Tidligere prosjekter (2025)
What you will do: The project will involve the bioinformatical analysis of raw sequencing data, from quality trimming through mapping to the genome and counting expression to statistical identification of differentially expressed genes. The project requires some basic experience working on the command-line (Unix, R, python, or others).
What you will learn: You will join group meetings and learn about the diverse yet complementary ongoing projects in our group and get first-hand experience in the analysis of RNAseq data (transcriptomics). Two PhD students in our group, Magdalena Winklhofer and Laura Valencia, will assist and train you to perform the different analytical tasks.
What you will be part of: You will join an international and stimulating research environment with 2 postdoctoral researchers, 2 PhD students, and 1 master student in the “Adaptation Group” led by Sjannie Lefevre and G?ran Nilsson. The project is part of a bigger project on ‘Epigenetics mechanisms and genes expression during anoxia’.
Are you interested? Contact Magdalena (magdalena.winklhofer@ibv.uio.no) or Laura (l.m.v.pesqueira@ibv.uio.no) for a meeting
Tidligere prosjekter (2023)
Project: Birds of Nygrotta
Bird species are incredibly good environmental indicators, due to their sensitivity to change and their high mobility. We have recently excavated a unique, large diversity of bird bones from Nygrotta cave in Northern Norway. This cave contains bones and sediments going all the way back to the last glaciation (~10-12?000 years). A more detailed assessment of the Nygrotta birds will help to inform us on past ecosystems in the area and the species which formed the local avian community, for a period we currently have little knowledge of.
As part of this project, you will learn basic zooarchaeological identification of Northern European bird species and how to perform detailed recording and analysis of bone remains. We will identify bird bones recovered from the most recent excavations at Nygrotta cave, which was excavated as part of the EvoCave project (https://tinyurl.com/EvoCave). Most of the specimens date to the early Holocene (~8000 years ago), a period defined by general warming. The bird species identified will be compared to modern-day bird distributions and help to inform us about past avifaunal distributions in Norway. Furthermore, you will take anatomical measurements of bone elements to look at size changes in species over time.
This project is integrated into the larger interdisciplinary EvoCave team which has specialists in evolutionary biology, palaeozoology, geology, sedimentology, geochronology, archaeology, aDNA, and genomics. Moreover, you will be part of the Archaeogenomics group with more than ten masters, PhDs, and postdocs who form a collaborative and stimulating research environment. You will be invited to take part in regular group meetings, learn about a diversity of ongoing projects, and become familiar with the general research environment in which we work.
Supervisors:
- Sam Walker (s.j.walker@ibv.uio.no)
- Sanne Boessenkool (sanne.boessenkool@ibv.uio.no)
Project: DNA extraction and analyses of bumblebees
Bumblebees are keystone pollinators: they pollinate a diverse array of both wild and agricultural plant species, many of which are pollinated exclusively or predominantly by bumblebees throughout their wide-ranging distribution across various temperate habitats. Widespread losses in bumblebee abundance and diversity therefore have severe implications for ecosystem function and food security. The causes of these declines are thought to be the result of a combination of anthropogenic stressors such as habitat loss and fragmentation, parasites introduced by humans, climate change and agrochemical exposure. However, the exact mechanisms driving bumblebee declines remain poorly understood. Whole genome sequencing approaches can provide valuable insights into a range of biological characteristics relevant to conservation biology, addressing questions involving genetic diversity, gene flow and local adaptation. As yet, these tools have not been widely applied to bumblebees.
In this project, you will contribute to laboratory work as part of a population genomics study of three bumblebee species sampled from a range of sites spread across North-Western Europe. You will be trained in DNA extraction methods and quantification of such extracts of modern-day bumblebees, with the possibility of also assisting with extractions of historical bumblebee specimens obtained from museum collections. Following this, libraries intended for whole genome sequencing will be generated from these DNA extracts, giving you an opportunity to also be trained in library preparation methods. You will work closely with a PhD candidate, and be part of the Archaeogenomics group with more than ten masters, PhDs and postdocs. The student will be invited to take part in regular group meetings, learn about other ongoing projects and become familiar with the general research environment we work in.
Supervisors:
- Lauren Cobb (l.l.cobb@ibv.uio.no)
- Bastiaan Star (bastiaan.star@ibv.uio.no)
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Project: The key to living without oxygen? Investigating succinate transport in the crucian carp
In animals, the most efficient way of producing energy (ATP) is through aerobic (oxygen demanding) metabolism in the mitochondria. In absence of oxygen (anoxia) this option is not available. For most animals, this rapidly causes energy failure and death. Even if they survived the initial anoxic period, reintroduction of oxygen leads to release of reactive oxygen species (ROS), which will soon cause oxidative damage to cells and eventually cell death. Succinate builds up during anoxia and is a major source of ROS at re-oxygenation due to the mitochondrial complex II enzyme (succinate dehydrogenase), going in reverse. Contrary to most animals, the crucian carp (Carassius carassius) has evolved unique mechanisms to survive months without oxygen by inhabiting lakes receiving limited oxygen supply during winter due to the thick ice layer. We have preliminary data indicating little oxidative damage after anoxia and re-oxygenation in several tissues of the anoxia tolerant crucian carp (e.g., liver, heart, brain, and gills), and that their mitochondria produce less ROS than anoxia intolerant species like the mouse, Mus musculus. Still, our recent metabolomics studies show accumulation of succinate in all tissues. Intriguingly succinate is accumulating to a larger extent in the crucian carp plasma (blood) and the liver compared to the brain and heart. We hypothesise that crucian carp circumvents the succinate-driven ROS production, by shuttling the succinate away from sensitive tissues, either into the water, or that it is metabolized in the liver, an organ where high constitutive activity of enzymes involved in the protection of cells from oxidative damage by ROS was observed.
What you will do: In this project, you will contribute to laboratory work?by measuring succinate level in the tissues and water samples taken from crucian carp during anoxia-reoxygenation exposure using a colorimetric assay (Succinate Assay Kit from Promega) and microplate reader.
What you will learn: You will join group meetings and learn about the diverse, yet complementary, ongoing projects in our group, get first-hand experience with carrying out a research assignment from samples preparation to data analyses and presentation. A postdoctoral researcher in our group, Lucie Gerber (main supervisor) will assist and train you to perform the different laboratory tasks and get familiar with the laboratory setting and the general research environment we work in.
What you will be part of: You will join an international and stimulating research environment with 2 postdoctoral researchers and 2 PhD students in the “Adaptation Group” led by Sjannie Lefevre and G?ran Nilsson. Moreover, the project is part of the UiO:Life Science convergence environment “Availability and function of donor organs: Debating the dead donor rule (3DR)”, a larger interdisciplinary and collaborative project involving more than 10 researchers and students from the Faculty of Medicine, Theology, and Oslo University Hospital, giving you the opportunity to interact with researchers with different research speciality and look at scientific research and collaboration through a larger lens.
Are you interested? Contact Lucie (lucie.gerber@ibv.uio.no) and ask for a meeting.
Project: Can air pollution reduce clover root growth?
Project: Reproductive barriers among fungi in Norway
Student project in the Oslo Mycology Group, Evogene.
Project: Previous glacial cycles have redistributed life on earth, especially so in the temperate and arctic regions. Postglacial migration patterns have been examined for numerous plants and animals in Europe, but less is known for microorganisms, including fungi. It is therefore not clear whether fungi have followed the same postglacial migration trajectories as plants and animals. We have inferred the postglacial history of the widespread wood-decay fungus Trichaptum abietinumin Europe. We found evidence for two different populations to have immigrated into Norway, one to western Norway and one to eastern Norway. In Norway these two groups stay genetically distinct, thus they may not mate with each other. We wonder whether they do not mate due to local adaptation to wet and drier climate which will retain different distributions or whether they cannot mate if they actually meet. ?
What you will learn: In this project you will mate fungal strains in the lab. We already have fungal strains from these two populations, ready to be mated. You will learn how to culture fungi in a clean lab environment, set up lab experiments where we mate fungal strains and evaluate the results in the microscope. You will further learn how to evaluate the significance of the results.
What you will be part of: You will be part of a large research environment in the Oslo Mycology Group at Evogene, IBV. We are currently 5 master students, 6 PhD students, 2 post docs, 2 researchers and 2 Professor/Associate professors. We arrange weekly journal clubs and meetings that you will be invited to.
Contact:
Inger Skrede (inger.skrede@ibv.uio.no)
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