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Sample records for program influences gene

  1. Sperm is epigenetically programmed to regulate gene transcription in embryos

    PubMed Central

    Teperek, Marta; Simeone, Angela; Gaggioli, Vincent; Miyamoto, Kei; Allen, George E.; Erkek, Serap; Kwon, Taejoon; Marcotte, Edward M.; Zegerman, Philip; Bradshaw, Charles R.; Peters, Antoine H.F.M.; Gurdon, John B.; Jullien, Jerome

    2016-01-01

    For a long time, it has been assumed that the only role of sperm at fertilization is to introduce the male genome into the egg. Recently, ideas have emerged that the epigenetic state of the sperm nucleus could influence transcription in the embryo. However, conflicting reports have challenged the existence of epigenetic marks on sperm genes, and there are no functional tests supporting the role of sperm epigenetic marking on embryonic gene expression. Here, we show that sperm is epigenetically programmed to regulate embryonic gene expression. By comparing the development of sperm- and spermatid-derived frog embryos, we show that the programming of sperm for successful development relates to its ability to regulate transcription of a set of developmentally important genes. During spermatid maturation into sperm, these genes lose H3K4me2/3 and retain H3K27me3 marks. Experimental removal of these epigenetic marks at fertilization de-regulates gene expression in the resulting embryos in a paternal chromatin-dependent manner. This demonstrates that epigenetic instructions delivered by the sperm at fertilization are required for correct regulation of gene expression in the future embryos. The epigenetic mechanisms of developmental programming revealed here are likely to relate to the mechanisms involved in transgenerational transmission of acquired traits. Understanding how parental experience can influence development of the progeny has broad potential for improving human health. PMID:27034506

  2. GAP: A computer program for gene assembly

    SciTech Connect

    Eisnstein, J.R.; Uberbacher, E.C.; Guan, X.; Mural, R.J.; Mann, R.C.

    1991-09-01

    A computer program, GAP (Gene Assembly Program), has been written to assemble and score hypothetical genes, given a DNA sequence containing the gene, and the outputs of several other programs which analyze the sequence. These programs include the codign-recognition and splice-junction-recognition modules developed in this laboratory. GAP is a prototype of a planned system in which it will be integrated with an expert system and rule base. Initial tests of GAP have been carried out with four sequences, the exons of which have been determined by biochemcial methods. The highest-scoring hypothetical genes for each of the four sequences had percent correct splice junctions ranging from 50 to 100% (average 81%) and percent correct bases ranging from 92 to 100% (average 96%). 9 refs., 1 tab.

  3. Radiopharmaceutical and Gene Therapy Program

    SciTech Connect

    Buchsbaum, Donald J.

    2006-02-09

    The objective of our research program was to determine whether novel receptors can be induced in solid cancers as a target for therapy with radiolabeled unmodified peptides that bind to the receptors. The hypothesis was that induction of a high number of receptors on the surface of these cancer cells would result in an increased uptake of the radiolabeled monomeric peptides as compared to published results with radiolabeled antibodies or peptides to naturally expressed antigens or receptors, and therefore a better therapeutic outcome. The following is a summary of published results.

  4. Influence of Rice Development on the Function of Bacterial Blight Resistance Genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Disease resistance genes most commonly used in breeding programs are single, dominant, resistance (R) genes with relative effectiveness influenced by plant developmental stage. Knowing the developmental stages at which an R gene is functional is important for disease management. In rice, resistanc...

  5. The influence of assortativity on the robustness and evolvability of gene regulatory networks upon gene birth

    PubMed Central

    Pechenick, Dov A.; Moore, Jason H.; Payne, Joshua L.

    2013-01-01

    Gene regulatory networks (GRNs) represent the interactions between genes and gene products, which drive the gene expression patterns that produce cellular phenotypes. GRNs display a number of characteristics that are beneficial for the development and evolution of organisms. For example, they are often robust to genetic perturbation, such as mutations in regulatory regions or loss of gene function. Simultaneously, GRNs are often evolvable as these genetic perturbations are occasionally exploited to innovate novel regulatory programs. Several topological properties, such as degree distribution, are known to influence the robustness and evolvability of GRNs. Assortativity, which measures the propensity of nodes of similar connectivity to connect to one another, is a separate topological property that has recently been shown to influence the robustness of GRNs to point mutations in cis-regulatory regions. However, it remains to be seen how assortativity may influence the robustness and evolvability of GRNs to other forms of genetic perturbation, such as gene birth via duplication or de novo origination. Here, we employ a computational model of genetic regulation to investigate whether the assortativity of a GRN influences its robustness and evolvability upon gene birth. We find that the robustness of a GRN generally increases with increasing assortativity, while its evolvability generally decreases. However, the rate of change in robustness outpaces that of evolvability, resulting in an increased proportion of assortative GRNs that are simultaneously robust and evolvable. By providing a mechanistic explanation for these observations, this work extends our understanding of how the assortativity of a GRN influences its robustness and evolvability upon gene birth. PMID:23542384

  6. Matching boxes: familiar size influences action programming.

    PubMed

    McIntosh, Robert D; Lashley, Gavin

    2008-01-01

    The perception/action model is the dominant account of the primary division of labour in the human visual pathway. Integral to this model is the idea that goal-directed actions are guided spatially by bottom-up vision, independent of perceptual recognition and top-down object knowledge. We question this idea by showing that the expected size of familiar objects (matchboxes) affects the amplitude of reaches made to grasp them, and the pre-shaping of the hand, even when binocular cues are available. This suggests that perceptual recognition routinely influences action programming.

  7. Programming gene expression with combinatorial promoters

    PubMed Central

    Cox, Robert Sidney; Surette, Michael G; Elowitz, Michael B

    2007-01-01

    Promoters control the expression of genes in response to one or more transcription factors (TFs). The architecture of a promoter is the arrangement and type of binding sites within it. To understand natural genetic circuits and to design promoters for synthetic biology, it is essential to understand the relationship between promoter function and architecture. We constructed a combinatorial library of random promoter architectures. We characterized 288 promoters in Escherichia coli, each containing up to three inputs from four different TFs. The library design allowed for multiple −10 and −35 boxes, and we observed varied promoter strength over five decades. To further analyze the functional repertoire, we defined a representation of promoter function in terms of regulatory range, logic type, and symmetry. Using these results, we identified heuristic rules for programming gene expression with combinatorial promoters. PMID:18004278

  8. More than genes: the advanced fetal programming hypothesis.

    PubMed

    Hocher, Berthold

    2014-10-01

    Many lines of data, initial epidemiologic studies as well as subsequent extensive experimental studies, indicate that early-life events play a powerful role in influencing later suceptibility to certain chronic diseases. Such events might be over- or undernutrition, exposure to environmental toxins, but also changes in hormones, in particular stress hormones. Typically, those events are triggered by the environmental challenges of the mother. However, recent studies have shown that paternal environmental or nutritional factors affect the phenotype of the offspring as well. The maternal and paternal environmental factors act on the phenotype of the offspring via epigenetic modification of its genome. The advanced fetal programming hypothesis proposes an additional non-environmentally driven mechanism: maternal and also paternal genes may influence the maturating sperm, the oocyte, and later the embryo/fetus, leading to their epigenetic alteration. Thus, the observed phenotype of the offspring may be altered by maternal/paternal genes independent of the fetal genome. Meanwhile, several independent association studies in humans dealing with metabolic and neurological traits also suggest that maternal genes might affect the offspring phenotype independent of the transmission of that particular gene to the offspring. Considering the implications of this hypothesis, some conclusions drawn from transgenic or knockout animal models and based on the causality between a genetic alteration and a phenotype, need to be challenged. Possible implications for the development, diagnostic and therapy of human genetic diseases have to be investigated.

  9. Maternal diet programs embryonic kidney gene expression.

    PubMed

    Welham, Simon J M; Riley, Paul R; Wade, Angie; Hubank, Mike; Woolf, Adrian S

    2005-06-16

    Human epidemiological data associating birth weight with adult disease suggest that organogenesis is "programmed" by maternal diet. In rats, protein restriction in pregnancy produces offspring with fewer renal glomeruli and higher systemic blood pressures than controls. We tested the hypothesis that maternal diet alters gene expression in the metanephros, the precursor of the definitive mammalian kidney. We demonstrated that maternal low-protein diet initiated when pregnancy starts and maintained to embryonic day 13, when the metanephros consists of mesenchyme surrounding a once-branched ureteric bud, is sufficient to significantly reduce glomerular numbers in offspring by about 20%. As assessed by representational difference analyses and real-time quantitative polymerase chain reactions, low-protein diet modulated gene expression in embryonic day 13 metanephroi. In particular, levels of prox-1, the ortholog of Drosophila transcription factor prospero, and cofilin-1, a regulator of the actin cytoskeleton, were reduced. During normal metanephrogenesis, prox-1 protein was first detected in mesenchymal cells around the ureteric tree and thereafter in nascent nephron epithelia, whereas cofilin-1 immunolocalized to bud derivatives and condensing mesenchyme. Previously, we reported that low-protein diets increased mesenchymal apoptosis cells when metanephrogenesis began and thereafter reduced numbers of precursor cells. Collectively, these studies prove that the maternal diet programs the embryonic kidney, altering cell turnover and gene expression at a time when nephrons and glomeruli have yet to form. The human implication is that the maternal diet ingested between conception and 5- 6-wk gestation contributes to the variation in glomerular numbers that are known to occur between healthy and hypertensive populations.

  10. Transposable element influences on gene expression in plants.

    PubMed

    Hirsch, Cory D; Springer, Nathan M

    2017-01-01

    Transposable elements (TEs) comprise a major portion of many plant genomes and bursts of TE movements cause novel genomic variation within species. In order to maintain proper gene function, plant genomes have evolved a variety of mechanisms to tolerate the presence of TEs within or near genes. Here, we review our understanding of the interactions between TEs and gene expression in plants by assessing three ways that transposons can influence gene expression. First, there is growing evidence that TE insertions within introns or untranslated regions of genes are often tolerated and have minimal impact on expression level or splicing. However, there are examples in which TE insertions within genes can result in aberrant or novel transcripts. Second, TEs can provide novel alternative promoters, which can lead to new expression patterns or original coding potential of an alternate transcript. Third, TE insertions near genes can influence regulation of gene expression through a variety of mechanisms. For example, TEs may provide novel cis-acting regulatory sites behaving as enhancers or insert within existing enhancers to influence transcript production. Alternatively, TEs may change chromatin modifications in regions near genes, which in turn can influence gene expression levels. Together, the interactions of genes and TEs provide abundant evidence for the role of TEs in changing basic functions within plant genomes beyond acting as latent genomic elements or as simple insertional mutagens. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

  11. Influence of Remedial Professional Development Programs for Poorly Performing Physicians

    ERIC Educational Resources Information Center

    Goulet, Francois; Gagnon, Robert; Gingras, Marie-Eve

    2007-01-01

    Introduction: The College des medecins du Quebec (CMQ) offers an individualized remedial professional development program to help physicians overcome selected clinical shortcomings. To measure the influence of the remedial professional development program, physicians who completed the program between 1993 and 2004 and who were assessed by peer…

  12. Factors Influencing Student Participation in College Study Abroad Programs

    ERIC Educational Resources Information Center

    Bandyopadhyay, Soumava; Bandyopadhyay, Kakoli

    2015-01-01

    This paper proposes a theoretical framework to investigate the factors that influence student participation in college study abroad programs. The authors posit that students' general perceptions regarding the study abroad experience and their expectations of intercultural awareness from study abroad programs will impact their perceptions of…

  13. Distal chromatin structure influences local nucleosome positions and gene expression.

    PubMed

    Jansen, An; van der Zande, Elisa; Meert, Wim; Fink, Gerald R; Verstrepen, Kevin J

    2012-05-01

    The positions of nucleosomes across the genome influence several cellular processes, including gene transcription. However, our understanding of the factors dictating where nucleosomes are located and how this affects gene regulation is still limited. Here, we perform an extensive in vivo study to investigate the influence of the neighboring chromatin structure on local nucleosome positioning and gene expression. Using truncated versions of the Saccharomyces cerevisiae URA3 gene, we show that nucleosome positions in the URA3 promoter are at least partly determined by the local DNA sequence, with so-called 'anti-nucleosomal elements' like poly(dA:dT) tracts being key determinants of nucleosome positions. In addition, we show that changes in the nucleosome positions in the URA3 promoter strongly affect the promoter activity. Most interestingly, in addition to demonstrating the effect of the local DNA sequence, our study provides novel in vivo evidence that nucleosome positions are also affected by the position of neighboring nucleosomes. Nucleosome structure may therefore be an important selective force for conservation of gene order on a chromosome, because relocating a gene to another genomic position (where the positions of neighboring nucleosomes are different from the original locus) can have dramatic consequences for the gene's nucleosome structure and thus its expression.

  14. Perspectives on best practices for gene therapy programs.

    PubMed

    Cheever, Thomas R; Berkley, Dale; Braun, Serge; Brown, Robert H; Byrne, Barry J; Chamberlain, Jeffrey S; Cwik, Valerie; Duan, Dongsheng; Federoff, Howard J; High, Katherine A; Kaspar, Brian K; Klinger, Katherine W; Larkindale, Jane; Lincecum, John; Mavilio, Fulvio; McDonald, Cheryl L; McLaughlin, James; Weiss McLeod, Bonnie; Mendell, Jerry R; Nuckolls, Glen; Stedman, Hansell H; Tagle, Danilo A; Vandenberghe, Luk H; Wang, Hao; Wernett, Pamela J; Wilson, James M; Porter, John D; Gubitz, Amelie K

    2015-03-01

    With recent successes in gene therapy trials for hemophilia and retinal diseases, the promise and prospects for gene therapy are once again garnering significant attention. To build on this momentum, the National Institute of Neurological Disorders and Stroke and the Muscular Dystrophy Association jointly hosted a workshop in April 2014 on "Best Practices for Gene Therapy Programs," with a focus on neuromuscular disorders. Workshop participants included researchers from academia and industry as well as representatives from the regulatory, legal, and patient advocacy sectors to cover the gamut from preclinical optimization to intellectual property concerns and regulatory approval. The workshop focused on three key issues in the field: (1) establishing adequate scientific premise for clinical trials in gene therapy, (2) addressing regulatory process issues, and (3) intellectual property and commercialization issues as they relate to gene therapy. The outcomes from the discussions at this workshop are intended to provide guidance for researchers and funders in the gene therapy field.

  15. Study of human dopamine sulfotransferases based on gene expression programming.

    PubMed

    Si, Hongzong; Zhao, Jiangang; Cui, Lianhua; Lian, Ning; Feng, Hanlin; Duan, Yun-Bo; Hu, Zhide

    2011-09-01

    A quantitative model is developed to predict the Km of 47 human dopamine sulfotransferases by gene expression programming. Each kind of compound is represented by several calculated structural descriptors of moment of inertia A, average electrophilic reactivity index for a C atom, relative number of triple bonds, RNCG relative negative charge, HA-dependent HDSA-1, and HBCA H-bonding charged surface area. Eight fitness functions of the gene expression programming method are used to find the best nonlinear model. The best quantitative model with squared standard error and square of correlation coefficient are 0.096 and 0.91 for training data set, and 0.102 and 0.88 for test set, respectively. It is shown that the gene expression programming-predicted results with fitness function are in good agreement with experimental ones.

  16. Exercise influences circadian gene expression in equine skeletal muscle.

    PubMed

    Murphy, B A; Wagner, A L; McGlynn, O F; Kharazyan, F; Browne, J A; Elliott, J A

    2014-07-01

    Circadian rhythms are endogenously generated 24-h oscillations that coordinate numerous aspects of mammalian physiology, metabolism and behaviour. The existence of a molecular circadian clock in equine skeletal muscle has previously been demonstrated. This study investigates how the circadian 24-h expression of exercise-relevant genes in skeletal muscle is influenced by a regular exercise regime. Mid-gluteal, percutaneous muscle biopsies were obtained over a 24-h period from six Thoroughbred mares before and after an 8-week exercise programme. Real-time qPCR assays were used to assess the expression patterns of core clock genes ARNTL, PER2, NR1D1, clock-controlled gene DBP, and muscle genes MYF6, UCP3, VEGFA, FOXO1, MYOD1, PPARGC1A, PPARGC1B, FBXO32 and PDK4. Two-way repeated measures ANOVA revealed a significant interaction between circadian time and exercise for muscle genes MYF6, UCP3, MYOD1 and PDK4. A significant effect of time was observed for all genes with the exception of VEGFA, where a main effect of exercise was observed. By cosinor analysis, the core clock genes, ARNTL (P <0.01) and NR1D1 (P <0.05), showed 24-h rhythmicity both pre- and post-exercise, while PER2 expression was rhythmic post-exercise (P <0.05) but not pre-exercise. The expression profiles of muscle genes MYOD1 and MYF6 showed significant fits to a 24-h cosine waveform indicative of circadian rhythmicity post-exercise only (P <0.01). This study suggests that the metabolic capacity of muscle is influenced by scheduled exercise and that optimal athletic performance may be achieved when exercise times and competition times coincide.

  17. Alternative Administrative Certification: Socializing Factors Influencing Program Choice

    ERIC Educational Resources Information Center

    Bickmore, Dana L.; Bickmore, Steven T.; Raines, Sarah

    2013-01-01

    This study used an organizational socialization lens to examine factors influencing participants' decision to pursue the principalship and choice to engage in an alternate administration certification program. Through an analysis of participant focus groups and interviews, factors emerged from the codes that were compared with dimensions of…

  18. Influence of Funding Cuts on Texas School Tobacco Programs

    ERIC Educational Resources Information Center

    Gingiss, Phyllis M.; Boerm, Melynda

    2009-01-01

    Background: Following the Master Settlement Agreement, state tobacco prevention spending peaked in 2002, but has subsequently been diminishing annually. This study compared the influence of 2004 Texas tobacco program budget cuts on school practices a year after funding loss. Methods: Three school groups were compared: continuously funded for a…

  19. Attendees' Perceptions of Commercial Influence in Noncommercially Funded CME Programs

    ERIC Educational Resources Information Center

    Goldfarb, Elizabeth; Baer, Lee; Fromson, John A.; Gorrindo, Tristan; Iodice, Kristin E.; Birnbaum, Robert J.

    2012-01-01

    Introduction: The controversy surrounding commercial support for continuing medical education (CME) programs has led to policy changes, but data show no significant difference in perceived bias between commercial and noncommercial CME. Indeed, what attendees perceive as commercial influence is not fully understood. We sought to clarify what…

  20. A Metacognitive Approach to Pair Programming: Influence on Metacognitive Awareness

    ERIC Educational Resources Information Center

    Breed, Betty; Mentz, Elsa; van der Westhuizen, Gert

    2014-01-01

    Introduction: The research focused on metacognition in a collaborative learning setting. Based on a comprehensive literature study the researchers designed a metacognitive teaching-learning strategy for pair programmers. Our purpose was to investigate the influence of this metacognitive teaching-learning strategy during pair programming in an…

  1. Quality Program: what influences the opinion of nursing team

    PubMed Central

    da Costa, Fernanda Mazzoni; Souza, Irene Duarte; Monteiro, Maria Inês; Lopes, Maria Helena Baena de Moraes; Greco, Rosangela Maria

    2016-01-01

    ABSTRACT Objective To analyze the major impact variables in the opinion of nursing staff about the Quality Program of a teaching hospital. Methods An exploratory-descriptive study was performed with 72 nursing staff. Data were collected through self-administered questionnaire containing 24 statements about the Quality Program; and the degree of agreement of the participants was expressed in a Likert scale. The collected data were analyzed by factor analysis and Pearson’s correlation coefficient. Results The analysis grouped the statements in six factors. The Pearson’s correlation coefficient defined a scale of influence of the variables within each factor, whose variable with the greatest impact in each factor is the priority issue for improving worker opinion about the Quality Program. The priority variables were to believe the Quality Program contributes to the hospital; to understand the program orientations; interest in hospital quality direction; and do not feel exhausted due to the program. Conclusion These variables must be focused during the implementation and execution of Quality Program, as they have greater impact on improving opinion regarding the Quality Program and thus helping to increase compliance of the nursing staff to the program. PMID:28076604

  2. Can Thrifty Gene(s) or Predictive Fetal Programming for Thriftiness Lead to Obesity?

    PubMed

    Baig, Ulfat; Belsare, Prajakta; Watve, Milind; Jog, Maithili

    2011-01-01

    Obesity and related disorders are thought to have their roots in metabolic "thriftiness" that evolved to combat periodic starvation. The association of low birth weight with obesity in later life caused a shift in the concept from thrifty gene to thrifty phenotype or anticipatory fetal programming. The assumption of thriftiness is implicit in obesity research. We examine here, with the help of a mathematical model, the conditions for evolution of thrifty genes or fetal programming for thriftiness. The model suggests that a thrifty gene cannot exist in a stable polymorphic state in a population. The conditions for evolution of thrifty fetal programming are restricted if the correlation between intrauterine and lifetime conditions is poor. Such a correlation is not observed in natural courses of famine. If there is fetal programming for thriftiness, it could have evolved in anticipation of social factors affecting nutrition that can result in a positive correlation.

  3. Factors that Influence the Effectiveness of Sanitation Programs

    PubMed Central

    Fernandez-Haddad, Marilu; Ingram, Maia

    2015-01-01

    Local governments in both Mexico and the U.S. spend considerable money on public services, which do not always bring the expected results. For instance, a large part of the public budget is destined to solve social and health problems, such as public sanitation. Government has attacked the problem by providing public sanitation infrastructure (such as garbage and recycling receptacles) and by using social ad campaigns. However, these efforts do not always affect the habits of residents and bring the desired changes in city sanitation. This article presents a case study that used a participatory method to address an innovative city sanitation effort: The Clean City Program in Puebla, Mexico. This program adopted social marketing techniques, a discipline born in the 70s when the principles and practices developed to sell products and services started to be applied to sell ideas, attitudes, or behaviors. Social marketing programs have been adopted by governments to change attitudes and behavior in areas such as public services. The article first describes the context and strategies of the program, which included the use of the promotora model to engage community members. The researchers then make use of qualitative data gathered throughout program planning and implementation to evaluate the impact of the social marketing programs and its effectiveness. The article analyzes social, educational, economic, demographic, and cultural factors that influence the effectiveness of sanitation programs and presents recommendations for strategies to engage community members in community sanitation programs. PMID:26389106

  4. Factors that Influence the Effectiveness of Sanitation Programs.

    PubMed

    Fernandez-Haddad, Marilu; Ingram, Maia

    2015-01-01

    Local governments in both Mexico and the U.S. spend considerable money on public services, which do not always bring the expected results. For instance, a large part of the public budget is destined to solve social and health problems, such as public sanitation. Government has attacked the problem by providing public sanitation infrastructure (such as garbage and recycling receptacles) and by using social ad campaigns. However, these efforts do not always affect the habits of residents and bring the desired changes in city sanitation. This article presents a case study that used a participatory method to address an innovative city sanitation effort: The Clean City Program in Puebla, Mexico. This program adopted social marketing techniques, a discipline born in the 70s when the principles and practices developed to sell products and services started to be applied to sell ideas, attitudes, or behaviors. Social marketing programs have been adopted by governments to change attitudes and behavior in areas such as public services. The article first describes the context and strategies of the program, which included the use of the promotora model to engage community members. The researchers then make use of qualitative data gathered throughout program planning and implementation to evaluate the impact of the social marketing programs and its effectiveness. The article analyzes social, educational, economic, demographic, and cultural factors that influence the effectiveness of sanitation programs and presents recommendations for strategies to engage community members in community sanitation programs.

  5. EXCAVATOR: a computer program for efficiently mining gene expression data.

    PubMed

    Xu, Dong; Olman, Victor; Wang, Li; Xu, Ying

    2003-10-01

    Massive amounts of gene expression data are generated using microarrays for functional studies of genes and gene expression data clustering is a useful tool for studying the functional relationship among genes in a biological process. We have developed a computer package EXCAVATOR for clustering gene expression profiles based on our new framework for representing gene expression data as a minimum spanning tree. EXCAVATOR uses a number of rigorous and efficient clustering algorithms. This program has a number of unique features, including capabilities for: (i) data- constrained clustering; (ii) identification of genes with similar expression profiles to pre-specified seed genes; (iii) cluster identification from a noisy background; (iv) computational comparison between different clustering results of the same data set. EXCAVATOR can be run from a Unix/Linux/DOS shell, from a Java interface or from a Web server. The clustering results can be visualized as colored figures and 2-dimensional plots. Moreover, EXCAVATOR provides a wide range of options for data formats, distance measures, objective functions, clustering algorithms, methods to choose number of clusters, etc. The effectiveness of EXCAVATOR has been demonstrated on several experimental data sets. Its performance compares favorably against the popular K-means clustering method in terms of clustering quality and computing time.

  6. Current status of the Gene-Tox Program.

    PubMed Central

    Auletta, A E; Brown, M; Wassom, J S; Cimino, M C

    1991-01-01

    The U.S. Environmental Protection Agency's Gene-Tox Program is a multiphased effort to review and evaluate the existing literature in assay systems available in the field of genetic toxicology. The first phase of the Gene-Tox Program selected assay systems for evaluation, generated expert panel reviews of the data from the scientific literature, and recommended testing protocols for the systems. Phase II established and evaluated the database of chemical genetic toxicity data for its relevance to identifying human health hazards. The ongoing phase III continues reviewing and updating chemical data in selected assay systems. Currently, data exist on over 4000 chemicals in 27 assay systems; two additional assay systems will be included in phase III. The review data are published in the scientific literature and are also publicly available through the National Library of Medicine TOXNET system. The review and analysis components of Gene-Tox comprise 45 published papers, and several others are in preparation. Differences that have been observed between Gene-Tox and National Toxicology Program databases relative to the sensitivity, specificity, accuracy, and predictivity of genetic toxicity data compared to carcinogenesis data are ascribable to differences between the two databases in chemical selection criteria, testing protocols, and chemical class distributions. PMID:1820273

  7. Garlic Influences Gene Expression In Vivo and In Vitro.

    PubMed

    Charron, Craig S; Dawson, Harry D; Novotny, Janet A

    2016-02-01

    There is a large body of preclinical research aimed at understanding the roles of garlic and garlic-derived preparations in the promotion of human health. Most of this research has targeted the possible functions of garlic in maintaining cardiovascular health and in preventing and treating cancer. A wide range of outcome variables has been used to investigate the bioactivity of garlic, ranging from direct measures of health status such as cholesterol concentrations, blood pressure, and changes in tumor size and number, to molecular and biochemical measures such as mRNA gene expression, protein concentration, enzyme activity, and histone acetylation status. Determination of how garlic influences mRNA gene expression has proven to be a valuable approach to elucidating the mechanisms of garlic bioactivity. Preclinical studies investigating the health benefits of garlic far outnumber human studies and have made frequent use of mRNA gene expression measurement. There is an immediate need to understand mRNA gene expression in humans as well. Although safety and ethical constraints limit the types of available human tissue, peripheral whole blood is readily accessible, and measuring mRNA gene expression in whole blood may provide a unique window to understanding how garlic intake affects human health.

  8. Factors Influencing Learning Environments in an Integrated Experiential Program

    NASA Astrophysics Data System (ADS)

    Koci, Peter

    The research conducted for this dissertation examined the learning environment of a specific high school program that delivered the explicit curriculum through an integrated experiential manner, which utilized field and outdoor experiences. The program ran over one semester (five months) and it integrated the grade 10 British Columbian curriculum in five subjects. A mixed methods approach was employed to identify the students' perceptions and provide richer descriptions of their experiences related to their unique learning environment. Quantitative instruments were used to assess changes in students' perspectives of their learning environment, as well as other supporting factors including students' mindfulness, and behaviours towards the environment. Qualitative data collection included observations, open-ended questions, and impromptu interviews with the teacher. The qualitative data describe the factors and processes that influenced the learning environment and give a richer, deeper interpretation which complements the quantitative findings. The research results showed positive scores on all the quantitative measures conducted, and the qualitative data provided further insight into descriptions of learning environment constructs that the students perceived as most important. A major finding was that the group cohesion measure was perceived by students as the most important attribute of their preferred learning environment. A flow chart was developed to help the researcher conceptualize how the learning environment, learning process, and outcomes relate to one another in the studied program. This research attempts to explain through the consideration of this case study: how learning environments can influence behavioural change and how an interconnectedness among several factors in the learning process is influenced by the type of learning environment facilitated. Considerably more research is needed in this area to understand fully the complexity learning

  9. Perspectives on Best Practices for Gene Therapy Programs

    PubMed Central

    Cheever, Thomas R.; Berkley, Dale; Braun, Serge; Brown, Robert H.; Byrne, Barry J.; Chamberlain, Jeffrey S.; Cwik, Valerie; Duan, Dongsheng; Federoff, Howard J.; High, Katherine A.; Kaspar, Brian K.; Klinger, Katherine W.; Larkindale, Jane; Lincecum, John; Mavilio, Fulvio; McDonald, Cheryl L.; McLaughlin, James; Weiss McLeod, Bonnie; Mendell, Jerry R.; Nuckolls, Glen; Stedman, Hansell H.; Tagle, Danilo A.; Vandenberghe, Luk H.; Wang, Hao; Wernett, Pamela J.; Wilson, James M.; Porter, John D.

    2015-01-01

    Abstract With recent successes in gene therapy trials for hemophilia and retinal diseases, the promise and prospects for gene therapy are once again garnering significant attention. To build on this momentum, the National Institute of Neurological Disorders and Stroke and the Muscular Dystrophy Association jointly hosted a workshop in April 2014 on “Best Practices for Gene Therapy Programs,” with a focus on neuromuscular disorders. Workshop participants included researchers from academia and industry as well as representatives from the regulatory, legal, and patient advocacy sectors to cover the gamut from preclinical optimization to intellectual property concerns and regulatory approval. The workshop focused on three key issues in the field: (1) establishing adequate scientific premise for clinical trials in gene therapy, (2) addressing regulatory process issues, and (3) intellectual property and commercialization issues as they relate to gene therapy. The outcomes from the discussions at this workshop are intended to provide guidance for researchers and funders in the gene therapy field. PMID:25654329

  10. Conserved Gene Expression Programs in Developing Roots from Diverse Plants

    PubMed Central

    Huang, Ling; Schiefelbein, John

    2015-01-01

    The molecular basis for the origin and diversification of morphological adaptations is a central issue in evolutionary developmental biology. Here, we defined temporal transcript accumulation in developing roots from seven vascular plants, permitting a genome-wide comparative analysis of the molecular programs used by a single organ across diverse species. The resulting gene expression maps uncover significant similarity in the genes employed in roots and their developmental expression profiles. The detailed analysis of a subset of 133 genes known to be associated with root development in Arabidopsis thaliana indicates that most of these are used in all plant species. Strikingly, this was also true for root development in a lycophyte (Selaginella moellendorffii), which forms morphologically different roots and is thought to have evolved roots independently. Thus, despite vast differences in size and anatomy of roots from diverse plants, the basic molecular mechanisms employed during root formation appear to be conserved. This suggests that roots evolved in the two major vascular plant lineages either by parallel recruitment of largely the same developmental program or by elaboration of an existing root program in the common ancestor of vascular plants. PMID:26265761

  11. Conserved Gene Expression Programs in Developing Roots from Diverse Plants.

    PubMed

    Huang, Ling; Schiefelbein, John

    2015-08-01

    The molecular basis for the origin and diversification of morphological adaptations is a central issue in evolutionary developmental biology. Here, we defined temporal transcript accumulation in developing roots from seven vascular plants, permitting a genome-wide comparative analysis of the molecular programs used by a single organ across diverse species. The resulting gene expression maps uncover significant similarity in the genes employed in roots and their developmental expression profiles. The detailed analysis of a subset of 133 genes known to be associated with root development in Arabidopsis thaliana indicates that most of these are used in all plant species. Strikingly, this was also true for root development in a lycophyte (Selaginella moellendorffii), which forms morphologically different roots and is thought to have evolved roots independently. Thus, despite vast differences in size and anatomy of roots from diverse plants, the basic molecular mechanisms employed during root formation appear to be conserved. This suggests that roots evolved in the two major vascular plant lineages either by parallel recruitment of largely the same developmental program or by elaboration of an existing root program in the common ancestor of vascular plants.

  12. Influence of Neonatal Hypothyroidism on Hepatic Gene Expression and Lipid Metabolism in Adulthood

    PubMed Central

    Bocos, Carlos; Henríquez-Hernández, Luis A.; Kahlon, Nusrat; Herrera, Emilio; Norstedt, Gunnar; Parini, Paolo; Flores-Morales, Amilcar; Fernández-Pérez, Leandro

    2012-01-01

    Thyroid hormones are required for normal growth and development in mammals. Congenital-neonatal hypothyroidism (CH) has a profound impact on physiology, but its specific influence in liver is less understood. Here, we studied how CH influences the liver gene expression program in adulthood. Pregnant rats were given the antithyroid drug methimazole (MMI) from GD12 until PND30 to induce CH in male offspring. Growth defects due to CH were evident as reductions in body weight and tail length from the second week of life. Once the MMI treatment was discontinued, the feed efficiency increased in CH, and this was accompanied by significant catch-up growth. On PND80, significant reductions in body mass, tail length, and circulating IGF-I levels remained in CH rats. Conversely, the mRNA levels of known GH target genes were significantly upregulated. The serum levels of thyroid hormones, cholesterol, and triglycerides showed no significant differences. In contrast, CH rats showed significant changes in the expression of hepatic genes involved in lipid metabolism, including an increased transcription of PPARα and a reduced expression of genes involved in fatty acid and cholesterol uptake, cellular sterol efflux, triglyceride assembly, bile acid synthesis, and lipogenesis. These changes were associated with a decrease of intrahepatic lipids. Finally, CH rats responded to the onset of hypothyroidism in adulthood with a reduction of serum fatty acids and hepatic cholesteryl esters and to T3 replacement with an enhanced activation of malic enzyme. In summary, we provide in vivo evidence that neonatal hypothyroidism influences the hepatic transcriptional program and tissue sensitivity to hormone treatment in adulthood. This highlights the critical role that a euthyroid state during development plays on normal liver physiology in adulthood. PMID:22666351

  13. Reverse engineering of gene regulatory network using restricted gene expression programming.

    PubMed

    Yang, Bin; Liu, Sanrong; Zhang, Wei

    2016-10-01

    Inference of gene regulatory networks has been becoming a major area of interest in the field of systems biology over the past decade. In this paper, we present a novel representation of S-system model, named restricted gene expression programming (RGEP), to infer gene regulatory network. A new hybrid evolutionary algorithm based on structure-based evolutionary algorithm and cuckoo search (CS) is proposed to optimize the architecture and corresponding parameters of model, respectively. Two synthetic benchmark datasets and one real biological dataset from SOS DNA repair network in E. coli are used to test the validity of our method. Experimental results demonstrate that our proposed method performs better than previously proposed popular methods.

  14. Iris phenotypes and pigment dispersion caused by genes influencing pigmentation.

    PubMed

    Anderson, Michael G; Hawes, Norman L; Trantow, Colleen M; Chang, Bo; John, Simon W M

    2008-10-01

    Spontaneous mutations altering mouse coat colors have been a classic resource for discovery of numerous molecular pathways. Although often overlooked, the mouse iris is also densely pigmented and easily observed, thus representing a similarly powerful opportunity for studying pigment cell biology. Here, we present an analysis of iris phenotypes among 16 mouse strains with mutations influencing melanosomes. Many of these strains exhibit biologically and medically relevant phenotypes, including pigment dispersion, a common feature of several human ocular diseases. Pigment dispersion was identified in several strains with mutant alleles known to influence melanosomes, including beige, light, and vitiligo. Pigment dispersion was also detected in the recently arising spontaneous coat color variant, nm2798. We have identified the nm2798 mutation as a missense mutation in the Dct gene, an identical re-occurrence of the slaty light mutation. These results suggest that dysregulated events of melanosomes can be potent contributors to the pigment dispersion phenotype. Combined, these findings illustrate the utility of studying iris phenotypes as a means of discovering new pathways, and re-linking old ones, to processes of pigmented cells in health and disease.

  15. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

    SciTech Connect

    Pimentel, Harold; Parra, Marilyn; Gee, Sherry L.; Mohandas, Narla; Pachter, Lior; Conboy, John G.

    2015-11-03

    Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentallydynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclearlocalized. Splice site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. Finally, we conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.

  16. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

    DOE PAGES

    Pimentel, Harold; Parra, Marilyn; Gee, Sherry L.; ...

    2015-11-03

    Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentallydynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclearlocalized. Splicemore » site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. Finally, we conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.« less

  17. Simulated microgravity influenced the expression of DNA damage repair genes

    NASA Astrophysics Data System (ADS)

    Zhang, Meng; Sun, Yeqing; Jiawei, Liu; Wang, Ting

    2016-07-01

    Ionizing radiation and microgravity were considered to be the most important stress factors of space environmental the respective study of the biological effects of the radiation and microgravity carried out earlier, but the interaction of the effects of radiation with microgravity started later, and due to difference of the materials and methods the result of this experiment were not consistent. To further investigate the influence of microgravity on the expression of the radiation damage repair genes, the seed of Arabidopsis (Col) and its gravity-insensitive mutant (PIN2) were exposed to 0.1Gy of the dose of energetic carbon-ion beam radiation (LET = 30KeV / μm), and the germinated seed were than fixed in the 3D random positioning apparatus immediately for a 10-day simulated microgravity. By measuring the deflection angle of root tip and the changes of the expression of Ku70 and RAD51 protein, we investigated the impact of microgravity effect on radiation damage repair systems. The results shown that radiation, microgravity and microgravity with radiation could increase the angle of the root of the Col significantly, but no obvious effect on PIN2 type. The radiation could increase the expression of Ku70 significantly in both Col and PIN2, microgravity does not affect the expression, but the microgravity with radiation could decrease the expression of Ku70. This result shown that the microgravity could influence the radiation damage repair systems in molecular level. Moreover, our findings were important to understand the molecular mechanism of the impact of microgravity effect on radiation damage repair systems in vivo.

  18. IL18 Gene Variants Influence the Susceptibility to Chagas Disease

    PubMed Central

    Leon Rodriguez, Daniel A; Carmona, F. David; Echeverría, Luis Eduardo; González, Clara Isabel; Martin, Javier

    2016-01-01

    Chagas disease is a parasitic disorder caused by the infection with the flagellated protozoan Trypanosoma cruzi. According to the World Health Organization, more than six million people are currently infected in endemic regions. Genetic factors have been proposed to influence predisposition to infection and development of severe clinical phenotypes like chronic Chagas cardiomyopathy (CCC). Interleukin 18 (IL18) encodes a proinflammatory cytokine that has been proposed to be involved in controlling T. cruzi infection. In this study, we analyzed the possible role of six IL18 gene variants (rs5744258, rs360722, rs2043055, rs187238, rs1946518 and rs360719), which cover most of the variation within the locus, in the susceptibility to infection by T. cruzi and/or CCC. In total, 1,171 individuals from a Colombian region endemic for Chagas disease, classified as seronegative (n = 595), seropositive asymptomatic (n = 175) and CCC (n = 401), were genotyped using TaqMan probes. Significant associations with T. cruzi infection were observed when comparing seronegative and seropositive individuals for rs187238 (P = 2.18E-03, OR = 0.77), rs360719 (P = 1.49E-03, OR = 0.76), rs2043055 (P = 2.52E-03, OR = 1.29), and rs1946518 (P = 0.0162, OR = 1.22). However, dependence analyses suggested that the association was mainly driven by the polymorphism rs360719. This variant is located within the promoter region of the IL18 gene, and it has been described that it creates a binding site for the transcription factor OCT-1 affecting IL-18 expression levels. In addition, no evidence of association was observed between any of the analyzed IL18 gene polymorphisms and the development of CCC. In summary, our data suggest that genetic variation within the promoter region of IL18 is directly involved in the susceptibility to infection by T. cruzi, which provides novel insight into disease pathophysiology and adds new perspectives to achieve a more effective disease control. PMID:27027876

  19. Intron retention as a component of regulated gene expression programs.

    PubMed

    Jacob, Aishwarya G; Smith, Christopher W J

    2017-04-08

    Intron retention has long been an exemplar of regulated splicing with case studies of individual events serving as models that provided key mechanistic insights into the process of splicing control. In organisms such as plants and budding yeast, intron retention is well understood as a major mechanism of gene expression regulation. In contrast, in mammalian systems, the extent and functional significance of intron retention have, until recently, remained greatly underappreciated. Technical challenges to the global detection and quantitation of transcripts with retained introns have often led to intron retention being overlooked or dismissed as "noise". Now, however, with the wealth of information available from high-throughput deep sequencing, combined with focused computational and statistical analyses, we are able to distinguish clear intron retention patterns in various physiological and pathological contexts. Several recent studies have demonstrated intron retention as a central component of gene expression programs during normal development as well as in response to stress and disease. Furthermore, these studies revealed various ways in which intron retention regulates protein isoform production, RNA stability and translation efficiency, and rapid induction of expression via post-transcriptional splicing of retained introns. In this review, we highlight critical findings from these transcriptomic studies and discuss commonalties in the patterns prevalent in intron retention networks at the functional and regulatory levels.

  20. Gene-expression programming for flip-bucket spillway scour.

    PubMed

    Guven, Aytac; Azamathulla, H Md

    2012-01-01

    During the last two decades, researchers have noticed that the use of soft computing techniques as an alternative to conventional statistical methods based on controlled laboratory or field data, gave significantly better results. Gene-expression programming (GEP), which is an extension to genetic programming (GP), has nowadays attracted the attention of researchers in prediction of hydraulic data. This study presents GEP as an alternative tool in the prediction of scour downstream of a flip-bucket spillway. Actual field measurements were used to develop GEP models. The proposed GEP models are compared with the earlier conventional GP results of others (Azamathulla et al. 2008b; RMSE = 2.347, δ = 0.377, R = 0.842) and those of commonly used regression-based formulae. The predictions of GEP models were observed to be in strictly good agreement with measured ones, and quite a bit better than conventional GP and the regression-based formulae. The results are tabulated in terms of statistical error measures (GEP1; RMSE = 1.596, δ = 0.109, R = 0.917) and illustrated via scatter plots.

  1. Effects of Metabolic Programming on Juvenile Play Behavior and Gene Expression in the Prefrontal Cortex of Rats.

    PubMed

    Hehar, Harleen; Ma, Irene; Mychasiuk, Richelle

    2016-01-01

    Early developmental processes, such as metabolic programming, can provide cues to an organism, which allow it to make modifications that are predicted to be beneficial for survival. Similarly, social play has a multifaceted role in promoting survival and fitness of animals. Play is a complex behavior that is greatly influenced by motivational and reward circuits, as well as the energy reserves and metabolism of an organism. This study examined the association between metabolic programming and juvenile play behavior in an effort to further elucidate insight into the consequences that early adaptions have on developmental trajectories. The study also examined changes in expression of four genes (Drd2, IGF1, Opa1, and OxyR) in the prefrontal cortex known to play significant roles in reward, bioenergetics, and social-emotional functioning. Using four distinct variations in developmental programming (high-fat diet, caloric restriction, exercise, or high-fat diet combined with exercise), we found that dietary programming (high-fat diet vs. caloric restriction) had the greatest impact on play behavior and gene expression. However, exercise also induced changes in both measures. This study demonstrates that metabolic programming can alter neural circuits and bioenergetics involved in play behavior, thus providing new insights into mechanisms that allow programming to influence the evolutionary success of an organism.

  2. Longevity is not influenced by prenatal programming of body size.

    PubMed

    Conover, Cheryl A; Bale, Laurie K; Grell, Jacquelyn A; Mader, Jessica R; Mason, Megan A

    2010-08-01

    Insulin-like growth factor (IGF) signaling is essential for achieving optimal body size during fetal development, whereas, in the adult, IGFs are associated with aging and age-related diseases. However, it is unclear as to what extent lifespan is influenced by events that occur during development. Here, we provide direct evidence that the exceptional longevity of mice with altered IGF signaling is not linked to prenatal programming of body size. Mice null for pregnancy-associated plasma protein-A (PAPP-A), an IGF-binding protein proteinase that increases local IGF bioavailability, are 60-70% the size of their wild-type littermates at birth and have extended median and maximum lifespan of 30-40%. In this study, PAPP-A(-/-) mice whose body size was normalized during fetal development through disruption of IgfII imprinting did not lose their longevity advantage. Adult-specific moderation of IGF signaling through PAPP-A inhibition may present a unique opportunity to improve lifespan without affecting important aspects of early life physiology.

  3. Influence of Formal Academic Leadership Programs on Undergraduates' Leadership Mindset: An Assessment of a Corps of Cadets Program

    ERIC Educational Resources Information Center

    Dunn, Allison L.; Ho, Sarah P.; Odom, Summer F.; Perdue, Emily R.

    2016-01-01

    Students enrolled in a Corps of Cadets program at Texas A&M University [N = 336] were surveyed to examine their leadership mindsets and whether their participation in a formal academic leadership program simultaneously influenced their hierarchical and systemic-thinking preferences. No significant differences were found between students…

  4. Network activity-independent coordinated gene expression program for synapse assembly.

    PubMed

    Valor, Luis M; Charlesworth, Paul; Humphreys, Lawrence; Anderson, Chris N G; Grant, Seth G N

    2007-03-13

    Global biological datasets generated by genomics, transcriptomics, and proteomics provide new approaches to understanding the relationship between the genome and the synapse. Combined transcriptome analysis and multielectrode recordings of neuronal network activity were used in mouse embryonic primary neuronal cultures to examine synapse formation and activity-dependent gene regulation. Evidence for a coordinated gene expression program for assembly of synapses was observed in the expression of 642 genes encoding postsynaptic and plasticity proteins. This synaptogenesis gene expression program preceded protein expression of synapse markers and onset of spiking activity. Continued expression was followed by maturation of morphology and electrical neuronal networks, which was then followed by the expression of activity-dependent genes. Thus, two distinct sequentially active gene expression programs underlie the genomic programs of synapse function.

  5. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences

    PubMed Central

    Laslett, Dean; Canback, Bjorn

    2004-01-01

    A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the ‘green’ algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags. PMID:14704338

  6. How the Number of Alleles Influences Gene Expression

    NASA Astrophysics Data System (ADS)

    Hat, Beata; Paszek, Pawel; Kimmel, Marek; Piechor, Kazimierz; Lipniacki, Tomasz

    2007-07-01

    The higher organisms, eukaryotes, are diploid and most of their genes have two homological copies (alleles). However, the number of alleles in a cell is not constant. In the S phase of the cell cycle all the genome is duplicated and then in the G2 phase and mitosis, which together last for several hours, most of the genes have four copies instead of two. Cancer development is, in many cases, associated with a change in allele number. Several genetic diseases are caused by haploinsufficiency: Lack of one of the alleles or its improper functioning. In the paper we consider the stochastic expression of a gene having a variable number of copies. We applied our previously developed method in which the reaction channels are split into slow (connected with change of gene state) and fast (connected with mRNA/protein synthesis/decay), the later being approximated by deterministic reaction rate equations. As a result we represent gene expression as a piecewise deterministic time-continuous Markov process, which is further related with a system of partial differential hyperbolic equations for probability density functions (pdfs) of protein distribution. The stationary pdfs are calculated analytically for haploidal gene or numerically for diploidal and tetraploidal ones. We distinguished nine classes of simultaneous activation of haploid, diploid and tetraploid genes. This allows for analysis of potential consequences of gene duplication or allele loss. We show that when gene activity is autoregulated by a positive feedback, the change in number of gene alleles may have dramatic consequences for its regulation and may not be compensated by the change of efficiency of mRNA synthesis per allele.

  7. Influence matrix program for aerodynamic lifting surface theory. [in subsonic flows

    NASA Technical Reports Server (NTRS)

    Medan, R. T.; Ray, K. S.

    1973-01-01

    A users manual is described for a USA FORTRAN 4 computer program which computes an aerodynamic influence matrix and is one of several computer programs used to analyze lifting, thin wings in steady, subsonic flow according to a kernel function method lifting surface theory. The most significant features of the program are that it can treat unsymmetrical wings, control points can be placed on the leading and/or trailing edges, and a stable, efficient algorithm is used to compute the influence matrix.

  8. Genes influencing circadian differences in blood pressure in hypertensive mice.

    PubMed

    Marques, Francine Z; Campain, Anna E; Davern, Pamela J; Yang, Yee Hwa J; Head, Geoffrey A; Morris, Brian J

    2011-04-26

    Essential hypertension is a common multifactorial heritable condition in which increased sympathetic outflow from the central nervous system is involved in the elevation in blood pressure (BP), as well as the exaggerated morning surge in BP that is a risk factor for myocardial infarction and stroke in hypertensive patients. The Schlager BPH/2J mouse is a genetic model of hypertension in which increased sympathetic outflow from the hypothalamus has an important etiological role in the elevation of BP. Schlager hypertensive mice exhibit a large variation in BP between the active and inactive periods of the day, and also show a morning surge in BP. To investigate the genes responsible for the circadian variation in BP in hypertension, hypothalamic tissue was collected from BPH/2J and normotensive BPN/3J mice at the 'peak' (n = 12) and 'trough' (n = 6) of diurnal BP. Using Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays, validation by quantitative real-time PCR and a statistical method that adjusted for clock genes, we identified 212 hypothalamic genes whose expression differed between 'peak' and 'trough' BP in the hypertensive strain. These included genes with known roles in BP regulation, such as vasopressin, oxytocin and thyrotropin releasing hormone, as well as genes not recognized previously as regulators of BP, including chemokine (C-C motif) ligand 19, hypocretin and zinc finger and BTB domain containing 16. Gene ontology analysis showed an enrichment of terms for inflammatory response, mitochondrial proton-transporting ATP synthase complex, structural constituent of ribosome, amongst others. In conclusion, we have identified genes whose expression differs between the peak and trough of 24-hour circadian BP in BPH/2J mice, pointing to mechanisms responsible for diurnal variation in BP. The findings may assist in the elucidation of the mechanism for the morning surge in BP in essential hypertension.

  9. Influence of leukotriene gene polymorphisms on chronic rhinosinusitis

    PubMed Central

    Al-Shemari, Hasan; Bossé, Yohan; Hudson, Thomas J; Cabaluna, Myrna; Duval, Melanie; Lemire, Mathieu; Vallee-Smedja, Sophie; Frenkiel, Saul; Desrosiers, Martin

    2008-01-01

    Background Chronic rhinosinusitis (CRS) is increasingly viewed as an inflammatory condition of the sinonasal mucosa interacting with bacteria and/or fungi. However, factors conferring susceptibility to disease remain unknown. Advances in genomics offer powerful tools to explore this disorder. The goal of this study was to evaluate the effect of single nucleotide polymorphisms (SNP) on CRS in a panel of genes related to cysteinyl leukotriene metabolism. Methods Severe cases of CRS and postal code match controls were recruited prospectively. A total of 206 cases and 200 controls were available for the present study. Using a candidate gene approach, five genes related to cysteinyl leukotriene metabolism were assessed. For each gene, we selected the maximally informative set of common SNPs (tagSNPs) using the European-derived (CEU) HapMap dataset. These SNPs are in arachidonate 5-lipoxygenase (ALOX5), arachidonate 5-lipoxygenase-activating protein (ALOX5AP), leukotriene C4 synthase (LTC4S), cysteinyl leukotriene receptor 1 (CYSLTR1) and cysteinyl leukotriene receptor 2 (CYSLTR2) genes. Results A total of 59 SNPs were genotyped to capture the common genetic variations within these genes. Three SNPs located within the ALOX5, CYSLTR1 and ALOX5AP genes reached the nominal p-value threshold (p < 0.05) for association with CRS. However, none of these SNPs resist multiple testing adjustment. Conclusion While these initial results do not support that polymorphsims in genes assessed involved in the leukotriene pathways are contributing to the pathogenesis of CRS, this initial study was not powered to detect polymorphisms with relative risk of 2.0 or less, where we could expect many gene effects for complex diseases to occur. Thus, despite this lack of significant association noted in this study, we believe that validation with external populations and the use of better-powered studies in the future may allow more conclusive findings. PMID:18366797

  10. The Program of Gene Transcription for a Single Differentiating Cell Type during Sporulation in Bacillus subtilis

    PubMed Central

    Eichenberger, Patrick; Fujita, Masaya; Jensen, Shane T; Conlon, Erin M; Rudner, David Z; Wang, Stephanie T; Ferguson, Caitlin; Haga, Koki; Sato, Tsutomu; Liu, Jun S

    2004-01-01

    Asymmetric division during sporulation by Bacillus subtilis generates a mother cell that undergoes a 5-h program of differentiation. The program is governed by a hierarchical cascade consisting of the transcription factors: σE, σK, GerE, GerR, and SpoIIID. The program consists of the activation and repression of 383 genes. The σE factor turns on 262 genes, including those for GerR and SpoIIID. These DNA-binding proteins downregulate almost half of the genes in the σE regulon. In addition, SpoIIID turns on ten genes, including genes involved in the appearance of σK . Next, σK activates 75 additional genes, including that for GerE. This DNA-binding protein, in turn, represses half of the genes that had been activated by σK while switching on a final set of 36 genes. Evidence is presented that repression and activation contribute to proper morphogenesis. The program of gene expression is driven forward by its hierarchical organization and by the repressive effects of the DNA-binding proteins. The logic of the program is that of a linked series of feed-forward loops, which generate successive pulses of gene transcription. Similar regulatory circuits could be a common feature of other systems of cellular differentiation. PMID:15383836

  11. Factors Influencing Job Satisfaction of New Graduate Nurses Participating in Nurse Residency Programs: A Systematic Review

    PubMed Central

    Lin, Patrice S.; Viscardi, Molly Kreider; McHugh, Matthew D.

    2016-01-01

    Nurse residency programs are designed to increase competence and skill, and ease the transition from student to new graduate nurse. These programs also offer the possibility to positively influence the job satisfaction of new graduate nurses, which could decrease poor nursing outcomes. However, little is known about the impact of participation in a nurse residency program on new graduate nurses’ satisfaction. This review examines factors that influence job satisfaction of nurse residency program participants. Eleven studies were selected for inclusion, and seven domains influencing new graduate nurses’ satisfaction during participation in nurse residency programs were identified: extrinsic rewards, scheduling, interactions and support, praise and recognition, professional opportunities, work environment, and hospital system. Within these domains, the evidence for improved satisfaction with nurse residency program participation was mixed. Further research is necessary to understand how nurse residency programs can be designed to improve satisfaction and increase positive nurse outcomes. PMID:25280192

  12. Factors influencing job satisfaction of new graduate nurses participating in nurse residency programs: a systematic review.

    PubMed

    Lin, Patrice S; Viscardi, Molly Kreider; McHugh, Matthew D

    2014-10-01

    Nurse residency programs are designed to increase competence and skill, and ease the transition from student to new graduate nurse. These programs also offer the possibility to positively influence the job satisfaction of new graduate nurses, which could decrease poor nursing outcomes. However, little is known about the impact of participation in a nurse residency program on new graduate nurses' satisfaction. This review examines factors that influence job satisfaction of nurse residency program participants. Eleven studies were selected for inclusion, and seven domains influencing new graduate nurses' satisfaction during participation in nurse residency programs were identified: extrinsic rewards, scheduling, interactions and support, praise and recognition, professional opportunities, work environment, and hospital system. Within these domains, the evidence for improved satisfaction with nurse residency program participation was mixed. Further research is necessary to understand how nurse residency programs can be designed to improve satisfaction and increase positive nurse outcomes.

  13. The Influence of Perceived Characteristics of Management Development Programs on Employee Outcomes

    ERIC Educational Resources Information Center

    Ardts, Joost C. A.; van der Velde, Mandy E. G.; Maurer, Todd J.

    2010-01-01

    Employees' perceptions of Management Development (MD) programs is the topic of this study. The purpose is to examine the influence of three important perceived characteristics of MD programs on relevant MD outcomes. The MD characteristics are: availability of role models, perceived control, and understanding the MD program. Outcomes are:…

  14. Investigating GEAR-Up College Readiness Program's Influence on Postsecondary Decisions of Rural Hispanic Youth

    ERIC Educational Resources Information Center

    Boydstun, Kelli Dawn

    2016-01-01

    This qualitative case study investigated how the GEAR-Up college readiness program influenced the postsecondary decisions of Hispanic students who participated in the GEAR-Up program for the recommended six-year period in a rural school district in Texas. It was not known how long-term participation in the GEAR-Up program at a rural school…

  15. Sleep Deprivation Influences Circadian Gene Expression in the Lateral Habenula.

    PubMed

    Zhang, Beilin; Gao, Yanxia; Li, Yang; Yang, Jing; Zhao, Hua

    2016-01-01

    Sleep is governed by homeostasis and the circadian clock. Clock genes play an important role in the generation and maintenance of circadian rhythms but are also involved in regulating sleep homeostasis. The lateral habenular nucleus (LHb) has been implicated in sleep-wake regulation, since LHb gene expression demonstrates circadian oscillation characteristics. This study focuses on the participation of LHb clock genes in regulating sleep homeostasis, as the nature of their involvement is unclear. In this study, we observed changes in sleep pattern following sleep deprivation in LHb-lesioned rats using EEG recording techniques. And then the changes of clock gene expression (Per1, Per2, and Bmal1) in the LHb after 6 hours of sleep deprivation were detected by using real-time quantitative PCR (qPCR). We found that sleep deprivation increased the length of Non-Rapid Eye Movement Sleep (NREMS) and decreased wakefulness. LHb-lesioning decreased the amplitude of reduced wake time and increased NREMS following sleep deprivation in rats. qPCR results demonstrated that Per2 expression was elevated after sleep deprivation, while the other two genes were unaffected. Following sleep recovery, Per2 expression was comparable to the control group. This study provides the basis for further research on the role of LHb Per2 gene in the regulation of sleep homeostasis.

  16. Sleep Deprivation Influences Circadian Gene Expression in the Lateral Habenula

    PubMed Central

    Gao, Yanxia

    2016-01-01

    Sleep is governed by homeostasis and the circadian clock. Clock genes play an important role in the generation and maintenance of circadian rhythms but are also involved in regulating sleep homeostasis. The lateral habenular nucleus (LHb) has been implicated in sleep-wake regulation, since LHb gene expression demonstrates circadian oscillation characteristics. This study focuses on the participation of LHb clock genes in regulating sleep homeostasis, as the nature of their involvement is unclear. In this study, we observed changes in sleep pattern following sleep deprivation in LHb-lesioned rats using EEG recording techniques. And then the changes of clock gene expression (Per1, Per2, and Bmal1) in the LHb after 6 hours of sleep deprivation were detected by using real-time quantitative PCR (qPCR). We found that sleep deprivation increased the length of Non-Rapid Eye Movement Sleep (NREMS) and decreased wakefulness. LHb-lesioning decreased the amplitude of reduced wake time and increased NREMS following sleep deprivation in rats. qPCR results demonstrated that Per2 expression was elevated after sleep deprivation, while the other two genes were unaffected. Following sleep recovery, Per2 expression was comparable to the control group. This study provides the basis for further research on the role of LHb Per2 gene in the regulation of sleep homeostasis. PMID:27413249

  17. Influence of Gene Expression on Hardness in Wheat.

    PubMed

    Nirmal, Ravi C; Furtado, Agnelo; Wrigley, Colin; Henry, Robert J

    2016-01-01

    Puroindoline (Pina and Pinb) genes control grain texture or hardness in wheat. Wild-type/soft alleles lead to softer grain while a mutation in one or both of these genes results in a hard grain. Variation in hardness in genotypes with identical Pin alleles (wild-type or mutant) is known but the molecular basis of this is not known. We now report the identification of wheat genotypes with hard grain texture and wild-type/soft Pin alleles indicating that hardness in wheat may be controlled by factors other than mutations in the coding region of the Pin genes. RNA-Seq analysis was used to determine the variation in the transcriptome of developing grains of thirty three diverse wheat genotypes including hard (mutant Pin) and soft (wild type) and those that were hard without having Pin mutations. This defined the role of pin gene expression and identified other candidate genes associated with hardness. Pina was not expressed in hard wheat with a mutation in the Pina gene. The ratio of Pina to Pinb expression was generally lower in the hard non mutant genotypes. Hardness may be associated with differences in Pin expression and other factors and is not simply associated with mutations in the PIN protein coding sequences.

  18. Influence of Gene Expression on Hardness in Wheat

    PubMed Central

    Nirmal, Ravi C.; Wrigley, Colin

    2016-01-01

    Puroindoline (Pina and Pinb) genes control grain texture or hardness in wheat. Wild-type/soft alleles lead to softer grain while a mutation in one or both of these genes results in a hard grain. Variation in hardness in genotypes with identical Pin alleles (wild-type or mutant) is known but the molecular basis of this is not known. We now report the identification of wheat genotypes with hard grain texture and wild-type/soft Pin alleles indicating that hardness in wheat may be controlled by factors other than mutations in the coding region of the Pin genes. RNA-Seq analysis was used to determine the variation in the transcriptome of developing grains of thirty three diverse wheat genotypes including hard (mutant Pin) and soft (wild type) and those that were hard without having Pin mutations. This defined the role of pin gene expression and identified other candidate genes associated with hardness. Pina was not expressed in hard wheat with a mutation in the Pina gene. The ratio of Pina to Pinb expression was generally lower in the hard non mutant genotypes. Hardness may be associated with differences in Pin expression and other factors and is not simply associated with mutations in the PIN protein coding sequences. PMID:27741295

  19. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.

    PubMed

    Haas, Brian J; Salzberg, Steven L; Zhu, Wei; Pertea, Mihaela; Allen, Jonathan E; Orvis, Joshua; White, Owen; Buell, C Robin; Wortman, Jennifer R

    2008-01-11

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  20. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    SciTech Connect

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  1. Identification of genes influencing dendrite morphogenesis in developing peripheral sensory and central motor neurons

    PubMed Central

    Ou, Yimiao; Chwalla, Barbara; Landgraf, Matthias; van Meyel, Donald J

    2008-01-01

    Background Developing neurons form dendritic trees with cell type-specific patterns of growth, branching and targeting. Dendrites of Drosophila peripheral sensory neurons have emerged as a premier genetic model, though the molecular mechanisms that underlie and regulate their morphogenesis remain incompletely understood. Still less is known about this process in central neurons and the extent to which central and peripheral dendrites share common organisational principles and molecular features. To address these issues, we have carried out two comparable gain-of-function screens for genes that influence dendrite morphologies in peripheral dendritic arborisation (da) neurons and central RP2 motor neurons. Results We found 35 unique loci that influenced da neuron dendrites, including five previously shown as required for da dendrite patterning. Several phenotypes were class-specific and many resembled those of known mutants, suggesting that genes identified in this study may converge with and extend known molecular pathways for dendrite development in da neurons. The second screen used a novel technique for cell-autonomous gene misexpression in RP2 motor neurons. We found 51 unique loci affecting RP2 dendrite morphology, 84% expressed in the central nervous system. The phenotypic classes from both screens demonstrate that gene misexpression can affect specific aspects of dendritic development, such as growth, branching and targeting. We demonstrate that these processes are genetically separable. Targeting phenotypes were specific to the RP2 screen, and we propose that dendrites in the central nervous system are targeted to territories defined by Cartesian co-ordinates along the antero-posterior and the medio-lateral axes of the central neuropile. Comparisons between the screens suggest that the dendrites of peripheral da and central RP2 neurons are shaped by regulatory programs that only partially overlap. We focused on one common candidate pathway controlled by the

  2. Modelling Programming Performance: Beyond the Influence of Learner Characteristics

    ERIC Educational Resources Information Center

    Lau, Wilfred W. F.; Yuen, Allan H. K.

    2011-01-01

    In the 21st century, the ubiquitous nature of technology today is evident and to a large extent, most of us benefit from the modern convenience brought about by technology. Yet to be technology literate, it is argued that learning to program still plays an important role. One area of research in programming concerns the identification of…

  3. Learning to Program with Personal Robots: Influences on Student Motivation

    ERIC Educational Resources Information Center

    McGill, Monica M.

    2012-01-01

    One of the goals of using robots in introductory programming courses is to increase motivation among learners. There have been several types of robots that have been used extensively in the classroom to teach a variety of computer science concepts. A more recently introduced robot designed to teach programming to novice students is the Institute…

  4. Multi-Vendor Loyalty Programs: Influencing Customer Behavioral Loyalty?

    PubMed Central

    Villacé-Molinero, Teresa; Reinares-Lara, Pedro; Reinares-Lara, Eva

    2016-01-01

    Loyalty programs are a consolidated marketing instrument whose adoption in many sectors has not been associated with appropriate comprehension of either their management elements or their effects. The purpose of this research is to contribute to knowledge about the effect of loyalty programs on repeat purchase behavior. More specifically, it seeks to discover whether joining a program changes the buying behavior of its members, and, if so, to study the profile of those whose behavior changes most. The intention was also to provide new study variables pertaining to multi-vendor loyalty programs, such as where they are joined or purchases in associated outlets as a result of behavioral loyalty. Research was carried out using a sample of 1200 individuals (31,746 purchases) belonging to a multi-vendor loyalty program. The study period was 13 years, 4 months, and split into two phases: before and after the joining the program. Different methodological approaches, such as the use of transactional databases that included pre-program-enrollment data and of the same sampling units throughout the study, were incorporated into the research with the aim of advancing academic knowledge regarding multi-vendor loyalty programs. Moreover, a type of program and market hardly dealt with in the relevant literature was analyzed. The results showed while the loyalty program had managed to reduce the time between purchases, it had not affected purchase volume or average expenditure. They also demonstrated the existence of a differential profile of customers who had changed their buying behavior to a greater extent. Finally, recency was identified as being the decisive variable in behavioral change. PMID:26941677

  5. Multi-Vendor Loyalty Programs: Influencing Customer Behavioral Loyalty?

    PubMed

    Villacé-Molinero, Teresa; Reinares-Lara, Pedro; Reinares-Lara, Eva

    2016-01-01

    Loyalty programs are a consolidated marketing instrument whose adoption in many sectors has not been associated with appropriate comprehension of either their management elements or their effects. The purpose of this research is to contribute to knowledge about the effect of loyalty programs on repeat purchase behavior. More specifically, it seeks to discover whether joining a program changes the buying behavior of its members, and, if so, to study the profile of those whose behavior changes most. The intention was also to provide new study variables pertaining to multi-vendor loyalty programs, such as where they are joined or purchases in associated outlets as a result of behavioral loyalty. Research was carried out using a sample of 1200 individuals (31,746 purchases) belonging to a multi-vendor loyalty program. The study period was 13 years, 4 months, and split into two phases: before and after the joining the program. Different methodological approaches, such as the use of transactional databases that included pre-program-enrollment data and of the same sampling units throughout the study, were incorporated into the research with the aim of advancing academic knowledge regarding multi-vendor loyalty programs. Moreover, a type of program and market hardly dealt with in the relevant literature was analyzed. The results showed while the loyalty program had managed to reduce the time between purchases, it had not affected purchase volume or average expenditure. They also demonstrated the existence of a differential profile of customers who had changed their buying behavior to a greater extent. Finally, recency was identified as being the decisive variable in behavioral change.

  6. [Influence of semantic stress on the motor program structure].

    PubMed

    Shalimov, P M; Ermolaev, B V

    1998-01-01

    To approach the applied aspects of support to operator interacting with the aerospace technical systems, the authors are working on the problems of structuring the motor programs and deformation caused to them by semantic stressful agents. Possibility for varying the composition of locomotion programs to ensure success of a general motor task had been experimentally demonstrated. Data obtained are viewed from the standpoint of revision of the motor image in the psychic control system.

  7. Transcriptome Analysis in Rat Kidneys: Importance of Genes Involved in Programmed Hypertension

    PubMed Central

    Tain, You-Lin; Huang, Li-Tung; Chan, Julie Y. H.; Lee, Chien-Te

    2015-01-01

    Suboptimal conditions in pregnancy can elicit long-term effects on the health of offspring. The most common outcome is programmed hypertension. We examined whether there are common genes and pathways in the kidney are responsible for generating programmed hypertension among three different models using next generation RNA sequencing (RNA-Seq) technology. Pregnant Sprague-Dawley rats received dexamethasone (DEX, 0.1 mg/kg) from gestational day 16 to 22, 60% high-fructose (HF) diet, or NG-nitro-l-arginine-methyester (l-NAME, 60 mg/kg/day) to conduct DEX, HF, or l-NAME model respectively. All three models elicited programmed hypertension in adult male offspring. We observed five shared genes (Bcl6, Dmrtc1c, Egr1, Inmt, and Olr1668) among three different models. The identified differential genes (DEGs) that are related to regulation of blood pressure included Aqp2, Ptgs1, Eph2x, Hba-a2, Apln, Guca2b, Hmox1, and Npy. RNA-Seq identified genes in arachidonic acid metabolism are potentially gatekeeper genes contributing to programmed hypertension. In addition, HF and DEX increased expression and activity of soluble epoxide hydrolase (Ephx2 gene encoding protein). Conclusively, the DEGs in arachidonic acid metabolism are potentially gatekeeper genes in programmed hypertension. The roles of DEGs identified by the RNA-Seq in this study deserve further clarification, to develop the potential interventions in the prevention of programmed hypertension. PMID:25739086

  8. The relative influence of natural selection and geography on gene flow in guppies.

    PubMed

    Crispo, Erika; Bentzen, Paul; Reznick, David N; Kinnison, Michael T; Hendry, Andrew P

    2006-01-01

    Two general processes may influence gene flow among populations. One involves divergent selection, wherein the maladaptation of immigrants and hybrids impedes gene flow between ecological environments (i.e. ecological speciation). The other involves geographic features that limit dispersal. We determined the relative influence of these two processes in natural populations of Trinidadian guppies (Poecilia reticulata). If selection is important, gene flow should be reduced between different selective environments. If geography is important, gene flow should be impeded by geographic distance and physical barriers. We examined how genetic divergence, long-term gene flow, and contemporary dispersal within a watershed were influenced by waterfalls, geographic distance, predation, and habitat features. We found that waterfalls and geographic distance increased genetic divergence and reduced dispersal and long-term gene flow. Differences in predation or habitat features did not influence genetic divergence or gene flow. In contrast, differences in predation did appear to reduce contemporary dispersal. We suggest that the standard predictions of ecological speciation may be heavily nuanced by the mating behaviour and life history strategies of guppies.

  9. Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors.

    PubMed

    Emmert-Streib, Frank

    2013-01-01

    The inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance of network inference algorithms. Specifically, we study five network inference methods, Aracne, BC3NET, CLR, C3NET and MRNET, and compare the results for three different conditions: (I) observational gene expression data: normal environmental condition, (II) interventional gene expression data: growth in rich media, (III) interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. Overall, we find that different statistical inference methods lead to comparable, but condition-specific results. Further, our results suggest that non-steady-state data enhance the inferability of regulatory networks.

  10. Cell Cycle Programs of Gene Expression Control Morphogenetic Protein Localization

    PubMed Central

    Lord, Matthew; Yang, Melody C.; Mischke, Michelle; Chant, John

    2000-01-01

    Genomic studies in yeast have revealed that one eighth of genes are cell cycle regulated in their expression. Almost without exception, the significance of cell cycle periodic gene expression has not been tested. Given that many such genes are critical to cellular morphogenesis, we wanted to examine the importance of periodic gene expression to this process. The expression profiles of two genes required for the axial pattern of cell division, BUD3 and BUD10/AXL2/SRO4, are strongly cell cycle regulated. BUD3 is expressed close to the onset of mitosis. BUD10 is expressed in late G1. Through promotor-swap experiments, the expression profile of each gene was altered and the consequences examined. We found that an S/G2 pulse of BUD3 expression controls the timing of Bud3p localization, but that this timing is not critical to Bud3p function. In contrast, a G1 pulse of BUD10 expression plays a direct role in Bud10p localization and function. Bud10p, a membrane protein, relies on the polarized secretory machinery specific to G1 to be delivered to its proper location. Such a secretion-based targeting mechanism for membrane proteins provides cells with flexibility in remodeling their architecture or evolving new forms. PMID:11134078

  11. Integrative Gene Regulatory Network Analysis Reveals Light-Induced Regional Gene Expression Phase Shift Programs in the Mouse Suprachiasmatic Nucleus

    PubMed Central

    Zhu, Haisun; Vadigepalli, Rajanikanth; Rafferty, Rachel; Gonye, Gregory E.; Weaver, David R.; Schwaber, James S.

    2012-01-01

    We use the multigenic pattern of gene expression across suprachiasmatic nuclei (SCN) regions and time to understand the dynamics within the SCN in response to a circadian phase-resetting light pulse. Global gene expression studies of the SCN indicate that circadian functions like phase resetting are complex multigenic processes. While the molecular dynamics of phase resetting are not well understood, it is clear they involve a “functional gene expression program”, e.g., the coordinated behavior of functionally related genes in space and time. In the present study we selected a set of 89 of these functionally related genes in order to further understand this multigenic program. By use of high-throughput qPCR we studied 52 small samples taken by anatomically precise laser capture from within the core and shell SCN regions, and taken at time points with and without phase resetting light exposure. The results show striking regional differences in light response to be present in the mouse SCN. By using network-based analyses, we are able to establish a highly specific multigenic correlation between genes expressed in response to light at night and genes normally activated during the day. The light pulse triggers a complex and highly coordinated network of gene regulation. The largest differences marking neuroanatomical location are in transmitter receptors, and the largest time-dependent differences occur in clock-related genes. Nighttime phase resetting appears to recruit transcriptional regulatory processes normally active in the day. This program, or mechanism, causes the pattern of core region gene expression to transiently shift to become more like that of the shell region. PMID:22662235

  12. Deviant Peer Influences in Programs for Youth Problems and Solutions

    ERIC Educational Resources Information Center

    Dodge, Kenneth A., Ed.; Dishion, Thomas J., Ed.; Lansford, Jennifer E., Ed.

    2006-01-01

    Most interventions for at-risk youth are group based. Yet, emerging research indicates that young people often learn to become deviant by interacting with deviant peers. In this important volume, leading intervention and prevention experts from psychology, education, criminology, and related fields analyze how, and to what extent, programs that…

  13. From "Hesitant" to "Environmental Leader": The Influence of a Professional Development Program on the Environmental Citizenship of Preschool Teachers

    ERIC Educational Resources Information Center

    Spektor-Levy, Ornit; Abramovich, Anat

    2017-01-01

    This study investigated the influence that the "Environmental Leadership Professional Development" program had on preschool teachers. The program's aim is to enhance environmental awareness, thus developing environmental citizenship and leadership. The program offered experiential and reflective learning, meetings with environmental…

  14. Saving the Seneca Outdoor Recreation Program: A Case Study in Exerting Political Influence.

    ERIC Educational Resources Information Center

    Magee, Clare

    1998-01-01

    This case study demonstrates the process of exerting political influence in faculty's systematic efforts to save the outdoor recreation program at Seneca College (Ontario). A chart and explanatory list present a seven-stage plan for influencing political decision-making. (SAS)

  15. The Influence of Early Childhood Program Participation on Academic Achievement at the Elementary Level

    ERIC Educational Resources Information Center

    Villani, Gina Marie

    2014-01-01

    The purpose of this study was to examine the influence of early childhood program participation on academic achievement by grade 3. This case study utilized a quantitative approach to data collection. For purposes of this research, one P-12 school district in central New Jersey was studied to look at the influence of early childhood program…

  16. Factors Influencing the ABT Phenomenon among Graduate Students in a Master Program in Mexico

    ERIC Educational Resources Information Center

    Gonzalez-Castillo, Vicente; Cisneros-Cohernour, Edith J.

    2007-01-01

    This paper presents the findings of a study examining the factors that influence the ABT phenomenon (all but thesis) among graduate students of a Master in Education program in the Southeast of Mexico. Findings of the study identified individual and organizational factors influencing ABT. The study allowed for a better understanding about how…

  17. Socio-Cultural Influences in Eating Disorders: Focus on Sports/Fitness Program.

    ERIC Educational Resources Information Center

    Moriarty, Dick; Moriarty, Mary

    This report notes that eating disorders are frequently described as a diet and fitness program gone wild. It outlines and describes five sociocultural influences which have been identified for eating disorders: (1) emphasis on thinness; (2) glorification of youth; (3) changing roles of women; (4) emphasis on fitness and sport programs; and (5) the…

  18. The Life Skills Program IPSY: Positive Influences on School Bonding and Prevention of Substance Misuse

    ERIC Educational Resources Information Center

    Wenzel, Victoria; Weichold, Karina; Silbereisen, Rainer K.

    2009-01-01

    The present study investigated whether a life skills program (LSP) for the prevention of adolescent substance misuse can have positive influences on a school context and on school bonding. The study also explored whether effects on alcohol use are mediated by positive effects on school bonding resulting from program participation. The LSP IPSY…

  19. Response to "Exploring the Influence of the ROC Integrated High School Program"

    ERIC Educational Resources Information Center

    Elrick, Michael

    2007-01-01

    In this article, the author provides a response to Scott Caspell's article "Exploring the Influence of the ROC Integrated High School Program." The author states that Caspell picked an excellent time frame to interview former students as they had participated in the integrated program between 10 and 13 years ago. Ideally, then,…

  20. The Australian Science Facilities Program: A Study of Its Influence on Science Education in Australian Schools.

    ERIC Educational Resources Information Center

    Ainley, John G.

    This report is a study conducted by the Australian Council for Educational Research to evaluate the influence of science material resources, provided under the Australian Science Facilities Program, on science education in Australia. Under the Australian Science Facilities Program some $123 million was spent, between July 1964 and June 1975, on…

  1. Factors Influencing Transfer of Responsibility-Based Physical Activity Program Goals into Classrooms

    ERIC Educational Resources Information Center

    Lee, Okseon; Martinek, Tom

    2012-01-01

    The purpose of this study was to investigate what influences the transfer of responsibility-based physical activity program goals into classrooms. Participants were the two boys and three girls (age range 9-11) who had participated in the program one to three semesters, with at least an 80% attendance rate. Data were collected from individual…

  2. Factors Influencing Curriculum Change in Professional Programs. ASHE Annual Meeting Paper.

    ERIC Educational Resources Information Center

    Boss, Michelle A.; Lowther, Malcolm A.

    This paper addresses the following issues concerning curriculum change in professional programs: (1) the degree of influence exhibited by external, internal, and intraorganizational factors as they interact to stimulate curriculum change in three professional programs (business, pharmacy, and accounting); (2) planning strategies used by faculty to…

  3. Influences on Students Selecting Cooperative Education Programs in Michigan High Schools. Final Report.

    ERIC Educational Resources Information Center

    Woloszyk, Carl A.

    Factors influencing the decision of high school students to enroll in cooperative education programs were investigated in a survey. The stratified random sample consisted of 275 high school students currently enrolled in cooperative education programs in five different types of communities throughout Michigan. The survey questionnaire included 8…

  4. Influence of the myopia gene on brain development.

    PubMed

    Karlsson, J L

    1975-11-01

    Evaluation of the performance of 17-18-year-old high school students on standard intelligence tests confirms previous reports that nearsighted persons consistently achieve scores approximately eight I.O. points higher than non-myopes. Comparison of tests administered to the same students 10 years earlier suggests that the intellectual gain precedes the development of nearsightedness. Since there is convincing evidence from genetic studies that myopia is an inherited condition, probably transmitted as a recessive characteristic, it is concluded that the myopia gene has a stimulant action on the brain in addition to its effect on the eye. The high frequency of myopia in urbanized societies is explained in terms of an evolutionary adjustment, myopes probably having a survival advantage under conditions of industrialization.

  5. Tobacco industry sociological programs to influence public beliefs about smoking

    PubMed Central

    Glantz, Stanton; Landman, Anne; Cortese, Daniel K

    2008-01-01

    The multinational tobacco companies responded to arguments about the social costs of smoking and hazards of secondhand smoke by quietly implementing the Social Costs/Social Values project (1979–1989), which relied upon the knowledge and authoritative power of social scientists to construct an alternate cultural repertoire of smoking. Social scientists created and disseminated non-health based, pro-tobacco arguments without fully acknowledging their relationship with the industry. After the U.S. Surgeon General concluded that nicotine was addictive in 1988, the industry responded by forming “Associates for Research in the Science of Enjoyment” (c.1988–1999), whose members toured the world promoting the health benefits of the use of legal substances, including tobacco, for stress relief and relaxation, without acknowledging the industry’s role. In this paper we draw on previously secret tobacco industry documents, now available on the internet to show how both of these programs utilized academic sociologists, political scientists, anthropologists, psychologists, philosophers and economists, and allowed the industry to develop and widely disseminate friendly research through credible channels. Strategies included creating favorable surveys and opinions, infusing them into the lay press and media through press releases, articles and conferences, publishing, promoting and disseminating books, commissioning and placing favorable book reviews, providing media training for book authors and organizing media tours. These programs allowed the tobacco industry to affect public and academic discourse on the social acceptability of smoking. PMID:18164524

  6. Quantitative influence of macromolecular crowding on gene regulation kinetics

    PubMed Central

    Tabaka, Marcin; Kalwarczyk, Tomasz; Hołyst, Robert

    2014-01-01

    We introduce macromolecular crowding quantitatively into the model for kinetics of gene regulation in Escherichia coli. We analyse and compute the specific-site searching time for 180 known transcription factors (TFs) regulating 1300 operons. The time is between 160 s (e.g. for SoxS Mw = 12.91 kDa) and 1550 s (e.g. for PepA6 of Mw = 329.28 kDa). Diffusion coefficients for one-dimensional sliding are between for large proteins up to for small monomers or dimers. Three-dimensional diffusion coefficients in the cytoplasm are 2 orders of magnitude larger than 1D sliding coefficients, nevertheless the sliding enhances the binding rates of TF to specific sites by 1–2 orders of magnitude. The latter effect is due to ubiquitous non-specific binding. We compare the model to experimental data for LacI repressor and find that non-specific binding of the protein to DNA is activation- and not diffusion-limited. We show that the target location rate by LacI repressor is optimized with respect to microscopic rate constant for association to non-specific sites on DNA. We analyse the effect of oligomerization of TFs and DNA looping effects on searching kinetics. We show that optimal searching strategy depends on TF abundance. PMID:24121687

  7. Creating Programs to Help Latino Youth Thrive at School: The Influence of Latino Parent Involvement Programs

    ERIC Educational Resources Information Center

    Behnke, Andrew O.; Kelly, Christine

    2011-01-01

    Parent involvement programs can play an essential role in the academic success of Latino youth. This article reports the effectiveness and evaluation of two new Extension programs that help Latino parents become more involved in their youths' academics. The Latino Parent and Family Advocacy and Support Training (LPFAST) targets parents of K- 8th…

  8. The Influence of an Academic Pharmacy Mentorship Program on Mentees' Commitment to Pursue an Academic Career.

    PubMed

    Sierra, Caroline M; Adams, Jennifer

    2017-02-25

    The objective of this study was to determine the influence of the American Association of Colleges of Pharmacy (AACP) Walmart Scholars Program on mentees' attitudes towards and decision to pursue a career in academia. Upon completion of the AACP Walmart Scholars Program, wherein mentor-mentee pairs attend the AACP Annual Meeting to learn about academic pharmacy careers, mentees wrote essays evaluating the program. Their views on academic pharmacy careers were analyzed for themes in the evaluations. Of the mentees who addressed the impact of the program on their perspectives on a career in academic pharmacy, over half stated the program positively influenced pursuit of such a career. This reinforces the importance of mentorship for those interested in or new to academic pharmacy.

  9. The Influence of an Academic Pharmacy Mentorship Program on Mentees’ Commitment to Pursue an Academic Career

    PubMed Central

    Sierra, Caroline M.

    2017-01-01

    The objective of this study was to determine the influence of the American Association of Colleges of Pharmacy (AACP) Walmart Scholars Program on mentees’ attitudes towards and decision to pursue a career in academia. Upon completion of the AACP Walmart* Scholars Program, wherein mentor-mentee pairs attend the AACP Annual Meeting to learn about academic pharmacy careers, mentees wrote essays evaluating the program. Their views on academic pharmacy careers were analyzed for themes in the evaluations. Of the mentees who addressed the impact of the program on their perspectives on a career in academic pharmacy, over half stated the program positively influenced pursuit of such a career. This reinforces the importance of mentorship for those interested in or new to academic pharmacy. PMID:28289293

  10. The maize rough sheath2 gene and leaf development programs in monocot and dicot plants.

    PubMed

    Tsiantis, M; Schneeberger, R; Golz, J F; Freeling, M; Langdale, J A

    1999-04-02

    Leaves of higher plants develop in a sequential manner from the shoot apical meristem. Previously it was determined that perturbed leaf development in maize rough sheath2 (rs2) mutant plants results from ectopic expression of knotted1-like (knox) homeobox genes. Here, the rs2 gene sequence was found to be similar to the Antirrhinum PHANTASTICA (PHAN) gene sequence, which encodes a Myb-like transcription factor. RS2 and PHAN are both required to prevent the accumulation of knox gene products in maize and Antirrhinum leaves, respectively. However, rs2 and phan mutant phenotypes differ, highlighting fundamental differences in monocot and dicot leaf development programs.

  11. Glucocorticoid Effects on the Programming of AT1b Angiotensin Receptor Gene Methylation and Expression in the Rat

    PubMed Central

    Bogdarina, Irina; Haase, Andrea; Langley-Evans, Simon; Clark, Adrian J. L.

    2010-01-01

    Adverse events in pregnancy may ‘programme’ offspring for the later development of cardiovascular disease and hypertension. Previously, using a rodent model of programmed hypertension we have demonstrated the role of the renin-angiotensin system in this process. More recently we showed that a maternal low protein diet resulted in undermethylation of the At1b angiotensin receptor promoter and the early overexpression of this gene in the adrenal of offspring. Here, we investigate the hypothesis that maternal glucocorticoid modulates this effect on fetal DNA methylation and gene expression. We investigated whether treatment of rat dams with the 11β-hydroxylase inhibitor metyrapone, could prevent the epigenetic and gene expression changes we observed. Offspring of mothers subjected to a low protein diet in pregnancy showed reduced adrenal Agtr1b methylation and increased adrenal gene expression as we observed previously. Treatment of mothers with metyrapone for the first 14 days of pregnancy reversed these changes and prevented the appearance of hypertension in the offspring at 4 weeks of age. As a control for non-specific effects of programmed hypertension we studied offspring of mothers treated with dexamethasone from day 15 of pregnancy and showed that, whilst they had raised blood pressure, they failed to show any evidence of Agtr1b methylation or increase in gene expression. We conclude that maternal glucocorticoid in early pregnancy may induce changes in methylation and expression of the Agtr1b gene as these are clearly reversed by an 11 beta-hydroxylase inhibitor. However in later pregnancy a converse effect with dexamethasone could not be demonstrated and this may reflect either an alternative mechanism of this glucocorticoid or a stage-specific influence. PMID:20169056

  12. Number of X-chromosome genes influences social behavior and vasopressin gene expression in mice.

    PubMed

    Cox, Kimberly H; Quinnies, Kayla M; Eschendroeder, Alex; Didrick, Paula M; Eugster, Erica A; Rissman, Emilie F

    2015-01-01

    Sex differences in behavior are widespread and often caused by hormonal differences between the sexes. In addition to hormones, the composition and numbers of the sex chromosomes also affect a variety of sex differences. In humans, X-chromosome genes are implicated in neurobehavioral disorders (i.e. fragile-X, autism). To investigate the role of X-chromosome genes in social behavior, we used a mouse model that has atypical sex chromosome configurations resembling Turner (45, XO) and Klinefelter syndromes (47, XXY). We examined a number of behaviors in juvenile mice. Mice with only one copy of most X-chromosome genes, regardless of gonadal sex, were less social in dyadic interaction and social preference tasks. In the elevated plus maze, mice with one X-chromosome spent less time in the distal ends of the open arms as compared to mice with two copies of X-chromosome genes. Using qRTPCR, we noted that amygdala from female mice with one X-chromosome had higher expression levels of vasopressin (Avp) as compared to mice in the other groups. Finally, in plasma from girls with Turner syndrome we detected reduced vasopressin (AVP) concentrations as compared to control patients. These novel findings link sex chromosome genes with social behavior via concentrations of AVP in brain, adding to our understanding of sex differences in neurobehavioral disorders.

  13. Influence of Gene Flow and Breeding Tactics on Gene Diversity within Populations

    PubMed Central

    Chesser, R. K.

    1991-01-01

    Expressions describing the accumulation of gene correlations within and among lineages and individuals of a population are derived. The model permits different migration rates by males and females and accounts for various breeding tactics within lineages. The resultant equations enable calculation of the probabilistic quantities for the fixation indices, rates of loss of genetic variation, accumulation of inbreeding, and coefficients of relationship for the population at any generation. All fixation indices were found to attain asymptotic values rapidly despite the consistent loss of genetic variation and accumulation of inbreeding within the population. The time required to attain asymptotic values, however, was prolonged when gene flow among lineages was relatively low (<20%). The degree of genetic differentiation among breeding groups, inbreeding coefficients, and gene correlations within lineages were found to be primarily functions of breeding tactics within groups rather than gene flow among groups. Thus, the asymptotic value of S. Wright's island model is not appropriate for describing genetic differences among groups within populations. An alternative solution is provided that under limited conditions will reduce to the original island model. The evolution of polygynous breeding tactics appears to be more favorable for promoting intragroup gene correlations than modification of migration rates. Inbreeding and variance effective sizes are derived for populations that are structured by different migration and breeding tactics. Processes that reduce the inbreeding effective population size result in a concomitant increase in variance effective population size. PMID:1743493

  14. Influence of CFH gene on symptom severity of schizophrenia

    PubMed Central

    Zhang, Chen; Lv, Qinyu; Fan, Weixing; Tang, Wei; Yi, Zhenghui

    2017-01-01

    Objective Recent advances have provided compelling evidence for the role of excessive complement activity in the pathophysiology of schizophrenia. In this study, we aimed to detect the association of the gene encoding complement factor H (CFH), a regulator in complement activation, with schizophrenia. Materials and methods A sample of 1783 individuals with or without schizophrenia was recruited for genetic analysis. Genomic DNA samples were extracted from peripheral blood cells using multiplex polymerase chain reaction and the SNaPshot assay. A Database for Schizophrenia Genetic Research (SZDB) was used to detect the association of brain CFH expression with schizophrenia. Next, we performed a genotype–phenotype analysis to identify the relationship between CFH Y402H polymorphism and clinical features of schizophrenia. Results There was a significant association of hippocampal CFH expression with schizophrenia (P=0.017), whereas this significance did not survive after adjusting for false discovery rate (P=0.105). Comparing the genotype and allele frequencies of the genotyped single-nucleotide polymorphisms between case and control groups showed no significant difference. There were significant differences in the scores of negative symptoms and delayed memory between the patients with C allele and those without C allele (P<0.01 and P=0.04 after Bonferroni correction, respectively). Furthermore, we observed a marginally significant association between the Y402H polymorphism and CFH expression in the hippocampus (P=0.051); however, this significance was lost after multiple testing correction (P=0.51, after Bonferroni correction). Conclusion Our findings provide suggestive evidence for the role of CFH in the development of negative symptoms and cognitive dysfunction in schizophrenia. PMID:28293111

  15. Tudor Nuclease Genes and Programmed DNA Rearrangements in Tetrahymena thermophila▿

    PubMed Central

    Howard-Till, Rachel A.; Yao, Meng-Chao

    2007-01-01

    Proteins containing a Tudor domain and domains homologous to staphylococcal nucleases are found in a number of eukaryotes. These “Tudor nucleases” have been found to be associated with the RNA-induced silencing complex (A. A. Caudy, R. F. Ketting, S. M. Hammond, A. M. Denli, A. M. Bathoorn, B. B. Tops, J. M. Silva, M. M. Myers, G. J. Hannon, and R. H. Plasterk, Nature 425:411-414, 2003). We have identified two Tudor nuclease gene homologs, TTN1 and TTN2, in the ciliate Tetrahymena thermophila, which has two distinct small-RNA pathways. Characterization of single and double KOs of TTN1 and TTN2 shows that neither of these genes is essential for growth or sexual reproduction. Progeny of TTN2 KOs and double knockouts occasionally show minor defects in the small-RNA-guided process of DNA deletion but appear to be normal in hairpin RNA-induced gene silencing, suggesting that Tudor nucleases play only a minor role in RNA interference in Tetrahymena. Previous studies of Tetrahymena have shown that inserted copies of the neo gene from Escherichia coli are often deleted from the developing macronucleus during sexual reproduction (Y. Liu, X. Song, M. A. Gorovsky, and K. M. Karrer, Eukaryot. Cell 4:421-431, 2005; M. C. Yao, P. Fuller, and X. Xi, Science 300:1581-1584, 2003). This transgene deletion phenomenon is hypothesized to be a form of genome defense. Analysis of the Tudor nuclease mutants revealed exceptionally high rates of deletion of the neo transgene at the TTN2 locus but no deletion at the TTN1 locus. When present in the same genome, however, the neo gene is deleted at high rates even at the TTN1 locus, further supporting a role for trans-acting RNA in this process. This deletion is not affected by the presence of the same sequence in the macronucleus, thus providing a counterargument for the role of the macronuclear genome in specifying all sequences for deletion. PMID:17715366

  16. Genome size diversity in angiosperms and its influence on gene space.

    PubMed

    Dodsworth, Steven; Leitch, Andrew R; Leitch, Ilia J

    2015-12-01

    Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of 1C=5.7Gb. One of the most crucial factors governing genome size in angiosperms is the relative amount and activity of repetitive elements. Recently, there have been new insights into how these repeats, previously discarded as 'junk' DNA, can have a significant impact on gene space (i.e. the part of the genome comprising all the genes and gene-related DNA). Here we review these new findings and explore in what ways genome size itself plays a role in influencing how repeats impact genome dynamics and gene space, including gene expression.

  17. Array data extractor (ADE): a LabVIEW program to extract and merge gene array data

    PubMed Central

    2013-01-01

    Background Large data sets from gene expression array studies are publicly available offering information highly valuable for research across many disciplines ranging from fundamental to clinical research. Highly advanced bioinformatics tools have been made available to researchers, but a demand for user-friendly software allowing researchers to quickly extract expression information for multiple genes from multiple studies persists. Findings Here, we present a user-friendly LabVIEW program to automatically extract gene expression data for a list of genes from multiple normalized microarray datasets. Functionality was tested for 288 class A G protein-coupled receptors (GPCRs) and expression data from 12 studies comparing normal and diseased human hearts. Results confirmed known regulation of a beta 1 adrenergic receptor and further indicate novel research targets. Conclusions Although existing software allows for complex data analyses, the LabVIEW based program presented here, “Array Data Extractor (ADE)”, provides users with a tool to retrieve meaningful information from multiple normalized gene expression datasets in a fast and easy way. Further, the graphical programming language used in LabVIEW allows applying changes to the program without the need of advanced programming knowledge. PMID:24289243

  18. Silencing of the SlNAP7 gene influences plastid development and lycopene accumulation in tomato

    NASA Astrophysics Data System (ADS)

    Fu, Da-Qi; Meng, Lan-Huan; Zhu, Ben-Zhong; Zhu, Hong-Liang; Yan, Hua-Xue; Luo, Yun-Bo

    2016-12-01

    Ripening is an important stage of fruit development. To screen the genes associated with pigment formation in tomato fruit, a suppression subtractive hybridization (SSH) cDNA library was constructed by using tomato fruit in the green ripe and break ripe stages, and 129 differential genes were obtained. Using redness as a screening marker, virus-induced gene silencing (VIGS) of the differential genes was performed with a sprout vacuum-infiltration system (SVI). The results showed that silencing the SlNAP7 gene affected the chloroplast development of tomato leaves, manifesting as a photo-bleaching phenotype, and silenced fruit significantly affected the accumulation of lycopene, manifested as a yellow phenotype. In our study, we found that silencing the SlNAP7 gene downregulates the expression of the POR and PORA genes and destroys the normal development of the chloroplast. The expression of related genes included in the lycopene biosynthesis pathway was not significantly changed, but lycopene accumulation was significantly reduced in tomato fruit. Perhaps it was caused by the destruction of the chromoplast, which leads to the oxidation of lycopene. The results show that the SlNAP7 gene influences chloroplast development and lycopene accumulation in tomato.

  19. Silencing of the SlNAP7 gene influences plastid development and lycopene accumulation in tomato.

    PubMed

    Fu, Da-Qi; Meng, Lan-Huan; Zhu, Ben-Zhong; Zhu, Hong-Liang; Yan, Hua-Xue; Luo, Yun-Bo

    2016-12-08

    Ripening is an important stage of fruit development. To screen the genes associated with pigment formation in tomato fruit, a suppression subtractive hybridization (SSH) cDNA library was constructed by using tomato fruit in the green ripe and break ripe stages, and 129 differential genes were obtained. Using redness as a screening marker, virus-induced gene silencing (VIGS) of the differential genes was performed with a sprout vacuum-infiltration system (SVI). The results showed that silencing the SlNAP7 gene affected the chloroplast development of tomato leaves, manifesting as a photo-bleaching phenotype, and silenced fruit significantly affected the accumulation of lycopene, manifested as a yellow phenotype. In our study, we found that silencing the SlNAP7 gene downregulates the expression of the POR and PORA genes and destroys the normal development of the chloroplast. The expression of related genes included in the lycopene biosynthesis pathway was not significantly changed, but lycopene accumulation was significantly reduced in tomato fruit. Perhaps it was caused by the destruction of the chromoplast, which leads to the oxidation of lycopene. The results show that the SlNAP7 gene influences chloroplast development and lycopene accumulation in tomato.

  20. Silencing of the SlNAP7 gene influences plastid development and lycopene accumulation in tomato

    PubMed Central

    Fu, Da-Qi; Meng, Lan-Huan; Zhu, Ben-Zhong; Zhu, Hong-Liang; Yan, Hua-Xue; Luo, Yun-Bo

    2016-01-01

    Ripening is an important stage of fruit development. To screen the genes associated with pigment formation in tomato fruit, a suppression subtractive hybridization (SSH) cDNA library was constructed by using tomato fruit in the green ripe and break ripe stages, and 129 differential genes were obtained. Using redness as a screening marker, virus-induced gene silencing (VIGS) of the differential genes was performed with a sprout vacuum-infiltration system (SVI). The results showed that silencing the SlNAP7 gene affected the chloroplast development of tomato leaves, manifesting as a photo-bleaching phenotype, and silenced fruit significantly affected the accumulation of lycopene, manifested as a yellow phenotype. In our study, we found that silencing the SlNAP7 gene downregulates the expression of the POR and PORA genes and destroys the normal development of the chloroplast. The expression of related genes included in the lycopene biosynthesis pathway was not significantly changed, but lycopene accumulation was significantly reduced in tomato fruit. Perhaps it was caused by the destruction of the chromoplast, which leads to the oxidation of lycopene. The results show that the SlNAP7 gene influences chloroplast development and lycopene accumulation in tomato. PMID:27929131

  1. Aging related methylation influences the gene expression of key control genes in colorectal cancer and adenoma

    PubMed Central

    Galamb, Orsolya; Kalmár, Alexandra; Barták, Barbara Kinga; Patai, Árpád V; Leiszter, Katalin; Péterfia, Bálint; Wichmann, Barnabás; Valcz, Gábor; Veres, Gábor; Tulassay, Zsolt; Molnár, Béla

    2016-01-01

    AIM To analyze colorectal carcinogenesis and age-related DNA methylation alterations of gene sequences associated with epigenetic clock CpG sites. METHODS In silico DNA methylation analysis of 353 epigenetic clock CpG sites published by Steve Horvath was performed using methylation array data for a set of 123 colonic tissue samples [64 colorectal cancer (CRC), 42 adenoma, 17 normal; GEO accession number: GSE48684]. Among the differentially methylated age-related genes, secreted frizzled related protein 1 (SFRP1) promoter methylation was further investigated in colonic tissue from 8 healthy adults, 19 normal children, 20 adenoma and 8 CRC patients using bisulfite-specific PCR followed by methylation-specific high resolution melting (MS-HRM) analysis. mRNA expression of age-related “epigenetic clock” genes was studied using Affymetrix HGU133 Plus2.0 whole transcriptome data of 153 colonic biopsy samples (49 healthy adult, 49 adenoma, 49 CRC, 6 healthy children) (GEO accession numbers: GSE37364, GSE10714, GSE4183, GSE37267). Whole promoter methylation analysis of genes showing inverse DNA methylation-gene expression data was performed on 30 colonic samples using methyl capture sequencing. RESULTS Fifty-seven age-related CpG sites including hypermethylated PPP1R16B, SFRP1, SYNE1 and hypomethylated MGP, PIPOX were differentially methylated between CRC and normal tissues (P < 0.05, Δβ ≥ 10%). In the adenoma vs normal comparison, 70 CpG sites differed significantly, including hypermethylated DKK3, SDC2, SFRP1, SYNE1 and hypomethylated CEMIP, SPATA18 (P < 0.05, Δβ ≥ 10%). In MS-HRM analysis, the SFRP1 promoter region was significantly hypermethylated in CRC (55.0% ± 8.4 %) and adenoma tissue samples (49.9% ± 18.1%) compared to normal adult (5.2% ± 2.7%) and young (2.2% ± 0.7%) colonic tissue (P < 0.0001). DNA methylation of SFRP1 promoter was slightly, but significantly increased in healthy adults compared to normal young samples (P < 0.02). This correlated

  2. Genetic Influences on Brain Gene Expression in Rats Selected for Tameness and Aggression

    PubMed Central

    Heyne, Henrike O.; Lautenschläger, Susann; Nelson, Ronald; Besnier, François; Rotival, Maxime; Cagan, Alexander; Kozhemyakina, Rimma; Plyusnina, Irina Z.; Trut, Lyudmila; Carlborg, Örjan; Petretto, Enrico; Kruglyak, Leonid; Pääbo, Svante; Schöneberg, Torsten; Albert, Frank W.

    2014-01-01

    Interindividual differences in many behaviors are partly due to genetic differences, but the identification of the genes and variants that influence behavior remains challenging. Here, we studied an F2 intercross of two outbred lines of rats selected for tame and aggressive behavior toward humans for >64 generations. By using a mapping approach that is able to identify genetic loci segregating within the lines, we identified four times more loci influencing tameness and aggression than by an approach that assumes fixation of causative alleles, suggesting that many causative loci were not driven to fixation by the selection. We used RNA sequencing in 150 F2 animals to identify hundreds of loci that influence brain gene expression. Several of these loci colocalize with tameness loci and may reflect the same genetic variants. Through analyses of correlations between allele effects on behavior and gene expression, differential expression between the tame and aggressive rat selection lines, and correlations between gene expression and tameness in F2 animals, we identify the genes Gltscr2, Lgi4, Zfp40, and Slc17a7 as candidate contributors to the strikingly different behavior of the tame and aggressive animals. PMID:25189874

  3. Factors influencing law enforcement decisions to adopt an evidence-based robbery prevention program.

    PubMed

    Cabell, A; Casteel, C; Chronister, T; Nocera, M; Vladutiu, C J; Peek-Asa, C

    2013-12-01

    Homicide is the leading cause of workplace death among small retail and service businesses in the United States. Evidence-based programs have been shown to reduce robbery and robbery-related crimes in small retail businesses; however, reaching small businesses with programs has been difficult. As small businesses typically have no corporate backing or trade affiliation, police departments have been identified as potential vehicles for program dissemination. A national sample of 300 law enforcement agencies was surveyed to identify facilitators and barriers to adoption and sustainability of an evidence-based program. The questionnaire was developed using behavioral theory concepts and administered via telephone. Preliminary findings suggest the primary facilitators to program adoption included organizational capacity factors such as staff buy-in, dedicated personnel and financial support. Competing responsibilities was the primary barrier identified by agencies. Agency size and program complexity were identified as potential predictors of program adoption. Identifying agency and program-specific characteristics that influence program adoption by law enforcement agencies will be valuable for marketing programs to agencies that have the infrastructure to support and sustain program dissemination. Understanding these factors will optimize the reach of evidence-based strategies to small businesses.

  4. Identification of key pathways and genes influencing prognosis in bladder urothelial carcinoma

    PubMed Central

    Ning, Xin; Deng, Yaoliang

    2017-01-01

    and cancer prognosis. Conclusion Genes and pathways related to cell cycle and DNA damage and repair may play a crucial role in BUC pathogenesis, whereas those pertaining to tumor angiogenesis may be key factors in influencing BUC prognosis, especially in advanced disease stages. PMID:28356754

  5. The Influence of the Global Gene Expression Shift on Downstream Analyses.

    PubMed

    Xu, Qifeng; Zhang, Xuegong

    2016-01-01

    The assumption that total abundance of RNAs in a cell is roughly the same in different cells is underlying most studies based on gene expression analyses. But experiments have shown that changes in the expression of some master regulators such as c-MYC can cause global shift in the expression of almost all genes in some cell types like cancers. Such shift will violate this assumption and can cause wrong or biased conclusions for standard data analysis practices, such as detection of differentially expressed (DE) genes and molecular classification of tumors based on gene expression. Most existing gene expression data were generated without considering this possibility, and are therefore at the risk of having produced unreliable results if such global shift effect exists in the data. To evaluate this risk, we conducted a systematic study on the possible influence of the global gene expression shift effect on differential expression analysis and on molecular classification analysis. We collected data with known global shift effect and also generated data to simulate different situations of the effect based on a wide collection of real gene expression data, and conducted comparative studies on representative existing methods. We observed that some DE analysis methods are more tolerant to the global shift while others are very sensitive to it. Classification accuracy is not sensitive to the shift and actually can benefit from it, but genes selected for the classification can be greatly affected.

  6. Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula.

    PubMed

    Ingvarsson, Pär K

    2007-03-01

    Codon bias is generally thought to be determined by a balance between mutation, genetic drift, and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes. In this paper, I study associations between codon usage, gene expression, and molecular evolution at synonymous and nonsynonymous sites in the long-lived, woody perennial plant Populus tremula (Salicaceae). Using expression data for 558 genes derived from expressed sequence tags (EST) libraries from 19 different tissues and developmental stages, I study how gene expression levels within single tissues as well as across tissues affect codon usage and rates sequence evolution at synonymous and nonsynonymous sites. I show that gene expression have direct effects on both codon usage and the level of selective constraint of proteins in P. tremula, although in different ways. Codon usage genes is primarily determined by how highly expressed a genes is, whereas rates of sequence evolution are primarily determined by how widely expressed genes are. In addition to the effects of gene expression, protein length appear to be an important factor influencing virtually all aspects of molecular evolution in P. tremula.

  7. Development of Genomic Resources for a thraustochytrid Pathogen and Investigation of Temperature Influences on Gene Expression

    PubMed Central

    Garcia-Vedrenne, Ana Elisa; Groner, Maya; Page-Karjian, Annie; Siegmund, Gregor-Fausto; Singhal, Sonia; Sziklay, Jamie; Roberts, Steven

    2013-01-01

    Understanding how environmental changes influence the pathogenicity and virulence of infectious agents is critical for predicting epidemiological patterns of disease. Thraustochytrids, part of the larger taxonomic class Labyrinthulomycetes, contain several highly pathogenic species, including the hard clam pathogen quahog parasite unknown (QPX). QPX has been associated with large-scale mortality events along the northeastern coast of North America. Growth and physiology of QPX is temperature-dependent, and changes in local temperature profiles influence pathogenicity. In this study we characterize the partial genome of QPX and examine the influence of temperature on gene expression. Genes involved in several biological processes are differentially expressed upon temperature change, including those associated with altered growth and metabolism and virulence. The genomic and transcriptomic resources developed in this study provide a foundation for better understanding virulence, pathogenicity and life history of thraustochytrid pathogens. PMID:24069279

  8. Genes involved in copper resistance influence survival of Pseudomonas aeruginosa on copper surfaces

    PubMed Central

    Elguindi, Jutta; Wagner, Janine; Rensing, Christopher

    2013-01-01

    Aims To evaluate the killing of Pseudomonas aeruginosa PAO1 on copper cast alloys and the influence of genes on survival on copper containing medium and surfaces. Methods and Results Different strains of P. aeruginosa were inoculated on copper containing medium or different copper cast alloys and the survival rate determined. The survival rates were compared to rates on copper-free medium and stainless steel as control. In addition, the effect of temperature on survival was examined. Conclusions Copper cast alloys had previously shown to be bactericidal to various bacteria but the mechanism of copper-mediated killing is still not known. In this report we demonstrate that P. aeruginosa PAO1 is rapidly killed on different copper cast alloys and that genes involved in conferring copper resistance in copper-containing medium also influenced survival on copper cast alloys. We also show that the rate of killing is influenced by temperature. PMID:19239551

  9. QSAR study of 1,4-dihydropyridine calcium channel antagonists based on gene expression programming.

    PubMed

    Si, Hong Zong; Wang, Tao; Zhang, Ke Jun; Hu, Zhi De; Fan, Bo Tao

    2006-07-15

    The gene expression programming, a novel machine learning algorithm, is used to develop quantitative model as a potential screening mechanism for a series of 1,4-dihydropyridine calcium channel antagonists for the first time. The heuristic method was used to search the descriptor space and select the descriptors responsible for activity. A nonlinear, six-descriptor model based on gene expression programming with mean-square errors 0.19 was set up with a predicted correlation coefficient (R2) 0.92. This paper provides a new and effective method for drug design and screening.

  10. Phosphorylation Events in the Multiple Gene Regulator of Group A Streptococcus Significantly Influence Global Gene Expression and Virulence

    PubMed Central

    Sanson, Misu; Makthal, Nishanth; Gavagan, Maire; Cantu, Concepcion; Olsen, Randall J.; Musser, James M.

    2015-01-01

    Whole-genome sequencing analysis of ∼800 strains of group A Streptococcus (GAS) found that the gene encoding the multiple virulence gene regulator of GAS (mga) is highly polymorphic in serotype M59 strains but not in strains of other serotypes. To help understand the molecular mechanism of gene regulation by Mga and its contribution to GAS pathogenesis in serotype M59 GAS, we constructed an isogenic mga mutant strain. Transcriptome studies indicated a significant regulatory influence of Mga and altered metabolic capabilities conferred by Mga-regulated genes. We assessed the phosphorylation status of Mga in GAS cell lysates with Phos-tag gels. The results revealed that Mga is phosphorylated at histidines in vivo. Using phosphomimetic and nonphosphomimetic substitutions at conserved phosphoenolpyruvate:carbohydrate phosphotransferase regulation domain (PRD) histidines of Mga, we demonstrated that phosphorylation-mimicking aspartate replacements at H207 and H273 of PRD-1 and at H327 of PRD-2 are inhibitory to Mga-dependent gene expression. Conversely, non-phosphorylation-mimicking alanine substitutions at H273 and H327 relieved inhibition, and the mutant strains exhibited a wild-type phenotype. The opposing regulatory profiles observed for phosphorylation- and non-phosphorylation-mimicking substitutions at H273 extended to global gene regulation by Mga. Consistent with these observations, the H273D mutant strain attenuated GAS virulence, whereas the H273A strain exhibited a wild-type virulence phenotype in a mouse model of necrotizing fasciitis. Together, our results demonstrate phosphoregulation of Mga and its direct link to virulence in M59 GAS strains. These data also lay a foundation toward understanding how naturally occurring gain-of-function variations in mga, such as H201R, may confer an advantage to the pathogen and contribute to M59 GAS pathogenesis. PMID:25824840

  11. Modelling gene and protein regulatory networks with answer set programming.

    PubMed

    Fayruzov, Timur; Janssen, Jeroen; Vermeir, Dirk; Cornelis, Chris; De Cock, Martine

    2011-01-01

    Recently, many approaches to model regulatory networks have been proposed in the systems biology domain. However, the task is far from being solved. In this paper, we propose an Answer Set Programming (ASP)-based approach to model interaction networks. We build a general ASP framework that describes the network semantics and allows modelling specific networks with little effort. ASP provides a rich and flexible toolbox that allows expanding the framework with desired features. In this paper, we tune our framework to mimic Boolean network behaviour and apply it to model the Budding Yeast and Fission Yeast cell cycle networks. The obtained steady states of these networks correspond to those of the Boolean networks.

  12. Internal and External Influences on Program-Level Curriculum Development in Higher Education Fashion Merchandising Programs

    ERIC Educational Resources Information Center

    King, Janice E.

    2010-01-01

    In an ever changing global economy, higher education experiences accountability issues in educating the workforce. Graduates require the knowledge and skills necessary to succeed in the global workplace. For graduates to have the opportunity to attain this understanding and expertise, it is critical to identify what influences curriculum…

  13. Random transposon mutagenesis of the Saccharopolyspora erythraea genome reveals additional genes influencing erythromycin biosynthesis

    PubMed Central

    Fedashchin, Andrij; Cernota, William H.; Gonzalez, Melissa C.; Leach, Benjamin I.; Kwan, Noelle; Wesley, Roy K.; Weber, J. Mark

    2015-01-01

    A single cycle of strain improvement was performed in Saccharopolyspora erythraea mutB and 15 genotypes influencing erythromycin production were found. Genotypes generated by transposon mutagenesis appeared in the screen at a frequency of ∼3%. Mutations affecting central metabolism and regulatory genes were found, as well as hydrolases, peptidases, glycosyl transferases and unknown genes. Only one mutant retained high erythromycin production when scaled-up from micro-agar plug fermentations to shake flasks. This mutant had a knockout of the cwh1 gene (SACE_1598), encoding a cell-wall-associated hydrolase. The cwh1 knockout produced visible growth and morphological defects on solid medium. This study demonstrated that random transposon mutagenesis uncovers strain improvement-related genes potentially useful for strain engineering. PMID:26468041

  14. Factors influencing participant enrolment in a diabetes prevention program in general practice: lessons from the Sydney diabetes prevention program

    PubMed Central

    2012-01-01

    Background The effectiveness of lifestyle interventions in reducing diabetes incidence has been well established. Little is known, however, about factors influencing the reach of diabetes prevention programs. This study examines the predictors of enrolment in the Sydney Diabetes Prevention Program (SDPP), a community-based diabetes prevention program conducted in general practice, New South Wales, Australia from 2008–2011. Methods SDPP was an effectiveness trial. Participating general practitioners (GPs) from three Divisions of General Practice invited individuals aged 50–65 years without known diabetes to complete the Australian Type 2 Diabetes Risk Assessment tool. Individuals at high risk of diabetes were invited to participate in a lifestyle modification program. A multivariate model using generalized estimating equations to control for clustering of enrolment outcomes by GPs was used to examine independent predictors of enrolment in the program. Predictors included age, gender, indigenous status, region of birth, socio-economic status, family history of diabetes, history of high glucose, use of anti-hypertensive medication, smoking status, fruit and vegetable intake, physical activity level and waist measurement. Results Of the 1821 eligible people identified as high risk, one third chose not to enrol in the lifestyle program. In multivariant analysis, physically inactive individuals (OR: 1.48, P = 0.004) and those with a family history of diabetes (OR: 1.67, P = 0.000) and history of high blood glucose levels (OR: 1.48, P = 0.001) were significantly more likely to enrol in the program. However, high risk individuals who smoked (OR: 0.52, P = 0.000), were born in a country with high diabetes risk (OR: 0.52, P = 0.000), were taking blood pressure lowering medications (OR: 0.80, P = 0.040) and consumed little fruit and vegetables (OR: 0.76, P = 0.047) were significantly less likely to take up the program. Conclusions Targeted

  15. Pain interference in individuals in driver intervention programs for driving under the influence offenders.

    PubMed

    Ilgen, Mark Andrew; McLouth, Christopher; Barry, Kristen L; Walton, Maureen; Cole, Phyllis A; Dabrowski, Michael P; Booth, Brenda M; Blow, Frederic C

    2010-07-01

    Pain-related problems among individuals in court-mandated Driver Intervention Programs (DIPs) for "driving under the influence" (DUI) offenders have not been well studied. This project examines 3,189 individuals from a DIP in Dayton, Ohio. Over 11% of participants reported significant pain-related interference in the past 4 weeks. Pain was significantly more likely in those with depression, more childhood conduct problems, and recent use of multiple illicit drugs. Many individuals seen in court-mandated DIP programs for DUI offenders also report difficulties with pain. DIP programming should address pain in relation to substance use and mental health issues.

  16. Influence of maternal health literacy on child participation in social welfare programs: the Philadelphia experience.

    PubMed

    Pati, Susmita; Mohamad, Zeinab; Cnaan, Avital; Kavanagh, Jane; Shea, Judy A

    2010-09-01

    We examined the influence of maternal health literacy on child participation in social welfare programs. In this cohort, 20% of the mothers had inadequate or marginal health literacy. Initially, more than 50% of the families participated in Temporary Assistance for Needy Families (TANF), the Food Stamp Program, and Special Supplemental Nutrition Program for Women, Infants, and Children, whereas fewer than 15% received child care subsidies or public housing. In multivariate regression, TANF participation was more than twice as common among children whose mothers had adequate health literacy compared with children whose mothers had inadequate health literacy.

  17. Influence of Maternal Health Literacy on Child Participation in Social Welfare Programs: The Philadelphia Experience

    PubMed Central

    Mohamad, Zeinab; Cnaan, Avital; Kavanagh, Jane; Shea, Judy A.

    2010-01-01

    We examined the influence of maternal health literacy on child participation in social welfare programs. In this cohort, 20% of the mothers had inadequate or marginal health literacy. Initially, more than 50% of the families participated in Temporary Assistance for Needy Families (TANF), the Food Stamp Program, and Special Supplemental Nutrition Program for Women, Infants, and Children, whereas fewer than 15% received child care subsidies or public housing. In multivariate regression, TANF participation was more than twice as common among children whose mothers had adequate health literacy compared with children whose mothers had inadequate health literacy. PMID:20634468

  18. Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis

    NASA Astrophysics Data System (ADS)

    Kaminski, Naftali; Allard, John D.; Pittet, Jean F.; Zuo, Fengrong; Griffiths, Mark J. D.; Morris, David; Huang, Xiaozhu; Sheppard, Dean; Heller, Renu A.

    2000-02-01

    The molecular mechanisms of pulmonary fibrosis are poorly understood. We have used oligonucleotide arrays to analyze the gene expression programs that underlie pulmonary fibrosis in response to bleomycin, a drug that causes lung inflammation and fibrosis, in two strains of susceptible mice (129 and C57BL/6). We then compared the gene expression patterns in these mice with 129 mice carrying a null mutation in the epithelial-restricted integrin 6 subunit (6/-), which develop inflammation but are protected from pulmonary fibrosis. Cluster analysis identified two distinct groups of genes involved in the inflammatory and fibrotic responses. Analysis of gene expression at multiple time points after bleomycin administration revealed sequential induction of subsets of genes that characterize each response. The availability of this comprehensive data set should accelerate the development of more effective strategies for intervention at the various stages in the development of fibrotic diseases of the lungs and other organs.

  19. Enamel Formation Genes Influence Enamel Microhardness Before and After Cariogenic Challenge

    PubMed Central

    Shimizu, Takehiko; Ho, Bao; Deeley, Kathleen; Briseño-Ruiz, Jessica; Faraco, Italo M.; Schupack, Brett I.; Brancher, João A.; Pecharki, Giovana D.; Küchler, Erika C.; Tannure, Patricia N.; Lips, Andrea; Vieira, Thays C. S.; Patir, Asli; Yildirim, Mine; Poletta, Fernando A.; Mereb, Juan C.; Resick, Judith M.; Brandon, Carla A.; Orioli, Iêda M.; Castilla, Eduardo E.; Marazita, Mary L.; Seymen, Figen; Costa, Marcelo C.; Granjeiro, José M.; Trevilatto, Paula C.; Vieira, Alexandre R.

    2012-01-01

    There is evidence for a genetic component in caries susceptibility, and studies in humans have suggested that variation in enamel formation genes may contribute to caries. For the present study, we used DNA samples collected from 1,831 individuals from various population data sets. Single nucleotide polymorphism markers were genotyped in selected genes (ameloblastin, amelogenin, enamelin, tuftelin, and tuftelin interacting protein 11) that influence enamel formation. Allele and genotype frequencies were compared between groups with distinct caries experience. Associations with caries experience can be detected but they are not necessarily replicated in all population groups and the most expressive results was for a marker in AMELX (p = 0.0007). To help interpret these results, we evaluated if enamel microhardness changes under simulated cariogenic challenges are associated with genetic variations in these same genes. After creating an artificial caries lesion, associations could be seen between genetic variation in TUFT1 (p = 0.006) and TUIP11 (p = 0.0006) with enamel microhardness. Our results suggest that the influence of genetic variation of enamel formation genes may influence the dynamic interactions between the enamel surface and the oral cavity. PMID:23028741

  20. Influence of sex on gene expression in human corneal epithelial cells

    PubMed Central

    Suzuki, Tomo; Richards, Stephen M.; Liu, Shaohui; Jensen, Roderick V.

    2009-01-01

    Purpose Sex-associated differences have been identified in the anatomy, physiology and pathophysiology of the human cornea. We hypothesize that many of these differences are due to fundamental variations in gene expression. Our objective in this study was to determine whether such differences exist in human corneal epithelial cells both in vivo and in vitro. Methods Human corneal epithelial cells were isolated from the corneoscleral rims of male and female donors. Cells were processed either directly for RNA extraction, or first cultured in phenol red-free keratinocyte serum-free media. The RNA samples were examined for differentially expressed mRNAs by using of CodeLink Bioarrays and Affymetrix GeneChips. Data were analyzed with GeneSifter.Net software. Results Our results demonstrate that sex significantly influences the expression of over 600 genes in human corneal epithelial cells in vivo. These genes are involved in a broad spectrum of biologic processes, molecular functions and cellular components, such as metabolic processes, DNA replication, cell migration, RNA binding, oxidoreductase activity and nucleoli. We also identified significant, sex-related effects on gene expression in human corneal epithelial cells in vitro. However, with few exceptions (e.g., X- and Y-linked genes), these sex-related differences in gene expression in vitro were typically different than those in vivo. Conclusions Our findings support our hypothesis that sex-related differences exist in the gene expression of human corneal epithelial cells. Variations in gene expression may contribute to sex-related differences in the prevalence of certain corneal diseases. PMID:20011627

  1. Environmental factors influencing gene transfer agent (GTA) mediated transduction in the subtropical ocean.

    PubMed

    McDaniel, Lauren D; Young, Elizabeth C; Ritchie, Kimberly B; Paul, John H

    2012-01-01

    Microbial genomic sequence analyses have indicated widespread horizontal gene transfer (HGT). However, an adequate mechanism accounting for the ubiquity of HGT has been lacking. Recently, high frequencies of interspecific gene transfer have been documented, catalyzed by Gene Transfer Agents (GTAs) of marine α-Proteobacteria. It has been proposed that the presence of bacterial genes in highly purified viral metagenomes may be due to GTAs. However, factors influencing GTA-mediated gene transfer in the environment have not yet been determined. Several genomically sequenced strains containing complete GTA sequences similar to Rhodobacter capsulatus (RcGTA, type strain) were screened to ascertain if they produced putative GTAs, and at what abundance. Five of nine marine strains screened to date spontaneously produced virus-like particles (VLP's) in stationary phase. Three of these strains have demonstrated gene transfer activity, two of which were documented by this lab. These two strains Roseovarius nubinhibens ISM and Nitratireductor 44B9s, were utilized to produce GTAs designated RnGTA and NrGTA and gene transfer activity was verified in culture. Cell-free preparations of purified RnGTA and NrGTA particles from marked donor strains were incubated with natural microbial assemblages to determine the level of GTA-mediated gene transfer. In conjunction, several ambient environmental parameters were measured including lysogeny indicated by prophage induction. GTA production in culture systems indicated that approximately half of the strains produced GTA-like particles and maximal GTA counts ranged from 10-30% of host abundance. Modeling of GTA-mediated gene transfer frequencies in natural samples, along with other measured environmental variables, indicated a strong relationship between GTA mediated gene transfer and the combined factors of salinity, multiplicity of infection (MOI) and ambient bacterial abundance. These results indicate that GTA-mediated HGT in the

  2. Influence of tetracycline on tetracycline-resistant heterotrophs and tet genes in activated sludge process.

    PubMed

    Yu, Jie; Liu, Dongfang; Li, Kexun

    2015-03-01

    The concentrations of tetracycline-intermediate resistant, tetracycline-resistant heterotrophic bacteria, and total heterotrophic bacteria were examined to assess the influence of tetracycline on tetracycline-resistant heterotrophs by the R2A agar cultivation method in the tetracycline fortified activated sludge process and in the natural background. Results showed that the percentages of both tetracycline-intermediate resistant and tetracycline-resistant heterotrophic bacteria in total heterotrophic bacteria were significantly increased, after tetracycline was fed to activated sludge for a 3 months period under four different operating conditions, as compared with the background. In order to investigate the mechanism of activated sludge resistance to tetracycline, polymerase chain reaction experiments were carried out to analyze the existence and evolution of tet genes in the presence of tetracycline. Results revealed that only tet A and tet B genes out of the 11 target tet genes were observed in tetracycline treated activated sludge while no tet gene was detected in background. This indicated that tet A gene could accumulate in activated sludge with slower and continuous influent, while the accumulation of tet B gene could be attributed to shorter hydraulic retention time. Therefore, it was proposed in this study that tetracycline-resistant genes created by efflux pumps spread earlier and quicker to encode resistance to tetracycline, which facilitated the increase in tetracycline-resistance.

  3. Interethnic differences of cytochrome P450 gene polymorphisms may influence outcome of taxane therapy in Roma and Hungarian populations.

    PubMed

    Szalai, Renata; Ganczer, Alma; Magyari, Lili; Matyas, Petra; Bene, Judit; Melegh, Bela

    2015-12-01

    Taxanes are widely used microtubule-stabilizing chemotherapeutic agents in the treatment of cancers. Several cytochrome P450 gene variants have been proven to influence taxane metabolism and therapy. The purpose of this work was to determine the distribution of genetic variations of CYP1B1, CYP2C8 and CYP3A5 genes as the first report on taxane metabolizer cytochrome P450 gene polymorphisms in Roma and Hungarian populations. A total of 397 Roma and 412 Hungarian healthy subjects were genotyped for CYP1B1 c.4326C > G, CYP2C8 c.792C > G and CYP3A5 c.6986A > G variant alleles by PCR-RFLP assay and direct sequencing. We found significant differences in the frequencies of homozygous variant genotypes of CYP1B1 4326 GG (p = 0.002) and CYP3A5 6986 GG (p < 0.001) between Roma and Hungarian populations. Regarding minor allele frequencies, for CYP2C8 a significantly increased prevalence was found in 792G allele frequency in the Hungarian population compared to the Roma population (5.83% vs. 2.14%, p = 0.001). Our results can be used as possible predictive factors in population specific treatment algorithms to developing effective programs for a better outcome in patients treated with taxanes.

  4. Examining the Influence of Campus Leadership Programs at a Catholic University

    ERIC Educational Resources Information Center

    Whitney, Rich; Meents-DeCaigny, Ellen

    2014-01-01

    This study uses the socially responsible leadership and leadership efficacy scales in the Multi-Institutional Study of Leadership (MSL) to examine leadership programs at one Catholic campus, and their influence on socially responsible leadership and leadership efficacy. Examining students that identified as involved in 14 campus leadership…

  5. Secondary Agricultural Education Program and Human Influences on Career Decision Self-Efficacy

    ERIC Educational Resources Information Center

    Marx, Adam A.; Simonsen, Jon C.; Kitchel, Tracy

    2014-01-01

    The purpose of this study was to determine the relationship between career decision self-efficacy (CDSE) and components of the secondary agricultural education program. Additionally, the authors sought to describe secondary students' CDSE and career decision influences. This study's design was descriptive and relational and incorporated high…

  6. Influence of Multiculturalism on the Study Programs in Malaysian Public Universities: International Students' Perceptions

    ERIC Educational Resources Information Center

    Pandian, Ambigapathy; Baboo, Shanthi Balraj; Mahfoodh, Omer Hassan Ali

    2016-01-01

    In response to the emphasis on the benefits of enhanced multicultural educational experiences of international students in higher education, this study examined international students' perceptions of the influence of multiculturalism on the study programs in Malaysian public universities. Both quantitative and qualitative data were collected. The…

  7. Limitations on Change: Current Conditions Influencing Academic Intransigence in Educational Administration Programs.

    ERIC Educational Resources Information Center

    Logan, Connie Stokes; Pounder, Diana G.

    An analysis of academic intransigence (resistance to change) in educational administrative preparation programs is presented in this paper. Drawing upon two conceptual frameworks, the stakeholder perspective and Porter's (1980) five-force model of industry structure and competitive influence, two factors contributing to academic intransigence are…

  8. Government Influence and Community Involvement on Abstinence-Only Programs in 1999 and 2003

    ERIC Educational Resources Information Center

    Gusrang, Jamie L.; Cheng, Simon

    2010-01-01

    In this study, we compare federal government influence on abstinence-only programs in 1999 and 2003 to better see how shifts in the federal government's sex education polices impacted other government and community actors. Using data from the Sex Education in America Surveys (SEAS), we find that changes in federal policy, particularly after the…

  9. Activating Interpersonal Influence in Health Promotion: A Field Test of Iowa's Program Against Smoking.

    ERIC Educational Resources Information Center

    Burke, Julie A.; And Others

    This study examined a smoking intervention program, which employed group competitions with rewards, to determine its effects on adolescents' smoking-relevant beliefs, their subjective norms, and peer influence. Initially, 1,187 seventh graders in Burlington, Clinton, and Muscatine, Iowa were surveyed in 1984. Data were gathered from a re-survey…

  10. Assessing the Positive Influence of Music Activities in Community Development Programs

    ERIC Educational Resources Information Center

    Dillon, Steve

    2006-01-01

    This article describes a framework for assessing the positive influence of music activities in community development programs. It examines hybrid music, health and rich media approaches to creative case study with the purpose of developing more compelling evidence based advocacy that examines the claims of a causal link. This preliminary study…

  11. Influence Based Learning Program Scientific Learning Approach to Science Students Generic Skills

    ERIC Educational Resources Information Center

    Wahyuni, Ida; Amdani, Khairul

    2016-01-01

    This study aims to determine the influence of scientific approach based learning program (P2BPS) against generic science skills of students. The method used in this research is "quasi experiment" with "two-group pretest posttest" design.The population in this study were all students who take courses in general physics II at the…

  12. The Influence of Precollege Access Programs on Postsecondary Enrollment and Persistence

    ERIC Educational Resources Information Center

    Glennie, Elizabeth J.; Dalton, Ben W.; Knapp, Laura G.

    2015-01-01

    Using a nationally representative longitudinal data-set, we examine the influence of precollege access programs on high school achievement, college preparation, postsecondary enrollment, and postsecondary persistence. Results do not show much difference in the level of academic preparation between participants and non-participants. However,…

  13. Evaluating the Effectiveness of an Intervention Program to Influence Attitudes of Students towards Peers with Disabilities

    ERIC Educational Resources Information Center

    de Boer, Anke; Pijl, Sip Jan; Minnaert, Alexander; Post, Wendy

    2014-01-01

    In this study we examine the effectiveness of an intervention program to influence attitudes of elementary school students towards peers with intellectual, physical and severe physical and intellectual disabilities. A quasi-experimental longitudinal study was designed with an experimental group and a control group, both comprising two rural…

  14. Network Influences on Dissemination of Evidence-Based Guidelines in State Tobacco Control Programs

    ERIC Educational Resources Information Center

    Luke, Douglas A.; Wald, Lana M.; Carothers, Bobbi J.; Bach, Laura E.; Harris, Jenine K.

    2013-01-01

    Little is known regarding the social network relationships that influence dissemination of evidence-based public health practices and policies. In public health, it is critical that evidence-based guidelines, such as the Centers for Disease Control and Prevention's "Best Practices for Comprehensive Tobacco Control Programs," are…

  15. Factors Influencing Rural Elementary School Principals' Decisions Concerning Building-Based Special Education Programming

    ERIC Educational Resources Information Center

    Voss, Terri B.

    2009-01-01

    The decisions rural elementary school principals make related to special education programming at their building sites are influenced by a variety of factors. This study employed a qualitative research methodology to investigate the perspectives of four rural elementary school principals concerning the decision-making processes they use as they…

  16. Structural influence of gene networks on their inference: analysis of C3NET

    PubMed Central

    2011-01-01

    Background The availability of large-scale high-throughput data possesses considerable challenges toward their functional analysis. For this reason gene network inference methods gained considerable interest. However, our current knowledge, especially about the influence of the structure of a gene network on its inference, is limited. Results In this paper we present a comprehensive investigation of the structural influence of gene networks on the inferential characteristics of C3NET - a recently introduced gene network inference algorithm. We employ local as well as global performance metrics in combination with an ensemble approach. The results from our numerical study for various biological and synthetic network structures and simulation conditions, also comparing C3NET with other inference algorithms, lead a multitude of theoretical and practical insights into the working behavior of C3NET. In addition, in order to facilitate the practical usage of C3NET we provide an user-friendly R package, called c3net, and describe its functionality. It is available from https://r-forge.r-project.org/projects/c3net and from the CRAN package repository. Conclusions The availability of gene network inference algorithms with known inferential properties opens a new era of large-scale screening experiments that could be equally beneficial for basic biological and biomedical research with auspicious prospects. The availability of our easy to use software package c3net may contribute to the popularization of such methods. Reviewers This article was reviewed by Lev Klebanov, Joel Bader and Yuriy Gusev. PMID:21696592

  17. Non-coding RNA in control of gene regulatory programs in cardiac development and disease.

    PubMed

    Philippen, Leonne E; Dirkx, Ellen; da Costa-Martins, Paula A; De Windt, Leon J

    2015-12-01

    Organogenesis of the vertebrate heart is a highly specialized process involving progressive specification and differentiation of distinct embryonic cardiac progenitor cell populations driven by specialized gene programming events. Likewise, the onset of pathologies in the adult heart, including cardiac hypertrophy, involves the reactivation of embryonic gene programs. In both cases, these intricate genomic events are temporally and spatially regulated by complex signaling networks and gene regulatory networks. Apart from well-established transcriptional mechanisms, increasing evidence indicates that gene programming in both the developing and the diseased myocardium are under epigenetic control by non-coding RNAs (ncRNAs). MicroRNAs regulate gene expression at the post-transcriptional level, and numerous studies have now established critical roles for this species of tiny RNAs in a broad range of aspects from cardiogenesis towards adult heart failure. Recent reports now also implicate the larger family of long non-coding RNAs (lncRNAs) in these processes as well. Here we discuss the involvement of these two ncRNA classes in proper cardiac development and hypertrophic disease processes of the adult myocardium. This article is part of a Special Issue entitled: Non-coding RNAs.

  18. IL-7 signalling represses Bcl-6 and the TFH gene program.

    PubMed

    McDonald, Paul W; Read, Kaitlin A; Baker, Chandra E; Anderson, Ashlyn E; Powell, Michael D; Ballesteros-Tato, André; Oestreich, Kenneth J

    2016-01-08

    The transcriptional repressor Bcl-6 is linked to the development of both CD4(+) T follicular helper (TFH) and central memory T (TCM) cells. Here, we demonstrate that in response to decreased IL-2 signalling, T helper 1 (TH1) cells upregulate Bcl-6 and co-initiate TFH- and TCM-like gene programs, including expression of the cytokine receptors IL-6Rα and IL-7R. Exposure of this potentially bi-potent cell population to IL-6 favours the TFH gene program, whereas IL-7 signalling represses TFH-associated genes including Bcl6 and Cxcr5, but not the TCM-related genes Klf2 and Sell. Mechanistically, IL-7-dependent activation of STAT5 contributes to Bcl-6 repression. Importantly, antigen-specific IL-6Rα(+)IL-7R(+) CD4(+) T cells emerge from the effector population at late time points post influenza infection. These data support a novel role for IL-7 in the repression of the TFH gene program and evoke a divergent regulatory mechanism by which post-effector TH1 cells may contribute to long-term cell-mediated and humoral immunity.

  19. Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits

    PubMed Central

    González-Prendes, Rayner; Quintanilla, Raquel; Cánovas, Angela; Manunza, Arianna; Figueiredo Cardoso, Tainã; Jordana, Jordi; Noguera, José Luis; Pena, Ramona N.; Amills, Marcel

    2017-01-01

    Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (~104 Mb), SSC5 (~15 Mb) and SSC13 (~137 Mb), while several additional regions were significantly associated with meat quality traits at the chromosome-wide level. There was a low positional concordance between the associations found for LD and GM traits, a feature that reflects the existence of differences in the genetic determinism of meat quality phenotypes in these two muscles. The performance of an eQTL search for SNPs mapping to the regions associated with meat quality traits demonstrated that the GM a* SSC3 and pH24 SSC17 QTL display positional concordance with cis-eQTL regulating the expression of several genes with a potential role on muscle metabolism. PMID:28054563

  20. Influence of testosterone and a novel SARM on gene expression in whole blood of Macaca fascicularis.

    PubMed

    Riedmaier, Irmgard; Tichopad, Ales; Reiter, Martina; Pfaffl, Michael W; Meyer, Heinrich H D

    2009-04-01

    Anabolic hormones, including testosterone, have been suggested as a therapy for aging-related conditions, such as osteoporosis and sarcopenia. These therapies are sometimes associated with severe androgenic side effects. A promising alternative to testosterone replacement therapy are selective androgen receptor modulators (SARMs). SARMs have the potential to mimic the desirable central and peripheral androgenic anabolic effects of testosterone without having its side effects. In this study we evaluated the effects of LGD2941, in comparison to testosterone, on mRNA expression of selected target genes in whole blood in an non-human model. The regulated genes can act as potential blood biomarker candidates in future studies with AR ligands. Cynomolgus monkeys (Macaca fascicularis) were treated either with testosterone or LGD2941 for 90 days in order to compare their effects on mRNA expression in blood. Blood samples were taken before SARM application, on day 16 and on day 90 of treatment. Gene expression of 37 candidate genes was measured using quantitative real-time RT-PCR (qRT-PCR) technology. Our study shows that both testosterone and LGD2941 influence mRNA expression of 6 selected genes out of 37 in whole blood. The apoptosis regulators CD30L, Fas, TNFR1 and TNFR2 and the interleukins IL-12B and IL-15 showed significant changes in gene expression between control and the treatment groups and represent potential biomarkers for androgen receptor ligands in whole blood.

  1. Genetic influences on insight problem solving: the role of catechol-O-methyltransferase (COMT) gene polymorphisms

    PubMed Central

    Jiang, Weili; Shang, Siyuan; Su, Yanjie

    2015-01-01

    People may experience an “aha” moment, when suddenly realizing a solution of a puzzling problem. This experience is called insight problem solving. Several findings suggest that catecholamine-related genes may contribute to insight problem solving, among which the catechol-O-methyltransferase (COMT) gene is the most promising candidate. The current study examined 753 healthy individuals to determine the associations between 7 candidate single nucleotide polymorphisms on the COMT gene and insight problem-solving performance, while considering gender differences. The results showed that individuals carrying A allele of rs4680 or T allele of rs4633 scored significantly higher on insight problem-solving tasks, and the COMT gene rs5993883 combined with gender interacted with correct solutions of insight problems, specifically showing that this gene only influenced insight problem-solving performance in males. This study presents the first investigation of the genetic impact on insight problem solving and provides evidence that highlights the role that the COMT gene plays in insight problem solving. PMID:26528222

  2. Gene Expression Under the Influence: Transcriptional Profiling of Ethanol in the Brain

    PubMed Central

    Contet, Candice

    2013-01-01

    Sensitivity to ethanol intoxication, propensity to drink ethanol and vulnerability to develop alcoholism are all influenced by genetic factors. Conversely, exposure to ethanol or subsequent withdrawal produce gene expression changes, which, in combination with environmental variables, may participate in the emergence of compulsive drinking and relapse. The present review offers an integrated perspective on brain gene expression profiling in rodent models of predisposition to differential ethanol sensitivity or consumption, in rats and mice subjected to acute or chronic ethanol exposure, as well as in human alcoholics. The functional categories over-represented among differentially expressed genes suggest that the transcriptional effects of chronic ethanol consumption contribute to the neuroplasticity and neurotoxicity characteristic of alcoholism. Importantly, ethanol produces distinct transcriptional changes within the different brain regions involved in intoxication, reinforcement and addiction. Special emphasis is put on recent profiling studies that have provided some insights into the molecular mechanisms potentially mediating genome-wide regulation of gene expression by ethanol. In particular, current evidence for a role of transcription factors, chromatin remodeling and microRNAs in coordinating the expression of large sets of genes in animals predisposed to excessive ethanol drinking or exposed to protracted abstinence, as well as in human alcoholics, is presented. Finally, studies that have compared ethanol with other drugs of abuse have highlighted common gene expression patterns that may play a central role in drug addiction. The availability of novel technologies and a focus on mechanistic approaches are shaping the future of ethanol transcriptomics. PMID:24078902

  3. Genetic influences on insight problem solving: the role of catechol-O-methyltransferase (COMT) gene polymorphisms.

    PubMed

    Jiang, Weili; Shang, Siyuan; Su, Yanjie

    2015-01-01

    People may experience an "aha" moment, when suddenly realizing a solution of a puzzling problem. This experience is called insight problem solving. Several findings suggest that catecholamine-related genes may contribute to insight problem solving, among which the catechol-O-methyltransferase (COMT) gene is the most promising candidate. The current study examined 753 healthy individuals to determine the associations between 7 candidate single nucleotide polymorphisms on the COMT gene and insight problem-solving performance, while considering gender differences. The results showed that individuals carrying A allele of rs4680 or T allele of rs4633 scored significantly higher on insight problem-solving tasks, and the COMT gene rs5993883 combined with gender interacted with correct solutions of insight problems, specifically showing that this gene only influenced insight problem-solving performance in males. This study presents the first investigation of the genetic impact on insight problem solving and provides evidence that highlights the role that the COMT gene plays in insight problem solving.

  4. The Influence of Assortativity on the Robustness of Signal-Integration Logic in Gene Regulatory Networks

    PubMed Central

    Pechenick, Dov A.; Payne, Joshua L.; Moore, Jason H.

    2011-01-01

    Gene regulatory networks (GRNs) drive the cellular processes that sustain life. To do so reliably, GRNs must be robust to perturbations, such as gene deletion and the addition or removal of regulatory interactions. GRNs must also be robust to genetic changes in regulatory regions that define the logic of signal-integration, as these changes can affect how specific combinations of regulatory signals are mapped to particular gene expression states. Previous theoretical analyses have demonstrated that the robustness of a GRN is influenced by its underlying topological properties, such as degree distribution and modularity. Another important topological property is assortativity, which measures the propensity with which nodes of similar connectivity are connected to one another. How assortativity influences the robustness of the signal-integration logic of GRNs remains an open question. Here, we use computational models of GRNs to investigate this relationship. We separately consider each of the three dynamical regimes of this model for a variety of degree distributions. We find that in the chaotic regime, robustness exhibits a pronounced increase as assortativity becomes more positive, while in the critical and ordered regimes, robustness is generally less sensitive to changes in assortativity. We attribute the increased robustness to a decrease in the duration of the gene expression pattern, which is caused by a reduction in the average size of a GRN’s in-components. This study provides the first direct evidence that assortativity influences the robustness of the signal-integration logic of computational models of GRNs, illuminates a mechanistic explanation for this influence, and furthers our understanding of the relationship between topology and robustness in complex biological systems. PMID:22155134

  5. Burkholderia cenocepacia ShvR-regulated genes that influence colony morphology, biofilm formation, and virulence.

    PubMed

    Subramoni, Sujatha; Nguyen, David T; Sokol, Pamela A

    2011-08-01

    Burkholderia cenocepacia is an opportunistic pathogen that primarily infects cystic fibrosis (CF) patients. Previously, we reported that ShvR, a LysR regulator, influences colony morphology, virulence, and biofilm formation and regulates the expression of an adjacent 24-kb genomic region encoding 24 genes. In this study, we report the functional characterization of selected genes in this region. A Tn5 mutant with shiny colony morphology was identified with a polar mutation in BCAS0208, predicted to encode an acyl-coenzyme A dehydrogenase. Mutagenesis of BCAS0208 and complementation analyses revealed that BCAS0208 is required for rough colony morphology, biofilm formation, and virulence on alfalfa seedlings. It was not possible to complement with BCAS0208 containing a mutation in the catalytic site. BCAS0201, encoding a putative flavin adenine dinucleotide (FAD)-dependent oxidoreductase, and BCAS0207, encoding a putative citrate synthase, do not influence colony morphology but are required for optimum levels of biofilm formation and virulence. Both BCAS0208 and BCAS0201 contribute to pellicle formation, although individual mutations in each of these genes had no appreciable effect on pellicle formation. A mutant with a polar insertion in BCAS0208 was significantly less virulent in a rat model of chronic lung infection as well as in the alfalfa model. Genes in this region were shown to influence utilization of branched-chain fatty acids, tricarboxylic acid cycle substrates, l-arabinose, and branched-chain amino acids. Together, our data show that the ShvR-regulated genes BCAS0208 to BCAS0201 are required for the rough colony morphotype, biofilm and pellicle formation, and virulence in B. cenocepacia.

  6. Forced Running Endurance Is Influenced by Gene(s) on Mouse Chromosome 10

    PubMed Central

    Kvedaras, Mindaugas; Minderis, Petras; Fokin, Andrej; Ratkevicius, Aivaras; Venckunas, Tomas; Lionikas, Arimantas

    2017-01-01

    Phenotypic diversity between laboratory mouse strains provides a model for studying the underlying genetic mechanisms. The A/J strain performs poorly in various endurance exercise models. The aim of the study was to test if endurance capacity and contractility of the fast- and slow-twitch muscles are affected by the genes on mouse chromosome 10. The C57BL/6J (B6) strain and C57BL/6J-Chr 10A/J/NaJ (B6.A10) consomic strain which carries the A/J chromosome 10 on a B6 strain background were compared. The B6.A10 mice compared to B6 were larger in body weight (p < 0.02): 27.2 ± 1.9 vs. 23.8 ± 2.7 and 23.4 ± 1.9 vs. 22.9 ± 2.3 g, for males and females, respectively, and in male soleus weight (p < 0.02): 9.7 ± 0.4 vs. 8.6 ± 0.9 mg. In the forced running test the B6.A10 mice completed only 64% of the B6 covered distance (p < 0.0001). However, there was no difference in voluntary wheel running (p = 0.6) or in fatigability of isolated soleus (p = 0.24) or extensor digitorum longus (EDL, p = 0.7) muscles. We conclude that chromosome 10 of the A/J strain contributes to reduced endurance performance. We also discuss physiological mechanisms and methodological aspects relevant to interpretation of these findings. PMID:28167917

  7. Identification of landscape features influencing gene flow: How useful are habitat selection models?

    PubMed

    Roffler, Gretchen H; Schwartz, Michael K; Pilgrim, Kristy L; Talbot, Sandra L; Sage, George K; Adams, Layne G; Luikart, Gordon

    2016-07-01

    Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid-range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long-term genetic connectivity.

  8. Identification of landscape features influencing gene flow: How useful are habitat selection models?

    USGS Publications Warehouse

    Roffler, Gretchen H.; Schwartz, Michael K.; Pilgrim, Kristy L.; Talbot, Sandra; Sage, Kevin; Adams, Layne G.; Luikart, Gordon

    2016-01-01

    Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid-range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long-term genetic connectivity.

  9. Multiple OPR genes influence personality traits in substance dependent and healthy subjects in two American populations

    PubMed Central

    Luo, Xingguang; Zuo, Lingjun; Kranzler, Henry; Zhang, Huiping; Wang, Shuang; Gelernter, Joel

    2011-01-01

    Background Personality traits are among the most complex quantitative traits. Certain personality traits are associated with substance dependence (SD); genetic factors may influence both. Associations between opioid receptor (OPR) genes and SD have been reported. This study investigated the relationship between OPR genes and personality traits in a case-control sample. Methods We assessed dimensions of the five-factor model of personality in 556 subjects: 250 with SD [181 European-Americans (EAs) and 69 African-Americans (AAs)] and 306 healthy subjects (266 EAs and 40 AAs). We genotyped 20 OPRM1 markers, 8 OPRD1 markers, and 7 OPRK1 markers, and 38 unlinked ancestry-informative markers in these subjects. The relationships between OPR genes and personality traits were examined using MANCOVA, controlling for gene-gene interaction effects and potential confounders. Associations were decomposed by Roy-Bargmann Stepdown ANCOVA. Results Personality traits were associated as main or interaction effects with the haplotypes, diplotypes, alleles and genotypes at the three OPR genes (0.002genes encoding the mu-, delta-, and kappa-opioid receptors may contribute to variation in personality traits. Further, the three OPR genes have significant interaction effects on personality traits. This work provides additional evidence that personality traits and SD have a partially overlapping genetic basis. PMID:18213616

  10. Multiple OPR genes influence personality traits in substance dependent and healthy subjects in two American populations.

    PubMed

    Luo, Xingguang; Zuo, Lingjun; Kranzler, Henry; Zhang, Huiping; Wang, Shuang; Gelernter, Joel

    2008-10-05

    Personality traits are among the most complex quantitative traits. Certain personality traits are associated with substance dependence (SD); genetic factors may influence both. Associations between opioid receptor (OPR) genes and SD have been reported. This study investigated the relationship between OPR genes and personality traits in a case-control sample. We assessed dimensions of the five-factor model of personality in 556 subjects: 250 with SD [181 European-Americans (EAs) and 69 African-Americans (AAs)] and 306 healthy subjects (266 EAs and 40 AAs). We genotyped 20 OPRM1 markers, 8 OPRD1 markers, and 7 OPRK1 markers, and 38 unlinked ancestry-informative markers in these subjects. The relationships between OPR genes and personality traits were examined using MANCOVA, controlling for gene-gene interaction effects and potential confounders. Associations were decomposed by Roy-Bargmann Stepdown ANCOVA. We found that personality traits were associated as main or interaction effects with the haplotypes, diplotypes, alleles and genotypes at the three OPR genes (0.002 < P < 0.046 from MANCOVA; 0.0004 < P < 0.049 from ANCOVA). Diplotype TTAGGA/TTCAGA at OPRM1 had main effects on Extraversion (P = 0.008), and diplotypes OPRM1(insertion mark)TTCAGA/TTCAGA and OPRD1(insertion mark)CAC/TAC had interaction effects on Openness (P = 0.010) after conservative correction for multiple testing. The present study demonstrates that the genes encoding the mu-, delta-, and kappa-opioid receptors may contribute to variation in personality traits. Further, the three OPR genes have significant interaction effects on personality traits. This work provides additional evidence that personality traits and SD have a partially overlapping genetic basis.

  11. Common genetic variants in NEFL influence gene expression and neuroblastoma risk.

    PubMed

    Capasso, Mario; Diskin, Sharon; Cimmino, Flora; Acierno, Giovanni; Totaro, Francesca; Petrosino, Giuseppe; Pezone, Lucia; Diamond, Maura; McDaniel, Lee; Hakonarson, Hakon; Iolascon, Achille; Devoto, Marcella; Maris, John M

    2014-12-01

    The genetic etiology of sporadic neuroblastoma is still largely obscure. In a genome-wide association study, we identified single-nucleotide polymorphisms (SNP) associated with neuroblastoma at the CASC15, BARD1, LMO1, DUSP12, HSD17B12, HACE1, and LIN28B gene loci, but these explain only a small fraction of neuroblastoma heritability. Other neuroblastoma susceptibility genes are likely hidden among signals discarded by the multiple testing corrections. In this study, we evaluated eight additional genes selected as candidates for further study based on proven involvement in neuroblastoma differentiation. SNPs at these candidate genes were tested for association with disease susceptibility in 2,101 cases and 4,202 controls, with the associations found replicated in an independent cohort of 459 cases and 809 controls. Replicated associations were further studied for cis-effect using gene expression, transient overexpression, silencing, and cellular differentiation assays. The neurofilament gene NEFL harbored three SNPs associated with neuroblastoma (rs11994014: Pcombined = 0.0050; OR, 0.88; rs2979704: Pcombined = 0.0072; OR, 0.87; rs1059111: Pcombined = 0.0049; OR, 0.86). The protective allele of rs1059111 correlated with increased NEFL expression. Biologic investigations showed that ectopic overexpression of NEFL inhibited cell growth specifically in neuroblastoma cells carrying the protective allele. NEFL overexpression also enhanced differentiation and impaired the proliferation and anchorage-independent growth of cells with protective allele and basal NEFL expression, while impairing invasiveness and proliferation of cells homozygous for the risk genotype. Clinically, high levels of NEFL expression in primary neuroblastoma specimens were associated with better overall survival (P = 0.03; HR, 0.68). Our results show that common variants of NEFL influence neuroblastoma susceptibility and they establish that NEFL expression influences disease initiation and

  12. Inside the Black Box of Doctoral Education: What Program Characteristics Influence Doctoral Students' Attrition and Graduation Probabilities?

    ERIC Educational Resources Information Center

    Ehrenberg, Ronald G.; Jakubson, George H.; Groen, Jeffrey A.; So, Eric; Price, Joseph

    2007-01-01

    The Andrew W. Mellon Foundation's Graduate Education Initiative (GEI) provided funding to 54 departments in the humanities and related social sciences during the 1990s to improve their PhD programs. This article estimates the aspects of PhD programs the GEI influenced and how these aspects influenced attrition and graduation probabilities. It uses…

  13. Programmed translational frameshift in the bacteriophage P2 FETUD tail gene operon.

    PubMed

    Christie, Gail E; Temple, Louise M; Bartlett, Becky A; Goodwin, Tina S

    2002-12-01

    The major structural components of the P2 contractile tail are encoded in the FETUD tail gene operon. The sequences of genes F(I) and F(II), encoding the major tail sheath and tail tube proteins, have been reported previously (L. M. Temple, S. L. Forsburg, R. Calendar, and G. E. Christie, Virology 181:353-358, 1991). Sequence analysis of the remainder of this operon and the locations of amber mutations Eam30, Tam5, Tam64, Tam215, Uam25, Uam77, Uam92, and Dam6 and missense mutation Ets55 identified the coding regions for genes E, T, U, and D, completing the sequence determination of the P2 genome. Inspection of the DNA sequence revealed a new open reading frame overlapping the end of the essential tail gene E. Lack of an apparent translation initiation site and identification of a putative sequence for a programmed translational frameshift within the E gene suggested that this new reading frame (E') might be translated as an extension of gene E, following a -1 translational frameshift. Complementation analysis demonstrated that E' was essential for P2 lytic growth. Analysis of fusion polypeptides verified that this reading frame was translated as a -1 frameshift extension of gpE, with a frequency of approximately 10%. The arrangement of these two genes within the tail gene cluster of phage P2 and their coupling via a translational frameshift appears to be conserved among P2-related phages. This arrangement shows a striking parallel to the organization in the tail gene cluster of phage lambda, despite a lack of amino acid sequence similarity between the tail gene products of these phage families.

  14. The Gene Expression Program for the Formation of Wing Cuticle in Drosophila

    PubMed Central

    Adler, Paul N.

    2016-01-01

    The cuticular exoskeleton of insects and other arthropods is a remarkably versatile material with a complex multilayer structure. We made use of the ability to isolate cuticle synthesizing cells in relatively pure form by dissecting pupal wings and we used RNAseq to identify genes expressed during the formation of the adult wing cuticle. We observed dramatic changes in gene expression during cuticle deposition, and combined with transmission electron microscopy, we were able to identify candidate genes for the deposition of the different cuticular layers. Among genes of interest that dramatically change their expression during the cuticle deposition program are ones that encode cuticle proteins, ZP domain proteins, cuticle modifying proteins and transcription factors, as well as genes of unknown function. A striking finding is that mutations in a number of genes that are expressed almost exclusively during the deposition of the envelope (the thin outermost layer that is deposited first) result in gross defects in the procuticle (the thick chitinous layer that is deposited last). An attractive hypothesis to explain this is that the deposition of the different cuticle layers is not independent with the envelope instructing the formation of later layers. Alternatively, some of the genes expressed during the deposition of the envelope could form a platform that is essential for the deposition of all cuticle layers. PMID:27232182

  15. Factors Influencing Engagement, Perceived Usefulness and Behavioral Mechanisms Associated with a Text Message Support Program

    PubMed Central

    Redfern, Julie; Santo, Karla; Coorey, Genevieve; Thakkar, Jay; Hackett, Maree; Thiagalingam, Aravinda; Chow, Clara K.

    2016-01-01

    Introduction Many studies have now demonstrated the efficacy of text messaging in positively changing behaviours. We aimed to identify features and factors that explain the effectiveness of a successful text messaging program in terms of user engagement, perceived usefulness, behavior change and program delivery preferences. Methods Mixed methods qualitative design combining four data sources; (i) analytic data extracted directly from the software system, (ii) participant survey, (iii) focus groups to identify barriers and enablers to implementation and mechanisms of effect and (iv) recruitment screening logs and text message responses to examine engagement. This evaluation was conducted within the TEXT ME trial—a parallel design, single-blind randomized controlled trial (RCT) of 710 patients with coronary heart disease (CHD). Qualitative data were interpreted using inductive thematic analysis. Results 307/352 (87% response rate) of recruited patients with CHD completed the program evaluation survey at six months and 25 participated in a focus group. Factors increasing engagement included (i) ability to save and share messages, (ii) having the support of providers and family, (iii) a feeling of support through participation in the program, (iv) the program being initiated close to the time of a cardiovascular event, (v) personalization of the messages, (vi) opportunity for initial face-to-face contact with a provider and (vii) that program and content was perceived to be from a credible source. Clear themes relating to program delivery were that diet and physical activity messages were most valued, four messages per week was ideal and most participants felt program duration should be provided for at least for six months or longer. Conclusions This study provides context and insight into the factors influencing consumer engagement with a text message program aimed at improving health-related behavior. The study suggests program components that may enhance

  16. How do interactions between early caregiving environment and genes influence health and behavior?

    PubMed

    Letourneau, Nicole; Giesbrecht, Gerald F; Bernier, Francois P; Joschko, Justin

    2014-01-01

    To promote optimal health and behavioral outcomes in children, nurses have long supported parents in providing the best possible care and nurturance to their offspring. A growing body of neuroscience research argues convincingly for the combined influences of genes and early caregiving on producing an individual's unique health and behavioral phenotype. In this article, we systematically review studies that demonstrate the relationship between qualities of early caregiving and genetic propensity to health and behavioral outcomes. From an initial set of 255 articles, 24 articles met our inclusion criteria. The outcomes fall into four distinct groups: hypothalamic-pituitary-adrenal (HPA) response to stress, externalizing behavior, internalizing behavior, and disorganized attachment. In the articles, authors examined genes that code for the 5-hydroxy tryptamine (serotonin) transporter genes linked polymorphic region [5-HTTLPR] serotonin transporter promoter, D4 dopamine receptor, brain-derived neurotrophic factor, and monoamine oxidase A promoter. The reviewed studies suggest that the effect of the early rearing environment on gene expression relates mainly to HPA response to stress, whereas interactions between genes and caregiving mainly relate to behavior and attachment. Findings have implications for nurses focused on advocacy, prevention, and intervention to support the healthy development of children in families faced with adversity.

  17. Language impairment and dyslexia genes influence language skills in children with autism spectrum disorders

    PubMed Central

    Eicher, John D.; Gruen, Jeffrey R.

    2014-01-01

    Language and communication development is a complex process influenced by numerous environmental and genetic factors. Many neurodevelopment disorders include deficits in language and communication skills in their diagnostic criteria, including autism spectrum disorders (ASD), language impairment (LI), and dyslexia. These disorders are polygenic and complex with a significant genetic component contributing to each. The similarity of language phenotypes and comorbidity of these disorders suggest that they may share genetic contributors. To test this, we examined the association of genes previously implicated in dyslexia, LI, and/or language-related traits with language skills in children with ASD. We used genetic and language data collected in the Autism Genome Research Exchange (AGRE) and Simons Simplex Collection (SSC) cohorts to perform a meta-analysis on performance on a receptive vocabulary task. There were associations with LI risk gene ATP2C2 and dyslexia risk gene MRPL19. Additionally, we found suggestive evidence of association with CMIP, GCFC2, KIAA0319L, the DYX2 locus (ACOT13, GPLD1, and FAM65B), and DRD2. Our results show that LI and dyslexia genes also contribute to language traits in children with ASD. These associations add to the growing literature of generalist genes that contribute to multiple related neurobehavioral traits. Future studies should examine whether other genetic contributors may be shared among these disorders and how risk variants interact with each other and the environment to modify clinical presentations. PMID:25448322

  18. Language impairment and dyslexia genes influence language skills in children with autism spectrum disorders.

    PubMed

    Eicher, John D; Gruen, Jeffrey R

    2015-04-01

    Language and communication development is a complex process influenced by numerous environmental and genetic factors. Many neurodevelopment disorders include deficits in language and communication skills in their diagnostic criteria, including autism spectrum disorders (ASD), language impairment (LI), and dyslexia. These disorders are polygenic and complex with a significant genetic component contributing to each. The similarity of language phenotypes and comorbidity of these disorders suggest that they may share genetic contributors. To test this, we examined the association of genes previously implicated in dyslexia, LI, and/or language-related traits with language skills in children with ASD. We used genetic and language data collected in the Autism Genome Research Exchange (AGRE) and Simons Simplex Collection (SSC) cohorts to perform a meta-analysis on performance on a receptive vocabulary task. There were associations with LI risk gene ATP2C2 and dyslexia risk gene MRPL19. Additionally, we found suggestive evidence of association with CMIP, GCFC2, KIAA0319L, the DYX2 locus (ACOT13, GPLD1, and FAM65B), and DRD2. Our results show that LI and dyslexia genes also contribute to language traits in children with ASD. These associations add to the growing literature of generalist genes that contribute to multiple related neurobehavioral traits. Future studies should examine whether other genetic contributors may be shared among these disorders and how risk variants interact with each other and the environment to modify clinical presentations.

  19. Renin-Angiotensin System Gene Variants and Type 2 Diabetes Mellitus: Influence of Angiotensinogen.

    PubMed

    Joyce-Tan, Siew Mei; Zain, Shamsul Mohd; Abdul Sattar, Munavvar Zubaid; Abdullah, Nor Azizan

    2016-01-01

    Genome-wide association studies (GWAS) have been successfully used to call for variants associated with diseases including type 2 diabetes mellitus (T2DM). However, some variants are not included in the GWAS to avoid penalty in multiple hypothetic testing. Thus, candidate gene approach is still useful even at GWAS era. This study attempted to assess whether genetic variations in the renin-angiotensin system (RAS) and their gene interactions are associated with T2DM risk. We genotyped 290 T2DM patients and 267 controls using three genes of the RAS, namely, angiotensin converting enzyme (ACE), angiotensinogen (AGT), and angiotensin II type 1 receptor (AGTR1). There were significant differences in allele frequencies between cases and controls for AGT variants (P = 0.05) but not for ACE and AGTR1. Haplotype TCG of the AGT was associated with increased risk of T2DM (OR 1.92, 95% CI 1.15-3.20, permuted P = 0.012); however, no evidence of significant gene-gene interactions was seen. Nonetheless, our analysis revealed that the associations of the AGT variants with T2DM were independently associated. Thus, this study suggests that genetic variants of the RAS can modestly influence the T2DM risk.

  20. The transcription factor ultraspiracle influences honey bee social behavior and behavior-related gene expression.

    PubMed

    Ament, Seth A; Wang, Ying; Chen, Chieh-Chun; Blatti, Charles A; Hong, Feng; Liang, Zhengzheng S; Negre, Nicolas; White, Kevin P; Rodriguez-Zas, Sandra L; Mizzen, Craig A; Sinha, Saurabh; Zhong, Sheng; Robinson, Gene E

    2012-01-01

    Behavior is among the most dynamic animal phenotypes, modulated by a variety of internal and external stimuli. Behavioral differences are associated with large-scale changes in gene expression, but little is known about how these changes are regulated. Here we show how a transcription factor (TF), ultraspiracle (usp; the insect homolog of the Retinoid X Receptor), working in complex transcriptional networks, can regulate behavioral plasticity and associated changes in gene expression. We first show that RNAi knockdown of USP in honey bee abdominal fat bodies delayed the transition from working in the hive (primarily "nursing" brood) to foraging outside. We then demonstrate through transcriptomics experiments that USP induced many maturation-related transcriptional changes in the fat bodies by mediating transcriptional responses to juvenile hormone. These maturation-related transcriptional responses to USP occurred without changes in USP's genomic binding sites, as revealed by ChIP-chip. Instead, behaviorally related gene expression is likely determined by combinatorial interactions between USP and other TFs whose cis-regulatory motifs were enriched at USP's binding sites. Many modules of JH- and maturation-related genes were co-regulated in both the fat body and brain, predicting that usp and cofactors influence shared transcriptional networks in both of these maturation-related tissues. Our findings demonstrate how "single gene effects" on behavioral plasticity can involve complex transcriptional networks, in both brain and peripheral tissues.

  1. The Transcription Factor Ultraspiracle Influences Honey Bee Social Behavior and Behavior-Related Gene Expression

    PubMed Central

    Chen, Chieh-Chun; Blatti, Charles A.; Hong, Feng; Liang, Zhengzheng S.; Negre, Nicolas; White, Kevin P.; Rodriguez-Zas, Sandra L.; Mizzen, Craig A.; Sinha, Saurabh; Zhong, Sheng; Robinson, Gene E.

    2012-01-01

    Behavior is among the most dynamic animal phenotypes, modulated by a variety of internal and external stimuli. Behavioral differences are associated with large-scale changes in gene expression, but little is known about how these changes are regulated. Here we show how a transcription factor (TF), ultraspiracle (usp; the insect homolog of the Retinoid X Receptor), working in complex transcriptional networks, can regulate behavioral plasticity and associated changes in gene expression. We first show that RNAi knockdown of USP in honey bee abdominal fat bodies delayed the transition from working in the hive (primarily “nursing” brood) to foraging outside. We then demonstrate through transcriptomics experiments that USP induced many maturation-related transcriptional changes in the fat bodies by mediating transcriptional responses to juvenile hormone. These maturation-related transcriptional responses to USP occurred without changes in USP's genomic binding sites, as revealed by ChIP–chip. Instead, behaviorally related gene expression is likely determined by combinatorial interactions between USP and other TFs whose cis-regulatory motifs were enriched at USP's binding sites. Many modules of JH– and maturation-related genes were co-regulated in both the fat body and brain, predicting that usp and cofactors influence shared transcriptional networks in both of these maturation-related tissues. Our findings demonstrate how “single gene effects” on behavioral plasticity can involve complex transcriptional networks, in both brain and peripheral tissues. PMID:22479195

  2. Transcription factor AP-2α regulates acute myeloid leukemia cell proliferation by influencing Hoxa gene expression.

    PubMed

    Ding, Xiaofeng; Yang, Zijian; Zhou, Fangliang; Wang, Fangmei; Li, Xinxin; Chen, Cheng; Li, Xiaofeng; Hu, Xiang; Xiang, Shuanglin; Zhang, Jian

    2013-08-01

    Transcription factor AP-2α mediates transcription of a number of genes implicated in mammalian development, cell proliferation and carcinogenesis. In the current study, we identified Hoxa7, Hoxa9 and Hox cofactor Meis1 as AP-2α target genes, which are involved in myeloid leukemogenesis. Luciferase reporter assays revealed that overexpression of AP-2α activated transcription activities of Hoxa7, Hoxa9 and Meis1, whereas siRNA of AP-2α inhibited their transcription activities. We found that AP-2 binding sites in regulatory regions of three genes activated their transcription by mutant analysis and AP-2α could interact with AP-2 binding sites in vivo by chromatin immunoprecipitation (ChIP). Further results showed that the AP-2α shRNA efficiently inhibited mRNA and protein levels of Hoxa7, Hoxa9 and Meis1 in AML cell lines U937 and HL60. Moreover, decreased expression of AP-2α resulted in a significant reduction in the growth and proliferation of AML cells in vitro. Remarkably, AP-2α knockdown leukemia cells exhibit decreased tumorigenicity in vivo compared with controls. Finally, AP-2α and target genes in clinical acute myeloid leukemia samples of M5b subtype revealed variable expression levels and broadly paralleled expression. These data support a role of AP-2α in mediating the expression of Hoxa genes in acute myeloid leukemia to influence the proliferation and cell survival.

  3. Integer programming-based approach to allocation of reporter genes for cell array analysis.

    PubMed

    Hayashida, Morihiro; Sun, Fuyan; Aburatani, Sachiyo; Horimoto, Katsuhisa; Akutsu, Tatsuya

    2008-01-01

    In this paper, we consider the problem of selecting the most effective set of reporter genes for analysis of biological networks using cell microarrays. We propose two graph theoretic formulations of the reporter gene allocation problem, and show that both problems are hard to approximate. We propose integer programming-based methods for solving practical instances of these problems optimally. We apply them to apoptosis pathway maps, and discuss the biological significance of the result. We also apply them to artificial networks, the result of which shows that optimal solutions can be obtained within several seconds for networks with 10,000 nodes.

  4. Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity.

    PubMed

    Jahanshad, Neda; Rajagopalan, Priya; Hua, Xue; Hibar, Derrek P; Nir, Talia M; Toga, Arthur W; Jack, Clifford R; Saykin, Andrew J; Green, Robert C; Weiner, Michael W; Medland, Sarah E; Montgomery, Grant W; Hansell, Narelle K; McMahon, Katie L; de Zubicaray, Greig I; Martin, Nicholas G; Wright, Margaret J; Thompson, Paul M

    2013-03-19

    Aberrant connectivity is implicated in many neurological and psychiatric disorders, including Alzheimer's disease and schizophrenia. However, other than a few disease-associated candidate genes, we know little about the degree to which genetics play a role in the brain networks; we know even less about specific genes that influence brain connections. Twin and family-based studies can generate estimates of overall genetic influences on a trait, but genome-wide association scans (GWASs) can screen the genome for specific variants influencing the brain or risk for disease. To identify the heritability of various brain connections, we scanned healthy young adult twins with high-field, high-angular resolution diffusion MRI. We adapted GWASs to screen the brain's connectivity pattern, allowing us to discover genetic variants that affect the human brain's wiring. The association of connectivity with the SPON1 variant at rs2618516 on chromosome 11 (11p15.2) reached connectome-wide, genome-wide significance after stringent statistical corrections were enforced, and it was replicated in an independent subsample. rs2618516 was shown to affect brain structure in an elderly population with varying degrees of dementia. Older people who carried the connectivity variant had significantly milder clinical dementia scores and lower risk of Alzheimer's disease. As a posthoc analysis, we conducted GWASs on several organizational and topological network measures derived from the matrices to discover variants in and around genes associated with autism (MACROD2), development (NEDD4), and mental retardation (UBE2A) significantly associated with connectivity. Connectome-wide, genome-wide screening offers substantial promise to discover genes affecting brain connectivity and risk for brain diseases.

  5. Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity

    PubMed Central

    Jahanshad, Neda; Rajagopalan, Priya; Hua, Xue; Hibar, Derrek P.; Nir, Talia M.; Toga, Arthur W.; Jack, Clifford R.; Saykin, Andrew J.; Green, Robert C.; Weiner, Michael W.; Medland, Sarah E.; Montgomery, Grant W.; Hansell, Narelle K.; McMahon, Katie L.; de Zubicaray, Greig I.; Martin, Nicholas G.; Wright, Margaret J.; Thompson, Paul M.; Weiner, Michael; Aisen, Paul; Weiner, Michael; Aisen, Paul; Petersen, Ronald; Jack, Clifford R.; Jagust, William; Trojanowski, John Q.; Toga, Arthur W.; Beckett, Laurel; Green, Robert C.; Saykin, Andrew J.; Morris, John; Liu, Enchi; Green, Robert C.; Montine, Tom; Petersen, Ronald; Aisen, Paul; Gamst, Anthony; Thomas, Ronald G.; Donohue, Michael; Walter, Sarah; Gessert, Devon; Sather, Tamie; Beckett, Laurel; Harvey, Danielle; Gamst, Anthony; Donohue, Michael; Kornak, John; Jack, Clifford R.; Dale, Anders; Bernstein, Matthew; Felmlee, Joel; Fox, Nick; Thompson, Paul; Schuff, Norbert; Alexander, Gene; DeCarli, Charles; Jagust, William; Bandy, Dan; Koeppe, Robert A.; Foster, Norm; Reiman, Eric M.; Chen, Kewei; Mathis, Chet; Morris, John; Cairns, Nigel J.; Taylor-Reinwald, Lisa; Trojanowki, J.Q.; Shaw, Les; Lee, Virginia M.Y.; Korecka, Magdalena; Toga, Arthur W.; Crawford, Karen; Neu, Scott; Saykin, Andrew J.; Foroud, Tatiana M.; Potkin, Steven; Shen, Li; Khachaturian, Zaven; Frank, Richard; Snyder, Peter J.; Molchan, Susan; Kaye, Jeffrey; Quinn, Joseph; Lind, Betty; Dolen, Sara; Schneider, Lon S.; Pawluczyk, Sonia; Spann, Bryan M.; Brewer, James; Vanderswag, Helen; Heidebrink, Judith L.; Lord, Joanne L.; Petersen, Ronald; Johnson, Kris; Doody, Rachelle S.; Villanueva-Meyer, Javier; Chowdhury, Munir; Stern, Yaakov; Honig, Lawrence S.; Bell, Karen L.; Morris, John C.; Ances, Beau; Carroll, Maria; Leon, Sue; Mintun, Mark A.; Schneider, Stacy; Marson, Daniel; Griffith, Randall; Clark, David; Grossman, Hillel; Mitsis, Effie; Romirowsky, Aliza; deToledo-Morrell, Leyla; Shah, Raj C.; Duara, Ranjan; Varon, Daniel; Roberts, Peggy; Albert, Marilyn; Onyike, Chiadi; Kielb, Stephanie; Rusinek, Henry; de Leon, Mony J.; Glodzik, Lidia; De Santi, Susan; Doraiswamy, P. Murali; Petrella, Jeffrey R.; Coleman, R. Edward; Arnold, Steven E.; Karlawish, Jason H.; Wolk, David; Smith, Charles D.; Jicha, Greg; Hardy, Peter; Lopez, Oscar L.; Oakley, MaryAnn; Simpson, Donna M.; Porsteinsson, Anton P.; Goldstein, Bonnie S.; Martin, Kim; Makino, Kelly M.; Ismail, M. Saleem; Brand, Connie; Mulnard, Ruth A.; Thai, Gaby; Mc-Adams-Ortiz, Catherine; Womack, Kyle; Mathews, Dana; Quiceno, Mary; Diaz-Arrastia, Ramon; King, Richard; Weiner, Myron; Martin-Cook, Kristen; DeVous, Michael; Levey, Allan I.; Lah, James J.; Cellar, Janet S.; Burns, Jeffrey M.; Anderson, Heather S.; Swerdlow, Russell H.; Apostolova, Liana; Lu, Po H.; Bartzokis, George; Silverman, Daniel H.S.; Graff-Radford, Neill R.; Parfitt, Francine; Johnson, Heather; Farlow, Martin R.; Hake, Ann Marie; Matthews, Brandy R.; Herring, Scott; van Dyck, Christopher H.; Carson, Richard E.; MacAvoy, Martha G.; Chertkow, Howard; Bergman, Howard; Hosein, Chris; Black, Sandra; Stefanovic, Bojana; Caldwell, Curtis; Hsiung, Ging-Yuek Robin; Feldman, Howard; Mudge, Benita; Assaly, Michele; Kertesz, Andrew; Rogers, John; Trost, Dick; Bernick, Charles; Munic, Donna; Kerwin, Diana; Mesulam, Marek-Marsel; Lipowski, Kristina; Wu, Chuang-Kuo; Johnson, Nancy; Sadowsky, Carl; Martinez, Walter; Villena, Teresa; Turner, Raymond Scott; Johnson, Kathleen; Reynolds, Brigid; Sperling, Reisa A.; Johnson, Keith A.; Marshall, Gad; Frey, Meghan; Yesavage, Jerome; Taylor, Joy L.; Lane, Barton; Rosen, Allyson; Tinklenberg, Jared; Sabbagh, Marwan; Belden, Christine; Jacobson, Sandra; Kowall, Neil; Killiany, Ronald; Budson, Andrew E.; Norbash, Alexander; Johnson, Patricia Lynn; Obisesan, Thomas O.; Wolday, Saba; Bwayo, Salome K.; Lerner, Alan; Hudson, Leon; Ogrocki, Paula; Fletcher, Evan; Carmichael, Owen; Olichney, John; DeCarli, Charles; Kittur, Smita; Borrie, Michael; Lee, T.-Y.; Bartha, Rob; Johnson, Sterling; Asthana, Sanjay; Carlsson, Cynthia M.; Potkin, Steven G.; Preda, Adrian; Nguyen, Dana; Tariot, Pierre; Fleisher, Adam; Reeder, Stephanie; Bates, Vernice; Capote, Horacio; Rainka, Michelle; Scharre, Douglas W.; Kataki, Maria; Zimmerman, Earl A.; Celmins, Dzintra; Brown, Alice D.; Pearlson, Godfrey D.; Blank, Karen; Anderson, Karen; Saykin, Andrew J.; Santulli, Robert B.; Schwartz, Eben S.; Sink, Kaycee M.; Williamson, Jeff D.; Garg, Pradeep; Watkins, Franklin; Ott, Brian R.; Querfurth, Henry; Tremont, Geoffrey; Salloway, Stephen; Malloy, Paul; Correia, Stephen; Rosen, Howard J.; Miller, Bruce L.; Mintzer, Jacobo; Longmire, Crystal Flynn; Spicer, Kenneth; Finger, Elizabeth; Rachinsky, Irina; Rogers, John; Kertesz, Andrew; Drost, Dick

    2013-01-01

    Aberrant connectivity is implicated in many neurological and psychiatric disorders, including Alzheimer’s disease and schizophrenia. However, other than a few disease-associated candidate genes, we know little about the degree to which genetics play a role in the brain networks; we know even less about specific genes that influence brain connections. Twin and family-based studies can generate estimates of overall genetic influences on a trait, but genome-wide association scans (GWASs) can screen the genome for specific variants influencing the brain or risk for disease. To identify the heritability of various brain connections, we scanned healthy young adult twins with high-field, high-angular resolution diffusion MRI. We adapted GWASs to screen the brain’s connectivity pattern, allowing us to discover genetic variants that affect the human brain’s wiring. The association of connectivity with the SPON1 variant at rs2618516 on chromosome 11 (11p15.2) reached connectome-wide, genome-wide significance after stringent statistical corrections were enforced, and it was replicated in an independent subsample. rs2618516 was shown to affect brain structure in an elderly population with varying degrees of dementia. Older people who carried the connectivity variant had significantly milder clinical dementia scores and lower risk of Alzheimer’s disease. As a posthoc analysis, we conducted GWASs on several organizational and topological network measures derived from the matrices to discover variants in and around genes associated with autism (MACROD2), development (NEDD4), and mental retardation (UBE2A) significantly associated with connectivity. Connectome-wide, genome-wide screening offers substantial promise to discover genes affecting brain connectivity and risk for brain diseases. PMID:23471985

  6. Organic carbon source in formulated sediments influences life traits and gene expression of Caenorhabditis elegans.

    PubMed

    Franzen, Julia; Menzel, Ralph; Höss, Sebastian; Claus, Evelyn; Steinberg, Christian E W

    2012-03-01

    River water quality is strongly influenced by their sediments and their associated pollutants. To assess the toxic potential of sediments, sediment toxicity tests require reliable control sediments, potentially including formulated control sediments as one major option. Although some standardization has been carried out, one critical issue still remains the quality of sediment organic matter (SOM). Organic carbon not only binds hydrophobic contaminants, but may be a source of mild toxicity, even if the SOM is essentially uncontaminated. We tested two different sources of organic carbon and the mixture of both (Sphagnum peat (P) and one commercial humic substances preparation-HuminFeed(®), HF) in terms of life trait variables and expression profiles of selected life performance and stress genes of the nematode Caenorhabditis elegans. In synchronous cultures, gene expression profiling was done after 6 and 48 h, respectively. The uncontaminated Sphagnum P reduced growth, but increased numbers of offspring, whereas HF did not significantly alter life trait variables. The 6 h expression profile showed most of the studied stress genes repressed, except for slight to strong induction in cyp-35B1 (all exposures), gst-38 (only mixture), and small hsp-16 genes (all exposures). After 48 h, the expression of almost all studied genes increased, particularly genes coding for antioxidative defense, multiple xenobiotic resistance, vitellogenin-like proteins, and genes regulating lifespan. Overall, even essentially uncontaminated SOM may induce several modes of action on the molecular level in C. elegans which may lead to false results if testing synthetic xenobiotics. This contribution is a plea for a strict standardization of the SOM quality in formulated sediments and to check for corresponding effects in other model sediment organisms, especially if using molecular toxicity endpoints.

  7. MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance.

    PubMed

    McGivney, Beatrice A; Browne, John A; Fonseca, Rita G; Katz, Lisa M; Machugh, David E; Whiston, Ronan; Hill, Emmeline W

    2012-12-01

    Myostatin, encoded by the MSTN gene, is a member of the TGF-β superfamily that regulates skeletal muscle development. A MSTN SNP significantly associated with Thoroughbred horse racing phenotypes has recently been identified as well as significant reductions in Thoroughbred skeletal muscle gene expression for three transcripts 400-1500 base pairs downstream of the MSTN gene following a period of training. Together, these findings indicate that MSTN genotypes may influence MSTN gene expression. To investigate this, MSTN mRNA expression was measured in biopsies from the middle gluteal muscle from 60 untrained yearling Thoroughbreds (C/C, n = 15; C/T, n = 28; T/T, n = 17) using two independent real-time qRT-PCR assays. MSTN gene expression was also evaluated in a subset (N = 33) of these animals using samples collected after a ten-month period of training. A significant association was observed between genotype and mRNA abundance for the untrained horses (assay I, P = 0.0237; assay II, P = 0.003559), with the C/C cohort having the highest MSTN mRNA levels, the T/T group the lowest levels and the C/T group intermediate levels. Following training, there was a significant decrease in MSTN mRNA (-3.35-fold; P = 6.9 × 10(-7) ), which was most apparent for the C/C cohort (-5.88-fold, P = 0.001). These data demonstrate the tight relationship between phenotype, genotype and gene expression at the MSTN gene in Thoroughbred racehorses.

  8. Evidence for a major gene influencing 7-year increases in diastolic blood pressure with age

    SciTech Connect

    Li Shu-Chuan Cheng; Carmelli, D.; Hunt, S.C.

    1995-11-01

    The contribution of genetic factors to blood pressure levels is well established. The contribution of genes to the longitudinal change in blood pressure has been less well studied, because of the lack of longitudinal family data. The present study investigated a possible major-gene effect on the observed increase with age in diastolic blood pressure (DBP) levels. Subjects included 965 unmedicated adults (age {ge}18 years) in 73 pedigrees collected in Utah as part of a longitudinal cardiovascular family study. Segregation analysis of DBP change over 7.2 years of follow-up identified a recessive major-gene effect with a gene frequency of p = .23. There was also a significant age effect on the genotypic means, which decreased expression of the major gene at older ages. For those inferred to have the genotype responsible for large DBP increases, DBP increased 32.3%, compared with a 1.5% increase in the nonsusceptible group (P < .0001). The relative risk of developing hypertension between the susceptible and nonsusceptible groups after 7.2 years was 2.4 (P = .006). Baseline DBP reactivities to mental arithmetic (P < .0001) and isometric hand-grip (P < .0001) stress tests were greatest in those assigned to the susceptible genotype. We conclude that age-related changes in DBP are influenced by a major gene. Characteristics of this major-gene effect for greater age-related blood pressure increases include greater reactivity to mental and physical stressors. The present study thus provides evidence for genetic control of changes in blood pressure, in addition to the previously suggested genetic control of absolute blood pressure level. 28 refs., 6 tabs.

  9. Identification of human gene structure using linear discriminant functions and dynamic programming

    SciTech Connect

    Solovyev, V.V.; Salamov, A.A.; Lawrence, C.B.

    1995-12-31

    Development of advanced technique to identify gene structure is one of the main challenges of the Human Genome Project. Discriminant analysis was applied to the construction of recognition functions for various components of gene structure. Linear discriminant functions for splice sites, 5{prime}-coding, internal exon, and Y-coding region recognition have been developed. A gene structure prediction system FGENE has been developed based on the exon recognition functions. We compute a graph of mutual compatibility of different exons and present a gene structure models as paths of this directed acyclic graph. For an optimal model selection we apply a variant of dynamic programming algorithm to search for the path in the graph with the maximal value of the corresponding discriminant functions. Prediction by FGENE for 185 complete human gene sequences has 81% exact exon recognition accuracy and 91% accuracy at the level of individual exon nucleotides with the correlation coefficient (C) equals 0.90. Testing FGENE on 35 genes not used in the development of discriminant functions shows 71% accuracy of exact exon prediction and 89% at the nucleotide level (C=0.86). FGENE compares very favorably with the other programs currently used to predict protein-coding regions. Analysis of uncharacterized human sequences based on our methods for splice site (HSPL, RNASPL), internal exons (HEXON), all type of exons (FEXH) and human (FGENEH) and bacterial (CDSB) gene structure prediction and recognition of human and bacterial sequences (HBR) (to test a library for E. coli contamination) is available through the University of Houston, Weizmann Institute of Science network server and a WWW page of the Human Genome Center at Baylor College of Medicine.

  10. Gene-gene interactions in the folate metabolic pathway influence the risk for acute lymphoblastic leukemia in children.

    PubMed

    Petra, Bohanec Grabar; Janez, Jazbec; Vita, Dolzan

    2007-04-01

    Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer. Genetic polymorphisms in the folate metabolic pathway may contribute to the susceptibility to childhood ALL because they affect the DNA synthesis, methylation and repair. We analysed common genetic polymorphisms of 5,10-methylenetetrahydrofolate reductase (MTHFR), thymidylate synthase (TS), methionine synthase (MS) and methionine synthase reductase (MTRR) in 68 children with ALL and 258 healthy controls to investigate their influence on the risk for ALL. No significant differences in frequencies of separate polymorphisms were observed between both groups. Combined MTHFR 677CT/TT and MS 2756AG/GG genotypes showed a nonsignificant tendency to reduce the risk for ALL 2.24-fold (CI: 0.191 - 1.037, P: 0.061). The risk was significantly reduced in carriers of combined MTHFR 677CT/TT, MS 2756AG/GG and MTRR 66AG/GG genotypes (OR: 0.312; CI: 0.107 - 0.907; P: 0.032). Our results suggest that gene - gene interactions that may decrease the methylation capacity might have a protective effect on the risk for childhood ALL.

  11. Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.

    PubMed

    McIsaac, R Scott; Gibney, Patrick A; Chandran, Sunil S; Benjamin, Kirsten R; Botstein, David

    2014-04-01

    A conditional gene expression system that is fast-acting, is tunable and achieves single-gene specificity was recently developed for yeast. A gene placed directly downstream of a modified GAL1 promoter containing six Zif268 binding sequences (with single nucleotide spacing) was shown to be selectively inducible in the presence of β-estradiol, so long as cells express the artificial transcription factor, Z3EV (a fusion of the Zif268 DNA binding domain, the ligand binding domain of the human estrogen receptor and viral protein 16). We show the strength of Z3EV-responsive promoters can be modified using straightforward design principles. By moving Zif268 binding sites toward the transcription start site, expression output can be nearly doubled. Despite the reported requirement of estrogen receptor dimerization for hormone-dependent activation, a single binding site suffices for target gene activation. Target gene expression levels correlate with promoter binding site copy number and we engineer a set of inducible promoter chassis with different input-output characteristics. Finally, the coupling between inducer identity and gene activation is flexible: the ligand specificity of Z3EV can be re-programmed to respond to a non-hormone small molecule with only five amino acid substitutions in the human estrogen receptor domain, which may prove useful for industrial applications.

  12. Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae

    PubMed Central

    McIsaac, R. Scott; Gibney, Patrick A.; Chandran, Sunil S.; Benjamin, Kirsten R.; Botstein, David

    2014-01-01

    A conditional gene expression system that is fast-acting, is tunable and achieves single-gene specificity was recently developed for yeast. A gene placed directly downstream of a modified GAL1 promoter containing six Zif268 binding sequences (with single nucleotide spacing) was shown to be selectively inducible in the presence of β-estradiol, so long as cells express the artificial transcription factor, Z3EV (a fusion of the Zif268 DNA binding domain, the ligand binding domain of the human estrogen receptor and viral protein 16). We show the strength of Z3EV-responsive promoters can be modified using straightforward design principles. By moving Zif268 binding sites toward the transcription start site, expression output can be nearly doubled. Despite the reported requirement of estrogen receptor dimerization for hormone-dependent activation, a single binding site suffices for target gene activation. Target gene expression levels correlate with promoter binding site copy number and we engineer a set of inducible promoter chassis with different input–output characteristics. Finally, the coupling between inducer identity and gene activation is flexible: the ligand specificity of Z3EV can be re-programmed to respond to a non-hormone small molecule with only five amino acid substitutions in the human estrogen receptor domain, which may prove useful for industrial applications. PMID:24445804

  13. Influence of a quality improvement learning collaborative program on team functioning in primary healthcare.

    PubMed

    Kotecha, Jyoti; Brown, Judith Belle; Han, Han; Harris, Stewart B; Green, Michael; Russell, Grant; Roberts, Sharon; Webster-Bogaert, Susan; Fournie, Meghan; Thind, Amardeep; Reichert, Sonja M; Birtwhistle, Richard

    2015-09-01

    Quality improvement (QI) programs are frequently implemented to support primary healthcare (PHC) team development and to improve care outcomes. In Ontario, Canada, the Quality Improvement and Innovation Partnership (QIIP) offered a learning collaborative (LC) program to support the development of interdisciplinary team function and improve chronic disease management, disease prevention, and access to care. A qualitative study using a phenomenological approach was conducted as part of a mixed-method evaluation to explore the influence of the program on team functioning in participating PHC teams. A purposive sampling strategy was used to identify PHC teams (n = 10), from which participants of different professional roles were selected through a purposeful recruitment process to reflect maximum variation of team roles. Additionally, QI coaches working with the interview participants and the LC administrators were also interviewed. Data were collected through semistructured telephone interviews that were audiotaped and transcribed verbatim. Thematic analysis was conducted through an iterative and interpretive approach. The shared experience of participating in the program appeared to improve team functioning. Participants described increased trust and respect for each other's clinical and administrative roles and were inspired by learning about different approaches to interdisciplinary care. This appeared to enhance collegial relationships, collapse professional silos, improve communication, and increase interdisciplinary collaboration. Teamwork involves more than just physically grouping healthcare providers from multiple disciplines and mandating them to work together. The LC program provided opportunities for participants to learn how to work collaboratively, and participation in the LC program appeared to enhance team functioning.

  14. Epigenetic Influence of Dam Methylation on Gene Expression and Attachment in Uropathogenic Escherichia coli

    PubMed Central

    Stephenson, Stacy Ann-Marie; Brown, Paul D.

    2016-01-01

    Urinary tract infections (UTI) are among the most frequently encountered infections in clinical practice globally. Predominantly a burden among female adults and infants, UTIs primarily caused by uropathogenic Escherichia coli (UPEC) results in high morbidity and fiscal health strains. During pathogenesis, colonization of the urinary tract via fimbrial adhesion to mucosal cells is the most critical point in infection and has been linked to DNA methylation. Furthermore, with continuous exposure to antibiotics as the standard therapeutic strategy, UPEC has evolved to become highly adaptable in circumventing the effect of antimicrobial agents and host defenses. Hence, the need for alternative treatment strategies arises. Since differential DNA methylation is observed as a critical precursor to virulence in various pathogenic bacteria, this body of work sought to assess the influence of the DNA adenine methylase (dam) gene on gene expression and cellular adhesion in UPEC and its potential as a therapeutic target. To monitor the influence of dam on attachment and FQ resistance, selected UPEC dam mutants created via one-step allelic exchange were transformed with cloned qnrA and dam complement plasmid for comparative analysis of growth rate, antimicrobial susceptibility, biofilm formation, gene expression, and mammalian cell attachment. The absence of DNA methylation among dam mutants was apparent. Varying deficiencies in cell growth, antimicrobial resistance and biofilm formation, alongside low-level increases in gene expression (recA and papI), and adherence to HEK-293 and HTB-9 mammalian cells were also detected as a factor of SOS induction to result in increased mutability. Phenotypic characteristics of parental strains were restored in dam complement strains. Dam’s vital role in DNA methylation and gene expression in local UPEC isolates was confirmed. Similarly to dam-deficient Enterohemorrhagic E. coli (EHEC), these findings suggest unsuccessful therapeutic use

  15. Epigenetic Influence of Dam Methylation on Gene Expression and Attachment in Uropathogenic Escherichia coli.

    PubMed

    Stephenson, Stacy Ann-Marie; Brown, Paul D

    2016-01-01

    Urinary tract infections (UTI) are among the most frequently encountered infections in clinical practice globally. Predominantly a burden among female adults and infants, UTIs primarily caused by uropathogenic Escherichia coli (UPEC) results in high morbidity and fiscal health strains. During pathogenesis, colonization of the urinary tract via fimbrial adhesion to mucosal cells is the most critical point in infection and has been linked to DNA methylation. Furthermore, with continuous exposure to antibiotics as the standard therapeutic strategy, UPEC has evolved to become highly adaptable in circumventing the effect of antimicrobial agents and host defenses. Hence, the need for alternative treatment strategies arises. Since differential DNA methylation is observed as a critical precursor to virulence in various pathogenic bacteria, this body of work sought to assess the influence of the DNA adenine methylase (dam) gene on gene expression and cellular adhesion in UPEC and its potential as a therapeutic target. To monitor the influence of dam on attachment and FQ resistance, selected UPEC dam mutants created via one-step allelic exchange were transformed with cloned qnrA and dam complement plasmid for comparative analysis of growth rate, antimicrobial susceptibility, biofilm formation, gene expression, and mammalian cell attachment. The absence of DNA methylation among dam mutants was apparent. Varying deficiencies in cell growth, antimicrobial resistance and biofilm formation, alongside low-level increases in gene expression (recA and papI), and adherence to HEK-293 and HTB-9 mammalian cells were also detected as a factor of SOS induction to result in increased mutability. Phenotypic characteristics of parental strains were restored in dam complement strains. Dam's vital role in DNA methylation and gene expression in local UPEC isolates was confirmed. Similarly to dam-deficient Enterohemorrhagic E. coli (EHEC), these findings suggest unsuccessful therapeutic use of

  16. Distributed Function Mining for Gene Expression Programming Based on Fast Reduction

    PubMed Central

    Deng, Song; Yue, Dong; Yang, Le-chan; Fu, Xiong; Feng, Ya-zhou

    2016-01-01

    For high-dimensional and massive data sets, traditional centralized gene expression programming (GEP) or improved algorithms lead to increased run-time and decreased prediction accuracy. To solve this problem, this paper proposes a new improved algorithm called distributed function mining for gene expression programming based on fast reduction (DFMGEP-FR). In DFMGEP-FR, fast attribution reduction in binary search algorithms (FAR-BSA) is proposed to quickly find the optimal attribution set, and the function consistency replacement algorithm is given to solve integration of the local function model. Thorough comparative experiments for DFMGEP-FR, centralized GEP and the parallel gene expression programming algorithm based on simulated annealing (parallel GEPSA) are included in this paper. For the waveform, mushroom, connect-4 and musk datasets, the comparative results show that the average time-consumption of DFMGEP-FR drops by 89.09%%, 88.85%, 85.79% and 93.06%, respectively, in contrast to centralized GEP and by 12.5%, 8.42%, 9.62% and 13.75%, respectively, compared with parallel GEPSA. Six well-studied UCI test data sets demonstrate the efficiency and capability of our proposed DFMGEP-FR algorithm for distributed function mining. PMID:26751200

  17. Paternal Low Protein Diet Programs Preimplantation Embryo Gene Expression, Fetal Growth and Skeletal Development in Mice.

    PubMed

    Watkins, Adam J; Sirovica, Slobodan; Stokes, Ben; Isaacs, Mark; Addison, Owen; Martin, Richard A

    2017-02-08

    Defining the mechanisms underlying the programming of early life growth is fundamental for improving adult health and wellbeing. While the association between maternal diet, offspring growth and adult disease risk is well-established, the effect of father's diet on offspring development are largely unknown. Therefore, we fed male mice an imbalanced low protein diet (LPD) to determine the impact on post-fertilisation development and fetal growth. We observed that in preimplantation embryos derived from LPD fed males, expression of multiple genes within the central metabolic AMPK pathway was reduced. In late gestation, paternal LPD programmed increased fetal weight, however, placental weight was reduced, resulting in an elevated fetal:placental weight ratio. Analysis of gene expression patterns revealed increased levels of transporters for calcium, amino acids and glucose within LPD placentas. Furthermore, placental expression of the epigenetic regulators Dnmt1 and Dnmt3L were increased also, coinciding with altered patterns of maternal and paternal imprinted genes. More strikingly, we observed fetal skeletal development was perturbed in response to paternal LPD. Here, while offspring of LPD fed males possessed larger skeletons, their bones comprised lower volumes of high mineral density in combination with reduced maturity of bone apatite. These data offer new insight in the underlying programming mechanisms linking poor paternal diet at the time of conception with the development and growth of his offspring.

  18. Distributed Function Mining for Gene Expression Programming Based on Fast Reduction.

    PubMed

    Deng, Song; Yue, Dong; Yang, Le-chan; Fu, Xiong; Feng, Ya-zhou

    2016-01-01

    For high-dimensional and massive data sets, traditional centralized gene expression programming (GEP) or improved algorithms lead to increased run-time and decreased prediction accuracy. To solve this problem, this paper proposes a new improved algorithm called distributed function mining for gene expression programming based on fast reduction (DFMGEP-FR). In DFMGEP-FR, fast attribution reduction in binary search algorithms (FAR-BSA) is proposed to quickly find the optimal attribution set, and the function consistency replacement algorithm is given to solve integration of the local function model. Thorough comparative experiments for DFMGEP-FR, centralized GEP and the parallel gene expression programming algorithm based on simulated annealing (parallel GEPSA) are included in this paper. For the waveform, mushroom, connect-4 and musk datasets, the comparative results show that the average time-consumption of DFMGEP-FR drops by 89.09%%, 88.85%, 85.79% and 93.06%, respectively, in contrast to centralized GEP and by 12.5%, 8.42%, 9.62% and 13.75%, respectively, compared with parallel GEPSA. Six well-studied UCI test data sets demonstrate the efficiency and capability of our proposed DFMGEP-FR algorithm for distributed function mining.

  19. Determinants of nucleosome positioning and their influence on plant gene expression.

    PubMed

    Liu, Ming-Jung; Seddon, Alexander E; Tsai, Zing Tsung-Yeh; Major, Ian T; Floer, Monique; Howe, Gregg A; Shiu, Shin-Han

    2015-08-01

    Nucleosome positioning influences the access of transcription factors (TFs) to their binding sites and gene expression. Studies in plant, animal, and fungal models demonstrate similar nucleosome positioning patterns along genes and correlations between occupancy and expression. However, the relationships among nucleosome positioning, cis-regulatory element accessibility, and gene expression in plants remain undefined. Here we showed that plant nucleosome depletion occurs on specific 6-mer motifs and this sequence-specific nucleosome depletion is predictive of expression levels. Nucleosome-depleted regions in Arabidopsis thaliana tend to have higher G/C content, unlike yeast, and are centered on specific G/C-rich 6-mers, suggesting that intrinsic sequence properties, such as G/C content, cannot fully explain plant nucleosome positioning. These 6-mer motif sites showed higher DNase I hypersensitivity and are flanked by strongly phased nucleosomes, consistent with known TF binding sites. Intriguingly, this 6-mer-specific nucleosome depletion pattern occurs not only in promoter but also in genic regions and is significantly correlated with higher gene expression level, a phenomenon also found in rice but not in yeast. Among the 6-mer motifs enriched in genes responsive to treatment with the defense hormone jasmonate, there are no significant changes in nucleosome occupancy, suggesting that these sites are potentially preconditioned to enable rapid response without changing chromatin state significantly. Our study provides a global assessment of the joint contribution of nucleosome occupancy and motif sequences that are likely cis-elements to the control of gene expression in plants. Our findings pave the way for further understanding the impact of chromatin state on plant transcriptional regulatory circuits.

  20. Genetic influences on adolescent sexual behavior: Why genes matter for environmentally oriented researchers.

    PubMed

    Harden, K Paige

    2014-03-01

    There are dramatic individual differences among adolescents in how and when they become sexually active adults, and early sexual activity is frequently cited as a cause of concern for scientists, policymakers, and the general public. Understanding the causes and developmental impact of adolescent sexual activity can be furthered by considering genes as a source of individual differences. Quantitative behavioral genetics (i.e., twin and family studies) and candidate gene association studies now provide clear evidence for the genetic underpinnings of individual differences in adolescent sexual behavior and related phenotypes. Genetic influences on sexual behavior may operate through a variety of direct and indirect mechanisms, including pubertal development, testosterone levels, and dopaminergic systems. Genetic differences may be systematically associated with exposure to environments that are commonly treated as causes of sexual behavior (gene-environment correlation). Possible gene-environment correlations pose a serious challenge for interpreting the results of much behavioral research. Multivariate, genetically informed research on adolescent sexual behavior compares twins and family members as a form of quasi experiment: How do twins who differ in their sexual experiences differ in their later development? The small but growing body of genetically informed research has already challenged dominant assumptions regarding the etiology and sequelae of adolescent sexual behavior, with some studies indicating possible positive effects of teenage sexuality. Studies of Gene × Environment interaction may further elucidate the mechanisms by which genes and environments combine to shape the development of sexual behavior and its psychosocial consequences. Overall, the existence of heritable variation in adolescent sexual behavior has profound implications for environmentally oriented theory and research.

  1. Genetic Influences on Adolescent Sexual Behavior: Why Genes Matter for Environmentally-Oriented Researchers

    PubMed Central

    Harden, K. Paige

    2013-01-01

    There are dramatic individual differences among adolescents in how and when they become sexually active adults, and “early” sexual activity is frequently cited as a cause of concern for scientists, policymakers, and the general public. Understanding the causes and developmental impact of adolescent sexual activity can be furthered by considering genes as a source of individual differences. Quantitative behavioral genetics (i.e., twin and family studies) and candidate gene association studies now provide clear evidence for the genetic underpinnings of individual differences in adolescent sexual behavior and related phenotypes. Genetic influences on sexual behavior may operate through a variety of direct and indirect mechanisms, including pubertal development, testosterone levels, and dopaminergic systems. Genetic differences may be systematically associated with exposure to environments that are commonly treated as causes of sexual behavior (gene-environment correlation). Possible gene-environment correlations pose a serious challenge for interpreting the results of much behavioral research. Multivariate, genetically-informed research on adolescent sexual behavior compares twins and family members as a form of “quasi-experiment”: How do twins who differ in their sexual experiences differ in their later development? The small but growing body of genetically-informed research has already challenged dominant assumptions regarding the etiology and sequelae of adolescent sexual behavior, with some studies indicating possible positive effects of teenage sexuality. Studies of gene × environment interaction may further elucidate the mechanisms by which genes and environments combine to shape the development of sexual behavior and its psychosocial consequences. Overall, the existence of heritable variation in adolescent sexual behavior has profound implications for environmentally-oriented theory and research. PMID:23855958

  2. Searching for genes influencing a complex disease: the case of coeliac disease.

    PubMed

    Naluai, Asa Torinsson; Ascher, Henry; Nilsson, Staffan; Wahlström, Jan

    2008-05-01

    Recently, a few genes have been reported to be causative in inflammatory diseases. Still, we are waiting for the vast majority to be discovered. New tools for genotyping and statistical analysis have been developed and emphasis has been put on study design. Coeliac disease (CD) is a disorder, where prolamins in dietary wheat gluten and related proteins from rye or barley are not tolerated. It is one of the most common chronic diseases in humans exceeding a population prevalence of 1%. In this article, we will summarise what is currently known about the genetics influencing CD with the emphasis on the non-HLA genetic component. We will discuss some difficulties when searching for susceptibility genes in disorders with complex inheritance patterns.

  3. A single dose of lysergic acid diethylamide influences gene expression patterns within the mammalian brain.

    PubMed

    Nichols, Charles D; Sanders-Bush, Elaine

    2002-05-01

    Hallucinogenic drugs such as lysergic acid diethylamide (LSD) have profound effects on humans including hallucinations and detachment from reality. These remarkable behavioral effects have many similarities to the debilitating symptoms of neuropsychiatric disorders such as schizophrenia. The effects of hallucinogens are thought to be mediated by serotonin receptor activation; however, how these drugs elicit the unusual behavioral effects remains largely a mystery, despite much research. We have undertaken the first comprehensive analysis of gene expression influenced by acute LSD administration in the mammalian brain. These studies represent a novel approach to elucidate the mechanism of action of this class of drugs. We have identified a number of genes that are predicted to be involved in the processes of synaptic plasticity, glutamatergic signaling and cytoskeletal architecture. Understanding these molecular events will lead to new insights into the etiology of disorders whose behavioral symptoms resemble the temporary effects of hallucinogenic drugs, and also may ultimately result in new therapies.

  4. Let them experience a ride under the influence of alcohol; a successful intervention program?

    PubMed

    Brookhuis, K A; de Waard, D; Steyvers, F J J M; Bijsterveld, H

    2011-05-01

    A considerable amount of all traffic accidents can be attributed to driving under the influence of alcohol. In particular the group of drivers aged 18-24 years is involved in many serious traffic accidents where alcohol turns out to be a major factor. In fact this age group shows about three times as many alcohol related traffic fatalities as all other categories of road users. The intervention program "Alcohol-free on the road" (Dutch: "Alcoholvrij op weg") aims to enhance young people's awareness of the effects of alcohol by letting them personally experience the effect of alcohol on their driving abilities. To this end, young drivers were invited to a closed circuit and allowed to drive first sober and then intoxicated, guided and guarded by driving instructors. Based on several other studies it was thought that a realistic experience of the effects of alcohol on driving abilities may contribute to a better understanding of the impact of alcohol and may stimulate attitudes that are needed to support the conscious decision not to drive while intoxicated. After more than ten years of running and data collection, 1200 young drivers have participated in the intervention program. In a quasi-experimental study with a non-equivalent group design, the program is evaluated in order to assess its effectiveness both with respect to the attitudes of the participants and the actual relevant behaviour in the years after the alcohol experience intervention program they attended, i.e. the incidence of actually driving under the influence of alcohol. To do this, a questionnaire was sent to a subset (415) of the participants who have completed the program, along with a control group (450), to compare attitudes and actual behaviour. In addition, the Public Prosecutor checked the files of those who responded, for the occurrence of driving under the influence of alcohol. The group that participated in the alcohol intervention program showed more awareness about the dangers of

  5. Children's acceptance of others with disability: the influence of a disability-simulation program.

    PubMed

    Hurst, Christina; Corning, Ken; Ferrante, Richard

    2012-12-01

    Elementary school is a transitional and impressionable period for any child. In inclusive classroom settings, children with disabilities may experience the challenges of acceptance and integration into peer relationships. The experience of children with disabilities in such classrooms can be positive if their classmates are accepting and open. One way to encourage these attitudes is by increasing awareness through disability-simulation. This study evaluates an existing school program, whose goal is to increase acceptance of others with disability. We surveyed students to assess the influence of the program. An adapted acceptance scale was distributed to students before and after participation in the program. Our hypothesis was that student acceptance would increase after participating in the program. Additionally, we hypothesized that physical, visual, and auditory disabilities would be easier for students to understand, making acceptance scores for these disabilities higher than those for a learning disability. We report changes in acceptance using group means. Our results reveal that post-survey responses showed higher acceptance than pre-survey responses, especially for auditory disabilities. Other significant findings include differences in attitudes between the two schools and differences based on prior experience with someone with a disability. By evaluating the effectiveness of this type of program (whose efficacy has been controversial in the literature), this study can provide teachers, administrators, genetic counselors, and parents with a better idea of how to address children's attitudes towards peers. In our study, the effectiveness of promoting understanding through disability-simulation has proven its worth to improve children's acceptance.

  6. Which factors influence students' selection of advanced graduate programs? One institution's experience.

    PubMed

    Saeed, Sophia; Jimenez, Monik; Howell, Howard; Karimbux, Nadeem; Sukotjo, Cortino

    2008-06-01

    The reasons that students choose certain specialties may be integral to the quality of specialty programs and the future of those specialties. The Harvard School of Dental Medicine (HSDM) has a high percentage (87.6 percent) of students who enroll in postgraduate programs. The goals of this study were to establish a baseline of factors that affect postgraduate program selection at HSDM and to determine if there was a significant difference in factor selection by gender, relationship status, graduation year, or choice to specialize versus choice to pursue advanced training in general dentistry. As a pilot study, we asked HSDM graduates from the classes of 2005 to 2007 to rank the importance of forty-two factors in selecting a field of dentistry and a particular program or institution within a specialty. Overall, students felt that intellectual content, challenging diagnostic problems, and possessing a special skill or talent unique to a specialty were the most important factors in choosing a field of dentistry. Influence of family members in dentistry was ranked as least important. In choice of a certain program or institution within a given field, clinical training and philosophy of training were ranked most highly. Students felt that the opportunity to moonlight was least important. Significant differences (p<0.05) were found regarding gender, relationship status, and students who chose to specialize versus those pursuing advanced general dentistry training. No significant differences were found among the students in different graduating classes.

  7. Vitamin D receptor gene FokI polymorphisms influence bone mass in adolescent football (soccer) players.

    PubMed

    Diogenes, Maria Eduarda L; Bezerra, Flávia Fioruci; Cabello, Giselda M K; Cabello, Pedro H; Mendonça, Laura M C; Oliveira Júnior, Astrogildo V; Donangelo, Carmen M

    2010-01-01

    The genetic influence on bone mineralization during adolescence is unclear possibly due to modifying factors such as skeletal maturation and lifestyle. We evaluated the influence of polymorphisms of the vitamin D receptor (VDR) gene on longitudinal changes in bone mass, bone- and calcium-related hormones in 46 adolescent soccer players (11.8-14.2 years). Total body bone mineral content (TBMC) and density (TBMD) were measured at baseline and after 6 months. Insulin-like growth factor-I (IGF-1), testosterone, intact parathyroid hormone, and activity of plasma bone alkaline phosphatase were measured at baseline and after 3 months. The influence of FokI or TaqI VDR genotypes on changes in the outcome variables were analyzed by univariate ANOVA with adjustment for chronological age, skeletal age and body weight at baseline. At baseline, boys with Ff genotype had higher TBMC, TBMD, TBMD Z-score compared to those with FF genotype (P < 0.05). After 3 months, Ff boys also had higher increment in plasma IGF-1 (P < 0.05). FokI polymorphism did not influence changes in bone mass measurements after 6 months, although differences detected at baseline remained significant after 6 months. There were no differences in the outcome variables according to TaqI genotypes. This study demonstrates that FokI polymorphisms affect bone mass in Brazilian adolescent soccer players and suggests that the FokI effect on bone mineralization occurs during bone maturation, possibly at the initial pubertal stages.

  8. The influence of maternal health literacy and child's age on participation in social welfare programs.

    PubMed

    Pati, Susmita; Siewert, Elizabeth; Wong, Angie T; Bhatt, Suraj K; Calixte, Rose E; Cnaan, Avital

    2014-07-01

    The objective of this study is to determine the influence of maternal health literacy and child's age on participation in social welfare programs benefiting children. In a longitudinal prospective cohort study of 560 Medicaid-eligible mother-infant dyads recruited in Philadelphia, maternal health literacy was assessed using the test of functional health literacy in adults (short version). Participation in social welfare programs [Temporary Assistance to Needy Families (TANF), Supplemental Nutrition Assistance Program (SNAP), Special Supplemental Nutrition Program for Women, Infants, and Children (WIC), child care subsidy, and public housing] was self-reported at child's birth, and at the 6, 12, 18, 24 month follow-up interviews. Generalized estimating equations quantified the strength of maternal health literacy as an estimator of program participation. The mothers were primarily African-Americans (83%), single (87%), with multiple children (62%). Nearly 24% of the mothers had inadequate or marginal health literacy. Children whose mothers had inadequate health literacy were less likely to receive child care subsidy (adjusted OR = 0.54, 95% CI 0.34-0.85) than children whose mothers had adequate health literacy. Health literacy was not a significant predictor for TANF, SNAP, WIC or housing assistance. The predicted probability for participation in all programs decreased from birth to 24 months. Most notably, predicted WIC participation declined rapidly after age one. During the first 24 months, mothers with inadequate health literacy could benefit from simplified or facilitated child care subsidy application processes. Targeted outreach and enrollment efforts conducted by social welfare programs need to take into account the changing needs of families as children age.

  9. Analysis of HLA and disease susceptibility: Chromosome 6 genes and sex influence long-QT phenotype

    SciTech Connect

    Weitkamp, L.R.; Moss, A.J.; Hall, W.J.; Robinson, J.L.; Guttormsen, S.A.; Lewis, R.A.; MacCluer, J.W.; Schwartz, P.J.; Locati, E.H.; Tzivoni, D.

    1994-12-01

    The long-QT (LQT) syndrome is a genetically complex disorder that is characterized by syncope and fatal ventricular arrhythmias. LQT syndrome, as defined by a prolonged electrocardiographic QT interval, has a higher incidence in females than in males and does not exhibit Mendelian transmission patterns in all families. Among those families that are nearly consistent with Mendelian transmission, linkage between a locus for LQT syndrome and the H-ras-1 locus on the short arm of chromosome 11 has been reported in some families but not in others. Earlier analyses suggesting that LQT syndrome might be caused by a gene in the HLA region of chromosome 6 were not confirmed by standard linkage analyses. Here, we present an analysis of HLA haplotype sharing among affected pedigree members, showing an excess of haplotype sharing in a previously published Japanese pedigree and possibly also in 15 families of European descent. The haplotypes shared by affected individuals derive from both affected and unaffected parents. In an analysis of independent (unrelated) HLA haplotypes, we also found a nonrandom distribution of HLA-DR genes in LQT syndrome patients compared with controls, suggesting an association between the LQT phenotype and specific HLA-DR genes. Our data indicate that DR2 has a protective effect and, particularly in males, that DR7 may increase susceptibility to the LQT syndrome. Thus, LQT syndrome may be influenced by genes on chromosomes 11 and 6, possibly with a sex-specific effect. These results provide a model for an effect of HLA-region genes inherited from either parent on the expression of an illness that may be determined principally by alleles at loci not linked to HLA.

  10. The influence of genes on "positive valence systems" constructs: A systematic review.

    PubMed

    Hess, Jonathan L; Kawaguchi, Daniel M; Wagner, Kayla E; Faraone, Stephen V; Glatt, Stephen J

    2016-01-01

    In 2009, the U.S. National Institute of Mental Health (NIMH) proposed an approach toward the deconstruction of psychiatric nosology under the research domain criteria (RDoC) framework. The overarching goal of RDoC is to identify robust, objective measures of behavior, emotion, cognition, and other domains that are more closely related to neurobiology than are diagnoses. A preliminary framework has been constructed, which has connected molecules, genes, brain circuits, behaviors, and other elements to dimensional psychiatric constructs. Although the RDoC framework has salience in emerging studies, foundational literature that pre-dated this framework requires synthesis and translation to the evolving objectives and nomenclature of RDoC. Toward this end, we review the candidate-gene association, linkage, and genome-wide studies that have implicated a variety of loci and genetic polymorphisms in selected Positive Valence Systems (PVS) constructs. Our goal is to review supporting evidence to currently listed genes implicated in this domain and novel candidates. We systematically searched and reviewed literature based on keywords listed under the June, 2011, edition of the PVS matrix on the RDoC website (http://www.nimh.nih.gov/research-priorities/rdoc/positive-valence-systems-workshop-proceedings.shtml), which were supplemented with de novo keywords pertinent to the scope of our review. Several candidate genes linked to the PVS framework were identified from candidate-gene association studies. We also identified novel candidates with loose association to PVS traits from genome-wide studies. There is strong evidence suggesting that PVS constructs, as currently conceptualized under the RDoC initiative, index genetically influenced traits; however, future research, including genetic epidemiological, and psychometric analyses, must be performed.

  11. A Comprehensive Examination of the Influence of State Tobacco Control Programs and Policies on Youth Smoking

    PubMed Central

    Loomis, Brett R.; Han, Beth; Gfroerer, Joe; Kuiper, Nicole; Couzens, G. Lance; Dube, Shanta; Caraballo, Ralph S.

    2013-01-01

    Objectives. We examined the influence of tobacco control policies (tobacco control program expenditures, smoke-free air laws, youth access law compliance, and cigarette prices) on youth smoking outcomes (smoking susceptibility, past-year initiation, current smoking, and established smoking). Methods. We combined data from the 2002 to 2008 National Surveys on Drug Use and Health with state and municipality population data from the US Census Bureau to assess the associations between state tobacco control policy variables and youth smoking outcomes, focusing on youths aged 12 to 17 years. We also examined the influence of policy variables on youth access when these variables were held at 2002 levels. Results. Per capita funding for state tobacco control programs was negatively associated with all 4 smoking outcomes. Smoke-free air laws were negatively associated with all outcomes except past-year initiation, and cigarette prices were associated only with current smoking. We found no association between these outcomes and retailer compliance with youth access laws. Conclusions. Smoke-free air laws and state tobacco control programs are effective strategies for curbing youth smoking. PMID:23327252

  12. Sirolimus and Everolimus Pathway: Reviewing Candidate Genes Influencing Their Intracellular Effects

    PubMed Central

    Granata, Simona; Dalla Gassa, Alessandra; Carraro, Amedeo; Brunelli, Matteo; Stallone, Giovanni; Lupo, Antonio; Zaza, Gianluigi

    2016-01-01

    Sirolimus (SRL) and everolimus (EVR) are mammalian targets of rapamycin inhibitors (mTOR-I) largely employed in renal transplantation and oncology as immunosuppressive/antiproliferative agents. SRL was the first mTOR-I produced by the bacterium Streptomyces hygroscopicus and approved for several medical purposes. EVR, derived from SRL, contains a 2-hydroxy-ethyl chain in the 40th position that makes the drug more hydrophilic than SRL and increases oral bioavailability. Their main mechanism of action is the inhibition of the mTOR complex 1 and the regulation of factors involved in a several crucial cellular functions including: protein synthesis, regulation of angiogenesis, lipid biosynthesis, mitochondrial biogenesis and function, cell cycle, and autophagy. Most of the proteins/enzymes belonging to the aforementioned biological processes are encoded by numerous and tightly regulated genes. However, at the moment, the polygenic influence on SRL/EVR cellular effects is still not completely defined, and its comprehension represents a key challenge for researchers. Therefore, to obtain a complete picture of the cellular network connected to SRL/EVR, we decided to review major evidences available in the literature regarding the genetic influence on mTOR-I biology/pharmacology and to build, for the first time, a useful and specific “SRL/EVR genes-focused pathway”, possibly employable as a starting point for future in-depth research projects. PMID:27187382

  13. DNASynth: A Computer Program for Assembly of Artificial Gene Parts in Decreasing Temperature

    PubMed Central

    Nowak, Robert M.; Wojtowicz-Krawiec, Anna; Plucienniczak, Andrzej

    2015-01-01

    Artificial gene synthesis requires consideration of nucleotide sequence development as well as long DNA molecule assembly protocols. The nucleotide sequence of the molecule must meet many conditions including particular preferences of the host organism for certain codons, avoidance of specific regulatory subsequences, and a lack of secondary structures that inhibit expression. The chemical synthesis of DNA molecule has limitations in terms of strand length; thus, the creation of artificial genes requires the assembly of long DNA molecules from shorter fragments. In the approach presented, the algorithm and the computer program address both tasks: developing the optimal nucleotide sequence to encode a given peptide for a given host organism and determining the long DNA assembly protocol. These tasks are closely connected; a change in codon usage may lead to changes in the optimal assembly protocol, and the lack of a simple assembly protocol may be addressed by changing the nucleotide sequence. The computer program presented in this study was tested with real data from an experiment in a wet biological laboratory to synthesize a peptide. The benefit of the presented algorithm and its application is the shorter time, compared to polymerase cycling assembly, needed to produce a ready synthetic gene. PMID:25629047

  14. Rapid gene expression changes in peripheral blood lymphocytes upon practice of a comprehensive yoga program.

    PubMed

    Qu, Su; Olafsrud, Solveig Mjelstad; Meza-Zepeda, Leonardo A; Saatcioglu, Fahri

    2013-01-01

    One of the most common integrative medicine (IM) modalities is yoga and related practices. Previous work has shown that yoga may improve wellness in healthy people and have benefits for patients. However, the mechanisms of how yoga may positively affect the mind-body system are largely unknown. Here we have assessed possible rapid changes in global gene expression profiles in the peripheral blood mononuclear cells (PBMCs) in healthy people that practiced either a comprehensive yoga program or a control regimen. The experimental sessions included gentle yoga postures, breathing exercises, and meditation (Sudarshan Kriya and Related Practices--SK&P) compared with a control regimen of a nature walk and listening to relaxing music. We show that the SK&P program has a rapid and significantly greater effect on gene expression in PBMCs compared with the control regimen. These data suggest that yoga and related practices result in rapid gene expression alterations which may be the basis for their longer term cell biological and higher level health effects.

  15. Rapid Gene Expression Changes in Peripheral Blood Lymphocytes upon Practice of a Comprehensive Yoga Program

    PubMed Central

    Qu, Su; Olafsrud, Solveig Mjelstad; Meza-Zepeda, Leonardo A.; Saatcioglu, Fahri

    2013-01-01

    One of the most common integrative medicine (IM) modalities is yoga and related practices. Previous work has shown that yoga may improve wellness in healthy people and have benefits for patients. However, the mechanisms of how yoga may positively affect the mind-body system are largely unknown. Here we have assessed possible rapid changes in global gene expression profiles in the peripheral blood mononuclear cells (PBMCs) in healthy people that practiced either a comprehensive yoga program or a control regimen. The experimental sessions included gentle yoga postures, breathing exercises, and meditation (Sudarshan Kriya and Related Practices – SK&P) compared with a control regimen of a nature walk and listening to relaxing music. We show that the SK&P program has a rapid and significantly greater effect on gene expression in PBMCs compared with the control regimen. These data suggest that yoga and related practices result in rapid gene expression alterations which may be the basis for their longer term cell biological and higher level health effects. PMID:23613970

  16. ECM proteins in a microporous scaffold influence hepatocyte morphology, function, and gene expression.

    PubMed

    Wang, Yan; Kim, Myung Hee; Shirahama, Hitomi; Lee, Jae Ho; Ng, Soon Seng; Glenn, Jeffrey S; Cho, Nam-Joon

    2016-11-29

    It is well known that a three-dimensional (3D) culture environment and the presence of extracellular matrix (ECM) proteins facilitate hepatocyte viability and maintenance of the liver-specific phenotype in vitro. However, it is not clear whether specific ECM components such as collagen or fibronectin differentially regulate such processes, especially in 3D scaffolds. In this study, a series of ECM-functionalized inverted colloidal crystal (ICC) microporous scaffolds were fabricated and their influence on Huh-7.5 cell proliferation, morphology, hepatic-specific functions, and patterns of gene expression were compared. Both collagen and fibronectin promoted albumin production and liver-specific gene expression of Huh-7.5 cells, compared with the bare ICC scaffold. Interestingly, cells in the fibronectin-functionalized scaffold exhibited different aggregation patterns to those in the collagen-functionalized scaffold, a variation that could be related to the distinct mRNA expression levels of cell adhesion-related genes. Based on these results, we can conclude that different ECM proteins, such as fibronectin and collagen, indeed play distinct roles in the phenotypic regulation of cells cultured in a 3D environment.

  17. ECM proteins in a microporous scaffold influence hepatocyte morphology, function, and gene expression

    PubMed Central

    Wang, Yan; Kim, Myung Hee; Shirahama, Hitomi; Lee, Jae Ho; Ng, Soon Seng; Glenn, Jeffrey S.; Cho, Nam-Joon

    2016-01-01

    It is well known that a three-dimensional (3D) culture environment and the presence of extracellular matrix (ECM) proteins facilitate hepatocyte viability and maintenance of the liver-specific phenotype in vitro. However, it is not clear whether specific ECM components such as collagen or fibronectin differentially regulate such processes, especially in 3D scaffolds. In this study, a series of ECM-functionalized inverted colloidal crystal (ICC) microporous scaffolds were fabricated and their influence on Huh-7.5 cell proliferation, morphology, hepatic-specific functions, and patterns of gene expression were compared. Both collagen and fibronectin promoted albumin production and liver-specific gene expression of Huh-7.5 cells, compared with the bare ICC scaffold. Interestingly, cells in the fibronectin-functionalized scaffold exhibited different aggregation patterns to those in the collagen-functionalized scaffold, a variation that could be related to the distinct mRNA expression levels of cell adhesion-related genes. Based on these results, we can conclude that different ECM proteins, such as fibronectin and collagen, indeed play distinct roles in the phenotypic regulation of cells cultured in a 3D environment. PMID:27897167

  18. Social Environment Influences Performance in a Cognitive Task in Natural Variants of the Foraging Gene

    PubMed Central

    Moreno, Celine; Burns, James G.; Sokolowski, Marla B.; Mery, Frederic

    2013-01-01

    In Drosophila melanogaster, natural genetic variation in the foraging gene affects the foraging behaviour of larval and adult flies, larval reward learning, adult visual learning, and adult aversive training tasks. Sitters (fors) are more sedentary and aggregate within food patches whereas rovers (forR) have greater movement within and between food patches, suggesting that these natural variants are likely to experience different social environments. We hypothesized that social context would differentially influence rover and sitter behaviour in a cognitive task. We measured adult rover and sitter performance in a classical olfactory training test in groups and alone. All flies were reared in groups, but fly training and testing were done alone and in groups. Sitters trained and tested in a group had significantly higher learning performances compared to sitters trained and tested alone. Rovers performed similarly when trained and tested alone and in a group. In other words, rovers learning ability is independent of group training and testing. This suggests that sitters may be more sensitive to the social context than rovers. These differences in learning performance can be altered by pharmacological manipulations of PKG activity levels, the foraging (for) gene's gene product. Learning and memory is also affected by the type of social interaction (being in a group of the same strain or in a group of a different strain) in rovers, but not in sitters. These results suggest that for mediates social learning and memory in D. melanogaster. PMID:24349049

  19. Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals.

    PubMed

    Baral, Aradhita; Kumar, Pankaj; Halder, Rashi; Mani, Prithvi; Yadav, Vinod Kumar; Singh, Ankita; Das, Swapan K; Chowdhury, Shantanu

    2012-05-01

    Non-canonical guanine quadruplex structures are not only predominant but also conserved among bacterial and mammalian promoters. Moreover recent findings directly implicate quadruplex structures in transcription. These argue for an intrinsic role of the structural motif and thereby posit that single nucleotide polymorphisms (SNP) that compromise the quadruplex architecture could influence function. To test this, we analysed SNPs within quadruplex motifs (Quad-SNP) and gene expression in 270 individuals across four populations (HapMap) representing more than 14,500 genotypes. Findings reveal significant association between quadruplex-SNPs and expression of the corresponding gene in individuals (P < 0.0001). Furthermore, analysis of Quad-SNPs obtained from population-scale sequencing of 1000 human genomes showed relative selection bias against alteration of the structural motif. To directly test the quadruplex-SNP-transcription connection, we constructed a reporter system using the RPS3 promoter-remarkable difference in promoter activity in the 'quadruplex-destabilized' versus 'quadruplex-intact' promoter was noticed. As a further test, we incorporated a quadruplex motif or its disrupted counterpart within a synthetic promoter reporter construct. The quadruplex motif, and not the disrupted-motif, enhanced transcription in human cell lines of different origin. Together, these findings build direct support for quadruplex-mediated transcription and suggest quadruplex-SNPs may play significant role in mechanistically understanding variations in gene expression among individuals.

  20. Genetic variability within the S100B gene influences the personality trait self-directedness.

    PubMed

    Suchankova, Petra; Baghaei, Fariba; Rosmond, Roland; Holm, Göran; Anckarsäter, Henrik; Ekman, Agneta

    2011-07-01

    Elevated serum levels of S100B have proven useful as an indicator of brain-injury but have also been shown in patients diagnosed with psychiatric disorders. Recently, associations were found between variations in the S100B gene and schizophrenia as well as bipolar affective disorder. The aim of the present study was to investigate whether some of these genetic variations influence general aspects of human behaviour as portrayed by normal dimensions of personality. Two single nucleotide polymorphisms within the S100B gene, 2757C>G and 5748C>T, were genotyped in two population based cohorts consisting of 42-year-old women (n=270) and 51-year-old men (n=247), respectively. The two polymorphisms were analysed with respect to personality traits assessed using the Temperament and Character Inventory (TCI). In men, the 2757C>G polymorphism was found to significantly influence the TCI dimension self-directedness with higher scores in 2757G homozygotes. A similar tendency towards association was seen in the female cohort; however, this correlation did not remain significant after correction for multiple comparisons. Furthermore, the 5748C>T polymorphism was highly associated with self-directedness in men. Self-directedness is an overall estimate of adaptive strategies to adjust behaviour to conceptual goals as well as coping strategies and is strongly correlated to general mental health and absence of personality disorder. These preliminary findings suggest that the S100B gene may be implicated not only in certain pathological brain conditions but also in processes involved in normal behaviour.

  1. Do conditional cash transfers influence migration? A study using experimental data from the Mexican PROGRESA program.

    PubMed

    Stecklov, Guy; Winters, Paul; Stampini, Marco; Davis, Benjamin

    2005-11-01

    Prior research on Mexican migration has shown that social networks and economic incentives play an important role in determining migration outcomes. We use experimental data from PROGRESA, Mexico's primary poverty-reduction program, to evaluate the effects of conditional cash transfers on migration both domestically and to the United States. Our study complements a growing body of literature aimed at overcoming longstanding hurdles to the establishment of causal validity in empirical studies of migration. Analysis based on the data collected before and after the program's onset shows that conditional transfers reduce U.S. migration but not domestic migration. The data also enable us to explore the role of existing family and community migration networks. The results show that migration networks strongly influence migration, but that the effect of conditional transfers on migration is apparently not mediated by existing migration network structures. Our results suggest that conditional transfers may be helpful in managing rural out-migration, particularly to the United States.

  2. Evaluating the effectiveness of an intervention program to influence attitudes of students towards peers with disabilities.

    PubMed

    de Boer, Anke; Pijl, Sip Jan; Minnaert, Alexander; Post, Wendy

    2014-03-01

    In this study we examine the effectiveness of an intervention program to influence attitudes of elementary school students towards peers with intellectual, physical and severe physical and intellectual disabilities. A quasi-experimental longitudinal study was designed with an experimental group and a control group, both comprising two rural schools. An intervention program was developed for kindergarten (n(experimental) = 22, n(control) = 31) and elementary school students without disabilities (n(experimental) = 91, n(control) = 127) (age range 4-12 years old). This intervention consisted of a 3 weeks education project comprising six lessons about disabilities. The Acceptance Scale for Kindergarten-revised and the Attitude Survey to Inclusive Education were used to measure attitudes at three moments: prior to the start of the intervention, after the intervention and 1 year later. The outcomes of the multilevel analysis showed positive, immediate effects on attitudes of kindergarten students, but limited effects on elementary school students' attitudes.

  3. Multi-gene genetic programming based predictive models for municipal solid waste gasification in a fluidized bed gasifier.

    PubMed

    Pandey, Daya Shankar; Pan, Indranil; Das, Saptarshi; Leahy, James J; Kwapinski, Witold

    2015-03-01

    A multi-gene genetic programming technique is proposed as a new method to predict syngas yield production and the lower heating value for municipal solid waste gasification in a fluidized bed gasifier. The study shows that the predicted outputs of the municipal solid waste gasification process are in good agreement with the experimental dataset and also generalise well to validation (untrained) data. Published experimental datasets are used for model training and validation purposes. The results show the effectiveness of the genetic programming technique for solving complex nonlinear regression problems. The multi-gene genetic programming are also compared with a single-gene genetic programming model to show the relative merits and demerits of the technique. This study demonstrates that the genetic programming based data-driven modelling strategy can be a good candidate for developing models for other types of fuels as well.

  4. The IFN-γ-induced Transcriptional Program of the CIITA Gene is Inhibited by Statins

    PubMed Central

    Lee, Sun Jung; Qin, Hongwei; Benveniste, Etty N.

    2009-01-01

    Summary Statins are 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase inhibitors that exert anti-inflammatory effects. IFN-γ induction of class II MHC expression, which requires the class II transactivator (CIITA), is inhibited by statins, however, the molecular basis for suppression is undetermined. We describe that statins inhibit IFN-γ-induced class II MHC expression by suppressing CIITA gene expression, which is dependent on the HMG-CoA reductase pathway. In addition, CIITA expression is inhibited by GGTI-298 or Clostridium difficile Toxin A, specific inhibitors of Rho family protein prenylation, indicating the involvement of small GTPases. Rac1 is involved in IFN-γ inducible expression of CIITA, and statins inhibit IFN-γ-induced Rac1 activation, contributing to the inhibitory effect of statins. IFN-γ induction of the CIITA gene is regulated by the transcription factors STAT-1α, IRF-1 and USF-1. We previously reported that statins inhibit constitutive STAT-1α expression. IRF-1, a STAT-1 dependent gene, is also inhibited by statins. Therefore, statin treatment results in decreased recruitment of STAT-1α and IRF-1 to the endogenous CIITA pIV promoter. The recruitment of USF-1 to CIITA pIV is also reduced by statins, as is the recruitment of RNA Polymerase II, p300 and Brg-1. These data indicate that statins inhibit the transcriptional program of the CIITA gene. PMID:18601229

  5. A MED13-dependent skeletal muscle gene program controls systemic glucose homeostasis and hepatic metabolism

    PubMed Central

    Amoasii, Leonela; Holland, William; Sanchez-Ortiz, Efrain; Baskin, Kedryn K.; Pearson, Mackenzie; Burgess, Shawn C.; Nelson, Benjamin R.; Bassel-Duby, Rhonda; Olson, Eric N.

    2016-01-01

    The Mediator complex governs gene expression by linking upstream signaling pathways with the basal transcriptional machinery. However, how individual Mediator subunits may function in different tissues remains to be investigated. Through skeletal muscle-specific deletion of the Mediator subunit MED13 in mice, we discovered a gene regulatory mechanism by which skeletal muscle modulates the response of the liver to a high-fat diet. Skeletal muscle-specific deletion of MED13 in mice conferred resistance to hepatic steatosis by activating a metabolic gene program that enhances muscle glucose uptake and storage as glycogen. The consequent insulin-sensitizing effect within skeletal muscle lowered systemic glucose and insulin levels independently of weight gain and adiposity and prevented hepatic lipid accumulation. MED13 suppressed the expression of genes involved in glucose uptake and metabolism in skeletal muscle by inhibiting the nuclear receptor NURR1 and the MEF2 transcription factor. These findings reveal a fundamental molecular mechanism for the governance of glucose metabolism and the control of hepatic lipid accumulation by skeletal muscle. Intriguingly, MED13 exerts opposing metabolic actions in skeletal muscle and the heart, highlighting the customized, tissue-specific functions of the Mediator complex. PMID:26883362

  6. Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming

    PubMed Central

    Huynh, Linh; Kececioglu, John; Köppe, Matthias; Tagkopoulos, Ilias

    2012-01-01

    Automatic design of synthetic gene circuits poses a significant challenge to synthetic biology, primarily due to the complexity of biological systems, and the lack of rigorous optimization methods that can cope with the combinatorial explosion as the number of biological parts increases. Current optimization methods for synthetic gene design rely on heuristic algorithms that are usually not deterministic, deliver sub-optimal solutions, and provide no guaranties on convergence or error bounds. Here, we introduce an optimization framework for the problem of part selection in synthetic gene circuits that is based on mixed integer non-linear programming (MINLP), which is a deterministic method that finds the globally optimal solution and guarantees convergence in finite time. Given a synthetic gene circuit, a library of characterized parts, and user-defined constraints, our method can find the optimal selection of parts that satisfy the constraints and best approximates the objective function given by the user. We evaluated the proposed method in the design of three synthetic circuits (a toggle switch, a transcriptional cascade, and a band detector), with both experimentally constructed and synthetic promoter libraries. Scalability and robustness analysis shows that the proposed framework scales well with the library size and the solution space. The work described here is a step towards a unifying, realistic framework for the automated design of biological circuits. PMID:22536398

  7. Multi-gene panel testing for hereditary cancer susceptibility in a rural Familial Cancer Program.

    PubMed

    Hermel, David J; McKinnon, Wendy C; Wood, Marie E; Greenblatt, Marc S

    2017-01-01

    This study explores our Familial Cancer Program's experience implementing multi-gene panel testing in a largely rural patient population. We conducted a retrospective review of patients undergoing panel testing between May 2011 and August 2015. Our goal was to evaluate factors that might be predictors of identifying variants (pathogenic or uncertain significance) and to assess clinical management changes due to testing. We utilized a structured family history tool to determine the significance of patient's family histories with respect to identification of genetic variants. A total of 227 patients underwent panel testing at our center and 67 patients (29.5 %) had variants identified, with 8 (3.5 %) having multiple variants. Overall, 44 patients (19.4 %) had a variant of uncertain significance (VUS) and 28 patients (12.3 %) had a pathogenic variant detected, with 10 (4.4 %) having pathogenic variants in highly penetrant genes. We found no statistical difference in patient familial and personal cancer history, age, rural status, Ashkenazi Jewish ancestry, insurance coverage and prior single-gene testing among those with pathogenic, VUS and negative panel testing results. There were no predictors of pathogenic variants on regression analysis. Panel testing changed cancer screening and management guidelines from that expected based on family history alone in 13.2 % of patients. Ultimately, cancer panel testing does yield critical information not identified by traditional single gene testing but maximal utility through a broad range of personal and family histories requires improved interpretation of variants.

  8. A MED13-dependent skeletal muscle gene program controls systemic glucose homeostasis and hepatic metabolism.

    PubMed

    Amoasii, Leonela; Holland, William; Sanchez-Ortiz, Efrain; Baskin, Kedryn K; Pearson, Mackenzie; Burgess, Shawn C; Nelson, Benjamin R; Bassel-Duby, Rhonda; Olson, Eric N

    2016-02-15

    The Mediator complex governs gene expression by linking upstream signaling pathways with the basal transcriptional machinery. However, how individual Mediator subunits may function in different tissues remains to be investigated. Through skeletal muscle-specific deletion of the Mediator subunit MED13 in mice, we discovered a gene regulatory mechanism by which skeletal muscle modulates the response of the liver to a high-fat diet. Skeletal muscle-specific deletion of MED13 in mice conferred resistance to hepatic steatosis by activating a metabolic gene program that enhances muscle glucose uptake and storage as glycogen. The consequent insulin-sensitizing effect within skeletal muscle lowered systemic glucose and insulin levels independently of weight gain and adiposity and prevented hepatic lipid accumulation. MED13 suppressed the expression of genes involved in glucose uptake and metabolism in skeletal muscle by inhibiting the nuclear receptor NURR1 and the MEF2 transcription factor. These findings reveal a fundamental molecular mechanism for the governance of glucose metabolism and the control of hepatic lipid accumulation by skeletal muscle. Intriguingly, MED13 exerts opposing metabolic actions in skeletal muscle and the heart, highlighting the customized, tissue-specific functions of the Mediator complex.

  9. Automatic design of synthetic gene circuits through mixed integer non-linear programming.

    PubMed

    Huynh, Linh; Kececioglu, John; Köppe, Matthias; Tagkopoulos, Ilias

    2012-01-01

    Automatic design of synthetic gene circuits poses a significant challenge to synthetic biology, primarily due to the complexity of biological systems, and the lack of rigorous optimization methods that can cope with the combinatorial explosion as the number of biological parts increases. Current optimization methods for synthetic gene design rely on heuristic algorithms that are usually not deterministic, deliver sub-optimal solutions, and provide no guaranties on convergence or error bounds. Here, we introduce an optimization framework for the problem of part selection in synthetic gene circuits that is based on mixed integer non-linear programming (MINLP), which is a deterministic method that finds the globally optimal solution and guarantees convergence in finite time. Given a synthetic gene circuit, a library of characterized parts, and user-defined constraints, our method can find the optimal selection of parts that satisfy the constraints and best approximates the objective function given by the user. We evaluated the proposed method in the design of three synthetic circuits (a toggle switch, a transcriptional cascade, and a band detector), with both experimentally constructed and synthetic promoter libraries. Scalability and robustness analysis shows that the proposed framework scales well with the library size and the solution space. The work described here is a step towards a unifying, realistic framework for the automated design of biological circuits.

  10. Early results of sarcomeric gene screening from the Egyptian National BA-HCM Program.

    PubMed

    Kassem, Heba Sh; Azer, Remon S; Saber-Ayad, Maha; Ayad, Maha S; Moharem-Elgamal, Sarah; Magdy, Gehan; Elguindy, Ahmed; Cecchi, Franco; Olivotto, Iacopo; Yacoub, Magdi H

    2013-02-01

    The present study comprised sarcomeric genotyping of the three most commonly involved sarcomeric genes: MYBPC3, MYH7, and TNNT2 in 192 unrelated Egyptian hypertrophic cardiomyopathy (HCM) index patients. Mutations were detected in 40 % of cases. Presence of positive family history was significantly (p=0.002) associated with a higher genetic positive yield (49/78, 62.8 %). The majority of the detected mutations in the three sarcomeric genes were novel (40/62, 65 %) and mostly private (47/62, 77 %). Single nucleotide substitution was the most frequently detected mutation type (51/62, 82 %). Over three quarters of these substitutions (21/27, 78 %) involved CpG dinucleotide sites and resulted from C>T or G>A transition in the three analyzed genes, highlighting the significance of CpG high mutability within the sarcomeric genes examined. This study could aid in global comparative studies in different ethnic populations and constitutes an important step in the evolution of the integrated clinical, translational, and basic science HCM program.

  11. The influence of rosuvastatin upon the gastrointestinal microbiota and host gene expression profiles.

    PubMed

    Nolan, James A; Skuse, Peter Henry; Govindarajan, Kalaimathi; Patterson, Elaine; Konstantinidou, Nina; Casey, Patrick G; MacSharry, John; Shanahan, Fergus; Stanton, Catherine; Hill, Colin; Cotter, P D; Joyce, Susan A; Gahan, Cormac Gm

    2017-02-16

    Statins are the most widely prescribed medications worldwide for the treatment of hypercholesterolemia. They inhibit the activity of 3-hydroxy-3-methylglutaryl co enzyme A reductase (HMG-R) an enzyme involved in cholesterol synthesis in higher organisms and in isoprenoid biosynthesis in some bacteria. We hypothesized that statins may influence the microbial community in the gut through either direct inhibition or indirect mechanisms involving alterations to host responses. We therefore examined the impact of rosuvastatin (RSV) on the community structure of the murine gastrointestinal microbiota. RSV was orally administered to mice and the effects upon the gut microbiota, host bile acid profiles and markers of inflammation were analysed. RSV significantly influenced the microbial community in both the caecum and faeces, causing a significant decrease in alpha diversity in the caecum and resulting in a reduction of several physiologically relevant bacterial groups. RSV treatment of mice significantly affected bile acid metabolism and impacted upon expression of inflammatory markers known to influence microbial community structure (including RegIIIγ and Camp) in the gut. This study suggests that a commonly used statin (RSV) leads to an altered gut microbial composition in normal mice with attendant impacts upon local gene expression profiles, a finding which should prompt further studies to investigate the implications of statins for gut microbiota stability and health in humans.

  12. Combining classifiers generated by multi-gene genetic programming for protein fold recognition using genetic algorithm.

    PubMed

    Bardsiri, Mahshid Khatibi; Eftekhari, Mahdi; Mousavi, Reza

    2015-01-01

    In this study the problem of protein fold recognition, that is a classification task, is solved via a hybrid of evolutionary algorithms namely multi-gene Genetic Programming (GP) and Genetic Algorithm (GA). Our proposed method consists of two main stages and is performed on three datasets taken from the literature. Each dataset contains different feature groups and classes. In the first step, multi-gene GP is used for producing binary classifiers based on various feature groups for each class. Then, different classifiers obtained for each class are combined via weighted voting so that the weights are determined through GA. At the end of the first step, there is a separate binary classifier for each class. In the second stage, the obtained binary classifiers are combined via GA weighting in order to generate the overall classifier. The final obtained classifier is superior to the previous works found in the literature in terms of classification accuracy.

  13. Innate-like functions of natural killer T cell subsets result from highly divergent gene programs.

    PubMed

    Engel, Isaac; Seumois, Grégory; Chavez, Lukas; Samaniego-Castruita, Daniela; White, Brandie; Chawla, Ashu; Mock, Dennis; Vijayanand, Pandurangan; Kronenberg, Mitchell

    2016-06-01

    Natural killer T cells (NKT cells) have stimulatory or inhibitory effects on the immune response that can be attributed in part to the existence of functional subsets of NKT cells. These subsets have been characterized only on the basis of the differential expression of a few transcription factors and cell-surface molecules. Here we have analyzed purified populations of thymic NKT cell subsets at both the transcriptomic level and epigenomic level and by single-cell RNA sequencing. Our data indicated that despite their similar antigen specificity, the functional NKT cell subsets were highly divergent populations with many gene-expression and epigenetic differences. Therefore, the thymus 'imprints' distinct gene programs on subsets of innate-like NKT cells that probably impart differences in proliferative capacity, homing, and effector functions.

  14. Innate-like functions of natural killer T cell subsets result from highly divergent gene programs

    PubMed Central

    Engel, Isaac; Seumois, Grégory; Chavez, Lukas; Samaniego-Castruita, Daniela; White, Brandie; Chawla, Ashu; Mock, Dennis; Vijayanand, Pandurangan; Kronenberg, Mitchell

    2016-01-01

    Natural killer T cells (NKT cells) have stimulatory or inhibitory effects on the immune response that can be attributed in part to the existence of functional subsets of NKT cells. These subsets have been characterized only on the basis of the differential expression of a few transcription factors and cell-surface molecules. Here we have analyzed purified populations of thymic NKT cell subsets at both the transcriptomic level and epigenomic level and by single-cell RNA sequencing. Our data indicated that despite their similar antigen specificity, the functional NKT cell subsets were highly divergent populations with many gene-expression and epigenetic differences. Therefore, the thymus ‘imprints’ distinct gene programs on subsets of innate-like NKT cells that probably impart differences in proliferative capacity, homing, and effector functions. PMID:27089380

  15. GRAIN: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach.

    PubMed

    Baumung, R; Farkas, J; Boichard, D; Mészáros, G; Sölkner, J; Curik, I

    2015-04-01

    GRain is freely available software intended to enable and promote testing of hypotheses with respect to purging and heterogeneity of inbreeding depression. The program is based on a stochastic approach, the gene dropping method, and calculates various coefficients from large and complex pedigrees. GRain calculates, together with the 'classical' inbreeding coefficient, ancestral inbreeding coefficients proposed by Ballou, (1997) J. Hered., 88, 169 and Kalinowski et al., (2000) Conserv. Biol., 14, 1375 as well as an ancestral history coefficient (AHC ), defined here for the first time. AHC is defined as the number that tells how many times during pedigree segregation (gene dropping) a randomly taken allele has been in IBD status. Furthermore, GRain enables testing of heterogeneity and/or purging of inbreeding depression with respect to different founders/ancestors by calculating partial coefficients for all previously obtained coefficients.

  16. Analysing gene regulatory networks by both constraint programming and model-checking.

    PubMed

    Fromentin, Jonathan; Comet, Jean-Paul; Le Gall, Pascale; Roux, Olivier

    2007-01-01

    In this article, we propose a formal method to analyse gene regulatory networks (GRN). The dynamics of such systems is often described by an ordinary differential equation system, but has also been abstracted into a discrete transition system. This modeling depends on parameters for which different values are possible. Each instantiation of these parameters defines a possible dynamics and verification tools can be used to select the tuples of values which lead to dynamics consistent with known behaviours. GRN are so complex that their discrete modeling gives a number of possible dynamics exponential in function of the GRN's size (number of genes and interactions). In this paper, we propose to use constraint programming and CTL formal language to determine the set of all dynamics consistent with the known behavioral properties without enumerating all of them. This approach allows us therefore to minimize the computation time necessary for the research of these parameters.

  17. Identification of Gender-Specific Candidate Genes That Influence Bone Microarchitecture in Chromosome 1

    PubMed Central

    Mohan, Subburaman; Hu, Yan; Edderkaoui, Bouchra

    2016-01-01

    The studies on the identification of the genetic basis for sexual dimorphism in peak bone mass are obviously important toward providing novel therapeutic approaches to prevent or treat metabolic bone diseases. Our goal in this study is to identify the bone microstructure that could lead to differences in volumetric (v) bone mineral density (BMD) and identify new candidate genes that regulate the gender effect on bone. Therefore, we used a congenic line of mice that carry the BMD1-4 locus from CAST/EiJ (CAST) mice in a C57BL/6J (B6) background and show greater vBMD in female but not male congenics compared to age and gender matched B6 mice. To assess the vBMD variations between the two lines of mice, we performed micro-CT measurements and found no difference in cortical bone volume by tissue volume (BV/TV) between congenics and B6 mice. However, trabecular BV/TV was significantly greater in female but not male congenics compared to corresponding B6 mice which was due to increased trabecular thickness but not reduced trabecular separation suggesting that a bone formation but not a bone resorption is responsible for the trabecular bone phenotype observed in the female but not male congenics. To identify the gender candidate genes, we have determined the polymorphisms between B6 and CAST within the BMD1-4 locus and performed gene expression profiling. We have identified ef-hand calcium binding domain (Efcab2), consortin, connexin sorting protein (Cnst) and presenilin 2 (Psen2) as potential candidate genes that regulate bone mass by influencing trabecular thickness in a gender specific manner. PMID:23263656

  18. Influence of catechol-O-methyltransferase (COMT) gene polymorphisms in pain sensibility of Brazilian fibromialgia patients.

    PubMed

    Barbosa, Flávia Regina; Matsuda, Josie Budag; Mazucato, Mendelson; de Castro França, Suzelei; Zingaretti, Sônia Marli; da Silva, Lucienir Maria; Martinez-Rossi, Nilce Maria; Júnior, Milton Faria; Marins, Mozart; Fachin, Ana Lúcia

    2012-02-01

    Fibromyalgia syndrome (FS) is a rheumatic syndrome affecting to 2-3% of individuals of productive age, mainly women. Neuroendocrine and genetic factors may play a significant role in development of the disease which is characterized by diffuse chronic pain and presence of tender points. Several studies have suggested an association between FS, especially pain sensitivity, and polymorphism of the catechol-O-methyltransferase (COMT) gene. The aim of the present study was to characterize the SNPs rs4680 and rs4818 of the COMT gene and assess its influence in pain sensitivity of patients with fibromyalgia screened by the Fibromyalgia Impact Questionnaire (FIQ). DNA was extracted from peripheral blood of 112 patients with fibromyalgia and 110 healthy individuals and was used as template in PCR for amplification of a 185-bp fragment of the COMT gene. The amplified fragment was sequenced for analyses of the SNPs rs4680 and rs4818. The frequency of mutant genotype AA of SNP rs6860 was 77.67% in patients with FS and 28.18% for the control group. For the SNP rs4818, the frequency of mutant genotype CC was 73.21 and 39.09% for patients with FS and controls, respectively. Moreover, the FIQ score was higher in patients with the homozygous mutant genotype for SNPs rs4680 (87.92 points) and rs4818 (86.14 points). These results suggest that SNPs rs4680 and rs4818 of the COMT gene may be associated with fibromyalgia and pain sensitivity in FS Brazilian patients.

  19. Transcriptomic Complexity of Aspergillus terreus Velvet Gene Family under the Influence of Butyrolactone I

    PubMed Central

    Palonen, Elina K.; Raina, Sheetal; Brandt, Annika; Meriluoto, Jussi; Keshavarz, Tajalli; Soini, Juhani T.

    2017-01-01

    Filamentous fungi of the Ascomycota phylum are known to contain a family of conserved conidiation regulating proteins with distinctive velvet domains. In Aspergilli, this velvet family includes four proteins, VeA, VelB, VelC and VosA, and is involved in conidiation and secondary metabolism along with a global regulator LaeA. In A. terreus, the overexpression of LaeA has been observed to increase the biogenesis of the pharmaceutically-important secondary metabolite, lovastatin, while the role of the velvet family has not been studied. The secondary metabolism and conidiation of A. terreus have also been observed to be increased by butyrolactone I in a quorum-sensing manner. An enlightenment of the interplay of these regulators will give potential advancement to the industrial use of this fungus, as well as in resolving the pathogenic features. In this study, the Aspergillus terreus MUCL 38669 transcriptome was strand-specifically sequenced to enable an in-depth gene expression analysis to further investigate the transcriptional role of butyrolactone I in these processes. The sequenced transcriptome revealed intriguing properties of the velvet family transcripts, including the regulator laeA, and uncovered the velC gene in A. terreus. The reliability refining microarray gene expression analysis disclosed a positive regulatory role for butyrolactone I in laeA expression, as well as an influence on the expression of the canonical conidiation-regulating genes under submerged culture. All of this supports the suggested regulative role of butyrolactone I in A. terreus secondary metabolism, as well as conidiation. PMID:28335447

  20. Genetic variation in the serotonin transporter gene influences ERP old/new effects during recognition memory

    PubMed Central

    Ross, Robert S.; Medrano, Paolo; Boyle, Kaitlin; Smolen, Andrew; Curran, Tim; Nyhus, Erika

    2015-01-01

    Recognition memory is defined as the ability to recognize a previously encountered stimulus and has been associated with spatially and temporally distinct event related potentials (ERPs). Allelic variations of the serotonin transporter gene (SLC6A4) have recently been shown to impact memory performance. Common variants of the serotonin transporter-linked polymorphic region (5HTTLPR) of the SLC6A4 gene result in long (l) and short (s) allelic variants with carriers of the s allele having lowered transcriptional efficiency. Thus, the current study examines the effects polymorphisms of the SLC6A4 gene have on performance and ERP amplitudes commonly associated with recognition memory. Electroencephalogram (EEG), genetic, and behavioral data were collected from sixty participants as they performed an item and source memory recognition task. In both tasks, participants studied and encoded 200 words, which were then mixed with 200 new words during retrieval. Participants were monitored with EEG during the retrieval portion of each memory task. EEG electrodes were grouped into four ROIs, left anterior superior, right anterior superior, left posterior superior, and right posterior superior. ERP mean amplitudes during hits in the item and source memory task were compared to correctly recognizing new items (correct rejections). Results show that s-carriers have decreased mean hit amplitudes in both the right anterior superior ROI 1000–1500 ms post stimulus during the source memory task and the left anterior superior ROI 300–500 ms post stimulus during the item memory task. These results suggest that individual differences due to genetic variation of the serotonin transporter gene influences recognition memory. PMID:26423665

  1. The Influence of Extracurricular Activities on Student Performance Perceived by Texas Rural High School Principals with Successful Extracurricular Programs

    ERIC Educational Resources Information Center

    Granger, Christopher John

    2014-01-01

    This study was designed to investigate the influence of student participation in extracurricular activities, as perceived by rural high school principals, with successful extracurricular programs. Participating principals were asked about their perceptions on the influence of student participation in extracurricular activities on student…

  2. Gene expression programming for total bed material load estimation--a case study.

    PubMed

    Zakaria, Nor Azazi; Azamathulla, H Md; Chang, Chun Kiat; Ghani, Aminuddin Ab

    2010-10-01

    This paper presents Gene-Expression Programming (GEP), which is an extension to the genetic programming (GP) approach to predict the total bed material load for three Malaysian rivers. The GEP is employed without any restriction to an extensive database compiled from measurements in the Muda, Langat, and Kurau rivers. The GEP approach demonstrated a superior performance compared to other traditional sediment load methods. The coefficient of determination, R(2) (=0.97) and the mean square error, MSE (=0.057) of the GEP method are higher than those of the traditional method. The performance of the GEP method demonstrates its predictive capability and the possibility of the generalization of the model to nonlinear problems for river engineering applications.

  3. The Influence of Rare Book and Manuscript Repositories on Graduate Research in the Humanities: The Graduate Research Fellowship Program

    ERIC Educational Resources Information Center

    James, Kathryn

    2007-01-01

    This article explores the influence of the rare book and manuscript repository on graduate student researchers in the humanities, through an examination of the graduate research fellowship program. Based on a comparison of residential research fellowship programs at twenty-three rare book and manuscript repositories, this article argues that…

  4. Black Teachers Matter: Qualitative Study of Factors Influencing African American Candidates Success in a Teacher Preparation Program

    ERIC Educational Resources Information Center

    Dinkins, Elizabeth; Thomas, Kevin

    2016-01-01

    This qualitative study examined the perspectives and experiences of ten African American students at a predominantly White institution to understand why students persisted or discontinued in the teacher preparation program. Findings indicate three predominant factors influence Black candidates' decision to complete or leave the program: the role…

  5. Continuous enteral and parenteral feeding each reduces heart rate variability but differentially influences monocyte gene expression in humans.

    PubMed

    Gale, Stephen C; Shanker, Beth-Ann; Coyle, Susette M; Macor, Marie A; Choi, Chun W; Calvano, Steve E; Corbett, Siobhan A; Lowry, Stephen F

    2012-08-01

    Enteral (EN) or parenteral (PN) nutrition is used to support critically ill patients until oral feeding resumes. Enteral nutrition is assumed preferable to PN, but the differential influence on immune function is not well defined. Autonomic nervous activity is known to influence innate immune responses, and we hypothesized that EN and PN could influence both autonomic signaling and gene activation in peripheral blood monocytes (PBMs). Ten subjects (aged 18-36 years) received continuous EN or PN for 72 h. Peripheral blood monocytes were isolated from whole blood before and after continuous feeding and were analyzed for gene expression using a microarray platform. Gene expression after feeding was compared from baseline and between groups. To measure autonomic outflow, subjects also underwent heart rate variability (HRV) monitoring during feeding. Time and frequency domain HRV data were compared between groups and five orally fed subjects for changes from baseline and changes over time. During continuous EN and PN, subjects exhibited declines in both time and frequency domain HRV parameters compared with baseline and with PO subjects, indicating a loss of vagal/parasympathetic tone. However, PN feeding had a much greater influence on PBM gene expression compared with baseline than EN, including genes important to innate immunity. Continuous EN and PN are both associated with decreasing vagal tone over time, yet contribute differently to PBM gene expression, in humans. These preliminary findings support assumptions that PN imposes a systemic inflammatory risk but also imply that continuous feeding, independent of route, may impart additional risk through different mechanisms.

  6. Influence of Horse and Rider on Stress during Horse-riding Lesson Program

    PubMed Central

    Kang, Ok-Deuk; Yun, Young-Min

    2016-01-01

    The present study aims to confirm the influence of a horse-riding lesson program (HRLP) on the stress level of horses and riders by respectively analyzing their salivary cortisol concentration. Twenty-four healthy horses and 23 riders participated in this study. The horses were randomly classified into two groups for the horse riding lesson program: Class 1 (for the beginner lesson) and Class 2 (for the intermediate lesson). The Class 1 group consisted of 12 horses and 12 riders, while the Class 2 group consisted of 12 horses and 11 riders. Salivettes cotton wool swabs were used for saliva collection and the saliva analyses were conducted using a two-way analysis of variance for repeated measures with SAS version 8. As for the results, the average salivary cortisol concentration of all horses before HRLP significantly increased compared to the baseline (p<0.001) while it decreased after the HRLP. The results of the salivary cortisol concentration of the riders were similar to the horses’ results. However, there was no difference during the HRLP between Class 1 and Class 2 in the horse or rider groups. The results suggest that the HRLP did not influence the stress level of the horses or riders. Thus, this study provides the necessary information and guidelines for future studies on stress in horses during riding and gives insight into better horse welfare and management options. PMID:27004819

  7. Influence of material removal programming on ion beam figuring of high-precision optical surfaces

    NASA Astrophysics Data System (ADS)

    Liao, Wenlin; Dai, Yifan; Xie, Xuhui

    2014-09-01

    Ion beam figuring (IBF) provides a nanometer/subnanometer precision fabrication technology for optical components, where the surface materials on highlands are gradually removed by the physical sputtering effect. In this deterministic method, the figuring process is usually divided into several iterations and the sum of the removed material in each iteration is expected to approach the ideally removed material as nearly as possible. However, we find that the material removal programming in each iteration would influence the surface error convergence of the figuring process. The influence of material removal programming on the surface error evolution is investigated through the comparative study of the contour removal method (CRM) and the geometric proportion removal method (PRM). The research results indicate that the PRM can maintenance the smoothness of the surface topography during the whole figuring process, which would benefit the stable operation of the machine tool and avoid the production of mid-to-high spatial frequency surface errors. Additionally, the CRM only has the corrective effect on the area above the contour line in each iteration, which would result in the nonuniform convergence of the surface errors in various areas. All these advantages distinguish PRM as an appropriate material removal method for ultraprecision optical surfaces.

  8. RESIN, a FORTRAN IV program for determining the area of influence of samples or drill holes in resource target search

    USGS Publications Warehouse

    Singer, D.A.

    1976-01-01

    A FORTRAN IV program that calculates the area of influence of drill holes or samples with respect to the size and shape of elliptical or circular resource targets is presented. Program options include determination of the degree to which areas within a region have been explored and estimation of probabilities that points are centers of undiscovered deposits. Errors of recognition can be utilized in the program input. ?? 1976.

  9. Programmed cell death genes are linked to elevated creatine kinase levels in unhealthy male nonagenarians

    PubMed Central

    Kim, Sangkyu; Simon, Eric; Myers, Leann; Hamm, L. Lee; Jazwinski, S. Michal

    2016-01-01

    Declining health in the oldest-old takes an energy toll for simple maintenance of body functions. The underlying mechanisms, however, differ in males and females. In females, the declines are explained by loss of muscle mass, but this is not the case in males in whom they are associated with increased levels of circulating creatine kinase. This relationship raises the possibility that muscle damage rather than muscle loss is the cause of the increased energy demands of unhealthy aging in males. We have now examined factors that contribute to the increase in creatine kinase. Much of it (60%) can be explained by a history of cardiac problems and lower kidney function, while being mitigated by moderate physical activity, reinforcing the notion that tissue damage is a likely source. In a search for genetic risk factors associated with elevated creatine kinase, the Ku70 gene XRCC6 and the ceramide synthase gene LASS1 were investigated because of their roles in telomere length and longevity and healthy aging, respectively. Single-nucleotide polymorphisms in these two genes were independently associated with creatine kinase levels. The XRCC6 variant was epistatic to one of the LASS1 variants but not to the other. These gene variants have potential regulatory activity. Ku70 is an inhibitor of the pro-apoptotic Bax, while the product of Lass1, ceramide, operates in both caspase-dependent and independent pathways of programmed cell death, providing a potential cellular mechanism for the effects of these genes on tissue damage and circulating creatine kinase. PMID:26913518

  10. The Influence of Sleep Disordered Breathing on Weight Loss in a National Weight Management Program

    PubMed Central

    Janney, Carol A.; Kilbourne, Amy M.; Germain, Anne; Lai, Zongshan; Hoerster, Katherine D.; Goodrich, David E.; Klingaman, Elizabeth A.; Verchinina, Lilia; Richardson, Caroline R.

    2016-01-01

    Study Objective: To investigate the influence of sleep disordered breathing (SDB) on weight loss in overweight/obese veterans enrolled in MOVE!, a nationally implemented behavioral weight management program delivered by the National Veterans Health Administration health system. Methods: This observational study evaluated weight loss by SDB status in overweight/obese veterans enrolled in MOVE! from May 2008–February 2012 who had at least two MOVE! visits, baseline weight, and at least one follow-up weight (n = 84,770). SDB was defined by International Classification of Diseases, Ninth Revision, Clinical Modification codes. Primary outcome was weight change (lb) from MOVE! enrollment to 6- and 12-mo assessments. Weight change over time was modeled with repeated-measures analyses. Results: SDB was diagnosed in one-third of the cohort (n = 28,269). At baseline, veterans with SDB weighed 29 [48] lb more than those without SDB (P < 0.001). On average, veterans attended eight MOVE! visits. Weight loss patterns over time were statistically different between veterans with and without SDB (P < 0.001); veterans with SDB lost less weight (−2.5 [0.1] lb) compared to those without SDB (−3.3 [0.1] lb; P = 0.001) at 6 months. At 12 mo, veterans with SDB continued to lose weight whereas veterans without SDB started to re-gain weight. Conclusions: Veterans with sleep disordered breathing (SDB) had significantly less weight loss over time than veterans without SDB. SDB should be considered in the development and implementation of weight loss programs due to its high prevalence and negative effect on health. Citation: Janney CA, Kilbourne AM, Germain A, Lai Z, Hoerster KD, Goodrich DE, Klingaman EA, Verchinina L, Richardson CR. The influence of sleep disordered breathing on weight loss in a national weight management program. SLEEP 2016;39(1):59–65. PMID:26350475

  11. The influences and factors of an undergraduate research program in preparing women for science careers

    NASA Astrophysics Data System (ADS)

    Campbell, Ashley Mcdowell

    Progress has been made in diminishing barriers experienced by women in science in recent years, however obstacles still remain. One of the key elements of the Texas Tech University Howard Hughes Medical Institute (TTU/HHMI) Undergraduate Biological Sciences Education Program is to "support activities that broaden access to science for women." In light of the barriers women in science face, this dissertation examined how the experiences of females in the TTU/HHMI fellows program prepared them for a career in science. This study employed mixed methods, utilizing both a questionnaire involving all past female fellows, and in-depth interviews with seven fellows who chose a career as a professional scientist. According to the quantitative data, research experience, the relationship with mentors, and opportunities to present at state or national meetings were program factors that fellows identified as contributing to their career success. The TTU/HHMI program experiences positively influenced the fellows' level of interest in science, confidence in science, and motivation to pursue a science-related career. Encouragement from the mentor and increased confidence regarding the ability to be successful in science were significant predictors of career advantages. Motivation to pursue a science-related career was the most significant predictor of the fellows' preparation to overcome barriers. Qualitatively, six themes were identified for coding, which included (1) research experience, (2) the mentor, (3) support and interactions, (4) self-confidence, (5) career decisions, and (6) time demands related to a science career. The themes identified were important factors in preparing these past female fellows for a career in science by initiating a change in their attitudes, knowledge, and skills. With over 90% of past fellows currently pursuing a science career, the program, through research experience and encouraging mentors, made a large impact on the career paths of fellows

  12. Fatty acid translocase gene CD36 rs1527483 variant influences oral fat perception in Malaysian subjects.

    PubMed

    Ong, Hing-Huat; Tan, Yen-Nee; Say, Yee-How

    2017-01-01

    We determined whether single nucleotide polymorphisms (SNPs; rs1761667 and rs1527483) in the fatty acid translocase CD36 gene - a receptor for fatty acids - is associated with oral fat perception (OFP) of different fat contents in custards and commercially-available foods, and obesity measures in Malaysian subjects (n=313; 118 males, 293 ethnic Chinese; 20 ethnic Indians). A 170-mm visual analogue scale was used to assess the ratings of perceived fat content, oiliness and creaminess of 0%, 2%, 6% and 10% fat content-by-weight custards and low-fat/regular versions of commercially-available milk, mayonnaise and cream crackers. Overall, the subjects managed to significantly discriminate the fat content, oiliness and creaminess between low-fat/regular versions of milk and mayonnaise. Females rated the perception of fat content and oiliness of both milks higher, but ethnicity, obesity and adiposity status did not seem to play a role in influencing most of OFP. The overall minor allele frequencies for rs1761667 and rs1527483 were 0.30 and 0.26, respectively. Females and individuals with rs1527483 TT genotype significantly perceived greater creaminess of 10% fat-by-weight custard. Also, individuals with rs1527483 TT genotype and T allele significantly perceived greater fat content of cream crackers, independent of fat concentration. rs1761667 SNP did not significantly affect OFP, except for cream crackers. Both gene variants were also not associated with obesity measures. Taken together, this study supports the notion that CD36 - specifically rs1527483, plays a role in OFP, but not in influencing obesity in Malaysian subjects. Besides, gender is an important factor for OFP, where females had higher sensitivity.

  13. Genetic Influences on Hand Osteoarthritis in Finnish Women – A Replication Study of Candidate Genes

    PubMed Central

    Hämäläinen, Satu; Solovieva, Svetlana; Vehmas, Tapio; Luoma, Katariina; Leino-Arjas, Päivi; Hirvonen, Ari

    2014-01-01

    Objectives Our aims were to replicate some previously reported associations of single nucleotide polymorphisms (SNPs) in five genes (A2BP1, COG5, GDF5, HFE, ESR1) with hand osteoarthritis (OA), and to examine whether genes (BCAP29, DIO2, DUS4L, DVWA, HLA, PTGS2, PARD3B, TGFB1 and TRIB1) associated with OA at other joint sites were associated with hand OA among Finnish women. Design We examined the bilateral hand radiographs of 542 occupationally active Finnish female dentists and teachers aged 45 to 63 and classified them according to the presence of OA by using reference images. Data regarding finger joint pain and other risk factors were collected using a questionnaire. We defined two hand OA phenotypes: radiographic OA in at least three joints (ROA) and symptomatic DIP OA. The genotypes were determined by PCR-based methods. In statistical analysis, we used SNPStats software, the chi-square test and logistic regression. Results Of the SNPs, rs716508 in A2BP1 was associated with ROA (OR = 0.7, 95% CI 0.5–0.9) and rs1800470 in TGFB1 with symptomatic DIP OA (1.8, 1.2–2.9). We found an interaction between ESR1 (rs9340799) and occupation: teachers with the minor allele were at an increased risk of symptomatic DIP OA (2.8, 1.3–6.5). We saw no association among the dentists. We also found that the carriage of the COG5 rs3757713 C allele increased the risk of ROA only among women with the BCAP29 rs10953541 CC genotype (2.6; 1.1–6.1). There was also a suggestive interaction between the HFE rs179945 and the ESR1 rs9340799, and the carriage of the minor allele of either of these SNPs was associated with an increased risk of symptomatic DIP OA (2.1, 1.3–2.5). Conclusions Our results support the earlier findings of A2BP1 and TBGF1 being OA susceptibility genes and provide evidence of a possible gene-gene interaction in the genetic influence on hand OA predisposition. PMID:24825461

  14. Human influence and biotic homogenization drive the distribution of Escherichia coli virulence genes in natural habitats.

    PubMed

    Cabal, Adriana; Vicente, Joaquin; Alvarez, Julio; Barasona, Jose Angel; Boadella, Mariana; Dominguez, Lucas; Gortazar, Christian

    2017-02-18

    Cattle are the main reservoirs for Shiga-toxin-producing Escherichia coli (STEC), the only known zoonotic intestinal E. coli pathotype. However, there are other intestinal pathotypes that can cause disease in humans, whose presence has been seldom investigated. Thus, our aim was to identify the effects of anthropic pressure and of wild and domestic ungulate abundance on the distribution and diversity of the main human E. coli pathotypes and nine of their representative virulence genes (VGs). We used a quantitative real-time PCR (qPCR) for the direct detection and quantification of the genus-specific gene uidA, nine E. coli VGs (stx1, sxt2, eae, ehxA, aggR, est, elt, bfpA, invA), as well as four genes related to O157:H7 (rfbO157 , fliCH7 ) and O104:H4 (wzxO104 , fliCH4 ) serotypes in animals (feces from deer, cattle, and wild boar) and water samples collected in three areas of Doñana National Park (DNP), Spain. Eight of the nine VGs were detected, being invA, eae, and stx2 followed by stx1, aggR, and ehxA the most abundant ones. In quantitative terms (gene copies per mg of sample), stx1 and stx2 gave the highest values. Significant differences were seen regarding VGs in the three animal species in the three sampled areas. The serotype-related genes were found in all but one sample types. In general, VGs were more diverse and abundant in the northern part of the Park, where the surface waters are more contaminated by human waste and farms. In the current study, we demonstrated that human influence is more relevant than host species in shaping the E. coli VGs spatial pattern and diversity in DNP. In addition, wildlife could be potential reservoirs for other pathotypes different from STEC, however further isolation steps would be needed to completely characterize those E. coli.

  15. Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

    PubMed Central

    Camp, J. Gray; Badsha, Farhath; Florio, Marta; Kanton, Sabina; Gerber, Tobias; Wilsch-Bräuninger, Michaela; Lewitus, Eric; Sykes, Alex; Hevers, Wulf; Lancaster, Madeline; Knoblich, Juergen A.; Lachmann, Robert; Pääbo, Svante; Huttner, Wieland B.; Treutlein, Barbara

    2015-01-01

    Cerebral organoids—3D cultures of human cerebral tissue derived from pluripotent stem cells—have emerged as models of human cortical development. However, the extent to which in vitro organoid systems recapitulate neural progenitor cell proliferation and neuronal differentiation programs observed in vivo remains unclear. Here we use single-cell RNA sequencing (scRNA-seq) to dissect and compare cell composition and progenitor-to-neuron lineage relationships in human cerebral organoids and fetal neocortex. Covariation network analysis using the fetal neocortex data reveals known and previously unidentified interactions among genes central to neural progenitor proliferation and neuronal differentiation. In the organoid, we detect diverse progenitors and differentiated cell types of neuronal and mesenchymal lineages and identify cells that derived from regions resembling the fetal neocortex. We find that these organoid cortical cells use gene expression programs remarkably similar to those of the fetal tissue to organize into cerebral cortex-like regions. Our comparison of in vivo and in vitro cortical single-cell transcriptomes illuminates the genetic features underlying human cortical development that can be studied in organoid cultures. PMID:26644564

  16. A physical map of important QTLs, functional markers and genes available for sesame breeding programs.

    PubMed

    Dossa, Komivi

    2016-10-01

    Sesame is one of the oldest oilseed crops grown mainly in Africa and Asia. Although genetic and genomic studies on sesame have started late, the past 5 years have witnessed extensive progresses in these areas on this crop. Important genomic sequence resources such as functional markers, genes and QTLs linked to agronomically important traits, have been generated through linkage mapping and association analysis to assist sesame improvement programs. However, most of these data are scattered in different maps making them hard to be exploited efficiently in breeding programs. In this study, we report a comprehensive physical map gathering 151 published genomic sequence resources which highlighted some hotspot functional regions in the sesame genome. Moreover, 83,135 non-redundant SSRs have been supplied along with their physical position and motif composition. This will assist future research in fine mapping or pinpointing more functional genes based on the already published QTLs and functional markers. This physical map represents a good landmark for further non-overlapping genetic and genomic studies working towards sesame improvement.

  17. Human cerebral organoids recapitulate gene expression programs of fetal neocortex development.

    PubMed

    Camp, J Gray; Badsha, Farhath; Florio, Marta; Kanton, Sabina; Gerber, Tobias; Wilsch-Bräuninger, Michaela; Lewitus, Eric; Sykes, Alex; Hevers, Wulf; Lancaster, Madeline; Knoblich, Juergen A; Lachmann, Robert; Pääbo, Svante; Huttner, Wieland B; Treutlein, Barbara

    2015-12-22

    Cerebral organoids-3D cultures of human cerebral tissue derived from pluripotent stem cells-have emerged as models of human cortical development. However, the extent to which in vitro organoid systems recapitulate neural progenitor cell proliferation and neuronal differentiation programs observed in vivo remains unclear. Here we use single-cell RNA sequencing (scRNA-seq) to dissect and compare cell composition and progenitor-to-neuron lineage relationships in human cerebral organoids and fetal neocortex. Covariation network analysis using the fetal neocortex data reveals known and previously unidentified interactions among genes central to neural progenitor proliferation and neuronal differentiation. In the organoid, we detect diverse progenitors and differentiated cell types of neuronal and mesenchymal lineages and identify cells that derived from regions resembling the fetal neocortex. We find that these organoid cortical cells use gene expression programs remarkably similar to those of the fetal tissue to organize into cerebral cortex-like regions. Our comparison of in vivo and in vitro cortical single-cell transcriptomes illuminates the genetic features underlying human cortical development that can be studied in organoid cultures.

  18. FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences.

    PubMed

    Schiex, Thomas; Gouzy, Jérôme; Moisan, Annick; de Oliveira, Yannick

    2003-07-01

    We describe FrameD, a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction and frameshift correction in unfinished sequences such as EST and EST cluster sequences. Like recent eukaryotic gene prediction programs, FrameD also includes the ability to take into account protein similarity information both in its prediction and its graphical output. Its performances are evaluated on different bacterial genomes. The web site (http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD) allows direct prediction, sequence correction and translation and the ability to learn new models for new organisms.

  19. FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences

    PubMed Central

    Schiex, Thomas; Gouzy, Jérôme; Moisan, Annick; de Oliveira, Yannick

    2003-01-01

    We describe FrameD, a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction and frameshift correction in unfinished sequences such as EST and EST cluster sequences. Like recent eukaryotic gene prediction programs, FrameD also includes the ability to take into account protein similarity information both in its prediction and its graphical output. Its performances are evaluated on different bacterial genomes. The web site (http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD) allows direct prediction, sequence correction and translation and the ability to learn new models for new organisms. PMID:12824407

  20. The Bacterial iprA Gene Is Conserved across Enterobacteriaceae, Is Involved in Oxidative Stress Resistance, and Influences Gene Expression in Salmonella enterica Serovar Typhimurium

    PubMed Central

    Herman, Allison; Serfecz, Jacquelyn; Kinnally, Alexandra; Crosby, Kathleen; Youngman, Matthew; Wykoff, Dennis

    2016-01-01

    ABSTRACT The iprA gene (formerly known as yaiV or STM0374) is located in a two-gene operon in the Salmonella enterica serovar Typhimurium genome and is associated with altered expression during spaceflight and rotating-wall-vessel culture conditions that increase virulence. However, iprA is uncharacterized in the literature. In this report, we present the first targeted characterization of this gene, which revealed that iprA is highly conserved across Enterobacteriaceae. We found that S. Typhimurium, Escherichia coli, and Enterobacter cloacae ΔiprA mutant strains display a multi-log-fold increase in oxidative stress resistance that is complemented using a plasmid-borne wild-type (WT) copy of the S. Typhimurium iprA gene. This observation was also associated with increased catalase activity, increased S. Typhimurium survival in macrophages, and partial dependence on the katE gene and full dependence on the rpoS gene. Our results indicate that IprA protein activity is sensitive to deletion of the N- and C-terminal 10 amino acids, while a region that includes amino acids 56 to 80 is dispensable for activity. RNA sequencing (RNA-Seq) analysis revealed several genes altered in expression in the S. Typhimurium ΔiprA mutant strain compared to the WT, including those involved in fimbria formation, spvABCD-mediated virulence, ethanolamine utilization, the phosphotransferase system (PTS) transport, and flagellin phase switching from FlgB to FliC (likely a stochastic event) and several genes of hypothetical or putative function. IMPORTANCE Overall, this work reveals that the conserved iprA gene measurably influences bacterial biology and highlights the pool of currently uncharacterized genes that are conserved across bacterial genomes. These genes represent potentially useful targets for bacterial engineering, vaccine design, and other possible applications. PMID:27246569

  1. Influence of interactions between genes and childhood trauma on refractoriness in psychiatric disorders.

    PubMed

    Kim, Ji Sun; Lee, Seung-Hwan

    2016-10-03

    Psychiatric disorders are excellent disease models in which gene-environmental interaction play a significant role in the pathogenesis. Childhood trauma has been known as a significant environmental factor in the progress of, and prognosis for psychiatric illness. Patients with refractory illness usually have more severe symptoms, greater disability, lower quality of life and are at greater risk of suicide than other psychiatric patients. Our literature review uncovered some important clinical factors which modulate response to treatment in psychiatric patients who have experienced childhood trauma. Childhood trauma seems to be a critical determinant of treatment refractoriness in psychotic disorder, bipolar disorder, major depressive disorder, and post-traumatic stress disorder. In patients with psychotic disorders, the relationship between childhood trauma and treatment-refractoriness appears to be mediated by cognitive impairment. In the case of bipolar disorder, the relationship appears to be mediated by greater affective disturbance and earlier onset, while in major depressive disorder the mediating factors are persistent, severe symptoms and frequent recurrence. In suicidal individuals, childhood maltreatment was associated with violent suicidal attempts. In the case of PTSD patients, it appears that childhood trauma makes the brain more vulnerable to subsequent trauma, thus resulting in more severe, refractory symptoms. Given that several studies have suggested that there are distinct subtypes of genetic vulnerability to childhood trauma, it is important to understand how gene-environment interactions influence the course of psychiatric illnesses in order to improve therapeutic strategies.

  2. Evidence for a gene influencing reading disability on chromosome 6p in two populations

    SciTech Connect

    Smith, S.D.; Brower, A.M.; Kimberling, W.J.

    1994-09-01

    A genetic contribution to specific reading disability has been demonstrated by twin studies, and segregation analysis has supported a dominant gene effect. In an effort to localize genes influencing reading disability, we have ascertained two independent populations of families: kindreds which were selected to have a three generation history of reading diability in an autosomal dominant pattern; and families with dizygotic twins, at least one of which has been diagnosed with reading disability. All available family members were given a battery of tests to measure reading and spelling ability and intelligence, and qualitative and quantitative phenotypes for reading disability were derived. Blood samples were obtained for genotyping on all consenting family members, in concordance with IRB requirements. Linkage analysis was performed by the sib pair method utilizing the S.A.G.E. (1992) package and by a differential regression technique developed by DeFries and Fulker (1985). In both populations and by both linkage techniques, several markers in the HLA region of chromosome 6p showed results suggestive of linkage, with the effect most pronounced in the twin families. Significance levels were enhanced when only the more severely affected subjects were analyzed with the differential regression technique.

  3. Thrombin and exercise similarly influence expression of cell cycle genes in cultured putative endothelial progenitor cells.

    PubMed

    Lockard, Michael M; Witkowski, Sarah; Jenkins, Nathan T; Spangenburg, Espen E; Obisesan, Thomas O; Hagberg, James M

    2010-06-01

    Acute exercise and exercise training may influence putative endothelial progenitor cell (EPC) number and colony forming units (CFU-ECs), although the mechanisms remain unclear. This study examined the effects of in vitro thrombin supplementation and acute exercise on CFU-EC gene expression, associated with cellular proliferation and differentiation. The effect of habitual physical activity was evaluated through analysis of EPCs from chronically high- and low-active men. Participants were healthy high- and low-active men (n=23), aged 55-80 yr. Circulating CD34+/VEGFR2+ number, CFU-ECs, plasma prothrombin fragment (F1+2), and thrombin-antithrombin III were measured at rest and after 30 min of exercise. Gene expression of cyclin A2, cyclin D1, p27, VE-cadherin, and VEGFR2 was assessed in postexercise CFU-ECs and resting CFU-ECs treated with 0, 1, 5, or 10 U/ml of thrombin. Outcomes were compared between high- and low-active participants. F1+2 and thrombin-antithrombin III, but not CD34+/VEGFR2+ number and CFU-ECs, increased with exercise. Exercise-induced changes in F1+2 correlated with changes in CD34+/VEGFR2+ number in both groups. Thrombin treatments and acute exercise increased cyclin A2 and cyclin D1 expression and decreased p27 expression. One unit per milliliter thrombin increased VEGFR2 and VE-cadherin expression, whereas 5 U/ml, 10 U/ml, and acute exercise did not elicit any changes. An exercise training effect was observed with greater decreases in p27 expression with 5 and 10 U/ml thrombin and greater increases in VEGFR2 and VE-cadherin expression with 1 U/ml thrombin in high-active men. Exercise-induced changes in putative EPC gene expression are associated with thrombin production and may be modulated by long-term exercise training.

  4. Thrombin and exercise similarly influence expression of cell cycle genes in cultured putative endothelial progenitor cells

    PubMed Central

    Lockard, Michael M.; Witkowski, Sarah; Jenkins, Nathan T.; Spangenburg, Espen E.; Obisesan, Thomas O.

    2010-01-01

    Acute exercise and exercise training may influence putative endothelial progenitor cell (EPC) number and colony forming units (CFU-ECs), although the mechanisms remain unclear. This study examined the effects of in vitro thrombin supplementation and acute exercise on CFU-EC gene expression, associated with cellular proliferation and differentiation. The effect of habitual physical activity was evaluated through analysis of EPCs from chronically high- and low-active men. Participants were healthy high- and low-active men (n = 23), aged 55–80 yr. Circulating CD34+/VEGFR2+ number, CFU-ECs, plasma prothrombin fragment (F1+2), and thrombin-antithrombin III were measured at rest and after 30 min of exercise. Gene expression of cyclin A2, cyclin D1, p27, VE-cadherin, and VEGFR2 was assessed in postexercise CFU-ECs and resting CFU-ECs treated with 0, 1, 5, or 10 U/ml of thrombin. Outcomes were compared between high- and low-active participants. F1+2 and thrombin-antithrombin III, but not CD34+/VEGFR2+ number and CFU-ECs, increased with exercise. Exercise-induced changes in F1+2 correlated with changes in CD34+/VEGFR2+ number in both groups. Thrombin treatments and acute exercise increased cyclin A2 and cyclin D1 expression and decreased p27 expression. One unit per milliliter thrombin increased VEGFR2 and VE-cadherin expression, whereas 5 U/ml, 10 U/ml, and acute exercise did not elicit any changes. An exercise training effect was observed with greater decreases in p27 expression with 5 and 10 U/ml thrombin and greater increases in VEGFR2 and VE-cadherin expression with 1 U/ml thrombin in high-active men. Exercise-induced changes in putative EPC gene expression are associated with thrombin production and may be modulated by long-term exercise training. PMID:20378705

  5. Variants in toll-like receptor 9 gene influence susceptibility to tuberculosis in a Mexican population

    PubMed Central

    2013-01-01

    Background The control of Mycobacterium tuberculosis (Mtb) infection begins with the recognition of mycobacterial structural components by toll like receptors (TLRs) and other pattern recognition receptors. Our objective was to determine the influence of TLRs polymorphisms in the susceptibility to develop tuberculosis (TB) in Amerindian individuals from a rural area of Oaxaca, Mexico with high TB incidence. Methods We carried out a case–control association community based study, genotyping 12 polymorphisms of TLR2, TLR4, TLR6 and TLR9 genes in 90 patients with confirmed pulmonary TB and 90 unrelated exposed but asymptomatic household contacts. Results We found a significant increase in the frequency of the allele A of the TLR9 gene polymorphism rs352139 (A>G) in the group of TB patients (g.f. = 0.522) when compared with controls (g.f. = 0.383), (Pcorr = 0.01, OR = 1.75). Under the recessive model (A/G + A/A vs G/G) this polymorphism was also significantly associated with TB (Pcorr = 0.01, OR= 2.37). The association of the SNP rs352139 was statistically significant after adjustment by age, gender and comorbidities by regression logistic analysis (Dominant model: p value = 0.016, OR = 2.31; Additive model: p value = 0.023, OR = 1.68). The haplotype GAA of TLR9 SNPs was also associated with TB susceptibility (Pcorr = 0.02). Differences in the genotype or allele frequencies of TLR2, TLR4 and TLR6 polymorphisms between TB patients and healthy contacts were not detected. Conclusions Our study suggests that the allele A of the intronic polymorphism rs352139 on TLR9 gene might contribute to the risk of developing TB in Mexican Amerindians. PMID:24053111

  6. Induction of a program gene expression during osteoblast differentiation with strontium ranelate

    SciTech Connect

    Zhu Lingling; Zaidi, Samir; Peng Yuanzhen; Zhou Hang; Moonga, Baljit S.; Blesius, Alexia; Dupin-Roger, Isabelle; Zaidi, Mone . E-mail: mone.zaidi@mssm.edu; Sun Li

    2007-04-06

    Strontium ranelate, a new agent for the treatment of osteoporosis, has been shown stimulate bone formation in various experimental models. This study examines the effect of strontium ranelate on gene expression in osteoblasts, as well as the formation of mineralized (von Kossa-positive) colony-forming unit-osteoblasts (CFU-obs). Bone marrow-derived stromal cells cultured for 21 days under differentiating conditions, when exposed to strontium ranelate, displayed a significant time- and concentration-dependent increase in the expression of the master gene, Runx2, as well as bone sialoprotein (BSP), but interestingly without effects on osteocalcin. This was associated with a significant increase in the formation of CFU-obs at day 21 of culture. In U-33 pre-osteoblastic cells, strontium ranelate significantly enhanced the expression of Runx2 and osteocalcin, but not BSP. Late, more mature osteoblastic OB-6 cells showed significant elevations in BSP and osteocalcin, but with only minimal effects on Runx2. In conclusion, strontium ranelate stimulates osteoblast differentiation, but the induction of the program of gene expression appears to be cell type-specific. The increased osteoblastic differentiation is the likely basis underlying the therapeutic bone-forming actions of strontium ranelate.

  7. A tomato metacaspase gene is upregulated during programmed cell death in Botrytis cinerea-infected leaves.

    PubMed

    Hoeberichts, Frank A; ten Have, Arjen; Woltering, Ernst J

    2003-07-01

    Programmed cell death (PCD) in plant cells is often accompanied by biochemical and morphological hallmarks similar to those of animal apoptosis. However, orthologs of animal caspases, cysteinyl aspartate-specific proteases that constitute the core component of animal apoptosis, have not yet been identified in plants. Recent studies have revealed the presence of a family of genes encoding proteins with distant homology to mammalian caspases, designated metacaspases, in the Arabidopsis thaliana genome. Here, we describe the isolation of LeMCA1, a type-II metacaspase cDNA clone from tomato (Lycopersicon esculentum Mill.). BLAST analysis demonstrated that the LeMCA1 gene is located in close vicinity of several genes that have been linked with PCD. Southern analysis indicated the existence of at least one more metacaspase in the tomato genome. LeMCA1 mRNA levels rapidly increased upon infection of tomato leaves with Botrytis cinerea, a fungal pathogen that induces cell death in several plant species. LeMCA1 was not upregulated during chemical-induced PCD in suspension-cultured tomato cells.

  8. A computer program for the simulation of folds of different sizes under the influence of gravity

    NASA Astrophysics Data System (ADS)

    Vacas Peña, José M.; Martínez Catalán, José R.

    2004-02-01

    Folding&g is a computer program, based on the finite element method, developed to simulate the process of natural folding from small to large scales in two dimensions. Written in Pascal code and compiled with Borland Delphi 3.0, the program has a friendly interactive user interface and can be used for research as well as educational purposes. Four main menu options allow the user to import or to build and to save a model data file, select the type of graphic output, introduce and modify several physical parameters and enter the calculation routines. The program employs isoparametric, initially rectangular elements with eight nodes, which can sustain large deformations. The mathematical procedure is based on the elasticity equations, but has been modified to simulate a viscous rheology, either linear or of power-law type. The parameters to be introduced include either the linear viscosity, or, when the viscosity is non-linear, the material constant, activation energy, temperature and power of the differential stress. All the parameters can be set by rows, which simulate layers. A toggle permits gravity to be introduced into the calculations. In this case, the density of the different rows must be specified, and the sizes of the finite elements and of the whole model become meaningful. Viscosity values can also be assigned to blocks of several rows and columns, which permits the modelling of heterogeneities such as rectangular areas of high strength, which can be used to simulate shearing components interfering with the buckling process. The program is applied to several cases of folding, including a single competent bed and multilayers, and its results compared with analytical and experimental results. The influence of gravity is illustrated by the modelling of diapiric structures and of a large recumbent fold.

  9. Assessment of the influence of field size on maize gene flow using SSR analysis.

    PubMed

    Palaudelmàs, M; Melé, E; Monfort, A; Serra, J; Salvia, J; Messeguer, J

    2012-06-01

    One of the factors that may influence the rate of cross-fertilization is the relative size of the pollen donor and receptor fields. We designed a spatial distribution with four varieties of genetically-modified (GM) yellow maize to generate different sized fields while maintaining a constant distance to neighbouring fields of conventional white kernel maize. Samples of cross-fertilized, yellow kernels in white cobs were collected from all of the adjacent fields at different distances. A special series of samples was collected at distances of 0, 2, 5, 10, 20, 40, 80 and 120 m following a transect traced in the dominant down-wind direction in order to identify the origin of the pollen through SSR analysis. The size of the receptor fields should be taken into account, especially when they extend in the same direction than the GM pollen flow is coming. From collected data, we then validated a function that takes into account the gene flow found in the field border and that is very useful for estimating the % of GM that can be found in any point of the field. It also serves to predict the total GM content of the field due to cross fertilization. Using SSR analysis to identify the origin of pollen showed that while changes in the size of the donor field clearly influence the percentage of GMO detected, this effect is moderate. This study demonstrates that doubling the donor field size resulted in an approximate increase of GM content in the receptor field of 7%. This indicates that variations in the size of the donor field have a smaller influence on GM content than variations in the size of the receptor field.

  10. Polymorphisms in MIR137HG and microRNA-137-regulated genes influence gray matter structure in schizophrenia

    DOE PAGES

    Wright, C.; Gupta, C. N.; Chen, J.; ...

    2016-02-02

    Evidence suggests that microRNA-137 (miR-137) is involved in the genetic basis of schizophrenia. Risk variants within the miR-137 host gene (MIR137HG) influence structural and functional brain-imaging measures, and miR-137 itself is predicted to regulate hundreds of genes. We evaluated the influence of a MIR137HG risk variant (rs1625579) in combination with variants in miR-137- regulated genes TCF4, PTGS2, MAPK1 and MAPK3 on gray matter concentration (GMC). These genes were selected based on our previous work assessing schizophrenia risk within possible miR-137-regulated gene sets using the same cohort of subjects. A genetic risk score (GRS) was determined based on genotypes of thesemore » four schizophrenia risk-associated genes in 221 Caucasian subjects (89 schizophrenia patients and 132 controls). The effects of the rs1625579 genotype with the GRS of miR-137-regulated genes in a three-way interaction with diagnosis on GMC patterns were assessed using a multivariate analysis. We found that schizophrenia subjects homozygous for the MIR137HG risk allele show significant decreases in occipital, parietal and temporal lobe GMC with increasing miR-137-regulated GRS, whereas those carrying the protective minor allele show significant increases in GMC with GRS. No correlations of GMC and GRS were found in control subjects. Variants within or upstream of genes regulated by miR-137 in combination with the MIR137HG risk variant may influence GMC in schizophrenia-related regions in patients. Furthermore, given that the genes evaluated here are involved in protein kinase A signaling, dysregulation of this pathway through alterations in miR-137 biogenesis may underlie the gray matter loss seen in the disease.« less

  11. Polymorphisms in MIR137HG and microRNA-137-regulated genes influence gray matter structure in schizophrenia.

    PubMed

    Wright, C; Gupta, C N; Chen, J; Patel, V; Calhoun, V D; Ehrlich, S; Wang, L; Bustillo, J R; Perrone-Bizzozero, N I; Turner, J A

    2016-02-02

    Evidence suggests that microRNA-137 (miR-137) is involved in the genetic basis of schizophrenia. Risk variants within the miR-137 host gene (MIR137HG) influence structural and functional brain-imaging measures, and miR-137 itself is predicted to regulate hundreds of genes. We evaluated the influence of a MIR137HG risk variant (rs1625579) in combination with variants in miR-137-regulated genes TCF4, PTGS2, MAPK1 and MAPK3 on gray matter concentration (GMC). These genes were selected based on our previous work assessing schizophrenia risk within possible miR-137-regulated gene sets using the same cohort of subjects. A genetic risk score (GRS) was determined based on genotypes of these four schizophrenia risk-associated genes in 221 Caucasian subjects (89 schizophrenia patients and 132 controls). The effects of the rs1625579 genotype with the GRS of miR-137-regulated genes in a three-way interaction with diagnosis on GMC patterns were assessed using a multivariate analysis. We found that schizophrenia subjects homozygous for the MIR137HG risk allele show significant decreases in occipital, parietal and temporal lobe GMC with increasing miR-137-regulated GRS, whereas those carrying the protective minor allele show significant increases in GMC with GRS. No correlations of GMC and GRS were found in control subjects. Variants within or upstream of genes regulated by miR-137 in combination with the MIR137HG risk variant may influence GMC in schizophrenia-related regions in patients. Given that the genes evaluated here are involved in protein kinase A signaling, dysregulation of this pathway through alterations in miR-137 biogenesis may underlie the gray matter loss seen in the disease.

  12. LIN28A Modulates Splicing and Gene Expression Programs in Breast Cancer Cells.

    PubMed

    Yang, Jun; Bennett, Brian D; Luo, Shujun; Inoue, Kaoru; Grimm, Sara A; Schroth, Gary P; Bushel, Pierre R; Kinyamu, H Karimi; Archer, Trevor K

    2015-09-01

    LIN28 is an evolutionarily conserved RNA-binding protein with critical functions in developmental timing and cancer. However, the molecular mechanisms underlying LIN28's oncogenic properties are yet to be described. RNA-protein immunoprecipitation coupled with genome-wide sequencing (RIP-Seq) analysis revealed significant LIN28 binding within 843 mRNAs in breast cancer cells. Many of the LIN28-bound mRNAs are implicated in the regulation of RNA and cell metabolism. We identify heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), a protein with multiple roles in mRNA metabolism, as a LIN28-interacting partner. Subsequently, we used a custom computational method to identify differentially spliced gene isoforms in LIN28 and hnRNP A1 small interfering RNA (siRNA)-treated cells. The results reveal that these proteins regulate alternative splicing and steady-state mRNA expression of genes implicated in aspects of breast cancer biology. Notably, cells lacking LIN28 undergo significant isoform switching of the ENAH gene, resulting in a decrease in the expression of the ENAH exon 11a isoform. The expression of ENAH isoform 11a has been shown to be elevated in breast cancers that express HER2. Intriguingly, analysis of publicly available array data from the Cancer Genome Atlas (TCGA) reveals that LIN28 expression in the HER2 subtype is significantly different from that in other breast cancer subtypes. Collectively, our data suggest that LIN28 may regulate splicing and gene expression programs that drive breast cancer subtype phenotypes.

  13. [Influence of silver and titanium dioxide nanoparticles on the expression of genes of biomarkers of inflammatory responses and apoptosis].

    PubMed

    Baranova, L A; Zhornik, E V; Volotovski, I D

    2015-01-01

    In order to evaluate the toxic effect of silver (AgNP) and titanium dioxide (TiO2) nanoparticles their influence on the expression of genes of biomarkers of inflammatory responses and apoptosis in human lymphocytes was studied. An increase in the IL-6, IL-8, TNF-α and p53 genes expression in the concentration range of silver and titanium dioxide nanoparticles of 10-40 μk g/ml was found. Increased expression of IL-6, IL-8, TNF-α and p53 genes under the nanoparticles action indicates the stimulation of the immune system and of apoptosis, respectively.

  14. A polymorphic (GA/CT)n- SSR influences promoter activity of Tryptophan decarboxylase gene in Catharanthus roseus L. Don

    PubMed Central

    Kumar, Santosh; Bhatia, Sabhyata

    2016-01-01

    Simple Sequence Repeats (SSRs) of polypurine-polypyrimidine type motifs occur very frequently in the 5′ flanks of genes in plants and have recently been implicated to have a role in regulation of gene expression. In this study, 2 accessions of Catharanthus roseus having (CT)8 and (CT)21 varying motifs in the 5′UTR of Tryptophan decarboxylase (Tdc) gene, were investigated for its role in regulation of gene expression. Extensive Tdc gene expression analysis in the 2 accessions was carried out both at the level of transcription and translation. Transcript abundance was estimated using Northern analysis and qRT-PCR, whereas the rate of Tdc gene transcription was assessed using in-situ nuclear run-on transcription assay. Translation status of Tdc gene was monitored by quantification of polysome associated Tdc mRNA using qRT-PCR. These observations were validated through transient expression analysis using the fusion construct [CaM35S:(CT)8–21:GUS]. Our study demonstrated that not only does the length of (CT)n -SSRs influences the promoter activity, but the presence of SSRs per se in the 5′-UTR significantly enhances the level of gene expression. We termed this phenomenon as “microsatellite mediated enhancement” (MME) of gene expression. Results presented here will provide leads for engineering plants with enhanced amounts of medicinally important alkaloids. PMID:27623355

  15. Socio-environmental and endocrine influences on developmental and caste-regulatory gene expression in the eusocial termite Reticulitermes flavipes

    PubMed Central

    2010-01-01

    Background Strict regulation of caste differentiation, at the molecular level, is thought to be important to maintain social structure in insect societies. Previously, a number of extrinsic and intrinsic factors have been shown to influence caste composition in termite colonies. One important factor is the influence of nestmates; in particular, soldier termites are known to inhibit hormone-dependent worker-to-soldier differentiation. However, soldier influences on nestmates at the molecular level are virtually unknown. Here, to test the hypothesis that soldiers can influence nestmate gene expression, we investigated the impact of four treatments on whole-body gene expression in totipotent Reticulitermes flavipes workers: (i) juvenile hormone III (JHIII; a morphogenetic hormone), (ii) soldier head extracts (SHE), (iii) JHIII+SHE, and (iv) live soldiers. Results Using quantitative-real-time PCR we determined the expression patterns of 49 previously identified candidate genes in response to the four treatments at assay days 1, 5, and 10. Thirty-eight total genes from three categories (chemical production/degradation, hemolymph protein, and developmental) showed significant differential expression among treatments. Most importantly, SHE and live soldier treatments had a significant impact on a number of genes from families known to play roles in insect development, supporting previous findings and hypotheses that soldiers regulate nestmate caste differentiation via terpene primer pheromones contained in their heads. Conclusions This research provides new insights into the impacts that socio-environmental factors (JH, soldiers, primer pheromones) can have on termite gene expression and caste differentiation, and reveals a number of socially-relevant genes for investigation in subsequent caste differentiation research. PMID:20416061

  16. Benefits of mother goose: influence of a community-based program on parent-child attachment relationships in typical families.

    PubMed

    Scharfe, Elaine

    2011-01-01

    An estimated 50 to 60% of children from typical families develop secure attachment relationships with their parents (Ainsworth, Blehar, Waters, & Wall, 1978; Van IJzendoorn & Kroonenberg, 1988); however, intervention research has focused primarily on interventions for high-risk clinical samples (Berlin, Zeanah, & Lieberman, 2008). In this project, the influence of a popular community-based parent-child program was assessed in a non-clinical sample of families. Families participating in a 10-week Parent-Child Mother Goose Program (n.d.) and families on the waitlist for the program were asked to complete questionnaires to assess parenting efficacy and satisfaction as well as parents' perception of their own and their child's attachment styles at the beginning of the program, the end of the program, and six months later. Mothers in the program group reported significantly more positive change in their reports of parenting efficacy over time and also reported significantly more change in their children's attachment category. Specifically, children in the program group were significantly more likely to be classified as secure over time (55% at T1 to 81% at T3) as compared to the waitlist participants (45% at T1 to 62% at T2). In this popular 10-week, community-based program, parents learned skills that continued to influence their relationship with their children six months after the conclusion of the program.

  17. Developing the leadership skills of new graduates to influence practice environments: a novice nurse leadership program.

    PubMed

    Dyess, Susan; Sherman, Rose

    2011-01-01

    The authors of the recently published Institute of Medicine on the Future of Nursing report emphasized the importance of preparing nurses to lead change to advance health care in the United States. Other scholars linked practice environments to safe quality care. In order for nurses to fully actualize this role in practice environments, they need to possess leadership skills sets that identify and respond to challenges faced. New nurses are no exception. This article presents a program with a 5-year track record that is designed to support transition and enhance the skill sets of leadership for new nurses in their first year of practice. Qualitative and quantitative evaluation measurements at baseline and postprogram provided data for evaluation of the first 4 cohorts in the program. Evaluative outcomes presented indicate that new nurses gained leadership and translational research skills that contributed to their ability to influence practice environments. Nonetheless, practice environments continue to need improvement and ongoing leadership from all levels of nursing must be upheld.

  18. Transcriptome-Wide Mapping of Pea Seed Ageing Reveals a Pivotal Role for Genes Related to Oxidative Stress and Programmed Cell Death

    PubMed Central

    Colville, Louise; Lorenzo, Oscar; Graeber, Kai; Küster, Helge; Leubner-Metzger, Gerhard; Kranner, Ilse

    2013-01-01

    Understanding of seed ageing, which leads to viability loss during storage, is vital for ex situ plant conservation and agriculture alike. Yet the potential for regulation at the transcriptional level has not been fully investigated. Here, we studied the relationship between seed viability, gene expression and glutathione redox status during artificial ageing of pea (Pisum sativum) seeds. Transcriptome-wide analysis using microarrays was complemented with qRT-PCR analysis of selected genes and a multilevel analysis of the antioxidant glutathione. Partial degradation of DNA and RNA occurred from the onset of artificial ageing at 60% RH and 50°C, and transcriptome profiling showed that the expression of genes associated with programmed cell death, oxidative stress and protein ubiquitination were altered prior to any sign of viability loss. After 25 days of ageing viability started to decline in conjunction with progressively oxidising cellular conditions, as indicated by a shift of the glutathione redox state towards more positive values (>−190 mV). The unravelling of the molecular basis of seed ageing revealed that transcriptome reprogramming is a key component of the ageing process, which influences the progression of programmed cell death and decline in antioxidant capacity that ultimately lead to seed viability loss. PMID:24205239

  19. Transcriptome-wide mapping of pea seed ageing reveals a pivotal role for genes related to oxidative stress and programmed cell death.

    PubMed

    Chen, Hongying; Osuna, Daniel; Colville, Louise; Lorenzo, Oscar; Graeber, Kai; Küster, Helge; Leubner-Metzger, Gerhard; Kranner, Ilse

    2013-01-01

    Understanding of seed ageing, which leads to viability loss during storage, is vital for ex situ plant conservation and agriculture alike. Yet the potential for regulation at the transcriptional level has not been fully investigated. Here, we studied the relationship between seed viability, gene expression and glutathione redox status during artificial ageing of pea (Pisum sativum) seeds. Transcriptome-wide analysis using microarrays was complemented with qRT-PCR analysis of selected genes and a multilevel analysis of the antioxidant glutathione. Partial degradation of DNA and RNA occurred from the onset of artificial ageing at 60% RH and 50°C, and transcriptome profiling showed that the expression of genes associated with programmed cell death, oxidative stress and protein ubiquitination were altered prior to any sign of viability loss. After 25 days of ageing viability started to decline in conjunction with progressively oxidising cellular conditions, as indicated by a shift of the glutathione redox state towards more positive values (>-190 mV). The unravelling of the molecular basis of seed ageing revealed that transcriptome reprogramming is a key component of the ageing process, which influences the progression of programmed cell death and decline in antioxidant capacity that ultimately lead to seed viability loss.

  20. The Earth Education Program Sunship™ Earth: A Mixed Methods Study of the Long-Term Influence on Environmental Attitudes and Actions

    ERIC Educational Resources Information Center

    Bires, Nancy K.

    2013-01-01

    There have been a limited number of studies on the short-term influence of environmental and earth education programs, however, not much information is available about the long-term influence of these programs on participants' environmental attitudes and actions. This mixed methods study explores the long-term influence of the earth education…

  1. Factors Influencing the Improved Academic Success in Literacy at the Knowledge Is Power Program (KIPP) Schools in the Delta Region According to Adult Perceptions

    ERIC Educational Resources Information Center

    Brown, Kimberly J.; Holt, Carleton R.

    2014-01-01

    This qualitative case study explored factors that have influenced literacy success of Knowledge is Power Program (KIPP) students in the low-income, poverty stricken Delta Region of Arkansas. The study examined progress made since implementation of the KIPP Program and the influence the program had made upon student achievement in literacy at the…

  2. Factors Influencing the Improved Academic Success in Literacy at the Knowledge Is Power Program School in the Delta Region According to Administrator, Teacher, and Student Perceptions: Case Study

    ERIC Educational Resources Information Center

    Brown, Kimberly Jonetta

    2012-01-01

    The purpose of this study was to explore the factors that have influenced the literacy success of the Knowledge is Power Program (KIPP) students in the low-income, poverty stricken Delta Region of a mid-south state. The study examined the progress made since the implementation of the KIPP Program and the influence the program has made upon student…

  3. Serum influences the expression of Pseudomonas aeruginosa quorum-sensing genes and QS-controlled virulence genes during early and late stages of growth

    PubMed Central

    Kruczek, Cassandra; Qaisar, Uzma; Colmer-Hamood, Jane A; Hamood, Abdul N

    2014-01-01

    In response to diverse environmental stimuli at different infection sites, Pseudomonas aeruginosa, a serious nosocomial pathogen, coordinates the production of different virulence factors through a complicated network of the hierarchical quorum-sensing (QS) systems including the las, rhl, and the 2-alkyl-4-quinolone-related QS systems. We recently showed that at early stages of growth serum alters the expression of numerous P. aeruginosa genes. In this study, we utilized transcriptional analysis and enzyme assays to examine the effect of serum on the QS and QS-controlled virulence factors during early and late phases of growth of the P. aeruginosa strain PAO1. At early phase, serum repressed the transcription of lasI, rhlI, and pqsA but not lasR or rhlR. However, at late phase, serum enhanced the expression of all QS genes. Serum produced a similar effect on the synthesis of the autoinducers 3OC12-HSL, C4-HSL, and HHQ/PQS. Additionally, serum repressed the expression of several QS-controlled genes in the early phase, but enhanced them in the late phase. Furthermore, serum influenced the expression of different QS-positive (vqsR, gacA, and vfr) as well as QS-negative (rpoN, qscR, mvaT, and rsmA) regulatory genes at either early or late phases of growth. However, with the exception of PAOΔvfr, we detected comparable levels of lasI/lasR expression in PAO1 and PAO1 mutants defective in these regulatory genes. At late stationary phase, serum failed to enhance lasI/lasR expression in PAOΔvfr. These results suggest that depending on the phase of growth, serum differentially influenced the expression of P. aeruginosa QS and QS-controlled virulence genes. In late phase, serum enhanced the expression of las genes through vfr. PMID:24436158

  4. The urease gene cluster of Vibrio parahaemolyticus does not influence the expression of the thermostable direct hemolysin (TDH) gene or the TDH-related hemolysin gene.

    PubMed

    Nakaguchi, Yoshitsugu; Okuda, Jun; Iida, Tetsuya; Nishibuchi, Mitsuaki

    2003-01-01

    In order to investigate why the thermostable direct hemolysin (TDH) and the TDH-related hemolysin (TRH) of Vibrio parahaemolyticus are produced at low levels from urease-positive strains, the effect of the functional urease gene cluster of V. parahaemolyticus on the expression of the tdh and trh genes was examined. Transcriptional lacZ fusions with the tdh1, tdh2, trh1 and trh2 genes representing variants of the tdh and trh genes were integrated into the chromosome of an Escherichia coli strain and a urease-negative V. parahaemolyticus strain. The plasmid-borne urease gene cluster introduced and expressed in these constructs did not affect expression of any of the fusion genes. The amount of TDH produced from a Kanagawa phenomenon-positive V. parahaemolyticus did not change by introduction of the urease gene cluster either. It was concluded therefore that the urease gene cluster is not involved in the regulation of tdh and trh expression.

  5. EXONSAMPLER: a computer program for genome-wide and candidate gene exon sampling for targeted next-generation sequencing.

    PubMed

    Cosart, Ted; Beja-Pereira, Albano; Luikart, Gordon

    2014-11-01

    The computer program EXONSAMPLER automates the sampling of thousands of exon sequences from publicly available reference genome sequences and gene annotation databases. It was designed to provide exon sequences for the efficient, next-generation gene sequencing method called exon capture. The exon sequences can be sampled by a list of gene name abbreviations (e.g. IFNG, TLR1), or by sampling exons from genes spaced evenly across chromosomes. It provides a list of genomic coordinates (a bed file), as well as a set of sequences in fasta format. User-adjustable parameters for collecting exon sequences include a minimum and maximum acceptable exon length, maximum number of exonic base pairs (bp) to sample per gene, and maximum total bp for the entire collection. It allows for partial sampling of very large exons. It can preferentially sample upstream (5 prime) exons, downstream (3 prime) exons, both external exons, or all internal exons. It is written in the Python programming language using its free libraries. We describe the use of EXONSAMPLER to collect exon sequences from the domestic cow (Bos taurus) genome for the design of an exon-capture microarray to sequence exons from related species, including the zebu cow and wild bison. We collected ~10% of the exome (~3 million bp), including 155 candidate genes, and ~16,000 exons evenly spaced genomewide. We prioritized the collection of 5 prime exons to facilitate discovery and genotyping of SNPs near upstream gene regulatory DNA sequences, which control gene expression and are often under natural selection.

  6. Maternal programming of defensive responses through sustained effects on gene expression.

    PubMed

    Zhang, Tie-Yuan; Bagot, Rose; Parent, Carine; Nesbitt, Cathy; Bredy, Timothy W; Caldji, Christian; Fish, Eric; Anisman, Hymie; Szyf, Moshe; Meaney, Michael J

    2006-07-01

    There are profound maternal effects on individual differences in defensive responses and reproductive strategies in species ranging literally from plants to insects to birds. Maternal effects commonly reflect the quality of the environment and are most likely mediated by the quality of the maternal provision (egg, propagule, etc.), which in turn determines growth rates and adult phenotype. In this paper we review data from the rat that suggest comparable forms of maternal effects on defensive responses stress, which are mediated by the effects of variations in maternal behavior on gene expression. Under conditions of environmental adversity maternal effects enhance the capacity for defensive responses in the offspring. In mammals, these effects appear to 'program' emotional, cognitive and endocrine systems towards increased sensitivity to adversity. In environments with an increased level of adversity, such effects can be considered adaptive, enhancing the probability of offspring survival to sexual maturity; the cost is that of an increased risk for multiple forms of pathology in later life.

  7. Unpredictable Variable Prenatal Stress Programs Expression of Genes Involved in Appetite Control and Energy Expenditure

    NASA Technical Reports Server (NTRS)

    Moyer, E. L.; Al-Shayeb, B.; Baer, L. A.; Ronca, A. E.

    2016-01-01

    Exposure to stress in the womb shapes neurobiological and physiological outcomes of offspring in later life, including body weight regulation and metabolic profiles. Our previous work utilizing a centrifugation-induced hyper-gravity demonstrated significantly increased (8-15%) body mass in male, but not female, rats exposed throughout gestation to chronic 2-g from conception to birth. We reported a similar outcome in adult offspring exposed throughout gestation to Unpredictable Variable Prenatal Stress (UVPS). Here we examine gene expression changes and the plasma of animals treated with our UVPS model to identify a potential role for prenatal stress in this hypergravity programming effect. Specifically we focused on appetite control and energy expenditure pathways in prenatally stressed adult (90-day-old) male Sprague-Dawley rats.

  8. Modelling formulations using gene expression programming--a comparative analysis with artificial neural networks.

    PubMed

    Colbourn, E A; Roskilly, S J; Rowe, R C; York, P

    2011-10-09

    This study has investigated the utility and potential advantages of gene expression programming (GEP)--a new development in evolutionary computing for modelling data and automatically generating equations that describe the cause-and-effect relationships in a system--to four types of pharmaceutical formulation and compared the models with those generated by neural networks, a technique now widely used in the formulation development. Both methods were capable of discovering subtle and non-linear relationships within the data, with no requirement from the user to specify the functional forms that should be used. Although the neural networks rapidly developed models with higher values for the ANOVA R(2) these were black box and provided little insight into the key relationships. However, GEP, although significantly slower at developing models, generated relatively simple equations describing the relationships that could be interpreted directly. The results indicate that GEP can be considered an effective and efficient modelling technique for formulation data.

  9. Prediction on the inhibition ratio of pyrrolidine derivatives on matrix metalloproteinase based on gene expression programming.

    PubMed

    Li, Yuqin; You, Guirong; Jia, Baoxiu; Si, Hongzong; Yao, Xiaojun

    2014-01-01

    Quantitative structure-activity relationships (QSAR) were developed to predict the inhibition ratio of pyrrolidine derivatives on matrix metalloproteinase via heuristic method (HM) and gene expression programming (GEP). The descriptors of 33 pyrrolidine derivatives were calculated by the software CODESSA, which can calculate quantum chemical, topological, geometrical, constitutional, and electrostatic descriptors. HM was also used for the preselection of 5 appropriate molecular descriptors. Linear and nonlinear QSAR models were developed based on the HM and GEP separately and two prediction models lead to a good correlation coefficient (R (2)) of 0.93 and 0.94. The two QSAR models are useful in predicting the inhibition ratio of pyrrolidine derivatives on matrix metalloproteinase during the discovery of new anticancer drugs and providing theory information for studying the new drugs.

  10. Use of Gene Expression Programming in regionalization of flow duration curve

    NASA Astrophysics Data System (ADS)

    Hashmi, Muhammad Z.; Shamseldin, Asaad Y.

    2014-06-01

    In this paper, a recently introduced artificial intelligence technique known as Gene Expression Programming (GEP) has been employed to perform symbolic regression for developing a parametric scheme of flow duration curve (FDC) regionalization, to relate selected FDC characteristics to catchment characteristics. Stream flow records of selected catchments located in the Auckland Region of New Zealand were used. FDCs of the selected catchments were normalised by dividing the ordinates by their median value. Input for the symbolic regression analysis using GEP was (a) selected characteristics of normalised FDCs; and (b) 26 catchment characteristics related to climate, morphology, soil properties and land cover properties obtained using the observed data and GIS analysis. Our study showed that application of this artificial intelligence technique expedites the selection of a set of the most relevant independent variables out of a large set, because these are automatically selected through the GEP process. Values of the FDC characteristics obtained from the developed relationships have high correlations with the observed values.

  11. The Aeromonas caviae AHA0618 gene modulates cell length and influences swimming and swarming motility.

    PubMed

    Lowry, Rebecca C; Parker, Jennifer L; Kumbhar, Ramhari; Mesnage, Stephane; Shaw, Jonathan G; Stafford, Graham P

    2014-12-17

    Aeromonas caviae is motile via a polar flagellum in liquid culture, with a lateral flagella system used for swarming on solid surfaces. The polar flagellum also has a role in cellular adherence and biofilm formation. The two subunits of the polar flagellum, FlaA and FlaB, are posttranslationally modified by O-linked glycosylation with pseudaminic acid on 6-8 serine and threonine residues within the central region of these proteins. This modification is essential for the formation of the flagellum. Aeromonas caviae possesses the simplest set of genes required for bacterial glycosylation currently known, with the putative glycosyltransferase, Maf1, being described recently. Here, we investigated the role of the AHA0618 gene, which shares homology (37% at the amino acid level) with the central region of a putative deglycosylation enzyme (HP0518) from the human pathogen Helicobacter pylori, which also glycosylates its flagellin and is proposed to be part of a flagellin deglycosylation pathway. Phenotypic analysis of an AHA0618 A. caviae mutant revealed increased swimming and swarming motility compared to the wild-type strain but without any detectable effects on the glycosylation status of the polar flagellins when analyzed by western blot analysis or mass spectroscopy. Bioinformatic analysis of the protein AHA0618, demonstrated homology to a family of l,d-transpeptidases involved in cell wall biology and peptidoglycan cross-linking (YkuD-like). Scanning electron microscopy (SEM) and fluorescence microscopy analysis of the wild-type and AHA0618-mutant A. caviae strains revealed the mutant to be subtly but significantly shorter than wild-type cells; a phenomenon that could be recovered when either AHA0618 or H. pylori HP0518 were introduced. We can therefore conclude that AHA0618 does not affect A. caviae behavior by altering polar flagellin glycosylation levels but is likely to have a role in peptidoglycan processing at the bacterial cell wall, consequently altering

  12. Notochordal Cells Influence Gene Expression of Inflammatory Mediators of Annulus Fibrosus Cells in Proinflammatory Cytokines Stimulation

    PubMed Central

    Moon, Hong Joo; Joe, Hoon; Kwon, Taek Hyun; Choi, Hye-Kyoung; Park, Youn Kwan

    2010-01-01

    Objective Notochordal cells in the intervertebral disc interact with nucleus pulposus (NP) cells and support the maintenance of disc homeostasis by regulation of matrix production. However, the influence of notochordal cells has not been evaluated in the annulus fibrosus (AF), which is the primary pain generator in the disc. We hypothesized that the notochordal cell has the capacity to modulate inflammatory mediators secreted by AF cells secondary to stimulation. Methods Notochordal and AF cells were isolated from adult New Zealand white rabbits. AF pellets were cultured with notochordal cell clusters or in notochordal cell-conditioned media (NCCM) for 24 or 48 hours with proinflammatory cytokines at varying concentrations. Gene expression in AF pellets were assayed for nitric oxide synthase (iNOS), cyclo-oxygenase (COX)-2, and interleukin (IL)-6 by real time reverse transcriptase polymerase chain reaction (RT-PCR). Results AF pellet in NCCM significantly decreased the iNOS and COX-2 messenger ribonucleic acid (mRNA) levels compared to AF pellets alone and AF pellets with notochordal cells (p < 0.05). AF pellet resulted in dose-dependent iNOS and COX-2 expression in response to IL-1β, stimulation, demonstrating that 1 ng/ml for 24 hours yielded a maximal response. AF pellet in NCCM significantly decreased the expression of iNOS and COX-2 in response to 1ng/ml IL-1β, stimulation at 24 hours (p < 0.05). There was no difference in IL-6 expression compared to AF pellets alone or AF pellets with notochordal cell clusters. Conclusion We conclude that soluble factors from notochordal cells mitigate the gene expression of inflammatory mediators in stimulated AF, as expected after annular injury, suggesting that notochordal cells could serve as a novel therapeutic approach in symptomatic disc development. PMID:20717505

  13. Influence of earthworm activity on gene transfer from Pseudomonas fluorescens to indigenous soil bacteria.

    PubMed Central

    Daane, L L; Molina, J A; Berry, E C; Sadowsky, M J

    1996-01-01

    We have developed a model system to assess the influence of earthworm activity on the transfer of plasmid pJP4 from an inoculated donor bacterium, Pseudomonas fluorescens C5t (pJP4), to indigenous soil microorganisms. Three different earthworm species (Lumbricus terrestris, Lumbricus rubellus, and Aporrectodea trapezoides), each with unique burrowing, casting, and feeding behaviors, were evaluated. Soil columns were inoculated on the surface with 10(8) cells per g of soil of the donor bacterium, and after a 2-week incubation period, donor, transconjugant, and total bacteria were enumerated at 5-cm-depth intervals. Transconjugants were confirmed by use of colony hybridization with a mer gene probe. In situ gene transfer of plasmid pJP4 from P. fluorescens C5t to indigenous soil bacteria was detected in all inoculated microcosms. In the absence of earthworms, the depth of recovery was limited to the top 5 cm of the column, with approximately 10(3) transconjugants per g of soil. However, the total number of transconjugants recovered from soil was significantly greater in microcosms containing either L. rubellus or A. trapezoides, with levels reaching about 10(5) CFU/g of soil. In addition, earthworms distributed donor and transconjugant bacteria throughout the microcosm columns, with the depth of recovery dependent on the burrowing behavior of each earthworm species. Donor and transconjugant bacteria were also recovered from earthworm casts and inside developing cocoons. Transconjugant bacteria from the indigenous soil microflora were classified as belonging to Acidovorax spp., Acinetobacter spp., Agrobacterium spp., Pasteurella spp., Pseudomonas spp., and Xanthomonas spp. PMID:8593052

  14. Genetic Variation in Autophagy-Related Genes Influences the Risk and Phenotype of Buruli Ulcer

    PubMed Central

    Capela, Carlos; Dossou, Ange Dodji; Silva-Gomes, Rita; Sopoh, Ghislain Emmanuel; Makoutode, Michel; Menino, João Filipe; Fraga, Alexandra Gabriel; Cunha, Cristina; Carvalho, Agostinho; Rodrigues, Fernando; Pedrosa, Jorge

    2016-01-01

    Introduction Buruli ulcer (BU) is a severe necrotizing human skin disease caused by Mycobacterium ulcerans. Clinically, presentation is a sum of these diverse pathogenic hits subjected to critical immune-regulatory mechanisms. Among them, autophagy has been demonstrated as a cellular process of critical importance. Since microtubules and dynein are affected by mycolactone, the critical pathogenic exotoxin produced by M. ulcerans, cytoskeleton-related changes might potentially impair the autophagic process and impact the risk and progression of infection. Objective Genetic variants in the autophagy-related genes NOD2, PARK2 and ATG16L1 has been associated with susceptibility to mycobacterial diseases. Here, we investigated their association with BU risk, its severe phenotypes and its progression to an ulcerative form. Methods Genetic variants were genotyped using KASPar chemistry in 208 BU patients (70.2% with an ulcerative form and 28% in severe WHO category 3 phenotype) and 300 healthy endemic controls. Results The rs1333955 SNP in PARK2 was significantly associated with increased susceptibility to BU [odds ratio (OR), 1.43; P = 0.05]. In addition, both the rs9302752 and rs2066842 SNPs in NOD2 gee significantly increased the predisposition of patients to develop category 3 (OR, 2.23; P = 0.02; and OR 12.7; P = 0.03, respectively, whereas the rs2241880 SNP in ATG16L1 was found to significantly protect patients from presenting the ulcer phenotype (OR, 0.35; P = 0.02). Conclusion Our findings indicate that specific genetic variants in autophagy-related genes influence susceptibility to the development of BU and its progression to severe phenotypes. PMID:27128681

  15. Mutations within the programmed cell death 10 gene cause cerebral cavernous malformations.

    PubMed

    Bergametti, F; Denier, C; Labauge, P; Arnoult, M; Boetto, S; Clanet, M; Coubes, P; Echenne, B; Ibrahim, R; Irthum, B; Jacquet, G; Lonjon, M; Moreau, J J; Neau, J P; Parker, F; Tremoulet, M; Tournier-Lasserve, E

    2005-01-01

    Cerebral cavernous malformations (CCMs) are hamartomatous vascular malformations characterized by abnormally enlarged capillary cavities without intervening brain parenchyma. They cause seizures and cerebral hemorrhages, which can result in focal neurological deficits. Three CCM loci have been mapped, and loss-of-function mutations were identified in the KRIT1 (CCM1) and MGC4607 (CCM2) genes. We report herein the identification of PDCD10 (programmed cell death 10) as the CCM3 gene. The CCM3 locus has been previously mapped to 3q26-27 within a 22-cM interval that is bracketed by D3S1763 and D3S1262. We hypothesized that genomic deletions might occur at the CCM3 locus, as reported previously to occur at the CCM2 locus. Through high-density microsatellite genotyping of 20 families, we identified, in one family, null alleles that resulted from a deletion within a 4-Mb interval flanked by markers D3S3668 and D3S1614. This de novo deletion encompassed D3S1763, which strongly suggests that the CCM3 gene lies within a 970-kb region bracketed by D3S1763 and D3S1614. Six additional distinct deleterious mutations within PDCD10, one of the five known genes mapped within this interval, were identified in seven families. Three of these mutations were nonsense mutations, and two led to an aberrant splicing of exon 9, with a frameshift and a longer open reading frame within exon 10. The last of the six mutations led to an aberrant splicing of exon 5, without frameshift. Three of these mutations occurred de novo. All of them cosegregated with the disease in the families and were not observed in 200 control chromosomes. PDCD10, also called "TFAR15," had been initially identified through a screening for genes differentially expressed during the induction of apoptosis in the TF-1 premyeloid cell line. It is highly conserved in both vertebrates and invertebrates. Its implication in cerebral cavernous malformations strongly suggests that it is a new player in vascular morphogenesis and

  16. A factors influencing applicant selection of entry-level physical therapist education programs in the United States.

    PubMed

    Wilcox, Kim Curbow; Weber, Mark

    2005-01-01

    Physical therapist education programs must compete for qualified applicants due to a nationwide reduction in the applicant pool. To develop successful recruitment strategies, faculty members need information on factors influencing applicant selection of a program. The purpose of this study was to analyze factors influencing selection of an entry-level physical therapist education program. Survey subjects were students enrolled in the first professional year of an accredited entry-level physical therapist education program. A survey instrument was developed based on the literature and interviews with physical therapist students and faculty members. Results of pilot studies to determine face and content validity were acceptable. Stratified random cluster sampling was applied to select 66 entry-level physical therapy programs from an available population of 150 of the 199 accredited programs. Forty-nine programs were not included in the population for various reasons. Using a five-point Likert scale, subjects rated the influence of 51 items on their selection of a specific physical therapist education program. The overall return rate was 70.4% (1,250 surveys returned). Data were analyzed by response frequency. Four factors were selected as "very influential" by 50% or more of the subjects: degree offered, accreditation status, perception of educational quality, and program atmosphere. Additional factors selected by 45% or more of respondents as "very influential" were pass rate on licensing examination, marketability of degree, student/faculty ratio, and small class size. Factors rated "not influential" by 50% or more of subjects included ethnic, cultural, and gender issues. Since 1998, the physical therapy profession has experienced changes in entry-level degree requirements, practice requirements, and employment opportunities, resulting in increased competition for qualified applicants to education programs. The information gained in this study may assist faculty in

  17. Dietary intake alters gene expression in colon tissue: possible underlying mechanism for the influence of diet on disease

    PubMed Central

    Pellatt, Andrew J.; Mullany, Lila E.; Wolff, Roger K.; Pellatt, Daniel F.

    2016-01-01

    Background Although the association between diet and disease is well documented, the biologic mechanisms involved have not been entirely elucidated. In this study, we evaluate how dietary intake influences gene expression to better understand the underlying mechanisms through which diet operates. Methods We used data from 144 individuals who had comprehensive dietary intake and gene expression data from RNAseq using normal colonic mucosa. Using the DESeq2 statistical package, we identified genes that showed statistically significant differences in expression between individuals in high-intake and low-intake categories for several dietary variables of interest adjusting for age and sex. We examined total calories, total fats, vegetable protein, animal protein, carbohydrates, trans-fatty acids, mutagen index, red meat, processed meat, whole grains, vegetables, fruits, fiber, folate, dairy products, calcium, and prudent and western dietary patterns. Results Using a false discovery rate of less than 0.1, meat-related foods were statistically associated with 68 dysregulated genes, calcium with three dysregulated genes, folate with four dysregulated genes, and nonmeat-related foods with 65 dysregulated genes. With a more stringent false discovery rate of less than 0.05, there were nine meat-related dysregulated genes and 23 nonmeat-related genes. Ingenuity pathway analysis identified three major networks among genes identified as dysregulated with respect to meat-related dietary variables and three networks among genes identified as dysregulated with respect to nonmeat-related variables. The top networks (Ingenuity Pathway Analysis network score >30) associated with meat-related genes were (i) cancer, organismal injury, and abnormalities, tumor morphology, and (ii) cellular function and maintenance, cellular movement, cell death, and survival. Among genes related to nonmeat consumption variables, the top networks were (i) hematological system development and function

  18. A Multidisciplinary Sepsis Program Enabled by a Two-Stage Clinical Decision Support System: Factors That Influence Patient Outcomes.

    PubMed

    Amland, Robert C; Haley, James M; Lyons, Jason J

    2016-11-01

    Sepsis is an inflammatory response triggered by infection, with risk of in-hospital mortality fueled by disease progression. Early recognition and intervention by multidisciplinary sepsis programs may reverse the inflammatory response among at-risk patient populations, potentially improving outcomes. This retrospective study of a sepsis program enabled by a 2-stage sepsis Clinical Decision Support (CDS) system sought to evaluate the program's impact, identify early indicators that may influence outcomes, and uncover opportunities for quality improvement. Data encompassed 16 527 adult hospitalizations from 2014 and 2015. Of 2108 non-intensive care unit patients screened-in by sepsis CDS, 97% patients were stratified by 177 providers. Risk of adverse outcome improved 30% from baseline to year end, with gains materializing and stabilizing at month 7 after sepsis program go-live. Early indicators likely to influence outcomes include patient age, recent hospitalization, electrolyte abnormalities, hypovolemic shock, hypoxemia, patient location when sepsis CDS activated, and specific alert patterns.

  19. Foxp transcription factors suppress a non-pulmonary gene expression program to permit proper lung development.

    PubMed

    Li, Shanru; Morley, Michael; Lu, MinMin; Zhou, Su; Stewart, Kathleen; French, Catherine A; Tucker, Haley O; Fisher, Simon E; Morrisey, Edward E

    2016-08-15

    The inhibitory mechanisms that prevent gene expression programs from one tissue to be expressed in another are poorly understood. Foxp1/2/4 are forkhead transcription factors that repress gene expression and are individually important for endoderm development. We show that combined loss of all three Foxp1/2/4 family members in the developing anterior foregut endoderm leads to a loss of lung endoderm lineage commitment and subsequent development. Foxp1/2/4 deficient lungs express high levels of transcriptional regulators not normally expressed in the developing lung, including Pax2, Pax8, Pax9 and the Hoxa9-13 cluster. Ectopic expression of these transcriptional regulators is accompanied by decreased expression of lung restricted transcription factors including Nkx2-1, Sox2, and Sox9. Foxp1 binds to conserved forkhead DNA binding sites within the Hoxa9-13 cluster, indicating a direct repression mechanism. Thus, Foxp1/2/4 are essential for promoting lung endoderm development by repressing expression of non-pulmonary transcription factors.

  20. Histone Deacetylases and Mood Disorders: Epigenetic Programming in Gene-Environment Interactions

    PubMed Central

    Machado-Vieira, Rodrigo; Ibrahim, Lobna; Zarate, Carlos A.

    2010-01-01

    Epigenetics involves molecular mechanisms related to gene expression independent of DNA sequence, mostly mediated by modification of chromatin histones. It has recently been suggested that these transcriptional changes may be implicated in the pathophysiology of mood disorders. In addition, histone deacetylase (HDAC) inhibitors have been shown to control epigenetic programming associated with the regulation of cognition and behavior, and may reverse dysfunctional epigenetic regulation associated with early life events in preclinical models. In this context, the active and continuous adaptation of chromatin, and the access of gene promoters to transcription factor mechanisms may represent a potential therapeutic target in the treatment of mood disorders such as bipolar disorder (BD) and major depressive disorder (MDD). Notably, the standard mood stabilizer valproate (VPA) has been shown to modulate the epigenome by inhibiting HDACs. However, several potential limitations are associated with this class of agents, including lack of selectivity for specific HDAC isoforms as well as risk of potentially serious side effects. Further studies regarding the potential role of chromatin remodeling in the mechanism of action of antidepressants and mood stabilizers are necessary to clarify the potential role of this class of agents as therapeutics for mood disorders. PMID:20961400

  1. Newborn Screening Quality Assurance Program for CFTR Mutation Detection and Gene Sequencing to Identify Cystic Fibrosis

    PubMed Central

    Hendrix, Miyono M.; Foster, Stephanie L.; Cordovado, Suzanne K.

    2016-01-01

    All newborn screening laboratories in the United States and many worldwide screen for cystic fibrosis. Most laboratories use a second-tier genotyping assay to identify a panel of mutations in the CF transmembrane regulator (CFTR) gene. Centers for Disease Control and Prevention’s Newborn Screening Quality Assurance Program houses a dried blood spot repository of samples containing CFTR mutations to assist newborn screening laboratories and ensure high-quality mutation detection in a high-throughput environment. Recently, CFTR mutation detection has increased in complexity with expanded genotyping panels and gene sequencing. To accommodate the growing quality assurance needs, the repository samples were characterized with several multiplex genotyping methods, Sanger sequencing, and 3 next-generation sequencing assays using a high-throughput, low-concentration DNA extraction method. The samples performed well in all of the assays, providing newborn screening laboratories with a resource for complex CFTR mutation detection and next-generation sequencing as they transition to new methods. PMID:28261631

  2. Interaction between serotonin 5-HT2A receptor gene and dopamine transporter (DAT1) gene polymorphisms influences personality trait of persistence in Austrian Caucasians.

    PubMed

    Schosser, Alexandra; Fuchs, Karoline; Scharl, Theresa; Schloegelhofer, Monika; Kindler, Jochen; Mossaheb, Nilufar; Kaufmann, Rainer M; Leisch, Friedrich; Kasper, Siegfried; Sieghart, Werner; Aschauer, Harald N

    2010-03-01

    We examined 89 normal volunteers using Cloninger's Temperament and Character Inventory (TCI). Genotyping the 102T/C polymorphism of the serotonin 5HT2A receptor gene and the ser9gly polymorphism in exon 1 of the dopamine D3 receptor (DRD3) gene was performed using PCR-RFLP, whereas the dopamine transporter (DAT1) gene variable number of tandem repeats (VNTR) polymorphism was investigated using PCR amplification followed by electrophoresis in an 8% acrylamide gel with a set of size markers. We found a nominally significant association between gender and harm avoidance (P=0.017; women showing higher scores). There was no association of either DAT1, DRD3 or 5HT2A alleles or genotypes with any dimension of the TCI applying Kruskal-Wallis rank-sum tests. Comparing homozygote and heterozygote DAT1 genotypes, we found higher novelty seeking scores in homozygotes (P=0.054). We further found a nominally significant interaction between DAT1 and 5HT2A homo-/heterozygous gene variants (P=0.0071; DAT1 and 5HT2A genotypes P value of 0.05), performing multivariate analysis of variance (MANOVA). Examining the temperamental TCI subscales, this interaction was associated with persistence (genotypes: P=0.004; homo-/heterozygous gene variants: P=0.0004). We conclude that an interaction between DAT1 and 5HT2A genes might influence the temperamental personality trait persistence.

  3. Maternal obesity programs mitochondrial and lipid metabolism gene expression in infant umbilical vein endothelial cells

    PubMed Central

    Ramos Costa, Suzana Maria; Isganaitis, Elvira; Matthews, Tucker; Hughes, Katelyn; Daher, Grace; Dreyfuss, Jonathan M.; Pontes da Silva, Giselia Alves; Patti, Mary-Elizabeth

    2016-01-01

    Background/Objectives Maternal obesity increases risk for childhood obesity, but molecular mechanisms are not well understood. We hypothesized that primary umbilical vein endothelial cells (HUVEC) from infants of overweight and obese mothers would harbor transcriptional patterns reflecting offspring obesity risk. Subjects/Methods In this observational cohort study, we recruited 13 lean (pre-pregnancy BMI <25.0 kg/m2) and 24 overweight-obese (‘ov-ob’, BMI ≥25.0 kg/m2) women. We isolated primary HUVEC, and analyzed both gene expression (Primeview, Affymetrix) and cord blood levels of hormones and adipokines. Results 142 transcripts were differentially expressed in HUVEC from infants of overweight-obese mothers (false discovery rate, FDR <0.05). Pathway analysis revealed that genes involved in mitochondrial and lipid metabolism were negatively correlated with maternal BMI (FDR <0.05). To test whether these transcriptomic patterns were associated with distinct nutrient exposures in the setting of maternal obesity, we analyzed the cord blood lipidome and noted significant increases in levels of total free fatty acids (lean: 95.5 ± 37.1 ug/ml, ov-ob: 124.1 ± 46.0 ug/ml, P=0.049), palmitate (lean: 34.5 ± 12.7 ug/ml, ov-ob: 46.3 ± 18.4 ug/ml, P=0.03) and stearate (lean: 20.8 ± 8.2 ug/ml, ov-ob: 29.7 ± 17.2 ug/ml, P=0.04), in infants of overweight-obese mothers. Conclusion Prenatal exposure to maternal obesity alters HUVEC expression of genes involved in mitochondrial and lipid metabolism, potentially reflecting developmentally-programmed differences in oxidative and lipid metabolism. PMID:27531045

  4. Tumor suppressor genes are larger than apoptosis-effector genes and have more regions of active chromatin: Connection to a stochastic paradigm for sequential gene expression programs.

    PubMed

    Garcia, Marlene; Mauro, James A; Ramsamooj, Michael; Blanck, George

    2015-08-03

    Apoptosis- and proliferation-effector genes are substantially regulated by the same transactivators, with E2F-1 and Oct-1 being notable examples. The larger proliferation-effector genes have more binding sites for the transactivators that regulate both sets of genes, and proliferation-effector genes have more regions of active chromatin, i.e, DNase I hypersensitive and histone 3, lysine-4 trimethylation sites. Thus, the size differences between the 2 classes of genes suggest a transcriptional regulation paradigm whereby the accumulation of transcription factors that regulate both sets of genes, merely as an aspect of stochastic behavior, accumulate first on the larger proliferation-effector gene "traps," and then accumulate on the apoptosis effector genes, thereby effecting sequential activation of the 2 different gene sets. As IRF-1 and p53 levels increase, tumor suppressor proteins are first activated, followed by the activation of apoptosis-effector genes, for example during S-phase pausing for DNA repair. Tumor suppressor genes are larger than apoptosis-effector genes and have more IRF-1 and p53 binding sites, thereby likewise suggesting a paradigm for transcription sequencing based on stochastic interactions of transcription factors with different gene classes. In this report, using the ENCODE database, we determined that tumor suppressor genes have a greater number of open chromatin regions and histone 3 lysine-4 trimethylation sites, consistent with the idea that a larger gene size can facilitate earlier transcriptional activation via the inclusion of more transactivator binding sites.

  5. Identification of Notch target genes in uncommitted T-cell progenitors: No direct induction of a T-cell specific gene program.

    PubMed

    Weerkamp, F; Luis, T C; Naber, B A E; Koster, E E L; Jeannotte, L; van Dongen, J J M; Staal, F J T

    2006-11-01

    Deregulated Notch signaling occurs in the majority of human T-ALL. During normal lymphoid development, activation of the Notch signaling pathway poses a T-cell fate on hematopoietic progenitors. However, the transcriptional targets of the Notch pathway are largely unknown. We sought to identify Notch target genes by inducing Notch signaling in human hematopoietic progenitors using two different methods: an intracellular signal through transfection of activated Notch and a Notch-receptor dependent signal by interaction with its ligand Delta1. Gene expression profiles were generated and evaluated with respect to expression profiles of immature thymic subpopulations. We confirmed HES1, NOTCH1 and NRARP as Notch target genes, but other reported Notch targets, including the genes for Deltex1, pre-T-cell receptor alpha and E2A, were not found to be differentially expressed. Remarkably, no induction of T-cell receptor gene rearrangements or transcription of known T-cell specific genes was found after activation of the Notch pathway. A number of novel Notch target genes, including the transcription factor TCFL5 and the HOXA cluster, were identified and functionally tested. Apparently, Notch signaling is essential to open the T-cell pathway, but does not initiate the T-cell program itself.

  6. Inherited Variants in Wnt Pathway Genes Influence Outcomes of Prostate Cancer Patients Receiving Androgen Deprivation Therapy

    PubMed Central

    Geng, Jiun-Hung; Lin, Victor C.; Yu, Chia-Cheng; Huang, Chao-Yuan; Yin, Hsin-Ling; Chang, Ta-Yuan; Lu, Te-Ling; Huang, Shu-Pin; Bao, Bo-Ying

    2016-01-01

    Aberrant Wnt signaling has been associated with many types of cancer. However, the association of inherited Wnt pathway variants with clinical outcomes in prostate cancer patients receiving androgen deprivation therapy (ADT) has not been determined. Here, we comprehensively studied the contribution of common single nucleotide polymorphisms (SNPs) in Wnt pathway genes to the clinical outcomes of 465 advanced prostate cancer patients treated with ADT. Two SNPs, adenomatous polyposis coli (APC) rs2707765 and rs497844, were significantly (p ≤ 0.009 and q ≤ 0.043) associated with both prostate cancer progression and all-cause mortality, even after multivariate analyses and multiple testing correction. Patients with a greater number of favorable alleles had a longer time to disease progression and better overall survival during ADT (p for trend ≤ 0.003). Additional, cDNA array and in silico analyses of prostate cancer tissue suggested that rs2707765 affects APC expression, which in turn is correlated with tumor aggressiveness and patient prognosis. This study identifies the influence of inherited variants in the Wnt pathway on the efficacy of ADT and highlights a preclinical rationale for using APC as a prognostic marker in advanced prostate cancer. PMID:27898031

  7. Influence of the Great Megathrust Earthquakes of the Past Decade on Risk Assessment and Outreach Programs

    NASA Astrophysics Data System (ADS)

    Dengler, L. A.

    2014-12-01

    Four subduction zone earthquakes of magnitude ≥ 8.6 occurred between 2004 and 2013. No earthquakes of this size were reported anywhere in the world in the preceding 36 years. The wealth of seismic, geodetic, geologic and tsunami data from these great megathrust events has advanced the understanding of subduction zones and challenged a number of previously accepted ideas. This talk focuses on how they have also influenced risk assessment and preparedness programs. Megathrust earthquakes differ from other large damaging earthquakes. The size of the megathrust source means a much larger area may be impacted by earthquake shakingaffecting not only the amount of damage, but posing response and recovery challenges. A second factor is tsunami generation. About a third of the 760,000 casualties in the decade were caused by the four mega-earthquakes. All four produced deadly tsunamis and over 95% of the death total was attributed to tsunami. Even when the extraordinarily deadly 2004 Andaman Sumatra tsunami is removed from the data set, 85% of the casualties in the remaining three earthquakes were caused by tsunami. In contrast, in the non-megathrust events caused over two-thirds of the decade's casualties but less than 1 % were caused by tsunami. The Cascadia subduction zone along the coast of northern California, Oregon, Washington and southern British Columbia is the only location in the contiguous 48 states where a great megathrust earthquake will someday occur. Assessing the risk posed by Cascadia and developing effective preparedness programs pose a number of challenges. Awareness of Cascadia is relatively recent and assessing the magnitude, recurrence and nature of past events depends primarily on paleoseismology. The megathrust events of the past decade provide a proxy for and a general picture of the likely impacts of a future Cascadia earthquake and have influenced preparedness efforts throughout the Cascadia region. The recent events have also posed problems for

  8. The Influence of Health Literacy on Reach, Retention, and Success in a Worksite Weight Loss Program.

    PubMed

    Zoellner, Jamie; You, Wendy; Almeida, Fabio; Blackman, Kacie C A; Harden, Samantha; Glasgow, Russell E; Linnan, Laura; Hill, Jennie L; Estabrooks, Paul A

    2015-05-14

    Purpose . To examine if employee health literacy (HL) status moderated reach, retention, and weight outcomes in a worksite weight loss program. Design . The study was a two-group cluster randomized controlled weight loss trial. Setting . The study was conducted in 28 worksites. Subjects . Subjects comprised 1460 employees with a body mass index >25 kg/m(2). Interventions . Two 12-month weight loss interventions targeted diet and physical activity behaviors: incentaHEALTH (INCENT; incentivized individually targeted Internet-based intervention) and Livin' My Weigh (LMW; less-intense quarterly newsletters). Measures . A validated three-item HL screening measure was self-completed at baseline. Weight was objectively assessed with the Health Spot scale at baseline and 12-month follow-up. Analysis . The impact of HL on program effectiveness was assessed through fixed-effect parametric models that controlled for individual (i.e., age, gender, race, ethnicity, income, education) and worksite fixed effects. Results . Enrolled employees had significantly higher HL status [13.54 (1.68)] as compared to unenrolled [13.04 (2.17)] (p < .001). This finding was consistent in both interventions. Also, HL moderated weight loss effects (beta = .66; SE = 027; p = .014) and losing >5% weight (beta = -1.53; SE = .77; p < .047). For those with lower baseline HL, the INCENT intervention produced greater weight loss outcomes compared to LMW. The HL level of employees retained was not significantly different from those lost to follow-up. Conclusion . HL influences reach and moderates weight effects. These findings underscore the need to integrate recruitment strategies and further evaluate programmatic approaches that attend to the needs of low-HL audiences.

  9. The Influence of Major Life Events on Economic Attitudes in a World of Gene-Environment Interplay.

    PubMed

    Hatemi, Peter K

    2013-10-01

    The role of "genes" on political attitudes has gained attention across disciplines. However, person-specific experiences have yet to be incorporated into models that consider genetic influences. Relying on a gene-environment interplay approach, this study explicates how life-events, such as losing one's job or suffering a financial loss, influence economic policy attitudes. The results indicate genetic and environmental variance on support for unions, immigration, capitalism, socialism and property tax is moderated by financial risks. Changes in the magnitude of genetic influences, however, are temporary. After two years, the phenotypic effects of the life events remain on most attitudes, but changes in the sources of individual differences do not. Univariate twin models that estimate the independent contributions of genes and environment on the variation of attitudes appear to provide robust baseline indicators of sources of individual differences. These estimates, however, are not event or day specific. In this way, genetic influences add stability, while environment cues change, and this process is continually updated.

  10. Differences between Faculty and Students' Perception of Recruitment Techniques that Influence Students To Attend Four-Year Automotive Programs.

    ERIC Educational Resources Information Center

    Belcher, Gregory; Frisbee, Robert; Sanford, Brian

    2003-01-01

    Responses were obtained from 382 of 607 students and 27 of 36 faculty in automotive technology. Both groups cited program reputation, university reputation, campus visits and high school/community college teachers/counselors as effective recruitment influences. Students thought parents and relatives were more influential than faculty did.…

  11. Two Case Studies of Beginning Teachers in State-Mandated Induction Programs: The Influence of Institutional Factors.

    ERIC Educational Resources Information Center

    Paulissen, Margaret O.; And Others

    The Teacher Induction Study investigated 2 state-mandated beginning teacher programs and examined the translation of state policy by 4 school districts, 13 individual schools, and 32 classrooms. From the case histories of 16 teams, 2 case histories were selected for further study. One case illustrated how institutional factors influenced team…

  12. Factors Influencing Rural Women Cassava Processors' Intention to Participate in an Agricultural Extension Education Program. Summary of Research 80.

    ERIC Educational Resources Information Center

    Ojomo, Christian O.; McCaslin, N. L.

    A study examined factors influencing female cassava processors' intentions regarding participation in an extension education program on cassava processing in rural Nigeria. Interviews were conducted with 224 women who were purposely selected from areas of zone 3 of Ondo State, Nigeria, which has large concentrations of cassava processors.…

  13. Significant Life Experience: Exploring the Lifelong Influence of Place-Based Environmental and Science Education on Program Participants

    ERIC Educational Resources Information Center

    Colvin, Corrie Ruth

    2013-01-01

    Current research provides a limited understanding of the life long influence of nonformal place-based environmental and science education programs on past participants. This study looks to address this gap, exploring the ways in which these learning environments have contributed to environmental identity and stewardship. Using Dorothy Holland's…

  14. The influence of one-carbon metabolism on gene promoter methylation in a population-based breast cancer study

    PubMed Central

    Gammon, Marilie D; Jefferson, Elizabeth; Zhang, Yujing; Cho, Yoon Hee; Wetmur, James G; Teitelbaum, Susan L; Bradshaw, Patrick T; Terry, Mary Beth; Garbowski, Gail; Hibshoosh, Hanina; Neugut, Alfred I; Santella, Regina M

    2011-01-01

    Abnormal methylation in gene promoters is a hallmark of the cancer genome; however, factors that may influence promoter methylation have not been well elucidated. As the one-carbon metabolism pathway provides the universal methyl donor for methylation reactions, perturbation of this pathway might influence DNA methylation and, ultimately, affect gene functions. Utilizing approximately 800 breast cancer tumor tissues from a large population-based study, we investigated the relationships between dietary and genetic factors involved in the one-carbon metabolism pathway and promoter methylation of a panel of 13 breast cancer-related genes. We found that CCND2, HIN1 and CHD1 were the most “dietary sensitive” genes, as methylation of their promoters was associated with intakes of at least two out of the eight dietary methyl factors examined. On the other hand, some micronutrients (i.e., B2 and B6) were more “epigenetically active” as their intake levels correlated with promoter methylation status in 3 out of the 13 breast cancer genes evaluated. Both positive (hypermethylation) and inverse (hypomethylation) associations with high micronutrient intake were observed. Unlike what we saw for dietary factors, we did not observe any clear patterns between one-carbon genetic polymorphisms and the promoter methylation status of the genes examined. Our results provide preliminary evidence that one-carbon metabolism may have the capacity to influence the breast cancer epigenome. Given that epigenetic alterations are thought to occur early in cancer development and are potentially reversible, dietary modifications may offer promising venues for cancer intervention and prevention. PMID:22048254

  15. Influence of CTLA-4 gene polymorphism in autoimmune and infectious diseases.

    PubMed

    Fernández-Mestre, Mercedes; Sánchez, Karen; Balbás, Omar; Gendzekhzadze, Ketevan; Ogando, Violeta; Cabrera, Mayra; Layrisse, Zulay

    2009-07-01

    Cell-mediated immunity requires costimulatory activity to initiate or inhibit antigen-specific T-cell responses. CTLA-4 is an inhibitory receptor expressed by activated and regulatory T cells. The single nucleotide polymorphism (SNP) +49 A/G of the CTLA-4 gene alters intracellular distribution of CTLA-4, interleukin-2 production, and, as a consequence, T-cell proliferation. The aim of this study was to analyze the only coding SNP CTLA-4 +49 A/G polymorphism in patients with either infectious (Chagas's, Dengue, and American cutaneous leishmaniasis) or autoimmune diseases (myasthenia gravis, pemphigus, and psoriasis). No statistically significant differences were reported when all patients of each disease group were compared with healthy individuals. However, the +49 G/G genotype was moderately increased in pemphigus and myasthenia gravis. Patients with diffuse cutaneous leishmaniasis (DCL) exhibited an increased frequency of the A/G +49 genotype compared with patients with localized cutaneous leishmaniasis (LCL; p = 0.009; odds ratio [OR] = 4.25; 95% confidence interval [CI] = 1.245-14.501) and intermediate cutaneous leishmaniasis (ICL; p = 0.027; OR = 4.44; 95% CI = 1.273-15.516), indicating that the heterozygous genotype, associated with overactivation of T-cell proliferation, could confer susceptibility to the development of the more severe clinical form of cutaneous leishmaniasis. The A/A +49 genotype was increased in LCL patients compared with DCL patients (p = 0.019; OR = 0.25; 95% CI = 0.067-0.953), indicating that this genotype, which has been associated with normal proliferation of T cells, could confer protection to the development of DCL. The results indicate that the polymorphism of CTLA-4 is an important genetic factor associated with risk or protection for the development of diffuse cutaneous leishmaniasis and has influence in the pathogenesis of autoimmune diseases. However, other closely linked candidate genes in linkage disequilibrium with CTLA4

  16. Myosin Light Chain Kinase (MLCK) Gene Influences Exercise Induced Muscle Damage during a Competitive Marathon

    PubMed Central

    Valero, Marjorie; Lara, Beatriz; Salinero, Juan José; Gallo-Salazar, César; Areces, Francisco

    2016-01-01

    Myosin light chain kinase (MLCK) phosphorylates the regulatory light chain (RLC) of myosin producing increases in force development during skeletal muscle contraction. It has been suggested that MLCK gene polymorphisms might alter RLC phosphorylation thereby decreasing the ability to produce force and to resist strain during voluntary muscle contractions. Thus, the genetic variations in the MLCK gene might predispose some individuals to higher values of muscle damage during exercise, especially during endurance competitions. The aim of this investigation was to determine the influence of MLCK genetic variants on exercise-induced muscle damage produced during a marathon. Sixty-seven experienced runners competed in a marathon race. The MLCK genotype (C37885A) of these marathoners was determined. Before and after the race, a sample of venous blood was obtained to assess changes in serum myoglobin concentrations and leg muscle power changes were measured during a countermovement jump. Self-reported leg muscle pain and fatigue were determined by questionnaires. A total of 59 marathoners (88.1%) were CC homozygotes and 8 marathoners (11.9%) were CA heterozygotes. The two groups of participants completed the race with a similar time (228 ± 33 vs 234 ± 39 min; P = 0.30) and similar self-reported values for fatigue (15 ± 2 vs 16 ± 2 A.U.; P = 0.21) and lower-limb muscle pain (6.2 ± 1.7 vs 6.6 ± 1.8 cm; P = 0.29). However, CC marathoners presented higher serum myoglobin concentrations (739 ± 792 vs 348 ± 144 μg·mL-1; P = 0.03) and greater pre-to-post- race leg muscle power reduction (-32.7 ± 15.7 vs -21.2 ± 21.6%; P = 0.05) than CA marathoners. CA heterozygotes for MLCK C37885A might present higher exercise-induced muscle damage after a marathon competition than CC counterparts. PMID:27483374

  17. Do universal media literacy programs have an effect on weight and shape concern by influencing media internalization?

    PubMed

    Wade, Tracey D; Wilksch, Simon M; Paxton, Susan J; Byrne, Susan M; Austin, S Bryn

    2017-02-02

    The current study examined whether media internalization, found to mediate the relationship between selected prevention programs and outcomes, mediated the impact of two universal prevention programs that targeted risk factors for eating disorders and obesity, namely weight concern, and shape concern. Students randomized to a media literacy (Media Smart) program (N = 269, 65% females, mean age 12.97 years) and a healthy lifestyle (Life Smart) program (N = 347, 69% females, mean age 13.07 years) were included in the analyses. There were four waves of data (baseline, end of intervention, 6- and 12-month follow-up). Latent growth curve modeling was used to explore whether group assignment influenced levels of media internalization, and whether that in turn influenced change over time of our two outcome variables. Being randomly allocated to Media Smart as opposed to Life Smart resulted in less growth of both outcome variables through the influence on decreasing levels of media internalization. Findings provided support for the suggestion that media literacy programs exert an impact on outcomes related to eating disorder risk through changes to media internalization. Future research should examine whether these mechanisms of change differ between girls and boys.

  18. The influence of the autochthonous wastewater microbiota and gene host on the fate of invasive antibiotic resistance genes.

    PubMed

    Narciso-da-Rocha, Carlos; Manaia, Célia M

    2017-01-01

    The aim of this study was to assess the fate of invasive antibiotic resistance genes (ARG) discharged in wastewater. With this objective, antibiotic resistant bacteria (ARB) known to harbor specific ARG were inoculated in wastewater (hospital effluent, or municipal raw and treated wastewater) and in ultra-pure sterile water microcosms. Two sets of wastewater ARB isolates were used - set 1, Enterococcus faecalis, Acinetobacter johnsonii, Klebsiella pneumoniae and set 2, Enterococcus faecium, Acinetobacter johnsonii, Escherichia coli. Non-inoculated controls were run in parallel. Samples were collected at the beginning and at the end (15days) of the incubation period and the abundance of the genes 16S rRNA, intI1, blaTEM and vanA and the bacterial community composition were analyzed. In general, the genes blaTEM and vanA had lower persistence in wastewater and in ultra-pure water than the genes 16S rRNA or the class 1 integron integrase intI1. This effect was more pronounced in wastewater than in ultra-pure water, evidencing the importance of the autochthonous microbiota on the elimination of invasive ARG. Wastewater autochthonous bacterial groups most correlated with variations of the genes intI1, blaTEM and vanA were members of the classes Gammaproteobacteria, Bacilli or Bacteroidia. For blaTEM, but not for vanA, the species of the ARB host was important to determine its fate. These are novel findings on the ecology of ARB in wastewater environments.

  19. The influence of modifications of a fatigue loading history program on fatigue lifetime

    NASA Technical Reports Server (NTRS)

    Branger, J.

    1972-01-01

    Rectangular specimens of 7075 and 2014 aluminum alloys with two holes (stress concentration factor of 3.24) have been tested under axial fatigue loading on a six-rod test bed with modifications of the loading program, the surface particulars, and the frequency. The length of the precrack stage was investigated by use of a new crack detector. In most cases the two alloys behaved similarly, with similar life to crack start under the same loading. Some overloads lengthened the life. Truncation by omission of the lowest peak loads should be limited to about 20 percent of the ultimate load. Simplifying counting methods gave misleading results. Very thin surface layers of anodizing, protection by vinyl, dry nitrogen atmosphere, as well as stepwise reaming or grinding the surface of the holes, lengthened the life; thick anodized layers shortened the life. Compressing the hole surface by rolling had no influence. Frequencies at about 210 to 240 cpm produced shorter lives than those at 40 cpm. At 5.4 cpm the life was considerably longer. A model to better understand the precrack-stage fatigue mechanism is discussed.

  20. The International Geophysical Year: Its influence on the beginning of the French space program

    NASA Astrophysics Data System (ADS)

    Moulin, Hervé

    2010-03-01

    In 1957-1958, the International Geophysical Year (IGY) was the most important scientific cooperation programme in the World, after the Second World War. Thousands of scientists from 67 countries were involved in this large operation, among them a lot of French scientists. IGY was previously called the IPY (International Polar Year) and France, as many other countries, has been involved in the Arctic and Antarctic regions researches. Everybody knows that the IGY is at the origin of Sputnik and the first launch of Russian and American satellites. But, we know less about the IGY rockets programme itself in which France had intended to participate. This paper will discuss this programme with a special highlight on some aspects of the French participation and their relationship with the IGY programme. This approach arises several questions, such as: Which French scientists have been involved? What was the attitude of the French Government about this program, etc. We focus our analysis on the interrogation: did the IGY have any real influence on the origin of the French space research activities?

  1. Patient perceptions of care as influenced by a large institutional pharmacogenomic implementation program.

    PubMed

    McKillip, Ryan P; Borden, Brittany A; Galecki, Paige; Ham, Sandra A; Patrick-Miller, Linda; Hall, Julianne P; Hussain, Sheena; Danahey, Keith; Siegler, Mark; Sorrentino, Matthew J; Sacro, Yasmin; Davis, Andrew M; Rubin, David T; Lipstreuer, Kristen; Polonsky, Tamar S; Nanda, Rita; Harper, William R; Koyner, Jay L; Burnet, Deborah L; Stadler, Walter M; Ratain, Mark J; Meltzer, David O; O'Donnell, Peter H

    2016-12-16

    Despite growing clinical use of genomic information, patient perceptions of genomic-based care are poorly understood. We prospectively studied patient-physician pairs who participated in an institutional pharmacogenomic implementation program. Trust/Privacy/Empathy/Medical Decision-Making (MDM)/Personalized Care (PC) dimensions were assessed through patient surveys after clinic visits at which physicians had access to preemptive pharmacogenomic results (Likert scale, 1-minimum/5-maximum; mean [SD]). From 2012-2015, 1,261 surveys were issued to 507 patients, with 792 (62.8%) returned. Privacy, Empathy, MDM and PC scores were significantly higher following visits when physicians considered pharmacogenomic results. Importantly, PC scores were significantly higher after physicians used pharmacogenomic information to guide medication changes (4.0[1.4] vs. 3.0[1.6], P<0.001) compared to prescribing visits without genomic guidance. Multivariable modeling controlling for clinical factors confirmed PC scores were more favorable following visits with genomic-influenced prescribing (OR=3.26 [1.31-8.14], P<0.05). Physicians appear to individualize care when utilizing pharmacogenomic results and this decision-making augmentation is perceived positively by patients. This article is protected by copyright. All rights reserved.

  2. The influence of military service on auditory health and the efficacy of a Hearing Conservation Program.

    PubMed

    Muhr, Per; Rosenhall, Ulf

    2011-01-01

    The influence of military service on self-assessed hearing symptoms and measured auditory function was studied as well as the efficacy of the Hearing Conservation Program (HCP) of the Swedish Armed Forces. 839 conscripts were recruited for the study at reporting to military service. They were all exposed to noise over the risk-limits from weapons and vehicles and used earmuffs and/or earplugs. Questionnaires and pure tone screening audiometry were studied at the start and the end of the military service. Retrospective information regarding audiometry at conscription before military service was included as control. The prevalence values of tinnitus were 23% before and 32% after the service and of sensitivity to noise 16% and 19% respectively. The prevalence values of hearing impairment were 6.3% at conscription, 14.5% at reporting to military service, and 24% after the training period. The incidence values of hearing decline were 3.7% during the period with no military noise exposure and 6.6% during the military service. Acoustic accident increased the risk of worsened tinnitus and sensitivity to noise four times and for a high frequency hearing decline six times. We observed elevated prevalence values of tinnitus, sensitivity to noise and hearing impairment at discharge compared to before military service. We observed an elevated risk of hearing decline during military service. Acoustic accident increased the risk of tinnitus, noise sensitivity and hearing decline. We suggest improvements regarding inclusion criteria for military service, and for education regarding the HCP.

  3. Influence of conservation programs on amphibians using seasonal wetlands in the Prairie Pothole Region

    USGS Publications Warehouse

    Balas, Caleb J.; Euliss, Ned H.; Mushnet, David M.

    2012-01-01

    Extensive modification of upland habitats surrounding wetlands to facilitate agricultural production has negatively impacted amphibian communities in the Prairie Pothole Region of North America. In attempts to mitigate ecosystem damage associated with extensive landscape alteration, vast tracks of upland croplands have been returned to perennial vegetative cover (i.e., conservation grasslands) under a variety of U.S. Department of Agriculture programs. We evaluated the influence of these conservation grasslands on amphibian occupancy of seasonal wetlands in the Prairie Pothole Region. Using automated call surveys, aquatic funnel traps, and visual encounter surveys, we detected eight amphibian species using wetlands within three land-use categories (farmed, conservation grasslands, and native prairie grasslands) during the summers of 2005 and 2006. Seasonal wetlands within farmlands were used less frequently by amphibians than those within conservation and native prairie grasslands, and wetlands within conservation grasslands were used less frequently than those within native prairie grasslands by all species and life-stages we successfully modeled. Our results suggest that, while not occupied as frequently as wetlands within native prairie, wetlands within conservation grasslands provide important habitat for maintaining amphibian biodiversity in the Prairie Pothole Region

  4. Evaluation of the All Stars Program: student and teacher factors that influence mediators of substance use.

    PubMed

    Giles, S M; Harrington, N G; Fearnow-Kenney, M

    2001-01-01

    The authors examined the relationship between students' perceptions of a problem behavior prevention program, All Stars, and changes in the program variables. Three factors--Program Enjoyment, Student Engagement, and Teacher Relationship--were used to predict changes in the four variables targeted by the All Stars program. Student Engagement was related to greater changes in student idealism, commitment, and bonding. Program Enjoyment was related to positive changes in student idealism and normative beliefs. Teacher Relationship had little impact on the program variables. Students who were taught All Stars by regular classroom teachers reported greater Program Enjoyment and Student Engagement than students taught by health education specialists.

  5. Study of programmed cell death 1 (PDCD1) gene polymorphims in Iranian patients with ankylosing spondylitis.

    PubMed

    Soleimanifar, Narjes; Amirzargar, Ali Akbar; Mahmoudi, Mahdi; Pourfathollah, Ali Akbar; Azizi, Esfandiar; Jamshidi, Ahmad Reza; Rezaei, Nima; Tahoori, Mohammad Taher; Bidad, Katayoon; Nikbin, Behrouz; Nicknam, Mohammad Hossein

    2011-12-01

    Ankylosing spondylitis (AS) is a chronic inflammatory disease, characterized by axial arthritis in which the genetic-environmental factors seem to be involved in the pathogenesis of the disease. This study was performed to investigate the role of polymorphisms of the programmed cell death 1 (PDCD1) gene on susceptibility to AS. In this study, 161 Iranian patients with AS and 208 normal controls were enrolled; two single-nucleotide polymorphisms (SNPs) of the PDCD1 gene PD-1.3 (G, A) in nucleotide position +7146 of intron 4 and PD-1.9 (C, T) in nucleotide +7625 of exon 5 were studied. Analysis of PD-1.3 revealed that 82% of patients and 79% of controls had GG genotype, while GA and AA genotypes were detected in 17% and 0.6% of patients, respectively, and 20% and 1.4% of controls, respectively. Moreover, the genotype CC (PD-1.9) was present in 92% of patients and 97% of controls. Although these differences were not statistically significant between patients and controls, comparisons of genotypes frequencies in the AS patients, based on human leukocyte antigen (HLA)-B27, revealed that all patients who had CT genotype (PD-1.9) were HLA-B27 positive, whereas 30% of patients with CC genotype were HLA-B27 negative. There was no evidence of association for PDCD1 SNPs with AS in our study, but CT genotype (PD-1.9) seems to be associated with HLA-B27 positivity in the patients with AS.

  6. Myoglobin-deficient mice activate a distinct cardiac gene expression program in response to isoproterenol-induced hypertrophy.

    PubMed

    Molojavyi, Andrei; Lindecke, Antje; Raupach, Annika; Moellendorf, Sarah; Köhrer, Karl; Gödecke, Axel

    2010-04-01

    Myoglobin knockout mice (myo-/-) adapt to the loss of myoglobin by the activation of a variety of compensatory mechanisms acting on the structural and functional level. To analyze to what extent myo-/- mice would tolerate cardiac stress we used the model of chronic isoproterenol application to induce cardiac hypertrophy in myo-/- mice and wild-type (WT) controls. After 14 days of isoproterenol infusion cardiac hypertrophy in WT and myo-/- mice reached a similar level. WT mice developed lung edema and left ventricular dilatation suggesting the development of heart failure. In contrast, myo-/- mice displayed conserved cardiac function and no signs of left ventricular dilatation. Analysis of the cardiac gene expression profiles using 40K mouse oligonucleotide arrays showed that isoproterenol affected the expression of 180 genes in WT but only 92 genes of myo-/- hearts. Only 40 of these genes were regulated in WT as well as in myo-/- hearts. In WT hearts a pronounced induction of genes of the extracellular matrix occurred suggesting a higher level of cardiac remodeling. myo-/- hearts showed altered transcription of genes involved in carbon metabolism, inhibition of apoptosis and muscular repair. Interestingly, a subset of genes that was altered in myo-/- mice already under basal conditions was differentially expressed in WT hearts under isoproterenol treatment. In summary, our data show a high capacity of myoglobin-deficient mice to adapt to catecholamine induced cardiac stress which is associated with activation of a distinct cardiac gene expression program.

  7. The influence of ignoring secondary structure on divergence time estimates from ribosomal RNA genes.

    PubMed

    Dohrmann, Martin

    2014-02-01

    Genes coding for ribosomal RNA molecules (rDNA) are among the most popular markers in molecular phylogenetics and evolution. However, coevolution of sites that code for pairing regions (stems) in the RNA secondary structure can make it challenging to obtain accurate results from such loci. While the influence of ignoring secondary structure on multiple sequence alignment and tree topology has been investigated in numerous studies, its effect on molecular divergence time estimates is still poorly known. Here, I investigate this issue in Bayesian Markov Chain Monte Carlo (BMCMC) and penalized likelihood (PL) frameworks, using empirical datasets from dragonflies (Odonata: Anisoptera) and glass sponges (Porifera: Hexactinellida). My results indicate that highly biased inferences under substitution models that ignore secondary structure only occur if maximum-likelihood estimates of branch lengths are used as input to PL dating, whereas in a BMCMC framework and in PL dating based on Bayesian consensus branch lengths, the effect is far less severe. I conclude that accounting for coevolution of paired sites in molecular dating studies is not as important as previously suggested, as long as the estimates are based on Bayesian consensus branch lengths instead of ML point estimates. This finding is especially relevant for studies where computational limitations do not allow the use of secondary-structure specific substitution models, or where accurate consensus structures cannot be predicted. I also found that the magnitude and direction (over- vs. underestimating node ages) of bias in age estimates when secondary structure is ignored was not distributed randomly across the nodes of the phylogenies, a phenomenon that requires further investigation.

  8. More Aroused, Less Fatigued: Fatty Acid Amide Hydrolase Gene Polymorphisms Influence Acute Response to Amphetamine

    PubMed Central

    Dlugos, Andrea M; Hamidovic, Ajna; Hodgkinson, Colin A; Goldman, David; Palmer, Abraham A; de Wit, Harriet

    2010-01-01

    Amphetamine is a stimulant drug that enhances attention and feelings of alertness. Amphetamine's effects are known to be modulated by endogenous cannabinoids, which are degraded by the enzyme fatty acid amide hydrolase (FAAH). In this study we investigated inter-individual differences in mood response to amphetamine in relation to four polymorphisms in the FAAH gene, including the FAAH missense variant rs324420C → A (Pro129Thr), which was previously found to be associated with street drug use and addictive traits. One hundred and fifty-nine healthy Caucasian volunteers participated in a three-session, double-blind crossover study receiving either placebo or oral d-amphetamine (10 and 20 mg). Associations between individual genotypes and levels of self-reported Arousal (Profile of Mood States) after d-amphetamine ingestion were investigated using two-way ANOVAs/ANCOVAs. Association analyses for haplotypes were performed using the adaptive permutation approach implemented in PLINK. Genotypes at rs3766246 and rs2295633 were significantly associated with increased ratings of Arousal (p<0.05) and Fatigue (p<0.01) after the 10-mg dose. Fatigue levels were also found to be associated with the haplotypes CCC and TAT formed from rs3766246, rs324420, and rs2295633 (p<0.05). These data suggest that the endocannabinoid system influences variation in subjective response to amphetamine. This has important implications for understanding the role of endogenous cannabinoids in response to amphetamine, studies of poly-substance abuse, and understanding the genetic determinants of inter-individual differences in stimulant effects and risk of abuse. PMID:19890266

  9. Bidirectional promoters of insects: genome-wide comparison, evolutionary implication and influence on gene expression.

    PubMed

    Behura, Susanta K; Severson, David W

    2015-01-30

    Bidirectional promoters are widespread in insect genomes. By analyzing 23 insect genomes we show that the frequency of bidirectional gene pairs varies according to genome compactness and density of genes among the species. The density of bidirectional genes expected based on number of genes per megabase of genome explains the observed density suggesting that bidirectional pairing of genes may be due to random event. We identified specific transcription factor binding motifs that are enriched in bidirectional promoters across insect species. Furthermore, we observed that bidirectional promoters may act as transcriptional hotspots in insect genomes where protein coding genes tend to aggregate in significantly biased (p < 0.001) manner compared to unidirectional promoters. Natural selection seems to have an association with the extent of bidirectionality of genes among the species. The rate of non-synonymous-to-synonymous changes (dN/dS) shows a second-order polynomial distribution with bidirectionality between species indicating that bidirectionality is dependent upon evolutionary pressure acting on the genomes. Analysis of genome-wide microarray expression data of multiple insect species suggested that bidirectionality has a similar association with transcriptome variation across species. Furthermore, bidirectional promoters show significant association with correlated expression of the divergent gene pairs depending upon their motif composition. Analysis of gene ontology showed that bidirectional genes tend to have a common association with functions related to "binding" (including ion binding, nucleotide binding and protein binding) across genomes. Such functional constraint of bidirectional genes may explain their widespread persistence in genome of diverse insect species.

  10. Serine 574 phosphorylation alters transcriptional programming of FOXO3 by selectively enhancing apoptotic gene expression.

    PubMed

    Li, Z; Zhao, J; Tikhanovich, I; Kuravi, S; Helzberg, J; Dorko, K; Roberts, B; Kumer, S; Weinman, S A

    2016-04-01

    Forkhead box O3 (FOXO3) is a multispecific transcription factor that is responsible for multiple and conflicting transcriptional programs such as cell survival and apoptosis. The protein is heavily post-translationally modified and there is considerable evidence that post-transcriptional modifications (PTMs) regulate protein stability and nuclear-cytosolic translocation. Much less is known about how FOXO3 PTMs determine the specificity of its transcriptional program. In this study we demonstrate that exposure of hepatocytes to ethanol or exposure of macrophages to lipopolysaccharide (LPS) induces the c-Jun N-terminal kinase (JNK)-dependent phosphorylation of FOXO3 at serine-574. Chromatin immunoprecipitation (ChIP), mRNA and protein measurements demonstrate that p-574-FOXO3 selectively binds to promoters of pro-apoptotic genes but not to other well-described FOXO3 targets. Both unphosphorylated and p-574-FOXO3 bound to the B-cell lymphoma 2 (Bcl-2) promoter, but the unphosphorylated form was a transcriptional activator, whereas p-574-FOXO3 was a transcriptional repressor. The combination of increased TRAIL (TNF-related apoptosis-inducing ligand) and decreased Bcl-2 was both necessary and sufficient to induce apoptosis. LPS treatment of a human monocyte cell line (THP-1) induced FOXO3 S-574 phosphorylation and apoptosis. LPS-induced apoptosis was prevented by knockdown of FOXO3. It was restored by overexpressing wild-type FOXO3 but not by overexpressing a nonphosphorylatable S-574A FOXO3. Expression of an S-574D phosphomimetic form of FOXO3 induced apoptosis even in the absence of LPS. A similar result was obtained with mouse peritoneal macrophages where LPS treatment increased TRAIL, decreased Bcl-2 and induced apoptosis in wild-type but not FOXO3(-/-) cells. This work thus demonstrates that S-574 phosphorylation generates a specifically apoptotic form of FOXO3 with decreased transcriptional activity for other well-described FOXO3 functions.

  11. Significant life experience: Exploring the lifelong influence of place-based environmental and science education on program participants

    NASA Astrophysics Data System (ADS)

    Colvin, Corrie Ruth

    Current research provides a limited understanding of the life long influence of nonformal place-based environmental and science education programs on past participants. This study looks to address this gap, exploring the ways in which these learning environments have contributed to environmental identity and stewardship. Using Dorothy Holland's approach to social practice theory's understanding of identity formation, this study employed narrative interviews and a close-ended survey to understand past participants' experience over time. Participants from two place-based environmental education programs and one science-inquiry program were asked to share their reflections on their program experience and the influence they attribute to that experience. Among all participants, the element of hands-on learning, supportive instructors, and engaging learning environments remained salient over time. Participants of nature-based programs demonstrated that these programs in particular were formative in contributing to an environmental stewardship identity. Social practice theory can serve as a helpful theoretical framework for significant life experience research, which has largely been missing from this body of research. This study also holds implications for the fields of place-based environmental education, conservation psychology, and sustainability planning, all of which look to understand and increase environmentally sustainable practices.

  12. Cationized bovine serum albumin as gene carrier: Influence of specific secondary structure on DNA complexibility and gene transfection.

    PubMed

    Du, Jianwei; Li, Bangbang; Zhang, Peng; Wang, Youxiang

    2016-07-01

    In this research, BSA, one of the natural rigid globular proteins with ca. 51% of α-helix secondary structure, was utilized to prepare cationized BSA (cBSA) as gene carrier. Tetraethylenepentamine (TEPA) or polyethylenimine (PEI1800) was grafted to BSA with different grafting levels. Based on the circular dichoism (CD) spectra, all cBSA remained α-helical structure to some degree. This was exciting to endow cBSA with quite different DNA complexibility and cellular biology behavior from the random coiled and flexible polycations such as PEI and poly-l-lysine (PLL). Strangely, the DNA condensability decreased with the increment of TEPA or PEI1800 grafting level. Also, the cBSA could condense DNA effectively to form irregular nanoparticles around 50-200nm above N/P ratio of 10. On account of the excellent hydration of BSA, the cBSA/DNA complexes revealed good colloidal stability under physiological salt condition. Cell culture experiments indicated this BSA-based gene carrier possessed good cellular compatibility. Surprisingly, cBSA/DNA complexes could be uptaken excellently by up to 90% cells. This might be owing to the agitation effect of α-helical structure and the positive potential of these complexes. BSA-PEI1800/DNA complexes with quick endosome escape even had transfection efficiency as high as PEI25k/DNA complexes. Overall, this paper provided us the potential of cBSA as gene carrier and might have some instructions in the design of protein-based gene delivery system.

  13. Volunteer Educators' Influence on Youth Participation and Learning in 4-H STEM Learning by Design Programs

    NASA Astrophysics Data System (ADS)

    Worker, Steven Michael

    The purpose of this study was to describe the co-construction of three 4-H STEM (science, technology, engineering, and mathematics) learning by design programs by volunteer educators and youth participants in the 4-H Youth Development Program. The programs advanced STEM learning through design, a pedagogical approach to support youth in planning, designing, and making shareable artifacts. This pedagogical approach is a special case of project-based learning, related to the practices found in the science learning through design literature as well as the making and tinkering movements. Specifically, I explored adult volunteer educators' roles and pedagogical strategies implementing the 4-H Junk Drawer Robotics curriculum (Mahacek, Worker, and Mahacek, 2011) and how that, in turn, afforded and constrained opportunities for youth to display or report engagement in design practices; learning of STEM content; strengthening tool competencies; dispositions of resilience, reciprocity, and playfulness; and psychological ownership. The curriculum targeted middle school youth with a sequence of science inquiry activities and engineering design challenges. This study employed naturalist and multiple-case study methodology relying on participant observations and video, interviews with educators, and focus groups with youth within three 4-H educational robotics programs organized by adult 4-H volunteer educators. Data collection took place in 2014 and 2015 at Santa Clara with an educator and seven youth; Solano with three educators and eight youth; and Alameda with an educator and seven youth. Data analysis revealed six discrete categories of pedagogy and interactions that I labeled as participation structures that included lecture, demonstration, learning activity, group sharing, scripted build, and design & build. These participation structures were related to the observed pedagogical practices employed by the educators. There was evidence of youth engagement in design

  14. Toward a Rosetta stone for the stem cell genome: stochastic gene expression, network architecture, and external influences.

    PubMed

    Halley, Julianne D; Winkler, David A; Burden, Frank R

    2008-09-01

    We review literature relating to three types of factors known to influence stem cell behavior. These factors are stochastic gene expression, regulatory network architecture, and the influence of external signals, such as those emanating from the niche. Although these factors are considered separately, their shared evolutionary history necessitates integration. Stochastic gene expression pervades network components; network architecture controls, modulates, or exploits this noise while performing additional computation; and such complexity also interplays with factors external to cells. Adequate understanding of each of these components, and how they interact, will lead to a conceptual model of the stem cell regulatory system that can be used to drive hypothesis-driven research and facilitate interpretation of experimental data.

  15. The influence of gene flow and drift on genetic and phenotypic divergence in two species of Zosterops in Vanuatu.

    PubMed

    Clegg, Sonya M; Phillimore, Albert B

    2010-04-12

    Colonization of an archipelago sets the stage for adaptive radiation. However, some archipelagos are home to spectacular radiations, while others have much lower levels of diversification. The amount of gene flow among allopatric populations is one factor proposed to contribute to this variation. In island colonizing birds, selection for reduced dispersal ability is predicted to produce changing patterns of regional population genetic structure as gene flow-dominated systems give way to drift-mediated divergence. If this transition is important in facilitating phenotypic divergence, levels of genetic and phenotypic divergence should be associated. We consider population genetic structure and phenotypic divergence among two co-distributed, congeneric (Genus: Zosterops) bird species inhabiting the Vanuatu archipelago. The more recent colonist, Z. lateralis, exhibits genetic patterns consistent with a strong influence of distance-mediated gene flow. However, complex patterns of asymmetrical gene flow indicate variation in dispersal ability or inclination among populations. The endemic species, Z. flavifrons, shows only a partial transition towards a drift-mediated system, despite a long evolutionary history on the archipelago. We find no strong evidence that gene flow constrains phenotypic divergence in either species, suggesting that levels of inter-island gene flow do not explain the absence of a radiation across this archipelago.

  16. The influence of gene flow and drift on genetic and phenotypic divergence in two species of Zosterops in Vanuatu

    PubMed Central

    Clegg, Sonya M.; Phillimore, Albert B.

    2010-01-01

    Colonization of an archipelago sets the stage for adaptive radiation. However, some archipelagos are home to spectacular radiations, while others have much lower levels of diversification. The amount of gene flow among allopatric populations is one factor proposed to contribute to this variation. In island colonizing birds, selection for reduced dispersal ability is predicted to produce changing patterns of regional population genetic structure as gene flow-dominated systems give way to drift-mediated divergence. If this transition is important in facilitating phenotypic divergence, levels of genetic and phenotypic divergence should be associated. We consider population genetic structure and phenotypic divergence among two co-distributed, congeneric (Genus: Zosterops) bird species inhabiting the Vanuatu archipelago. The more recent colonist, Z. lateralis, exhibits genetic patterns consistent with a strong influence of distance-mediated gene flow. However, complex patterns of asymmetrical gene flow indicate variation in dispersal ability or inclination among populations. The endemic species, Z. flavifrons, shows only a partial transition towards a drift-mediated system, despite a long evolutionary history on the archipelago. We find no strong evidence that gene flow constrains phenotypic divergence in either species, suggesting that levels of inter-island gene flow do not explain the absence of a radiation across this archipelago. PMID:20194170

  17. Possible influence of B chromosomes on genes included in immune response and parasite burden in Apodemus flavicollis.

    PubMed

    Adnađević, Tanja; Jovanović, Vladimir M; Blagojević, Jelena; Budinski, Ivana; Cabrilo, Borislav; Bjelić-Čabrilo, Olivera; Bijelić-Čabrilo, Olivera; Vujošević, Mladen

    2014-01-01

    Genetic background underlying wild populations immune response to different parasites is still not well understood. We studied immune response to multiple infections and to competition between different parasite species at different developmental stages in population of yellow-necked mouse, Apodemus flavicollis. Quantitative real-time PCR was used to investigate associations of MHC II-DRB, IL-10 and Tgf-β genes expressions with presence of intestinal parasites at different developmental stages. Furthermore, we were interested whether the host related characteristics (sex, age, body condition, presence of B chromosomes or expression of other genes) or characteristics of present parasites (number of adult parasites of each identified species, egg count of each parasite genus, total number of nematode individuals) affect differential expression of the studied genes. A significant invert association between the expression of MHC II-DRB and Tgf-β gene was found, which together with absence of IL-10 association confirmed modified Th2 as the main type of immune response to nematode infections. Effect of recorded parasites and parasite life-cycle stage on expression levels of MHC II-DRB gene was detected only through interactions with host-related characteristics such as sex, age, and the presence of B chromosomes. The presence of B chromosomes is associated with lower expression level of Tgf-β gene. Although the influence of host genetic background on parasite infection has already been well documented, this is the first study in mammals that gave presence of B chromosomes on immune response full consideration.

  18. Temperature and food influence shell growth and mantle gene expression of shell matrix proteins in the pearl oyster Pinctada margaritifera.

    PubMed

    Joubert, Caroline; Linard, Clémentine; Le Moullac, Gilles; Soyez, Claude; Saulnier, Denis; Teaniniuraitemoana, Vaihiti; Ky, Chin Long; Gueguen, Yannick

    2014-01-01

    In this study, we analyzed the combined effect of microalgal concentration and temperature on the shell growth of the bivalve Pinctada margaritifera and the molecular mechanisms underlying this biomineralization process. Shell growth was measured after two months of rearing in experimental conditions, using calcein staining of the calcified structures. Molecular mechanisms were studied though the expression of 11 genes encoding proteins implicated in the biomineralization process, which was assessed in the mantle. We showed that shell growth is influenced by both microalgal concentration and temperature, and that these environmental factors also regulate the expression of most of the genes studied. Gene expression measurement of shell matrix protein thereby appears to be an appropriate indicator for the evaluation of the biomineralization activity in the pearl oyster P. margaritifera under varying environmental conditions. This study provides valuable information on the molecular mechanisms of mollusk shell growth and its environmental control.

  19. Common Variants in 40 Genes Assessed for Diabetes Incidence and Response to Metformin and Lifestyle Intervention in the Diabetes Prevention Program

    PubMed Central

    Jablonski, Kathleen A.; McAteer, Jarred B.; de Bakker, Paul I.W.; Franks, Paul W.; Pollin, Toni I.; Hanson, Robert L.; Saxena, Richa; Fowler, Sarah; Shuldiner, Alan R.; Knowler, William C.; Altshuler, David; Florez, Jose C.

    2010-01-01

    OBJECTIVE Genome-wide association studies have begun to elucidate the genetic architecture of type 2 diabetes. We examined whether single nucleotide polymorphisms (SNPs) identified through targeted complementary approaches affect diabetes incidence in the at-risk population of the Diabetes Prevention Program (DPP) and whether they influence a response to preventive interventions. RESEARCH DESIGN AND METHODS We selected SNPs identified by prior genome-wide association studies for type 2 diabetes and related traits, or capturing common variation in 40 candidate genes previously associated with type 2 diabetes, implicated in monogenic diabetes, encoding type 2 diabetes drug targets or drug-metabolizing/transporting enzymes, or involved in relevant physiological processes. We analyzed 1,590 SNPs for association with incident diabetes and their interaction with response to metformin or lifestyle interventions in 2,994 DPP participants. We controlled for multiple hypothesis testing by assessing false discovery rates. RESULTS We replicated the association of variants in the metformin transporter gene SLC47A1 with metformin response and detected nominal interactions in the AMP kinase (AMPK) gene STK11, the AMPK subunit genes PRKAA1 and PRKAA2, and a missense SNP in SLC22A1, which encodes another metformin transporter. The most significant association with diabetes incidence occurred in the AMPK subunit gene PRKAG2 (hazard ratio 1.24, 95% CI 1.09–1.40, P = 7 × 10−4). Overall, there were nominal associations with diabetes incidence at 85 SNPs and nominal interactions with the metformin and lifestyle interventions at 91 and 69 mostly nonoverlapping SNPs, respectively. The lowest P values were consistent with experiment-wide 33% false discovery rates. CONCLUSIONS We have identified potential genetic determinants of metformin response. These results merit confirmation in independent samples. PMID:20682687

  20. Genome-Wide RNAi Screens in C. elegans to Identify Genes Influencing Lifespan and Innate Immunity.

    PubMed

    Sinha, Amit; Rae, Robbie

    2016-01-01

    RNA interference is a rapid, inexpensive, and highly effective tool used to inhibit gene function. In C. elegans, whole genome screens have been used to identify genes involved with numerous traits including aging and innate immunity. RNAi in C. elegans can be carried out via feeding, soaking, or injection. Here we outline protocols used to maintain, grow, and carry out RNAi via feeding in C. elegans and determine whether the inhibited genes are essential for lifespan or innate immunity.

  1. Arabidopsis flowering locus D influences systemic-acquired-resistance- induced expression and histone modifications of WRKY genes.

    PubMed

    Singh, Vijayata; Roy, Shweta; Singh, Deepjyoti; Nandi, Ashis Kumar

    2014-03-01

    A plant that is in part infected by a pathogen is more resistant throughout its whole body to subsequent infections--a phenomenon known as systemic acquired resistance (SAR). Mobile signals are synthesized at the site of infection and distributed throughout the plant through vascular tissues. Mechanism of SAR development subsequent to reaching the mobile signal in the distal tissue is largely unknown. Recently we showed that flowering locus D (FLD) gene of Arabidopsis thaliana is required in the distal tissue to activate SAR. FLD codes for a homologue of human-lysine-specific histone demethylase. Here we show that FLD function is required for priming (SAR induced elevated expression during challenge inoculation) of WRKY29 and WRKY6 genes. FLD also differentially influences basal and SAR-induced expression of WRKY38, WRKY65 and WRKY53 genes. In addition, we also show that FLD partly localizes in nucleus and influences histone modifications at the promoters of WRKY29 and WRKY6 genes. The results altogether indicate to the possibility of FLD's involvement in epigenetic regulation of SAR.

  2. Microarray assessment of the influence of the conceptus on gene expression in the mouse uterus during decidualization.

    PubMed

    McConaha, M E; Eckstrum, K; An, J; Steinle, J J; Bany, B M

    2011-04-01

    During pregnancy in several species including humans and rodents, the endometrium undergoes decidualization. This process of differentiation from endometrial to decidual tissue occurs only after the onset of implantation in mice. It can also be artificially induced causing the formation of deciduomal tissue. The purpose of this study was to compare the gene expression profile of the developing decidua in pregnant mice with the deciduoma formed after artificial induction in an effort to identify conceptus-influenced changes in uterine gene expression during decidualization. We induced decidualization artificially by transferring blastocyst-sized ConA-coated agarose beads into the uterus on day 2.5 of pseudopregnancy. Recently published work has found this model to be more 'physiological' than other methods. Total RNA was isolated from blastocyst and bead-induced 'implantation' sites of the uteri of day 7.5 pregnant (decidua) and pseudopregnant (deciduoma) mice respectively. This RNA was then used for microarray analysis using Mouse Illumina BeadArray chips. This analysis revealed potential differential mRNA levels of only 45 genes between the decidua and bead-induced deciduoma tissues. We confirmed the differential mRNA levels of 31 of these genes using quantitative RT-PCR. Finally, the level and localization of some of the mRNAs for select genes (Aldh3a1, Bcmo1, Guca2b, and Inhbb) identified by our microarray analysis were examined in more detail. This study provides the identity of a small set of genes whose expression in the uterus during decidualization may be influenced by molecular signals from the conceptus.

  3. An Evaluation of the Influence of the Expanded Food and Nutrition Education Program in Missouri.

    ERIC Educational Resources Information Center

    Nolan, Nelda M.; Gross, John G.

    The report evaluates the Expanded Food and Nutrition Education Program (EFNEP) in Missouri by comparing the dietary adequacy and nutrition knowledge of 200 program families representative of urban, small town and rural areas with that of 200 similarly representative non-program families. Data were gathered by personal interviews taken in March,…

  4. A Qualitative Examination of Challenges Influencing Doctoral Students in an Online Doctoral Program

    ERIC Educational Resources Information Center

    Deshpande, Anant

    2016-01-01

    The main purpose of the study was to investigate the challenges faced by students in completion of an online doctoral program at the University of Liverpool, Online Doctoral Business Administration program. We analyse the responses of 91 doctoral students in an online DBA program. Based on the exploratory qualitative study themes were developed…

  5. Study Abroad Programs as Tools of Internationalization: Which Factors Influence Hungarian Business Students to Participate?

    ERIC Educational Resources Information Center

    Huják, Janka

    2015-01-01

    The internationalization of higher education has been on the agenda for decades now all over the world. Study abroad programs are undoubtedly tools of the internationalization endeavors. The ERASMUS Student Mobility Program is one of the flagships of the European Union's educational exchange programs implicitly aiming for the internationalization…

  6. Evaluation of the All Stars Program: Student and Teacher Factors that Influence Mediators of Substance Use.

    ERIC Educational Resources Information Center

    Giles, Steven M.; Harrington, Nancy Grant; Fearnow-Kenney, Melodie

    2001-01-01

    Examined the relationship between students' perceptions of a problem behavior prevention program, All Stars, and changes in program variables-bonding; normative beliefs; ideals; and commitment. Three factors-Program Enjoyment, Student Engagement, and Teacher Relationship-were used to predict changes in four variables. Results indicate Student…

  7. Attributions, Influences and Outcomes for Underrepresented and Disadvantaged Participants of a Medical Sciences Enrichment Pipeline Program

    ERIC Educational Resources Information Center

    Pinckney, Charlyene Carol

    2014-01-01

    The current study was undertaken to examine the effectiveness of the Rowan University-School of Osteopathic Medicine - Summer Pre-Medical Research and Education Program (Summer PREP), a postsecondary medical sciences enrichment pipeline program for under-represented and disadvantaged students. Thirty-four former program participants were surveyed…

  8. The Influence of Major Life Events on Economic Attitudes in a World of Gene-Environment Interplay

    PubMed Central

    Hatemi, Peter K.

    2014-01-01

    The role of “genes” on political attitudes has gained attention across disciplines. However, person-specific experiences have yet to be incorporated into models that consider genetic influences. Relying on a gene-environment interplay approach, this study explicates how life-events, such as losing one’s job or suffering a financial loss, influence economic policy attitudes. The results indicate genetic and environmental variance on support for unions, immigration, capitalism, socialism and property tax is moderated by financial risks. Changes in the magnitude of genetic influences, however, are temporary. After two years, the phenotypic effects of the life events remain on most attitudes, but changes in the sources of individual differences do not. Univariate twin models that estimate the independent contributions of genes and environment on the variation of attitudes appear to provide robust baseline indicators of sources of individual differences. These estimates, however, are not event or day specific. In this way, genetic influences add stability, while environment cues change, and this process is continually updated. PMID:24860199

  9. Global profiling of influence of intra-ischemic brain temperature on gene expression in rat brain.

    PubMed

    Kobayashi, Megumi Sugahara; Asai, Satoshi; Ishikawa, Koichi; Nishida, Yayoi; Nagata, Toshihito; Takahashi, Yasuo

    2008-06-01

    Mild to moderate differences in brain temperature are known to greatly affect the outcome of cerebral ischemia. The impact of brain temperature on ischemic disorders has been mainly evaluated through pathological analysis. However, no comprehensive analyses have been conducted at the gene expression level. Using a high-density oligonucleotide microarray, we screened 24000 genes in the hippocampus under hypothermic (32 degrees C), normothermic (37 degrees C), and hyperthermic (39 degrees C) conditions in a rat ischemia-reperfusion model. When the ischemic group at each intra-ischemic brain temperature was compared to a sham-operated control group, genes whose expression levels changed more than three-fold with statistical significance could be detected. In our screening condition, thirty-three genes (some of them novel) were obtained after screening, and extensive functional surveys and literature reviews were subsequently performed. In the hypothermic condition, many neuroprotective factor genes were obtained, whereas cell death- and cell damage-associated genes were detected as the brain temperature increased. At all intra-ischemic brain temperatures, multiple molecular chaperone genes were obtained. The finding that intra-ischemic brain temperature affects the expression level of many genes related to neuroprotection or neurotoxicity coincides with the different pathological outcomes at different brain temperatures, demonstrating the utility of the genetic approach.

  10. Gene regulation of Salmonella enterica serovar Typhimurium as influenced by LuxS/AI-2

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quorum sensing is mediated by small signaling molecules, autoinducer molecules. The luxS gene which is conserved in several Gram-positive and Gram-negative bacteria is involved in the synthesis of the autoinducer molecule-2 (AI-2). Genes controlled by luxS in S. Typhimurium were identified using mic...

  11. Photoperiod and E-genes Directly Influence the Duration of Soybean Reproductive Development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Duration of the reproductive phase (DRP) is critical for soybean [Glycine max (L.) Merr.] yield. Manipulation of this phase may benefit breeding for higher yield. The soybean E-gene series control time to flowering and maturity through a photoperiod-mediated response. It is possible that E-genes and...

  12. Influence of Sex on Basal and Dickkopf-1 Regulated Gene Expression in the Bovine Morula

    PubMed Central

    Denicol, Anna C.; Leão, Beatriz C. S.; Dobbs, Kyle B.; Mingoti, Gisele Z.; Hansen, Peter J.

    2015-01-01

    Sex affects function of the developing mammalian embryo as early as the preimplantation period. There were two goals of the current objective. The first was to determine the degree and nature of differences in gene expression between female and male embryos in the cow at the morula stage of development. The second objective was to determine whether DKK1, a molecule known to alter differentiation of the blastocyst, would affect gene expression differently for female and male morulae. In Experiment 1, female and male embryos were treated with DKK1 at Day 5 after insemination. Morulae were harvested 24 h after treatment, pooled in groups of 20 for microarray analysis and RNA subjected to analysis of gene expression by microarray hybridization. There were 662 differentially expressed genes between females and males and 128 of these genes had a fold change ≥ 1.5 between the two sexes. Of the genes upregulated in females, 49.5% were located in the X chromosome. Functional analysis predicted that cell survival was greater in female embryos. Experiment 2 involved a similar design except that transcripts for 12 genes previously reported to be affected by sex, DKK1 or the interaction were quantified by quantitative polymerase chain reaction. Expression of all genes tested that were affected by sex in experiment 1 was affected in a similar manner in Experiment 2. In contrast, effects of DKK1 on gene expression were largely not repeatable in Experiment 2. The exception was for the Hippo signaling gene AMOT, which was inhibited by DKK1. In Experiment 3, embryos produced by fertilization with unsorted sperm were treated with DKK1 at Day 5 and abundance of transcripts for CDX2, GATA6, and NANOG determined at Days 5, 6 and 7 after insemination. There was no effect of DKK1 on expression of any of the three genes. In conclusion, female and male bovine embryos have a different pattern of gene expression as early as the morula stage, and this is due to a large extent to expression

  13. Influence of Sex on Basal and Dickkopf-1 Regulated Gene Expression in the Bovine Morula.

    PubMed

    Denicol, Anna C; Leão, Beatriz C S; Dobbs, Kyle B; Mingoti, Gisele Z; Hansen, Peter J

    2015-01-01

    Sex affects function of the developing mammalian embryo as early as the preimplantation period. There were two goals of the current objective. The first was to determine the degree and nature of differences in gene expression between female and male embryos in the cow at the morula stage of development. The second objective was to determine whether DKK1, a molecule known to alter differentiation of the blastocyst, would affect gene expression differently for female and male morulae. In Experiment 1, female and male embryos were treated with DKK1 at Day 5 after insemination. Morulae were harvested 24 h after treatment, pooled in groups of 20 for microarray analysis and RNA subjected to analysis of gene expression by microarray hybridization. There were 662 differentially expressed genes between females and males and 128 of these genes had a fold change ≥ 1.5 between the two sexes. Of the genes upregulated in females, 49.5% were located in the X chromosome. Functional analysis predicted that cell survival was greater in female embryos. Experiment 2 involved a similar design except that transcripts for 12 genes previously reported to be affected by sex, DKK1 or the interaction were quantified by quantitative polymerase chain reaction. Expression of all genes tested that were affected by sex in experiment 1 was affected in a similar manner in Experiment 2. In contrast, effects of DKK1 on gene expression were largely not repeatable in Experiment 2. The exception was for the Hippo signaling gene AMOT, which was inhibited by DKK1. In Experiment 3, embryos produced by fertilization with unsorted sperm were treated with DKK1 at Day 5 and abundance of transcripts for CDX2, GATA6, and NANOG determined at Days 5, 6 and 7 after insemination. There was no effect of DKK1 on expression of any of the three genes. In conclusion, female and male bovine embryos have a different pattern of gene expression as early as the morula stage, and this is due to a large extent to expression

  14. Factors influencing student selection of marriage and family therapy graduate programs.

    PubMed

    Hertlein, Katherine M; Lambert-Shute, Jennifer

    2007-01-01

    To understand which factors students consider most important in choosing a marriage and family therapy (MFT) graduate program and how programs met or did not meet these expectations of students over the course of graduate study, we conducted an online mixed-method investigation. One hundred twelve graduate students in Commission on Accreditation for Marriage and Family Therapy Education-accredited programs responded to an online survey assessing what factors led them to select a specific graduate program in MFT. In the quantitative portion, students ranked each factor (personal fit, faculty, funding, research, clinical work, and teaching) as well as characteristics of each factor in relation to its importance in their selection of an MFT program. Additionally, students indicated to what level their programs meet their expectations. In the qualitative portion, students described how they believed their chosen program was or was not meeting their expectations. Both doctoral and master's students ranked personal fit as the top factor affecting their choice of graduate program in MFT, but they differed on the characteristics of each of these factors and their importance in selecting an MFT program. Implications for this research include program evaluation and program advertising, and are consistent with the scientist-practitioner model.

  15. Prediction of lung cancer based on serum biomarkers by gene expression programming methods.

    PubMed

    Yu, Zhuang; Chen, Xiao-Zheng; Cui, Lian-Hua; Si, Hong-Zong; Lu, Hai-Jiao; Liu, Shi-Hai

    2014-01-01

    In diagnosis of lung cancer, rapid distinction between small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) tumors is very important. Serum markers, including lactate dehydrogenase (LDH), C-reactive protein (CRP), carcino-embryonic antigen (CEA), neurone specific enolase (NSE) and Cyfra21-1, are reported to reflect lung cancer characteristics. In this study classification of lung tumors was made based on biomarkers (measured in 120 NSCLC and 60 SCLC patients) by setting up optimal biomarker joint models with a powerful computerized tool - gene expression programming (GEP). GEP is a learning algorithm that combines the advantages of genetic programming (GP) and genetic algorithms (GA). It specifically focuses on relationships between variables in sets of data and then builds models to explain these relationships, and has been successfully used in formula finding and function mining. As a basis for defining a GEP environment for SCLC and NSCLC prediction, three explicit predictive models were constructed. CEA and NSE are frequently- used lung cancer markers in clinical trials, CRP, LDH and Cyfra21-1 have significant meaning in lung cancer, basis on CEA and NSE we set up three GEP models-GEP 1(CEA, NSE, Cyfra21-1), GEP2 (CEA, NSE, LDH), GEP3 (CEA, NSE, CRP). The best classification result of GEP gained when CEA, NSE and Cyfra21-1 were combined: 128 of 135 subjects in the training set and 40 of 45 subjects in the test set were classified correctly, the accuracy rate is 94.8% in training set; on collection of samples for testing, the accuracy rate is 88.9%. With GEP2, the accuracy was significantly decreased by 1.5% and 6.6% in training set and test set, in GEP3 was 0.82% and 4.45% respectively. Serum Cyfra21-1 is a useful and sensitive serum biomarker in discriminating between NSCLC and SCLC. GEP modeling is a promising and excellent tool in diagnosis of lung cancer.

  16. Surface EMG-based Sketching Recognition Using Two Analysis Windows and Gene Expression Programming

    PubMed Central

    Yang, Zhongliang; Chen, Yumiao

    2016-01-01

    Sketching is one of the most important processes in the conceptual stage of design. Previous studies have relied largely on the analyses of sketching process and outcomes; whereas surface electromyographic (sEMG) signals associated with sketching have received little attention. In this study, we propose a method in which 11 basic one-stroke sketching shapes are identified from the sEMG signals generated by the forearm and upper arm muscles from 4 subjects. Time domain features such as integrated electromyography, root mean square and mean absolute value were extracted with analysis windows of two length conditions for pattern recognition. After reducing data dimensionality using principal component analysis, the shapes were classified using Gene Expression Programming (GEP). The performance of the GEP classifier was compared to the Back Propagation neural network (BPNN) and the Elman neural network (ENN). Feature extraction with the short analysis window (250 ms with a 250 ms increment) improved the recognition rate by around 6.4% averagely compared with the long analysis window (2500 ms with a 2500 ms increment). The average recognition rate for the eleven basic one-stroke sketching patterns achieved by the GEP classifier was 96.26% in the training set and 95.62% in the test set, which was superior to the performance of the BPNN and ENN classifiers. The results show that the GEP classifier is able to perform well with either length of the analysis window. Thus, the proposed GEP model show promise for recognizing sketching based on sEMG signals. PMID:27790083

  17. A dynamic multiarmed bandit-gene expression programming hyper-heuristic for combinatorial optimization problems.

    PubMed

    Sabar, Nasser R; Ayob, Masri; Kendall, Graham; Qu, Rong

    2015-02-01

    Hyper-heuristics are search methodologies that aim to provide high-quality solutions across a wide variety of problem domains, rather than developing tailor-made methodologies for each problem instance/domain. A traditional hyper-heuristic framework has two levels, namely, the high level strategy (heuristic selection mechanism and the acceptance criterion) and low level heuristics (a set of problem specific heuristics). Due to the different landscape structures of different problem instances, the high level strategy plays an important role in the design of a hyper-heuristic framework. In this paper, we propose a new high level strategy for a hyper-heuristic framework. The proposed high-level strategy utilizes a dynamic multiarmed bandit-extreme value-based reward as an online heuristic selection mechanism to select the appropriate heuristic to be applied at each iteration. In addition, we propose a gene expression programming framework to automatically generate the acceptance criterion for each problem instance, instead of using human-designed criteria. Two well-known, and very different, combinatorial optimization problems, one static (exam timetabling) and one dynamic (dynamic vehicle routing) are used to demonstrate the generality of the proposed framework. Compared with state-of-the-art hyper-heuristics and other bespoke methods, empirical results demonstrate that the proposed framework is able to generalize well across both domains. We obtain competitive, if not better results, when compared to the best known results obtained from other methods that have been presented in the scientific literature. We also compare our approach against the recently released hyper-heuristic competition test suite. We again demonstrate the generality of our approach when we compare against other methods that have utilized the same six benchmark datasets from this test suite.

  18. Surface EMG-based Sketching Recognition Using Two Analysis Windows and Gene Expression Programming.

    PubMed

    Yang, Zhongliang; Chen, Yumiao

    2016-01-01

    Sketching is one of the most important processes in the conceptual stage of design. Previous studies have relied largely on the analyses of sketching process and outcomes; whereas surface electromyographic (sEMG) signals associated with sketching have received little attention. In this study, we propose a method in which 11 basic one-stroke sketching shapes are identified from the sEMG signals generated by the forearm and upper arm muscles from 4 subjects. Time domain features such as integrated electromyography, root mean square and mean absolute value were extracted with analysis windows of two length conditions for pattern recognition. After reducing data dimensionality using principal component analysis, the shapes were classified using Gene Expression Programming (GEP). The performance of the GEP classifier was compared to the Back Propagation neural network (BPNN) and the Elman neural network (ENN). Feature extraction with the short analysis window (250 ms with a 250 ms increment) improved the recognition rate by around 6.4% averagely compared with the long analysis window (2500 ms with a 2500 ms increment). The average recognition rate for the eleven basic one-stroke sketching patterns achieved by the GEP classifier was 96.26% in the training set and 95.62% in the test set, which was superior to the performance of the BPNN and ENN classifiers. The results show that the GEP classifier is able to perform well with either length of the analysis window. Thus, the proposed GEP model show promise for recognizing sketching based on sEMG signals.

  19. Transporter Molecules influence the Gene Expression in HeLa Cells

    PubMed Central

    Waldeck, Waldemar; Pipkorn, Ruediger; Korn, Bernhard; Mueller, Gabriele; Schick, Matthias; Tóth, Katalin; Wiessler, Manfred; Didinger, Bernd; Braun, Klaus

    2009-01-01

    Progresses in biology and pharmacology led to highly specific bioactive substances, but their poor bioavailability at the site of action is a result of their physico-chemical properties. Various design approaches for transport carrier molecules facilitating the cellular entry of bioactive substances could help to reach their molecular target in cells and tissues. The transfer efficacy and the subsequent pharmacological effects of the cargo molecules are well investigated, but the investigations of effects of the carrier molecules themselves on the target cells or tissues remain necessary. A special attention should be paid to the differential gene expression, particularly in the interpretation of the data achieved by highly specific active pharmaceutical products. After application of transmembrane transport peptides, particularly the pAnt and also the HIV-1 Tat, cells respond with a conspicuous altered gene expression of at least three genes. The PKN1 gene was induced and two genes (ZCD1 and BSG) were slightly repressed. The genes and the chromosomes are described, the moderate differential gene expression graphed, and the ontology is listed. PMID:19214198

  20. Habitat fragmentation influences gene structure and gene differentiation among the Loxoblemmus aomoriensis populations in the Thousand Island Lake.

    PubMed

    Lv, Kun; Zhou, Jing; Gu, Jian-Qiang; Zhou, Guo-Xing; Wang, Wei; Xu, Zhi-Hong

    2017-02-16

    Thousand Island Lake (TIL) is a fragmented landscape consisting of more than 1000 land-bridge islands isolated during reservoir formation. To evaluate the effects of fragmentation and island attributes on insect populations, we examined the genetic structure of Loxoblemmus aomoriensis, a species of cricket widely distributed in TIL, and compared genetic diversity between islands samples. Population genetic analyses was conducted based on mitochondrial DNA haplotype frequencies of 10 sample islands. By comparing three island attributes with population genetic diversity reveals that island area influenced population genetic diversity (r(2 )=( )0.5094, p = 0.00204). Using Pairwise Fst values, we also found that long-distance isolation increased the genetic differentiation, while short-distance isolation can be offset by dispersal. These results indicate that fragmentation can impact populations on a genetic level.

  1. Contamination with bacterial zoonotic pathogen genes in U.S. streams influenced by varying types of animal agriculture

    USGS Publications Warehouse

    Haack, Sheridan K.; Duris, Joseph W.; Kolpin, Dana W.; Focazio, Michael J.; Meyer, Michael T.; Johnson, Heather E.; Oster, Ryan J.; Foreman, William T.

    2016-01-01

    Animal waste, stream water, and streambed sediment from 19 small (< 32 km2) watersheds in 12 U.S. states having either no major animal agriculture (control, n = 4), or predominantly beef (n = 4), dairy (n = 3), swine (n = 5), or poultry (n = 3) were tested for: 1) cholesterol, coprostanol, estrone, and fecal indicator bacteria (FIB) concentrations, and 2) shiga-toxin producing and enterotoxigenic Escherichia coli, Salmonella, Campylobacter, and pathogenic and vancomycin-resistant enterococci by polymerase chain reaction (PCR) on enrichments, and/or direct quantitative PCR. Pathogen genes were most frequently detected in dairy wastes, followed by beef, swine and poultry wastes in that order; there was only one detection of an animal-source-specific pathogen gene (stx1) in any water or sediment sample in any control watershed. Post-rainfall pathogen gene numbers in stream water were significantly correlated with FIB, cholesterol and coprostanol concentrations, and were most highly correlated in dairy watershed samples collected from 3 different states. Although collected across multiple states and ecoregions, animal-waste gene profiles were distinctive via discriminant analysis. Stream water gene profiles could also be discriminated by the watershed animal type. Although pathogen genes were not abundant in stream water or streambed samples, PCR on enrichments indicated that many genes were from viable organisms, including several (shiga-toxin producing or enterotoxigenic E. coli, Salmonella, vancomycin-resistant enterococci) that could potentially affect either human or animal health. Pathogen gene numbers and types in stream water samples were influenced most by animal type, by local factors such as whether animals had stream access, and by the amount of local rainfall, and not by studied watershed soil or physical characteristics. Our results indicated that stream water in small agricultural U.S. watersheds was susceptible to pathogen gene inputs under

  2. Ocean Drilling Program Leg 178 (Antarctic Peninsula): Sedimentology of glacially influenced continental margin topsets and foresets

    USGS Publications Warehouse

    Eyles, N.; Daniels, J.; Osterman, L.E.; Januszczak, N.

    2001-01-01

    Ocean Drilling Program Leg 178 (February-April 1998) drilled two sites (Sites 1097 and 1103) on the outer Antarctic Peninsula Pacific continental shelf. Recovered strata are no older than late Miocene or early Pliocene (<4.6 Ma). Recovery at shallow depths in loosely consolidated and iceberg-turbated bouldery sediment was poor but improved with increasing depth and consolidation to allow description of lithofacies and biofacies and interpretation of depositional environment. Site 1097 lies on the outer shelf within Marguerite Trough which is a major outlet for ice expanding seaward from the Antarctic Peninsula and reached a maximum depth drilled of 436.6 m below the sea floor (mbsf). Seismic stratigraphic data show flat-lying upper strata resting on strata that dip gently seaward. Uppermost strata, to a depth of 150 mbsf, were poorly recovered, but data suggest they consist of diamictites containing reworked and abraded marine microfauna. This interval is interpreted as having been deposited largely as till produced by subglacial cannibalization of marine sediments (deformation till) recording ice sheet expansion across the shelf. Underlying gently dipping strata show massive, stratified and graded diamictite facies with common bioturbation and slump stuctures that are interbedded with laminated and massive mudstones with dropstones. The succession contains a well-preserved in situ marine microfauna typical of open marine and proglacial marine environments. The lower gently dipping succession at Site 1097 is interpreted as a complex of sediment gravity flows formed of poorly sorted glacial debris. Site 1103 was drilled in that part of the continental margin that shows uppermost flat-lying continental shelf topsets overlying steeper dipping slope foresets seaward of a structural mid-shelf high. Drilling reached a depth of 363 mbsf with good recovery in steeply dipping continental slope foreset strata. Foreset strata are dominated by massive and chaotically

  3. Influence of a screening navigation program on social inequalities in health beliefs about colorectal cancer screening.

    PubMed

    Vallet, Fanny; Guillaume, Elodie; Dejardin, Olivier; Guittet, Lydia; Bouvier, Véronique; Mignon, Astrid; Berchi, Célia; Salinas, Agnès; Launoy, Guy; Christophe, Véronique

    2016-08-01

    The aim of the study was to test whether a screening navigation program leads to more favorable health beliefs and decreases social inequalities in them. The selected 261 noncompliant participants in a screening navigation versus a usual screening program arm had to respond to health belief measures inspired by the Protection Motivation Theory. Regression analyses showed that social inequalities in perceived efficacy of screening, favorable attitude, and perceived facility were reduced in the screening navigation compared to the usual screening program. These results highlight the importance of health beliefs to understand the mechanism of screening navigation programs in reducing social inequalities.

  4. The use and influence of employee incentives on participation and throughput in a telephonic disease management program.

    PubMed

    Wilhide, Calvin; Hayes, John R; Farah, J Ramsay

    2008-08-01

    Participation rates are often viewed by vendors and employer-based disease management (DM) services as an important benchmark of successful program implementation. Although participation is commonly understood to vary widely between and within employer groups, little is known about the role of incentives on rates of participation and graduation from DM programs. This study examined the use of incentives, employer characteristics, and perceptions of employee-employer communication on participation and program throughput. The relationship between incentive use and rates of participation and throughput among 87 employer groups from the 2004 company portfolio were assessed using existing account information. Detailed information on the highest and lowest third of the sample was obtained through interviews with account representatives. Wilcoxon, chi square, and regression analyses were used to examine the influence of employer characteristics and incentive factors on enrollee participation rates and program completion. Fifty-two percent of the accounts offered incentives for participation. From 1% to 23% of the eligible employees enrolled and completed the DM program. Incentives had a direct impact on participation, with amounts greater than $50 the most effective. Participation increased with communication tools including e-mail, high-blast (repeated) communications, and health fairs. Results suggest that cash incentives and communication play a significant role in rates of participation and program completion.

  5. Antibiotic Resistance Genes in Freshwater Biofilms May Reflect Influences from High-Intensity Agriculture.

    PubMed

    Winkworth-Lawrence, Cynthia; Lange, Katharina

    2016-11-01

    Antibiotic resistance is a major public health concern with growing evidence of environmental gene reservoirs, especially in freshwater. However, the presence of antibiotic resistance genes in freshwater, in addition to the wide spectrum of land use contaminants like nitrogen and phosphate, that waterways are subjected to is inconclusive. Using molecular analyses, freshwater benthic rock biofilms were screened for genes conferring resistance to antibiotics used in both humans and farmed animals (aacA-aphD to aminoglycosides; mecA to ß-lactams; ermA and ermB to macrolides; tetA, tetB, tetK, and tetM to tetracyclines; vanA and vanB to glycopeptides). We detected widespread low levels of antibiotic resistance genes from 20 waterways across southern New Zealand throughout the year (1.3 % overall detection rate; 480 samples from three rocks per site, 20 sites, eight occasions; July 2010-May 2011). Three of the ten genes, ermB, tetK, and tetM, were detected in 62 of the 4800 individual screens; representatives confirmed using Sanger sequencing. No distinction could be made between human and agricultural land use contamination sources based on gene presence distribution alone. However, land use pressures are suggested by moderate correlations between antibiotic resistance genes and high-intensity farming in winter. The detection of antibiotic resistance genes at several sites not subject to known agricultural pressures suggests human sources of resistance, like waterway contamination resulting from unsatisfactory toilet facilities at recreational sites.

  6. Diet-induced changes in maternal gut microbiota and metabolomic profiles influence programming of offspring obesity risk in rats

    PubMed Central

    Paul, Heather A.; Bomhof, Marc R.; Vogel, Hans J.; Reimer, Raylene A.

    2016-01-01

    Maternal obesity and overnutrition during pregnancy and lactation can program an increased risk of obesity in offspring. In this context, improving maternal metabolism may help reduce the intergenerational transmission of obesity. Here we show that, in Sprague-Dawley rats, selectively altering obese maternal gut microbial composition with prebiotic treatment reduces maternal energy intake, decreases gestational weight gain, and prevents increased adiposity in dams and their offspring. Maternal serum metabolomics analysis, along with satiety hormone and gut microbiota analysis, identified maternal metabolic signatures that could be implicated in programming offspring obesity risk and highlighted the potential influence of maternal gut microbiota on maternal and offspring metabolism. In particular, the metabolomic signature of insulin resistance in obese rats normalized when dams consumed the prebiotic. In summary, prebiotic intake during pregnancy and lactation improves maternal metabolism in diet-induced obese rats in a manner that attenuates the detrimental nutritional programming of offspring associated with maternal obesity. Overall, these findings contribute to our understanding of the maternal mechanisms influencing the developmental programming of offspring obesity and provide compelling pre-clinical evidence for a potential strategy to improve maternal and offspring metabolic outcomes in human pregnancy. PMID:26868870

  7. Social influence and bullying behavior: intervention-based network dynamics of the fairplayer.manual bullying prevention program.

    PubMed

    Wölfer, Ralf; Scheithauer, Herbert

    2014-01-01

    Bullying is a social phenomenon and although preventive interventions consequently address social mechanisms, evaluations hardly consider the complexity of peer processes. Therefore, the present study analyzes the efficacy of the fairplayer.manual bullying prevention program from a social network perspective. Within a pretest-posttest control group design, longitudinal data were available from 328 middle-school students (MAge  = 13.7 years; 51% girls), who provided information on bullying behavior and interaction patterns. The revealed network parameters were utilized to examine the network change (MANCOVA) and the network dynamics (SIENA). Across both forms of analyses, findings revealed the hypothesized intervention-based decrease of bullies' social influence. Hence the present bullying prevention program, as one example of programs that successfully addresses both individual skills and social mechanisms, demonstrates the desired effect of reducing contextual opportunities for the exhibition of bullying behavior.

  8. Molecular and Functional Characterization of Wheat ARGOS Genes Influencing Plant Growth and Stress Tolerance.

    PubMed

    Zhao, Yue; Tian, Xuejun; Li, Yuanyuan; Zhang, Liyuan; Guan, Panfeng; Kou, Xiaoxia; Wang, Xiaobo; Xin, Mingming; Hu, Zhaorong; Yao, Yingyin; Ni, Zhongfu; Sun, Qixin; Peng, Huiru

    2017-01-01

    Auxin Regulated Gene involved in Organ Size (ARGOS) is significantly and positively associated with organ size and is involved in abiotic stress responses in plants. However, no studies on wheat ARGOS genes have been reported to date. In the present study, three TaARGOS homoeologous genes were isolated and located on chromosomes 4A, 4B, and 4D of bread wheat, all of which are highly conserved in wheat and its wild relatives. Comparisons of gene expression in different tissues demonstrated that the TaARGOSs were mainly expressed in the stem. Furthermore, the TaARGOS transcripts were significantly induced by drought, salinity, and various phytohormones. Transient expression of the TaARGOS-D protein in wheat protoplasts showed that TaARGOS-D localized to the endoplasmic reticulum. Moreover, overexpression of TaARGOS-D in Arabidopsis resulted in an enhanced germination rate, larger rosette diameter, increased rosette leaf area, and higher silique number than in wild-type (WT) plants. The roles of TaARGOS-D in the control of plant growth were further studied via RNA-seq, and it was found that 105 genes were differentially expressed; most of these genes were involved in 'developmental processes.' Interestingly, we also found that overexpression of TaARGOS-D in Arabidopsis improved drought and salinity tolerance and insensitivity to ABA relative to that in WT plants. Taken together, these results demonstrate that the TaARGOSs are involved in seed germination, seedling growth, and abiotic stress tolerance.

  9. Unconjugated Bile Acids Influence Expression of Circadian Genes: A Potential Mechanism for Microbe-Host Crosstalk

    PubMed Central

    Govindarajan, Kalaimathi; MacSharry, John; Casey, Patrick G.; Shanahan, Fergus

    2016-01-01

    Disruptions to circadian rhythm in mice and humans have been associated with an increased risk of obesity and metabolic syndrome. The gut microbiota is known to be essential for the maintenance of circadian rhythm in the host suggesting a role for microbe-host interactions in the regulation of the peripheral circadian clock. Previous work suggested a role for gut bacterial bile salt hydrolase (BSH) activity in the regulation of host circadian gene expression. Here we demonstrate that unconjugated bile acids, known to be generated through the BSH activity of the gut microbiota, are potentially chronobiological regulators of host circadian gene expression. We utilised a synchronised Caco-2 epithelial colorectal cell model and demonstrated that unconjugated bile acids, but not the equivalent tauro-conjugated bile salts, enhance the expression levels of genes involved in circadian rhythm. In addition oral administration of mice with unconjugated bile acids significantly altered expression levels of circadian clock genes in the ileum and colon as well as the liver with significant changes to expression of hepatic regulators of circadian rhythm (including Dbp) and associated genes (Per2, Per3 and Cry2). The data demonstrate a potential mechanism for microbe-host crosstalk that significantly impacts upon host circadian gene expression. PMID:27907092

  10. Overexpression of HOX genes is prevalent in Ewing sarcoma and is associated with altered epigenetic regulation of developmental transcription programs.

    PubMed

    Svoboda, Laurie K; Harris, Ashley; Bailey, Natashay J; Schwentner, Raphaela; Tomazou, Eleni; von Levetzow, Cornelia; Magnuson, Brian; Ljungman, Mats; Kovar, Heinrich; Lawlor, Elizabeth R

    2014-12-01

    The polycomb proteins BMI-1 and EZH2 are highly overexpressed by Ewing sarcoma (ES), a tumor of stem cell origin that is driven by EWS-ETS fusion oncogenes, most commonly EWS-FLI1. In the current study we analyzed expression of transcription programs that are controlled by polycomb proteins during embryonic development to determine if they are abnormal in ES. Our results show that polycomb target gene expression in ES deviates from normal tissues and stem cells and that, as expected, most targets are relatively repressed. However, we also discovered a paradoxical up regulation of numerous polycomb targets and these were highly enriched for homeobox (HOX) genes. Comparison of HOX profiles between malignant and non-malignant tissues revealed a distinctive HOX profile in ES, which was characterized by overexpression of posterior HOXD genes. In addition, ectopic expression of EWS-FLI1 during stem cell differentiation led to aberrant up regulation of posterior HOXD genes. Mechanistically, this up regulation was associated with altered epigenetic regulation. Specifically, ES and EWS-FLI1+ stem cells displayed a relative loss of polycomb-dependent H3K27me3 and gain of trithorax-dependent H3K4me3 at the promoters of posterior HOXD genes and also at the HOXD11.12 polycomb response element. In addition, a striking correlation was evident between HOXD13 and other genes whose regulation is coordinately regulated during embryonic development by distal enhancer elements. Together, these studies demonstrate that epigenetic regulation of polycomb target genes, in particular HOXD genes, is altered in ES and that these changes are mediated downstream of EWS-FLI1.

  11. Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming.

    PubMed

    Saetrom, Pål; Sneve, Ragnhild; Kristiansen, Knut I; Snøve, Ola; Grünfeld, Thomas; Rognes, Torbjørn; Seeberg, Erling

    2005-01-01

    Several methods exist for predicting non-coding RNA (ncRNA) genes in Escherichia coli (E.coli). In addition to about sixty known ncRNA genes excluding tRNAs and rRNAs, various methods have predicted more than thousand ncRNA genes, but only 95 of these candidates were confirmed by more than one study. Here, we introduce a new method that uses automatic discovery of sequence patterns to predict ncRNA genes. The method predicts 135 novel candidates. In addition, the method predicts 152 genes that overlap with predictions in the literature. We test sixteen predictions experimentally, and show that twelve of these are actual ncRNA transcripts. Six of the twelve verified candidates were novel predictions. The relatively high confirmation rate indicates that many of the untested novel predictions are also ncRNAs, and we therefore speculate that E.coli contains more ncRNA genes than previously estimated.

  12. Factors Influencing Enrollment in Agricultural Education Programs as Expressed by Iowa Secondary Agricultural Education Students.

    ERIC Educational Resources Information Center

    Reis, Randal; Kahler, Alan A.

    1997-01-01

    Iowa secondary students (n=1,429) indicated that the people who most influenced agricultural education enrollment were parents, instructor, friend, and former ag student. Other influences included personal interest, farm background, and fun of participating. They were least satisfied with classroom facilities, agricultural mechanics, and…

  13. An Investigation of the Influence Acknowledgement Programs Have on Alumni Giving Behavior: Implications for Marketing Strategy

    ERIC Educational Resources Information Center

    Bingham, Frank G., Jr.; Quigley, Charles J., Jr.; Murray, Keith B.

    2002-01-01

    Understanding the factors that influence alumni giving is a critical task of institutional marketers and development officers. To better understand the factors that influence alumni support, this research reports the results of a field experiment in which the effect that acknowledgement of alumni contributions has on their subsequent donation…

  14. Individual and Institutional Influences on Faith-Based Health and Wellness Programming

    ERIC Educational Resources Information Center

    Bopp, Melissa; Fallon, Elizabeth A.

    2011-01-01

    The majority of the US population is affiliated with faith-based organizations (FBO). Health and wellness activities (HWAs) within FBOs have great potential for reach, though the factors influencing faith-based HWA are not well understood. The purpose of this study was to examine individual faith leader and institutional influences on HWAs offered…

  15. Large-Scale Transposition Mutagenesis of Streptomyces coelicolor Identifies Hundreds of Genes Influencing Antibiotic Biosynthesis.

    PubMed

    Xu, Zhong; Wang, Yemin; Chater, Keith F; Ou, Hong-Yu; Xu, H Howard; Deng, Zixin; Tao, Meifeng

    2017-03-15

    Gram-positive Streptomyces bacteria produce thousands of bioactive secondary metabolites, including antibiotics. To systematically investigate genes affecting secondary metabolism, we developed a hyperactive transposase-based Tn5 transposition system and employed it to mutagenize the model species Streptomyces coelicolor, leading to the identification of 51,443 transposition insertions. These insertions were distributed randomly along the chromosome except for some preferred regions associated with relatively low GC content in the chromosomal core. The base composition of the insertion site and its flanking sequences compiled from the 51,443 insertions implied a 19-bp expanded target site surrounding the insertion site, with a slight nucleic acid base preference in some positions, suggesting a relative randomness of Tn5 transposition targeting in the high-GC Streptomyces genome. From the mutagenesis library, 724 mutants involving 365 genes had altered levels of production of the tripyrrole antibiotic undecylprodigiosin (RED), including 17 genes in the RED biosynthetic gene cluster. Genetic complementation revealed that most of the insertions (more than two-thirds) were responsible for the changed antibiotic production. Genes associated with branched-chain amino acid biosynthesis, DNA metabolism, and protein modification affected RED production, and genes involved in signaling, stress, and transcriptional regulation were overrepresented. Some insertions caused dramatic changes in RED production, identifying future targets for strain improvement.IMPORTANCE High-GC Gram-positive streptomycetes and related actinomycetes have provided more than 100 clinical drugs used as antibiotics, immunosuppressants, and antitumor drugs. Their genomes harbor biosynthetic genes for many more unknown compounds with potential as future drugs. Here we developed a useful genome-wide mutagenesis tool based on the transposon Tn5 for the study of secondary metabolism and its regulation

  16. Factors Influencing Student Selection of Marriage and Family Therapy Graduate Programs

    ERIC Educational Resources Information Center

    Hertlein, Katherine M.; Lambert-Shute, Jennifer

    2007-01-01

    To understand which factors students consider most important in choosing a marriage and family therapy (MFT) graduate program and how programs met or did not meet these expectations of students over the course of graduate study, we conducted an online mixed-method investigation. One hundred twelve graduate students in Commission on Accreditation…

  17. The McNair Program as a Socializing Influence on Doctoral Degree Attainment

    ERIC Educational Resources Information Center

    Gittens, Cheryl Bailey

    2014-01-01

    The quality of doctoral students' academic and social experiences is a key element of their success in graduate school programs. These experiences support the completion of doctoral programs, especially for first-generation college students from low-income backgrounds. Framed by Weidman's (1989) undergraduate socialization model, the author…

  18. Influence of an Academic Intervention Program on Minority Student Career Choice

    ERIC Educational Resources Information Center

    Sweeney, Jennifer K.; Villarejo, Merna

    2013-01-01

    This qualitative, retrospective study explored how educational experiences provided as part of an undergraduate intervention program helped to shape career decisions for minority biology students. A key goal for the program is to increase minority entry into science research and teaching careers, yet actual career choice has not been studied.…

  19. Influences of School Latino Composition and Linguistic Acculturation on a Prevention Program for Youths

    ERIC Educational Resources Information Center

    Marsiglia, Flavio F.; Yabiku, Scott T.; Kulis, Stephen; Nieri, Tanya; Lewin, Benjamin

    2010-01-01

    This study examined how ethnic composition and linguistic acculturation within schools affected the efficacy of a youth substance use prevention model program. Data came from a randomized trial of the "keepin' it REAL" program, using a predominantly Mexican American sample of middle school students in Phoenix, Arizona. Schools were…

  20. The Effectiveness of an Interactive Multimedia Program to Influence Eating Habits

    ERIC Educational Resources Information Center

    Irvine, A. Blair; Ary, Dennis V.; Grove, Dean A.; Gilfillan-Morton, Lynn

    2004-01-01

    An interactive multimedia program to encourage individuals to decrease their dietary fat consumption and to increase consumption of fruits and vegetables was developed and evaluated at two worksites. The program presented content tailored to the user by gender, content interests, race, and age group. It was tested using a randomized treatment and…

  1. Navy Organic Airborne and Surface Influence Sweep Program Needs Defense Contract Management Agency Support

    DTIC Science & Technology

    2012-04-27

    Requirements International Organization for Standardization ISO 9001 :2008 – Quality Management . Also, the Program Manager worked with Naval Sea Systems...9 • FAR 52.246-11, Higher Level Contract Quality ,” which specifies high-level quality requirements for Quality Management Systems...states that the DCMA program integrator will base the technical assessment on engineering, software acquisition management , and manufacturing and quality

  2. Beyond Cognitive Increase: Investigating the Influence of Computer Programming on Perception and Application of Mathematical Skills

    ERIC Educational Resources Information Center

    Rich, Peter J.; Bly, Neil; Leatham, Keith R.

    2014-01-01

    This study aimed to provide first-hand accounts of the perceived long-term effects of learning computer programming on a learner's approach to mathematics. These phenomenological accounts, garnered from individual interviews of seven different programmers, illustrate four specific areas of interest: (1) programming provides context for many…

  3. The Influence of Selected Variables on the Effectiveness of Preschool Programs for Disadvantaged Children.

    ERIC Educational Resources Information Center

    Spicker, Howard H.

    The purpose of this paper is to identify some variations among experimental programs and discuss the manner in which such variations seem to affect a program's success. To accomplish this purpose an in-depth analysis of a few major preschool intervention studies is made in terms of four pertinent variables: (1) Curriculum Model (2) Home…

  4. National Implications in Juvenile Justice: The Influence of Juvenile Mentoring Programs on At Risk Youth.

    ERIC Educational Resources Information Center

    Belshaw, Scott H.; Kritsonis, William Allan

    2007-01-01

    In 1972 the federal government created the Juvenile Justice Delinquency Prevention Act that procured funding for various governmental programs to combat the sudden increase in juvenile crime. A provision of this Act set out the creation of mentoring programs to help decrease the juvenile crime rate and dropout rates in secondary schools. This…

  5. The Rapid Adjustment Farm Program's Influence on Other Farms in the Community.

    ERIC Educational Resources Information Center

    Simeral, Kenneth D.

    The study investigated the diffusion of innovative farming practices from Rapid Adjustment Farms (RAF) to other farms in southeast Ohio. The RAF program, begun in 1968, introduced new technology and management practices to its participant farmers. After reviewing literature of farming programs' information diffusion, a descriptive survey was made…

  6. Youth with Disabilities in Work-Based Learning Programs: Factors that Influence Success

    ERIC Educational Resources Information Center

    Scholl, Linda; Mooney, Marianne

    2004-01-01

    This article presents the findings of a research study on the quality of the learning experiences of youth with disabilities who participated in Wisconsin's Youth Apprenticeship (YA) Program--a rigorous two-year work-based learning program for high school juniors and seniors. The researchers identify key factors that enhance the capacity of youth…

  7. The Influence of Using TI-84 Calculators with Programs on Algebra I High Stakes Examinations

    ERIC Educational Resources Information Center

    Spencer, Misty

    2013-01-01

    The purpose of this study was to determine if there was a significant difference in scores on the Mississippi Algebra I SATP2 when one group was allowed to use programs and the other group was not allowed to use programs on TI-84 calculators. An additional purpose of the study was also to determine if there was a significant difference in the…

  8. The Influence of Faculty Exchange Programs on Faculty Members' Professional Development

    ERIC Educational Resources Information Center

    Alkarzon, Awni

    2016-01-01

    This paper addresses the problems facing faculty members, who made short-term international exchange programs in foreign countries; in their attempts to internationalize the campus through teaching, research, and service. Some faculty members who participated in foreign exchange programs try to infuse their international experience through…

  9. Elements of the School Program, as Reported by Alumni, Which Most Influence Students' Religion

    ERIC Educational Resources Information Center

    Tannenbaum, Chana

    2012-01-01

    Yeshiva high schools strive to educate and inspire their students. In addition to the formal educational curriculum, a large portion of these schools' budget is spent on various types of programs in order to achieve these goals. The purpose of this study was to determine which elements of the high school program were perceived by students as…

  10. The Influence of Hormonal Fluctuations on Womens' Selection and Enjoyment of Television Programs.

    ERIC Educational Resources Information Center

    Meadowcroft, Jeanne; Zillmann, Dolf

    Existing theory suggests that women in the premenstrual and menstrual phases of their hormonal cycle would select and enjoy nonarousing television programs, sucy as nonhostile comedy and game shows, and would avoid action drama and hostile and arousing programs. To test this theory, female undergraduates from telecommunications and journalism…

  11. Characteristics influencing weight reduction among veterans in the MOVE!® Program.

    PubMed

    Garvin, Jane T; Marion, Lucy N; Narsavage, Georgia L; Finnegan, Lorna

    2015-01-01

    Obesity is a common health problem for veterans. This study explored background and program characteristics associated with a 5% weight reduction for veterans enrolled in MOVE!(®), a weight management program. For data analysis, 404 veteran records were examined using logistic regression. Background characteristics included socio-demographic variables, comorbidity, body mass index, rurality, and Veterans Administration (VA) priority group. Program characteristics included the program type (group attendee or self-managed) as well as the number and type of provider contacts. Thirteen percent of participants achieved a 5% weight reduction. Age in years (odds ratio [OR] = 1.04) and the number of group visits (OR = 1.05) were significant predictors for achieving a 5% weight reduction. Given the importance of weight reduction, health professionals should consider these significant predictors when planning weight-reduction programs for veterans.

  12. Influence of Coding Variability in APP-Aβ Metabolism Genes in Sporadic Alzheimer’s Disease

    PubMed Central

    Sassi, Celeste; Ridge, Perry G.; Nalls, Michael A.; Gibbs, Raphael; Ding, Jinhui; Lupton, Michelle K.; Troakes, Claire; Lunnon, Katie; Al-Sarraj, Safa; Brown, Kristelle S.; Medway, Christopher; Lord, Jenny; Turton, James; Morgan, Kevin; Powell, John F.; Kauwe, John S.; Cruchaga, Carlos; Bras, Jose; Goate, Alison M.; Singleton, Andrew B.; Guerreiro, Rita; Hardy, John

    2016-01-01

    The cerebral deposition of Aβ42, a neurotoxic proteolytic derivate of amyloid precursor protein (APP), is a central event in Alzheimer’s disease (AD)(Amyloid hypothesis). Given the key role of APP-Aβ metabolism in AD pathogenesis, we selected 29 genes involved in APP processing, Aβ degradation and clearance. We then used exome and genome sequencing to investigate the single independent (single-variant association test) and cumulative (gene-based association test) effect of coding variants in these genes as potential susceptibility factors for AD, in a cohort composed of 332 sporadic and mainly late-onset AD cases and 676 elderly controls from North America and the UK. Our study shows that common coding variability in these genes does not play a major role for the disease development. In the single-variant association analysis, the main hits, none of which statistically significant after multiple testing correction (1.9e-4genes mainly involved in Aβ extracellular degradation (TTR, ACE), clearance (LRP1) and APP trafficking and recycling (SORL1). These results were partially replicated in the gene-based analysis (c-alpha and SKAT tests), that reports ECE1, LYZ and TTR as nominally associated to AD (1.7e-3 genes is not a critical factor for AD development and 2) Aβ degradation and clearance, rather than Aβ production, may play a key role in the etiology of sporadic AD. PMID:27249223

  13. Influence of Coding Variability in APP-Aβ Metabolism Genes in Sporadic Alzheimer's Disease.

    PubMed

    Sassi, Celeste; Ridge, Perry G; Nalls, Michael A; Gibbs, Raphael; Ding, Jinhui; Lupton, Michelle K; Troakes, Claire; Lunnon, Katie; Al-Sarraj, Safa; Brown, Kristelle S; Medway, Christopher; Lord, Jenny; Turton, James; Morgan, Kevin; Powell, John F; Kauwe, John S; Cruchaga, Carlos; Bras, Jose; Goate, Alison M; Singleton, Andrew B; Guerreiro, Rita; Hardy, John

    2016-01-01

    The cerebral deposition of Aβ42, a neurotoxic proteolytic derivate of amyloid precursor protein (APP), is a central event in Alzheimer's disease (AD)(Amyloid hypothesis). Given the key role of APP-Aβ metabolism in AD pathogenesis, we selected 29 genes involved in APP processing, Aβ degradation and clearance. We then used exome and genome sequencing to investigate the single independent (single-variant association test) and cumulative (gene-based association test) effect of coding variants in these genes as potential susceptibility factors for AD, in a cohort composed of 332 sporadic and mainly late-onset AD cases and 676 elderly controls from North America and the UK. Our study shows that common coding variability in these genes does not play a major role for the disease development. In the single-variant association analysis, the main hits, none of which statistically significant after multiple testing correction (1.9e-4genes mainly involved in Aβ extracellular degradation (TTR, ACE), clearance (LRP1) and APP trafficking and recycling (SORL1). These results were partially replicated in the gene-based analysis (c-alpha and SKAT tests), that reports ECE1, LYZ and TTR as nominally associated to AD (1.7e-3 genes is not a critical factor for AD development and 2) Aβ degradation and clearance, rather than Aβ production, may play a key role in the etiology of sporadic AD.

  14. The Influence of Promoter Architectures and Regulatory Motifs on Gene Expression in Escherichia coli

    PubMed Central

    Rydenfelt, Mattias; Garcia, Hernan G.; Cox, Robert Sidney; Phillips, Rob

    2014-01-01

    The ability to regulate gene expression is of central importance for the adaptability of living organisms to changes in their external and internal environment. At the transcriptional level, binding of transcription factors (TFs) in the promoter region can modulate the transcription rate, hence making TFs central players in gene regulation. For some model organisms, information about the locations and identities of discovered TF binding sites have been collected in continually updated databases, such as RegulonDB for the well-studied case of E. coli. In order to reveal the general principles behind the binding-site arrangement and function of these regulatory architectures we propose a random promoter architecture model that preserves the overall abundance of binding sites to identify overrepresented binding site configurations. This model is analogous to the random network model used in the study of genetic network motifs, where regulatory motifs are identified through their overrepresentation with respect to a “randomly connected” genetic network. Using our model we identify TF pairs which coregulate operons in an overrepresented fashion, or individual TFs which act at multiple binding sites per promoter by, for example, cooperative binding, DNA looping, or through multiple binding domains. We furthermore explore the relationship between promoter architecture and gene expression, using three different genome-wide protein copy number censuses. Perhaps surprisingly, we find no systematic correlation between the number of activator and repressor binding sites regulating a gene and the level of gene expression. A position-weight-matrix model used to estimate the binding affinity of RNA polymerase (RNAP) to the promoters of activated and repressed genes suggests that this lack of correlation might in part be due to differences in basal transcription levels, with repressed genes having a higher basal activity level. This quantitative catalogue relating promoter

  15. Influence of statistical estimators of mutual information and data heterogeneity on the inference of gene regulatory networks.

    PubMed

    de Matos Simoes, Ricardo; Emmert-Streib, Frank

    2011-01-01

    The inference of gene regulatory networks from gene expression data is a difficult problem because the performance of the inference algorithms depends on a multitude of different factors. In this paper we study two of these. First, we investigate the influence of discrete mutual information (MI) estimators on the global and local network inference performance of the C3NET algorithm. More precisely, we study 4 different MI estimators (Empirical, Miller-Madow, Shrink and Schürmann-Grassberger) in combination with 3 discretization methods (equal frequency, equal width and global equal width discretization). We observe the best global and local inference performance of C3NET for the Miller-Madow estimator with an equal width discretization. Second, our numerical analysis can be considered as a systems approach because we simulate gene expression data from an underlying gene regulatory network, instead of making a distributional assumption to sample thereof. We demonstrate that despite the popularity of the latter approach, which is the traditional way of studying MI estimators, this is in fact not supported by simulated and biological expression data because of their heterogeneity. Hence, our study provides guidance for an efficient design of a simulation study in the context of network inference, supporting a systems approach.

  16. Influence of the plant extract complex "AdMax" on global gene expression levels in cultured human fibroblasts.

    PubMed

    Antoshechkin, Anatoly; Olalde, Jose; Antoshechkina, Marina; Briuzgin, Vladimir; Platinskiy, Leonid

    2008-01-01

    Ethanol/water extracts from roots of Leuzea carthamoides Iljin, Rhodiola rosea L., Eleutherococcus senticosus Maxim, and from dry berries of Schizandra chinensis Baill. are known as adaptogenic remedies, which enhance physical endurance, counteract fatigue and restore suppressed immunity. Molecular mechanisms underlying effects of the extracts are poorly understood. In this study, a combination of these four extracts called AdMax™ (Nulab, Inc., Florida) was examined for its ability to influence gene expression levels in cultured human fibroblasts in vitro with the help of whole-genome Affymetrix oligonucleotide microarrays. We showed that AdMax treatment results in significant changes (at least 2 fold, p <. 05) in expression of 67 genes that are involved in metabolism of protein, nucleic acids, lipid and carbohydrates, in regulation of transcription, protein and ion transport, response to stimulus and stress. Enhancing expression of the PANK2 gene is of special interest in connection with AdMax ability to enhance physical endurance and counteract fatigue. PANK2 encodes a mitochondrial enzyme pantothenate kinase 2, which provides coenzyme A biosynthesis and thereby plays crucial role in energy metabolism. Partial deficiency of PANK2 gene activity leads to pantothenate kinase-associated neurodegeneration. In this connection potential therapeutic use of AdMax in patients with neurodegenerative diseases is discussed.

  17. Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy.

    PubMed

    Deichmann, Annette; Hacein-Bey-Abina, Salima; Schmidt, Manfred; Garrigue, Alexandrine; Brugman, Martijn H; Hu, Jingqiong; Glimm, Hanno; Gyapay, Gabor; Prum, Bernard; Fraser, Christopher C; Fischer, Nicolas; Schwarzwaelder, Kerstin; Siegler, Maria-Luise; de Ridder, Dick; Pike-Overzet, Karin; Howe, Steven J; Thrasher, Adrian J; Wagemaker, Gerard; Abel, Ulrich; Staal, Frank J T; Delabesse, Eric; Villeval, Jean-Luc; Aronow, Bruce; Hue, Christophe; Prinz, Claudia; Wissler, Manuela; Klanke, Chuck; Weissenbach, Jean; Alexander, Ian; Fischer, Alain; von Kalle, Christof; Cavazzana-Calvo, Marina

    2007-08-01

    Recent reports have challenged the notion that retroviruses and retroviral vectors integrate randomly into the host genome. These reports pointed to a strong bias toward integration in and near gene coding regions and, for gammaretroviral vectors, around transcription start sites. Here, we report the results obtained from a large-scale mapping of 572 retroviral integration sites (RISs) isolated from cells of 9 patients with X-linked SCID (SCID-X1) treated with a retrovirus-based gene therapy protocol. Our data showed that two-thirds of insertions occurred in or very near to genes, of which more than half were highly expressed in CD34(+) progenitor cells. Strikingly, one-fourth of all integrations were clustered as common integration sites (CISs). The highly significant incidence of CISs in circulating T cells and the nature of their locations indicate that insertion in many gene loci has an influence on cell engraftment, survival, and proliferation. Beyond the observed cases of insertional mutagenesis in 3 patients, these data help to elucidate the relationship between vector insertion and long-term in vivo selection of transduced cells in human patients with SCID-X1.

  18. Social interaction influences blood cortisol values and brain aromatase genes in the protandrous false clown anemonefish, Amphiprion ocellaris.

    PubMed

    Iwata, Eri; Mikami, Kyohei; Manbo, Jun; Moriya-Ito, Keiko; Sasaki, Hideaki

    2012-12-01

    Anemonefish, Amphiprion spp., are socially controlled, protandrous sex changers with a monogamous mating system. Under certain conditions, sexually immature anemonefish with ambisexual gonads differentiate directly into males or females. Formation and maintenance of social rank in a group are considered key requirements for the induction of sex change or differentiation. Generally, each animal living in a social group experiences a different level of social stress in accordance with its social rank, and we hypothesize that the stress situation of individual anemonefish influences its sex determination. Groups of three sexually immature anemonefish were placed into each of five experimental tanks and kept for 10 days to allow for social rank formation and behavioral observation. The fish were then euthanized, and blood and brain samples were collected from each fish. The social rank of each individual was distinguishable from day 1 of the experiment. Aggressive behaviors were most frequent and blood Cortisol values were higher in dominant individuals. The transcription of mRNA for stress-related genes, i.e., those encoding for glucocorticoid and arginine vasotocin receptors, was higher in the brains of dominant individuals than in other social ranks. Furthermore, we detected higher transcription levels of gonad and brain aromatase genes, which encode the enzyme that converts androgens into estrogens, in the brains of dominant individuals. These results suggest that social rank reflects the blood Cortisol value, which in turn leads to sex differentiation by manipulating transcription of genes, including aromatase genes, in the brain.

  19. Influence of intron length on interaction characters between post-spliced intron and its CDS in ribosomal protein genes

    NASA Astrophysics Data System (ADS)

    Zhao, Xiaoqing; Li, Hong; Bao, Tonglaga; Ying, Zhiqiang

    2012-09-01

    Many experiment evidences showed that sequence structures of introns and intron loss/gain can influence gene expression, but current mechanisms did not refer to the functions of post-spliced introns directly. We propose that postspliced introns play their functions in gene expression by interacting with their mRNA sequences and the interaction is characterized by the matched segments between introns and their CDS. In this study, we investigated the interaction characters with length series by improved Smith-Waterman local alignment software for the ribosomal protein genes in C. elegans and D. melanogaster. Our results showed that RF values of five intron groups are significantly high in the central non-conserved region and very low in 5'-end and 3'-end splicing region. It is interesting that the number of the optimal matched regions gradually increases with intron length. Distributions of the optimal matched regions are different for five intron groups. Our study revealed that there are more interaction regions between longer introns and their CDS than shorter, and it provides a positive pattern for regulating the gene expression.

  20. The trehalose utilization gene thuA ortholog in Mesorhizobium loti does not influence competitiveness for nodulation on Lotus spp.

    PubMed

    Ampomah, Osei Yaw; Jensen, John Beck

    2014-03-01

    Competitiveness for nodulation is a desirable trait in rhizobia strains used as inoculant. In Sinorhizobium meliloti 1021 mutation in either of the trehalose utilization genes thuA or thuB influences its competitiveness for root colonization and nodule occupancy depending on the interacting host. We have therefore investigated whether mutation in the thuA ortholog in Mesorhizobium loti MAFF303099 also leads to a similar competitive phenotype on its hosts. The results show that M. loti thuA mutant Ml7023 was symbiotically effective and was as competitive as the wild type in colonization and nodule occupancy on Lotus corniculatus and Lotus japonicus. The thuA gene in M. loti was not induced during root colonization or in the infection threads unlike in S. meliloti, despite its induction by trehalose and high osmolarity in in vitro assays.

  1. The CYBA gene A640G polymorphism influences predispositions to coronary artery disease through interactions with cigarette smoking and hypercholesterolemia.

    PubMed

    Niemiec, Pawel; Nowak, Tomasz; Balcerzyk, Anna; Krauze, Jolanta; Zak, Iwona

    2011-08-01

    The CYBA gene encodes the p22phox peptide, an essential subunit of vascular NADPH oxidases. The aim of the study was to analyze potential interactions between CYBA gene A640G polymorphism and traditional risk factors of atherosclerosis. We studied 320 subjects: 160 patients with coronary artery disease (CAD) and 160 controls. The results of interactions were interpreted on the basis of synergy index values (SI, SIM). The 640G allele interacted with cigarette smoking (SI = 2.02, SIM = 2.32). Even greater increase of the CAD risk was found whenever the 640G allele interacted with both smoking and hypercholesterolemia (SI = 2.70, SIM = 3.60). The results suggest that the A640G polymorphism may influence individual predispositions to CAD through interactions with smoking and hypercholesterolemia.

  2. Cloning and expression of a putative cytochrome P450 gene that influences the colour of Phalaenopsis flowers.

    PubMed

    Su, Vincent; Hsu, Ban-Dar

    2003-11-01

    Anthocyanins are responsible for reds through blues in flowers. Blue and violet flowers generally contain derivatives of delphinidin, whereas red and pink flowers contain derivatives of cyanidin or pelargonidin. Differences in hydroxylation patterns of these three major classes of anthocyanidins are controlled by the cytochrome P450 enzymes. Flavonoid-3',5'-hydroxylase, a member of the cytochrome P450 family, is the key enzyme in the synthesis of 3',5'-hydroxylated anthocyanins, generally required for blue or purple flowers. Here we report on the isolation of a cDNA clone of a putative flavonoid-3',5'-hydroxylase gene from Phalaenopsis that was then cloned into a plant expression vector. Transient transformation was achieved by particle bombardment of Phalaenopsis petals. The transgenic petals changed from pink to magenta, indicating that the product of the putative flavonoid-3',5'-hydroxylase gene influences anthocyanin pigment synthesis.

  3. Sperm length is not influenced by haploid gene expression in the flies Drosophila melanogaster and Scathophaga stercoraria.

    PubMed

    Pitnick, Scott; Dobler, Ralph; Hosken, David J

    2009-11-22

    Recent theoretical models have postulated a role for haploid-diploid conflict and for kin selection favouring sperm cooperation and altruism in the diversification and specialization of sperm form. A critical assumption of these models-that haploid gene expression contributes to variation in sperm form-has never been demonstrated and remains contentious. By quantifying within-male variation in sperm length using crosses between males and females from populations that had been subjected to divergent experimental selection, we demonstrate that haploid gene expression does not contribute to variation in sperm length in both Drosophila melanogaster and Scathophaga stercoraria. This finding casts doubt on the importance of haploid-diploid conflict and kin selection as evolutionary influences of sperm phenotypes.

  4. The influence of tissue procurement procedures on RNA integrity, gene expression, and morphology in porcine and human liver tissue.

    PubMed

    Kap, Marcel; Sieuwerts, Anieta M; Kubista, Mikael; Oomen, Monique; Arshad, Shazia; Riegman, Peter

    2015-06-01

    The advent of molecular characterization of tissues has brought an increasing emphasis on the quality of biospecimens, starting with the tissue procurement process. RNA levels are particularly affected by factors in the collection process, but the influence of different pre-analytical factors is not well understood. Here we present the influence of tissue specimen size, as well as the transport and freezing protocols, on RNA quality. Large, medium, and smaller porcine liver samples were stored either dry, on moist gauze, or in salt solution for various times, and then frozen in either liquid nitrogen or in pre-cooled isopentane. Large and small human liver samples were frozen in pre-cooled isopentane either immediately or after one hour at room temperature. The small samples were stored dry, on moist gauze, or in salt solution. RNA was isolated and RIN values were measured. The RNA for six standard reference genes from human liver was analyzed by RT-qPCR, and tissue morphology was assessed for artifacts of freezing. Experiments using porcine liver samples showed that RNA derived from smaller samples was more degraded after one hour of cold ischemia, and that cooled transport is preferable. Human liver samples showed significant RNA degradation after 1 h of cold ischemia, which was more pronounced in smaller samples. RNA integrity was not significantly influenced by the transport or freezing method, but changes in gene expression were observed in samples either transported on gauze or in salt solution. Based on observations in liver samples, smaller samples are more subject to gene expression variability introduced by post-excision sample handling than are larger samples. Small biopsies should be transported on ice and snap frozen as soon as possible after acquisition from the patient.

  5. Interaction of mutant lpr gene with background strain influences renal disease.

    PubMed

    Kelley, V E; Roths, J B

    1985-11-01

    The mutant gene lpr on the MRL/Mp strain of mice is responsible for converting a late onset glomerulonephritis into an early, aggressive, and fatal renal disease. This gene induces the proliferation of a unique subset of lymphocytes, the production of a variety of autoantibodies and shortened survival in MRL/Mp as well as in the genetically distinct strains C3H/HeJ, C57BL/6J, and AKR/J. The present study examined in detail the role of the lpr gene in the formation of lupus nephritis. The results show that C3H-lpr and B6-lpr mice do not develop nephritis while the AKR-lpr strain has a mild form of renal disease. None of these newly constructed congenic mutant strains have the severity of proteinuria or the degree of renal pathology characteristic of MRL-lpr mice. Thus, the lpr gene alone is insufficient in producing severe renal injury. The interaction of the lpr gene with other factors is required for the induction of life-threatening lupus nephritis.

  6. Influence of sex and genetic variability on expression of X-linked genes in human monocytes.

    PubMed

    Castagné, Raphaële; Zeller, Tanja; Rotival, Maxime; Szymczak, Silke; Truong, Vinh; Schillert, Arne; Trégouët, David-Alexandre; Münzel, Thomas; Ziegler, Andreas; Cambien, François; Blankenberg, Stefan; Tiret, Laurence

    2011-11-01

    In humans, the fraction of X-linked genes with higher expression in females has been estimated to be 5% from microarray studies, a proportion lower than the 25% of genes thought to escape X inactivation. We analyzed 715 X-linked transcripts in circulating monocytes from 1,467 subjects and found an excess of female-biased transcripts on the X compared to autosomes (9.4% vs 5.5%, p<2×10(-5)). Among the genes not previously known to escape inactivation, the most significant one was EFHC2 whose 20% of variability was explained by sex. We also investigated cis expression quantitative trait loci (eQTLs) by analyzing 15,703 X-linked SNPs. The frequency and magnitude of X-linked cis eQTLs were quite similar in males and females. Few genes exhibited a stronger genetic effect in females than in males (ARSD, DCX, POLA1 and ITM2A). These genes would deserve further investigation since they may contribute to sex pathophysiological differences.

  7. Influence of Candidate Genes on Attention Problems in Children: A Longitudinal Study

    PubMed Central

    Middeldorp, Christel M.; Slof-Op’t Landt, Margarita C. T.; Bartels, Meike; Hottenga, Jouke-Jan; Suchiman, H. Eka D.; Slagboom, P. Eline; Boomsma, Dorret I.

    2010-01-01

    Attention problems form one of the core characteristics of Attention-Deficit Hyperactive Disorder (ADHD), a multifactorial neurodevelopmental disorder. From twin research it is clear that genes play a considerable role in the etiology and in the stability of ADHD in childhood. Association studies have focused on genes involved in the dopaminergic and serotoninergic systems, but with inconclusive results. This study investigated the effect of 26 Single Nucleotide Polymorphisms (SNPs) in genes encoding for serotonin receptors 2A (HTR2A), Catechol-O-Methyltransferase (COMT), Tryptophane Hydroxylase type 2 (TPH2), and Brain Derived Neurotrophic Factor (BDNF). Attention problems (AP) were assessed by parental report at ages 3, 7, 10, and 12 years in more than 16,000 twin pairs. There were 1148 genotyped children with AP data. We developed a longitudinal framework to test the genetic association effect. Based on all phenotypic data, a longitudinal model was formulated with one latent factor loading on all AP measures over time. The broad heritability for the AP latent factor was 82%, and the latent factor explained around 55% of the total phenotypic variance. The association of SNPs with AP was then modeled at the level of this factor. None of the SNPs showed a significant association with AP. The lowest p-value was found for the rs6265 SNP in the BDNF gene (p = 0.035). Overall, our results suggest no evidence for a role of these genes in childhood AP. PMID:21049304

  8. The Analysis of Polymorphism of Alcohol Dehydrogenase 3 (ADH3) Gene and Influence of Liver Function Status in Indonesia.

    PubMed

    Suhartini; Mustofa; Nurhantari, Yudha; Rianto, Bambang Udji Djoko

    2017-01-31

    Indonesian culture actually has no historical record of behaviors in consuming alcohol, but there are many recent reports of alcohol abuse among Asian people involving their traditional drink. In genotype studies, the damage of the liver caused by consuming alcohol is influenced by the presence of the polymorphism enzyme gene. The lack of study regarding such topic is a signal to further investigate ADH3 gene distribution and its effect on liver function status. The total of 197 research subjects of Javanese descent received alcohol dehydrogenase 3 (ADH3) genetic polymorphism and liver status tests in the city of Yogyakarta, Indonesian. An analytical study with a cross-sectional design was then conducted on the subjects, with the resulting isolated DNAs amplified through polymerase chain reaction (PCR). The genotype of ADH3 was determined by means of restriction fragment length polymorphism (RFLP) using Ssp1 restricting enzyme. Liver function status was assessed by measuring serum glutamic oxaloacetic transaminase (SGOT), serum glutamic pyruvate transaminase (SGPT) and gamma glutamyl transferase (GGT) using a photometric system. Gene types of ADH3*1 (2.1%), ADH3*2 (82.7%) and ADH3*1/3*2 (15.2%) on the subjects were concluded, finding that there is no difference between the gender. In conclusion most of the ADH3 gene polymorphism of the subjects were ADH3*2 (82.7%). The influence of genetic polymorphisms on the status of liver function in the subjects showed significant difference according to GGT measurement, but the same cannot be said on the other two values measuring SGOT and SGPT.

  9. Molecular and Functional Characterization of Wheat ARGOS Genes Influencing Plant Growth and Stress Tolerance

    PubMed Central

    Zhao, Yue; Tian, Xuejun; Li, Yuanyuan; Zhang, Liyuan; Guan, Panfeng; Kou, Xiaoxia; Wang, Xiaobo; Xin, Mingming; Hu, Zhaorong; Yao, Yingyin; Ni, Zhongfu; Sun, Qixin; Peng, Huiru

    2017-01-01

    Auxin Regulated Gene involved in Organ Size (ARGOS) is significantly and positively associated with organ size and is involved in abiotic stress responses in plants. However, no studies on wheat ARGOS genes have been reported to date. In the present study, three TaARGOS homoeologous genes were isolated and located on chromosomes 4A, 4B, and 4D of bread wheat, all of which are highly conserved in wheat and its wild relatives. Comparisons of gene expression in different tissues demonstrated that the TaARGOSs were mainly expressed in the stem. Furthermore, the TaARGOS transcripts were significantly induced by drought, salinity, and various phytohormones. Transient expression of the TaARGOS-D protein in wheat protoplasts showed that TaARGOS-D localized to the endoplasmic reticulum. Moreover, overexpression of TaARGOS-D in Arabidopsis resulted in an enhanced germination rate, larger rosette diameter, increased rosette leaf area, and higher silique number than in wild-type (WT) plants. The roles of TaARGOS-D in the control of plant growth were further studied via RNA-seq, and it was found that 105 genes were differentially expressed; most of these genes were involved in ‘developmental processes.’ Interestingly, we also found that overexpression of TaARGOS-D in Arabidopsis improved drought and salinity tolerance and insensitivity to ABA relative to that in WT plants. Taken together, these results demonstrate that the TaARGOSs are involved in seed germination, seedling growth, and abiotic stress tolerance. PMID:28228774

  10. Evidence of a major gene influencing hair length and heat tolerance in Bos taurus cattle.

    PubMed

    Olson, T A; Lucena, C; Chase, C C; Hammond, A C

    2003-01-01

    Evidence was found that supports the existence of a major gene (designated as the slick hair gene), dominant in mode of inheritance, that is responsible for producing a very short, sleek hair coat. Cattle with slick hair were observed to maintain lower rectal temperatures (RT). The gene is found in Senepol cattle and criollo (Spanish origin) breeds in Central and South America. This gene is also found in a Venezuelan composite breed, the Carora, formed from the Brown Swiss and a Venezuelan criollo breed. Two sets of backcross matings of normal-haired sire breeds to Senepol crossbred dams assumed to be heterozygous for the slick hair gene resulted in ratios of slick to normal-haired progeny that did not significantly differ from 1:1. Data from Carora x Holstein crossbred cows in Venezuela also support the concept of a major gene that is responsible for the slick hair coat of the Carora breed. Cows that were 75% Holstein: 25% Carora in breed composition segregated with a ratio that did not differ from 1:1, as would be expected from a backcross matinginvolving a dominant gene. The effect of the slick hair gene on RT depended on the degree of heat stress and appeared to be affected by age and/or lactation status. The decreased RT observed for slick-haired crossbred calves compared to normal-haired contemporaries ranged from 0.18 to 0.4 degrees C. An even larger decrease in RT (0.61 degrees C; P < 0.01) was observed in lactating Carora x Holstein F1 crossbred cows, even though it did not appear that these cows were under severe heat stress. The improved thermotolerance of crossbred calves due to their slick hair coats did not result in increased weaning weights, possibly because both the slick and normal-haired calves were being nursed by slick-haired dams. There were indications that the slick-haired calves grew faster immediately following weaning and that their growth during the cooler months of the year was not compromised significantly by their reduced quantity of

  11. The Influence of Marriage on Community College Student Achievement in Specific Programs of Study.

    ERIC Educational Resources Information Center

    Yess, James P.

    1981-01-01

    A study is reported that found marital status to be an important predictor of community college graduating quality point average in the following programs of study: Business Administration General, Business Administration Transfer, Executive Secretarial, and Nursing Education. (Author/MLW)

  12. Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation

    PubMed Central

    Skyba, Oleksandr; Cullen, Dan; Douglas, Carl J.

    2016-01-01

    ABSTRACT Identification of the specific genes and enzymes involved in the fungal degradation of lignocellulosic biomass derived from feedstocks with various compositions is essential to the development of improved bioenergy processes. In order to elucidate the effect of substrate composition on gene expression in wood-rotting fungi, we employed microarrays based on the annotated genomes of the brown- and white-rot fungi, Rhodonia placenta (formerly Postia placenta) and Phanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-old Populus trichocarpa (poplar) trees of genotypes with distinct cell wall chemistries, selected from a population of several hundred trees grown in a common garden. The woody substrates were incubated with wood decay fungi for 10, 20, and 30 days. An analysis of transcript abundance in all pairwise comparisons highlighted 64 and 84 differentially expressed genes (>2-fold, P < 0.05) in P. chrysosporium and P. placenta, respectively. Cross-fungal comparisons also revealed an array of highly differentially expressed genes (>4-fold, P < 0.01) across different substrates and time points. These results clearly demonstrate that gene expression profiles of P. chrysosporium and P. placenta are influenced by wood substrate composition and the duration of incubation. Many of the significantly expressed genes encode “proteins of unknown function,” and determining their role in lignocellulose degradation presents opportunities and challenges for future research. IMPORTANCE This study describes the variation in expression patterns of two wood-degrading fungi (brown- and white-rot fungi) during colonization and incubation on three different naturally occurring poplar substrates of differing chemical compositions, over time. The results clearly show that the two fungi respond differentially to their substrates and that several known and, more interestingly

  13. The influence of maternal health literacy and child’s age on participation in social welfare programs

    PubMed Central

    Pati, Susmita; Siewert, Elizabeth; Wong, Angie T.; Bhatt, Suraj K.; Calixte, Rose E.; Cnaan, Avital

    2013-01-01

    Objective To determine the influence of maternal health literacy and child’s age on participation in social welfare programs benefiting children. Methods In a longitudinal prospective cohort study of 560 Medicaid-eligible mother-infant dyads recruited in Philadelphia, maternal health literacy was assessed using the Test of Functional Health Literacy in Adults (short version). Participation in social welfare programs (Temporary Assistance to Needy Families [TANF], Supplemental Nutrition Assistance Program [SNAP], Special Supplemental Nutrition Program for Women, Infants, and Children [WIC], child care subsidy, and public housing) was self-reported at child’s birth, and at the 6, 12, 18, 24 month follow-up interviews. Generalized estimating equations quantified the strength of maternal health literacy as an estimator of program participation. Results The mothers were primarily African-Americans (83%), single (87%), with multiple children (62%). Nearly 24% of the mothers had inadequate or marginal health literacy. Children whose mothers had inadequate health literacy were less likely to receive child care subsidy (adjusted OR= 0.54, 95% CI: 0.34–0.85) than children whose mothers had adequate health literacy. Health literacy was not a significant predictor for TANF, SNAP, WIC or housing assistance. The predicted probability for participation in all programs decreased from birth to 24 months. Most notably, predicted WIC participation declined rapidly after age one. Conclusions During the first 24 months, mothers with inadequate health literacy could benefit from simplified or facilitated child care subsidy application processes. Targeted outreach and enrollment efforts conducted by social welfare programs need to take into account the changing needs of families as children age. PMID:23990157

  14. Factors influencing the number of applications submitted per applicant to orthopedic residency programs

    PubMed Central

    Finkler, Elissa S.; Fogel, Harold A.; Kroin, Ellen; Kliethermes, Stephanie; Wu, Karen; Nystrom, Lukas M.; Schiff, Adam P.

    2016-01-01

    Background From 2002 to 2014, the orthopedic surgery residency applicant pool increased by 25% while the number of applications submitted per applicant rose by 69%, resulting in an increase of 109% in the number of applications received per program. Objective This study aimed to identify applicant factors associated with an increased number of applications to orthopedic surgery residency programs. Design An anonymous survey was sent to all applicants applying to the orthopedic surgery residency program at Loyola University. Questions were designed to define the number of applications submitted per respondent as well as the strength of their application. Of 733 surveys sent, 140 (19.1%) responses were received. Setting An academic institution in Maywood, IL. Participants Fourth-year medical students applying to the orthopedic surgery residency program at Loyola University. Results An applicant's perception of how competitive he or she was (applicants who rated themselves as ‘average’ submitted more applications than those who rated themselves as either ‘good’ or ‘outstanding’, p=0.001) and the number of away rotations (those who completed >2 away rotations submitted more applications, p=0.03) were significantly associated with an increased number of applications submitted. No other responses were found to be associated with an increased number of applications submitted. Conclusion Less qualified candidates are not applying to significantly more programs than their more qualified counterparts. The increasing number of applications represents a financial strain on the applicant, given the costs required to apply to more programs, and a time burden on individual programs to screen increasing numbers of applicants. In order to stabilize or reverse this alarming trend, orthopedic surgery residency programs should openly disclose admission criteria to prospective candidates, and medical schools should provide additional guidance for candidates in this process

  15. The influence of a family program on adolescent tobacco and alcohol use.

    PubMed Central

    Bauman, K E; Foshee, V A; Ennett, S T; Pemberton, M; Hicks, K A; King, T S; Koch, G G

    2001-01-01

    OBJECTIVES: This study examined a family-directed program's effectiveness in preventing adolescent tobacco and alcohol use in a general population. METHODS: Adolescents aged 12 to 14 years and their families were identified by random-digit dialing throughout the contiguous United States. After providing baseline data by telephone interviews, they were randomly allocated to receive or not receive a family-directed program featuring mailed booklets and telephone contacts by health educators. Follow-up telephone interviews were conducted 3 and 12 months after program completion. RESULTS: The findings suggested that smoking onset was reduced by 16.4% at 1 year, with a 25.0% reduction for non-Hispanic Whites but no statistically significant program effect for other races/ethnicities. There were no statistically significant program effects for smokeless tobacco or alcohol use onset. CONCLUSIONS: The family-directed program was associated with reduced smoking onset for non-Hispanic Whites, suggesting that it is worthy of further application, development, and evaluation. PMID:11291373

  16. Diet-influenced chromatin modification and expression of chemopreventive genes by the soy peptide, lunasin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Epigenetic silencing of tumor suppressors and pro-apoptosis genes in cancer cells, unlike genetic mutations, can potentially be reversed by the use of DNA demethylating agents (to remove methylation marks on the DNA) and HDAC inhibitors (to increase histone acetylation). It is now well established t...

  17. Dietary wheat germ oil influences gene expression in larvae and eggs of the oriental fruit fly

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Changes in animal nutrition, particularly essential dietary components, alter global gene expression patterns. Our goal is to identify molecular markers that serve as early indicators of the quality of insect culture media. Markers of deficient culture media will increase the efficiency of develop...

  18. Parasitization by Scleroderma guani influences expression of superoxide dismutase genes in Tenebrio molitor

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Superoxide dismutase (SOD) is an antioxidant enzyme involved in detoxifying reactive oxygen species. In this study, we identified genes encoding the extracellular and intracellular copper-zinc SODs (ecCuZnSOD and icCuZnSOD) and a manganese SOD (MnSOD) in the yellow mealworm beetle, Tenebrio molitor....

  19. Parasitization by Scleroderma guani influences expression of superoxide dismutase genes in Tenebrio molitor.

    PubMed

    Zhu, Jia-Ying; Ze, Sang-Zi; Stanley, David W; Yang, Bin

    2014-09-01

    Superoxide dismutase (SOD) is an antioxidant enzyme involved in detoxifying reactive oxygen species. In this study, we identified genes encoding the extracellular and intracellular copper-zinc SODs (ecCuZnSOD and icCuZnSOD) and a manganese SOD (MnSOD) in the yellow mealworm beetle, Tenebrio molitor. The cDNAs for ecCuZnSOD, icCuZnSOD, and MnSOD, respectively, encode 24.55, 15.81, and 23.14 kDa polypeptides, which possess structural features typical of other insect SODs. They showed 20-94% identity to other known SOD sequences from Bombyx mori, Musca domestica, Nasonia vitripennis, Pediculus humanus corporis, and Tribolium castaneum. Expression of these genes was analyzed in selected tissues and developmental stages, and following exposure to Escherichia coli and parasitization by Scleroderma guani. We recorded expression of all three SODs in cuticle, fat body, and hemocytes and in the major developmental stages. Relatively higher expressions were detected in late-instar larvae and pupae, compared to other developmental stages. Transcriptional levels were upregulated following bacterial infection. Analysis of pupae parasitized by S. guani revealed that expression of T. molitor SOD genes was significantly induced following parasitization. We infer that these genes act in immune response and in host-parasitoid interactions.

  20. Influence of temperature regimes on resistance gene-mediated response to rice bacterial blight

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Increasing temperatures could reduce yield growth rate of rice by 10% in several rice production areas. Similarly, higher temperatures are predicted to accelerate the breakdown of plant disease resistance through higher disease pressure or altered resistance (R) gene effectiveness in many host-path...

  1. Maternal Environment Interacts with Modifier Genes to Influence Progression of Nephrotic Syndrome

    PubMed Central

    Ratelade, Julien; Lavin, Tiphaine Aguirre; Muda, Andrea Onetti; Morisset, Ludivine; Mollet, Géraldine; Boyer, Olivia; Chen, Deborah S.; Henger, Anna; Kretzler, Matthias; Hubner, Norbert; Théry, Clotilde; Gubler, Marie-Claire; Montagutelli, Xavier; Antignac, Corinne; Esquivel, Ernie L.

    2008-01-01

    Mutations in the NPHS2 gene, which encodes podocin, are responsible for some cases of sporadic and familial autosomal recessive steroid-resistant nephrotic syndrome. Inter- and intrafamilial variability in the progression of renal disease among patients bearing NPHS2 mutations suggests a potential role for modifier genes. Using a mouse model in which the podocin gene is constitutively inactivated, we sought to identify genetic determinants of the development and progression of renal disease as a result of the nephrotic syndrome. We report that the evolution of renal disease as a result of nephrotic syndrome in Nphs2-null mice depends on genetic background. Furthermore, the maternal environment significantly interacts with genetic determinants to modify survival and progression of renal disease. Quantitative trait locus mapping suggested that these genetic determinants may be encoded for by genes on the distal end of chromosome 3, which are linked to proteinuria, and on the distal end of chromosome 7, which are linked to a composite trait of urea, creatinine, and potassium. These loci demonstrate epistatic interactions with other chromosomal regions, highlighting the complex genetics of renal disease progression. In summary, constitutive inactivation of podocin models the complex interactions between maternal and genetically determined factors on the progression of renal disease as a result of nephrotic syndrome in mice. PMID:18385421

  2. Differential influence of distinct fatty acids on cardiomyocyte metabolic gene expression

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Diabetes mellitus increases risk for cardiovascular disease, and exposes the heart to high plasma fatty acid (FA) levels, which induce genes promoting FA oxidation (e.g., malonyl-CoA decarboxylase; mcd), as well as those suppressing carbohydrate oxidation (e.g., pyruvate dehydrogenase kinase 4; pdk4...

  3. Cognitive Influences of Students' Alternative Conceptions within a Hands-On Gene Technology Module

    ERIC Educational Resources Information Center

    Franke, Gaitano; Bogner, Franz X.

    2011-01-01

    In a German out-of-school laboratory, 293 medium-achieving 10th-grade students participated in a lesson unit about gene technology. They were divided into two groups (I-1, I-2), both of which followed the same hands-on lesson procedure. Students within I-2 were additionally confronted with alternative conceptions to central issues of the specific…

  4. New PAH gene promoter KLF1 and 3'-region C/EBPalpha motifs influence transcription in vitro.

    PubMed

    Klaassen, Kristel; Stankovic, Biljana; Kotur, Nikola; Djordjevic, Maja; Zukic, Branka; Nikcevic, Gordana; Ugrin, Milena; Spasovski, Vesna; Srzentic, Sanja; Pavlovic, Sonja; Stojiljkovic, Maja

    2017-02-01

    Phenylketonuria (PKU) is a metabolic disease caused by mutations in the phenylalanine hydroxylase (PAH) gene. Although the PAH genotype remains the main determinant of PKU phenotype severity, genotype-phenotype inconsistencies have been reported. In this study, we focused on unanalysed sequences in non-coding PAH gene regions to assess their possible influence on the PKU phenotype. We transiently transfected HepG2 cells with various chloramphenicol acetyl transferase (CAT) reporter constructs which included PAH gene non-coding regions. Selected non-coding regions were indicated by in silico prediction to contain transcription factor binding sites. Furthermore, electrophoretic mobility shift assay (EMSA) and supershift assays were performed to identify which transcriptional factors were engaged in the interaction. We found novel KLF1 motif in the PAH promoter, which decreases CAT activity by 50 % in comparison to basal transcription in vitro. The cytosine at the c.-170 promoter position creates an additional binding site for the protein complex involving KLF1 transcription factor. Moreover, we assessed for the first time the role of a multivariant variable number tandem repeat (VNTR) region located in the 3'-region of the PAH gene. We found that the VNTR3, VNTR7 and VNTR8 constructs had approximately 60 % of CAT activity. The regulation is mediated by the C/EBPalpha transcription factor, present in protein complex binding to VNTR3. Our study highlighted two novel promoter KLF1 and 3'-region C/EBPalpha motifs in the PAH gene which decrease transcription in vitro and, thus, could be considered as PAH expression modifiers. New transcription motifs in non-coding regions will contribute to better understanding of the PKU phenotype complexity and may become important for the optimisation of PKU treatment.

  5. Variation in the TLR4 gene influences the risk of organ failure and shock post-trauma: a cohort study

    PubMed Central

    Shalhub, Sherene; Junker, Christopher E.; Imahara, Scott D.; Mindrinos, Michael N.; Dissanaike, Sharmila; O’Keefe, Grant E.

    2009-01-01

    Background Genetic variation contributes to risk and outcomes of sepsis. We sought to determine if variation in inflammation related genes is associated with severity of sepsis in trauma patients. Methods A cohort of severely injured Caucasian patients was studied and genotyped for candidate single nucleotide polymorphisms (SNPs). These were toll-like receptor 4 (TLR4) A896G, tumor necrosis factor-α G-308A, interleukin-6 G-174C, interleukin-1β C-31T, and cluster of differentiation marker-14 C-159T. SNP genotypes among patients with sepsis and complicated sepsis were analyzed by chi-square and logistic regression. Six haplotype-tagging SNPs in the TLR4 gene were subsequently examined to determine their influence on TLR4 A896G SNP’s relationship to sepsis severity. Results We enrolled 598 patients. Complicated sepsis developed in 147 (25%). Adjusting for independent risk factors, carriage of the variant TLR4 896 G allele was associated with decreased risk of complicated sepsis (OR = 0.3, 95%CI = 0.1–0.7, p = 0.008). Furthermore, two haplotypes seemed to better characterize this risk than the variant TLR4 896 G allele. The variant TLR4 896G allele is linked to one common haplotype, which seems to confer a considerably reduced risk of complicated sepsis. (aOR = 0.2 95% CI = 0.05–0.7, p = 0.01) Conclusions Variation within TLR4 gene is associated with severity of post-traumatic sepsis. This risk may not be solely related to TLR4 A896G SNP. It is likely that other, uncharacterized variations in the TLR4 gene contribute to sepsis severity. A thorough evaluation of variability within the TLR4 gene is needed to characterize sepsis risk. PMID:19131814

  6. A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants1[OPEN

    PubMed Central

    Van Bel, Michiel; Van Hautegem, Tom; Fendrych, Matyáš; Simaskova, Maria; van Durme, Matthias; Buscaill, Pierre; Rivas, Susana; S. Coll, Nuria; Maere, Steven

    2015-01-01

    A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta. PMID:26438786

  7. Brain Gene Expression is Influenced by Incubation Temperature During Leopard Gecko (Eublepharis macularius) Development.

    PubMed

    Pallotta, Maria Michela; Turano, Mimmo; Ronca, Raffaele; Mezzasalma, Marcello; Petraccioli, Agnese; Odierna, Gaetano; Capriglione, Teresa

    2017-03-20

    Sexual differentiation (SD) during development results in anatomical, metabolic, and physiological differences that involve not only the gonads, but also a variety of other biological structures, such as the brain, determining differences in morphology, behavior, and response in the breeding season. In many reptiles, whose sex is determined by egg incubation temperature, such as the leopard gecko, Eublepharis macularius, embryos incubated at different temperatures clearly differ in the volume of brain nuclei that modulate behavior. Based on the premise that "the developmental decision of gender does not flow through a single gene", we performed an analysis on E. macularius using three approaches to gain insights into the genes that may be involved in brain SD during the thermosensitive period. Using quantitative RT-PCR, we studied the expression of genes known to be involved in gonadal SD such as WNT4, SOX9, DMRT1, Erα, Erβ, GnRH, P450 aromatase, PRL, and PRL-R. Then, further genes putatively involved in sex dimorphic brain differentiation were sought by differential display (DDRT-PCR) and PCR array. Our findings indicate that embryo exposure to different sex determining temperatures induces differential expression of several genes that are involved not only in gonadal differentiation (PRL-R, Wnt4, Erα, Erβ, p450 aromatase, and DMRT1), but also in neural differentiation (TN-R, Adora2A, and ASCL1) and metabolic pathways (GP1, RPS15, and NADH12). These data suggest that the brains of SDT reptiles might be dimorphic at birth, thus behavioral experiences in postnatal development would act on a structure already committed to male or female.

  8. Factors influencing participation in a vascular disease prevention lifestyle program among participants in a cluster randomized trial

    PubMed Central

    2013-01-01

    Background Previous research suggests that lifestyle intervention for the prevention of diabetes and cardiovascular disease (CVD) are effective, however little is known about factors affecting participation in such programs. This study aims to explore factors influencing levels of participation in a lifestyle modification program conducted as part of a cluster randomized controlled trial of CVD prevention in primary care. Methods This concurrent mixed methods study used data from the intervention arm of a cluster RCT which recruited 30 practices through two rural and three urban primary care organizations. Practices were randomly allocated to intervention (n = 16) and control (n = 14) groups. In each practice up to 160 eligible patients aged between 40 and 64 years old, were invited to participate. Intervention practice staff were trained in lifestyle assessment and counseling and referred high risk patients to a lifestyle modification program (LMP) consisting of two individual and six group sessions over a nine month period. Data included a patient survey, clinical audit, practice survey on capacity for preventive care, referral and attendance records at the LMP and qualitative interviews with Intervention Officers facilitating the LMP. Multi-level logistic regression modelling was used to examine independent predictors of attendance at the LMP, supplemented with qualitative data from interviews with Intervention Officers facilitating the program. Results A total of 197 individuals were referred to the LMP (63% of those eligible). Over a third of patients (36.5%) referred to the LMP did not attend any sessions, with 59.4% attending at least half of the planned sessions. The only independent predictors of attendance at the program were employment status - not working (OR: 2.39 95% CI 1.15-4.94) and having high psychological distress (OR: 2.17 95% CI: 1.10-4.30). Qualitative data revealed that physical access to the program was a barrier, while GP

  9. Epigenetics: Behavioral Influences on Gene Function, Part I: Maternal Behavior Permanently Affects Adult Behavior in Offspring

    ERIC Educational Resources Information Center

    Ogren, Marilee P.; Lombroso, Paul J.

    2008-01-01

    The article highlights the field of epigenetics and its relevance in determining the effects of maternal nurturing on behavioral patterns in offsprings. Results concluded that maternal behavior influences the offspring's behavior to stress in adulthood and the effects are transgenerational through epigenetic mechanisms.

  10. Social environment influences the relationship between genotype and gene expression in wild baboons

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Variation in the social environment can have profound effects on survival and reproduction in wild social mammals. However, we know little about the degree to which these effects are influenced by genetic differences among individuals, and, conversely, the degree to which social environmental variat...

  11. Reorganization of the FSU space program and its influence on worldwide space activities

    NASA Astrophysics Data System (ADS)

    Tarasenko, Maksim V.

    1993-10-01

    The paper examines changes in the organization of the former Soviet space program, current program status, and priorities, and analyzes the impact of these changes on world space activities. It is shown that after the breakup of the USSR Russia took over general responsibility for Soviet space activity. Space program management is being reorganized to split military and civil activities and to introduce a system of checks and balances. Attempts are being made to diversify the use of military space systems for civil application, including global environmental problems. Economic problems in the former Soviet republics and political tensions between them force them to search for the cooperation with the West. With a balanced Western response this trend could provide long-term mutual benefits.

  12. The influence of newborn early literacy intervention programs in three canadian provinces.

    PubMed

    Letourneau, Nicole; Whitty, Pam; Watson, Barry; Phillips, Jennifer; Joschko, Justin; Gillis, Doris

    2015-01-01

    Low levels of literacy in early childhood can have lasting effects on children's educational and intellectual development. Many countries have implemented newborn literacy programs designed to teach parents pre-literacy promoting activities to share with their children. We conducted 2 quasi-experimental studies using 1) a pre-test/post-test design and 2) a non-equivalent control group design to examine the effect of newborn literacy programs on parents' self-reported literacy intentions/behaviors, values toward literacy, and parent-child interactions. Parents were recruited from 3 provinces, 2 with newborn literacy programs (intervention) and 1 without (control). Parents in the intervention group completed prenatal and postnatal (after participation in program) questionnaires. Parents in the control group completed 1 questionnaire. Questionnaires were designed to capture parents' literacy intentions (prenatal), behaviors (postnatal), values, and parent-child interactions (postnatal). A total of 98 parents were included in study one and 174 were included in study two. Parents' self-reported prenatal intentions and values were higher than their postnatal behaviors and values. Parents in the intervention group exhibited higher literacy behaviors and values and greater enjoyment reading to their children than parents in the control group, though they also reported reading to their children less frequently. Parents in the intervention group had significantly higher Positive Interactive scores than controls. Overall, we found participation in newborn literacy programs positively impacted parenting behaviors and attitudes. Lower postnatal within-group scores (intentions and values versus behaviors and values) may have been the result of participants' high expectations. Given our findings, we recommend that these programs continue.

  13. The impact of a professional development program on teachers' practice and how context variables influenced such practice: a case study

    NASA Astrophysics Data System (ADS)

    Yarema, Sandra Lynn

    This case study investigated how context variables influenced the impact of a state-funded longitudinal professional development (PD) program on the participant teachers' practice. Data was collected to compare differences in Science Content Knowledge, Science Pedagogical Content Knowledge, and the teachers' practice over the course of the PD program. Contextual variables related to district restructuring and school implementation of district policy evidence a direct effect on time spent on science instruction, specific instructional strategies used, and on the development of a professional community among the participants. This case study substantiates the implication that districts and school policies must provide adequate support for teachers to implement what is learned in professional development to enact any effective science education reform at the elementary school level.

  14. Influence of gene flow on divergence dating - implications for the speciation history of Takydromus grass lizards.

    PubMed

    Tseng, Shu-Ping; Li, Shou-Hsien; Hsieh, Chia-Hung; Wang, Hurng-Yi; Lin, Si-Min

    2014-10-01

    Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species-tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.

  15. Individual letters of the RNA polymerase II CTD code govern distinct gene expression programs in fission yeast

    PubMed Central

    Schwer, Beate; Bitton, Danny Asher; Sanchez, Ana M.; Bähler, Jürg; Shuman, Stewart

    2014-01-01

    The primary structure and phosphorylation pattern of the tandem Y1S2P3T4S5P6S7 repeats of the RNA polymerase II carboxyl-terminal domain (CTD) comprise an informational code that coordinates transcription, chromatin modification, and RNA processing. To gauge the contributions of individual CTD coding “letters” to gene expression, we analyzed the poly(A)+ transcriptomes of fission yeast mutants that lack each of the four inessential CTD phosphoacceptors: Tyr1, Ser2, Thr4, and Ser7. There was a hierarchy of CTD mutational effects with respect to the number of dysregulated protein-coding RNAs, with S2A (n = 227) >> Y1F (n = 71) > S7A (n = 58) >> T4A (n = 7). The majority of the protein-coding RNAs affected in Y1F cells were coordinately affected by S2A, suggesting that Tyr1-Ser2 constitutes a two-letter code “word.” Y1F and S2A elicited increased expression of genes encoding proteins involved in iron uptake (Frp1, Fip1, Fio1, Str3, Str1, Sib1), without affecting the expression of the genes that repress the iron regulon, implying that Tyr1-Ser2 transduces a repressive signal. Y1F and S2A cells had increased levels of ferric reductase activity and were hypersensitive to phleomycin, indicative of elevated intracellular iron. The T4A and S7A mutations had opposing effects on the phosphate response pathway. T4A reduced the expression of two genes encoding proteins involved in phosphate acquisition (the Pho1 acid phosphatase and the phosphate transporter SPBC8E4.01c), without affecting the expression of known genes that regulate the phosphate response pathway, whereas S7A increased pho1+ expression. These results highlight specific cellular gene expression programs that are responsive to distinct CTD cues. PMID:24591591

  16. Estrogenic Endocrine Disrupting Chemicals Influencing NRF1 Regulated Gene Networks in the Development of Complex Human Brain Diseases.

    PubMed

    Preciados, Mark; Yoo, Changwon; Roy, Deodutta

    2016-12-13

    During the development of an individual from a single cell to prenatal stages to adolescence to adulthood and through the complete life span, humans are exposed to countless environmental and stochastic factors, including estrogenic endocrine disrupting chemicals. Brain cells and neural circuits are likely to be influenced by estrogenic endocrine disruptors (EEDs) because they strongly dependent on estrogens. In this review, we discuss both environmental, epidemiological, and experimental evidence on brain health with exposure to oral contraceptives, hormonal therapy, and EEDs such as bisphenol-A (BPA), polychlorinated biphenyls (PCBs), phthalates, and metalloestrogens, such as, arsenic, cadmium, and manganese. Also we discuss the brain health effects associated from exposure to EEDs including the promotion of neurodegeneration, protection against neurodegeneration, and involvement in various neurological deficits; changes in rearing behavior, locomotion, anxiety, learning difficulties, memory issues, and neuronal abnormalities. The effects of EEDs on the brain are varied during the entire life span and far-reaching with many different mechanisms. To understand endocrine disrupting chemicals mechanisms, we use bioinformatics, molecular, and epidemiologic approaches. Through those approaches, we learn how the effects of EEDs on the brain go beyond known mechanism to disrupt the circulatory and neural estrogen function and estrogen-mediated signaling. Effects on EEDs-modified estrogen and nuclear respiratory factor 1 (NRF1) signaling genes with exposure to natural estrogen, pharmacological estrogen-ethinyl estradiol, PCBs, phthalates, BPA, and metalloestrogens are presented here. Bioinformatics analysis of gene-EEDs interactions and brain disease associations identified hundreds of genes that were altered by exposure to estrogen, phthalate, PCBs, BPA or metalloestrogens. Many genes modified by EEDs are common targets of both 17 β-estradiol (E2) and NRF1. Some of

  17. KCNN Genes that Encode Small-Conductance Ca2+-Activated K+ Channels Influence Alcohol and Drug Addiction

    PubMed Central

    Padula, Audrey E; Griffin, William C; Lopez, Marcelo F; Nimitvilai, Sudarat; Cannady, Reginald; McGuier, Natalie S; Chesler, Elissa J; Miles, Michael F; Williams, Robert W; Randall, Patrick K; Woodward, John J; Becker, Howard C; Mulholland, Patrick J

    2015-01-01

    Small-conductance Ca2+-activated K+ (KCa2) channels control neuronal excitability and synaptic plasticity, and have been implicated in substance abuse. However, it is unknown if genes that encode KCa2 channels (KCNN1-3) influence alcohol and drug addiction. In the present study, an integrative functional genomics approach shows that genetic datasets for alcohol, nicotine, and illicit drugs contain the family of KCNN genes. Alcohol preference and dependence QTLs contain KCNN2 and KCNN3, and Kcnn3 transcript levels in the nucleus accumbens (NAc) of genetically diverse BXD strains of mice predicted voluntary alcohol consumption. Transcript levels of Kcnn3 in the NAc negatively correlated with alcohol intake levels in BXD strains, and alcohol dependence enhanced the strength of this association. Microinjections of the KCa2 channel inhibitor apamin into the NAc increased alcohol intake in control C57BL/6J mice, while spontaneous seizures developed in alcohol-dependent mice following apamin injection. Consistent with this finding, alcohol dependence enhanced the intrinsic excitability of medium spiny neurons in the NAc core and reduced the function and protein expression of KCa2 channels in the NAc. Altogether, these data implicate the family of KCNN genes in alcohol, nicotine, and drug addiction, and identify KCNN3 as a mediator of voluntary and excessive alcohol consumption. KCa2.3 channels represent a promising novel target in the pharmacogenetic treatment of alcohol and drug addiction. PMID:25662840

  18. The early onset of type 1 autoimmune hepatitis has a strong genetic influence: role of HLA and KIR genes.

    PubMed

    Podhorzer, A; Paladino, N; Cuarterolo, M L; Fainboim, H A; Paz, S; Theiler, G; Capucchio, M; López, S I; Machicote, A; Montal, S; Podesta, G; Fainboim, L

    2016-04-01

    We have previously reported a strong association between HLA-DRB1*1301 and type 1 pediatric autoimmune hepatitis (PAH) and between HLA-DR*0405 and adult autoimmune hepatitis (AAH). Because human killer cell immunoglobulin-like receptors are known to be associated with susceptibility to autoimmune diseases, we investigated the frequencies of HLA-A, B, C, DRB1 and KIR genes in 144 type 1 PAH and 86 AAH patients, which were compared with 273 healthy controls. We demonstrated in PAH the increased frequency of the functional form of KIR2DS4-Full Length (KIR2DS4-FL), which in combination with HLA-DRB1*1301 revealed a strong synergistic effect (odds ratio=36.5). PAH-KIR2DS4-FL+ subjects have shown an increased frequency of their putative HLA-C*02, 04 and 06 ligands. KIR analysis of PAH also revealed a decreased frequency of KIR2DL2 gene and its ligand. In contrast, AAH cases have shown a weaker increased frequency of KIR2DS4-FL, a lack of synergistic effect with HLA class II antigens and a moderate association with HLA-DRB1*0405. Of note, we demonstrated that liver T cells have a unique pattern of KIR expression. These results show a KIR gene involved in autoimmune hepatitis and suggest a stronger genetic influence for the early onset type I autoimmune hepatitis.

  19. Jasmonic acid influences mycorrhizal colonization in tomato plants by modifying the expression of genes involved in carbohydrate partitioning.

    PubMed

    Tejeda-Sartorius, Miriam; Martínez de la Vega, Octavio; Délano-Frier, John Paul

    2008-06-01

    The role of jasmonic acid (JA) on mycorrhizal colonization by Glomus fasciculatum in tomato plants was examined using mutant plants overexpressing prosystemin (PS) or affected in the synthesis of JA (suppressor of prosystemin-mediated responses 2, spr2). The degree of mycorrhizal colonization was determined by measuring frequency (F%) and intensity (M%) of colonization and arbuscule abundance (A%). Gene expression and biochemical analyses were also performed in roots to detect changes in carbon (C) partitioning. Colonization was similar in mycorrhizal PS and wild-type roots, except for a higher A% in the former. Conversely, colonization was severely reduced in roots of spr2 mutants. No association was found between levels of expression of genes coding for systemic wound responsive proteins (or SWRPs) and other defense-related proteins in roots and mycorrhization levels in these plants. On the other hand, the degree of mycorrhizal colonization correlated with changes in the transcriptional regulation of a number of genes involved in sucrose hydrolysis and transport, cell wall invertase activity and mycorrhizal-specific fatty acid content in roots. The results obtained suggest that one of the mechanisms by which JA might operate to modulate the mycorrhization process could be through its influence on the regulation of C partitioning in the plant. The significant colonization increase observed in mycorrhizal spr2 plants supplied with exogenous methyl jasmonate supports its role as a positive regulator of the symbiosis.

  20. Thioredoxin and thioredoxin reductase influence estrogen receptor α-mediated gene expression in human breast cancer cells

    PubMed Central

    Rao, Abhi K; Ziegler, Yvonne S; McLeod, Ian X; Yates, John R; Nardulli, Ann M

    2010-01-01

    Accumulation of reactive oxygen species (ROS) in cells damages resident proteins, lipids, and DNA. In order to overcome the oxidative stress that occurs with ROS accumulation, cells must balance free radical production with an increase in the level of antioxidant enzymes that convert free radicals to less harmful species. We identified two antioxidant enzymes, thioredoxin (Trx) and Trx reductase (TrxR), in a complex associated with the DNA-bound estrogen receptor α (ERα). Western analysis and immunocytochemistry were used to demonstrate that Trx and TrxR are expressed in the cytoplasm and in the nuclei of MCF-7 human breast cancer cells. More importantly, endogenously expressed ERα, Trx, and TrxR interact and ERα and TrxR associate with the native, estrogen-responsive pS2 and progesterone receptor genes in MCF-7 cells. RNA interference assays demonstrated that Trx and TrxR differentially influence estrogen-responsive gene expression and that together, 17β-estradiol, Trx, and TrxR alter hydrogen peroxide (H2O2) levels in MCF-7 cells. Our findings suggest that Trx and TrxR are multifunctional proteins that, in addition to modulating H2O2 levels and transcription factor activity, aid ERα in regulating the expression of estrogen-responsive genes in target cells. PMID:19620238

  1. Thioredoxin and thioredoxin reductase influence estrogen receptor alpha-mediated gene expression in human breast cancer cells.

    PubMed

    Rao, Abhi K; Ziegler, Yvonne S; McLeod, Ian X; Yates, John R; Nardulli, Ann M

    2009-12-01

    Accumulation of reactive oxygen species (ROS) in cells damages resident proteins, lipids, and DNA. In order to overcome the oxidative stress that occurs with ROS accumulation, cells must balance free radical production with an increase in the level of antioxidant enzymes that convert free radicals to less harmful species. We identified two antioxidant enzymes, thioredoxin (Trx) and Trx reductase (TrxR), in a complex associated with the DNA-bound estrogen receptor alpha (ERalpha). Western analysis and immunocytochemistry were used to demonstrate that Trx and TrxR are expressed in the cytoplasm and in the nuclei of MCF-7 human breast cancer cells. More importantly, endogenously expressed ERalpha, Trx, and TrxR interact and ERalpha and TrxR associate with the native, estrogen-responsive pS2 and progesterone receptor genes in MCF-7 cells. RNA interference assays demonstrated that Trx and TrxR differentially influence estrogen-responsive gene expression and that together, 17beta-estradiol, Trx, and TrxR alter hydrogen peroxide (H(2)O(2)) levels in MCF-7 cells. Our findings suggest that Trx and TrxR are multifunctional proteins that, in addition to modulating H(2)O(2) levels and transcription factor activity, aid ERalpha in regulating the expression of estrogen-responsive genes in target cells.

  2. KCNN Genes that Encode Small-Conductance Ca2+-Activated K+ Channels Influence Alcohol and Drug Addiction.

    PubMed

    Padula, Audrey E; Griffin, William C; Lopez, Marcelo F; Nimitvilai, Sudarat; Cannady, Reginald; McGuier, Natalie S; Chesler, Elissa J; Miles, Michael F; Williams, Robert W; Randall, Patrick K; Woodward, John J; Becker, Howard C; Mulholland, Patrick J

    2015-07-01

    Small-conductance Ca(2+)-activated K(+) (KCa2) channels control neuronal excitability and synaptic plasticity, and have been implicated in substance abuse. However, it is unknown if genes that encode KCa2 channels (KCNN1-3) influence alcohol and drug addiction. In the present study, an integrative functional genomics approach shows that genetic datasets for alcohol, nicotine, and illicit drugs contain the family of KCNN genes. Alcohol preference and dependence QTLs contain KCNN2 and KCNN3, and Kcnn3 transcript levels in the nucleus accumbens (NAc) of genetically diverse BXD strains of mice predicted voluntary alcohol consumption. Transcript levels of Kcnn3 in the NAc negatively correlated with alcohol intake levels in BXD strains, and alcohol dependence enhanced the strength of this association. Microinjections of the KCa2 channel inhibitor apamin into the NAc increased alcohol intake in control C57BL/6J mice, while spontaneous seizures developed in alcohol-dependent mice following apamin injection. Consistent with this finding, alcohol dependence enhanced the intrinsic excitability of medium spiny neurons in the NAc core and reduced the function and protein expression of KCa2 channels in the NAc. Altogether, these data implicate the family of KCNN genes in alcohol, nicotine, and drug addiction, and identify KCNN3 as a mediator of voluntary and excessive alcohol consumption. KCa2.3 channels represent a promising novel target in the pharmacogenetic treatment of alcohol and drug addiction.

  3. Polymorphisms in the Brain-Derived Neurotrophic Factor Gene Influence Memory and Processing Speed One Month after Brain Injury

    PubMed Central

    Tyler, Anna L.; Flashman, Laura A.; Rhodes, C. Harker; McDonald, Brenna C.; Saykin, Andrew J.; Tosteson, Tor D.; Tsongalis, Gregory J.; Moore, Jason H.

    2012-01-01

    Abstract Brain-derived neurotrophic factor (BDNF) plays a role in cognition, as well as neural survival and plasticity. There are several common polymorphisms in the BDNF gene, one of which (rs6265) is an extensively studied non-synonymous coding polymorphism (Val66Met) which has been linked to cognitive performance in healthy controls and some clinical populations. We hypothesized that the Met allele of rs6265 would be associated with poorer cognitive performance in individuals with mild-to-moderate traumatic brain injury, and that other polymorphisms in the BDNF gene would also affect cognition. Genotype at 9 single-nucleotide polymorphisms (SNPs) in the BDNF gene, and measures of speed of information processing, learning, and memory were assessed in 75 patients with mTBI and 38 healthy subjects. Consistent with previous reports, the Met allele of rs6265 was associated with cognition (slower processing speed) in the entire group. Two other SNPs were associated with processing speed in the mTBI group, but both are in linkage disequilibrium with rs6265, and neither remained significant after adjustment for rs6265 status. Within the mTBI group, but not the controls, 4 SNPs, but not rs6265, were associated with memory measures. These associations were not affected by adjustment for rs6265 status. Polymorphisms in BDNF influence cognitive performance shortly after mTBI. The results raise the possibility that a functional polymorphism other than rs6265 may contribute to memory function after mTBI. PMID:22188054

  4. The transcriptional regulator gene E2 of the Human Papillomavirus (HPV) 16 influences the radiosensitivity of cervical keratinocytes

    PubMed Central

    2012-01-01

    Background Clinical studies have demonstrated that HPV induced tumors constitute a specific subclass of cancer with a better response to radiation treatment. The purpose of this study was to investigate meaning of viral E2-gene for radiosensitivity. Methods W12 cells contain episomal HPV 16 genomes, whereas S12 cells, which derive from the W12 line, contain HPV DNA as integrated copies. Clonogenic survival was analyzed using 96-well in vitro test. Using flow cytometry cell cycle analyses were performed. Expression of pRb and p53 were analyzed using intracellular staining. Results W12 cells (intact E2 gene) showed a lower survival fraction than S12 cells. W12 cells developed a G2/M block 24 h after irradiation with 2 Gy whereas S12 showed no G2/M bloc. After irradiation S12 cells developed polyploidy and pRb-positive cells decreased. W12 cells showed no change of pRb-positive cells. Conclusions Depending on E2 gene status differences in cell cycle regulation might cause radioresistance. The E2/E7/pRb pathway seems to influence HPV-induced radiosensitivity. Our experiments demonstrated an effect of HPV on radiosensitivity of cervical keratinocytes via viral transcription regulator E2 pathway. PMID:23134732

  5. The putative zinc finger of a caulimovirus is essential for infectivity but does not influence gene expression.

    PubMed

    Scholthof, H B; Wu, F C; Kiernan, J M; Shepherd, R J

    1993-04-01

    Plant pararetroviruses, such as caulimoviruses, and animal retroviruses have in common the presence of a highly conserved arrangement of cysteines and a histidine in the precursor of the capsid protein. The composition of these amino acids resembles a zinc finger element, a structure that is common to a class of eukaryotic proteins that regulate gene expression. The role of the putative zinc finger in the life-cycle of caulimoviruses was investigated by introducing specific mutations in the coat protein coding region of a cloned and infectious form of figwort mosaic virus, a caulimovirus. This mutated viral genome, which no longer encoded the conserved cysteine and histidine residues, was not infectious in plants. Transient expression assays in protoplasts showed that expression of a reporter gene inserted at different places in the genome was not detectably influenced by the coat protein or its putative zinc finger. It appears that the zinc finger-like element of caulimoviruses is not involved in the regulation of gene expression. These observations support a model which predicts a function of the zinc finger in specific recognition and packaging of viral RNA into virions prior to reverse transcription.

  6. Influence of Different Levels of Lipoic Acid Synthase Gene Expression on Diabetic Nephropathy

    PubMed Central

    Xu, Longquan; Hiller, Sylvia; Simington, Stephen; Nickeleit, Volker; Maeda, Nobuyo; James, Leighton R.; Yi, Xianwen

    2016-01-01

    Oxidative stress is implicated in the pathogenesis of diabetic nephropathy (DN) but outcomes of many clinical trials are controversial. To define the role of antioxidants in kidney protection during the development of diabetic nephropathy, we have generated a novel genetic antioxidant mouse model with over- or under-expression of lipoic acid synthase gene (Lias). These models have been mated with Ins2Akita/+ mice, a type I diabetic mouse model. We compare the major pathologic changes and oxidative stress status in two new strains of the mice with controls. Our results show that Ins2Akita/+ mice with under-expressed Lias gene, exhibit higher oxidative stress and more severe DN features (albuminuria, glomerular basement membrane thickening and mesangial matrix expansion). In contrast, Ins2Akita/+ mice with highly-expressed Lias gene display lower oxidative stress and less DN pathologic changes. Our study demonstrates that strengthening endogenous antioxidant capacity could be an effective strategy for prevention and treatment of DN. PMID:27706190

  7. The HTR1A and HTR1B receptor genes influence stress-related information processing.

    PubMed

    Mekli, Krisztina; Payton, Antony; Miyajima, Fabio; Platt, Hazel; Thomas, Emma; Downey, Darragh; Lloyd-Williams, Kathryn; Chase, Diana; Toth, Zoltan G; Elliott, Rebecca; Ollier, William E; Anderson, Ian M; Deakin, J F William; Bagdy, Gyorgy; Juhasz, Gabriella

    2011-01-01

    The serotonergic system has been widely implicated in stress related psychiatric disorders such as depression and anxiety. We investigated the possible association between depression and anxiety scores and SNPs within the HTR1A and HTR1B genes in a population sample (n=1387). There was no direct SNP-phenotype association, but in interaction with recent stressful life events rs6295 G, rs878567 T alleles and rs6296 C alleles were associated with significantly higher symptom scores. A subset of control subjects (n=101) took part in a computerised face emotion processing task. Healthy rs6295 GG carriers did not show an affective bias to perceive more negative emotions but reacted more quickly to fearful faces. Thus we conclude that the serotonin-1A receptor conveys vulnerability to these psychiatric disorders by modulating threat-related information processing. Our results extend previous findings of an interaction between stressful life events and the serotonin transporter gene to two other genes in the serotonergic pathway and emphasise the possible role of increased threat-related information processing as an intermediate phenotype.

  8. Perinatal administration of a bitter tastant influences gene expression in chicken palate and duodenum.

    PubMed

    Cheled-Shoval, Shira L; Behrens, Maik; Meyerhof, Wolfgang; Niv, Masha Y; Uni, Zehava

    2014-12-31

    Bitter taste receptors (Tas2rs) and downstream effectors are responsible for mediating bitterness perception and regulation of food choice in mammals. Using RT-PCR, we demonstrated the expression of three Tas2rs and taste signal transduction molecules, α-gustducin, PLCβ2, and TRPM5, in the palate, tongue, and gastrointestinal tract sections in chicken. The bitter tastant quinine activates all three chicken Tas2rs in vitro as shown using calcium-imaging assays of transfected cells. Administration of quinine postnatally or perinatally (both pre- and posthatch) to chickens increased the expression of Tas2r genes in the palate by 6.45-fold (ggTas2r1 postnatal treatment), 4.86-fold (ggTas2r1 perinatal treatment), and 4.48-fold (ggTas2r7 postnatal treatment) compared to the genes' expression in the naı̈ve group respectively, and affected taste related gene expression in the duodenum. Whereas no-choice intake of quinine solution was not significantly lower than that of water in naı̈ve chicks, the treatment groups postnatal, prenatal, and perinatal showed significantly lower intake of quinine by 56.1, 47.7, and 50.2%, respectively, suggesting a possible trend toward sensitization. These results open new venues toward unraveling the formative stages shaping food intake and nutrition in chicken.

  9. Genetic interactions among cortical malformation genes that influence susceptibility to convulsions in C. elegans.

    PubMed

    Locke, Cody J; Williams, Shelli N; Schwarz, Erich M; Caldwell, Guy A; Caldwell, Kim A

    2006-11-20

    Epilepsy is estimated to affect 1-2% of the world population, yet remains poorly understood at a molecular level. We have previously established the roundworm Caenorhabditis elegans as a model for investigating genetic susceptibilities to seizure-like convulsions in vivo. Here we investigate the behavioral consequences of decreasing the activity of nematode gene homologs within the LIS1 pathway that are associated with a human cortical malformation termed lissencephaly. Bioinformatic analysis revealed the nud-2 gene, encoding the worm homolog of mammalian effectors of LIS1, termed NDE1 and NDEL1. Phenotypic analysis of animals targeted by RNA interference (RNAi) was performed using a pentylenetetrazole (PTZ) exposure paradigm to induce convulsions. Worms depleted for LIS1 pathway components (NUD-1, NUD-2, DHC-1, CDK-5, and CDKA-1) exhibited significant convulsions following PTZ and RNAi treatment. Strains harboring fluorescent markers for GABAergic neuronal architecture and synaptic vesicle trafficking were employed to discern putative mechanisms accounting for observed convulsion behaviors. We found that depletion of LIS1 pathway components resulted in defective GABA synaptic vesicle trafficking. We also utilized combinations of specific genetic backgrounds to create a sensitized state for convulsion susceptibility and discovered that convulsion effects were significantly enhanced when LIS-1 and other pathway components were compromised within the same animals. Thus, interactions among gene products with LIS-1 may mediate intrinsic thresholds of neuronal synchrony.

  10. Individual and combined influence of ACE and ACTN3 genes on muscle phenotypes in Polish athletes.

    PubMed

    Orysiak, Joanna; Mazur-Różycka, Joanna; Busko, Krzysztof; Gajewski, Jan; Szczepanska, Beata; Malczewska-Lenczowska, Jadwiga

    2017-02-08

    The aim of this study was to examine the association between ACE and ACTN3 genes, independently or in combination, and muscle strength and power in male and female athletes. The study involved 398 young male (n=266) and female (n=132) athletes representing various sport disciplines (ice hockey, canoeing, swimming, volleyball). All were Caucasians. The following measurements were taken: height of jump and mechanical power in countermovement jump (CMJ) and spike jump (SPJ), and muscle strength of 10 muscle groups (flexors and extensors of the elbow, shoulder, hip, knee and trunk). The ID polymorphism of ACE and the R577X polymorphism of ACTN3 were typed using PCR (polymerase chain reaction) and PCR-RFLP (polymerase chain reaction - restriction fragment length polymorphism), respectively. The genotype distribution of the ACE and ACTN3 genes did not differ significantly between groups of athletes for either sex. There was no association between ACE and ACTN3 genotypes (alone or in combination) and sum of muscle strength, height of jump or mechanical power in both jump tests (CMJ and SPJ) for male and female athletes. These findings do not support an influential role of the ACE and ACTN3 genes in determining power/strength performance of elite athletes.

  11. Influence of the dairy environment on gene expression and substrate utilization in lactic acid bacteria.

    PubMed

    Klaenhammer, Todd R; Azcarate-Peril, M Andrea; Altermann, Eric; Barrangou, Rodolphe

    2007-03-01

    Lactic acid bacteria (LAB) are widely used for the industrial production of fermented dairy products and form a group of related low-GC-content gram-positive bacteria. The major species used in dairy manufacturing are Lactobacillus, Lactococcus, Streptococcus, and Leuconostoc. Traditionally most are applied as starter cultures for dairy fermentations or used as probiotic cultures, delivered in dairy vehicles. The appearance of the genomes of Lactococcus lactis, Bidifobacterium longum, Lactobacillus plantarum, L. johnsonii, L. acidophilus, 2 strains of Streptococcus thermophilus, and pending completion of many draft genomic sequences, is now promoting in-depth investigation into the comparative genetic content of LAB. Moreover, whole-genome transcriptional arrays are quickly revealing critical genes/operons that are coordinately expressed and the impact of environmental factors on expression of multiple gene sets. Comparative genomics between multiple genomes is providing insights into genes that are important in metabolic, physiological, and functional roles for different LAB in the environments they inhabit, ranging from the gastrointestinal tract to milk and acidified dairy products.

  12. Mosaicism for the FMR1 gene influences adaptive skills development in fragile X-affected males

    SciTech Connect

    Cohen, I.L.; Sudhalter, V.; Nolin, S.L.

    1996-08-09

    Fragile X syndrome is one of the most common forms of inherited mental retardation, and the first of a new class of genetic disorders associated with expanded trinucleotide repeats. Previously, we found that about 41% of affected males are mosaic for this mutation in that some of their blood cells have an active fragile X gene and others do not. It has been hypothesized that these mosaic cases should show higher levels of functioning than those who have only the inactive full mutation gene, but previous studies have provided negative or equivocal results. In the present study, the cross-sectional development of communication, self-care, socialization, and motor skills was studied in 46 males with fragile X syndrome under age 20 years as a function of two variables: age and the presence or absence of mosaicism. The rate of adaptive skills development was 2-4 times as great in mosaic cases as in full mutation cases. There was also a trend for cases with autism to be more prevalent in the full-mutation group. These results have implications for prognosis, for the utility of gene or protein replacement therapies for this disorder, and for understanding the association between mental retardation, developmental disorders, and fragile X syndrome. 21 refs., 3 figs.

  13. c-Myb influences HIV type 1 gene expression and virus production.

    PubMed

    Churchill, M J; Ramsay, R G; Rhodes, D I; Deacon, N J

    2001-11-01

    c-Myb is expressed in proliferating T cells. Fifteen c-Myb-binding sites can be identified in the HIV-1 long terminal repeat (LTR), suggesting that c-Myb may regulate HIV-1 gene expression and virus replication. Increasing the cellular levels of c-Myb by transient transfection of CEM cells resulted in a 10- to 20-fold activation of HIV-1 LTR-driven gene expression and mutation of one high-affinity Myb-binding site within the LTR reduced this activation by 60 to 70%. Conversely, inhibition of c-Myb expression in MT-2 cells by treatment with c-myb antisense oligonucleotides decreased HIV-1 replication by 85%, as measured by reverse transcriptase activity and cytopathic effects. The effect of c-myb antisense oligonucleotides on HIV-1 gene expression and virus particle production appeared to be independent of cell proliferation, but dependent on the presence of c-Myb activity mediated through the HIV-1 LTR. These data show that c-myb expression affects HIV-1 replication in CD4(+) T cells.

  14. Two host microRNAs influence WSSV replication via STAT gene regulation

    PubMed Central

    Huang, Ying; Wang, Wen; Ren, Qian

    2016-01-01

    MicroRNAs (miRNAs) have important roles in post-transcriptional regulation of gene expression. During viral infection, viruses utilize hosts to enhance their replication by altering cellular miRNAs. The Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway plays crucial roles in the antiviral responses. In this study, two miRNAs (miR-9041 and miR-9850) from Macrobrachium rosenbergii were found to promote white spot syndrome virus (WSSV) replication. The up-regulation of miR-9041 or miR-9850 suppresses STAT expression in the gills of M. rosenbergii, which subsequently down-regulates the expression of its downstream dynamin (Dnm) genes: Dnm1, Dnm2, and Dnm3. Knockdown of miR-9041 and miR-9850 restricts WSSV replication by up-regulating STAT and Dnm gene expression. The silencing of STAT, Dnm1, Dnm2, or Dnm3 led to an increase of the number of WSSV copies in shrimp. The injection of recombinant Dnm1, Dnm2, or Dnm3 proteins could inhibit WSSV replication in vivo. Overall, our research indicates the roles of host miRNAs in the enhancement of WSSV replication by regulating the host JAK/STAT pathway. PMID:27029712

  15. Gene expression kinetics in individual plasmodial cells reveal alternative programs of differential regulation during commitment and differentiation.

    PubMed

    Rätzel, Viktoria; Marwan, Wolfgang

    2015-05-26

    During its life cycle, the amoebozoon Physarum polycephalum forms multinucleate plasmodial cells that can grow to macroscopic size while maintaining a naturally synchronous population of nuclei. Sporulation-competent plasmodia were stimulated through photoactivation of the phytochrome photoreceptor and the expression of sporulation marker genes was analyzed quantitatively by repeatedly taking samples of the same plasmodial cell at successive time points after the stimulus pulse. Principal component analysis of the gene expression data revealed that plasmodial cells take different trajectories leading to cell fate decision and differentiation and suggested that averaging over individual cells is inappropriate. Queries for genes with pairwise correlated expression kinetics revealed qualitatively different patterns of co-regulation, indicating that alternative programs of differential regulation are operational in individual plasmodial cells. At the single cell level, the response to stimulation of a non-sporulating mutant was qualitatively different as compared to the wild type with respect to the differentially regulated genes and their patterns of co-regulation. The observation of individual differences during commitment and differentiation supports the concept of a Waddington-type quasipotential landscape for the regulatory control of cell differentiation. Comparison of wild type and sporulation mutant data further supports the idea that mutations may impact the topology of this landscape.

  16. Micro-RNA-31 controls hair cycle-associated changes in gene expression programs of the skin and hair follicle.

    PubMed

    Mardaryev, Andrei N; Ahmed, Mohammed I; Vlahov, Nikola V; Fessing, Michael Y; Gill, Jason H; Sharov, Andrey A; Botchkareva, Natalia V

    2010-10-01

    The hair follicle is a cyclic biological system that progresses through stages of growth, regression, and quiescence, which involves dynamic changes in a program of gene regulation. Micro-RNAs (miRNAs) are critically important for the control of gene expression and silencing. Here, we show that global miRNA expression in the skin markedly changes during distinct stages of the hair cycle in mice. Furthermore, we show that expression of miR-31 markedly increases during anagen and decreases during catagen and telogen. Administration of antisense miR-31 inhibitor into mouse skin during the early- and midanagen phases of the hair cycle results in accelerated anagen development, and altered differentiation of hair matrix keratinocytes and hair shaft formation. Microarray, qRT-PCR and Western blot analyses revealed that miR-31 negatively regulates expression of Fgf10, the components of Wnt and BMP signaling pathways Sclerostin and BAMBI, and Dlx3 transcription factor, as well as selected keratin genes, both in vitro and in vivo. Using luciferase reporter assay, we show that Krt16, Krt17, Dlx3, and Fgf10 serve as direct miR-31 targets. Thus, by targeting a number of growth regulatory molecules and cytoskeletal proteins, miR-31 is involved in establishing an optimal balance of gene expression in the hair follicle required for its proper growth and hair fiber formation.

  17. Measuring the Accountability of CTE Programs: Factors that Influence Postcollege Earnings among Community College Students

    ERIC Educational Resources Information Center

    Maguire, Kenneth J.; Starobin, Soko S.; Laanan, Frankie Santos; Friedel, Janice N.

    2012-01-01

    In this study specific factors were examined to determine their ability to influence fifth-year earnings of community college students in the Manufacturing/Science, Technology, Engineering and Math (STEM) career cluster and the Arts/Audiovisual/Technology/ Communication career cluster. State and national data sets from Iowa's Management…

  18. Influence of Alice 3: Reducing the Hurdles to Success in a CS1 Programming Course

    ERIC Educational Resources Information Center

    Daly, Tebring

    2013-01-01

    Learning the syntax, semantics, and concepts behind software engineering can be a challenging task for many individuals. This paper examines the Alice 3 software, a three-dimensional visual environment for teaching programming concepts, to determine if it is an effective tool for improving student achievement, raising self-efficacy, and engaging…

  19. Individual Attitudes and Social Influences on College Students' Intent to Participate in Study Abroad Programs

    ERIC Educational Resources Information Center

    Wang, Liz C.; Gault, John; Christ, Paul; Diggin, Patricia A.

    2016-01-01

    Participation in study abroad programs (SAPs) is widely viewed as offering important professional and personal benefits for college students. This study applies the "Theory of Reasoned Action" [Ajzen, I., & Fishbein, M. (1980) and "Understanding attitudes and predicting social behavior," Englewood Cliffs, NJ:…

  20. Caregiver Involvement in the Intensive Mental Health Program: Influence on Changes in Child Functioning

    ERIC Educational Resources Information Center

    Richards, Margaret M.; Bowers, Mark J.; Lazicki, Tammy; Krall, Dan; Jacobs, Anne K.

    2008-01-01

    We examined behavioral markers of caregiver involvement and the ways in which family participation was related to treatment outcomes in 47 elementary school children with SED enrolled in a school-based intensive mental health program. Measures of caregiver involvement included therapeutic home visits, attendance at therapeutic meetings, completion…

  1. Examining the Influence of a Curriculum-Based Elementary Mathematics Professional Development Program

    ERIC Educational Resources Information Center

    Polly, Drew; Wang, Chuang; McGee, Jennifer; Lambert, Richard G.; Martin, Christie S.; Pugalee, David

    2014-01-01

    This study presents findings from the first cohort of teachers in a U.S. Department of Education Mathematics Science Partnership (MSP) grant designed to support the use of a standards-based elementary school mathematics curriculum, Investigations in Number, Data, and Space (Investigations). In line with the goals of the MSP program, the 84-hour…

  2. How People Choose Vocational Education and Training Programs: Social, Education and Personal Influences on Aspiration.

    ERIC Educational Resources Information Center

    Maxwell, Graham; Cooper, Maureen; Biggs, Neville

    The reasons why Australians choose to enroll in vocational education and training (VET) programs were examined through a questionnaire survey and site visits. The questionnaire yielded responses from 1,501 VET students of a target sample of 3,000 students who were equally representative of the following fields of study: business, engineering,…

  3. How Robotics Programs Influence Young Women's Career Choices: A Grounded Theory Model

    ERIC Educational Resources Information Center

    Craig, Cecilia Dosh-Bluhm

    2014-01-01

    The fields of engineering, computer science, and physics have a paucity of women despite decades of intervention by universities and organizations. Women's graduation rates in these fields continue to stagnate, posing a critical problem for society. This qualitative grounded theory (GT) study sought to understand how robotics programs influenced…

  4. A Comparison of the Influence of Four Different Reading Programs on Children's Expressed Attitudes Toward Reading.

    ERIC Educational Resources Information Center

    Knight, Jeanne Jensen

    The purpose of this study was to determine what differences in expressed attitudes toward reading existed after one school year's instruction in each of four different beginning reading programs. Four schools with similar populations using four different emphases in beginning reading were selected for sampling. The different emphases were Language…

  5. Influence of Materials on Teacher Adoption of Abstinence-Only-Until-Marriage Programs

    ERIC Educational Resources Information Center

    Wilson, Kelly L.; Wiley, David C.

    2009-01-01

    Background: Given the growing scientific evidence against abstinence-only-until-marriage education, health educators are supporting an evidence-based approach to teaching sexuality education. However, there is still an abundance of federal support and funding streams allocated to sustain abstinence-only programs. This study assessed indicators…

  6. The 12 Steps of Addiction Recovery Programs as an Influence on Leadership Development: A Personal Narrative

    ERIC Educational Resources Information Center

    Friedman, Mitchell

    2016-01-01

    My participation in a 12-step addiction program based on the principles and traditions of Alcoholics Anonymous (AA) has been critical for my leadership development. As I worked to refrain from addictive behaviors and practiced 12-step principles, I experienced a shift from individualistic, self-centered leadership towards a servant leader…

  7. Food, Fun and Fitness Internet program for girls: influencing log-on rate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Internet-based interventions hold promise as an effective channel for reaching large numbers of youth. However, log-on rates, a measure of program dose, have been highly variable. Methods to enhance log-on rate are needed. Incentives may be an effective method. This paper reports the effect of reinf...

  8. The Power of Plain Talk: Exploring One Program' Influence on the Adolescent Reproductive Health Field

    ERIC Educational Resources Information Center

    Summerville, Geri; Canova, Karen

    2006-01-01

    Launched by the Annie E. Casey Foundation in the early 1990s, Plain Talk is a community-based initiative that seeks to reduce the incidence of teen pregnancy and STDs by improving adult/teen communication about sex. A key component of the program is parental involvement--which was once seen by many in the adolescent reproductive health (ARH) field…

  9. Factors That Influence Student Selection of Educational Leadership Master's Programs at Regional Universities

    ERIC Educational Resources Information Center

    Winn, Pam; Leach, Lesley F.; Erwin, Susan; Benedict, Liza

    2014-01-01

    Graduate enrollment numbers in Educational Leadership programs have dwindled at many public higher education institutions. At the same time, for-profit institutions and institutions with private marketing partnerships have experienced increasingly greater enrollments. Many public institutions are reevaluating their marketing and recruiting…

  10. Factors Influencing College Attendance of Appalachian Kentucky Students Participating in a Federal Educational Talent Search Program

    ERIC Educational Resources Information Center

    Bowling, William D.

    2013-01-01

    Post-secondary education is quickly becoming a requirement for many growing careers. Because of this, an increased focused on post-secondary enrollment and attainment has been seen in the education community, particularly in the K-12 systems. To that end a large number of programs and organizations have begun to provide assistance to these…

  11. The Factors Influencing Teaching (FIT)-Choice Scale in a Dutch Teacher Education Program

    ERIC Educational Resources Information Center

    Fokkens-Bruinsma, Marjon; Canrinus, Esther T.

    2012-01-01

    This study examined the suitability of the FIT-Choice scale in a Dutch educational context among two cohorts of preservice teachers (Ns = 62, 89), surveyed at the end and the beginning of their one-year program respectively. The relationships between the motivations for becoming a teacher and concurrent commitment were examined, as well as the…

  12. The Influence of Current Television Programing on the Maintenance of Female Gender Identity.

    ERIC Educational Resources Information Center

    Arquette, Cecile M.; Horton, Julie

    Over the years, it has been shown that television has the tendency to use stereotypical gender imagery, and despite the continuing trend toward political correctness, the same types of gender bias are still very common today. Because of this tendency for bias, television programming continues to be an area of concern, especially in light of the…

  13. Influences of the Kentucky Cooperative Extension Home Economics Program. Part I.

    ERIC Educational Resources Information Center

    Mann, Opal

    In planning a reorganization of the Kentucky Cooperative Extension Service by re-grouping counties, a statewide study of home economics education was made to determine the audience for the programs, methods by which audiences were reached, and differences between members of homemakers clubs and nonmembers. Interviews were held with a 5% random…

  14. Do Rape Education Programs Influence Rape Patterns among New York State College Students?

    ERIC Educational Resources Information Center

    Parrot, Andrea

    This study examined the differences in patterns of college student reports of rape and the availability of educational programs among college students. College students (N=994) from 26 colleges and universities in New York State were studied to determine the extent of forced sex and rape experiences. Additionally, they were studied to determine if…

  15. Perspectives on Influencing Aspects for Students' Acceptance of Multimedia Materials in Training Programs

    ERIC Educational Resources Information Center

    Córdova, Mayra Lucía González; Zermeño, Marcela Georgina Gómez; Mejía, Irma Antonia García

    2015-01-01

    This study was carried out in order to improve the understanding and learning of participants enrolled in face-to-face training programs, and to enhance their learning and retention of content through multimedia materials. A qualitative study was conducted to inquire about the perception of the participants and instructors of an Administrative…

  16. Estrogenic Endocrine Disrupting Chemicals Influencing NRF1 Regulated Gene Networks in the Development of Complex Human Brain Diseases

    PubMed Central

    Preciados, Mark; Yoo, Changwon; Roy, Deodutta

    2016-01-01

    During the development of an individual from a single cell to prenatal stages to adolescence to adulthood and through the complete life span, humans are exposed to countless environmental and stochastic factors, including estrogenic endocrine disrupting chemicals. Brain cells and neural circuits are likely to be influenced by estrogenic endocrine disruptors (EEDs) because they strongly dependent on estrogens. In this review, we discuss both environmental, epidemiological, and experimental evidence on brain health with exposure to oral contraceptives, hormonal therapy, and EEDs such as bisphenol-A (BPA), polychlorinated biphenyls (PCBs), phthalates, and metalloestrogens, such as, arsenic, cadmium, and manganese. Also we discuss the brain health effects associated from exposure to EEDs including the promotion of neurodegeneration, protection against neurodegeneration, and involvement in various neurological deficits; changes in rearing behavior, locomotion, anxiety, learning difficulties, memory issues, and neuronal abnormalities. The effects of EEDs on the brain are varied during the entire life span and far-reaching with many different mechanisms. To understand endocrine disrupting chemicals mechanisms, we use bioinformatics, molecular, and epidemiologic approaches. Through those approaches, we learn how the effects of EEDs on the brain go beyond known mechanism to disrupt the circulatory and neural estrogen function and estrogen-mediated signaling. Effects on EEDs-modified estrogen and nuclear respiratory factor 1 (NRF1) signaling genes with exposure to natural estrogen, pharmacological estrogen-ethinyl estradiol, PCBs, phthalates, BPA, and metalloestrogens are presented here. Bioinformatics analysis of gene-EEDs interactions and brain disease associations identified hundreds of genes that were altered by exposure to estrogen, phthalate, PCBs, BPA or metalloestrogens. Many genes modified by EEDs are common targets of both 17 β-estradiol (E2) and NRF1. Some of

  17. Influences of graphene on microbial community and antibiotic resistance genes in mouse gut as determined by high-throughput sequencing.

    PubMed

    Xie, Yongchao; Wu, Bing; Zhang, Xu-Xiang; Yin, Jinbao; Mao, Liang; Hu, Maojie

    2016-02-01

    Graphene is a promising candidate as an antibacterial material owning to its bacterial toxicity. However, little information on influence of graphene on gut microbiota is available. In this study, mice were exposed to graphene for 4 weeks, and high-throughput sequencing was applied to characterize the changes in microbial community and antibiotic resistance genes (ARGs) in mouse gut. The results showed that graphene exposure increased biodiversity of gut microbiota, and changed their community. The 1 μg/d graphene exposure had higher influences on the gut microbiota than 10 μg/d and 100 μg/d graphene exposures, which might be due to higher aggregation of high-level graphene. The influence of graphene on gut microbiota might attribute to that graphene could induce oxidative stress and damage of cell membrane integrity. The results were verified by the increase of ratio of Gram-negative bacteria. Outer membrane of Gram-negative bacteria could reduce the membrane damage induced by graphene and make them more tolerance to graphene. Further, we found that graphene exposure significantly increased the abundance and types of ARGs, indicating a potential health risk of graphene. This study firstly provides new insight to the health effects of graphene on gut microbiota.

  18. Population size influences amphibian detection probability: implications for biodiversity monitoring programs.

    PubMed

    Tanadini, Lorenzo G; Schmidt, Benedikt R

    2011-01-01

    Monitoring is an integral part of species conservation. Monitoring programs must take imperfect detection of species into account in order to be reliable. Theory suggests that detection probability may be determined by population size but this relationship has not yet been assessed empirically. Population size is particularly important because it may induce heterogeneity in detection probability and thereby cause bias in estimates of biodiversity. We used a site occupancy model to analyse data from a volunteer-based amphibian monitoring program to assess how well different variables explain variation in detection probability. An index to population size best explained detection probabilities for four out of six species (to avoid circular reasoning, we used the count of individuals at a previous site visit as an index to current population size). The relationship between the population index and detection probability was positive. Commonly used weather variables best explained detection probabilities for two out of six species. Estimates of site occupancy probabilities differed depending on whether the population index was or was not used to model detection probability. The relationship between the population index and detectability has implications for the design of monitoring and species conservation. Most importantly, because many small populations are likely to be overlooked, monitoring programs should be designed in such a way that small populations are not overlooked. The results also imply that methods cannot be standardized in such a way that detection probabilities are constant. As we have shown here, one can easily account for variation in population size in the analysis of data from long-term monitoring programs by using counts of individuals from surveys at the same site in previous years. Accounting for variation in population size is important because it can affect the results of long-term monitoring programs and ultimately the conservation of

  19. Assessment of factors influencing retention in the Philippine National Rural Physician Deployment Program

    PubMed Central

    2012-01-01

    Background The ‘Doctors to the Barrios’ (DTTB) Program was launched in 1993 in response to the shortage of doctors in remote communities in the Philippines. While the Program has attracted physicians to work in such areas for the prescribed 2-year period, ongoing monitoring shows that very few chose to remain there for longer and be absorbed by their Local Government Unit (LGU). This assessment was carried out to explore the reasons for the low retention rates and to propose possible strategies to reverse the trend. Methods A mixed methods approach was used comprising a self-administered questionnaire for members of the current cohort of DTTBs, and oral interviews with former DTTBs. Results Among former DTTBs, the wish to serve rural populations was the most widely cited motivation. By comparison, among the current cohort of DTTBs, more than half joined the Program due to return of service obligations; a quarter to help rural populations, and some out of an interest in public health. Those who joined the Program to return service experienced significantly less satisfaction, whilst those who joined out of an interest in public health were significantly more satisfied with their rural work. Those who graduated from medical schools in the National Capital Region were significantly more critical about their compensation and perceived there to be fewer options for leisure in rural areas. With regard to the factors impeding retention, lack of support from the LGU was most frequently mentioned, followed by concerns about changes in compensation upon absorption by the LGU, family issues and career advancement. Conclusions Through improved collaboration with the Department of Health, LGUs need to strengthen the support provided to DTTBs. Priority could be given to those acting out of a desire to help rural populations or having an interest in public health, and those who have trained outside of the National Capital Region. Whether physicians should be able to use the

  20. Exercise, sex, menstrual cycle phase, and 17beta-estradiol influence metabolism-related genes in human skeletal muscle.

    PubMed

    Fu, Ming-hua H; Maher, Amy C; Hamadeh, Mazen J; Ye, Changhua; Tarnopolsky, Mark A

    2009-12-30

    Higher fat and lower carbohydrate and amino acid oxidation are observed in women compared with men during endurance exercise. We hypothesized that the observed sex difference is due to estrogen and that menstrual cycle phase or supplementation of men with 17beta-estradiol (E(2)) would coordinately influence the mRNA content of genes involved in lipid and/or carbohydrate metabolism in skeletal muscle. Twelve men and twelve women had muscle biopsies taken before and immediately after 90 min of cycling at 65% peak oxygen consumption (Vo(2peak)). Women were studied in the midfollicular (Fol) and midluteal (Lut) phases, and men were studied after 8 days of E(2) or placebo supplementation. Targeted RT-PCR was used to compare mRNA content for genes involved in transcriptional regulation and lipid, carbohydrate, and amino acid metabolism. Sex was the greatest predictor of substrate metabolism gene content. Sex affected the mRNA content of FATm, FABPc, SREBP-1c, mtGPAT, PPARdelta, PPARalpha, CPTI, TFP-alpha, GLUT4, HKII, PFK, and BCOADK (P < 0.05). E(2) administration significantly (P < 0.05) affected the mRNA content of PGC-1alpha, PPARalpha, PPARdelta, TFP-alpha, CPTI, SREBP-1c, mtGPAT, GLUT4, GS-1, and AST. Acute exercise increased the mRNA abundance for PGC-1alpha, HSL, FABPc, CPTI, GLUT4, HKII, and AST (P < 0.05). Menstrual cycle had a small effect on PPARdelta, GP, and glycogenin mRNA content. Overall, women have greater mRNA content for several genes involved in lipid metabolism, which is partially due to an effect of E(2).

  1. Blood and Bones: The Influence of the Mass Media on Australian Primary School Children's Understandings of Genes and DNA

    NASA Astrophysics Data System (ADS)

    Donovan, Jenny; Venville, Grady

    2012-06-01

    Previous research showed that primary school children held several misconceptions about genetics of concern for their future lives. Included were beliefs that genes and DNA are separate substances, with genes causing family resemblance and DNA identifying suspects at crime scenes. Responses to this work `blamed' the mass media for these misunderstandings. This study aimed to determine whether that blame had any foundation by examining the media habits and conceptions about genes and DNA of Australian children. With little prior research considering the influence of entertainment mass media on children's academically relevant knowledge, this was an exploratory study with a mixed modes design. Data were collected by detailed media questionnaires and face-to-face interviews with 62 children aged 10-12 years, and subjected to content and thematic analysis. Specific mass media examples children reported using were examined for genetics content. Results indicate 5 h/day of media use, mostly television including crime shows, and that children perceived television to be their main source of information about genetics. Most children (89 %) knew DNA, 60 % knew genes, and more was known about uses of DNA outside the body such as crime solving or resolving family relationships than about its biological nature and function. Half believed DNA is only in blood and body parts used for forensics. These concepts paralleled the themes emerging from the media examples. The results indicate that the mass media is a pervasive teacher of children, and that fundamental concepts could be introduced earlier in schools to establish scientific concepts before misconceptions arise.

  2. The Strengthening Families Initiative and Child Care Quality Improvement: How Strengthening Families Influenced Change in Child Care Programs in One State

    ERIC Educational Resources Information Center

    Douglass, Anne; Klerman, Lorraine

    2012-01-01

    Research Findings: This study investigated how the Strengthening Families through Early Care and Education initiative in Illinois (SFI) influenced change in 4 child care programs. Findings indicate that SFI influenced quality improvements through 4 primary pathways: (a) Learning Networks, (b) the quality of training, (c) the engagement of program…

  3. Genes

    MedlinePlus

    ... Search Search MedlinePlus GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español You Are Here: Home → Medical Encyclopedia → Genes URL of this page: //medlineplus.gov/ency/article/ ...

  4. Monitoring gene expression in muscle tissue of macaca fascicularis under the influence of testosterone and SARM.

    PubMed

    Reiter, Martina; Tichopad, Ales; Riedmaier, Irmgard; Pfaffl, Michael W; Meyer, Heinrich H D

    2010-01-01

    The focus of this study was to evaluate data on the gene expression profiles induced by testosterone and a selective androgen receptor modulator (SARM, TAP Pharmaceutical Products Inc., Lake Forest, IL, USA) in androgen sensitive muscle tissue to obtain a better understanding on the molecular mechanisms of action and to identify biomarkers for SARM function in primate organs. A total of 24 male cyomolgus monkeys were divided into four groups: testosterone group, SARM1 group, SARM10 group, and control group, each consisting of six animals. The testosterone group was treated i.m. with 3.0 mg/kg Testostoviron®-depot-250 (Schering, Berlin, Germany) every 2 weeks, the SARM1 and SARM10 groups with 1 mg/kg or 10 mg/kg SARM LGD2941 daily, and the control group was not treated. Muscle biopsies from musculus quadriceps and musculus triceps were collected at three time points: baseline time point before SARM application (control), on day 16, and on day 90 of treatment. A total of 30 candidate genes were selected according to their functionality by screening the actual literature and were composed to the following functional groups: cell cycle, endocrine factors, energy metabolism, muscle fiber proteins, muscle specific transcription factors, protein metabolism, and satellite cell biology. Biomarkers were identified as genes regulated from baseline in any of the three treatment groups at day 16 or day 90 using analysis of variance with baseline defined as the contrast group. Out of 23 tested candidate genes, 3 were significantly regulated in m. quadriceps after 90 days treatment; in m. triceps no significant differences were identified. Cathepsin L, calpain 3, and insulin like growth factor binding protein 3 could be identified as first biomarkers, and first physiological differences between control and treatment samples were determined. Both testosterone and SARM LGD2941 appear to have similar effects after 90 days treatment, and thus a longer-term therapy with these

  5. Influence of decoys on the noise and dynamics of gene expression

    NASA Astrophysics Data System (ADS)

    Burger, Anat; Walczak, Aleksandra M.; Wolynes, Peter G.

    2012-10-01

    Many transcription factors bind to DNA with a remarkable lack of specificity, so that regulatory binding sites compete with an enormous number of nonregulatory “decoy” sites. For an autoregulated gene, we show decoy sites decrease noise in the number of unbound proteins to a Poisson limit that results from binding and unbinding. This noise buffering is optimized for a given protein concentration when decoys have a 1/2 probability of being occupied. Decoys linearly increase the time to approach steady state and exponentially increase the time to switch epigenetically between bistable states.

  6. Ghrelin Gene Variants Influence on Metabolic Syndrome Components in Aged Spanish Population

    PubMed Central

    Mora, Mireia; Adam, Victoria; Palomera, Elisabet; Blesa, Sebastian; Díaz, Gonzalo; Buquet, Xavier; Serra-Prat, Mateu; Martín-Escudero, Juan Carlos; Palanca, Ana; Chaves, Javier Felipe; Puig-Domingo, Manuel

    2015-01-01

    Background The role of genetic variations within the ghrelin gene on cardiometabolic profile and nutritional status is still not clear in humans, particularly in elderly people. Objectives We investigated six SNPs of the ghrelin gene and their relationship with metabolic syndrome (MS) components. Subjects and Methods 824 subjects (413 men/411 women, age 77.31±5.04) participating in the Mataró aging study (n = 310) and the Hortega study (n = 514) were analyzed. Anthropometric variables, ghrelin, lipids, glucose and blood pressure levels were measured, and distribution of SNPs -994CT (rs26312), -604GA (rs27647), -501AC (rs26802), R51Q (rs34911341), M72L (rs696217) and L90G (rs4684677) of the ghrelin gene evaluated. Genotypes were determined by multiplex PCR and SNaPshot minisequencing. MS (IDF criteria) was found in 54.9%. Results No association between any of the SNPs and levels of total fasting circulating ghrelin levels was found. C/A-A/A genotype of M72L was associated with increased risk of central obesity according to IDF criteria, while G/A-G/G genotypes of -604GA with reduced risk. A/A genotype of -501AC polymorphism was associated to decreased BMI. In relation to lipid profile, the same genotypes of -604GA were associated with increased total cholesterol and LDL-cholesterol and -501AC with reduced triglycerides. There were no associations with systolic or diastolic blood pressure levels or with hypertension, glucose levels or diabetes and ghrelin polymorphisms. However, G/G genotype of -604GA was associated with glucose >100 mg/dL. Haplotype analysis showed that only one haplotype is associated with increased risk of waist circumference and central obesity. The analysis of subjects by gender showed an important and different association of these polymorphisms regarding MS parameters. Conclusion Ghrelin gene variants -604GA, -501AC and M72L are associated with certain components of MS, in particular to BMI and lipid profile in elderly Spanish subjects. PMID

  7. "I Could See Myself as a Scientist": The Potential of Out-of-School Time Programs to Influence Girls' Identities in Science

    ERIC Educational Resources Information Center

    Riedinger, Kelly; Taylor, Amy

    2016-01-01

    Out-of-school time (OST) programs like the Coastal Ecology science camp can positively influence science identities, particularly for youth from groups historically underserved and underrepresented in science, technology, engineering, and math (STEM). OST STEM programming gives youth opportunities to learn science outside the formal classroom in…

  8. Factors Influencing College Choice for Students in Agriculture Programs: A Comparative Study of Community College and Land-Grant University Students

    ERIC Educational Resources Information Center

    Cunningham, Shannon Kaye

    2013-01-01

    The purpose of this study was to identify factors that influenced college choice of students who recently enrolled (current freshmen and sophomores) in agriculture programs at Oklahoma's land-grant university, as compared to recently enrolled students (current freshmen and sophomores) in selected agriculture programs at public community colleges…

  9. Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen.

    PubMed

    Airoldi, Edoardo M; Miller, Darach; Athanasiadou, Rodoniki; Brandt, Nathan; Abdul-Rahman, Farah; Neymotin, Benjamin; Hashimoto, Tatsu; Bahmani, Tayebeh; Gresham, David

    2016-04-15

    Cell growth rate is regulated in response to the abundance and molecular form of essential nutrients. InSaccharomyces cerevisiae(budding yeast), the molecular form of environmental nitrogen is a major determinant of cell growth rate, supporting growth rates that vary at least threefold. Transcriptional control of nitrogen use is mediated in large part by nitrogen catabolite repression (NCR), which results in the repression of specific transcripts in the presence of a preferred nitrogen source that supports a fast growth rate, such as glutamine, that are otherwise expressed in the presence of a nonpreferred nitrogen source, such as proline, which supports a slower growth rate. Differential expression of the NCR regulon and additional nitrogen-responsive genes results in >500 transcripts that are differentially expressed in cells growing in the presence of different nitrogen sources in batch cultures. Here we find that in growth rate-controlled cultures using nitrogen-limited chemostats, gene expression programs are strikingly similar regardless of nitrogen source. NCR expression is derepressed in all nitrogen-limiting chemostat conditions regardless of nitrogen source, and in these conditions, only 34 transcripts exhibit nitrogen source-specific differential gene expression. Addition of either the preferred nitrogen source, glutamine, or the nonpreferred nitrogen source, proline, to cells growing in nitrogen-limited chemostats results in rapid, dose-dependent repression of the NCR regulon. Using a novel means of computational normalization to compare global gene expression programs in steady-state and dynamic conditions, we find evidence that the addition of nitrogen to nitrogen-limited cells results in the transient overproduction of transcripts required for protein translation. Simultaneously, we find that that accelerated mRNA degradation underlies the rapid clearing of a subset of transcripts, which is most pronounced for the highly expressed NCR

  10. Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen

    PubMed Central

    Airoldi, Edoardo M.; Miller, Darach; Athanasiadou, Rodoniki; Brandt, Nathan; Abdul-Rahman, Farah; Neymotin, Benjamin; Hashimoto, Tatsu; Bahmani, Tayebeh; Gresham, David

    2016-01-01

    Cell growth rate is regulated in response to the abundance and molecular form of essential nutrients. In Saccharomyces cerevisiae (budding yeast), the molecular form of environmental nitrogen is a major determinant of cell growth rate, supporting growth rates that vary at least threefold. Transcriptional control of nitrogen use is mediated in large part by nitrogen catabolite repression (NCR), which results in the repression of specific transcripts in the presence of a preferred nitrogen source that supports a fast growth rate, such as glutamine, that are otherwise expressed in the presence of a nonpreferred nitrogen source, such as proline, which supports a slower growth rate. Differential expression of the NCR regulon and additional nitrogen-responsive genes results in >500 transcripts that are differentially expressed in cells growing in the presence of different nitrogen sources in batch cultures. Here we find that in growth rate–controlled cultures using nitrogen-limited chemostats, gene expression programs are strikingly similar regardless of nitrogen source. NCR expression is derepressed in all nitrogen-limiting chemostat conditions regardless of nitrogen source, and in these conditions, only 34 transcripts exhibit nitrogen source–specific differential gene expression. Addition of either the preferred nitrogen source, glutamine, or the nonpreferred nitrogen source, proline, to cells growing in nitrogen-limited chemostats results in rapid, dose-dependent repression of the NCR regulon. Using a novel means of computational normalization to compare global gene expression programs in steady-state and dynamic conditions, we find evidence that the addition of nitrogen to nitrogen-limited cells results in the transient overproduction of transcripts required for protein translation. Simultaneously, we find that that accelerated mRNA degradation underlies the rapid clearing of a subset of transcripts, which is most pronounced for the highly expressed NCR

  11. Factors influencing the quality of implementation of a positive youth development program in Hong Kong.

    PubMed

    Shek, Daniel T L; Law, Moon Y M

    2013-01-01

    This study examines how social workers collaborate with school teachers in implementing a school-based positive youth development program in Hong Kong. Individual and focus group interviews are conducted with social workers cooperating with school teachers in implementing the Project P.A.T.H.S. in a school context. Through the interviews, strategies for establishing inter-disciplinary collaboration and factors that hinder or facilitate program implementation are identified. This case study highlights factors that facilitate the collaboration between social workers and school teachers, including the following: 1) sufficient training for instructors, 2) sharing of the practice wisdom and teaching experiences, 3) building up mutual support among different parties, 4) use of proactive communication, and 5) demonstration of self-disclosure.

  12. Web-based residency training program reviews influence applicants who use them.

    PubMed

    Zai, Adrian; Chung, Jeanhee; Chueh, Henry

    2005-01-01

    Scutwork.com is an online, peer-based residency review system. We report preliminary results of an online survey designed to investigate the impact of Scutwork on the residency application process. Overall, 68% of respondents believe that the reviews influenced their decision-making and 91% would use Scutwork again. These results and others reported below suggest that Scutwork may play a significant role in the residency selection process.

  13. Ditch network sustains functional connectivity and influences patterns of gene flow in an intensive agricultural landscape

    PubMed Central

    Favre-Bac, L; Mony, C; Ernoult, A; Burel, F; Arnaud, J-F

    2016-01-01

    In intensive agricultural landscapes, plant species previously relying on semi-natural habitats may persist as metapopulations within landscape linear elements. Maintenance of populations' connectivity through pollen and seed dispersal is a key factor in species persistence in the face of substantial habitat loss. The goals of this study were to investigate the potential corridor role of ditches and to identify the landscape components that significantly impact patterns of gene flow among remnant populations. Using microsatellite loci, we explored the spatial genetic structure of two hydrochorous wetland plants exhibiting contrasting local abundance and different habitat requirements: the rare and regionally protected Oenanthe aquatica and the more commonly distributed Lycopus europaeus, in an 83 km2 agricultural lowland located in northern France. Both species exhibited a significant spatial genetic structure, along with substantial levels of genetic differentiation, especially for L. europaeus, which also expressed high levels of inbreeding. Isolation-by-distance analysis revealed enhanced gene flow along ditches, indicating their key role in effective seed and pollen dispersal. Our data also suggested that the configuration of the ditch network and the landscape elements significantly affected population genetic structure, with (i) species-specific scale effects on the genetic neighborhood and (ii) detrimental impact of human ditch management on genetic diversity, especially for O. aquatica. Altogether, these findings highlighted the key role of ditches in the maintenance of plant biodiversity in intensive agricultural landscapes with few remnant wetland habitats. PMID:26486611

  14. Characterization of the bovine gene LIPE and possible influence on fatty acid composition of meat

    PubMed Central

    Goszczynski, Daniel Estanislao; Mazzucco, Juliana Papaleo; Ripoli, María Verónica; Villarreal, Edgardo Leopoldo; Rogberg-Muñoz, Andrés; Mezzadra, Carlos Alberto; Melucci, Lilia Magdalena; Giovambattista, Guillermo

    2014-01-01

    LIPE is an intracellular neutral lipase, which is capable of hydrolyzing a variety of esters and plays a key role in the mobilization of fatty acids from diacylglycerols. The objectives of this study were to characterize the genetic polymorphism of bovine LIPE gene and to evaluate the possible association between three SNPs in the coding regions of this gene with the fatty acid composition of meat in a cattle population. Forty-three unrelated animals from different cattle breeds were re-sequenced and 21 SNPs were detected over approximately 2600 bp, five of these SNPs were novel. Three SNPs were selected, on the basis of evolutionary conservation, to perform validation and association studies in a crossbred cattle population. Our results may suggest a possible association of SNP1 with contents of oleic acid and total monounsaturated fatty acids (p < 0.01), and SNP2 and SNP3 with Heneicosylic acid content (p < 0.01), may be helpful to improve the quality of meat and improve health. PMID:25606458

  15. Plasmid-encoded genes influence exosporium assembly and morphology in Bacillus megaterium QM B1551 spores.

    PubMed

    Manetsberger, Julia; Hall, Elizabeth A H; Christie, Graham

    2015-09-01

    Spores of Bacillus megaterium QM B1551 are encased in a morphologically distinctive exosporium. We demonstrate here that genes encoded on the indigenous pBM500 and pBM600 plasmids are required for exosporium assembly and or stability in spores of this strain. Bioinformatic analyses identified genes encoding orthologues of the B. cereus-family exosporium nap and basal layer proteins within the B. megaterium genome. Transcriptional analyses, supported by electron and fluorescent microscopy, indicate that the pole-localized nap, identified here for the first time in B. megaterium QM B1551 spores, is comprised of the BclA1 protein. The role of the BxpB protein, which forms the basal layer of the exosporium in B. cereus spores, is less clear since spores of a null mutant strain display an apparently normal morphology. Retention of the localized nap in bxpB null spores suggests that B. megaterium employs an alternative mechanism to that used by B. cereus spores in anchoring the nap to the spore surface.

  16. Genetic variation at the TPH2 gene influences impulsivity in addition to eating disorders.

    PubMed

    Slof-Op't Landt, Margarita C T; Bartels, Meike; Middeldorp, Christel M; van Beijsterveldt, Catherina E M; Slagboom, P Eline; Boomsma, Dorret I; van Furth, Eric F; Meulenbelt, Ingrid

    2013-01-01

    Genes are involved in eating disorders (EDs) and self-induced vomiting (SV), a key symptom of different types of EDs. Perfectionism and impulsivity are potential risk factors for EDs. TPH2 (tryptophan hydroxylase 2) SNP rs1473473 was previously associated with anorexia nervosa and EDs characterized by SV. Could perfectionism or impulsivity be underlying the association between rs1473473 and EDs? Genetic association between TPH2 SNP rs1473473 and perfectionism or impulsivity was first evaluated in a random control group (N = 512). The associations obtained in this control group were subsequently tested in a group of patients with an ED (N = 267). The minor allele of rs1473473 (OR = 1.49) was more frequent in impulsive controls, but also in impulsive patients with an ED (OR = 1.83). The largest effect was found in the patients with an ED characterized by SV (OR = 2.51, p = 0.02). Genetic variation at the TPH2 gene appeared to affect impulsivity which, in turn, might predispose to the SV phenotype.

  17. Plasmid-encoded genes influence exosporium assembly and morphology in Bacillus megaterium QM B1551 spores

    PubMed Central

    Manetsberger, Julia; Hall, Elizabeth A. H.; Christie, Graham

    2015-01-01

    Spores of Bacillus megaterium QM B1551 are encased in a morphologically distinctive exosporium. We demonstrate here that genes encoded on the indigenous pBM500 and pBM600 plasmids are required for exosporium assembly and or stability in spores of this strain. Bioinformatic analyses identified genes encoding orthologues of the B. cereus-family exosporium nap and basal layer proteins within the B. megaterium genome. Transcriptional analyses, supported by electron and fluorescent microscopy, indicate that the pole-localized nap, identified here for the first time in B. megaterium QM B1551 spores, is comprised of the BclA1 protein. The role of the BxpB protein, which forms the basal layer of the exosporium in B. cereus spores, is less clear since spores of a null mutant strain display an apparently normal morphology. Retention of the localized nap in bxpB null spores suggests that B. megaterium employs an alternative mechanism to that used by B. cereus spores in anchoring the nap to the spore surface. PMID:26316548

  18. Influence of the core circadian gene "Clock" on obesity and leptin resistance in mice.

    PubMed

    Xie, Xiaoping; Yang, Shuhong; Zou, Yan; Cheng, Shuting; Wang, Yuhui; Jiang, Zhou; Xiao, Jing; Wang, Zhengrong; Liu, Yanyou

    2013-01-23

    Alterations in metabolism could be due to cell-autonomous effects associated with altered expression of Clock in central nervous system feeding centers and/or peripheral tissues involved in metabolism. Clock mutant mice are hyperphagic and obese, which indicates that Clock is related to obesity. In the present study, we used intracerebroventricular injection of recombinant adenoviral vector harboring Clock genes to explore the role of Clock on diet induced obesity and the mechanisms involved in leptin resistance and leptin signaling in mice. The results demonstrated that expression of Clock in the arcuate nucleus of diet induced obesity mice was down-regulated. The recombinant adenoviral vector harboring Clock genes could reduce obesity indexes of diet induced obesity mice including body weight, BMI and total fat mass, attenuate hyperleptinemia, increase leptin sensitivity and decrease accumulated suppressor of cytokine signaling-3 in the arcuate nucleus. These results indicate that Clock plays an important role on obesity, which may be involved in leptin resistance and regulation of suppressor of cytokine signaling-3 in arcuate nucleus.

  19. Uropathogenic Escherichia coli isolates with different virulence genes content exhibit similar pathologic influence on Vero cells.

    PubMed

    Obaid, Jamil M A S; Mansour, Samira R; Elshahedy, Mohammed S; Rabie, Tarik E; Azab, Adel M H

    2014-01-01

    Uropathogenic Escherichia coli are the major causative agent of urinary tract infection--they may simultaneously express a number of virulence factors to cause disease. The aim of this study was to investigate the relation between virulence factors content of fifteen UPEC isolates and their pathogenic potential. The isolates belonged to the five serotypes O78:K80, O114:K90, O142:K86, O164 and O157. Nine of the virulence factors have been explored, ibeA, pap, sfa/foc, cnfl, hly, fyuA, pil, ompT and traT. Virulence factors profiling of the isolates revealed a different content ranging from 22% to 100% of the virulence genes explored. The pathogenic capacity of all fifteen isolates when tested on Vero cells showed that the cytotoxicity for all tested strains on Vero cells was approximately equal and enhanced after growth in syncase broth, leading mainly to cell lysis. The toxic effects reduced slightly after heat treatment of the toxin, and greatly after formalin detoxification, but not all the deleterious effect was abolished. Endotoxin also has cytotoxic effects on Vero cells, but longer time is needed for cytolysis which is greatly diminished with formalin treatment. In conclusion, our study revealed that pathogenic strains of UPEC can exert their pathogenic effect on live cells or system with limited virulence factors gene content.

  20. A review of the influence of treatment strategies on antibiotic resistant bacteria and antibiotic resistance genes.

    PubMed

    Sharma, Virender K; Johnson, Natalie; Cizmas, Leslie; McDonald, Thomas J; Kim, Hyunook

    2016-05-01

    Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) in the aquatic environment have become an emerging contaminant issue, which has implications for human and ecological health. This review begins with an introduction to the occurrence of ARB and ARG in different environmental systems such as natural environments and drinking water resources. For example, ARG or ARB with resistance to ciprofloxacin, sulfamethoxazole, trimethoprim, quinolone, vancomycin, or tetracycline (e.g., tet(A), tet(B), tet(C), tet(G), tet(O), tet(M), tet(W), sul I, and sul II) have been detected in the environment. The development of resistance may be intrinsic, may be acquired through spontaneous mutations (de novo), or may occur due to horizontal gene transfer from donor bacteria, phages, or free DNA to recipient bacteria. An overview is also provided of the current knowledge regarding inactivation of ARB and ARG, and the mechanism of the effects of different disinfection processes in water and wastewater (chlorination, UV irradiation, Fenton reaction, ozonation, and photocatalytic oxidation). The effects of constructed wetlands and nanotechnology on ARB and ARG are also summarized.

  1. Influence of DNA-repair gene variants on the micronucleus frequency in thyroid cancer patients.

    PubMed

    García-Quispes, W A; Pastor, S; Galofré, P; Biarnés, F; Castell, J; Velázquez, A; Marcos, R

    2013-01-20

    The role of different DNA-repair genes (OGG1, XRCC1, XRCC2 and XRCC3) on both the spontaneous and the induced frequency of micronuclei (MN) has been studied in the lymphocytes of a group of 114 patients with differentiated thyroid cancer (DTC). Induction of MN was achieved by treatment of the lymphocytes with 0.5Gy of gamma-radiation. The selected genes are involved in base-excision repair (BER) (OGG1, Ser326Cys; XRCC1, Arg280His and Arg399Gln), and in homologous recombination repair (HRR) (XRCC2, Arg188His and XRCC3, IVS5-14G). Genotyping was carried out by use of the iPLEX (Sequenom) technique. Results indicate that only the OGG1-Ser326Cys polymorphism was able to modulate the MN frequency. This effect was only observed in the spontaneous MN frequency (P=0.016), but not in the MN frequency induced after irradiation. In addition, a strong correlation was observed between spontaneous and induced MN frequency, which would suggest an underlying genetic background.

  2. Variations in critical morphine biosynthesis genes and their potential to influence human health.

    PubMed

    Mantione, Kirk; Kream, Richard M; Stefano, George B

    2010-01-01

    Endogenous morphine has been detected in human tissues from the vascular, immune and nervous systems. The genes/enzymes (CYP2D6, COMT and PNMT) that are involved in the biosynthesis of morphine have variations that affect their functionality. Some of these variations are the result of single nucleotide polymorphisms of DNA sequences. This review highlights some of the functional differences in the critical enzymes required for the biosynthesis of morphine that may affect human health. These variations have been shown to change the way animals react to stressors, perceive pain and behave. The presence of morphine signaling in almost all organ systems suggests that it is most likely playing a role in maintaining the health and promoting the normal functioning of these physiological systems.

  3. A major anti-myoglobin idiotype. Influence of H-2-linked Ir genes on idiotype expression

    PubMed Central

    1984-01-01

    A rabbit antiidiotypic antiserum raised against an A.SW IgG1K monoclonal anti-sperm whale myoglobin (Mb) antibody, HAL19, and extensively absorbed with normal mouse immunoglobulin and MOPC 21 (IgG1K), was found to detect a common or major anti-Mb idiotype expressed by some but not all anti-Mb monoclonal antibodies, regardless of immunoglobulin G (IgG) subclass, and by 40-50% of the anti-Mb antibodies in immune serum from five high responder strains of mice representing five different Igh allotypes. It did not inhibit antibodies to three unrelated protein antigens. The fraction of antibodies expressing this idiotype, denoted IdHAL19, was regulated by H-2-linked genes that correlated exactly in four independent haplotypes and an F1 with the known Mb immune response (Ir) genes and may be identical to these. Whereas less than 50% of antibodies from high responder mice were inhibitable by anti-IdHAL19, greater than 80% of antibodies from low responder mice, tested at comparable final antibody concentration, were inhibitable. This result was true for both low responder haplotypes, H-2b (B10) and H-2k (B10.BR). The idiotype was found to be present on antibodies that bound to native Mb but not fragments 1-55 or 132-153 of Mb or a denatured form, S-methyl Mb. This specificity for native Mb paralleled that of the monoclonal idiotype HAL19 itself. Therefore, the production of antibodies specific for native in contrast to denatured Mb was studied in H-2-congenic high and low responder strains. Strikingly, low responders produced antibodies that reacted almost exclusively with the native conformation, whereas a larger proportion of antibodies from high responder mice also reacted with the denatured form, S-methyl Mb. Bypassing of the Ir gene defect by immunization with Mb attached to a carrier, F gamma G, resulted in low responder antisera resembling higher responder sera in both idiotype expression and conformational specificity. The simplest explanation of these results is

  4. Segregation analysis of blood oxygen saturation in broilers suggests a major gene influence on ascites.

    PubMed

    Navarro, P; Visscher, P M; Chatziplis, D; Koerhuis, A N M; Haley, C S

    2006-12-01

    1. Blood oxygen saturation (SaO) is a potential indicator trait for resistance to ascites in chickens. 2. The objective of the study was to investigate the genetic architecture of SaO in a meat-type chicken line reared in commercial conditions. 3. Data were collected over 15 generations of selection and were divided into two data sets on the basis of a change in recording age from 6 to 5 weeks of age, approximately halfway through the period. The resulting pedigrees comprised in excess of 90,000 birds each and, on average, 12% of these birds had SaO records. 4. Segregation analyses of SaO were carried out assuming a mixed inheritance model that included a major locus segregating in a polygenic background. 5. The analyses suggest that a major gene is involved in the genetic control of SaO in this line. The putative gene acts in a dominant fashion and has an additive effect of around 0.90 sigma(p), equivalent to a predicted difference in SaO between the two homozygous classes of more than 10%. The frequency of the allele that increases SaO changed from 0.53 to 0.65 from the first to the second set of data, consistent with selection on SaO scores. 6. Using estimated genotype probabilities at the putative major locus, we inferred that it acts in an overdominant fashion on body weight and fleshing score. If the low SaO allele leads to susceptibility to ascites, its combined effects are consistent with it being maintained in the population by a balance of natural selection on fitness nad artificial selection on growth and carcase traits. 7. Even with selection on both SaO and growth traits, the combined genotypic effects would make it difficult to remove the unfavourable low-SaO allele by means of traditional selection without the use of genetic markers.

  5. Gibberellin 3-oxidase gene expression patterns influence gibberellin biosynthesis, growth, and development in pea.

    PubMed

    Reinecke, Dennis M; Wickramarathna, Aruna D; Ozga, Jocelyn A; Kurepin, Leonid V; Jin, Alena L; Good, Allen G; Pharis, Richard P

    2013-10-01

    Gibberellins (GAs) are key modulators of plant growth and development. PsGA3ox1 (LE) encodes a GA 3β-hydroxylase that catalyzes the conversion of GA20 to biologically active GA1. To further clarify the role of GA3ox expression during pea (Pisum sativum) plant growth and development, we generated transgenic pea lines (in a lele background) with cauliflower mosaic virus-35S-driven expression of PsGA3ox1 (LE). PsGA3ox1 transgene expression led to higher GA1 concentrations in a tissue-specific and development-specific manner, altering GA biosynthesis and catabolism gene expression and plant phenotype. PsGA3ox1 transgenic plants had longer internodes, tendrils, and fruits, larger stipules, and displayed delayed flowering, increased apical meristem life, and altered vascular development relative to the null controls. Transgenic PsGA3ox1 overexpression lines were then compared with lines where endogenous PsGA3ox1 (LE) was introduced, by a series of backcrosses, into the same genetic background (BC LEle). Most notably, the BC LEle plants had substantially longer internodes containing much greater GA1 levels than the transgenic PsGA3ox1 plants. Induction of expression of the GA deactivation gene PsGA2ox1 appears to make an important contribution to limiting the increase of internode GA1 to modest levels for the transgenic lines. In contrast, PsGA3ox1 (LE) expression driven by its endogenous promoter was coordinated within the internode tissue to avoid feed-forward regulation of PsGA2ox1, resulting in much greater GA1 accumulation. These studies further our fundamental understanding of the regulation of GA biosynthesis and catabolism at the tissue and organ level and demonstrate that the timing/localization of GA3ox expression within an organ affects both GA homeostasis and GA1 levels, and thereby growth.

  6. Mycorrhizal fungi influence on silver uptake and membrane protein gene expression following silver nanoparticle exposure

    NASA Astrophysics Data System (ADS)

    Noori, Azam; White, Jason C.; Newman, Lee A.

    2017-02-01

    The rapid growth of nanotechnology and the high demand for nanomaterial use have greatly increased the risk of particle release into the environment. Understanding nanomaterial interactions with crop species and their associated microorganisms is critical to food safety and security. In the current study, tomato was inoculated with mycorrhizal fungi and subsequently exposed to 12, 24, or 36 mg/kg of 2- or 15-nm silver nanoparticles (Ag-NPs). Mycorrhizal (M) and non-mycorrhizal (NM) tomatoes exposed to 36 mg/kg of 2-nm Ag-NPs accumulated 1300 and 1600 μg/g silver in their tissues, respectively. Mycorrhizal plants accumulated 14% less silver compared to non-mycorrhizal plants. To begin to understand the mechanisms by which plants accumulate NPs, the expression of two aquaporin channel genes, the plasma membrane intrinsic protein (PIP) and the tonoplast membrane intrinsic protein (TIP), and one potassium channel (KC) gene were studied. In non-mycorrhizal plants, the expression of KC, PIP, and TIP was eight, five, and nine times higher than the control, respectively. These expressions for mycorrhizal plants were 5.8, 3.5, and 2 times higher than controls, respectively. The expression of KC and PIP, which are located on the plasma membrane, was 3.5 and 2.5, respectively, times higher than TIP, which is located on the tonoplast. PIP expression was significantly higher in NM tomatoes exposed to 12 mg/kg of 2-nm Ag-NPs compared to M plants. These results show that mycorrhizal colonization decreases Ag accumulation in NP-exposed plants and also moderates changes in expression level of membrane transport proteins.

  7. Polyethylenimine-polyacrylic acid nanocomposites: Type of bonding does influence the gene transfer efficacy and cytotoxicity.

    PubMed

    Tripathi, Sushil K; Ahmadi, Zeba; Gupta, Kailash C; Kumar, Pradeep

    2016-04-01

    The main aim of the current study is to compare the physicochemical properties, cytotoxicity and gene-transfer ability of electrostatically and covalently linked nanocomposites of polyethylenimine (PEI) and polyacrylic acid (PAA) on mammalian cells. Two series of nanocomposites, ionic PEI-PAA (iPP) and covalent PEI-PAA (cPP), were synthesized by varying the amounts of polyacrylic acid (PAA). Physicochemical characterization revealed that iPP nanopcomposites were of bigger sized than cPP nanocomposites with zeta potential almost comparable. Nucleic acid binding assay displayed that iPP and cPP nanocomposites, having sufficient cationic charge, efficiently interacted with plasmid DNA and completely retarded its electrophoretic mobility on agarose gel. In vitro MTT assay showed slightly higher cell viability of cPP/pDNA complexes over their ionic counterparts. Both the series of nanocomposite/pDNA complexes exhibited considerably higher transfection efficacy compared to pDNA complexes of native bPEI and the standard transfection reagent, Lipofectamine, with cPP/pDNA complexes performed much better than iPP/pDNA complexes. Flow cytometry further confirmed these findings where cPP-4/pDNA complex showed transfection in ∼ 85% HEK293 cells, while iPP-2/pDNA complex transfected ∼ 67% HEK293 cells. Lipofectamine/pDNA and bPEI/pDNA complexes could transfect just ∼ 35% and ∼ 26% HEK293 cells. All these results demonstrate the superiority of covalently linked nanocomposites (cPP) which could be used as efficient carriers for nucleic acids in future gene delivery applications.

  8. Tryptophan hydroxylase-2 gene variation influences personality traits and disorders related to emotional dysregulation.

    PubMed

    Gutknecht, Lise; Jacob, Christian; Strobel, Alexander; Kriegebaum, Claudia; Müller, Johannes; Zeng, Yong; Markert, Christoph; Escher, Andrea; Wendland, Jens; Reif, Andreas; Mössner, Rainald; Gross, Cornelius; Brocke, Burkhard; Lesch, Klaus-Peter

    2007-06-01

    Variation in the tryptophan hydroxylase-2 gene (TPH2) coding for the rate-limiting enzyme of serotonin (5-HT) synthesis in the brain modulates responses of limbic circuits to emotional stimuli and has been linked to a spectrum of clinical populations characterized by emotional dysregulation. Here, we tested a set of common single nucleotide polymorphisms (SNPs) in and downstream of the transcriptional control region of TPH2 for association with personality traits and with risk for personality disorders in two cohorts comprising of 336 healthy individuals and 420 patients with personality disorders. Personality dimensions were assessed by the Tridimensional Personality Questionnaire (TPQ) and the revised NEO Personality Inventory (NEO-PI-R). Personality disorders were diagnosed with the Structured Clinical Interview of DSM-IV and were allocated to clusters A, B, and C. Individual SNP and haplotype analyses revealed significant differences in genotype frequencies between controls and cluster B as well as cluster C patients, respectively. In both patient groups, we observed overrepresentation of T allele carriers of a functional polymorphism in the upstream regulatory region of TPH2 (SNP G-703T, rs4570625) which was previously shown to bias responsiveness of the amygdala, a structure critically involved in emotionality. Furthermore, significant effects of TPH2 variants on anxiety-related traits defined primarily by the TPQ Harm Avoidance were found in healthy individuals. The results link potentially functional TPH2 variants to personality traits related to emotional instability as well as to cluster B and cluster C personality disorders. These findings implicate alterations of 5-HT synthesis in emotion regulation and confirm TPH2 as a susceptibility and/or modifier gene of affective spectrum disorders.

  9. Physical activity levels and patterns in older adults: the influence of a DVD-based exercise program.

    PubMed

    Gothe, Neha P; Wójcicki, Thomas R; Olson, Erin A; Fanning, Jason; Awick, Elizabeth; Chung, H David; Zuniga, Krystle E; Mackenzie, Michael J; Motl, Robert W; McAuley, Edward

    2015-02-01

    The use of multimedia to influence health behaviors offers unique advantages over more traditional center-based programs, however, little is known about the effectiveness of such approaches in improving physical activity levels over time. The purpose of this study was to examine the efficacy of a progressive and age-appropriate, DVD-delivered exercise program in promoting physical activity levels among older adult cohorts. Community dwelling older adults (N = 307, Mean age = 71 years) were randomized to one of two groups: a 6-month home-based DVD-delivered exercise (i.e., FlexToBa™) intervention group or a healthy aging DVD control group. Physical activity was assessed objectively using a standard 7-day accelerometer wear period and subjectively using the Godin Leisure Time Exercise Questionnaire, at baseline and follow-up. Analysis of covariances indicated a statistically significant treatment effect for subjectively [F(1,250) = 8.42, P = .004, η(2) = .03] and objectively [F(1,240) = 3.77, P = .05, η(2) = .02] measured physical activity. The older cohort (>70) in the FlexToBa condition further had significantly larger improvements in physical activity levels compared to their younger counterparts. From a public health perspective, media-delivered interventions such as the FlexToBa program might prove to be cost-effective, have a broader reach and at the same time be effective in improving physical activity levels in older adults.

  10. Do 12-week yoga program influence respiratory function of elderly women?

    PubMed

    Bezerra, Lídia Aguiar; de Melo, Helton Fabrício; Garay, Ana Paula; Reis, Victor Machado; Aidar, Felipe José; Bodas, Ana Rita; Garrido, Nuno Domingos; de Oliveira, Ricardo Jacó

    2014-09-29

    Aging produces several respiratory limitations and reduces tolerance to physical efforts, sometimes leading to pulmonary diseases in the elderly. The literature draws attention to the possible benefits of Yoga practice among the elderly, presenting evidence for significant improvements in quality of life. It was hypothesized that yoga practice can improve respiratory function in the elderly. The effects of a yoga program on pulmonary volumes and respiratory muscle strength were verified in 36 elderly women divided into a yoga group [YG] (63.1 ± 13.3 years of age) and a control group (61.0 ± 6.9 years of age). Maximal inspiratory and expiratory pressure (MIP and MEP) were assessed by a manovacuometer and tidal volume (VT), vital capacity (VC) and minute ventilation (VE) were measured by a ventilometer. The program comprised 65 min sessions, 3 times/week during 12 weeks. The heart rate and respiratory rate decreased significantly in the YG (76-39 ± 8-03 vs. 74-61±10.26 bpm and 18.61 ± 3.15 vs. 16.72 ± 3.12 resp/min, respectively). In the YG, VT and VE increased significantly (0.55 ± 0.22 vs. 0.64 ± 0.2 ml and 9.19 ± 2.39 vs. 10.05 ± 2.11 ml, respectively), as well as VC (1.48 ± 0.45 vs. 2.03 ± 0.72 ml). Improvements were also found in MIP and MEP in the YG (62.17 ± 14.77 vs. 73.06 ± 20.16 cmH2O and 80.56 ± 23.94 vs. 86.39 ± 20.16 cmH2O, respectively). It was concluded that a 12-week yoga program significantly improves pulmonary function of aged women.

  11. Do 12-Week Yoga Program Influence Respiratory Function of Elderly Women?

    PubMed Central

    Bezerra, Lídia Aguiar; de Melo, Helton Fabrício; Garay, Ana Paula; Reis, Victor Machado; Aidar, Felipe José; Bodas, Ana Rita; Garrido, Nuno Domingos; de Oliveira, Ricardo Jacó

    2014-01-01

    Aging produces several respiratory limitations and reduces tolerance to physical efforts, sometimes leading to pulmonary diseases in the elderly. The literature draws attention to the possible benefits of Yoga practice among the elderly, presenting evidence for significant improvements in quality of life. It was hypothesized that yoga practice can improve respiratory function in the elderly. The effects of a yoga program on pulmonary volumes and respiratory muscle strength were verified in 36 elderly women divided into a yoga group [YG] (63.1 ± 13.3 years of age) and a control group (61.0 ± 6.9 years of age). Maximal inspiratory and expiratory pressure (MIP and MEP) were assessed by a manovacuometer and tidal volume (VT), vital capacity (VC) and minute ventilation (VE) were measured by a ventilometer. The program comprised 65 min sessions, 3 times/week during 12 weeks. The heart rate and respiratory rate decreased significantly in the YG (76-39 ± 8-03 vs. 74-61±10.26 bpm and 18.61 ± 3.15 vs. 16.72 ± 3.12 resp/min, respectively). In the YG, VT and VE increased significantly (0.55 ± 0.22 vs. 0.64 ± 0.2 ml and 9.19 ± 2.39 vs. 10.05 ± 2.11 ml, respectively), as well as VC (1.48 ± 0.45 vs. 2.03 ± 0.72 ml). Improvements were also found in MIP and MEP in the YG (62.17 ± 14.77 vs. 73.06 ± 20.16 cmH2O and 80.56 ± 23.94 vs. 86.39 ± 20.16 cmH2O, respectively). It was concluded that a 12-week yoga program significantly improves pulmonary function of aged women. PMID:25713658

  12. The influence of Community Access to Child Health (CATCH) program on community pediatrics.

    PubMed

    Soares, Neelkamal S; Hobson, Wendy L; Ruch-Ross, Holly; Finneran, Maureen; Varrasso, Denia A; Keller, David

    2014-01-01

    The CATCH (Community Access to Child Health) Program, which supports pediatricians who engage with the community to improve child health, increase access to health care, and promote advocacy through small seed grants, was last evaluated in 1998. The objective was to describe the characteristics of CATCH grant recipients and projects and assess the community impact of funded projects. Prospective data was collected from CATCH applications (grantee characteristics, topic area and target population for projects funded from 2006-2012) and post-project 2-year follow-up survey (project outcomes, sustainability, and impact for projects funded from 2008 through 2010). From 2006 through 2012, the CATCH Program awarded 401 projects to grantees working mostly in general pediatrics. Eighty-five percent of projects targeted children covered by Medicaid, 33% targeted uninsured children, and 75% involved a Latino population. Main topic areas addressed were nutrition, access to health care, and medical home. Sixty-nine percent of grantees from 2008 to 2010 responded to the follow-up survey. Ninety percent reported completing their projects, and 86% of those projects continued to exist in some form. Grantees reported the development of community partnerships (77%) and enhanced recognition of child health issues in the community (73%) as the most frequent changes due to the projects. The CATCH Program funds community-based projects led by pediatricians that address the medical home and access to care. A majority of these projects and community partnerships are sustained beyond their original CATCH funding and, in many cases, are leveraged into additional financial or other community support.

  13. Rethinking the influence of hydroelectric development on gene flow in a long-lived fish, the Lake Sturgeon Acipenser fulvescens

    PubMed Central

    McDougall, Craig A.; Welsh, Amy B.; Gosselin, Thierry; Anderson, W. Gary; Nelson, Patrick A.

    2017-01-01

    Many hydroelectric dams have been in place for 50 - >100 years, which for most fish species means that enough generations have passed for fragmentation induced divergence to have accumulated. However, for long-lived species such as Lake Sturgeon, Acipenser fulvescens, it should be possible to discriminate between historical population structuring and contemporary gene flow and improve the broader understanding of anthropogenic influence. On the Winnipeg River, Manitoba, two hypotheses were tested: 1) Measureable quantities of former reservoir dwelling Lake Sturgeon now reside downstream of the Slave Falls Generating Station, and 2) genetically differentiated populations of Lake Sturgeon occur upstream and downstream, a result of historical structuring. Genetic methods based on ten microsatellite markers were employed, and simulations were conducted to provide context. With regards to contemporary upstream to downstream contributions, the inclusion of length-at-age data proved informative. Both pairwise relatedness and Bayesian clustering analysis substantiated that fast-growing outliers, apparently entrained after residing in the upstream reservoir for several years, accounted for ~15% of the Lake Sturgeon 525–750 mm fork length captured downstream. With regards to historical structuring, upstream and downstream populations were found to be differentiated (FST = 0.011, and 0.013–0.014 when fast-growing outliers were excluded), and heterozygosity metrics were higher for downstream versus upstream juveniles. Historical asymmetric (downstream) gene flow in the vicinity of the generating station was the most logical explanation for the observed genetic structuring. In this section of the Winnipeg River, construction of a major dam does not appear to have fragmented a previously panmictic Lake Sturgeon population, but alterations to habitat may be influencing upstream to downstream contributions in unexpected ways. PMID:28329005

  14. Rethinking the influence of hydroelectric development on gene flow in a long-lived fish, the Lake Sturgeon Acipenser fulvescens.

    PubMed

    McDougall, Craig A; Welsh, Amy B; Gosselin, Thierry; Anderson, W Gary; Nelson, Patrick A

    2017-01-01

    Many hydroelectric dams have been in place for 50 - >100 years, which for most fish species means that enough generations have passed for fragmentation induced divergence to have accumulated. However, for long-lived species such as Lake Sturgeon, Acipenser fulvescens, it should be possible to discriminate between historical population structuring and contemporary gene flow and improve the broader understanding of anthropogenic influence. On the Winnipeg River, Manitoba, two hypotheses were tested: 1) Measureable quantities of former reservoir dwelling Lake Sturgeon now reside downstream of the Slave Falls Generating Station, and 2) genetically differentiated populations of Lake Sturgeon occur upstream and downstream, a result of historical structuring. Genetic methods based on ten microsatellite markers were employed, and simulations were conducted to provide context. With regards to contemporary upstream to downstream contributions, the inclusion of length-at-age data proved informative. Both pairwise relatedness and Bayesian clustering analysis substantiated that fast-growing outliers, apparently entrained after residing in the upstream reservoir for several years, accounted for ~15% of the Lake Sturgeon 525-750 mm fork length captured downstream. With regards to historical structuring, upstream and downstream populations were found to be differentiated (FST = 0.011, and 0.013-0.014 when fast-growing outliers were excluded), and heterozygosity metrics were higher for downstream versus upstream juveniles. Historical asymmetric (downstream) gene flow in the vicinity of the generating station was the most logical explanation for the observed genetic structuring. In this section of the Winnipeg River, construction of a major dam does not appear to have fragmented a previously panmictic Lake Sturgeon population, but alterations to habitat may be influencing upstream to downstream contributions in unexpected ways.

  15. Fine-mapping butyrophilin family genes revealed several polymorphisms influencing viral genotype selection in hepatitis C infection.

    PubMed

    Ampuero, J; del Campo, J A; Rojas, L; García-Lozano, R J; Buti, M; Solá, R; Forns, X; Moreno-Otero, R; Andrade, R; Diago, M; Salmerón, J; Rodrigo, L; Pons, J A; Navarro, J M; Calleja, J L; García-Samaniego, J; García-Valdecasas, M; Rojas, Á; Millán, R; González-Escribano, M F; Romero-Gómez, M

    2015-01-01

    Host-viral genetic interaction has a key role in hepatitis C infection (HCV) and maybe in the viral selection. In a preliminary GWAS analysis, we identified BTN3A2 rs9104 to be associated with HCV genotype 1. Therefore, our aim was to determine the influence of BTN family on the selection of HCV genotype. We performed a fine-mapping analysis of BTN gene region in a cohort of chronic HCV infection (N=841), validating significant results in another independent chronic HCV infection cohort (N=637), according to selection of viral genotype. BTN3A2 rs9104, BTN3A2 rs733528, BTN2A1 rs6929846, BTN2A1 rs7763910 and BTN3A3 rs13220495 were associated with viral genotype selection. Interestingly, BTN3A2 rs9104 GG genotype was closely related to genotype 1 infection (80.7% (394/488) compared with genotype 3 infection (53.5% (23/43); P=0.0001) in patients harboring IL28B-CT/TT genotype, although this effect was not observed in IL28B-CC genotype. Similarly, BTN3A3 rs13220495 CC genotype was linked to genotype 3 infection (100% (32/32)) compared to genotype 1 (87.3% (137/157); P=0.028) in patients harboring IL28B-CC genotype, but did not in IL28B-CT/TT genotype. Genetic variants in the butyrophilin family genes may alter susceptibility to infection, selecting HCV genotype and influencing disease progression. BTN3A2 rs9104 was strongly associated with genotype 1 infection and the haplotype BTN3A3 rs13220495 CC+IL28B genotype CC was universal in patients with hepatitis C genotype 3a.

  16. The Garlic Allelochemical Diallyl Disulfide Affects Tomato Root Growth by Influencing Cell Division, Phytohormone Balance and Expansin Gene Expression

    PubMed Central

    Cheng, Fang; Cheng, Zhihui; Meng, Huanwen; Tang, Xiangwei

    2016-01-01

    Diallyl disulfide (DADS) is a volatile organosulfur compound derived from garlic (Allium sativum L.), and it is known as an allelochemical responsible for the strong allelopathic potential of garlic. The anticancer properties of DADS have been studied in experimental animals and various types of cancer cells, but to date, little is known about its mode of action as an allelochemical at the cytological level. The current research presents further studies on the effects of DADS on tomato (Solanum lycopersicum L.) seed germination, root growth, mitotic index, and cell size in root meristem, as well as the phytohormone levels and expression profile of auxin biosynthesis genes (FZYs), auxin transport genes (SlPINs), and expansin genes (EXPs) in tomato root. The results showed a biphasic, dose-dependent effect on tomato seed germination and root growth under different DADS concentrations. Lower concentrations (0.01–0.62 mM) of DADS significantly promoted root growth, whereas higher levels (6.20–20.67 mM) showed inhibitory effects. Cytological observations showed that the cell length of root meristem was increased and that the mitotic activity of meristematic cells in seedling root tips was enhanced at lower concentrations of DADS. In contrast, DADS at higher concentrations inhibited root growth by affecting both the length and division activity of meristematic cells. However, the cell width of the root meristem was not affected. Additionally, DADS increased the IAA and ZR contents of seedling roots in a dose-dependent manner. The influence on IAA content may be mediated by the up-regulation of FZYs and PINs. Further investigation into the underlying mechanism revealed that the expression levels of tomato EXPs were significantly affected by DADS. The expression levels of EXPB2 and beta-expansin precursor were increased after 3 d, and those of EXP1, EXPB3 and EXLB1 were increased after 5 d of DADS treatment (0.41 mM). This result suggests that tomato root growth may be

  17. The influence of managed care on U.S. baccalaureate nursing education programs.

    PubMed

    Jackson, Susan E

    2006-02-01

    The transformation of health care into managed care has raised many issues and concerns for nurse educators. The milieu in which nurses currently practice reflects the restructuring shaped by managed care principles. The shift from acute care to expanded community services has changed the way health care is provided within hospital settings. The organization of nursing programs has been affected by this shift, and the ramifications of these external forces on curriculum structure have altered the way nursing students are educated. This article presents research demonstrating the changes in the structure of the curricula for baccalaureate nursing education in 2001, which were caused by health care reform in effect since 1994.

  18. How does the employer contribution for the federal employees health benefits program influence plan selection?

    PubMed

    Florence, Curtis S; Thorpe, Kenneth E

    2003-01-01

    Market reform of health insurance is proposed to increase coverage and reduce growth in spending by providing an incentive to choose low-cost plans. However, having a choice of plans could result in risk segmentation. Risk-adjusted payments have been proposed to address risk segmentation but are criticized as ineffective. An alternative to risk adjustment is to subsidize premiums, as in the Federal Employees Health Benefits Program (FEHBP). Subsidizing premiums may also increase total premium spending. We find that there is little risk segmentation in the FEHBP and that reducing the premium subsidy would lower government premium spending and slightly increase risk segmentation.

  19. Suppression of Wnt1-induced mammary tumor growth and lower serum insulin in offspring exposed to maternal blueberry diet suggest early dietary influence on developmental programming.

    PubMed

    Rahal, Omar M; Pabona, John Mark P; Kelly, Thomas; Huang, Yan; Hennings, Leah J; Prior, Ronald L; Al-Dwairi, Ahmed; Simmen, Frank A; Simmen, Rosalia C M

    2013-02-01

    Despite the well-accepted notion that early maternal influences persist beyond fetal life and may underlie many adult diseases, the risks imposed by the maternal environment on breast cancer development and underlying biological mechanisms remain poorly understood. In this study, we investigated whether early exposure to blueberry (BB) via maternal diet alters oncogene Wnt1-induced mammary tumorigenesis in offspring. Wnt1-transgenic female mice were exposed to maternal Casein (CAS, control) or blueberry-supplemented (CAS + 3%BB) diets throughout pregnancy and lactation. Offspring were weaned to CAS and mammary tumor development was followed until age 8 months. Tumor incidence and latency were similar for both groups; however, tumor weight at killing and tumor volume within 2 weeks of initial detection were lower (by 50 and 60%, respectively) in offspring of BB- versus control-fed dams. Dietary BB exposure beginning at weaning did not alter mammary tumor parameters. Tumors from maternal BB-exposed offspring showed higher tumor suppressor (Pten and Cdh1) and lower proproliferative (Ccnd1), anti-apoptotic (Bcl2) and proangiogenic (Figf, Flt1 and Ephb4) transcript levels, and displayed attenuated microvessel density. Expression of Pten and Cdh1 genes was also higher in mammary tissues of maternal BB-exposed offspring. Mammary tissues and tumors of maternal BB-exposed offspring showed increased chromatin-modifying enzyme Dnmt1 and Ezh2 transcript levels. Body weight, serum insulin and serum leptin/adiponectin ratio were lower for maternal BB-exposed than control tumor-bearing offspring. Tumor weights and serum insulin were positively correlated. Results suggest that dietary influences on the maternal environment contribute to key developmental programs in the mammary gland to modify breast cancer outcome in adult progeny.

  20. Contribution of distinct homeodomain DNA binding specificities to Drosophila embryonic mesodermal cell-specific gene expression programs.

    PubMed

    Busser, Brian W; Gisselbrecht, Stephen S; Shokri, Leila; Tansey, Terese R; Gamble, Caitlin E; Bulyk, Martha L; Michelson, Alan M

    2013-01-01

    Homeodomain (HD) proteins are a large family of evolutionarily conserved transcription factors (TFs) having diverse developmental functions, often acting within the same cell types, yet many members of this family paradoxically recognize similar DNA sequences. Thus, with multiple family members having the potential to recognize the same DNA sequences in cis-regulatory elements, it is difficult to ascertain the role of an individual HD or a subclass of HDs in mediating a particular developmental function. To investigate this problem, we focused our studies on the Drosophila embryonic mesoderm where HD TFs are required to establish not only segmental identities (such as the Hox TFs), but also tissue and cell fate specification and differentiation (such as the NK-2 HDs, Six HDs and identity HDs (I-HDs)). Here we utilized the complete spectrum of DNA binding specificities determined by protein binding microarrays (PBMs) for a diverse collection of HDs to modify the nucleotide sequences of numerous mesodermal enhancers to be recognized by either no or a single subclass of HDs, and subsequently assayed the consequences of these changes on enhancer function in transgenic reporter assays. These studies show that individual mesodermal enhancers receive separate transcriptional input from both I-HD and Hox subclasses of HDs. In addition, we demonstrate that enhancers regulating upstream components of the mesodermal regulatory network are targeted by the Six class of HDs. Finally, we establish the necessity of NK-2 HD binding sequences to activate gene expression in multiple mesodermal tissues, supporting a potential role for the NK-2 HD TF Tinman (Tin) as a pioneer factor that cooperates with other factors to regulate cell-specific gene expression programs. Collectively, these results underscore the critical role played by HDs of multiple subclasses in inducing the unique genetic programs of individual mesodermal cells, and in coordinating the gene regulatory networks