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

Fine structure and distribution of antennal sensilla of stink bug Arma chinensis (Heteroptera: Pentatomidae)

Scanning electron microscopy was used to examine the morphology, ultrastructure, and distribution of antennal sensilla of the stink bug Arma chinensis. Two types of sensilla trichodea (ST1–2), four types of sensilla basiconica (SB 1– 4), one type of sensilla chaetica (SCH), one type of sensilla cavity (SCA) and one type of sensilla coeloconica (SCO) were distinguished on the antennae in both sexes. ST1 and ST2 were absent from the scape and pedicel. SB1 were absent from the scape. SB2 were distributed throughout the antennae. SB3 were located on the second pedicel and the two flagellomeres. SB4 were absent from the second flagellomere. SCH was observed on the second pedicel and the two flagellomeres. SCA and SCO occurred only on the second flagellomere. SB1 clusters occurred on the distal part of the second flagellomere. We compared the morphology and structure of these sensilla to other Heteroptera and discuss their possible functions

A Two-Year Surveillance of 2009 Pandemic Influenza A (H1N1) in Guangzhou, China: From Pandemic to Seasonal Influenza?

In this two-years surveillance of 2009 pandemic influenza A (H1N1) (pH1N1) in Guangzhou, China, we reported here that the scale and duration of pH1N1 outbreaks, severe disease and fatality rates of pH1N1 patients were significantly lower or shorter in the second epidemic year (May 2010-April 2011) than those in the first epidemic year (May 2009-April 2010) (P<0.05), but similar to those of seasonal influenza (P>0.05). Similar to seasonal influenza, pre-existing chronic pulmonary diseases was a risk factor associated with fatal cases of pH1N1 influenza. Different from seasonal influenza, which occurred in spring/summer seasons annually, pH1N1 influenza mainly occurred in autumn/winter seasons in the first epidemic year, but prolonged to winter/spring season in the second epidemic year. The information suggests a tendency that the epidemics of pH1N1 influenza may probably further shift to spring/summer seasons and become a predominant subtype of seasonal influenza in coming years in Guangzhou, China

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats

Metatranscriptomic analysis revealed Prevotella as a potential biomarker of oropharyngeal microbiomes in SARS-CoV-2 infection

Background and objectivesDisease severity and prognosis of coronavirus disease 2019 (COVID-19) disease with other viral infections can be affected by the oropharyngeal microbiome. However, limited research had been carried out to uncover how these diseases are differentially affected by the oropharyngeal microbiome of the patient. Here, we aimed to explore the characteristics of the oropharyngeal microbiota of COVID-19 patients and compare them with those of patients with similar symptoms.MethodsCOVID-19 was diagnosed in patients through the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Characterization of the oropharyngeal microbiome was performed by metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 144 COVID-19 patients, 100 patients infected with other viruses, and 40 healthy volunteers.ResultsThe oropharyngeal microbiome diversity in patients with SARS-CoV-2 infection was different from that of patients with other infections. Prevotella and Aspergillus could play a role in the differentiation between patients with SARS-CoV-2 infection and patients with other infections. Prevotella could also influence the prognosis of COVID-19 through a mechanism that potentially involved the sphingolipid metabolism regulation pathway.ConclusionThe oropharyngeal microbiome characterization was different between SARS-CoV-2 infection and infections caused by other viruses. Prevotella could act as a biomarker for COVID-19 diagnosis and of host immune response evaluation in SARS-CoV-2 infection. In addition, the cross-talk among Prevotella, SARS-CoV-2, and sphingolipid metabolism pathways could provide a basis for the precise diagnosis, prevention, control, and treatment of COVID-19

An investigation of the prevalence rate of fatty liver disease among people undergoing physical examination in Tangshan, China

ObjectiveTo investigate the prevalence rate of fatty liver disease among people undergoing physical examination in Tangshan, China, and to provide a reasonable basis for the prevention and treatment of fatty liver disease. MethodsThe clinical data of 12 808 individuals who underwent physical examination in Tangshan from March 2014 to February 2016 were collected, and among these individuals, 3540 had fatty liver disease. The data including age, sex, body mass index (BMI), fasting plasma glucose (FPG), total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), and liver ultrasound findings were analyzed. The t-test was used for comparison of continuous data between groups and the chi-square test was used for comparison of categorical data between groups. Results Of all 7151 male individuals who underwent physical examination, 2750 (38.46%) had fatty liver disease, and of all 5657 female individuals, 790 (13.96%) had fatty liver disease; there was a significant difference in the prevalence rate of fatty liver disease between male and female individuals (χ2=947.25, P＜0.01). There was a significant difference in the detection rate of fatty liver disease between male and female individuals in each age group of 18-29, 30-39, 40-49, and ≥50 years (χ2=337.58, 474.06, 449.38, and 12.86, all P＜0.01). There was a significant difference in the detection rate of fatty liver disease between male or female individuals with different BMIs ［obese (BMI ≥28), overweight (24≤BMI＜28), and normal (BMI＜24)］ (χ2=1104.01 and 500.23, both P＜0.01). In the three groups of obese (BMI ≥28), overweight (24≤BMI＜28), and normal (BMI＜24) individuals who underwent physical examination, there was a significant difference in the detection rate of fatty liver disease between male and female individuals in each group (χ2=71.24, 87.97, and 323.84, all P＜0.01). Male and female individuals with obesity (BMI ≥28) and overweight (24≤BMI＜28) had a significantly higher detection rate of fatty liver disease than those with normal BMI (both P＜0.01). There were significant differences in FPG, TC, TG, and LDL-C between the fatty liver group and the non-fatty liver group (t=17.482, 13.698, 22.133, and 27.334, all P＜0001). In male individuals who underwent physical examination, there were significant differences in FPG, TC, TG, and LDL-C between the individuals with and without fatty liver disease (t=11.288,8.652,11.671, and 20.118, all P＜0.01); in female individuals, there were also significant differences in FPG, TC, TG, and LDL-C between the individuals with and without fatty liver disease (t=16.816, 5.532, 15.154, and 18.507, all P＜0.01). ConclusionAmong the adults undergoing physical examination in Tangshan, male adults have a significantly higher prevalence rate of fatty liver disease than female adults. Overweight or obesity, hyperlipidemia, and abnormal glucose metabolism are major causes of fatty liver disease