Transcription factor networks and chromatin remodeler function in gene regulation on the eukaryotic genome

Numerous events – from histone modification and transcription factor binding to gene expression – take place on eukaryotic chromatin, while cells are constantly exposed to dynamic stimuli ranging from spatial and temporal cues to environmental and extracellular signals. The cell’s ability to respond and adjust accordingly is directly related to cell fitness and viability. With the advent of next-generation sequencing, investigating these events has been enabled at nucleotide resolution but across the entire genome. In this dissertation, I investigate changes on eukaryotic genomes including yeast and human, which are triggered by stress and by loss of a protein of interest, by analyzing genomics data generated mainly through next-generation sequencing. In Chapter 1, I determine how yeast cells achieve transcriptional reprogramming in response to heat stress by first identifying the complete set of transcription factors that are essential for heat stress conditions. This is further explored by identifying both the target loci bound by the transcription factors under conditions of heat-stress, as well as the genes that require the function of the transcription factor for normal transcriptional response to heat stress. In Chapter 2, I study a chromatin remodeling factor, CHD1 (Chromodomain Helicase DNA binding protein 1) with regard to two aspects: first, what factors provide specificity for Chd1 positioning on chromatin, by examining the role of proteins that physically or genetically interact with Chd1, and second, what is the relationship of Chd1 with the hallmark of chromatin modifications, histone H3 tri-methylation at Lys 4 and Lys 36, by investigating changes in these histone methylation marks in the absence of Chd1. Additionally, I show a novel functional link between Chd1 and RNA splicing through analysis of intron retention in transcripts produced in the Chd1 mutant. Lastly, I investigate Chd1 role in human glioblastoma cell line by generating a Chd1 knock-out via the CRISPR/Cas9 genome editing system. Taken together, the work presented in this dissertation provides novel approaches, discoveries, and intriguing insights into how eukaryotic chromatin experiences dynamic alterations in response to various perturbations on a genome-wide scale.Cellular and Molecular Biolog

Issues in Developing and Evaluating a Culturally Tailored Internet Cancer Support Group

The purpose of this paper is to explore practical issues in developing and implementing a culturally tailored Internet Cancer Support Group for a group of ethnic minority cancer patients—Asian American cancer patients. Throughout the research process of the original study testing the Internet cancer support group, research team made written records of practical issues and plausible rationales for the issues. Weekly group discussion among research team members was conducted, and the discussion records were evaluated and analyzed using a content analysis (with individual words as the unit of analysis). The codes from the analysis process were categorized into idea themes, through which the issues were extracted. The issues included those in: (a) difficulties in using multiple languages; (b) collaboration with the IT department and technical challenges (c) difficulties in recruitment; (d) difficulties in retention; (e) optimal timing; and (f) characteristics of the users. Based on the findings, we suggested researchers to plan a workable translation process, check technical needs in advance, use multiple strategies to recruit and retain research participants, plan the right time for data collection, and consider characteristics of the users in the study design

Internet Recruitment of Asian American Breast Cancer Survivors

The purpose of this paper is to identify practical issues in Internet recruitment of racial/ethnic minorities by analyzing an Internet intervention study conducted with Asian American breast cancer survivors, and to propose directions for recruitment of racial/ethnic minorities for future Internet research. Six practical issues were identified: (a) a relatively fewer number of Internet communities/groups; (b) hindrances in establishing authenticity; (c) difficulties in gaining entrée from the webmasters or website owners of Internet communities/groups; (d) the necessity of racially/ethnically matched research team members; (e) flexibility required in recruitment strategies; and (f) strategies to overcome the low response rate

Stress and premenstrual symptoms: A web-based causal-comparative study on Korean women studying in the U.S. and South Korea

Premenstrual symptoms are a common health condition in women that can impair their daily activities and overall quality of life. Although the severity of symptoms has been reported to be highly correlated with levels of perceived stress, how and to what extent these two are linked remains unclear. The objectives of this study were to identify the relationship between perceived stress and premenstrual symptoms, as well as to examine the impact of acculturative stress on this relationship among Korean international students. These students provide an excellent exemplar to study this phenomenon as they are the group with high stress levels due to additive acculturative stress while having common risk factors for premenstrual symptoms. The study used a 10-week longitudinal causal-comparative web-based study design. A convenience sampling method was used to recruit 98 Korean international students from the United States and 89 Korean domestic students from South Korea (comparison group). Weekly web-based surveys were administered for 10 weeks to capture the women’s levels of perceived stress, acculturative stress, and premenstrual symptoms for two consecutive menstrual cycles. The data were analyzed through descriptive analyses, linear multivariable mixed-model regressions, hierarchical multiple regressions, and path analyses, using SPSS 22.0 and Mplus 7.3. The levels of perceived stress and menstrual symptomatology were significantly higher during the premenstrual phase in Korean domestic students, while in Korean international students, levels of perceived stress did not differ by menstrual phases. Levels of perceived stress and menstrual symptomatology were significantly higher in Korean international students than in Korean domestic students throughout the menstrual cycle. Levels of perceived stress and acculturative stress were the strongest influencing factors for premenstrual symptoms in Korean international students. While perceived stress was a significant influencing factor for Korean domestic students, it was not the strongest factor. Psychological distress was a partial mediator between perceived stress and premenstrual symptoms in Korean international students, whereas perceived social support was a moderator between the relationship in Korean domestic students only. The findings of this study not only supported a significant relationship between perceived stress and premenstrual symptoms, but also the impact of acculturative stress on the relationship

Stress and premenstrual symptoms: A web-based causal-comparative study on Korean women studying in the U.S. and South Korea

Premenstrual symptoms are a common health condition in women that can impair their daily activities and overall quality of life. Although the severity of symptoms has been reported to be highly correlated with levels of perceived stress, how and to what extent these two are linked remains unclear. The objectives of this study were to identify the relationship between perceived stress and premenstrual symptoms, as well as to examine the impact of acculturative stress on this relationship among Korean international students. These students provide an excellent exemplar to study this phenomenon as they are the group with high stress levels due to additive acculturative stress while having common risk factors for premenstrual symptoms. The study used a 10-week longitudinal causal-comparative web-based study design. A convenience sampling method was used to recruit 98 Korean international students from the United States and 89 Korean domestic students from South Korea (comparison group). Weekly web-based surveys were administered for 10 weeks to capture the women’s levels of perceived stress, acculturative stress, and premenstrual symptoms for two consecutive menstrual cycles. The data were analyzed through descriptive analyses, linear multivariable mixed-model regressions, hierarchical multiple regressions, and path analyses, using SPSS 22.0 and Mplus 7.3. The levels of perceived stress and menstrual symptomatology were significantly higher during the premenstrual phase in Korean domestic students, while in Korean international students, levels of perceived stress did not differ by menstrual phases. Levels of perceived stress and menstrual symptomatology were significantly higher in Korean international students than in Korean domestic students throughout the menstrual cycle. Levels of perceived stress and acculturative stress were the strongest influencing factors for premenstrual symptoms in Korean international students. While perceived stress was a significant influencing factor for Korean domestic students, it was not the strongest factor. Psychological distress was a partial mediator between perceived stress and premenstrual symptoms in Korean international students, whereas perceived social support was a moderator between the relationship in Korean domestic students only. The findings of this study not only supported a significant relationship between perceived stress and premenstrual symptoms, but also the impact of acculturative stress on the relationship

Physiologic Changes during Sponge Bathing in Premature Infants

In this study, we observed physiological reactions of premature infants during sponge bathing in the neonatal intensive care unit (NICU). The infants’ body temperature, heart rate, and oxygen saturation were monitored to examine hypothermia risks during bathing. The participants of the study were 32 premature infants who were hospitalized right after their birth in the V hospital in Korea between December 2012 and August 2013. The informed consents of the study were received from the infants’ parents. The infants were randomly assigned into two-day and four-day bath cycle groups and their physiological reactions were monitored before bathing as well as 5 and 10 min after bathing. The collected data were analyzed using the SPSS statistical package through t-test. A significant drop in body temperature was noted in both groups; that is, 4-day bathing cycle and 2-day bathing cycle (p < 0.001). However, there were no significant changes in heart rate or transcutaneous oxygen levels. There was no significant change between groups at each measurement point. In order to minimize the physiological instability that may be caused during bathing, the care providers should try to complete bathing within the shortest possible time and to make bathing a pleasant and useful stimulus for infants

Analysis of transcriptional modules during human fibroblast ageing

For systematic identification of transcription signatures of human cell aging, we carried out Weighted Gene Co-expression Network Analysis (WGCNA) with the RNA-sequencing data generated with young to old human dermal fibroblasts. By relating the modules to the donor's traits, we uncovered the natural aging- and premature aging disease-associated modules. The STRING functional association networks built with the core module memberships provided a systematic overview of genome-wide transcriptional changes upon aging. We validated the selected candidates via quantitative reverse transcription PCR (RT-qPCR) assay with young and aged human fibroblasts, and uncovered several genes involved in ECM, cell, and nuclear mechanics as a potential aging biomarker. Collectively, our study not only provides a snapshot of functional changes during human fibroblast aging but also presents potential aging markers that are relevant to cell mechanics.ISSN:2045-232

Transcultural Nursing: Current Trends in Theoretical Works

Purpose: To explore the current trends in theoretical works related to transcultural nursing through an integrated literature review. Methods: The literature on theoretical works related to transcultural nursing during the past 10 years was searched through multiple databases and reviewed to determine themes reflecting the current trends in theoretical works related to transcultural nursing. Results: Through the review and analysis process, four themes reflecting the current trends in theoretical works related to transcultural nursing were found: (a) purposes of exploring, defining and clarifying, and reflecting; (b) various theorizing methods; (c) multiple sources of theorizing; and (d) clear linkages to nursing practice and research. Conclusion: Continuous efforts need to be made to further develop the theoretical works related to transcultural nursing to reflect changes in this ever-changing nursing world. Keywords: nursing research, nursing theory, transcultural nursin

Widespread misinterpretable ChIP-seq bias in yeast.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to detect genome-wide interactions between a protein of interest and DNA in vivo. Loci showing strong enrichment over adjacent background regions are typically considered to be sites of binding. Insufficient attention has been given to systematic artifacts inherent to the ChIP-seq procedure that might generate a misleading picture of protein binding to certain loci. We show here that unrelated transcription factors appear to consistently bind to the gene bodies of highly transcribed genes in yeast. Strikingly, several types of negative control experiments, including a protein that is not expected to bind chromatin, also showed similar patterns of strong binding within gene bodies. These false positive signals were evident across sequencing platforms and immunoprecipitation protocols, as well as in previously published datasets from other labs. We show that these false positive signals derive from high rates of transcription, and are inherent to the ChIP procedure, although they are exacerbated by sequencing library construction procedures. This expression bias is strong enough that a known transcriptional repressor like Tup1 can erroneously appear to be an activator. Another type of background bias stems from the inherent nucleosomal structure of chromatin, and can potentially make it seem like certain factors bind nucleosomes even when they don't. Our analysis suggests that a mock ChIP sample offers a better normalization control for the expression bias, whereas the ChIP input is more appropriate for the nucleosomal periodicity bias. While these controls alleviate the effect of the biases to some extent, they are unable to eliminate it completely. Caution is therefore warranted regarding the interpretation of data that seemingly show the association of various transcription and chromatin factors with highly transcribed genes in yeast

Isolation and characterization of five novel probiotic strains from Korean infant and children faeces.

Probiotics are dietary supplements containing viable, non-pathogenic microorganisms that interact with the gastrointestinal microflora and directly with the immune system. The possible health effects of probiotics include modulating the immune system and exerting antibacterial, anticancer, and anti-mutagenic effects. The purpose of this study was to isolate, identify, and characterize novel strains of probiotics from the faeces of Korean infants. Various assays were conducted to determine the physiological features of candidate probiotic isolates, including Gram staining, 16S rRNA gene sequencing, tolerance assays to stimulated gastric juice and bile salts, adherence ability assays, antibiotic susceptibility testing, and assays of immunomodulatory effects. Based on these morphological and biochemical characteristics, five potential probiotic isolates (Enterococcus faecalis BioE EF71, Lactobacillus fermentum BioE LF11, Lactobacillus plantarum BioE LPL59, Lactobacillus paracasei BioE LP08, and Streptococcus thermophilus BioE ST107) were selected. E. faecalis BioE EF71 and L. plantarum BioE LPL59 showed high tolerance to stimulated gastric juice and bile salts, and S. thermophilus BioE ST107 as well as these two strains exhibited stronger adherence ability than reference strain Lactobacillus rhamnosus GG. All five strains inhibited secretion of lipopolysaccharide-induced pro-inflammatory cytokines IL-6 and TNF-α in RAW264.7 macrophages in vitro. L. fermentum BioE LF11, L. plantarum BioE LPL59, and S. thermophilus BioE ST107 enhanced the production of anti-inflammatory cytokine IL-10. Overall, our findings demonstrate that the five novel strains have potential as safe probiotics and encouraged varying degrees of immunomodulatory effects