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The University of Southampton
Institute for Life Sciences

Omics, Organisms and Disease

Technological advances have allowed scientists to gather large amounts of data about a vast array of species, organisms and single cells. Our researchers are using mathematical modelling, machine learning and other algorithms to extract information and patterns from large data sets to further our understanding of disease.

Image credit: Prof Sarah Ennis

We are now in a world where large and complex data sets can be obtained efficiently and affordably, enabling researchers to discover more and more across various species – from humans to plants and viruses. But to make full use of the data available and to ensure it positively impacts on society, we need to be able to extract information in a meaningful way.

Interdisciplinary scientists across fields such as Medicine, Ocean and Earth Sciences, Engineering, Mathematics and Computer Sciences are coming together on a number of collaborations to analyse large sets of data, extract information and translate it into practices that will benefit society.

From analysing patient genomes, to carrying out metagenomic analysis of water samples, to using mass spectrometry metabolic profiling techniques, our scientists are studying the unique processes that take place within cells that can lead to disease or poor health outcomes in humans and help track changes in the environment.

We are using the data to answer clinical questions in areas such as cancer, autoimmune and respiratory disease and with the help of clinical colleagues we are translating our findings into novel techniques for clinicians to treat their patients, make predictions about prognosis and drug responsiveness.

Related Staff Member

Key words

Data, Complex Datasets, Disease, Epigenetics, Genes, Genetics, Complex Datasets, Interdisciplinary, Patients

Please see a selection of postgraduate courses related to this subject area below. 


For the full range of undergraduate and postgraduate courses at the University of Southampton, please visit our courses webpages:  https://www.southampton.ac.uk/courses.page

MSc Statistics

This programme includes options ranging from the more theoretical aspects of statistics to those which cover material focussed on real world applications of statistics.

MSc in Statistics with Applications in Medicine

The MSc in Statistics with Applications in Medicine provides training in statistical methodology, with an emphasis on solving practical problems arising in the context of collecting and analysing medical data.

PhD Programme - Medicine

Full and part-time PhDs in a broad range of specialist areas in Medicine, including biomedicine, research in clinical environments and population-based statistical studies.

MSc Genomic Medicine

This programme explores the genomics and informatics of rare and common diseases, cancer and infectious diseases, and the application of these for diagnostics, prognostics and stratified medicine.

Crohn’s disease

At least 115,000 people have Crohn's Disease in the UK with up to one third being under 21 years old when their condition is diagnosed. It is the most common form of Inflammatory Bowel Disease in children and incidence rates are increasing. 

Inflammation in the gut causes the symptoms - diarrhoea, abdominal pain and tiredness – but it is unclear what triggers this inflammation. It is thought that a combination of genetic and environmental factors are involved.

Our scientists are using next generation sequencing techniques to analyse patients’ genes, gene expression and the role the microbiome plays in triggering disease. The microbiome is the community of bacteria that live in the body.

The study aims to assess how the gut microbiome interacts with the other factors to cause disease: including the children’s genetic susceptibility to developing Crohn’s disease, the activity of the children’s immune system and which genes are turned on or turned off.

Previous studies have tried to investigate the underlying causes of Crohn’s Disease, but to date none have examined the microbiome alongside genetic risk and gene expression over a long period of time in the same patients. 

Our research will improve the understanding of the cause of the disease and potentially lead to more effective therapies and new ways of predicting how severe the disease will be in individuals and how well they will respond to treatments. 

https://www.action.org.uk/our-research/what-causes-crohns-disease 


Contacts Dr James Ashton, Prof Sarah Ennis

Chronic Lymphocytic Leukaemia 

Our scientists are using the latest single cell techniques and next generation sequencing to give greater insight into Chronic Lymphocytic Leukaemia (CLL), the most prevalent form of leukaemia in the western world.

In recent years, new treatment regimens for CLL have transformed outcomes for patients. However, CLL is a disease of subtypes where specific combinations of the cell of origin and mutations appear to program an aggressive form, prone to transformation and treatment resistance.

More research into the natural evolution of this subtype of CLL is needed to understand which mutations accumulate within individual leukaemia cells and how dysregulated gene expression facilitates cell growth and transformation when the disease progresses.

Using two cutting-edge approaches (developed independently at the Institute of Cancer Research and Harvard University), our scientists will separate patient blood and lymph node samples into single cancer cells and analyse them in microfluidic based machines to detect patterns of DNA mutations and then use next generation sequencing to capture a snapshot of gene expression changes in the different leukaemia clones.

The data collected will generate evolutionary maps and catalogue the diversity of leukaemia cell populations in patients’ samples. It is hoped, that this information will further our understanding of how leukaemia cells may be programmed to evolve into an aggressive form that requires specific monitoring and management.

https://www.southampton.ac.uk/ifls/news/2016/09/27-microfluidics-in-medicine.page

https://www.leuka.org.uk 

ContactDr Matthew Rose-Zerilli

Genetic susceptibility to asthma

Researchers across the University are working together with international partners to study genetics and epigenetics in the developmental origins of allergy and respiratory disease. 

Asthma remains one of the most common health conditions in the UK with more than 5.4 million people receiving treatment for it. There is strong evidence that a person’s health as they grow can be determined before birth through modifications to their DNA known as epigenetic modifications, which control the activity of our genes without changing the actual DNA sequence.

One significant epigenetic modification is DNA methylation, which plays a key role in the development of the embryo and the formation of different cell types, regulating when and where genes are switched on. DNA methylation can be affected by a range of environmental factors such as parental health, diet and lifestyle.

Using samples taken from three generations of families, the parents, participants and children of the Isle of Wight longitudinal birth cohort our researchers are examining genome-wide DNA methylation and comparing it to environmental exposures of the participants and other measurements in samples of blood, buccal cells, nasal samples, and lung epithelial cells taken from the participants’ children who may or may not experience respiratory conditions.

The study will further our understanding of whether epigenetic modifications alter the risk for allergy and asthma; whether the epigenome, in particular the methylation of CpG sites is vertically transmitted from parents to offspring; and what environmental factors impact epigenetic marks and in which developmental periods (pregnancy, infancy, or both) are epigenetic marks established. The insight will help our teams will develop new preventative and treatment strategies that could help millions of people.

ContactsProf John Holloway, Prof Hasan Arshad

Remineralisation in the Ocean’s Twilight Zone

Global oceans absorb about 40% of the CO2 released by human activities.  For this CO2 capture to be effective, it requires an efficient oceanic ‘biological carbon pump’, primarily as sinking particles that delivers the carbon fixed by photosynthesis at the sunlit surface to the deep dark ocean, where the carbon can stay trapped for centuries.  However, the majority of this carbon – in the form of organic matter – exported from the surface ocean, cannot make it into the deep ocean due to active remineralisation in the ocean’s twilight, or mesopelagic zone – the intermediate layer between the sunlit surface and deep ocean (ca. 100-1000m depth) where photosynthesis ceases to occur. Remineralisation is the breakdown of organic matter back into CO2 and other inorganic nutrients. Therefore, remineralisation in the mesopelagic is critical to controlling the ocean's ability to absorb atmospheric CO2.

Nitrogen (N) is often the limiting nutrient for biological production in surface oceans, and as such, its remineralisation in the twilight ocean (and subsequent upward transport) is key to replenish the much-needed nitrogen at surface to facilitate biological carbon pump. In other words, remineralisation in twilight ocean reduces the efficiency of the biological pump, but it is vital to regain the nutrient nitrogen for the overall running of the biological pump itself.

However, the mechanisms of N-remineralisation are poorly characterised, and there have so far been no rate measurements of this process in the ocean’s twilight zone. Neither well understood is how and how much organic carbon within particles are degraded back to CO2 in the mesopelagic, apart from the fact that they are usual ‘hotspots’ of microbial colonisation.

Using a combination of state-of-the-art geochemical rate measurements and molecular biological analyses, our ocean scientists will be establishing the most complete dataset of directly measured N-remineralisation fluxes ever attempted in the oceans. They will determine exactly how and how much nitrogen is remineralised in the twilight ocean and elucidate the remineralisation pathways of how organic nitrogen is converted back to nitrate – the most abundant and preferred form of nutrient nitrogen taken by phytoplankton – based on combined omics analyses ranging from metatranscriptomics to metaproteomics.

Teaming up with biogeochemists, ecologists and modelers at the National Oceanography Centre in a separate project (COMICS), our teams will also examine the microbial remineralisation processes especially on sinking and non-sinking particles, to determine the extent and manners they impact oceanic biological pump from a carbon perspective.

Contacts: Dr Phyllis LamProf Tom Bibby, Prof Mark MooreDr Paul Skipp
 

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