Motivation: Network interpretation using correlations has several known difficulties. Firstly, the data structure has discrete counts with an excess of zeros creating non-normal non-continuous data. Secondly, correlations, often used as similarity measures in network inference, are not causal. Thirdly, there is a masking effect of mutualism on commensalism and competition on amensalism in ecological networks that interfere with interpretation (Faust and Raes, 2012). More explicitly, the symmetric nature of correlations (cor(X,Y)=cor(Y,X)) can mask the affect of the asymmetric ecology relationship (commensalism and amensalism). We aim to solve the third issue which may speed up targeted drug therapies or disease diagnosis based on specific relationships in gut microbiomes. Methods: We apply a non-symmetric correlation method, Gini Correlations which should serve as a better classifier of ecological relationships revealing a fuller picture of microbiomes. First, create simulated correlated and independent Zero-Inflated Negative Binomial data. Second, validate Gini correlations by comparing Gini with Pearson Spearman and Kendall correlations; calculate false positive rate, true positive rate, accuracy, ROC, AUC after applying Benjamini-Hochberg (1995) multiple testing correction. Simulation Result: Gini is consistent and out performs other methods for small sample sizes of 10 and 25 producing consistently low false positive rates across 64+ simulation settings as well as consistently high accuracy rates. When sample size is increased to 50 Gini performs as well as other methods. Real Data Result: For well-defined microbial communities Gini correlations found novel biologically and medically relevant relationships. However, Gini's ability to unmask non-symmetric ecological relationships is yet to be determined.

The collective microbial genomes within our gut(microbiome) represent a powerful metabolic force, leading many authors to call our GI flora an "organ within an organ", and the metagenomic sequencing of our microbiome, "the second human genome project". Bile acids, endogenously produced by the host liver, represent both a strong selective pressure for potential colonizers, aswell as substrates for microbial metabolism. Indeed, microbes have evolved enzymes to deconjugate bile salts, epimerize bile acid hydroxyl groups, and 7alpha-dehydroxylateprimary bile acids. The products of microbial 7alpha-dehydroxylation, secondary bile acids, are suggested by numerous lines of evidence to be involved in promoting colon carcinogenesis. 7alpha-dehydroxylating activity is a multi-step pathway, genes of which have only been identified in a small number of organisms within the genusClostridium. The biochemistry of this pathway has been largely worked out. The third step in the pathway is introduction of a delta-4-double bond; however, the gene product(s) responsible have not been identified. The baiCD and baiH genes were cloned, expressed and shown to have NAD-dependent 3-oxo-delta-4-steroid oxidoreductase activity showing stereospecificity for 7alpha-hydroxy and 7beta-hydroxy bile acid, respectively.In addition, bai genes were isolated from C.hylemonae TN271 by bidirectional genome-walking by PCR. This represents the first report of bai genes from a "low activity" 7alpha-dehydroxylating bacterium. The gene organization and sequence of the baiBCDEFGHI operon was highly conserved between C. hylemonae TN271 and the "high activity" 7alpha-dehydroxylating bacterium C. scindens VPI12708. The baiA gene was located by PCR using degenerate oligonucleotides. Bi-directional genome-walking revealed what appears to be several novel genes involved in bile acid metabolism which were also located in C. scindens VPI 12708. Expression of a 62 kDa flavoprotein and reactionwith [24-14C] 3-oxo-DCA and NADP resulted in a product of greater hydrophilicity than deoxycholic acid. The identity of this product was not determined. A second gene appears to share a common evolutionary origin with the baiF gene. A hypothesis is offered regarding the function of these homologues as Type III CoA transferasesrecognizing 5alpha-bile acids, or 5beta-bile acids (allo-bile acids). A third gene encodes a putative short chain reductase, similar in size and predicted function to the baiA gene, which may be involved in the final reductive step in the pathway. These novel genes also contained a conserved upstream regulatory region with the baioxidative genes. Finally, two genes were identified which may serve as potential drug targets to inhibit bile acid 7alpha-dehydroxylation. The first is an ABC transporter which may be co-transcribed with the other novel bile acid metabolizing genes, and what appears to be a bile acid sensor/regulator similar to the Tryptophan-rich sensory protein (TspO)/mitochondrial peripheral benzodiazepinereceptor (MBR) family of proteins.

Master of Science / Department of Anatomy and Physiology / Lei Wang / Jishu Shi / Interleukin-1 beta (IL-1β) is an important mediator of inflammatory response, and the elevated expression of IL-1β is correlated with tumor growth and metastasis. Epithelial-mesenchymal transition (EMT) is a reversible transition between epithelial phenotype and mesenchymal phenotype. Usually, EMT can be identified by its unique morphology change and expression of EMT markers. In our study, we have found after treated HCT-116, a colon cancer cell line, and human primary colon cancer cells with IL-1β, cells began to display mesenchymal phenotype with highly down-regulated E-cadherin expression and up-regulated ZEB factors expression. For colon cancer cells, sphere formation assay in serum free medium (SFM) with the presence of growth factors is used to identify cancer stem cell population. We have shown that IL-1β can induce colon cancer stem cell proliferation and express stem cell markers (Bmi1, Nanog, and Nestin). In addition, besides the stem cell markers, we also found ZEB factors were highly up-regulated in spheroid cells as well. We silenced Zeb1 expression and investigated the effect of IL-1β on shZeb1 HCT-116 cells. The results indicated Zeb1 knockdown not only inhibited IL-1β-induced EMT but also reduced proliferation of spheroid cells and inhibited Bmi1 expression. Therefore, ZEB factors must play an important role in both EMT process and cancer stem cell development. From our data, we conclude that IL-1β promotes epithelial-mesenchymal transition and a stem cell phenotype in colon cancer via ZEB factors.

Sulforafan är en isotiacyanat som beskrivs ha effektiva cancerpreventativa egenskaper. Kemikalien görs tillgänglig för människan genom konsumtion av korsblommiga grönsaker så som broccoli och grönkål. Cancer är vanligt, och i Sverige räknar man med att var tredje människa kommer att drabbas under sin livstid. I följande litteraturstudie var syftet att sammanställa information om på vilket sätt sulforafan påverkar koloncancerceller, samt söka evidens för att konsumtion av sulforafanrika grönsaker bidrar till minskad risk att drabbas av koloncancer. Sulforafan har cancerpreventativa egenskaper i cellkultur så som inhibering av histondeacetylas-aktivitet, inducering av cellcykelarrest och apoptos och minskad proliferation hos cancercellerna. Det minskar även uttryck av gener som är inblandade i angiogenes.Det finns inte nog med evidens om broccolikonsumtion, på grund av sitt höga innehåll av sulforafan, skulle vara cancerpreventativt hos människan. / Sulforaphane is an isothiocyanate that is described as having chemopreventative effects. The phytochemical is made available to humans by dietary consumption of cruciferous vegetables such as broccoli and kale. Cancer is a common disease, and in Sweden it is estimated that one in three will be diagnosed with cancer during their lifetime. This review study aims to summarize the effect of sulforaphane on human colon cancer cells, and seek evidence that consumption of cruciferous vegetables reduces the risk of developing colon cancer. Sulforaphane is considered chemopreventative in vitro through inhibition of histone deacetylas activity, induction of cell cycle arrest and apoptosis and through reduction of cell proliferation. It has also been shown to reduces expression of genes involved in angiogenesis.There is not enough evidence to confirm that dietary broccoli consumption, through its high content of sulforaphane, would be chemopreventative.

Introdução - Estudos sobre o câncer de cólon mostram que a sua incidência, no mundo, tem aumentado de maneira significativa no último século. Acredita-se que este resultado esteja relacionado, entre outros aspectos, com a industrialização, a urbanização ocorridas neste período e mudanças no estilo de vida. A morbimortalidade associada ao câncer de cólon observada em países desenvolvidos é maior do que em países em desenvolvimento e o que se tem observado é que, embora a tendência da incidência seja crescente para ambos os sexos, a mortalidade permanece estável. Objetivo - Analisar as tendências da incidência e da mortalidade de pacientes com câncer de cólon, registrados no Registro de Câncer de Base Populacional (RCBP) do Município de São Paulo. Métodos - Foram analisadas as tendências temporais da incidência no período de 1997 a 2005 e da mortalidade no período de 1980 a 2007. As análises foram feitas separadamente por sexo e faixa etária e os efeitos da idade, do período e da coorte foram estimados através do modelo de regressão de Poisson. Resultados - Houve aumento na incidência por câncer de cólon no município de São Paulo, em quase todas as faixas etárias estudadas. O aumento da mortalidade foi menor do que o aumento da incidência e parece coincidir com um efeito de coorte presente durante todo o período do estudo. Tanto na incidência quanto na mortalidade, os aumentos foram mais pronunciados entre os homens. O modelo idade-período apresentou o melhor ajuste para os coeficientes de incidência para ambos os sexos, e o modelo completo (idade-período-coorte) se mostrou com melhor ajuste para os coeficientes de mortalidade para ambos os sexos. Não foi identificada interação estatisticamente significativa do sexo para os coeficientes de incidência e de mortalidade. Conclusão: Os resultados encontrados no presente estudo mostraram um aumento da incidência e da mortalidade, em ambos os sexos, em quase todas as faixas etárias. Observamos uma tendência da estabilização nas coortes de nascimento do câncer de cólon para ambos os sexos, sugerindo que as mudanças de estilo de vida podem contribuir para a redução da mortalidade por câncer de cólon, principalmente nas coortes mais jovens. / Introduction Studies on colon cancer show that its incidence worldwide has been increasing in the last century. There is evidence suggesting that this can be partially related to the industrialisation and urbanisation which occurred in the period and life style changes. Morbi-mortality associated with colon cancer observed in industrialised countries is greater than in developing countries. Colon cancer incidence presents an increasing trend for both sexes, probably due to a wider access to available diagnostic methods, while mortality rates remain stable. Objective: To assess incidence and mortality trends in patients with colon cancer, registered in São Paulo Cancer Registry. Methods: Temporal trends between 1997 and 2005 for incidence and between 1980 and 2007 for mortality were assessed. Analyses were performed separately by sex and age group, and effects of age, period and cohort were estimated by using Poisson´s regression model. Results: For all age groups assessed, there was an increase in colon cancer incidence in the city of São Paulo. The increase in mortality rates was lower than the increase in incidence which seems to coincide with a cohort effect present during the period studied. Increases in both incidence and mortality rates, were more pronounced among men. The age-period model presented the best adjustment to incidence coefficients for both sexes and the complete age-periodcohort model showed the best adjustment to mortality coefficients for both sexes. No significant statistical interaction for sex and incidence coefficient or sex and mortality coefficient was found. Conclusion: Results found in the present study revealed an increase in incidence and mortality rates, for both sexes and all age groups. A stabilisation in birth cohorts of colon cancer for both sexes was observed, suggesting that life style changes may contribute to the reduction in colon cancer mortality, especially in younger cohorts.

In Canada, colorectal cancer is the second leading cause of death from cancer in men and the third leading cause of death from cancer in women. Several factors contribute to the development of cancer. Genetic predisposition, diet, and lifestyle habits are some of the major factors for colorectal cancer development. In the diet related factors, epidemiological studies suggest that consumption of whole grains rich in dietary fiber are associated with low incidence of human colon cancer. Recent studies have also shown that, in addition to dietary fiber, the type of dietary fiber and other compounds such as phenolic acids present in cereal grain bran may also have a role to play in colon cancer prevention. In a recent study, eleven major phenolic acids which differed in anti-oxidant activity were identified in wheat bran from wheat varieties belonging to six different market classes. The main objective of this study was to develop an in vitro cell culture based assay system to study the effect of phenolic acids on colon cancer development. Another objective was to study the effect of phenolic acids on selected molecular markers associated with cell proliferation, apoptosis and inflammation. Two well established colon carcinoma cell lines HT-29 and HCT 116 were treated with varying concentrations of fourteen phenolic acids to study their effect on cell survival and proliferation. In addition, immunohistochemical assays were performed on treated cells for two cell proliferation markers (Cyclin D1 and Ki67), an apoptosis marker (Bax) and three inflammatory markers (Beta-catenin, COX-2 and iNOS). Treatment of phenolic acids inhibited the growth of both the cell lines, however the effects varied with phenolic acid and cell line used in the assay. As determined by IC50, the growth of HCT 116 cells was inhibited the most by caffeic, ellagic, and gallic acids with IC50 of 0.22 mM, 0.17 mM, and 0.15 mM, respectively. On the other hand, caffeic, chlorogenic, and gallic acids are most effective in preventing the growth of HT-29 cells, with IC50 at 0.06 mM, 0.28 mM, and 0.30 mM, respectively. Immunohistochemical and Western Blotting studies revealed that phenolic acids differentially affected markers for cell proliferation, apoptosis and cell inflammation. In most of the cases, phenolic acid treatments up-regulated the pro-apoptosis marker Bax, while it down-regulated cell proliferation marker Cyclin D1. The results clearly show that a cell culture based assay can be used to study the effect of phenolic acids or other chemical constituents isolated from plants to study their effect on colon cancer cell lines. Statistical analysis revealed that only in very limited cases, results of molecular markers correlated to cell growth and proliferation. Therefore, to draw firm conclusions, more detailed and extensive studied need to be completed using different phenolic acids, the two cell lines and more replications. However, this study has developed the necessary protocols and provided some indicative results such as most of the phenolic acids induced pro-apoptosis pathway in both the colon cancer lines. Future studies with extracted phenolic acids from wheat bran using the cell culture system optimized in this study can be used to define the role of different wheat varieties in colon cancer prevention.

Apoptosis is a genetically regulated form of cell death that occurs when the cell is exposed to physiological, pathogenic, or cytotoxic stimuli. Unregulated apoptosis (too much or too little apoptosis) at any time from embryogenesis to adulthood, can result in a variety of disease states, such as neurodegenerative disorders, autoimmunity, cardiovascular disease, liver and kidney problems, and cancer. A reasonable estimation is that either too little or too much cell death contributes to half of the main medical illnesses for which adequate therapy or prevention is lacking. The apoptotic pathways can be initiated by reactive oxygen species (ROS) and inflammatory molecules, both of which are believed to be up-regulated in a state of obesity. In addition, multiple studies have shown that the risk of developing cardiovascular disease, type 2 diabetes mellitus, nonalcoholic fatty liver disease, and certain types of cancers increase with increasing degree of obesity in both men and women. Despite the well characterized association of obesity and disease incidence, the mechanisms by which obesity contributes to disease pathology are poorly understood. Previously, in our research group, it was shown that obese Zucker rats, which are the animal model of human obesity, are more prone to colon cancer and hepatic steatosis compare to their relative lean counterparts. Therefore, applying Real-Time RT-PCR, the expression levels of some pro- and anti-apoptotic members of the BCL-2 family of genes were investigated to figure out the possible effect of obesity on apoptotic gene expression levels. Also, apoptotic gene expression patterns of obese and lean Zucker rats after DNA damage induction were compared to each other in order to find the possible connection of apoptotic gene expression with disease progression in obese individuals. This is the first study comparing the expression level of BCL-2 family of genes in obese versus lean liver and colon tissue. In this study, it was shown that an obese genotype affects pro- and anti-apoptotic gene expression levels and patterns whether or not DNA damage has been induced in both liver and colon. The results show a clear alteration in apoptotic gene expression levels in obese individuals compared to their lean counterparts leading to the proposal that apoptosis may be involved in the obesity related colon cancer and liver steatosis.

BackgroundIn this study, we describe a Quality Improvement (QI) intervention in three radiology departments within the Swedish health care system, with a special focus on access and methodology. AimThe goals for the QI-intervention were to implement best practice for patients with suspected colon cancer, and reduce the Turn Around Time (TAT).The aim of the study was to identify relevant factors for successful QI in order to further develop the organisation to create a system of continuous QI (CQI) for the radiological service. MethodsInitially, a multiprofessional QI-team was formed. To identify waste and areas for improvement, process mapping and lead time analysis were conducted during a collaborative learning approach. A focus group interview was carried out with the participants in the QI-intervention and the local managers, and a qualitative content analysis of the focus group transcript was performed. ResultsBest practise was gradually introduced, and overall access was improved, but TAT was not changed. Four key factors for CQI were revealed; Communication, Engagement, Context, and Patient- and Customer focus. Moreover, the impact of providing useful and reliable measurements to the frontline staff was found to be high DiscussionThe lack of decreased TAT indicates that further redesign of the radiology process is needed. As the impact of measurements was considered high, an improved system for obtaining and providing useful information to all parts in the organization is essential. Moreover, the infrastructure for CQI needs to be developed further, e.g. by clarifying roles, educating in improvement knowledge, and developing multiprofessional meetings. Finally, motivating and engaging staff is crucial to improve healthcare. It is important with a deeper understanding what triggers this, patient centeredness could be one.

Apoptosis is a genetically regulated form of cell death that occurs when the cell is exposed to physiological, pathogenic, or cytotoxic stimuli. Unregulated apoptosis (too much or too little apoptosis) at any time from embryogenesis to adulthood, can result in a variety of disease states, such as neurodegenerative disorders, autoimmunity, cardiovascular disease, liver and kidney problems, and cancer. A reasonable estimation is that either too little or too much cell death contributes to half of the main medical illnesses for which adequate therapy or prevention is lacking. The apoptotic pathways can be initiated by reactive oxygen species (ROS) and inflammatory molecules, both of which are believed to be up-regulated in a state of obesity. In addition, multiple studies have shown that the risk of developing cardiovascular disease, type 2 diabetes mellitus, nonalcoholic fatty liver disease, and certain types of cancers increase with increasing degree of obesity in both men and women. Despite the well characterized association of obesity and disease incidence, the mechanisms by which obesity contributes to disease pathology are poorly understood. Previously, in our research group, it was shown that obese Zucker rats, which are the animal model of human obesity, are more prone to colon cancer and hepatic steatosis compare to their relative lean counterparts. Therefore, applying Real-Time RT-PCR, the expression levels of some pro- and anti-apoptotic members of the BCL-2 family of genes were investigated to figure out the possible effect of obesity on apoptotic gene expression levels. Also, apoptotic gene expression patterns of obese and lean Zucker rats after DNA damage induction were compared to each other in order to find the possible connection of apoptotic gene expression with disease progression in obese individuals. This is the first study comparing the expression level of BCL-2 family of genes in obese versus lean liver and colon tissue. In this study, it was shown that an obese genotype affects pro- and anti-apoptotic gene expression levels and patterns whether or not DNA damage has been induced in both liver and colon. The results show a clear alteration in apoptotic gene expression levels in obese individuals compared to their lean counterparts leading to the proposal that apoptosis may be involved in the obesity related colon cancer and liver steatosis.

Recent experiments are bringing to the fore more and more information about the effects of different treatments on the gene expression of different genes. The results obtained from these experiments show that some definite trends are observed in different genes in the Human Embryonic Kidney and Human Colon Adenocarcinoma Grade II cell lines. The difference in the gene expressions of the two cell lines motivates the problem in this thesis. The thesis provided intervention methods to make the colon cancer cell line genes behave more like their Human Embryonic Kidney cell line counterparts. Two methods of intervention were introduced. The first method was the simpler on-off control intervention while the second method used a more advanced proportional integral control to meet the goal. A comparison of these two intervention methods showed the clear implementational advantages of proportional integral control over on-off control.