Browsing by Author "Cauchi, Michael"

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    Analysis of volatile organic compounds of bacterial origin in chronic gastrointestinal diseases
    (Wiley, 2013-07-17) Walton, Christopher; Fowler, Dawn P.; Turner, Claire; Jia, W.; Whitehead, Rebekah N.; Griffiths, Lesley; Dawson, Claire; Waring, Rosemary H.; Ramsden, David B.; Cole, Jeffrey A.; Cauchi, Michael; Bessant, Conrad M.; Hunter, John O.
    BACKGROUND: The aim of this study was to determine whether volatile organic compounds (VOCs) present in the headspace of feces could be used to diagnose or distinguish between chronic diseases of the gastrointestinal tract and apparently healthy volunteers. METHODS: A total of 87 people were recruited, divided between 4 categories: healthy volunteers (n = 19), Crohn's disease (n = 22), ulcerative colitis (n = 20), and irritable bowel syndrome (n = 26). They each supplied fecal samples before, and except for the healthy volunteers, after treatment. Fecal samples were incubated in a sample bag with added purified air at 40°C and headspace samples were taken and concentrated on thermal sorption tubes. Gas chromatography-mass spectrometry then desorbed and analyzed these. The concentrations of a selection of high-abundance compounds were determined and assessed for differences in concentration between the groups. RESULTS: Crohn's disease samples showed significant elevations in the concentrations of ester and alcohol derivates of short-chain fatty acids and indole compared with the other groups; indole and phenol were elevated in ulcerative colitis and irritable bowel syndrome but not at a statistically significant level. After treatment, the levels of many of the VOCs were significantly reduced and were more similar to those concentrations in healthy controls. CONCLUSIONS: The abundance of a number of VOCs in feces differs markedly between Crohn's disease and other gastrointestinal conditions. Following treatment, the VOC profile is altered to more closely resemble that of healthy volunteers.
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    Data analysis tools for safe drinking water production
    (Cranfield University, Cranfield University at Silsoe, 2006-11-08T17:00:01Z) Cauchi, Michael; Setford, S.; Bessant, Conrad
    Providing safe and high quality drinking water is essential for a high quality of life. However, the water resources in Europe are threatened by various sources of contamination. This has led to the development of concepts and technologies to create a basis for provision of safe and high quality drinking water, which had thus resulted in the formation of the Artificial Recharge Demonstration project (ARTDEMO). The overall aim of this thesis in relation to the ARTDEMO project was to develop a realtime automated water monitoring system, capable of using data from various complementary sources to determine the amounts of inorganic and organic pollutants. The application of multivariate calibration to differential pulse anodic stripping voltammograms and fluorescence spectra (emission and excitation-emission matrix) is presented. The quantitative determination of cadmium, lead and copper acquired on carbon-ink screen-printed electrodes, arsenic and mercury acquired on gold-ink screen-printed electrodes, in addition to the quantitative determination of anthracene, phenanthrene and naphthalene have been realised. The statistically inspired modification of partial least squares (SIMPLS) algorithm has been shown to be the better modelling tool, in terms of the root mean square error of prediction (RMSEP), in conjunction with application of data pre-treatment techniques involving rangescaling, filtering and weighting of variables. The % recoveries of cadmium, lead and copper in a certified reference material by graphite furnace atomic absorption spectrometry (GF-AAS) and multivariate calibration are in good agreement. The development of a prototype application on a personal digital assistant (PDA) device is described. At-line analysis at potential contamination sites in which an instant response is required is thus possible. This provides quantitative screening of target metal ions. The application imports the acquired voltammograms, standardises them against the laboratory-acquired voltammograms (using piecewise direct standardisation), and predicts the concentrations of the target metal ions using previously trained SIMPLS models. This work represents significant progress in the development of analytical techniques for water quality determination, in line with the ARTDEMO project's aim of maintaining a high quality of drinking water.
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    Diversity and distribution of sulphate-reducing bacteria in human faeces from healthy subjects and patients with inflammatory bowel disease
    (2012-06-01T00:00:00Z) Jia, Wenjing; Whitehead, Rebekah N.; Griffiths, Lesley; Dawson, Claire; Bai, Hao; Waring, Rosemary H.; Ramsden, David B.; Hunter, John O.; Cauchi, Michael; Bessant, Conrad M.; Fowler, Dawn P.; Walton, Christopher; Turner, Claire; Cole, Jeffrey A.
    The relative abundance of different groups of sulphate-reducing bacteria (SRB) in faecal DNA collected before and after therapy from patients suffering from Crohn's disease (CD), irritable bowel syndrome (IBS) or ulcerative colitis (UC) has been compared with that from healthy controls. Growth tests revealed that SRB were not more abundant in samples from patients with CD before treatment than in the healthy control group. For most of the 128 samples available, these preliminary results were confirmed using degenerate PCR primers that amplify the dsrAB gene. However, some samples from patients with CD before treatment contained a growth inhibitor that was absent from IBS or UC samples. In-depth sequencing of PCR-generated dsrB fragments revealed that the diversity detected was surprisingly low, with only eight strains of SRB and the sulphite-reducing bacterium, Bilophila wadsworthia, detected above the 0.1% threshold. The proportion of the two major species detected, B.wadsworthia and Desulfovibrio piger, was as high as 93.5% of the total SRB population in the healthy control group and lower in all patient groups. Four previously undescribed species were found: it is impossible to predict whether they are sulphate or sulphite-reducing bacteria.
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    Enteral feeding reduces metabolic activity of the intestinal microbiome in Crohn’s disease: an observational study
    (Nature Publishing Group, 2016-05-11) Walton, Christopher; Montoya, M. P. B.; Fowler, Dawn P.; Turner, Claire; Jia, W.; Whitehead, Rebekah N.; Griffiths, Lesley; Waring, Rosemary H.; Ramsden, David B.; Cole, Jeffrey A.; Cauchi, Michael; Bessant, Conrad M.; Naylor, J.; Hunter, John O.
    BACKGROUND/OBJECTIVES: Enteral feeding will induce remission in as many as 80–90% of compliant patients with active Crohn’s disease (CD), but its method of action remains uncertain. This study was designed to examine its effects on the colonic microbiome. METHODS/SUBJECTS: Healthy volunteers and patients with CD followed a regimen confined to enteral feeds alone for 1 or 2 weeks, respectively. Chemicals excreted on breath or in faeces were characterised at the start and at the end of the feeding period by gas chromatography/mass spectrometry. RESULTS: One week of feeding in healthy volunteers caused significant changes in stool colour and deterioration in breath odour, together with increased excretion of phenol and indoles on the breath. Feeding for 2 weeks in patients with CD produced significant improvements in symptoms and a decrease in the concentration of C-reactive protein. The faecal concentrations of microbial products, including short-chain fatty acids (SCFAs), and potentially toxic substances, including 1-propanol, 1-butanol and the methyl and ethyl esters of SCFAs, showed significant falls. CONCLUSIONS: A significant change occurs in the production of microbial metabolites after enteral feeding in both healthy volunteers and patients with CD. Many of those detected in CD are toxic and may feasibly lead to the immunological attack on the gut microbiota, which is characteristic of inflammatory bowel disease. The reduction in the production of such metabolites after enteral feeding may be the reason for its effectiveness in CD.
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    Evaluation of a gas sensor array and pattern recognition for the identification of bladder cancer from urine headspace.
    (Royal Society of Chemistry, 2011-01-21T00:00:00Z) Weber, Christina M.; Cauchi, Michael; Patel, Mitesh; Bessant, Conrad M.; Turner, Claire; Britton, Lezlie E.; Willis, Carolyn M.
    Previous studies have indicated that volatile compounds specific to bladder cancer may exist in urine headspace, raising the possibility that headspace analysis could be used for diagnosis of this particular cancer. In this paper, we evaluate the use of a commercially available gas sensor array coupled with a specifically designed pattern recognition algorithm for this purpose. The best diagnostic performance that we were able to obtain with independent test data provided by healthy volunteers and bladder cancer patients was 70% overall accuracy (70% sensitivity and 70% specificity). When the data of patients suffering from other non-cancerous urological diseases were added to those of the healthy controls, the classification accuracy fell to 65% with 60% sensitivity and 67% specificity. While this is not sufficient for a diagnostic test, it is significantly better than random chance, leading us to conclude that there is useful information in the urine headspace but that a more informative analytical technique, such as mass spectrometry, is required if this is to be exploited fully.
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    Evaluation of gas chromatography mass spectrometry and pattern recognition for the identification of bladder cancer from urine headspace
    (Royal Society of Chemistry, 2016-05-03) Cauchi, Michael; Weber, C. M.; Bolt, B. J.; Spratt, P. B.; Bessant, C.; Turner, D. C.; Willis, C. M.; Britton, L. E.; Turner, Claire; Morgan, G.
    Previous studies have indicated that volatile organic compounds specific to bladder cancer may exist in urine headspace, raising the possibility that they may be of diagnostic value for this particular cancer. To further examine this hypothesis, urine samples were collected from patients diagnosed with either bladder cancer or a non‐cancerous urological disease/infection, and from healthy volunteers, from which the volatile metabolomes were analysed using gas chromatography mass spectrometry. The acquired data were subjected to a specifically designed pattern recognition algorithm, involving cross‐model validation. The best diagnostic performance, achieved with independent test data provided by healthy volunteers and bladder cancer patients, was 89% overall accuracy (90% sensitivity and 88% specificity). Permutation tests showed that these were statistically significant, providing further evidence of the potential for volatile biomarkers to form the basis of a non‐invasive diagnostic technique.
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    Identification of meat spoilage gene biomarkers in Pseudomonas putida using gene profiling
    (Elsevier, 2015-04-20) Mohareb, Fady R.; Iriondo, Maite; Doulgeraki, Agapi I.; van Hoek, Angela; Aarts, Henk; Cauchi, Michael; Nychas, George-John E.
    While current food science research mainly focuses on microbial changes in food products that lead to foodborne illnesses, meat spoilage remains as an unsolved problem for the meat industry. This can result in important economic losses, food waste and loss of consumer confidence in the meat market. Gram-negative bacteria involved in meat spoilage are aerobes or facultative anaerobes. These represent the group with the greatest meat spoilage potential, where Pseudomonas tend to dominate the microbial consortium under refrigeration and aerobic conditions. Identifying stress response genes under different environmental conditions can help researchers gain an understanding of how Pseudomonas adapts to current packaging and storage conditions. We examined the gene expression profile of Pseudomonas putida KT2440, which plays an important role in the spoilage of meat products. Gene expression profiles were evaluated to select the most differentially expressed genes at different temperatures (30 °C and 10 °C) and decreasing glucose concentrations, in order to identify key genes actively involved with the spoilage process. A total of 739 and 1269 were found to be differentially expressed at 30 °C and 10 °C respectively; of which 430 and 568 genes were overexpressed, and 309 and 701 genes were repressed at 30 °C and 10 °C respectively.
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    MMpred: functional miRNA – mRNA interaction analyses by miRNA expression prediction
    (BioMed Central, 2012-11-14) Stempor, Przemyslaw A.; Cauchi, Michael; Wilson, Paul
    Background: MicroRNA (miRNA) directed gene repression is an important mechanism of posttranscriptional regulation. Comprehensive analyses of how microRNA influence biological processes requires paired miRNA-mRNA expression datasets. However, a review of both GEO and ArrayExpress repositories revealed few such datasets, which was in stark contrast to the large number of messenger RNA (mRNA) only datasets. It is of interest that numerous primary miRNAs (precursors of microRNA) are known to be co-expressed with coding genes (host genes). Results: We developed a miRNA-mRNA interaction analyses pipeline. The proposed solution is based on two miRNA expression prediction methods – a scaling function and a linear model. Additionally, miRNA-mRNA anticorrelation analyses are used to determine the most probable miRNA gene targets (i.e. the differentially expressed genes under the influence of up- or down-regulated microRNA). Both the consistency and accuracy of the prediction method is ensured by the application of stringent statistical methods. Finally, the predicted targets are subjected to functional enrichment analyses including GO, KEGG and DO, to better understand the predicted interactions. Conclusions: The MMpred pipeline requires only mRNA expression data as input and is independent of third party miRNA target prediction methods. The method passed extensive numerical validation based on the binding energy between the mature miRNA and 3’ UTR region of the target gene. We report that MMpred is capable of generating results similar to that obtained using paired datasets. For the reported test cases we generated consistent output and predicted biological relationships that will help formulate further testable hypotheses.
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    Optical assay for biotechnology and clinical diagnosis
    (IEEE Institute of Electrical and Electronics, 2011-12-31T00:00:00Z) Moczko, Ewa; Cauchi, Michael; Turner, Claire; Meglinski, I. V.; Piletsky, Sergey A.
    In this paper, we present an optical diagnostic assay consisting of a mixture of environmental-sensitive fluorescent dyes combined with multivariate data analysis for quantitative and qualitative examination of biological and clinical samples. The performance of the assay is based on the analysis of spectrum of the selected fluorescent dyes with the operational principle similar to electronic nose and electronic tongue systems. This approach has been successfully applied for monitoring of growing cell cultures and identification of gastrointestinal diseases in humans.
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    A systems biology approach to target discovery in regulatory T cells
    (Cranfield University, 2011-08) Weston, Marie C.; Cauchi, Michael; Page, Matt
    Regulatory T cells (Tregs) have a central role in the maintenance of tolerance to self- antigens and the prevention of autoimmune disease. This study used an integrative systems biology approach to identify tolerogenic genes in Tregs which could potentially serve as novel therapeutic targets for immunological disorders. A consensus Treg gene signature was generated by comparing gene expression in Treg vs naïve or conventional T cells across multiple public studies. Ingenuity Pathway Analysis software was then used to expand the Treg consensus gene list to include interacting proteins accessible to intervention by antibody therapeutics. Many viruses co-opt genes for host proteins that modulate the host’s immune system. It is hypothesized that some viruses may have co-opted genes that can induce tolerance, allowing the virus to evade elimination by the host’s immune system. Putative tolerogenic genes were therefore selected for further investigation based upon their presence in viral genomes. The presence of human genes in viral genomes was investigated by performing a batch reciprocal BLAST search. The biological significance of the human vs viral alignments was evaluated by manual inspection of the alignments and searching for the presence of shared motifs and protein family domains in the viral and human sequences. A final list of ten putative tolerogenic genes included genes known to be associated with immune function and some already established therapeutic targets for autoimmune diseases, as well as four potentially novel therapeutic targets. The biological rationale for the putative targets’ involvement in tolerance was explored in the context of Treg gene expression and protein-protein interaction (PPI) network topology. A PPI network was generated and annotated with confidence scores for each of the interactions. The Cytoscape plugin JActiveModules was used to find putative functional network modules.
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    Use of the analysis of the volatile faecal metabolome in screening for colorectal cancer
    (PLOS (Public Library of Science), 2015-06-18) Batty, Claire A.; Cauchi, Michael; Lourenço, Célia; Hunter, John O.; Turner, Claire
    Diagnosis of colorectal cancer is an invasive and expensive colonoscopy, which is usually carried out after a positive screening test. Unfortunately, existing screening tests lack specificity and sensitivity, hence many unnecessary colonoscopies are performed. Here we report on a potential new screening test for colorectal cancer based on the analysis of volatile organic compounds (VOCs) in the headspace of faecal samples. Faecal samples were obtained from subjects who had a positive faecal occult blood sample (FOBT). Subjects subsequently had colonoscopies performed to classify them into low risk (non-cancer) and high risk (colorectal cancer) groups. Volatile organic compounds were analysed by selected ion flow tube mass spectrometry (SIFT-MS) and then data were analysed using both univariate and multivariate statistical methods. Ions most likely from hydrogen sulphide, dimethyl sulphide and dimethyl disulphide are statistically significantly higher in samples from high risk rather than low risk subjects. Results using multivariate methods show that the test gives a correct classification of 75% with 78% specificity and 72% sensitivity on FOBT positive samples, offering a potentially effective alternative to FOBT.