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Distinct Responses of Mycobacterium smegmatis to Exposure to Low and High Levels of Hydrogen Peroxide

Hydrogen peroxide (H2O2) is a natural oxidant produced by aerobic organisms and gives rise to oxidative damage, including DNA mutations, protein inactivation and lipid damage. The genus Mycobacterium utilizes redox sensors and H2O2 scavenging enzymes for the detoxification of H2O2. To date, the precise response to oxidative stress has not been fully elucidated. Here, we compared...

Comparative genomic analysis of Acinetobacter baumannii clinical isolates reveals extensive genomic variation and diverse antibiotic resistance determinants

Background Acinetobacter baumannii is an important nosocomial pathogen that poses a serious health threat to immune-compromised patients. Due to its rapid ability to develop multidrug resistance (MDR), A. baumannii has increasingly become a focus of attention worldwide. To better understand the genetic variation and antibiotic resistance mechanisms of this bacterium at the...

RAID v2.0: an updated resource of RNA-associated interactions across organisms

With the development of biotechnologies and computational prediction algorithms, the number of experimental and computational prediction RNA-associated interactions has grown rapidly in recent years. However, diverse RNA-associated interactions are scattered over a wide variety of resources and organisms, whereas a fully comprehensive view of diverse RNA-associated interactions...

Comparative genomic analysis of Mycobacterium tuberculosis clinical isolates

Background Due to excessive antibiotic use, drug-resistant Mycobacterium tuberculosis has become a serious public health threat and a major obstacle to disease control in many countries. To better understand the evolution of drug-resistant M. tuberculosis strains, we performed whole genome sequencing for 7 M. tuberculosis clinical isolates with different antibiotic resistance...

A functional module-based exploration between inflammation and cancer in esophagus

• Google ScholarSearch for Yongfei Hu in:Nature Research journals • PubMed • Google ScholarSearch for Kongning Li in:Nature Research journals • PubMed • Google ScholarSearch for Hong Wang in:Nature Research ... contributed equally to this work. AffiliationsCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, ChinaNannan Liu, Chunhua Li, Yan Huang, Ying Yi, Yongfei

Structural Diversity of Class 1 Integrons and Their Associated Gene Cassettes in Klebsiella pneumoniae Isolates from a Hospital in China

BackgroundKlebsiella pneumoniae strains carrying class 1 integrons are becoming more common worldwide, and their role in the dissemination of drug resistance is significant. The aim of this study was to characterize the structural diversity of class 1 integrons and their associated gene cassettes in K. pneumoniae isolates from hospital settings. Methodology/Principal FindingsWe...

DNA microarray analysis reveals that antibiotic resistance-gene diversity in human gut microbiota is age related

Program. Author information Author notesNa Lu, Yongfei Hu & Liying Zhu These authors contributed equally to this work. AffiliationsCAS key Laboratory of Pathogenic Microbiology and Immunology, Institute ... of Microbiology, Chinese Academy of Sciences, Beijing, ChinaNa Lu, Yongfei Hu, Xi Yang & Baoli ZhuBeijing Key Laboratory of Microbial Drug Resistance and Resistome, Institute of Microbiology, Chinese

ViRBase: a resource for virus–host ncRNA-associated interactions

Increasing evidence reveals that diverse non-coding RNAs (ncRNAs) play critically important roles in viral infection. Viruses can use diverse ncRNAs to manipulate both cellular and viral gene expression to establish a host environment conducive to the completion of the viral life cycle. Many host cellular ncRNAs can also directly or indirectly influence viral replication and even...

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, ChinaGeorge F. Gao AuthorsSearch for Yongfei Hu in:Nature Research journals • PubMed • Google

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

Vega-Thurber Dionysios A. Antonopoulos Katie Barott Matthew T. Cottrell Christelle Desnues Elizabeth A. Dinsdale Mike Furlan Matthew Haynes Matthew R. Henn Yongfei Hu David L. Kirchman Tracey McDole John