Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

Abstract Background In eukaryotic organisms, DNA is packaged into chromatin structure, where most of DNA is wrapped into nucleosomes. DNA compaction and nucleosome positioning have clear functional implications, since they modulate the accessibility of genomic regions to regulatory proteins. Despite the intensive research effort focused in this area, the rules defining nucleosome positioning and the location of DNA regulatory regions still remain elusive. Results Naked (histone-free) and nucleosomal DNA from yeast were digested by microccocal nuclease (MNase) and sequenced genome-wide. MNase cutting preferences were determined for both naked and nucleosomal DNAs. Integration of their sequencing profiles with DNA conformational descriptors derived from atomistic molecular dynamic simulations enabled us to extract the physical properties of DNA on a genomic scale and to correlate them with chromatin structure and gene regulation. The local structure of DNA around regulatory regions was found to be unusually flexible and to display a unique pattern of nucleosome positioning. Ab initio physical descriptors derived from molecular dynamics were used to develop a computational method that accurately predicts nucleosome enriched and depleted regions. Conclusions Our experimental and computational analyses jointly demonstrate a clear correlation between sequence-dependent physical properties of naked DNA and regulatory signals in the chromatin structure. These results demonstrate that nucleosome positioning around TSS (Transcription Start Site) and TTS (Transcription Termination Site) (at least in yeast) is strongly dependent on DNA physical properties, which can define a basal regulatory mechanism of gene expression

Study of Factors Affecting Students' Performance in three Sci- ence Classes: General Biology, Botany, and Microbiology at Fayetteville State University

Abstract Several studies have reported the effects of class time on overall students' performances, but there are just few on the influence of factors as absences, gender, class section, class difficulty or semester. The objectives of this study were to analyze the effects of the above mentioned factors (absences, class time, gender, class difficulty and semester) on college students' performance in three science classes: Principles of Biology (BIOL 150), General Botany (BOTN 210), and Microbiology & Immunology (BIOL 330) over a period of 3 years. Analysis of variance (ANOVA) for absences showed significant differences for the number of those between the different semesters (fall, spring, and summer) and that students tend to miss more classes (P>0.05) during fall and spring than summer semesters. Gender (P>0.3515) and class section (P>0.0608) do not seem to significantly affect the average grades in general biology and microbiology. Regarding gender, significant differences were observed in BOTN 210 between females and males average grades. Females tend to do better than males at least in this class. There was a moderate but strongly significant negative correlation (-0.59, P>0.0001***) between the average grades and the number of absences in almost all classes. ANOVA also showed significant differences for the average grades between the different class times at P>0.0020*. The Tukey-Kramer test revealed that students perform better in morning classes compared to afternoon classes. The class time plays a significant role in the number of absences as well. Analysis showed that the most "convenient" time for students is late morning or after __________________________________________________ E-mail: [email protected] noon given that they tend to result in fewer absences. In addition, students tend to receive better grades in BOTN 210 that they do in BIOL 330 and BIOL 150 (Means 77.33, 69.42, and 67.82, respectively) which can be justified by the fact that the latter two are more intense than the first. Overall, absences are the only factor among those studied (absences, gender, class section, class difficulty and semester) that seem to affect student's grades negatively in all three classes (BIOL 150, BOTN 210 and BIOL 330). Typically, factors such as gender, and class section do not have any effect on students' performance. Results for class time show that students may perform better in morning or evening classes. In other cases time does not play any significant role to efficiency

Ganoderma lucidum reduces obesity in mice by modulating the composition of the gut microbiota

Obesity is associated with low-grade chronic inflammation and intestinal dysbiosis. Ganoderma lucidum is a medicinal mushroom used in traditional Chinese medicine with putative anti-diabetic effects. Here, we show that a water extract of Ganoderma lucidum mycelium (WEGL) reduces body weight, inflammation and insulin resistance in mice fed a high-fat diet (HFD). Our data indicate that WEGL not only reverses HFD-induced gut dysbiosis—as indicated by the decreased Firmicutes-to-Bacteroidetes ratios and endotoxin-bearing Proteobacteria levels—but also maintains intestinal barrier integrity and reduces metabolic endotoxemia. The anti-obesity and microbiota-modulating effects are transmissible via horizontal faeces transfer from WEGL-treated mice to HFD-fed mice. We further show that high molecular weight polysaccharides (>300 kDa) isolated from the WEGL extract produce similar anti-obesity and microbiota-modulating effects. Our results indicate that G. lucidum and its high molecular weight polysaccharides may be used as prebiotic agents to prevent gut dysbiosis and obesity-related metabolic disorders in obese individuals