Doctoral Training Partnerships: a range of postgraduate training is funded by the Research Councils. For information on current funding routes, see the common terminology at https://www.ukri.org/apply-for-funding/how-we-fund-studentships/. Training grants may be to one organisation or to a consortia of research organisations. This portal will show the lead organisation only.

The microbiota of the skin forms a vital component of the body's ecosystem, particularly in preventing colonisation by pathogenic bacteria (microflora protection). The microbial community has also been implicated in non infective skin conditions such as eczema and Acne (Cogen et al. Br J Dermatol.158:442-55; Segre J Clin Invest. 116:1150-8.). Cutaneous bacteria are responsible for individual body odour characteristics (Austin & Ellis J Steroid Biochem Mol Biol. 87:105-10.), which are largely defined by the metabolic end products they produce. The composition of the skin surface microbial community must be understood to enable the development of new generations of personal care products. Previous attempts to study the skin microbial communities have had limited success primarily due to technological hurdles -the sampling inadequacy of culture-based techniques and the limited penetration obtained by conventional analysis of clone libraries. Here, traditional community profiling techniques will be followed by deep 16S ribosomal RNA gene sequencing and metagenomic shotgun DNA sequencing. The student will carry out all steps from sampling through to molecular biology and bioinformatic analysis and they will receive training in this at the School of Biological Sciences while drawing on the expertise of the industrial partner, located nearby, in sampling the skin microflora and determining its biochemistry and general microbiology. The experimental programme has three components: 1. Profiling microbial communities using trRFLP; 2. In depth elucidation of the composition of selected microbial communities by pyrosequencing of16S ribosomal RNA 3. Metabolic reconstruction via metagenomic shotgun sequencing. The student will first establish a baseline by investigating the stability of skin microbial community structure from a number of individuals within a volunteer population. The CASE partner has experience of this type of study and will ensure ethical compliance. The student will use TRFLP (Liu et al. Appl. Environ. Microbiol. 63: 4516-4522) to profile samples at multiple time-points to examine how populations change over time and between individuals. This will comprise the first year of the project at which point we we will have a much improved understanding of the stability of skin microbial communities and the extent of variation between individuals. This information will be vital for designing the subsequent experiments in which large databases of sequence information will be assembled and analysed.. 16S sequences will be interrogated directly using 454 pyrosequencing and species identified using alignment with public databases. The student will identify and differentiate those taxa that are cosmopolitan, specific to groups or individuals and those likely to change in abundance over time. Hypotheses will be generated on the relationships/correlations between microbial species identity and abundance, the age and sex of individuals and disease status for example. Simple qPCR- experiments will be designed to test hypotheses. To understand the metabolic processes present in microbial communities, the student will prepare whole genomic DNA and total RNA, and perform metagenomic shotgun sequencing on these samples using 454 pyrosequencing. Assembly and annotation of these data will be performed in order to reconstruct the metabolic potential of the microbial communities (using data from the DNA sample) as well as information about which pathways are active (using data from the RNA sample). Phylogenetic analysis of the genic sequences will be used to identify which bacterial taxa appear to be responsible for certain processes. Intensive bioinformatics training will be provided to the student for this part of the project, and will have the support of several postdoctoral bioinformatics scientists.

Doctoral Training Partnerships: a range of postgraduate training is funded by the Research Councils. For information on current funding routes, see the common terminology at www.rcuk.ac.uk/StudentshipTerminology. Training grants may be to one organisation or to a consortia of research organisations. This portal will show the lead organisation only.

We are exposed to a range of chemicals in day-to-day life, at home and at work, which may have unwanted health effects. In this study we are interested in the sensitivity of the lung to chemicals that are inhaled, usually while at work. Not everybody is affected, but when those who are affected are exposed to the same chemical again they may experience an asthma attack, and they may also react to other agents that they inhale from the air (this accounts for approximately 10% of adult-onset asthma). This is called respiratory sensitisation. It is important to determine whether existing or newly-developed chemicals will cause respiratory sensitisation, and if so, the magnitude of the response. It is also important to understand the cellular mechanisms that are involved. The immunological responses of the lung are complex, and no validated tests exist to determine the potential of chemicals to initiate these responses. Animal experiments are often used to help make these assessments, but they are not always very accurate, although they do help us understand some of the mechanisms involved. Furthermore, the 7th Amendment to the European Union Cosmetics Directive (European Commission, 2003) recommends that we develop new ways of testing compounds so that we reduce animal experimentation. The strategy is called the 3Rs, Reduction, Refinement and Replacement of the use of animals in scientific tests. One aim of this study is to establish testing methods that avoid using animals by using human cells. Use of human cells is important as it will ensure development of a more representative model for assessing the potency of these chemicals in man. The cells in the lung that respond to inhaled particles are the lung's 'skin', epithelial cells, as well as cells that act like a vacuum cleaner, internalising and neutralising inhaled material that settles on the 'skin'; which are called macrophages. Epithelial cells and macrophages send messages to dendritic cells that sit underneath the lung epithelial cells. Dendritic cells also extend long 'probes' onto the epithelial surface where they can directly interact with any inhaled chemicals. Depending on the messages received, dendritic cells then activate the immune response to fight infection and other foreign particles that reach the lung. However, sometimes the messages go wrong, and this is when the lung becomes very sensitive to some types of inhaled particles and chemicals. We aim to isolate cells from adult human lung tissue that is removed during an operation to remove a tumour. Normal regions of lung that are attached to, but not affected by, the tumour can be used. We will then culture epithelial, macrophage and dendritic cells alone, and together in a 3-dimensional model resembling the lung. We will expose the cells to chemicals that we know are respiratory sensitisers, as well as chemicals that do not cause respiratory sensitisation, to examine the cellular messaging pathways involved in respiratory sensitisation. We also want to determine whether there are unique responses that identify chemical sensitisers so that these culture models can be developed and used for routine testing of existing and new compounds that might affect the lung. In addition, with this knowledge, it should be possible to develop drugs that prevent these abnormal responses. These models could be used to avoid the use of animals to investigate respiratory sensitisers to understand mechanisms of respiratory sensitisation.

Doctoral Training Partnerships: a range of postgraduate training is funded by the Research Councils. For information on current funding routes, see the common terminology at https://www.ukri.org/apply-for-funding/how-we-fund-studentships/. Training grants may be to one organisation or to a consortia of research organisations. This portal will show the lead organisation only.