Under stress, chlamydiae can enter a non-infectious but viable state termed persistence. In the absence of a tractable genetic system, persistence induction provides an important experimental tool with which to study these fascinating organisms. This review will discuss examples of: i) persistence studies that have illuminated critical chlamydiae/host interactions; and ii) novel persistence models that will do so in the future.

No description available.

If unaccounted for, differences in human anatomy can lead to adverse clinical outcomes for patients. The literature describes numerous variations of branches of the brachial artery; the most common anomaly is found as high as 25% of the time, in which the brachial artery passes over the median nerve, splitting the brachial artery into superficial and deep branches. Another common variation of the forearm arterial supply includes branching of the radial artery from the brachial artery proximal to the antecubital fossa (12.5%). Herein, we report a unique variation found in a 96-year-old white whole-body formalin-fixed male donor, dissected with typical dissection techniques. Although predictably bifurcating at the cubital fossa, the relative calibers and distribution of the ulnar and radial arteries in the forearm were notably atypical. The common interosseous artery branched from the radial artery rather than the ulnar artery, and distally branched into the anterior and posterior interosseous arteries. This morphology resulted in the deep anterior forearm and entirety of the posterior forearm relying on the radial artery for perfusion. There was also a notable size difference between the ulnar and radial arteries in which the radial artery was much larger. A review of the literature revealed two articles reporting this unique anomaly. It is important clinically to understand this abnormal branching pattern, as various medical procedures involve the radial artery. The radial artery is commonly used to gain access to circulation for cardiac catheterization and stent placement and can also be accessed for cannulation for a variety of medical procedures. Awareness of radial artery dominance reduces the possibility of iatrogenic injury and increases positive clinical outcomes. This protocol was reviewed by the VCOM IRB (#2022-050).

Recent breakthroughs in high-throughput biotechnology have promoted the integration of multi-platform data to investigate signal transduction pathways within a cell. In order to model complicated dynamics and heterogeneity of biological pathways, sophisticated computational models are needed to address unique properties of both the biological hypothesis and the data. In this dissertation work, we have proposed and developed methods using Markov Chain Monte Carlo (MCMC) techniques to solve complex modeling problems in human cancer research by integrating multi-platform data. We focus on two research topics: 1) identification of transcriptional regulatory networks and 2) uncovering of aberrant intracellular signal transduction pathways. We propose a robust method, called GibbsOS, to identify condition specific gene regulatory patterns between transcription factors and their target genes. A Gibbs sampler is employed to sample target genes from the marginal function of outlier sum of regression t statistic. Numerical simulation has demonstrated significant performance improvement of GibbsOS over existing methods against noise and false positive connections in binding data. We have applied GibbsOS to breast cancer cell line datasets and identified condition specific regulatory rewiring in human breast cancer. We also propose a novel method, namely Gibbs sampler to Infer Signal Transduction (GIST), to detect aberrant pathways that are highly associated with biological phenotypes or clinical information. By converting predefined potential functions into a Gibbs distribution, GIST estimates edge directions by learning the distribution of linear signaling pathway structures. Through the sampling process, the algorithm is able to infer signal transduction directions which are jointly determined by both gene expression and network topology. We demonstrate the advantage of the proposed algorithms on simulation data with respect to different settings of noise level in gene expression and false-positive connections in protein-protein interaction (PPI) network. Another major contribution of the dissertation work is that we have improved traditional perspective towards understanding aberrant signal transductions by further investigating structural linkage of signaling pathways. We develop a method called Structural Organization to Uncover pathway Landscape (SOUL), which emphasizes on modularized pathways structures from reconstructed pathway landscape. GIST and SOUL provide a very unique angle to computationally model alternative pathways and pathway crosstalk. The proposed new methods can bring insight to drug discovery research by targeting nodal proteins that oversee multiple signaling pathways, rather than treating individual pathways separately. A complete pathway identification protocol, namely Infer Modularization of PAthway CrossTalk (IMPACT), is developed to bridge downstream regulatory networks with upstream signaling cascades. We have applied IMPACT to breast cancer treated patient datasets to investigate how estrogen receptor (ER) signaling pathways are related to drug resistance. The identified pathway proteins from patient datasets are well supported by breast cancer cell line models. We hypothesize from computational results that HSP90AA1 protein is an important nodal protein that oversees multiple signaling pathways to drive drug resistance. Cell viability analysis has supported our hypothesis by showing a significant decrease in viability of endocrine resistant cells compared with non-resistant cells when 17-AAG (a drug that inhibits HSP90AA1) is applied. We believe that this dissertation work not only offers novel computational tools towards understanding complicated biological problems, but more importantly, it provides a valuable paradigm where systems biology connects data with hypotheses using computational modeling. Initial success of using microarray datasets to study endocrine resistance in breast cancer has shed light on translating results from high throughput datasets to biological discoveries in complicated human disease studies. As the next generation biotechnology becomes more cost-effective, the power of the proposed methods to untangle complicated aberrant signaling rewiring and pathway crosstalk will be finally unleashed. / Ph. D.

The purpose of the present study was to demonstrate behavioral differences between high Machiavellians (MACHS) as described by Christie (1970a) and those exhibiting the aberrant self-promotion pattern proposed by Gustafson and Ritzer (1995). The aberrant self-promoter (ASP) was defined as having a high degree of narcissism, combined with a low need to appear conventionally "nice" along with pronounced antisocial behavior. The Machiavellian was described as one who is capable of manipulating others to obtain some advantage. The situation that was proposed differentiate the two groups is a legislature game which involves bargaining and forming alliances. ASPs and Machiavellians were identified by the same procedures used by Gustafson and Ritzer (1995). In Condition 1, the issues being voted upon were value laden in the sense that they were designed to elicit an affective response. In Condition 2, the issues were value and affect neutral. The experimental subjects were undergraduates enrolled in psychology courses. It was predicted that because Machiavellians are better at separating affect from rational thought than are either ASPs or non-Mach non-ASPs, Machiavellians would perform better than either of the other groups in the value laden issues condition. It was also predicted that participants would rate aberrant self-promoters less favorably than other players on trust, respect, and likability due to the ASPs ineffectiveness in bargaining and forming alliances. Two repeated measures ANOVAs were performed to test the hypotheses. Results supported only the last prediction regarding likability. Reasons for these findings and implications were discussed / Master of Science

Milk fat globule membrane surrounds the fat droplets of milk. It is a biopolymer containing primarily membrane glycoproteins and polar lipids which contribute to its properties as a possible neutraceutical. The aims of the studies were to determine if dietary milk fat globule membrane: (1) confers protection against colon carcinogenesis; and (2) promotes gut mucosal integrity while decreasing inflammation compared to diets containing corn oil or anhydrous milk fat. Aim 1. Three dietary treatments differing only in the fat source were formulated: (1) AIN-76A, corn oil; (2) AIN-76A, anhydrous milk fat; and (3) AIN-76A, 50% milk fat globule membrane, 50% anhydrous milk fat. Each diet was formulated to contain 50 g/kg diet of fat and to be identical in macro and micro nutrient content. To assess protection against colon carcinogenesis, male, weanling Fischer-344 rats were randomly assigned to one of the three dietary treatments. Animals were injected with 1,2-dimethylhydrazine once per week at weeks 3 and 4. After 13 weeks animals were sacrificed, colons were removed, and aberrant crypt foci were counted by microscopy. Rats fed the milk fat globule membrane diet (n = 16) had significantly fewer aberrant crypt foci (20.9 ± 5.7) compared to rats fed corn oil (n = 17) or anhydrous milk fat (n = 16) diets (31.3 ± 9.5 and 29.8 ± 11.4 respectively; P < 0.05). Aim 2. Male BALB/c mice were randomly assigned to one of two diets: AIN- 76A, corn oil or AIN-76A, 50% milk fat globule membrane, 50% anhydrous milk fat. After 5 weeks mice were injected with saline vehicle control or lipopolysaccharide and gavaged with dextran-FITC. To assess gut mucosal integrity and inflammation, serum samples were assayed for dextran-FITC 24 and 48 hours after gavage, and a panel of 16 cytokine concentrations was analyzed. Serum concentrations of IL-6, IL-10, IL-17, MCP-1, IFNγ, and TNFα decreased and gut permeability decreased 45% in lipopolysaccharide challenged mice fed milk fat globule membrane diet compared to control diet at 24 hours (P < 0.05). Overall, the results of these aims suggest that diets containing milk fat globule membrane are protective against colon carcinogenesis, inhibit the inflammatory response, and protect against gastrointestinal stress.

Background. Lynch syndrome is the most common genetic predisposition for hereditary cancer. Carriers of pathogenic changes in mismatch repair (MMR) genes have an increased risk of developing colorectal (CRC), endometrial, ovarian, urinary tract, prostate, and other cancers, depending on which gene is malfunctioning. In Lynch syndrome, differences in cancer incidence (penetrance) according to the gene involved have led to the stratification of cancer surveillance. By contrast, any differences in penetrance determined by the type of pathogenic variant remain unknown. Objective. To determine cumulative incidences of cancer in carriers of truncating and missense or aberrant splicing pathogenic variants of the MLH1 and MSH2 genes. Methods. Carriers of pathogenic variants of MLH1 (path_MLH1) and MSH2 (path_MSH2) genes filed in the Prospective Lynch Syndrome Database (PLSD) were categorized as truncating or missense/aberrant splicing according to the InSiGHT criteria for pathogenicity. Results. Among 5199 carriers, 1045 had missense or aberrant splicing variants, and 3930 had truncating variants. Prospective observation years for the two groups were 8205 and 34,141 years, respectively, after which there were no significant differences in incidences for cancer overall or for colorectal cancer or endometrial cancers separately. Conclusion. Truncating and missense or aberrant splicing pathogenic variants were associated with similar average cumulative incidences of cancer in carriers of path MLH1 and path_MSH2.

Submitted by Michele Mologni (mologni@unoeste.br) on 2019-01-29T18:40:59Z No. of bitstreams: 1 Sandra Cristina Genaro.pdf: 1632390 bytes, checksum: 89f6ec224705d20a5ce967976b70a4c3 (MD5) / Made available in DSpace on 2019-01-29T18:40:59Z (GMT). No. of bitstreams: 1 Sandra Cristina Genaro.pdf: 1632390 bytes, checksum: 89f6ec224705d20a5ce967976b70a4c3 (MD5) Previous issue date: 2018-11-22 / Among the existing types, colorectal cancer (CRC) affects approximately one million people per year, considered the second most common cause of death among women and the third most prevalent in men. Risk factors are genetic syndromes; inflammatory bowel diseases; family history; sedentary lifestyle; obesity, low fiber, high saturated fats, smoked foods or built-in food, excess red meat (> 300g/week), preparation mode in high temperatures and on the ember; medications; smoking, and excessive alcohol. These factors alter the intestinal microbiome which is colonized by pathogenic bacteria capable of provoking a local inflammatory response that, in chronic cases, activates carcinogenic components. Probiotics have increasingly attracted the attention of researchers in order to understand their action in the intestinal microbiota, aiding in the prevention and treatment of colorectal cancer. The objective of this study was to evaluate the effect of a probiotic In aggressiveness of the chemically induced colorectal tumor in rats. Twenty-five male Fisher 344 rats, 250 g, receiving ration and water ad libitum, were randomly divided into 5 groups (5 rats/group): GControl, without treatment; GTumor, tumor induction; GTumor + 5FU, tumor induction, 5-fluorouracil applied; GTumor + prob, tumor induction, supplemented with probiotic; GTumor + 5-FU + prob, tumor induction, applied 5-fluorouracil, supplemented with probiotic. For tumor induction, the animals received four intraperitoneal injections of the carcinogen 1.2-dimethylhidrazine (DMH) at the dose of 20 mg/kg body weight, being two applications per week, for four consecutive week. A 15-day interval was given and DMH applications were repeated for another four week. After 5 weeks of the last dose of the carcinogen, the treatment was initiated for ten consecutive weeks, applying a weekly dose of 15 mg/kg body weight of 5-fluorouracil, Intraperitoneal route and commercial probiotic containing Lactobacillus and Bifidobacterium at the dose of 1x109 UFC, administered by gavage, daily. Datas were analyzed by the analysis of variance One Way and the averages compared by the test of Dunnett. Used Software Statistical GraphPad Prism. The histopathologic analyses evaluated by the Chi-square ratio test. It was considered type-I error of 5% as statistically significant. Compared to the GTumor, the GTumor + prob (P < 0,0373) and GTumor + 5-FU + prob (P < 0,0003) showed attenuating effect on the aggressiveness of the colorectal tumor, with a reduction in the count of Aberrant Crypts Foci; and lower percentage of malignant neoplastic lesions in the GTumor + prob (40% of low-grade tubular adenoma, 40% of carcinoma in situ, 20% of low-grade adenocarcinoma) and GTumor + 5-FU + prob (40% of low-grade tubular adenoma and 60% of carcinoma in situ). The suplementation with probiotic has the potential to decrease the formation of aberrant crypts and mitigate the progression of tumor malignancy, potentializing the antitumor effect of 5-fluorouracil chemotherapy in the colic segments. / O câncer colorretal (CCR) acomete aproximadamente um milhão de pessoas por ano, considerado a segunda causa de morte mais comum entre mulheres e a terceira mais prevalente em homens. Os fatores de risco incluem as síndromes genéticas; doenças inflamatórias intestinais; história familiar; sedentarismo; obesidade, alimentação pobre em fibras, rica em gorduras saturadas, alimentos defumados ou embutidos, carne vermelha em excesso (>300g/sem), modo de preparação em altas temperaturas e na brasa; medicamentos; tabagismo e bebida alcoólica em excesso. Esses fatores levam a alteração da microbiota intestinal a qual é colonizada por bactérias patogênicas capazes de provocar uma resposta inflamatória local que, em casos crônicos, ativam componentes cancerígenos. Os probióticos têm atraído cada vez mais a atenção de pesquisadores com o intuito de compreender a sua ação na microbiota intestinal, auxiliando na prevenção e tratamento do câncer colorretal. O objetivo desse estudo foi avaliar o efeito de um probiótico na agressividade do tumor colorretal induzido quimicamente em ratos. Vinte e cinco ratos machos Fisher 344, 250 g, recebendo ração e água ad libitum, foram divididos aleatoriamente em 5 grupos (5 ratos/grupo): GControle, sem tratamento; GTumor, indução do tumor; GTumor+5FU, indução do tumor, aplicado 5-Fluorouracil; GTumor+Prob, indução do tumor, suplementado com probiótico; GTumor+5-FU+Prob, indução do tumor, aplicado 5-Fluorouracil, suplementado com probiótico. Para indução do tumor colorretal, os animais receberam quatro injeções intraperitoneais do carcinógeno 1,2-dimetilhidrazina (DMH) na dose de 20 mg/kg de peso corporal, sendo duas aplicações por semana, durante quatro semanas consecutivas. Deu-se um intervalo de 15 dias e as aplicações de DMH foram repetidas por mais quatro semanas. Após 5 semanas da última dose do carcinógeno, iniciou-se o tratamento por dez semanas consecutivas, com 5-Fluorouracil: uma dose de 15 mg/kg por semana, via intraperitoneal e probiótico comercial: 1x109 UFC, diariamente, por gavagem. Os dados foram analisados pela Análise de Variância One Way e as médias comparadas pelo teste de Dunnett. Utilizado software estatístico GraphPad Prism. As análises histopatológicas avaliadas pelo teste de proporção Qui-quadrado. Foi considerado erro tipo-I de 5% como estatisticamente significante. Comparados com o GTumor, o GTumor+Prob (p<0,0373) e GTumor+5-FU+Prob (p<0,0003) exibiram efeito atenuante na agressividade do tumor colorretal obervando redução na contagem de Focos de Criptas Aberrantes; e menor porcentagem de lesões neoplásicas malignas no GTumor+Prob (40% de adenoma tubular de baixo grau, 40% de carcinoma in situ, 20% de adenocarcinoma de baixo grau) e GTumor+5-FU+Prob (40% de adenoma tubular de baixo grau e 60% de carcinoma in situ). Concluimos que a suplementação com probiótico tem potencial para diminuir a formação de criptas aberrantes e amenizar a progressão da malignidade do tumor, potencializando o efeito antitumoral da quimioterapia com 5-Fluorouracil nos segmentos cólicos.

In an experiment to understand colon carcinogenesis, all animals were exposed to a carcinogen while half the animals were also exposed to radiation. Spatially, we measured the existence of aberrant crypt foci (ACF), namely morphologically changed colonic crypts that are known to be precursors of colon cancer development. The biological question of interest is whether the locations of these ACFs are spatially correlated: if so, this indicates that damage to the colon due to carcinogens and radiation is localized. Statistically, the data take the form of binary outcomes (corresponding to the existence of an ACF) on a regular grid. We develop score??type methods based upon the Matern and conditionally autoregression (CAR) correlation models to test for the spatial correlation in such data, while allowing for nonstationarity. Because of a technical peculiarity of the score??type test, we also develop robust versions of the method. The methods are compared to a generalization of Moran??s test for continuous outcomes, and are shown via simulation to have the potential for increased power. When applied to our data, the methods indicate the existence of spatial correlation, and hence indicate localization of damage. Assuming that there are correlations in the locations of the ACF, the questions are how great are these correlations, and whether the correlation structures di?er when an animal is exposed to radiation. To understand the extent of the correlation, we cast the problem as a spatial binary regression, where binary responses arise from an underlying Gaussian latent process. We model these marginal probabilities of ACF semiparametrically, using ?xed-knot penalized regression splines and single-index models. We ?t the models using pairwise pseudolikelihood methods. Assuming that the underlying latent process is strongly mixing, known to be the case for many Gaussian processes, we prove asymptotic normality of the methods. The penalized regression splines have penalty parameters that must converge to zero asymptotically: we derive rates for these parameters that do and do not lead to an asymptotic bias, and we derive the optimal rate of convergence for them. Finally, we apply the methods to the data from our experiment.

In an experiment to understand colon carcinogenesis, all animals were exposed to a carcinogen while half the animals were also exposed to radiation. Spatially, we measured the existence of aberrant crypt foci (ACF), namely morphologically changed colonic crypts that are known to be precursors of colon cancer development. The biological question of interest is whether the locations of these ACFs are spatially correlated: if so, this indicates that damage to the colon due to carcinogens and radiation is localized. Statistically, the data take the form of binary outcomes (corresponding to the existence of an ACF) on a regular grid. We develop score??type methods based upon the Matern and conditionally autoregression (CAR) correlation models to test for the spatial correlation in such data, while allowing for nonstationarity. Because of a technical peculiarity of the score??type test, we also develop robust versions of the method. The methods are compared to a generalization of Moran??s test for continuous outcomes, and are shown via simulation to have the potential for increased power. When applied to our data, the methods indicate the existence of spatial correlation, and hence indicate localization of damage. Assuming that there are correlations in the locations of the ACF, the questions are how great are these correlations, and whether the correlation structures di?er when an animal is exposed to radiation. To understand the extent of the correlation, we cast the problem as a spatial binary regression, where binary responses arise from an underlying Gaussian latent process. We model these marginal probabilities of ACF semiparametrically, using ?xed-knot penalized regression splines and single-index models. We ?t the models using pairwise pseudolikelihood methods. Assuming that the underlying latent process is strongly mixing, known to be the case for many Gaussian processes, we prove asymptotic normality of the methods. The penalized regression splines have penalty parameters that must converge to zero asymptotically: we derive rates for these parameters that do and do not lead to an asymptotic bias, and we derive the optimal rate of convergence for them. Finally, we apply the methods to the data from our experiment.