Project: Small mammal bones from a cave archive in Northern Norway
Small mammals are excellent indicators for changes in ecological conditions and climate. Reconstructing past small mammal biodiversity through the study of sub-fossil bones or DNA therefore provides unique insights into past environments, and in-depth studies of past small mammal diversity are lacking as their remains are rarely recovered. In the autumn of 2023 we have performed an excavation in Solvikhula, or Storhellerhola, a large cave in Fauske, Northern Norway. A rich diversity of small mammal bones was recovered, as well as bones from a variety of amphibia and birds. Analysing this recovered biodiversity and how it has changed through time will give us a better understanding on how climate, environment and ecosystems have developed during the past 1000s of years.
As part of this project, you will learn basic zooarchaeological and ecological identification of small mammal species and how to perform detailed recording and analysis of bone remains. We will identify small mammal teeth recovered from the most recent excavations at Solvikhula, which was excavated as part of the EvoCave (https://www.mn.uio.no/cees/english/research/projects/101491/) and SaveCave projects (https://www.mn.uio.no/cees/english/research/projects/savecave/index.html). You will also have the opportunity to analyse glacial sediments from another cave in Northern Norway. Furthermore, you will be introduced to the concept of bulk-bone metabarcoding – a technique where we use ancient DNA analyses to obtain taxonomic identifications of small bone fragments that cannot be identified by skeletal morphology (osteology). You will be able to familiarise yourself with the different steps that are performed in the DNA laboratories.
This project is integrated into the larger interdisciplinary SaveCave team which has specialists in evolutionary biology, zoo-archaeology, sedimentology, archaeology and ancient DNA. 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:
- Lea Frank (lea.frank@ibv.uio.no)
- Sanne Boessenkool (sanne.boessenkool@ibv.uio.no)
Project: Sampling, DNA extraction and high-throughput sequencing preparation of solitary bees
Bees comprise an important group of pollinators, and they are declining mainly due to habitat fragmentation and land use change. Approximately 75% of food crop species and 90% of wild flowering plants depend on animal pollination for reproductive success, so a loss of pollinating insects has fundamental implications both for biodiversity and food security. With over 20,000 bee species worldwide (210 in Norway), the bees are distributed unevenly in the landscape. By learning more about how different types of bees are distributed differently in the landscape, we can provide information that management can use in conservation efforts of these crucial creatures. To do this, we can use whole genome sequencing approaches to investigate the bees’ connectivity though geneflow as well as delineate population structure and local adaptation.
In this project, the student will contribute to laboratory work as part of a larger population genomics study of three solitary bee species sampled from a range of sites across North-Western Europe. The student will be trained in the entire sampling treatment process including photo-documentation, labelling, dissection and molecular laboratory procedures. The project includes DNA extraction and quantification methods (spin-column extractions, qubit fluorometry and gel electrophoresis). Following this, libraries intended for whole genome sequencing will be generated from these DNA extracts, giving the student an opportunity to also be trained in library preparation methods. The student will work closely with a PhD candidate who work on project: BEEDIVERSE: Improving wild bee conservation by integrating functional ecology with genome-wide biodiversity estimates.
Also see link: https://www.mn.uio.no/cees/english/research/groups/archaeogenomics/projects/beediverse.html
Supervisor:
- Bastiaan Star (bastiaan.star@ibv.uio.no)
- Emma Falkeid Eriksen (e.f.eriksen@ibv.uio.no)
Project: Reproductive barriers among fungi in Norway
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 abietinum in 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, but they can mate in our labs. We ask whether they do not mate in nature due to local adaptation to wet and drier climate, or if the hybrids are performing poorer when competing for resources or living in variable habitats?
In this project you will test if hybrids are less fit than their parental populations. 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 and set up lab experiments where we will test the fitness of hybrids in various environments. You will further learn how to evaluate the significance of the results.
This project can take two students, one that investigate growth and wood decay at variable conditions, and one that investigate competitive ability of these populations and their hybrid. You will be part of a large research environment in the Oslo Mycology Group at Evogene, IBV. We are currently 8 master students, 6 PhD students, 3 post docs, 2 researchers and 2 Professor/Associate professors. We arrange weekly journal clubs and meetings that you will be invited to.
Supervisor:
- Inger Skrede (inger.skrede@ibv.uio.no)
Project: Quantifying urban-rural variation in boldness in common bird species
Human activity has shaped the evolution and ecology of countless species. One of the starkest examples of this is behaviour, specifically responses to human presence. Birds are an excellent model for studying adaptation to human environments because of their visibility, strong associations with human activity and well-studied behaviour.
Do birds that live in close proximity to humans become acclimatised and habituated to their presence? Are some species more tolerant of a human presence than others? Perhaps there is individual variation in boldness and risk-taking behaviour that might lead to success in human-shaped environments? This project will seek to quantify differences in bird behaviour across urban-rural gradients in Oslo in response to human interaction.
You will be given the opportunity to perform fieldwork and behavioural assays on birds. Specifically, you will perform tests of flight initiation distance – i.e. measuring when a bird flies away upon human approach – across Oslo. You will be trained in data analysis using R and be given an introduction in identify within and between species variation in behaviour. You will work closely with a postdoctoral researcher and within the wider Ecological and Evolutionary Genetics group which includes PhD and Masters students. You will be invited to take part in group meetings, participate in other fieldwork ongoing in Oslo and become familiar with our research environment.
Supervisors:
- George Pacheco (george.pacheco@ibv.uio.no)
- Mark Ravinet (mark.ravinet@ibv.uio.no)
Project: How to use Artificial Intelligence (AI) image recognition to automatically identify specific fish species in medieval fish-market paintings?
Background
The abundance of historical paintings from the medieval period provides a captivating visual tapestry of bygone eras, depicting not only the societal and cultural norms of the time but also offering glimpses into the past natural world. Such paintings often feature meticulously detailed landscapes, flora, and fauna, that serve as a visual record that may be analyzed for historical ecological data. Specifically, medieval oil paintings depicting bustling market scenes often feature a wide array of fish species. Moreover, the often-meticulous attention to detail in these artworks allows for the identification of specific marine species, effectively providing anecdotal documentation of historical fish biodiversity. Yet in order to obtain a thorough spatiotemporal understanding of such past biodiversity, one would need to analyze hundreds to thousands of historical paintings, which requires a prohibitive amount of time. Such large-scale analyses would be greatly aided if these could be performed using Artificial Intelligence (AI) recognition software. Nonetheless, it is currently unclear if Artificial Intelligence (AI) recognition software can handle different painting styles to confidently identify different species of fish.
This project aims to investigate the potential of Artificial Intelligence (AI) image recognition to automate the identification of specific fish species in historical paintings. There are a number of open questions. For instance, what is the best training set? Can we use modern, species-specific images, or should we use (parts of) historical paintings where we first manually identify a few species? Can some species be easier recognized than others? Can we improve image recognition by asking AI to modify training set images to fit a specific historical painting style? Are some image recognition software packages better or perhaps easier to work with? The aim of the project is to come with recommendations of a “best practices work flow” for creating a training set of publicly available images of specific marine fish species and to assess the potential for the automated identification of specific marine species in number of publicly available historical paintings using AI.
This is an innovative project that may provide a number of future multi-disciplinary research directions. We currently have limited hands-on experience in Artificial Intelligence (AI) image recognition and this project therefore requires an independent student with an interest in learning and applying novel AI image tools to diverse biological problems.
Supervisor:
- Bastiaan Star (bastiaan.star@ibv.uio.no)
Project: Disentangling the toxicity of venom as a complex trait
Venoms are complex cocktails of bioactive compounds that are injected into other organisms to evoke a drastic physiological response, usually for predation or defensive purposes. They are among the most successful traits in evolutionary history and have evolved independently on over a hundred occasions throughout the animal kingdom. Venoms are typically composed of proteins and peptides, referred collectively as toxins, that each contribute to the toxic phenotype of the whole venom by targeting specific receptors and pathways in the victim. In this sense, venoms are complex traits whose overall phenotype can be deconstructed and studied by isolating and characterizing individual components. Although analyzing the toxicity of individual toxins is the typical approach from a pharmacological perspective, it is the toxicity of the overall venom phenotype that is subject to natural selection.
In this research internship, the student will contribute to the study of the evolution of venom as complex trait in the context of the Lacewing Venom project. Specifically, we will screen the toxicity of crude venom extracts from the green lacewing Chrysoperla carnea (Neuroptera: Chrysopidae) against Drosophila melanogaster in a quantitative genetic framework. This will produce unprecedented insights into the evolvability (potential for adaptive evolution) of animal venoms as complex characters. Although this study will be based in already collected venom samples, the student will be given the opportunity to learn venom extraction methods in the laboratory. The student will also learn to maintain and handle laboratory populations of model animals (C. carnea and D. melanogaster), perform toxicity assays, and conduct complex statistical analyses. There is also room, depending on the student interests, to learn biochemistry (e.g., HPLC), ‘omics’ (proteomics, transcriptomics), and bioinformatic techniques typically used in venom research (venomics).
About the Venomics group: the student will be part of a diverse and stimulating group of professionals with different backgrounds and a common interest: animal venoms. The Venomics group is led by Dr. Eivind Undheim and is currently composed by two postdocs, three PhDs, one principal engineer, and one visiting Erasmus student. The student will work closely with a postdoc, but interaction with other group members will be highly encouraged. Finally, the student will be invited to regular lab meetings, journal clubs and social activities.
Supervisors:
- Gustavo A. Agudelo-Cantero (g.a.agudelo-cantero@ibv.uio.no)
- Eivind Andreas Baste Undheim (e.a.b.undheim@ibv.uio.no)
Project: Creating plastic-eating worms by genome engineering
Microplastics pose a significant threat to ecosystems and human health. One proposed method for managing microplastics is their biodegradation. For example, waxworms have been shown to produce enzymes capable of degrading polyethylene plastics. Modified organisms expressing such enzymes could be used as tools towards environmental clean-up. In this project, the goal is to genetically engineer Caenorhabditis elegans, a well-known animal model, to enable biodegradation of microplastics.
The C. elegans is a microscopic roundworm that has been instrumental in uncovering important biological pathways such as apoptosis and RNAi. The animal is genetically tractable, easy to culture in the lab and has a transparent body that enables microscopic examination. The gene encoding the plastic-degrading enzyme identified from waxworms will be introduced into the C. elegans genome at a specific site using the Mos1-mediated Single Copy Insertion (MosSCI) method, which involves transposon-mediated gene insertion. C. elegans can ingest microplastics, which can be tracked using fluorescence microscopy. By feeding microplastics to the engineered strain expressing the plastic-degrading enzyme and tracking the microplastics, we can study if and how the microplastics are being degraded.
In the BIOS3060 course, the student will learn how to design and clone the constructs required for transgenics. They will use microinjection to create genetically engineered animals. Time-permitting, the student may establish the feeding assay and analyse microplastic degradation.
Supervisors:
- Pooja Kumari (pooja.kumari@ibv.uio.no)
- Rafal Ciosk (rafal.ciosk@ibv.uio.no)
Suggested reading:
Single-copy insertion of transgenes in Caenorhabditis elegans.
Project: Evolution of anoxia tolerance: comparing goldfish and crucian carp metabolism during anoxia survival
For most animals, absence of oxygen (anoxia) rapidly causes energy failure and death. Contrary to most animals, the crucian carp (Carassius carassius) and closely related goldfish (carassius auratus) have the ability to survive without oxygen in response to overwintering in oxygen-depleted frozen freshwater habitats. Yet, the domesticated goldfish is clearly less anoxia-tolerant than the wild crucian carp. During the long domestication history (at least 1000 years) the selection pressure from environmental anoxia will have been relaxed in goldfish and the tolerance may have been partially lost, offering an ideal comparative system. We are currently annotating the crucian carp genome and comparing it to the genome of goldfish to identify genes/mechanisms/pathways selected for anoxia tolerance, and potentially lost or inactive in goldfish.
What you will do: For this project, to get more physiological insights, you will contribute to laboratory work by measuring levels of stress and metabolic products (e.g., lactate, glycerol, ethanol and succinate) in blood (plasma) taken from both crucian carp and goldfish after 1 and 2-day exposure to anoxia. This means using commercial plate assay kits and a microplate reader as well as writing SOPs.
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, Elie Farhat, and PhD student in our group, Laura Valencia, 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 1 researcher, 1 postdoctoral researcher, 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 Elie (elie.farhat@ibv.uio.no) or Laura (l.m.v.pesqueira@ibv.uio.no) and ask for a meeting.
Project: Transcriptomics responses to anoxia in the heart of crucian
Crucian carp (Carassius carassius) overwinter in ice-covered lakes and can survive anoxia for several months, depending on the temperature. The physiological adaptations allowing this survival are well understood at the whole-organism level, but we know less about the molecular machinery coordinating the various adaptation elements to anoxia and re-oxygenation. Gene expression can be activated, altered, or repressed in response to external stressors. Previous experiments analyzing whole-brain transcriptome (RNAseq) data have shown that a considerable proportion of the transcriptome is regulated differentially in response to anoxia, and we hypothesize that to be true for the heart as well. We will perform a bioinformatic analysis to identify which genes are differentially expressed in the heart.
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)
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)