell types which in its turn requires single cell data thus, not available for data such as bulk sequencing. Cell deconvolution is a computational technique that plays a crucial role in unraveling the complexities of the TME. By analyzing bulk tumor data, cell deconvolution separates the mixed signals into individual proportions from various cell types, offering a clearer view of the cellular composition and interactions within the TME.

A recent methodology called “EcoTyper”, a machine-learning framework integrating transcriptome deconvolution and single-cell RNA sequencing that extends beyond quantification of each cell type to also characterize distinct cell states within those types, offering a more detailed view of the cellular dynamics within the TME.

The aim of this student project, part of a larger PhD project, is to combine “EcoTyper” with spatially resolved RNA data from the “GeoMx DSP” platform to characterize the TME of large cohorts of hundreds of patients, from two different types of B-cell lymphomas.

To read more about EcoTyper.

https://www.sciencedirect.com/science/article/pii/S1535610821004517?via%3Dihub#sec3

To read more about the spatial omic platform/ GeoMX DSP data. See the latest publication from our group – based on such analysis.

https://pubmed.ncbi.nlm.nih.gov/37139184/

 

If you are interested in this or similar spatial omic projects, contact:

Sara.Ek@immun.lth.se

 

We have ongoing and past experience in supervising short and long term projects for students at the Master program in Bioinformatics.

March 11, 2024

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Bioinformatics

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How do bees balance the nutrient content of pollen for their larvae?

The underlying causes of the global decline of wild bees is important to understand because bees are essential for pollination of both crops and wild plants (Potts et al. 2016). Bees forage on nectar and pollen, where the latter is the main resource used to feed the growing larvae (Lau et al. 2022). Many bees, either at species or individual level, show clear preferences for pollen from certain plant species or genera: at the species level for solitary bees (Persson et al. 2018; Yourstone et al. 2021;2023). It has been suggested that this is caused by an inability by the larvae to digest pollen from certain plant genera, likely because of their chemical protection (Praz et al. 2008; Sedivy et al. 2012). However, it may also be caused by the need to optimise the nutritional balance between macronutrients, i.e., carbohydrates, proteins, and lipids (Leonhardt et al. 2022), and a recent study has shown that the availability of specific macronutrients, rather than flower species per se, shape plant-pollinator networks in real landscapes (Vaudo et al. 2024).

Potential aims

In this project you will look closer into if and how bee species, such as Osmia bicornis (Red mason bee) and Bombus terrestris (Buff-taled bumblebee) optimise nutritional content of its pollen collection over time, and if this is restricted by the quality of the floral resources in the surrounding farmland landscape.

Methods and time plan

You will use existing data on pollen foraging collected by Persson et al. (2018) and Yourstone et al. (2021; 2023), combined with published data on pollen nutritional content (e.g. Hanley et al 2008; Pamminger et al 2019). Depending on your interests and the extent of the project you may also using image analysis to extract you own pollen data already collected from bees (Olsson et al. 2022), and, or make pollen collection in the field during summer and perform nutrient assessments in the lab.

Project duration: 15-30 credits using existing data only, 45-60 credits including field data collection/lab work

Supervisors and contact info:

References – read more!

Hanley et al 2008: https://doi.org/10.1111/j.1365-2435.2008.01415.x

Lau et al 2022: https://royalsocietypublishing.org/doi/abs/10.1098/rstb.2021.0510

Leonhardt et al 2022: https://royalsocietypublishing.org/doi/abs/10.1098/rstb.2021.0171

Olsson et al. 2021: https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13575

Pamminger et al 2019: https://doi.org/10.7717/peerj.7394

Persson et al 2018: https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.4116

Potts et al. 2016: https://www.nature.com/articles/nature20588

Praz et al 2008: http://dx.doi.org/10.1890/07-0751.1

Vaudo et al 2024: https://doi.org/10.1073/pnas.2317228120

Sedivy et al 2012: http://dx.doi.org/10.1111/j.1365-2435.2010.01828.x

Yourstone et al 2021: https://doi.org/10.1016/j.biocon.2021.109249

Yourstone et al 2023: https://doi.org/10.1093/beheco/arad028

March 3, 2024

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Biology

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Biology of blood parasite vectors in a bluetit population

In a bluetit population situated outside Lund the prevalence of blood parasites has increased in the population from around 45% in 1996 to over 85% being infected in the 2020s. The increase seems to be linked to an increase in temperature when the birds are newly hatched and are still in the nest boxes being feed by their parents. This is a time period where biting midges are known to visit the nest boxes and potentially spreading the disease.

We are now seeking a master student to investigate the role of temperature, brood sizes and seasonality on the abundance of vectors in the nest boxes. The project includes fieldwork, some level of invertebrate species identification (either through morphology or with the use of molecular methods) as well as an opportunity to investigate the level of parasite the caught vectors are carrying using molecular methods.

Supervisors: Olof Hellgren, Fredrik Andreasson and Jan-Åke Nilsson

 

If you think this sounds like an exciting and interesting project, please contact:

Olof Hellgren (olof.hellgren@biol.lu.se), Fredrik Andreasson (fredrik.andreasson@biol.lu.se)  or Jan-Åke Nilsson (Jan-ake.nilsson@biol.lu.se) via e-mail or come visit us on the second floor of the Ecology building.

February 28, 2024

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Biology

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How are bumblebees affected by pesticides and their mixtures? 

Pesticides play a crucial role in our environment and are essential for sustaining food production. However, our understanding of the impact pesticides can have on insects remains limited, particularly when used in combinations. This lack of knowledge is particularly concerning for insect pollinators, such as bumblebees, which are exposed to these substances while foraging. 

 

The goal of this project is to develop a method that allows to expose individual bumblebees with known doses of pesticides, both as single compounds and binary mixtures. Bumblebees will be exposed acutely (a single dose) and chronically (over days). You will quantify the impact on bumblebees by monitoring lethality and motor impairments resulting from the ingested doses of commonly used pesticides. The long-term goal is to use the data to test the sublethal effects of pesticides in behavioural assays. 

 

The laboratory work will involve the manipulation of insects, optimising a feeding method specifically designed for bumblebees to determine the intake dose for each individual, developing an ethogram, and analysing binary data using modelling techniques. 

If you are interested in this project and would like to know more, please contact me: silvia.ronnau@biol.lu.se 

 

February 28, 2024

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Biology

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Effect of urbanisation on sperm DNA damage in Great tits (Parus major)

In the last few decades, the populations of several wild bird species decreased dramatically worldwide. This is due to many factors associated with urbanization, including habitat loss, fragmentation, pollution, and other environmental stressors. It was shown that the average reproductive performance is lower in polluted areas, also in a recent review pointed out that 82% of the studies documented pollution-induced fitness reduction in birds. Many studies were shown that the clutch size does not vary among polluted and non-polluted areas, however, the hatching rate can be lower in polluted areas than in non-polluted areas. It was shown in medical studies that in a highly polluted area the percentage of sperm DNA fragmentation (measurement for DNA damage) can be above 30%, which can lead to miscarriage in women or lead to infertility in men. Since sperm DNA damage can cause miscarriage and infertility, it can be one of the causes of hatching failure in birds. However, it has been shown in humans that sperm DNA damage can cause infertility, we do not know whether pollution can affect sperm DNA integrity in bird populations. Therefore, the aim of this project is to investigate the effect of urbanisation caused pollution on sperm DNA integrity in Great tit Parus major comparing urban and a rural populations.

 

Main supervisor: Caroline Isaksson – caroline.isaksson@biol.lu.se

Co-supervisor: Zsófia Tóth – zsofia.toth@biol.lu.se

February 20, 2024

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Biology

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Investigating molecular mechanisms underlying sex differences in human immunity

The COVID-19 pandemic has highlighted sex differences during infection, with increased hospitalizations and deaths in SARS-CoV-2-infected men as compared to women. This observation is not exclusively seen in SARS-CoV-2 infection; in fact, biological sex has a prominent influence in regulating immune responses. Generally, women display enhanced innate and adaptive immune responses when compared to men, resulting in less severe infections and increased response to vaccinations. While sex differences are attributed to the combined effects of sex hormones, sex chromosomes and societal factors, it is still unknown how biological sex influences genes and pathways in immune cells that significantly impact immune responses. In the Systems Immunology Lab at Lund University (https://theconsigliolab.wordpress.com/), we investigate how biological sex impacts human immunity using systems immunology approaches.

 

We are looking for a MSc student (ideally over 20-week project) interested in wetlab training in human immunology, with the possibility of developing skills in computational methods of data analysis. We are located at BMC B12, and the projects in our lab entail performing human blood cell cultures, stimulating immune cells to assess immune function via different methods (i.e. flowcytometry, etc), and identifying genes and pathways regulated by sex hormone receptors (CRISPR, CUT&RUN sequencing). Training/knowledge of immunology, as well as experience with cell culture and molecular biology are both desired but not required.

 

If you have any questions you are welcome to email me directly at camila.consiglio@med.lu.se

February 20, 2024

This entry was posted in

Molecular Biology

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POLLINATOR StreETs as vital connections to maintain functional urban areas

This is an opportunity to work with pollinators in an urban setting and be part of a European project where we will investigate the pollinator communities in several different cities in Europe. The project consists of fieldwork in Lund and analysis of the data collected here and potentially also the data collected in other Swedish cities if that is of interest.

 

Fieldwork: Pan traps in urban setting

Where: within the urban area of Lund

When: from May to September 2024. 5-10 days each month

Requirements: Interest in pollinators and pollination. Knowledge of the English language

 

Contacts:

irene.piccini@up.poznan.pl

georg.andersson@biol.lu.se

 

Website: https://zoologia.up.poznan.pl/en/projects/pollinators-et-al/

February 13, 2024

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Biology

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What can trait diversity reveal about the sustainability of forest management?

  • What do traits tell us about species responses to environmental change and the resulting impacts for ecosystem function and services?
  • Which forest management practises have the greatest impact on biodiversity, ecosystem function and ecosystem services?

The research student will analyse long-term data sets for biological indicator species (birds, plants or butterflies) to evaluate how changes in biodiversity affect ecosystem function, and which management strategies yield the greatest conservation and ecosystem services benefits.

For further information contact:

Dr Richard Walters richard.walters@cec.lu.se;

Dr Avril Weinbach avril.weinbach@cec.lu.se;

Prof Henrik Smith Henrik.smith@biol.lu.se

 

February 13, 2024

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Biology

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