A5040820400- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Gut microbiota and health
- Antibiotic Resistance in Bacteria
- RNA and protein synthesis mechanisms
- Muscle Physiology and Disorders
- Microbial infections and disease research
- Probiotics and Fermented Foods
- Machine Learning in Bioinformatics
- Bacterial Genetics and Biotechnology
- Microbial Community Ecology and Physiology
- Bacterial biofilms and quorum sensing
- Animal Virus Infections Studies
- Hepatitis B Virus Studies
- Infant Nutrition and Health
- Adipokines, Inflammation, and Metabolic Diseases
- Exercise and Physiological Responses
- Virus-based gene therapy research
- Mycobacterium research and diagnosis
- Pediatric health and respiratory diseases
- Glycosylation and Glycoproteins Research
- Advanced Proteomics Techniques and Applications
- SARS-CoV-2 and COVID-19 Research
- Vibrio bacteria research studies
- Food Supply Chain Traceability
Qingdao Agricultural University
2025
Northwest A&F University
2024-2025
First Hospital of Jiaxing
2025
Chongqing Medical University
2021-2024
Dalian Medical University
2021-2024
Second Affiliated Hospital of Chongqing Medical University
2021-2024
Shanghai Veterinary Research Institute
2024
Wuhan Institute of Technology
2024
European Bioinformatics Institute
2024
Nanfang Hospital
2016-2023
FASTA and FASTQ are basic ubiquitous formats for storing nucleotide protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, sampling. Existing tools only implement some these manipulations, not particularly efficiently, available certain operating systems. Furthermore, the complicated installation process required packages running environments can render programs less user friendly. This paper describes a...
With the emergence of multidrug-resistant and extensively drug-resistant bacterial pathogens, phage therapy other alternative or additional therapeutic modalities are receiving resurgent attention. One major obstacles in developing effective therapies is evolution resistance host. When Pseudomonas aeruginosa was infected with a that uses O-antigen as receptor, resistances typically achieved through changing loss structure. In this study, we showed dsRNA phiYY core lipopolysaccharide receptor...
Abstract In the era of ubiquitous high‐throughput sequencing studies, there is a growing need for analysis tools that are not just performant but also comprehensive and user‐friendly enough to cater both novice advanced users. This article introduces SeqKit2, next iteration widely used sequence tool SeqKit, featuring expanded functionality, performance optimizations, support additional compression methods. Retaining pragmatic subcommand architecture, SeqKit2 represents substantial...
Abstract The bacterial sequence data publicly available at the global DNA archives is a vast source of information on evolution bacteria and their mobile elements. However, most it either unassembled or inconsistently assembled QC-ed. This makes unsuitable for large-scale analyses, inaccessible researchers to use. In 2021 Blackwell et al therefore released uniformly set 661,405 genomes, consisting all whole genome sequenced isolate as November 2018, along with various search indexes. this...
Recent studies have shown that myostatin, first identified as a negative regulator of skeletal muscle growth, may also be involved in the formation fibrosis within muscle. In this study, we further explored potential role myostatin fibrosis, well its interaction with both transforming growth factor-β1 and decorin. We discovered stimulated fibroblast proliferation vitro induced differentiation into myofibroblasts. found expression, conversely, secretion C2C12 myoblasts. Decorin, small...
Capsaicin reduces body weight mainly through activation of transient receptor potential vanilloid 1 (TRPV1) cation channel. However, recent evidence indicates that the gut microbiota influences many physiological processes in host and might provoke obesity. This study determined whether anti-obesity effect capsaicin is related to changes microbiota. C57BL/6 mice were fed either with high-fat diet (HFD) or HFD (HFD-CAP) for nine weeks. We observed a significantly reduced gain improved glucose...
Abstract Background and Aims The safety antibody responses of coronavirus disease 2019 (COVID‐19) vaccination in patients with chronic hepatitis B (CHB) virus infection is still unclear, exploration COVID‐19 CHB significant clinical practice. Methods 362 adult 87 healthy controls at an interval least 21 days after a full‐course (21–105 days) were enrolled. Adverse events (AEs) collected by questionnaire. profiles 1, 2 3 months elucidated determination anti‐spike IgG, anti‐receptor‐binding...
Abstract Motivation The growing number of microbial reference genomes enables the improvement metagenomic profiling accuracy but also imposes greater requirements on indexing efficiency, database size and runtime taxonomic profilers. Additionally, most profilers focus mainly bacterial, archaeal fungal populations, while less attention is paid to viral communities. Results We present KMCP (K-mer-based Metagenomic Classification Profiling), a novel k-mer-based tool that utilizes genome...
Bacteriophages (phages) play critical roles in modulating microbial ecology. Within the human microbiome, factors influencing long-term coexistence of phages and bacteria remain poorly investigated. Saccharibacteria (formerly TM7) are ubiquitous members oral microbiome. These ultrasmall form episymbiotic relationships with their host impact physiology. Here, we showed that during surface-associated growth, a isolate (named TM7x) protects its bacterium, Schaalia odontolytica strain XH001)...
As an important physiological indicator, wheat canopy temperature (CT) can be observed after flowering in attempt to predict yield and quality. However, the relationship between CT quality is not clear. In this study, CT, photosynthetic rate (Pn), filling rate, yield, of 68 lines were measured, establish a connection accelerate selection new varieties. This experiment used infrared imaging camera measure materials planted field 2022. Twenty with significant differences selected for planting...
Abstract Inflammation, an important phase of skeletal muscle healing, largely involves macrophages, TGF‐β1, and the COX‐2 pathway. To improve our understanding how these molecules interact during all phases we examined their roles in cells vitro vivo. Initially, found that depletion macrophages tissue led to reduced regeneration. Macrophages may influence healing by inducing production TGF‐β1 PGE 2 different cell types. We then addition induced cells, effect probably mediated enzyme. It was...
Abstract Summary TaxonKit is a command-line toolkit for rapid manipulation of NCBI taxonomy data. It provides executable binary files major operating systems including Windows, Linux, and Mac OS X, can be directly used without any dependencies nor local database buiding. demonstrates competitive performance in execution time compared to similar tools. The efficiency, scalability, usability enable researchers rapidly investigate Availability Taxonkit implemented Go programming language....
Nonsteroidal anti-inflammatory drugs (NSAIDs) are commonly used to treat skeletal muscle injury. However, studies have shown that NSAIDs may be detrimental the healing process. Mediated by prostaglandin F(2alpha) (PGF(2alpha)) and E(2) (PGE(2)), cycloxygenase-2 (COX-2) pathway plays an important role in healing. We hypothesize COX-2 is for fusion of cells regeneration injured muscle. For vitro experiments, we isolated myogenic precursor from wild-type (Wt) gene-deficient (COX-2(-/-)) mice...
Pseudomonas aeruginosa is an opportunistic pathogen with a relatively large genome, and has been shown to routinely lose genomic fragments during environmental selection. However, the underlying molecular mechanisms that promote chromosomal deletion are still poorly understood. In recent study, we showed by deleting fragment containing two closely situated genes, hmgA galU, P. was able form 'brown mutants', bacteriophage (phage) resistant mutants brown color phenotype. this show occur at...
Abstract The interactions between Bacteriophage (phage) and host bacteria are widespread in nature influences of phage replication on the cells complex extensive. Here, we investigate genome-wide Pseudomonas aeruginosa ( P. aeruginosa) its temperate PaP3 at five time points during infection. Compared to uninfected host, 38% (2160/5633) genes phage-infected were identified as differentially expressed (DEGs). Functional analysis repressed DEGs revealed infection-stage-dependent pathway...
Bacteriophages (phages) are widely distributed in the biosphere and play a key role modulating microbial ecology soil, ocean, humans. Although of DNA bacteriophages is well described, biology RNA poorly understood. More than 1900 phage genomes currently deposited NCBI, but only 6 dsRNA 12 ssRNA genome sequences reported. The were isolated from legume samples or lakes with Pseudomonas syringae as host. Here, we report first aeruginosa phiYY three-segmented genome. was hospital sewage China...
Acinetobacter baumannii has emerged as one of the most important hospital-acquired pathogens in world, because its resistance to almost all available antibiotic drugs. Endolysins from phages are attracting increasing interest potential antimicrobial agents, especially for drug-resistant bacteria. We previously isolated and characterized Abp1, a virulent phage targeting multidrug-resistant A. strain, AB1. To evaluate endolysin Abp1 phage, gene plyAB1 was cloned over-expressed Escherichia...
Toxin-antitoxin (TA) systems are small genetic modules that widely distributed in the genomes of bacteria and archaea have been proposed to fulfill numerous functions. Here, we describe identification characterization a type II TA system, comprising hicAB locus human opportunistic pathogen Pseudomonas aeruginosa. The consists genes hicA hicB encoding toxin its cognate antitoxin, respectively. BLAST analysis revealed is prevalent approximately 36% P. aeruginosa strains locates same genomic...
The basic biology of bacteriophage–host interactions has attracted increasing attention due to a renewed interest in the therapeutic potential bacteriophages. In addition, knowledge host pathways inhibited by phage may provide clues novel drug targets. However, effect on bacterial gene expression and metabolism is still poorly understood. this study, we tracked phage–host combining transcriptomic metabolomic analyses Pseudomonas aeruginosa infected with lytic bacteriophage, PaP1. Compared...