EASTBIO DTP invites applications by first and second-year undergraduate students for 2-month lab placements at one of our partner institutions in the summer of 2023.
Apply by the 18th of April 2023!
To apply, browse the available projects below, by institution, contact the lead supervisor (email provided) to discuss their support for your application and submit the completed Application Form by the closing date, 18 April 2023. Applications are competitive on the basis of a limited number of placements.
Email EASTBIO if you have any questions.
University of Edinburgh - College of Science and Engineering
Scotland's Rural College (SRUC)
Available projects at the University of Aberdeen:
Project title: The Impact of Deformed Wing Virus infection on Honeybee Cognition
Project supervisor: Dr Fabio Manfredini
Thematic area: Livestock & Aquaculture
Project Summary: Honeybees are important pollinators of many crop plants and essential for global food security, however honeybee health is declining due to a combination of factors, including climate change, pesticides, and pathogens. One of the most prevalent pathogens that is affecting honeybee colonies across the world is Deformed Wing Virus (or DWV). This virus is known to cause behavioural symptoms, including impaired learning ability, and accelerated behavioural maturation – i.e., a faster transition from nursing to foraging – which is also known to affect cognitive abilities. These symptoms threaten colonies, as complex learning is vital for honeybees to efficiently forage and navigate in the environment.
This research project will focus on improving our understanding of these behavioural symptoms in two ways: 1) measuring onset of foraging in infected bees, to assess how accelerated behavioural maturation correlate with viral loads, and 2) using a cognitive test (proboscis extension reflex or PER) to investigate how cognitive performance is influenced by accelerated behavioural maturation and viral infection. The student will gain a variety of basic lab skills in zoology and behavioural ecology, including bee-handling experience, observation of animal behaviour, and an understanding of how and why behavioural research is conducted.
Project dates: 5th of June to 31st of July 2023
Available projects at the University of Edinburgh - College of Science and Engineering
Project title: Investigation of a novel class of protozoan and fungal transmembrane proteins
Project supervisor: Jelena Baranovic
Thematic area: Health
Project Summary: Parasitic protozoa cause a range of diseases in animals and humans, including malaria, toxoplasmosis and meningitis. We have previously identified a new class of proteins in the malaria parasite, Plasmodium, and shown that they are essential for transmission of the parasite through the mosquito vector. The proteins are members of a novel 9 transmembrane helix protein superfamily that also includes a family of fungal proteins implicated in the regulation of calcium signal transduction pathways. Our bioinformatic analyses indicate these proteins are found exclusively in unicellular eukaryotes, including many parasitic protozoa, making them excellent targets for the development of novel drugs, required in the face of increasing drug resistance.
This project will explore these as yet uncharacterised proteins using human embryonic kidney (HEK) cells as in vitro cell expression system to test their potential role as calcium ion channels. The student will get the opportunity to express various members of this new protein family in HEK cells, explore their expression and subcellular localisation using immunofluorescence microscopy and a chance to perform live-cell calcium imaging to test whether the proteins can alter flow of calcium ions inside cells.
Project start date: 1st of June 2023
Project title: Ageing in a wild mouse population
Project supervisors: Tom Little and Amy Pederson
Thematic area: Rules of Life
Project Summary: Wild animals do not come with birth certificates. As we often do not know the age of a wild animal, studies of the ageing, or senescence, rate in the wild have been severely limited. Thus, while we know lots about human ageing, and the genetic, lifestyle or environmental factors that cause people to be ‘grey before their time’, we know very little about wild populations. In this project, you will be a part of a team that follows individual wood mice over time, determining chronological age and monitoring the ageing rate with a combination of analyses, including cutting edge molecular biomarkers of age. The student will participate in field work in a local woodland site, and use molecular or photographic techniques to determine the age of wild rodents. Thus, a range of skills will be acquired, including field work, rodent handling and molecular techniques in the laboratory, as well as data handling.
Project start date: 1st of June 2023
Project title: The role of ubiquitination in resistance to pathogens in plants
Project supervisor: Beatriz Orosa
Thematic area: Rules of Life
Project Summary: Pest represent the largest threat to crop production, causing yield losses of up to 40%. The interaction between plants and pathogens is complex, and in this interaction, ubiquitination acts as a central regulator of plant immunity. Ubiquitination involves the covalent attachment of the small polypeptide ubiquitin to substrate proteins, and it could be used to enhance resistance to pathogens. In order to do it, a real understanding of the role of the ubiquitome in regulating plant immune responses is needed it. During this project, the student will study how ubiquitination exerts a multi-layered regulation over plant immune responses, regulating different pathways through the use of mutants for different types of ubiquitin.
Project tasks:
• Infect Arabidopsis mutants with pathogens and characterize the effect of pathogenesis by measuring the lesions and pathogen biomass.
• Validate the activation of immune genes by PCR.
• Assess the accumulation of ubiquitinated targets and western blot.
This project will provide an excellent inter-disciplinary training opportunity, covering aspects of molecular biology and applying a wide variety of techniques. The student will be part of a large multidisciplinary and diverse team working in plant immunity at the University of Edinburgh, in close collaboration with world experts in synthetic biology and biochemistry.
Project dates: 1st June to 31st of July 2023
Project title: A new multi-partite virus
Project supervisor: Darren Obbard
Thematic area: Rules of Life
Project Summary: Viruses are arguably the strangest form of ‘life’, and one of the most surprising groups are multipartite viruses, in which each chromosome is separately packaged in its own viral particle. This life-history strategy seems to make no sense, as it means that multiple separate particles are needed to start an infection.
Although multipartite viruses are well known in plants, they have only recently been found in animals, and none has been extensively studied. We have recently discovered a completely new group of small DNA viruses in Drosophila that may be multipartite, and we would like to study them in the lab. This project will survey wild-caught flies by PCR to find infected individuals that can be used for future virus isolation and DNA sequencing.
Project dates: 5th of June to 21st of July 2023
Project title: Detection of virulence plasmids and antimicrobial resistance in Salmonella isolated from cattle
Project supervisor: Prerna Vohra
Thematic area: Livestock & Aquaculture
Project Summary: Salmonella enterica is a zoonotic pathogen of global importance. Cattle are a major reservoir of Salmonella serovars that cause disease in cattle and humans. The Salmonella virulence plasmids (pSV) are conserved and while their size may vary between serovars, they all carry the 7.8 kb spv operon, which is important for intracellular survival of Salmonella in host cells and systemic spread of the bacteria beyond the intestine. While commonly associated with some serovars, pSV can be transferred between strains. Similarly, plasmids carrying antimicrobial resistance genes can also be transferred between strains. In this study, the presence of pSV in Salmonella strains isolated from a cattle feedlot and their resistance to clinically relevant antibiotics will be investigated. The Salmonella strains belong to 11 different serovars and by (a) detecting the presence of pSV in these strains via PCR for genes of the spv operon and (b) performing antimicrobial susceptibility testing, we will gain insights into horizontal gene transfer within the Salmonella strains isolated from this feedlot. This project will provide skills in bacteriology (bacterial handling and culture), molecular microbiology (plasmid extraction, agarose gel electrophoresis, PCR) and antimicrobial susceptibility testing (disk diffusion, broth microdilution) as well as an understanding of bacterial surveillance.
Project dates: 21 June to 2 August 2023
Project title: Developing a validated method for the non-invasive analysis of an important biomarker to improve pig health and welfare
Project supervisors: Victoria Lee & Arianne Lowe
Thematic area: Health
Project Summary: Biomarkers, such as acute phase proteins (APPs), are an important tool for measuring animal health and welfare. APPs are often measured from blood samples, and sampling may be stressful for the animals concerned. Methods have been developed to measure some APPs from saliva as a non-invasive alternative, but these methods do not yet exist for all APPs. Developing validated laboratory methods to analyse these remaining biomarkers from saliva is a vital step to allow less stressful, non-invasive methods to be used. The project objective is to develop and validate new laboratory methods for analysing pig major acute phase protein (Pig-MAP) in saliva. Pig-MAP is an important indicator of inflammation and stress in pigs, but can currently only be analysed from blood. A validated salivary assay for Pig-MAP would represent a major step forward for the non-invasive measurement of biomarkers in pigs, with important applications in veterinary science and animal welfare research. This project offers students an opportunity to gain first-hand research experience in the SRUC Animal Welfare Biomarkers Laboratory, using state-of-the-art techniques including ELISA. The student will be supported to learn and develop their skills in the laboratory, with the potential to make an important contribution to scientific research.
Project start date:12th of June 2023 (start date flexible)
Project title: Phenotypic AMR resistance livestock and linked environments
Project supervisors: Lesley Smith and Arianne Lowe
Thematic area: Livestock & Aquaculture
Project Summary: Antimicrobial resistance (AMR) is widely recognised as a long-term global health challenge. The use of antibiotics in livestock production has been highlighted as a major contributor to the incidence of AMR in livestock. Previous SRUC studies have demonstrated that there are high levels of AMR gene carriage in livestock holdings, suggesting the potential for livestock units to be a source of AMR pollution into the surrounding environment. AMR is a complex One Health issue that spans over multiple settings, including the environment. However, few studies have sought to understand the role of the environment in the AMR system. This project will use classical culture-based phenotypic methods of testing for antimicrobial resistance of a bacteria to particular antibiotics. Thus, the objective of this project is to determine the phenotypic resistance of faecal samples from different livestock species, and their linked environments (e.g. soil and wildlife).
The student will gain experience in microbiology techniques such as making media, pouring plates, aseptic technique, maintaining and isolating cultures and carrying out antimicrobial resistance testing using biomerieux ETEST® strips.
The student will also gain experience of working within a busy research lab and have the opportunity to attend and present at regular lab meetings.
Project dates: 12th of June to 4th of August 2023
Project title: Vertical farming with speed hydroponics
Project supervisors: Ian Mackay, Rajiv Sharma, Chin Jian Yang
Thematic area: Crops & Soil
Project Summary: Controlled Environment Agriculture (CEA) is critical for delivering a sustainable and climate resilient crop production system with reduced food miles. Vertical Farming (VF) with a hydroponic system is an example of CEA with the benefit of efficient space use. However, the continuous rise in energy cost is prohibitive toward mainstreaming VF. There is an opportunity to reduce the cost by hastening the crop production cycle through Speed Breeding (SB)1. We will use pak choi (Brassica rapa ssp. chinensis) and barley (Hordeum vulgare) as horticultural and cereal crop models, respectively, for studying the potentials and impacts of SB in VF with hydroponics. (1) We will evaluate the variations in above- and below-“ground” morphologies using Image analysis and Machine Learning (ML) models. (2) We will test different light regime, temperature and media, and optimise the crop growth recipe under VF with SB and hydroponics.
Overall, this project is excellent for student to gain valuable skills and experience in plant biology and crop production. The training will provide the student with the knowledge and confidence to undertake further research and advance their future career. The student will have the opportunity to contribute to the research and development of VF with SB and hydroponics.
References:
1\Watson A et al. (2018) Speed breeding is a powerful tool to accelerate crop research and breeding. Nat Plants 4: 23-29.
Project dates: 5th of June to 28th of July 2023
Project title: Microbe-dependent heterosis in barley
Project supervisors: Rajiv Sharma, Chin Jian Yang
Thematic area: Crops & Soil
Project Summary: Soil microbiome plays an important role in plant development and its effect can vary depending on the genetics of the plants. A recent study reported the contributions of microbiome towards heterosis in maize1, revealing an interesting finding that heterosis in maize root biomass and germination rate was abolished when the plants were grown in sterile soil. We will test if the same conclusions can be drawn for heterosis in barley using a diverse set of inbred barley and their hybrids in untreated (field) and sterile (autoclaved) soil under standard growth conditions. The plants will be phenotyped for various below- and above-ground traits. The identities of soil microbiome will be determined using 16s ribosomal RNA (rRNA) sequencing and quantitative PCR (qPCR) methods. The root morphology will be imaged and simulated using the OpenSimRoot software2.
This project will provide valuable insights into the role of microbiome in barley heterosis and offers undergraduate students a solid foundation in scientific research methodology, data analysis, and interpretation, thereby boosting their confidence in considering and undertaking further research. Overall, this project presents an excellent opportunity for student to gain valuable skills training while contributing to advancing knowledge in the field of soil microbiomes and plant development.
References:
1\Wagner MR et al. (2021) Microbe-dependent heterosis in maize. Proc Natl Acad Sci USA 118: e2021965118.
2\Postma JA et al. (2017) OpenSimRoot: widening the scope and application of root architectural models. New Phytol 215: 1274-1286.
Project dates: 5th of June to 28th of July 2023
Project title: Impacts of speed breeding on barley epigenomics and shovelomics
Project supervisors: Rajiv Sharma, Chin Jian Yang
Thematic area: Crops and Soil
Project Summary: Speed Breeding (SB) improves the rate of genetic gain in modern crops by reducing the breeding cycle time. SB is achieved by disrupting the circadian clock through various imposed abiotic stresses such as extended photoperiod, elevated temperature and drought1. The focus in SB is largely on completing breeding cycles at the expense of above-ground architecture vigor, leaving the effects on the epigenome and below-ground largely unexplored. To study this we will use diverse barley accessions and then study three areas of research: (1) we will evaluate the variations in root morphology using image analysis and Machine Learning (ML) models, (2) we will use bisulfite PCR method to identify the methylation status (epigenetic marks) of key flowering-time genes, (3) we will simulate the root architecture2 and compare the simulate roots to the observed roots.
Overall, this project is an excellent opportunity for student to gain valuable skills training and experience in plant biology, which will help to boost their confidence in considering and undertaking further research in these fields. By contributing to a better understanding of the wider impacts of SB, students will have the chance to make meaningful contributions to advancing knowledge in this area of study.
References:
1\Watson A et al. (2018) Speed breeding is a powerful tool to accelerate crop research and breeding. Nat Plants 4: 23-29.
2\Postma JA et al. (2017) OpenSimRoot: widening the scope and application of root architectural models. New Phytol 215: 1274-1286.
Project dates: 5th of June to 28th of July 2023
Project title: Understanding the pathogenesis of equine pituitary tumours
Project supervisor: Ruth Morgan
Thematic area: Health
Project Summary: Equine Cushing’s Disease or Pituitary Pars Intermedia Dysfunction (PPID) affects more than 30% of horses over the age of 15. The disease has a significant impact on animal welfare, and its secondary complications are always life-limiting and often fatal. Despite the high prevalence, there are still big gaps in our understanding of the molecular pathogenesis of the disease. At post-mortem hyperplastic or adenomatous change of the melanotrophs is found, thought to be due to a loss of dopaminergic input but it is unclear if these are different diseases or a continuum. We hypothesise that ademomas can be distinguished from hyperplastic growth in the pituitary by the transcription and protein profile and that this can give us clues about the underlying pathogenesis. We will determine the protein and RNA levels of genes commonly associated with pituitary pathology in other species in pituitaries which are normal (n=10), hyperplastic (n=6) or adenomatous (n=7). The student will learn how to section and stain fixed pituitary sections and extract RNA from diseased and healthy pituitaries. They will quantify expression of regulators of Wnt signalling sonic hedgehog and BMP pathways (Andoniadou et al 2012) by immunohistochemistry and qPCR.
Project dates: 22nd of May to 14th of July 2023
Project title: Characterising the immune response to coinfections in lambs
Project supervisor: Naomi Fox
Thematic area: Livestock & Aquaculture
Project Summary: It is common for animals to be affected by more than one disease at any one time, and the presence of two infections can shift host resistance and impact disease severity. Despite coinfections being common, the progression of the immune response in the presence of such infections is not well known. This is partly due to the complexities of running large animal experiments with highly transmissible infections. Following a successful infection trial, we have a unique selection of samples that provide the rare opportunity to explore what happens when multiple pathogens spread through a flock of lambs simultaneously.
You will explore how the host’s immune system responds to the simultaneous challenge of multiple infections. During this lab-based project you will be working within an active research team and will receive tailored training in all lab techniques required.
Objective 1: Determine the bacterial communities in infected lambs.
Following training in DNA extractions and PCR, you will help to determine the bacterial communities present in pre-collected samples from a cohort of 96 lambs.
Objective 2: Characterise the immune response to mixed infections.
Using ELISAs you will characterise the hosts immune response over time.
Project start date: 1st of June 2023
