Genes Confer Similar Robustness to Environmental, Stochastic, and Genetic Perturbations in Yeast

Gene inactivation often has little or no apparent consequence for the phenotype of an organism. This property—enetic (or mutational) robustness—is pervasive, and has important implications for disease and evolution, but is not well understood. Dating back to at least Waddington, it has been suggested that mutational robustness may be related to the requirement to withstand environmental or stochastic perturbations. Here I show that global quantitative data from yeast are largely consistent with this idea. Considering the effects of mutations in all nonessential genes shows that genes that confer robustness to environmental or stochastic change also buffer the effects of genetic change, and with similar efficacy. This means that selection during evolution for environmental or stochastic robustness (also referred to as canalization) may frequently have the side effect of increasing genetic robustness. A dynamic environment may therefore promote the evolution of phenotypic complexity. It also means that “hub” genes in genetic interaction (synthetic lethal) networks are generally genes that confer environmental resilience and phenotypic stability

IRE1α Disruption Causes Histological Abnormality of Exocrine Tissues, Increase of Blood Glucose Level, and Decrease of Serum Immunoglobulin Level

Accumulation of unfolded proteins in the endoplasmic reticulum (ER) causes ER stress. As a cellular adaptive response to ER stress, unfolded protein response (UPR) activates molecules for the quality control of ER proteins. One enzyme that plays an important role in UPR is Inositol Requiring Enzyme-1 (IRE1), which is highly conserved from yeast to humans. In particular, mammalian IRE1α activates X-box-binding protein 1 (XBP1) by unconventional splicing of XBP1 mRNA during ER stress. From analysis of knockout mice, both IRE1α and XBP1 have been shown to be essential for development and that XBP1 is necessary for the secretory machinery of exocrine glands, plasma cell differentiation, and hepatic lipogenesis. However, the essentiality of IRE1α in specific organs and tissues remains incompletely understood. Here, we analyzed the phenotype of IRE1α conditional knockout mice and found that IRE1α-deficient mice exhibit mild hypoinsulinemia, hyperglycemia, and a low-weight trend. Moreover, IRE1α disruption causes histological abnormality of the pancreatic acinar and salivary serous tissues and decrease of serum level of immunoglobulin produced in the plasma cells, but not dysfunction of liver. Comparison of this report with previous reports regarding XBP1 conditional knockout mice might provide some clues for the discovery of the novel functions of IRE1α and XBP1. (196 words

Aspects of the Statistical Analysis of Data From Mixture Distributions

The purpose of this thesis is to give insight into major problems arising in the theory of mixture distributions, and, more importantly, to improve and extend some of the results that are given in the literature. We especially focus on the problem of estimating the number of components that underlie the probability distribution of a data sample. This is among the most difficult problems encountered in this area. In principle, there are two main approaches to the problem; the theoretical approach studies the asymptotic distribution of the likelihood ratio test under the null hypothesis for testing for k1 versus k2 components, where k1 < k2, and the algorithmic approach uses simulations in order to overcome some of the theoretical difficulties. In this work, we use both methodologies, and we give illustrations of the methods' performances in some practical examples. We emphasise, now, the approaches that we adopt for dealing with this problem. In a Monte-Carlo context, we propose a technique that uses an information theory criterion inside a parametric bootstrap procedure. The performance of this technique is then assessed, and comparison is made to a method using a similar type of bootstrap procedure, but where the decision criterion is based on likelihood ratio inference, and to Windham and Cutler's (1992) information theory based method. Another combined approach is also suggested. Using a stochastic algorithmic methodology, Celeux (1987) proposes a test for the number of components, and claims that it follows a Hotelling's distribution. We argue about the reasons why this does not hold, and we derive the asymptotic distribution of this test statistic. This theoretical investigation leads us to study some problems that go beyond the scope of the mixture framework, since they are related to the theory of autoregressive processes. Some simulation results are also provided in some simple situations. In the case where the mixing proportions are known, there is a result in the literature (Goffinet et al, 1992) that provides the asymptotic distribution of the likelihood ratio test under the null hypothesis. However, this result is not useful in some cases, corresponding to some values of the proportions. Using, then, theoretical arguments supported by simulation results, we provide this distribution in those cases. Thus, in summary, there are three main directions in this thesis: the information based approach that mainly uses computational tools arising from recent developments in the theory of the EM algorithm; the stochastic approach that uses mathematical tools from the theory of stochastic processes; and the study of the likelihood ratio test for known proportions, whose general techniques arise from the theory of asymptotic statistics

Yeast Sex: Surprisingly High Rates of Outcrossing between Asci

BACKGROUND: Saccharomyces yeasts are an important model system in many areas of biological research. Very little is known about their ecology and evolution in the wild, but interest in this natural history is growing. Extensive work with lab strains in the last century uncovered the Saccharomyces life cycle. When nutrient limited, a diploid yeast cell will form four haploid spores encased in a protective outer layer called the ascus. Confinement within the ascus is thought to enforce mating between products of the same meiotic division, minimizing outcrossing in this stage of the life cycle. METHODOLOGY/PRINCIPAL FINDINGS: Using a set of S. cerevisiae and S. paradoxus strains isolated from woodlands in North America, we set up trials in which pairs of asci were placed in contact with one another and allowed to germinate. We observed outcrossing in approximately 40% of the trials, and multiple outcrossing events in trials with three asci in contact with each other. When entire populations of densely crowded asci germinated, approximately 10-25% of the resulting colonies were outcrossed. There were differences between the species with S. cerevisiae having an increased tendency to outcross in mass mating conditions. CONCLUSIONS/SIGNIFICANCE: Our results highlight the potential for random mating between spores in natural strains, even in the presence of asci. If this type of mating does occur in nature and it is between close relatives, then a great deal of mating behavior may be undetectable from genome sequences

A rapid change in virulence gene expression during the transition from the intestinal lumen into tissue promotes systemic dissemination of Salmonella.

Bacterial pathogens causing systemic disease commonly evolve from organisms associated with localized infections but differ from their close relatives in their ability to overcome mucosal barriers by mechanisms that remain incompletely understood. Here we investigated whether acquisition of a regulatory gene, tviA, contributed to the ability of Salmonella enterica serotype Typhi to disseminate from the intestine to systemic sites of infection during typhoid fever. To study the consequences of acquiring a new regulator by horizontal gene transfer, tviA was introduced into the chromosome of S. enterica serotype Typhimurium, a closely related pathogen causing a localized gastrointestinal infection in immunocompetent individuals. TviA repressed expression of flagellin, a pathogen associated molecular pattern (PAMP), when bacteria were grown at osmotic conditions encountered in tissue, but not at higher osmolarity present in the intestinal lumen. TviA-mediated flagellin repression enabled bacteria to evade sentinel functions of human model epithelia and resulted in increased bacterial dissemination to the spleen in a chicken model. Collectively, our data point to PAMP repression as a novel pathogenic mechanism to overcome the mucosal barrier through innate immune evasion

A comparison of cecal colonization of Salmonella enterica serotype Typhimurium in white leghorn chicks and Salmonella-resistant mice

<p>Abstract</p> <p>Background</p> <p>Salmonellosis is one of the most important bacterial food borne illnesses worldwide. A major source of infection for humans is consumption of chicken or egg products that have been contaminated with <it>Salmonella enterica </it>serotype Typhimurium, however our knowledge regarding colonization and persistence factors in the chicken is small.</p> <p>Results</p> <p>We compared intestinal and systemic colonization of 1-week-old White Leghorn chicks and <it>Salmonella</it>-resistant CBA/J mice during infection with <it>Salmonella enterica </it>serotype Typhimurium ATCC14028, one of the most commonly studied isolates. We also studied the distribution of wild type serotype Typhimurium ATCC14028 and an isogenic <it>invA </it>mutant during competitive infection in the cecum of 1-week-old White Leghorn chicks and 8-week-old CBA/J mice. We found that although the systemic levels of serotype Typhimurium in both infected animal models are low, infected mice have significant splenomegaly beginning at 15 days post infection. In the intestinal tract itself, the cecal contents are the major site for recovery of serotype Typhimurium in the cecum of 1-week-old chicks and <it>Salmonella</it>-resistant mice. Additionally we show that only a small minority of <it>Salmonellae </it>are intracellular in the cecal epithelium of both infected animal models, and while SPI-1 is important for successful infection in the murine model, it is important for association with the cecal epithelium of 1-week-old chicks. Finally, we show that in chicks infected with serotype Typhimurium at 1 week of age, the level of fecal shedding of this organism does not reflect the level of cecal colonization as it does in murine models.</p> <p>Conclusion</p> <p>In our study, we highlight important differences in systemic and intestinal colonization levels between chick and murine serotype Typhimurium infections, and provide evidence that suggests that the role of SPI-1 may not be the same during colonization of both animal models.</p

Sulfur Metabolism Actively Promotes Initiation of Cell Division in Yeast

BACKGROUND:Sulfur metabolism is required for initiation of cell division, but whether or not it can actively promote cell division remains unknown. METHODOLOGY/PRINCIPAL FINDINGS:Here we show that yeast cells with more mtDNA have an expanded reductive phase of their metabolic cycle and an increased sulfur metabolic flux. We also show that in wild type cells manipulations of sulfur metabolic flux phenocopy the enhanced growth rate of cells with more mtDNA. Furthermore, introduction of a hyperactive cystathionine-beta-synthase (CBS) allele in wild type cells accelerates initiation of DNA replication. CONCLUSIONS/SIGNIFICANCE:Our results reveal a novel connection between a key sulfur metabolic enzyme, CBS, and the cell cycle. Since the analogous hyperactive CBS allele in human CBS suppresses other disease-causing CBS mutations, our findings may be relevant for human pathology. Taken together, our results demonstrate the importance of sulfur metabolism in actively promoting initiation of cell division

A comparison of cecal colonization of Salmonella enterica serotype Typhimurium in white leghorn chicks and Salmonella-resistant mice

<p>Abstract</p> <p>Background</p> <p>Salmonellosis is one of the most important bacterial food borne illnesses worldwide. A major source of infection for humans is consumption of chicken or egg products that have been contaminated with <it>Salmonella enterica </it>serotype Typhimurium, however our knowledge regarding colonization and persistence factors in the chicken is small.</p> <p>Results</p> <p>We compared intestinal and systemic colonization of 1-week-old White Leghorn chicks and <it>Salmonella</it>-resistant CBA/J mice during infection with <it>Salmonella enterica </it>serotype Typhimurium ATCC14028, one of the most commonly studied isolates. We also studied the distribution of wild type serotype Typhimurium ATCC14028 and an isogenic <it>invA </it>mutant during competitive infection in the cecum of 1-week-old White Leghorn chicks and 8-week-old CBA/J mice. We found that although the systemic levels of serotype Typhimurium in both infected animal models are low, infected mice have significant splenomegaly beginning at 15 days post infection. In the intestinal tract itself, the cecal contents are the major site for recovery of serotype Typhimurium in the cecum of 1-week-old chicks and <it>Salmonella</it>-resistant mice. Additionally we show that only a small minority of <it>Salmonellae </it>are intracellular in the cecal epithelium of both infected animal models, and while SPI-1 is important for successful infection in the murine model, it is important for association with the cecal epithelium of 1-week-old chicks. Finally, we show that in chicks infected with serotype Typhimurium at 1 week of age, the level of fecal shedding of this organism does not reflect the level of cecal colonization as it does in murine models.</p> <p>Conclusion</p> <p>In our study, we highlight important differences in systemic and intestinal colonization levels between chick and murine serotype Typhimurium infections, and provide evidence that suggests that the role of SPI-1 may not be the same during colonization of both animal models.</p

Translate to divide: сontrol of the cell cycle by protein synthesis

Protein synthesis underpins much of cell growth and, consequently, cell multiplication. Understanding how proliferating cells commit and progress into the cell cycle requires knowing not only which proteins need to be synthesized, but also what determines their rate of synthesis during cell division.The open access fee for this work was funded through the Texas A&M University Open Access to Knowledge (OAK) Fund