BIOS6010 Biomedical Science & Medical Project Brochure PDF

BIOS6010 Project Brochure for Biomedical Science and Medical Science students School of: Biological and Medical Sciences Faculty of: Health, Life and Physical Sciences “A wealth of information for the student choosing a project.” Andrew Jones – Module Leader of BIOS 6010...

BIOS6010 Project Brochure for Biomedical Science and Medical Science students School of: Biological and Medical Sciences Faculty of: Health, Life and Physical Sciences “A wealth of information for the student choosing a project.” Andrew Jones – Module Leader of BIOS 6010 “Investigating a topic of your choice was extremely rewarding and writing it up in the formal manner required is a massively valuable life skill.” Previous project student  2 Contents Foreword................................................................................................................................................. 3 Patrick Esser............................................................................................................................................ 4 Alison Forhead........................................................................................................................................ 5 Victor M Bolanos-Garcia......................................................................................................................... 6 Laura Gathercole..................................................................................................................................... 7 Caz Griffiths............................................................................................................................................. 8 Korneel Hens........................................................................................................................................... 9 Hee-Jeon Hong...................................................................................................................................... 10 Barbara Jennings................................................................................................................................... 11 Andrew Jones........................................................................................................................................ 12 Munira Kadhim..................................................................................................................................... 13 Ravinder Kanda..................................................................................................................................... 16 Kate Lines.............................................................................................................................................. 17 Shakeeb Moosavi.................................................................................................................................. 18 Ryan Pink............................................................................................................................................... 19 Paul K Potter......................................................................................................................................... 20 Priya Samuel.......................................................................................................................................... 21 Jack Sunter............................................................................................................................................ 22 Sue Vaughan......................................................................................................................................... 23 Oxford Brookes Centre for Functional Genomics................................................................................. 24 Oxford Target Therapeutics.................................................................................................................. 25 Projects at John Radcliffe Hospital........................................................................................................ 26 Publications with project students as authors...................................................................................... 27 Awards for project students................................................................................................................. 29  3 Foreword Welcome to BIOS6010 – Project! Hopefully this module will provide you with a unique experience during your studies at Oxford Brookes University. Here, you will be working with a supervisor and engaging in actual research, whether it be carrying out experiments in the lab, analysing data on the computer or doing a systematic review of the literature. Will you get any results? What will the results be? What does it all mean? That is the nature and excitement of research! Modules BIOS5002 and BIOS6010 work closely together to ensure the progression of your project journey. Thus, in BIOS5002 you will apply for projects you are interested in, be allocated a supervisor (hopefully one of your five choices), and under the guidance of your supervisor you will write a research proposal outlining the importance of the project. This, then, leads into BIOS6010, where you will do the actual research over a period of several weeks. What will you have to show for all this hard work? The answer to that is easy – a 9000 word dissertation. But have no fear, for the construction of this magnum opus will be broken down into two stages, first a literature review, which is an elaboration/extension of your research proposal. This review will be marked and you will get feedback for improvement, which is quite handy as the literature review will basically serve as the Introductory Chapter for your dissertation (stage two). Throughout this process, you should find yourself getting more familiar with the topic of your project so that, perhaps, you will give a ten minute oral presentation about your research with the enthusiasm and confidence of a mini-expert. Enough of the preliminaries – on to the first task at hand, choosing a research topic and therefore your potential supervisor. What follows are brief outlines of the available projects. Whilst going through them, hopefully you will begin to appreciate the wide diversity of research topics and techniques on offer. Also look out for supervisors external to Oxford Brookes who are offering projects for your consideration, giving you the opportunity to do research at other respectable institutions such as the John Radcliffe Hospital or the University of Oxford. Once you have identified projects of interest, you are strongly encouraged to contact the supervisors to find out more. This will show the supervisor that you are keen on doing his/her research, which will likely boost the chances of your application being successful. Also, it will help you in filling out the first page of your application form should that project be your first choice. You will need to submit the application form during the first couple of weeks of BIOS5002. Wishing you a memorable research experience (hopefully in a good way). Andrew Jones Module leader for BIOS6010 7 November 2019  4 Patrick Esser [email protected] MOReS, Staff Profile Type of projects available: Lab, computer or literature-based research Research interests The centre for Movement, Occupation and Rehabilitation Exercise Sciences (MORES) brings together a multidisciplinary team including allied health professionals (GPs, Physio and Occupational Therapists), Engineers (Bio and Mechanical), Data Scientists and Exercise physiologists ranging from PhD up to internationally recognised Professors in clinical rehabilitation. Projects on offer range from cardiovascular health to lung function in adolescents, and EMA and interventional approaches to explore and combat fatigue, movement and quality of life in clinical populations and trauma. Common techniques involved Measurement suite of Movement Quality and Quantity Measurement suite of Physical Activity & Physiology Remote delivery of Interventions (Digital Health) Development of new digital healthcare outcome measurements Gold Standard devices to validate kinetic and kinematic devices Relevant publications MOReS website, MOReS ResearchGate Patrick’s Google Scholar, Patrick’s ResearchGate  5 Alison Forhead [email protected] My web-site Type of projects available: Lab or literature-based research Research interests Towards term, a wide range of physiological systems in the fetus mature ready for, arguably, the most important event in life: the successful transition from the intrauterine to extrauterine environment. These include maturation of the fetal lungs to enable normal respiratory function; activation of heat production in brown adipose tissue; and changes to digestive and metabolic processes to maintain blood glucose levels at birth. In the UK, preterm delivery affects approximately 1 in 13 of pregnancies, and prematurity is the leading cause of neonatal mortality and morbidity. My research is focussed on understanding the mechanisms responsible for fetal maturation, especially the role of hormones such as glucocorticoids, thyroid hormones and leptin. It has an integrative approach to examine the process of fetal maturation from the gene to systems level and combines studies of whole animal physiology with stereological, biochemical and molecular biology techniques. Our research findings have important implications for understanding the normal processes of fetal growth and development, the consequences of prematurity and fetal endocrine disorders, and the mechanisms underlying developmental programming of adult health and disease. Common techniques involved Histology to assess the basic structure of tissues Immunohistochemistry to localise target proteins and identify cell types Western blotting to quantify tissue content of target proteins Relevant publications Fowden AL & Forhead AJ (2015) Glucocorticoids as regulatory signals during intrauterine development. Experimental Physiology 100: 1477-1487. Forhead AJ & Fowden AL (2014) Thyroid hormones in fetal growth and prepartum maturation. Journal of Endocrinology 221: R87-R103. Forhead AJ & Fowden AL (2009) The hungry fetus? Role of leptin as a nutritional signal before birth. Journal of Physiology 587: 1145-1152.  6 Victor M Bolanos-Garcia [email protected] https://www.brookes.ac.uk/profiles/staff/victor- bolanos-garcia Type of projects available: Lab or computer-based projects Research interests Maintenance of correct chromosome numbers is absolutely critical for all living organisms. An evolutionarily conserved and self-monitoring surveillance system, the spindle assembly for the mitotic checkpoint (SAC), has therefore emerged to ensure the timely and high fidelity transmission of the genetic material to an offspring. In humans, failure of the SAC is a major determinant of aberrant chromosome segregation and genome instability and represents the leading cause of pregnancy loss and of birth and development defects and oncogenesis. Research in my group aims to define the structural and functional basis of the SAC and to develop new therapies for the early diagnosis and the treatment of human malignancies including cancer and age-associated genetic disorders. Common techniques involved Recently considerable progress has been made in understanding the composition of the SAC and the recruitment hierarchy of its components. SAC genes overexpression. However, the molecular interactions of the SAC with the kinetochore have Yeast-two hybrid system. proved elusive, even though they are clearly indispensable for the accurate Differential scanning fluorimetry. segregation of chromosomes. The understanding of the function and mode Tissue culture techniques. of regulation of this surveillance system requires definition of the structural details of the individual subunits and different subcomplexes. For this, we Relevant have exploited publications biochemical, biophysical, structural and cell biology methods including X-ray protein crystallography, NMR, small-angle X-ray scattering, surface plasmon resonance, analytical ultracentrifugation, isothermal 1. Elowe S, Bolanos-Garcia VM. The Spindle Checkpoint Proteins BUB1 and BUBR1: (SLiM)ming down to the calorimetry basics. Trends inand ES-nanospray Biochem MS. The2.studies Sci (2022) 47:352-366. on the SACVM, Rus A, Bolanos-Garcia andBastida otherA,signalling Morales P. Identification of novel heparanase inhibitors using virtual screening. Catalysts (2022) 12:503. 3. Curtis NL, systems Ruda haveP, Bolanos-Garcia GF, Brennan shown thatVM.signalling Deregulation assemblies often involve of chromosome segregation concerted and cancer. Annu Rev Cancer Biol (2020). folding and binding and cooperative interactions to give extended multiprotein assemblies. These have led to a general model for high signal- to-noise signalling involving weak binary interactions to well-defined but  7 Laura Gathercole [email protected] My website Type of projects available: Computer-based projects Research interests Bile acids are potent regulators of metabolism. My research focuses on understanding how the dysregulation of bile acid synthesis impacts on obesity and metabolic diseases. In collaboration with the Oxford Biobank I have identified single nucleotide polymorphisms (SNPs) in bile acid synthesis genes which are associated with changes in the levels of bile acid metabolites in the blood and markers of metabolic health (Inc. body mass index, % fat mass, and serum lipids). In this project you will analyse our experimentally derived data, and data from open-access online repositories, to investigate how these SNPs impact on metabolism and metabolic health. Common techniques involved Bioinformatics Mapping SNPs on to a gene Phenotype-genotype correlations Function prediction Linkage disequilibrium Relevant publications Role of Bile Acids in Metabolic Control. Molinaro A, Wahlström A, Marschall HU. Trends Endocrinol Metab. 2017 Nov 28. pii: S1043-2760(17)30151-0. Genotype-phenotype associations in obesity dependent on definition of the obesity phenotype. Kring SI, Larsen LH, Holst C, Toubro S, Hansen T, Astrup A, Pedersen O, Sørensen TI. Obes Facts. 2008;1(3):138-45.  8 Caz Griffiths [email protected] Type of projects available: Literature-based research Literature-based projects I will be offering a different approach to research projects, for students who don’t like lab work! These research approaches are widely used in medical sciences. Be aware – they are just as much hard work as experimental projects! My main interest is viruses, so you may want to investigate antiviral drug or vaccine strategies, epidemiology of emerging diseases, or the mechanisms by which a virus might be leading to off-target outcomes. In recent years students have investigated virus roles in cancers, long-Covid, fertility, foetal development and post-viral fatigue. We can discuss your ideas together and start searching for a workable research question that interests you. Systematic Reviews can be designed to suit your scientific interest. The research approach involves finding and phrasing a suitable question that allows you to perform an extensive literature search. You will subsequently screen and select a core collection of well-matched publications and choose only those conducted with rigour, to reach your final collection. From these, you will extract and evaluate relevant data and evaluate it, bearing in mind the different experimental approaches used. Often, this can provide you with data that you can statistically analyse to address your own research question. Alternatively, it may offer data that allows you to propose a mechanism of action, or test a hypothesis that may explain an as-yet-unknown metabolic or causal link. You’ll learn and practice a professional-level scientific research approach, and follow a robust methodology to mining the scientific literature. You’ll have to thoroughly explore all accessible studies relevant to your research question, and judge the experimental design of the studies that your methods identify. Finally, you’ll offer a critical analysis of the collective data in your selected studies.  9 Korneel Hens [email protected] My website Type of projects available: Lab-based projects Research interests Why do we fancy a tasty dessert after a large meal but not a dry piece of bread? The motivation to eat can arise from the need to maintain body weight and metabolic function (homeostatic feeding), or from the sensory perception of pleasure upon food intake (hedonic feeding). Over the last 50 years, significant efforts have been made to understand the neural and molecular basis of homeostatic feeding regulation. Much less is known about hedonic feeding, although overconsumption of palatable food is considered a major factor contributing to the surge in obesity and diabetes. Our lab uses the fruit fly Drosophila melanogaster as a model organism to uncover the neural and molecular circuits that regulate hedonic feeding. We have identified several genes that are up- or downregulated in the brain upon changes in the fly’s diet. These genes are strong candidates as regulators of hedonic feeding and await further characterization. Common techniques involved Fly genetics Immunohistochemistry Molecular biology (PCR, cloning, bacterial transformation) Feeding assays Relevant publications Prasad N. and Hens K. (2018) Sugar promotes feeding in flies via the serine protease homolog scarface. Cell Rep. 24(12): 3194-3206. Dus M., Ai M. and Suh G.S. (2013) Taste-independent nutrient selection is mediated by a brain-specific Na+/solute co-transporter in Drosophila. Nat. Neurosci. 16(5): 526-528. Burke C.J. and Waddell S. (2011) Remembering nutrient quality of sugar in Drosophila. Curr. Biol. 21(9): 746-750.  10 Hee-Jeon Hong [email protected] Website Type of projects available: Lab-based projects Research interests A fundamental understanding of bacterial antibiotic tolerance and resistance mechanisms will be an important part of any future strategy aimed at solving the growing problems with treating microbial infections. We are using a harmless, soil derived Gram-positive bacteria, Actinomycetes, as a model system to investigate the mechanisms involved in sensing, responding and adapting to antibiotic attack. Through this study, we have developed several novel bioassays capable of detecting any compound that targets bacterial cell wall and the aim of this project is to screen natural product extract library through a bioassay system and discover novel antibiotics. Common techniques involved preparation of medium bacterial cell culture and antibiotic diffusion assay understanding and use of bioassay system understanding and use of a wide range of antibiotics Relevant publications Truman, A.W., Kwun, M.J., Cheng, J., Yang, S.H., Shu, J.-W., and Hong, H.-J. (2014) Antibiotic resistance mechanisms inform discovery: Identification and characterization of a novel Amycolatopsis strain producing Ristocetin. Antimicrob. Agents Chemother. 58:5687-5695.  11 Barbara Jennings [email protected] Link to my web page Type of projects available: Lab-based projects Research interests Precise control of gene expression is critical for the development and survival of all animals. Failure of gene regulation during development usually results in death of the embryo or birth defects, and in adult life leads to disease including cancer. Transcription factors that recognize specific DNA sequences play a central role in gene regulation. Their action can be either to enhance (activate) or inhibit (repress) transcription of specific target genes. Most transcription factors do not have intrinsic activating or repressive activity but recruit co-factors that regulate transcription. For example, the Groucho family of co-repressor proteins are recruited by many different transcription factors that repress transcription during animal development. Although the importance of gene repression by transcription factors is well established, the molecular mechanisms underlying repression by transcription factors is not well understood. The aim of the projects that I am offering will be to uncover molecular mechanisms used by transcription factors to repress transcription. We will use the fruit fly (Drosophila melanogaster) as a model system. Common techniques involved Genetics (Drosophila) Microscopy Relevant publications Kaul, A.K., Schuster, E.F., and Jennings, B.H. (2015). Recent insights into Groucho co-repressor recruitment and function. Transcription 6, pp7–11. Jennings, BH., (2011). “Drosophila – a versatile model in biology & medicine”. Materials Today: 14, pp190–195.  12 Andrew Jones [email protected] My website Type of projects available: Lab-based projects Research interests My research focuses on studying ion channels, which include nicotinic acetylcholine receptors, GABA receptors and voltage-gated sodium channels (VGSCs). These receptors play important roles in the nervous system and are targets of insecticides. The project will involve studying VGSCs from mosquitoes that spread malaria (Anopheles). The mosquitoes you will be working on have been sent from Nigeria, as part of a collaboration with the Nigerian Institute of Medical Research. You will be looking for mutations in the vgsc gene, which causes insecticide resistance, from these mosquitoes. The results from the project will provide information about the status of insecticide resistance in Africa and can inform the future use of insecticides to effectively control the spread of serious diseases. Common techniques involved, classic Molecular Biology! DNA extraction from mosquitoes PCR to amplify regions of the mosquito voltage-gated sodium channel Agarose gel electrophoresis DNA purification using spin columns Sequence Analysis to identify mutations Relevant publications Clarkson, C.S. et al. (2021). The genetic architecture of target-site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii. Mol Ecol Nov 30(21):5303-5317. CHECK OUT Marcombe et al. 2022 and 2024 in ‘Publications with project students as authors’ at the end. The highlighted students were my project students from previous years and their work led to these publications. I’m hoping that this year our findings on sodium channels will be included in a future publication.  13 Munira Kadhim UG Projects: 2023 - 2024 Munira Kadhim and John Harrison Munira Kadhim [email protected] ; John Harrison [email protected] Type of projects available: Literature-based research Project titles: 1) Individual sensitivity to radiation-induced cancer 2) Radiation and diseases of the circulatory system 3) Radiation and neurodegenerative diseases 1. Individual sensitivity to radiation We are all exposed to ionising radiation from natural sources and many of us will also be exposed during diagnostic medical procedures (CT scans and X-radiography). Some workers can receive higher doses and accidents can also expose workers and members of the public to higher doses. Epidemiological studies show that individuals differ in their response to ionizing radiation and the resulting risks of cancer and other health effects. In particular, young children are at greater risk than adults for most types of radiation-induced cancer. There is also an established difference between males and females, with females being more sensitive for most cancer types. Risk estimates also vary between populations in relations to differences in background cancer incidence. For example, stomach cancer tends to be higher in Asian populations, while breast cancer is higher in Western populations. It is also recognised that genetic diseases can result in greater radiation sensitivity, for example, in individuals with defective DNA repair genes, as in  14 Fanconi’s Anaemia and Ataxia Talangiectasia. Cellular studies that provide measures of DNA damage and other biological endpoints provide evidence of genetic variation in sensitivity to radiation between individuals in populations. In the future, it may be possible to assess the risks and likelihood of cancer for individuals. Currently, radiation protection standards do not take such differences into account. The project will involve literature search and data evaluation to: (a) briefly review the central findings from epidemiological studies on differences between males and females and age at exposure, (b) briefly review the effects of genetic disorders, (c) consider evidence of genetic variation and radiation sensitivity in populations, and (d) consider the implications of knowledge of individual sensitivity for the protection of workers and members of the public. 2. Radiation and diseases of the circulatory system We know from epidemiological studies that ionising radiation can increase risks of diseases of the circulatory system, such as heart attack and strokes, if the radiation dose is sufficiently high. An important question is whether there is a (lower) risk of disease associated with lower doses of radiation. Currently, protection practice accounts only for risks of cancer and heritable effects. Cardiovascular disease is the leading cause of death globally, so even a small increase in risk due to radiation exposure could have an important impact in terms of radiation-related deaths. The project will involve literature search and data evaluation to: (a) briefly review the central findings from epidemiological studies on the relationship between radiation exposure and incidence and death from circulatory diseases, (b) briefly review the mechanisms of damage that result in circulatory diseases and the possible role of radiation as a causative agent, and (c) consider the implications of knowledge of this topic for the protection of workers and members of the public. 3.Radiation and neurodegenerative diseases There is increasing epidemiological evidence that ionising radiation can increase risks of the development of neurodegenerative disease, particularly Parkinson’s Disease. Neurodegenerative diseases, including Alzheimer’s disease and Parkinson’s disease, are common and growing causes of morbidity and mortality worldwide, particularly in older people. Currently, general radiological protection practice does not take account of risks of these diseases. The project will involve literature search and data evaluation to: (a) briefly review the central findings from epidemiological studies on the relationship between radiation exposure and incidence and death from neurodegenerative diseases, (b) briefly review the mechanisms of damage that result in neurodegenerative diseases and the  15 possible role of radiation as a causative agent, and (c) consider the implications of knowledge of this topic for the protection of workers and members of the public. Relevant Publications: Goodhead, D.T. Initial events in the cellular effects of ionizing radiations : clustered damage in DNA. Int. J. Radiat. Biol. 65, 7-17 (1994). Shore, R.E. et al. Implications of recent epidemiologic studies for the linear nonthreshold model and radiation protection. J. Radiol. Prot. 38, 1217-1233 (2018) ICRP. 2007 Recommendations of the International Commission on Radiological Protection. Ann. ICRP 37 (2-4) (2007). ICRP. Use of dose quantities in radiological protection. Ann. ICRP 50 (1) (2021). Kadhim, M., Hill, M. Non-targeted effects of radiation exposure: recent advance and implications. Radiation Protection Dosimetry (10.1093/rpd/ncv167) (2015). Al-Mayah, H. et al. Possible role of Exosomes Containing RNA in mediating Non-Targeted Effect of Ionizing Radiation. Radiation Research 177: 539-545 (2012) Ammar, H. et al. Exosome-Mediated Telomere Instability in Human Breast Epithelial Cancer Cells Post X-Irradiation. Radiation Research 187, 98–106 (2017) DOI: 10.1667/RR14201.1 Wakeford, R. Risk of diseases of the circulatory system after low-level radiation-exposure – an assessment of evidence from occupational exposures. J. Radiol. Prot. 42 020201 (2022) Circulatory Disease Risk. Documents of the Health Protection Agency, RCE-16 (2010) Tapio, S. et al. Ionizing radiation-induced circulatory and metabolic diseases. Environmental International 146, 106235 (2021) Azizova, T. et al. Occupational exposure to chronic ionizing radiation increases risks of Parkinson’s disease incidence in Russia Mayak workers. Int. J. Epidemiol. 49 435-447 (2020) Miller, K.B. et al Ionizing radiation, cerebrovascular disease, and consequent dementia: a review and proposed framework relevant to space radiation exposure. Front/. Physiol. 1008640 (2022) S. Bhattacharya, A. Asaithamby, Ionizing radiation and heart risks, Semin Cell Dev Biol (2016), http://dx.doi.org/10.1016/j.semcdb.2016.01.045.  16 Ravinder Kanda [email protected] My website Type of projects available: Computer or literature-based research Research interests The study of retroviruses and their association with diseases, an example of which is cancer. Common techniques involved The use of Bio Linux and BLAST to analyse genome sequences. Relevant publications Kanda RK and Coulson T. (2015). The effect of life history on retroviral genome invasions. PLoS ONE 10 (2) (2015) pp.1-17  17 Kate Lines [email protected] My website Type of projects available: Lab-based projects Research interests Epigenetic regulation of gene expression is now one of the hallmarks of cancer. My research focusses on examining how these mechanisms, including DNA methylation, histone organisation and miRNA expression differ in cancer compared to normal cells. I’m particularly interested in studying epigenetic mechanisms in hormone secreting cancers, including pancreatic neuroendocrine tumours that are a rare phenomenon as they have a low mutation rate compared to other cancer types. Common techniques involved DNA and RNA extraction PCR to quantify expression of specific genes Western blot to quantify expression of specific proteins Histology to assess protein expression in different cell types Relevant publications English KA, Goldsworthy M, Willis B, Kooblall KG, Birla S, Selberherr A, Stevenson M, Shariq OA, Oberg AL, Wang T, Carmichael J, Mavrommatis K, Escoubet L, Thakker RV, Howles SA, Lines KE. Calcium sensing receptor expression is downregulated in gastroenteropancreatic neuroendocrine tumours via epigenetic mechanisms. Int J Cancer. 2024. Kooblall KG, Stokes VJ, Shariq OA, English KA, Stevenson M, Broxholme J, Wright B, Lockstone HE, Buck D, Grozinsky-Glasberg S, Yates CJ, Thakker RV, Lines KE. miR-3156-5p is downregulated in serum of MEN1 patients and regulates expression of MORF4L2. Endocr Relat Cancer. 2022;29(10):557-68. Lines KE, Stevenson M, Filippakopoulos P, Muller S, Lockstone HE, Wright B, Grozinsky- Glasberg S, Grossman AB, Knapp S, Buck D, Bountra C, Thakker RV. Epigenetic pathway inhibitors represent potential drugs for treating pancreatic and bronchial neuroendocrine tumors. Oncogenesis. 2017;6(5):e332.  18 Shakeeb Moosavi [email protected] My website Type of projects available: Lab or literature-based research Research interests My primary research interest is to find out how breathlessness (‘dyspnoea’) arises so that more effective drugs can be developed to relieve dyspnoea when the underlying disease r can’t be cured. The multidisciplinary research involves experiments on healthy volunteers and various patients who are inordinately breathless. I have tested hypotheses regarding ‘air hunger’ (an unpleasant component of dyspnoea), validated ways to induce specific components of dyspnoea using specially-constructed breathing circuits and developed a unique questionnaire that quantifies overall breathlessness (intensity and unpleasantness) and is based on the language patients use to describe their experience. The work has guided on-going clinical studies including randomised-controlled trials to test novel interventions. Common techniques involved Use of specially constructed breathing circuits (to test sensitivity to induced breathlessness), Cardiopulmonary Exercise Testing (to test response to exercise) and Transcranial Doppler Ultrasound (to measure cerebral blood flow) in healthy volunteers and patients. Non-invasive cardiorespiratory measurements including ECG, HR, BP, end-tidal PCO2, Oxygen saturation, O2 consumption, CO2 production, Ventilation, Respiratory Rate and Tidal Volume. Assessment of breathlessness using rating scales (e.g. visual analogue scale) and multidimensional dyspnoea questionnaires (e.g. D12) Relevant publications Grogono J, Butler C, Izadi H, Moosavi, SH (2018) Inhaled furosemide for relief of air hunger versus sense of breathing effort: A randomized controlled trial. Respiratory Research 19(1):181 View full text here Banzett RB, Moosavi SH (2017), 'Measuring dyspnoea: new multidimensional instruments to match our 21st century understanding' European Respiratory Journal 49 (3) Full-text link Binks AP, Evans KC, Reed JD, Moosavi SH, Banzett RB (2014) “The time-course of cortico-limbic neural responses to air hunger”. Respir Physiol Neurobiol, 208:78-85 Full-text link Yorke J, Moosavi SH, Shuldham C, Jones PW (2010) Quantification of dyspnoea using descriptors: development and initial testing of the Dyspnoea-12.Full-text link  19 Ryan Pink [email protected] My website Type of projects available: Computer-based projects Research interests Extracellular Vesicles Cancer Diagnostics Public Engagement of Science Common techniques involved Data mining Basic Bioinformatics Genomics Public Engagement of Science Relevant publications Cisplatin induces the release of extracellular vesicles from ovarian cancer cells that can induce invasiveness and drug resistance in bystander cells. DOI: 10.1098/rstb.2017.0065 Identification of novel cancer biomarkers of prognostic value using specific gene regulatory networks (GRN): a novel role of RAD51AP1 for ovarian and lung cancers. https://doi.org/10.1093/carcin/bgx122 Pink RC, Beaman E, Samuel P, Brooks SA, Carter DRF, 'Utilising extracellular vesicles for early cancer diagnostics: benefits, challenges and recommendations for the future' British Journal of Cancer 126 (2022) pp.323-333 Balestri M, Campera M, Beaman E, Bell D, Pink R, Nekaris KAI, 'Let’s get virtual! Reinventing a science festival during a pandemic: limitations and insights' International Journal of Science Education, Part B: Communication and Public Engagement 12 (3) (2022) pp.193- 202  20 Paul K Potter [email protected] My website Type of projects available: Lab-based projects Research interest Modelling disease has led to great advances in the treatment of disease. I am interested in developing and characterising novel models of disease to identify new genes and pathways associated with disease, with a particular emphasis on chronic and age-related disease. A particular emphasis is extracellular matrix dysfunction in relation to chronic disorders, and includes research into renal disease, bone disorders and osteoarthritis. I also have an interest in inflammatory bowel disease and consequences of mitochondrial dysfunction. Common techniques involved Genetic analysis; SNP mapping, PCR, sequencing Protein analysis; Western blotting, ELISA, Histology Relevant publications (1) Falcone et al. A novel model of nephrotic syndrome results from a point mutation in Lama5 and is modified by genetic background. Kidney International, in press Oct 2021. (2) Portero et al. Pro-arrhythmic effects of elevated branched chain amino acid levels. Cardiovascular Research, 2021; cvab207 (3) Randles et al. Identification of an Altered Matrix Signature in Kidney Aging and Disease. JASN, 2021, 32 (7) 1713-1732 (4) Bellantuono et al. A toolbox for the longitudinal assessment of healthspan in ageing mice. Nature Protocols, 2020, 15: 540–574 (PMID: 31915391) (5) Potter et al. Novel gene function revealed by mouse mutagenesis screens for models of age-related disease. Nature Communications, 2016, 7:12444  21 Priya Samuel [email protected] My website Type of projects available: Literature-based research Research interests I work with Dr. Dave Carter on cancer biology, in particular, drug resistance in cancer cells. I am interested in the various modulators, mechanisms and genetic factors by which cancer cells evade death when treated with a chemotherapeutic drug. I am exploring the role of microRNAs and Extracellular vesicles in drug resistance of cancer cells. The projects I am offering are systematic literature reviews. This involves following a prescribed method to review published studies extracting, analysing and interpreting data from these studies. The topics researched are flexible and can be tailored to your interests. While some topics have focused on specific microRNAs and their role in certain diseases, others have involved a range of themes such as “acupuncture in osteoarthritis” or “aldehyde dehydrogenases and their role in alcohol addiction”. Common techniques involved The projects that I offer are systematic literature reviews. These are literature-based projects which follow a defined and prescriptive methodology and involve unbiased choice of papers, methodical extraction of data from the papers followed by critical analysis and interpretation of the data. Relevant publications Samuel P, Mulcahy LA, Furlong F, McCarthy HO, Brooks S, Fabbri M, Pink RC, Carter DRF, 'Cisplatin induces the release of extracellular vesicles from ovarian cancer cells that can induce invasiveness and drug resistance in bystander cells.'Philosophical Transactions B: Biological Sciences 373 (1737) (2017) Samuel P, Fabbri M, Carter DRF, 'Mechanisms of drug resistance in cancer: the role of extracellular vesicles' Proteomics 17 (23/24) (2017) Pink RC, Samuel P, Massa D, Caley DP, Brooks SA, Carter DRF, 'The passenger strand, miR-21-3p, plays a role in mediating cisplatin resistance in ovarian cancer cells' Gynecologic Oncology 137 (1) (2015) pp.143-151 Samuel P, Pink RC, Brooks SA, Carter DR, 'miRNAs and ovarian cancer: a miRiad of mechanisms to induce cisplatin drug resistance.'Expert Review of Anticancer Therapy 16 (1) (2016) pp.57-70  22 Jack Sunter [email protected] My website Type of projects available: Lab-based projects Research interests My research focuses on the eukaryotic parasites, Leishmania mexicana and Trypanosoma brucei, which cause diseases that affect the poorest people in less developed countries around the world. These parasites have evolved an amazing diversity of shapes and forms that are adapted to the different ecological niches they encounter as they progress through their complex life cycles. In the lab we study how the cell shape of these parasites is formed, maintained, and changed. In the lab you will be looking at the effect of knocking out cytoskeletal proteins on the shape of these parasites. Common techniques involved Light microscopy Immunofluorescence Scanning electron microscopy Image analysis on ImageJ Relevant publications Sunter JD, Gull K. (2017) Shape, form, function and Leishmania pathogenicity: from textbook descriptions to biological understanding. Open Biology. Halliday C, Yanase R, Catta-Preta CMC, Moreira-Leite F, Myskova J, Pruzinova K, Volf P, Mottram JC, Sunter JD (2020) Role for the flagellum attachment zone in Leishmania anterior cell tip morphogenesis. PLoS Pathog.  23 Sue Vaughan [email protected] My website Type of projects available: Lab-based projects Research interests My research focuses on eukaryotic protozoal parasite Trypanosoma brucei, which causes African sleeping sickness in Humans and Nagana in Cattle. We are interested in the role of the flagellum in the pathogenicity of the parasite and use state of the art 3D microscopy techniques. Projects in my lab would involve looking at the effect of knocking out genes involved in assembling flagella and using our scanning electron microscope. Common techniques involved For this project you will use our scanning electron microscope (SEM). Relevant publications Hughes L, Borrett S, Towers K, Starborg T and Vaughan S. (2017). Patterns of organelle ontogeny through a cell cycle revealed by whole-cell reconstructions using 3D electron microscopy. J Cell Sci 130(3):637-647. Wheeler RJ, Scheumann N, Wickstead B, Gull K, Vaughan S (2013). Cytokinesis in Trypanosoma brucei differs between bloodstream and tsetse trypomastigote forms: implications for microtubule-based morphogenesis and mutant analysis. Mol Microbiol, 90(6):1339-55.  24 Oxford Brookes Centre for Functional Genomics [email protected] Centre website Type of projects available: Computer-based projects Research interests High-throughput sequencing has revolutionized the field of molecular biology by enabling large- scale whole genome sequencing as well as a plethora of genomics and transcriptomics techniques. The sheer amount of data produced however risks creating a gap between data production and understanding the underlying biological mechanisms. At the Centre for Functional Genomics, we explore different next generation sequencing approaches to understand the genomic and genetic principles that govern biological form and function. We use state-of-the-art methods to decipher how genes control life and how genetic changes cause differences between organisms. The Centre for Functional Genomics offers undergraduate bioinformatics projects applying genomic and transcriptomic data across a wide range of topics. You will learn to handle large data sets and to extract biological meaning from them. As data throughput continues to increase in virtually all aspects of science, these are essential skills for future scientists. Common techniques involved Bioinformatics Genome building and annotation Variant analysis (WGS, exome) Gene expression analysis (RNA-seq) Relevant publications Ang, Roesma, Nijman, Meier & Srivathsan, 2019. Faecal DNA to the rescue: Shotgun sequencing of non-invasive samples reveals two subspecies of Southeast Asian primates to be Critically Endangered species. bioRxiv: 867986. https://doi.org/10.1101/867986 Königer, Arif & Grath, 2019. Three Quantitative Trait Loci Explain More than 60% of Variation for Chill Coma Recovery Time in a Natural Population of Drosophila ananassae. G3 (Bethesda) 9(11):3715- 3725. https://doi.org/10.1534/g3.119.400453 Gaspar, Arif, Sumner-Rooney, Kittelmann, Bodey, Stern, Santos Nunes & McGregor, 2020. Characterization of the Genetic Architecture Underlying Eye Size Variation Within Drosophila melanogaster and Drosophila simulans. G3 (Bethesda) [Online ahead of print]. https://doi.org/10.1534/g3.119.400877 Herndon, Shelton, Gerischer et al., 2019. Enhanced genome assembly and a new official gene set for Tribolium castaneum. BMC Genomics, 21 (1), 47. https://doi.org/10.1186/s12864-019-6394-6  25 Oxford Target Therapeutics Contact: [email protected] Website: https://ottx.co.uk/ https://www.youtube.com/watch?v=P_dbB0cBOFM&feature=youtu.be Type of projects available: Lab, computer or literature-based research Research interests Oxford Target Therapeutics Ltd. (OTT) is a pioneering pharmaceutical company focused on advancing innovative cancer therapies. We specialise in identifying and developing novel drug candidates that target crucial cellular processes involved in cancer progression. Our mission is to bridge the gap between cutting-edge research and transformative cancer treatments, empowering hope for patients facing this challenging disease. Common techniques involved Computational biology (analysis of cancer protein target-drug interactions). Gene expression in heterologous expression systems (overproduction of cancer drug targets in bacteria and insect cells). Protein biochemistry and biophysics (high throughput purification of protein drug targets and quantification of protein-ligand binding affinities). Cell culture-based assays (quantification of drug potency in cancer cells in culture). Relevant publications Pugh L, Pancholi A, Purat PC, Agudo-Alvarez S, Benito-Arenas R, Bastida A, Bolanos-Garcia VM. Computational Biology Dynamics of Mps1 Kinase Molecular Interactions with Isoflavones Reveals a Chemical Scaffold with Potential to Develop New Therapeutics for the Treatment of Cancer. Int J Mol Sci. 2022. DOI: 10.3390/ijms232214228. Tomoni A, Lees J, Santana AG, Bolanos-Garcia VM, Bastida A. Pseudokinases: From Allosteric Regulation of Catalytic Domains and the Formation of Macromolecular Assemblies to Emerging Drug Targets. Catalysts 2019. DOI: 10.3390/catal9090778.  26 Projects at John Radcliffe Hospital Title: Analytical evaluation of point of care testing glucometers for glucose and ketones Details: The project will involve assessing the analytical accuracy and precision of commercial glucometer devices as part of market engagement prior to procurement. The work will focus on comparing results across the analytical range to those produced by the laboratory analysers (Abbott Alinity) and the benchtop blood gas analysers (Radiometer ABL90 Flex Plus). The work will focus on patient cohorts with abnormal haematocrits (paediatrics) and low concentrations. Full training will be provided. The project will require efficient methodical working due to the labile nature of the analytes. Title: Assessing the impact of the Sysmex BT-50 module on QC performance, time- efficiency and instrumentation performance. Details: The Sysmex BT-50 is a new automated QC module which optimises the storage, preparation and processing of QC material on the Sysmex XR. The project will involve assessing the QC performance (accuracy and precision) of QC ran from the Sysmex BT-50 compared with standard manual preparation and processing of QC material and how the effect this new module has on staff time saved, how this saved time is used to enhance the service and how the instrumentation performance is effected (i.e. does it result in a reduction of service calls to Sysmex). For more information contact Simon Duffy [email protected].  27 Publications with project students as authors Bendell C, Moosavi SH and Herigstad M. (2019). Low-level carbon monoxide exposure affects BOLD fMRI response. J Cereb Blood Flow Metab Nov 11:271678X19887358. Camm EJ, Inzani I, De Blasio MJ, Davies KL, Lloyd IR, Wooding FBP, Blache D, Fowden AL and Forhead AJ. (2021). Thyroid hormone deficiency suppresses fetal pituitary-adrenal function near term: implications for the control of fetal maturation and parturition. Thyroid 31(6):861-869. Combes G, Barysz H, Garand C, Gama Braga L, Alharbi I, Thebault P, Murakami L, Bryne DP, Stankovic S, Eyers PA, Bolanos-Garcia VM, Earnshaw WC, Maciejowski J, Jallepalli PV and Elowe S. (2018). Mps1 phosphorylates its N-terminal extension to relieve autoinhibition and activate the spindle assembly checkpoint. Curr Biol 28(6):872-883.e5. Green L. (2014). Development of an anti-CD2/CD3/CD28 bead-based T-cell proliferation assay. The International Journal of Student Research 7, 1 January 2014, hzu012. Jacobs LA, Bewicke-Copley F, Poolman MG, Pink RC, Mulcahy LA, Baker I, Beaman EM, Brooks T, Caley DP, Cowling W, Currie JM, Horsburgh J, Kenehan L, Keyes E, Leite D, Massa D, McDermott- Rouse A, Samuel P, Wood H, Kadhim M and Carter DR. (2013). Meta-analysis using a novel database, miRStress, reveals miRNAs that are frequently associated with the radiation and hypoxia stress-responses. PLoS One 14;8(11):e80844. Kapanidou M, Curtis NL and Bolanos-Garcia VM. (2017). Cdc20: at the Crossroads between chromosome segregation and mitotic exit. Trends Biochem Sci 42(3):193-205. Marcombe S, Thammavong P, Luangamath P, Chonephetsarath S, Phommavanh N, Lakeomany K, Nilaxay S, Rahmani Z, Saverton PJ, Abdullateef OH, Forward J, Jacob AE, Khadam S, Ali W, Boer C, Kakinuma H, Hawkins J, Longstreeth R, Portwood NM, Smee M, Brown N, Kuyucu NC, Lechmere S, Stieger G, Maithaviphet S, Nambanya S, Brey PT and Jones AK. (2020). Malaria and Dengue mosquito vectors from Lao PDR show a lack of the rdl mutant allele responsible for cyclodiene insecticide resistance. J Medical Entomology 57(3):815-823. Marcombe S, Shimell K, Savage R, Howlett E, Luangamath P, Nilaxay S, Vungkyly V, Baby A, King M, Clarke J, Jeffries C, Jojo J, Lacey E, Bhatty F, Mabika D, Dela Cruz A, Fisher C, Mbadu M, Despiniadis I, Brey PT, Thammavong P and Jones AK. (2022). Detection of pyrethroid resistance mutations and intron variants in the voltage-gated sodium channel of Aedes (Stegomyia) aegypti and Aedes (Stegomyia) albopictus mosquitoes from Lao People's Democratic Republic. Medical and Veterinary Entomology 36(4):424-434. Marcombe S, Doeurk B, Thammavong P, Veseli T, Heafield C, Mills M-A, Kako S, Ferreira Prado M, Thomson S, Millett S, Hill T, Kentsley I, Davies S, Pathiraja G, Daniels B, Browne L, Nyamukanga M, Harvey J, Rubinstein L, Townsend C, Allen Z, Davey-Spence C, Hupi A, Jones AK and Boyer S. (2024). Metabolic Resistance and Not Voltage-Gated Sodium Channel Gene Mutation Is Associated with Pyrethroid Resistance of Aedes albopictus (Skuse, 1894) from Cambodia. Insects 15(5):358 Thulborn SJ, Dilpazir M, Haldar K, Mistry V, Brightling CE, Barer MR and Bafadhel M. (2017). Investigating the role of pentraxin 3 as a biomarker for bacterial infection in subjects with COPD. Int J Chron Obstruct Pulmon Dis 12:1199-1205. Tomoni A, Lees J, Santana GA, Bolanos-Garcia VM and Bastida A. (2019). Pseudokinases: from allosteric regulation of catalytic domains and the formation of macromolecular assemblies to emerging drug targets. Catalysts 9(9), 778.  28 Young R, Lewandowska D, Long E, Wooding FBP, De Blasio MJ, Davies KL, Camm EJ, Sangild PerT, Fowden AL and Forhead AJ. (2023). Hypothyroidism impairs development of the gastrointestinal tract in the ovine fetus. Front Physiol 3;14.  29 Awards for project students Burden S. 2019. The Rob Clarke Awards, Abstract Award.