Sheep scab is a highly contagious ectoparasitic disease caused by the mite, Psoroptes ovis, which causes intensely pruritic lesions with severe dermatitis and is a major welfare and production issue in the UK national flock. In an attempt to improve disease control, sheep scab was recently made notifiable in Scotland indicating that early diagnostic tests will be crucial to the success of this legislation. A sensitive and specific antibody based assay has been developed which can diagnose early infestation, but which does not indicate current disease status post-treatment due to residual circulating antibody levels. However, studies into host biology and response to disease have illustrated the potential use of biomarkers (BMs) in diagnostics as indicators of disease progression and the effectiveness of treatment regimes, including a recent microarray analysis which identified over 600 host genes differentially expressed in circulating leukocytes following P. ovis infestation. As many of these genes encoded proteins known to be involved in inflammatory responses, this data was used in the search for potential BMs. Initially the genes were filtered and ranked, using bioinformatic analysis, to identify the most promising BM candidates and then evaluated using Western blot analysis against a range of sera from P. ovis infested and naïve sheep. Promising results were obtained for a complement binding protein, C4BPB, showing it was rapidly up-regulated following infestation and correlated with disease progression as determined by lesion size development. The ovine C4BPB gene was successfully sequenced for the first time and a recombinant form of this protein expressed in E. coli. Antibodies, raised in rabbits against ovine rC4BPB, were used to develop a sandwich ELISA, results from which suggested the potential of C4BPB as a BM for sheep scab as it indicated current disease status postinfestation and post-treatment. The major ruminant acute phase proteins (APPs) serum amyloid A (SAA) and haptoglobin (Hp) were then investigated using commercially available assays, as previous studies indicated they were effective markers of inflammatory disease in ruminants. Results from these analyses indicated that both APPs responded positively to infestation with P. ovis but this was not statistically significant until 4 weeks post-infestation. After treatment, the APPs declined rapidly, as described by their short half life of less than 3 days following successful treatment, compared with 56 days for the estimated half life of the host antibody against the mite antigen Pso o 2. Further statistical analysis of the APP response suggested that SAA was the more discriminatory marker, with lower pre-infestation levels and higher sensitivity at the estimated optimum cut-off values. The possibility of using a signature of BMs, as an alternative to a single BM, was discussed as a method of increasing the sensitivity and specificity of the improved test, along with the potential of combining the BM diagnostic with the existing antibody assay. It was concluded that this would provide a highly sensitive and specific test for sheep scab which would diagnose early infestation as well as indicating current disease status post-treatment, providing a highly beneficial tool to the sheep industry to aid the control of this disease.

Les îles Kerguelen (40°S, 70°E) renferment des écosystèmes d’eau douce parmi les plus isolés du monde des activités anthropiques directes. Le but de ce travail était d’étudier les facteurs bio-écologiques influençant les niveaux de bioaccumulation des contaminants chimiques dans les tissus des salmonidés des îles Kerguelen (truite commune, Salmo trutta et omble de fontaine, Salvelinus fontinalis) et les effets toxiques potentiellement associés. Nos travaux ont permis de démontrer que les teneurs hépatiques et musculaires en Cd et en Cu, mais aussi les teneurs musculaires en PCB étaient élevées et comparables à celles détectées chez des populations de salmonidés de zones géographiques plus anthropisées. Par ailleurs, des différences de contamination selon l’espèce, la saison et le morphotype (lac, rivière et base) ont été mises en évidence. L’analyse histologique des foies des truites a mis en évidence des atteintes hépatiques (fibrose, infiltration des cellules immunitaires, développement de centres mélanomacrophagiques) et hepatocytaires (nécrose, altérations nucléaires) nettes de l’ensemble des poissons étudiés qui révelent un état de stress important en cohérence avec les forts taux de toxiques dans cet organe. D’autre part, les biomarqueurs des défenses anti-oxydantes ont mis en évidence des différences entre les morphotypes étudiés. Par ailleurs, l’analyse de l’activité sérique de lysozyme a montré que ces salmonidés sont caractérisés par des niveaux de compétences immunitaires réduits. Les îles Kerguelen constitue un site atelier pour les études écotoxicologiques. Le suivi sur le long terme, devrait améliorer la connaissance des variations des réponses écophysiologiques des populations de poissons d'eau douce face à la pression chimique globale. / The Kerguelen Islands (40°S, 70°E) contain freshwater ecosystems among the most isolated from human activities in the world. The aim of this work was to study the bio-ecological factors influencing levels of chemical bioaccumulation in Kergueln salmonids tissue (brown trout, Salmo trutta and brook trout, Salvelinus fontinalis) and their potential toxic effects. Our work demonstrated that the hepatic and muscular Cu and Cd levels, and also, the muscular PCB levels were hight and similar to those of salmonids from impacted areas. Moreover, differences in contamination according to species, season and morphotype (lake, river and base) were noted. Histological analysis of trouts livers showed clear damage of liver (fibrosis, infiltration of immune cells, development centers mélanomacrophagiques) and of hepatocytes (necrosis, nuclear alteration) in all studied fish traducing an important level of stress consistently with the high concentration of toxicant in this organ. On the other hand, antioxidant defenses biomarkers revealed differences between the studied morphotypes. Moreover, analysis of serum lysozyme activity showed that these salmonids were characterized by reduced immune competences. Kerguelen Islands constitute a workshop site for ecotoxicological studies. The long-term monitoring should improve the knowledge of changes in eco-physiological responses of freshwater fish populations dealing with the global chemical pressure.

A thesis submitted to the Faculty of Medicine, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Science (Medicine). / The publications forming this submission cover two broad fields. A series of papers deal with experimental hypertension ; possible roles for angiotensin and prostanoid substances in the pathogenesis of hypertension were investigated. The results indicated that the capacity of kidney to inactivate angiotensin II could be quite profoundly altered by inducing hypertension using the one and two-clip Goldblatt methods or by altering the sodium chloride content of the diet. / IT2018

Thesis advisor: Thomas C. Chiles / Sensitive, real-time detection of biomarkers is of critical importance for rapid and accurate diagnosis of disease for point-of-care (POC) technologies. Current methods, while sensitive, do not adequately allow for POC applications due to several limitations, including complex instrumentation, high reagent consumption, and cost. We have investigated two novel nanoarchitectures, the nanocoax and the nanodendrite, as electrochemical biosensors towards the POC detection of infectious disease biomarkers to overcome these limitations. The nanocoax architecture is composed of vertically-oriented, nanoscale coaxial electrodes, with coax cores and shields serving as integrated working and counter electrodes, respectively. The dendritic structure consists of metallic nanocrystals extending from the working electrode, increasing sensor surface area. Nanocoaxial- and nanodendritic-based electrochemical sensors were fabricated and developed for the detection of bacterial toxins using an electrochemical enzyme-linked immunosorbent assay (ELISA) and differential pulse voltammetry (DPV). Proof-of-concept was demonstrated for the detection of cholera toxin (CT). Both nanoarchitectures exhibited levels of sensitivity that are comparable to the standard optical ELISA used widely in clinical applications. In addition to matching the detection profile of the standard ELISA, these electrochemical nanosensors provide a simple electrochemical readout and a miniaturized platform with multiplexing capabilities toward POC implementation. Further development as suggested in this thesis may lead to increases in sensitivity, enhancing the attractiveness of the architectures for future POC devices. / Thesis (PhD) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Lei Ieng Kit Kenny. / "April 2002." / Thesis (M.D.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (p. 89-118). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web.

The diagnostic pathway for prostate cancer involves the blood test prostate specific antigen (PSA) which has high sensitivity but low specificity at age related reference ranges. The resultant clinical consequence is a large number of negative diagnostic studies (transrectal ultrasound guided biopsies - TRUS). There is a need for a secondary screening test to help improve on the current diagnostic pathway. Mechanical markers have been used previously to assess the prostate for disease with numerous ex-vivo reports of differences between benign and malignant prostates. There have been no in-vivo studies with direct elasticity assessment devices for prostate cancer detection. This thesis forms part of work in a collaborative study in conjunction with engineers who have created a microscale device, capable of dynamic elasticity assessment. The specific objectives of this thesis were to a) assess dynamic micromechanical markers for the detection and differentiation of clinically significant from insignificant prostate cancer b) to identify relationships between mechanical and histopathological variables in the ex-vivo and in-vivo environments and c) assess the potential for these markers to differentiate peri-prostatic tissues. A prospective study was set-up with full ethics and management approvals with patients undergoing a systematic mechanical assessment of their prostate using the E-finger device and after prostate excision a systematic ex-vivo mechanical assessment on a calibrated stage. The ex-vivo assessment allowed accurate histopathological and mechanical variable assessment in a controlled environment. 7-Tesla ex-vivo MRI scanning aided in assessing the limitations of mechanical assessment of the prostate. There were clear consistent differences between individual dynamic micromechanical markers for benign and tumour containing measurement areas in both environments. Modelling of these dynamic micromechanical markers yielded encouraging accuracy levels for the detection of prostate cancer and differentiation of significant from insignificant disease. There were associations between individual mechanical markers and important histopathological features associated with cancer (acinar size, tumour volume and reactive stroma). These markers showed promise and utility in the differentiation of prostate from bladder and rhabdosphincter. This work demonstrates the clear potential translational uses for dynamic micromechanical markers in the assessment of the prostate for cancer.

Biomarkers have important clinical uses as diagnostic, prognostic, and predictive tools for cancer therapy. However, translation from biomarkers claimed in literature to clinical use has been traditionally poor. Importantly, clinical covariates have been shown to be important factors in biomarker discovery in small-scale studies. Yet, traditional differential gene expression analysis for expression biomarkers ignores covariates, which are only accounted for later, if at all. We conjecture that covariate-sensitive biomarker identification should lead to the discovery of more robust and true biomarkers as confounding effects are considered. Here we examine gene expression in more than 750 breast invasive ductal carcinoma cases from The Cancer Genome Atlas (TCGA-BRCA) in the form of RNA-Seq data. Specifically, we focus on differential gene expression with respect to understanding HER2, ER, and PR biology – the three key receptors in breast cancer. We explore methods of differential expression analysis, including non-parametric Mann-Whitney-Wilcoxon analysis, generalized linear models with covariates, and a novel categorical method for covariates. We tested the influence of common patient characteristics, such as age and race, and clinical covariates such as HER2, ER, and PR receptor statuses. More importantly, we show that inclusion of a correlated covariate (e.g. PR status as a covariate in ER analysis) substantially changes the list of differentially expressed genes, removing many likely false positives and revealing genes obscured by the covariate. Incorporation of relevant covariates in differential gene expression analysis holds strong biological importance with respect to biomarker discovery and may be the next step towards better translation of biomarkers to clinical use.

BACKGROUND: Elucidation of candidate colorectal cancer biomarkers often begins by comparing the expression profiles of cancerous and normal tissue by performing high throughput gene expression profiling. While many such studies have been performed, the resulting lists of differentially expressed genes tend to be inconsistent with each other, suggesting that there are some false positives and negatives. One logical solution to this problem is to determine the intersection of the lists of differentially expressed genes from independent studies. It is expected that genes that are biologically relevant to cancer tumorigenesis will be reported most often, while sporadically reported genes are due to the inherent biases and limitations of each of the profiling platforms used. However, the statistical significance of the observed intersection among many independent studies is usually not considered. PURPOSE: To address these issues, we developed a computational meta-analysis method that ranked differentially expressed genes based on the following criteria, which are presented in order of importance: the amount of intersection among studies, total tissue sample sizes, and average fold change in expression. We applied this meta-analysis method to 25 independent colorectal cancer profiling studies that compared cancer versus normal, adenoma versus normal, and cancer versus adenoma tissues. RESULTS: We observed that some genes were consistently reported as differentially expressed with a statistically significant frequency (P <.0001) in the cancer versus normal and adenoma versus normal comparisons, but not in the cancer versus adenoma comparison. We performed a review of some of the high ranking candidates and determined that some have previously been shown to have diagnostic and/or prognostic utility in colorectal cancer. More interestingly, the meta-analysis method also identified genes that had yet to be tested and validated as biomarkers. Thus, these candidates are currently being validated at the protein level on colorectal tissue microarrays. CONCLUSION: Our meta-analysis method identified genes that were consistently reported as differentially expressed. Besides identifying new biomarker candidates, our meta-analysis method also provides another filter to remove false positive genes from further consideration. In conclusion, the genes presented here will aid in the identification of highly sensitive and specific biomarkers in colorectal cancer.

Windblown dust is a significant source of sediment and organic matter for many basins, but its influence on ancient basins can be difficult to detect and quantify. We quantified the biomarker content, including n-alkanes, hopanes, and steranes of the Brushy Canyon Formation sandstones and siltstones to evaluate the significance of windblown dust in delivery of sediment and terrestrial organic matter to the Middle Permian Delaware Basin. Ramp siltstones of the basin have been interpreted as representing deposits of unconfined low-density turbidity currents or "aeolo-marine" sediments. We analyzed the organic contents of five samples of channel-confined turbiditic sandstones and siltstones and five samples of ramp siltstones outcropping in the Guadalupe Mountains National Park, West Texas, to estimate the relative proportions of terrestrial and marine organic matter in the two types of host rocks. The total organic carbon content of all samples varied from 0.07 percent - 2.04 percent. The abundance of high molecular weight n-alkanes (n-C27 and greater) suggests that terrestrial organic matter was present in nearly all samples. Terrestrial organic matter input to the basin was characterized using a crossplot of pristane/n-C17 versus phytane/n-C18. Ramp siltstones showed ~10-fold greater variation in terrestrial content than did turbiditic sandstones and siltstones. This observation is more consistent with the aeolo-marine interpretation of ramp siltstones, and suggests that terrestrial organic matter was delivered to the Delaware Basin by wind transport during deposition of the Brushy Canyon Formation.

In 2007, there will be an estimated 178,480 new cases of breast cancer diagnosed in women in the United States. The elucidation of the vast heterogeneity of individual tumors has led to a paradigm shift from a one-size fits all treatment strategy to more individualized treatment based on the molecular profile of the tumor. Identifying biomarkers that respond to or predict the action of drugs is important in identifying efficacious targets and drugs that will improve clinical outcome. To examine this, we first identified two breast cancer cell lines (ACC-3199 and ACC-3171) from a panel of low passage breast cells lines that were capable of growing serially as tumor xenografts. This was followed by the in vivo molecular characterization of these two cell lines. In ACC-3199 tumors, we identified a gain of pAKT expression compared to cultured cells. Based on this finding, we investigated the role of diffusion-weighted (DW) and dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) as potential imaging biomarkers in identifying early response to PX-866, a PI3K inhibitor, in ACC-3199 tumors as represented by changes in tumor cellularity and hemodynamic parameters, respectively. Our results indicated that DW-MRI was able to identify an early response to PX-886 in ACC-3199 tumors as defined by an increase in the apparent diffusion coefficient (ADC) value of the tumors prior to changes in tumor volumes. Using DCE-MRI, we were able to conclude that PX-866 was not an effective anti-angiogenic agent as indicated by an increase in tumor permeability following therapy. Based on the VEGFR2 expression observed in ACC-3171 tumor xenografts, we examined the response of MDA-MB-231/GFP and ACC-3171 tumor xenografts to the anti-angiogenic agent, sunitinib, using the same imaging modalities. DW-MRI was able to detect increases in ADC values as early as 12 h post-treatment in both MDA-MB-231/GFP and ACC-3171 tumors. Thus, it appears that DW-MRI may be a useful clinical test in predicting the early response to PI3K and anti-angiogenic inhibitors. These imaging approaches, in addition to the further molecular characterization of breast tumors may lead to the improvement and development of medical therapies for breast cancer patients.