Modeling Gene Networks in Saccharomyces cerevisiae

Detailed and innovative analysis of gene regulatory network structures may reveal novel insights to biological mechanisms. Here we study how gene regulatory network in Saccharomyces cerevisiae can differ under aerobic and anaerobic conditions. To achieve this, we discretized the gene expression profiles and calculated the self-entropy of down- and upregulation of gene expression as well as joint entropy. Based on these quantities the uncertainty coefficient was calculated for each gene triplet, following which, separate gene logic networks were constructed for the aerobic and anaerobic conditions. Four structural parameters such as average degree, average clustering coefficient, average shortest path, and average betweenness were used to compare the structure of the corresponding aerobic and anaerobic logic networks. Five genes were identified to be putative key components of the two energy metabolisms. Furthermore, community analysis using the Newman fast algorithm revealed two significant communities for the aerobic but only one for the anaerobic network. David Gene Functional Classification suggests that, under aerobic conditions, one such community reflects the cell cycle and cell replication, while the other one is linked to the mitochondrial respiratory chain function

Short sleep time may be the main reason for irregular breakfast to cause overweight—a cross-sectional study

IntroductionIn recent years, the relationship between circadian rhythm and overweight and obesity has attracted the attention of many scholars.MethodsTo evaluate association between the duration of sleep and the regularity of breakfast and overweight. A total of 1,178 students from Qingdao University were selected by stratified cluster sampling. There were 601 males (24.69 ± 0.80 years old) and 569 females (24.54 ± 0.70 years old). We used body mass index (BMI), waist circumference (WC), and waist-to-hip ratio (WHR) to define overweight levels. Chi-square test, Pearson correlation test, and logistic regression were applied to test association among overweight, sleep duration, sleep onset time, and breakfast regularity. Pittsburgh sleep quality index was used to assess the overall sleep quality of the study subjects. Mediation effect and Sobel test were used to analyze the effect of sleep duration on breakfast regularity and overweight.ResultsOnly 34.1% of the population ate breakfast every day, and eating breakfast 1–3 times per week was associated with a higher risk of overweight (BMI: OR = 2.183, 95%CI: 1.369,3,481; WC: OR = 2.101, 95%CI: 1.232,3,583; WHR: OR = 2.108, 95%CI: 1.331,3,337). The effects of all types of Usual Breakfast Consumption Frequency on overweight were fully mediated by sleep duration (p < 0.05). In particular, the subjects exercised outdoors more than five times per week slept longer (p < 0.05).ConclusionShort sleep duration may be the main reason for irregular breakfast leading to overweight. Adequate outdoor exercise is essential for weight maintenance

Benazepril hydrochloride improves diabetic nephropathy and decreases proteinuria by decreasing ANGPTL-4 expression

Abstract Background This study aimed to investigate the effects of benazepril hydrochloride (BH) on proteinuria and ANGPTL-4 expression in a diabetic nephropathy (DN) rat model. Methods A total of 72 Wistar male rats were randomly divided into three groups: normal control (NC), DN group and BH treatment (BH) groups. The DN model was induced by streptozotocin (STZ). Weight, glucose, proteinuria, biochemical indicators and the kidney weight index were examined at 8, 12 and 16 weeks. In addition, ANGPTL-4 protein and mRNA expressions were assessed by immunohistochemistry and qRT-PCR, respectively. Relationships between ANGPTL-4 and biochemical indicators were investigated using Spearman analysis. Results Weight was significantly lower but glucose levels were significantly higher in both the DN and BH groups than in the NC group (P < 0.05). Compared with the DN group, proteinuria, urea, creatinine, triglycerides and total cholesterol levels were decreased, whereas the albumin level was increased after BH treatment (all P < 0.05). Furthermore, BH diminished kidney volume and ameliorated the pathological changes associated with DN. ANGPTL-4 expression was significantly decreased after BH treatment, and ANGPTL-4 expression was highly correlated with biochemical indicators of DN (P < 0.05). Conclusions Benazepril hydrochloride improves DN and decreases proteinuria by decreasing ANGPTL-4 expression

Biotransformation of HSP into 2,5-DHP by HSP hydroxylase from <i>A. tumefaciens</i> S33.

<p>Effects of temperature (a) and pH (b) on the enzymatic formation of 2,5-DHP (<i>squares</i>) from HSP (<i>circles</i>). (a) The reactions were carried out in 50 mM sodium phosphate (pH 8.0) at the temperature indicated. (b) The reactions were performed at 35°C in sodium phosphate buffer at pH indicated. (c) The reaction was performed in 50 mM sodium phosphate (pH 8.0) at 35°C. The values are means of three replicates, and the error bars indicate the standard deviations.</p

Purification of HSP hydroxylase from <i>A. tumefaciens</i> S33.

<p>Purification of HSP hydroxylase from <i>A. tumefaciens</i> S33.</p

LC-MS profiles of the reaction catalyzed by purified HSP hydroxylase from <i>A. tumefaciens</i> S33.

<p>(a) HPLC profile monitored with PDA detector; (b–d) mass spectra of products 2,5-DHP (<i>m/z</i> 110.18) and succinic acid (<i>m/z</i> 117.15) and substrate HSP (<i>m/z</i> 194.04), respectively. Negatively charged ions were detected.</p

Effects of temperature and pH on the activity of HSP hydroxylase from A. <i>tumefaciens</i> S33.

<p>(a) The reactions were carried out in 50 mM Tris-HCl (pH 8.0) at the temperature indicated. (b) The reactions were performed at 30°C in different buffers: citric acid-sodium hydrogen phosphate (pH 5.0 and pH 6.0), sodium phosphate (pH 6.0, pH 7.0 and pH 8.0), Tris-HCl (pH 8.0, pH 9.0 and pH 10.0) and sodium bicarbonate-sodium hydroxide (pH 10.0 and pH 11.0). The values are means of three replicates, and the error bars indicate the standard deviations.</p

Proposed pathway for nicotine degradation by <i>A. tumefaciens</i> S33.

<p>The steps from nicotine to 6-hydroxy-pseudooxynicotine are same to part of the pyridine pathway, and the step catalyzed by 6-hydroxy-3-succinoylpyridine hydroxylase, which is indicated in the box, is same to the pyrrolidine pathway.</p