A5064240120- RNA and protein synthesis mechanisms
- Tuberculosis Research and Epidemiology
- Mycobacterium research and diagnosis
- Molecular Biology Techniques and Applications
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Antibiotic Resistance in Bacteria
- CRISPR and Genetic Engineering
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- RNA modifications and cancer
- Cocoa and Sweet Potato Agronomy
- DNA Repair Mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Biochemical and Molecular Research
- Plant-Microbe Interactions and Immunity
- Infectious Diseases and Tuberculosis
- Plant Gene Expression Analysis
- HIV/AIDS drug development and treatment
- Microbial Metabolism and Applications
- RNA Interference and Gene Delivery
- Pneumocystis jirovecii pneumonia detection and treatment
- Innovative Microfluidic and Catalytic Techniques Innovation
- Advanced Electron Microscopy Techniques and Applications
- Circular RNAs in diseases
Fujian Agriculture and Forestry University
2007-2025
Longyan University
2023
National Institute of Diabetes and Digestive and Kidney Diseases
2014-2019
National Institutes of Health
2014-2019
Institute of Biophysics
2011
Chinese Academy of Sciences
2011
University of Chinese Academy of Sciences
2011
Structures of the simplest replisome The DNA performs concerted parental-strand separation and synthesis on both strands. Gao et al. report cryo–electron microscopy structures minimum set bacteriophage T7 proteins that can carry out leading- lagging-strand at replication fork (see Perspective by Li O'Donnell). Three key enzymes involved in replication—DNA polymerase, helicase, primase—were visualized complex with substrate DNA, demonstrating their highly dynamic organizations Comparison...
To investigate the mutations within whole rpoB gene of Mycobacterium tuberculosis and analyze their effects on rifampin (RIF) resistance based crystal structure.We sequenced entire in 175 isolates quantified minimum inhibitory concentrations using microplate-based assays. Additionally, structural interactions between wild-type/mutant RpoB RIF were also analyzed.Results revealed that a total 34 distributed across 17 different sites identified. Of mutations, 25 could alter interaction...
To assess the mutation effects of ethambutol (EMB) resistance-associated genes, including embCAB operon, ubiA, embR, and aftA, on EMB resistance levels among multidrug-resistant tuberculosis (MDR-TB) isolates from China. A total 159 MDR-TB China had their MICs quantified, sequences four regions were analyzed. multivariate regression model was established to evaluate mutations resistance. Our results showed that overall 95.6% (109/114 isolates) EMB-resistant harbored at least one within...
The enzyme MGG_00097 from rice blast fungus (<i>Magnaporthe grisea</i>) is a NADPH-dependent oxidoreductase, involved in synthesizing glycerol dihydroxyacetone phosphate and dihydroxyacetone. 35.5-kDa monomer belongs to the aldo-keto reductase superfamily, characterized by highly conserved catalytic tetrad. This study, elucidates expression, purification, kinetic properties of recombinant MGG_00097. ternary complex with NADP<sup>+</sup> was refined 2.9 Å resolution,...
The DNA cutting and joining reactions of HIV-1 integration are catalyzed by integrase (IN), a viral protein that functions as tetramer bridging the two ends (intasome). Two major obstacles for biochemical structural studies intasomes 1) low efficiency assembly with oligonucleotide substrates, 2) non-specific aggregation both free IN in reaction mixture. By fusing small binding protein, Sulfolobus solfataricus chromosomal Sso7d (PDB: 1BNZ), we have engineered highly soluble hyperactive IN....
Sweet potato production is constrained by Fusarium wilt, which caused oxysporum f. sp. batatas (Fob). The identification of genes related to disease resistance and the underlying mechanisms will contribute improving via sweet breeding programs. In present study, we performed de novo transcriptome assembly digital gene expression (DGE) profiling challenged with Fob using Illumina HiSeq technology. total, 89,944,188 clean reads were generated from 12 samples assembled into 101,988 unigenes an...
With the increasing incidence of drug-resistant tuberculosis (DR-TB), determining a rapid and accurate drug susceptibility testing (DST) method to identify ethambutol (EMB) resistance in Mycobacterium has become essential for patient management China. Herein, we evaluated correlation between three phenotypic DST methods, namely, proportion (PM), MGIT 960 system, microplate alamar Blue assay (MABA), DNA sequencing embAB 118 M. isolates from When results methods were compared with those...
Abstract DNA polymerase III (DNA pol III) is a multi-subunit replication machine responsible for the accurate and rapid of bacterial genomes, however, how it functions in Mycobacterium tuberculosis ( Mtb ) requires further investigation. We have reconstituted leading-strand process holoenzyme vitro investigated physical functional relationships between its key components. verify presence an αβ 2 ε polymerase-clamp-exonuclease replicase complex by biochemical methods protein-protein...
To assess the relationship between variant rpoB mutations and degree of rifampin (RIF)/rifabutin (RFB) resistance in Mycobacterium tuberculosis (M. tuberculosis).We analyzed whole gene 177 M. clinical isolates quantified their minimum inhibitory concentrations (MICs) using microplate-based assays.The results revealed that isolates, 116 were resistant to both RIF RFB. There 38 mutated patterns within sequenced 120 isolates. Statistical analysis indicated mutations, S450L, H445D, H445Y, H445R,...
Researchers often need to synthesize genes of interest in this era synthetic biology. Gene synthesis by PCR assembly multiple DNA fragments is a quick and economical method that widely applied. Up now, there have been few software solutions for designing gene synthesis. However, some these use programming languages are not popular other products commercial or require users visit servers. In study, we propose Python program design The algorithm designed meet the experimental needs. Also,...
Retroviral DNA integration is mediated by nucleoprotein complexes (intasomes) comprising a pair of viral ends synapsed tetramer integrase. Current integrase inhibitors act on intasomes rather than free protein. Structural and functional studies are essential to understand their mechanism action how the virus can escape mutation. To date, prototype foamy (PFV) only retrovirus for which high-resolution structures have been determined. In PFV intasome structure, core domains outer subunits...
To determine which genes are important in placenta by network analysis.Placenta expressing were screened from RNA-Seq data. Protein-protein interaction data downloaded STRING (v11.0) database. Google PageRank (PR) algorithm was used to identify placental protein network. Six disease-related datasets NCBI GEO database, and the differential expression of 99 identified.We calculated PR for each gene defined top with high as genes. GAPDH has highest PR. The had different pattern cell types. FN1...
Primer design is essential to conduct whole plasmid site-directed mutagenesis for protein study. Traditionally, primers of are designed manually that time-consuming and fallible. Here, we present a Python script searching by presetting parameters nucleotide composition percentage guanine-cytosine (GC content). The running results showed the able search with mutations target residue automatically. This may facilitate primer aid mutant construction.
The Fusarium wilt disease caused by oxysporum f. sp. batatas (Fob) is one of the devastating diseases sweetpotato. However, molecular mechanisms sweetpotato response to Fob poorly understood. In present study, comparative quantitative proteomic analysis was conducted investigate defense involved. Two cultivars with differential infection responses were inoculated spore suspensions and quantitatively analyzed Tandem Mass Tags (TMT). 2267 proteins identified 1897 them quantified. There 817...
Gene cloning is an important step in investigating gene structure and function. To verify sequence, Sanger sequencing used, which may produce several overlapping files that need to be merged before alignment the target sequence performed. Previously, we reported Python program Merge sequences ( https://peerj.com/articles/11354/ ), ran command line relied heavily on EMBOSS suite. In this updated version of program, have made remarkable improvements. It provides a graphical user interface...
Objective: To explore the association between variant mutations within embB and ubiA , degree of ethambutol (EMB) resistance Mycobacterium tuberculosis ( M. ) isolates. Methods: A total 146 isolates were used to determine minimum inhibitory concentrations (MICs) EMB with a 96-well microplate-based assay. The among these identified DNA sequencing. Moreover, multivariate regression model computer established assess effects on resistance. Results: Our data showed that overall 100 exhibited 28...
Due to the codon bias of different species, optimization is usually carried out in process heterologous protein expression. At present, there are a variety tools. However, optimized sequences may still have high or low points local guanine and cytosine (GC) content, which not conducive primer design gene subcloning, also makes it difficult perform experiment synthesizing whole with DNA fragments by polymerase chain reaction (PCR) reaction. In this study, we present stand-alone software...
Abstract Machine learning is used to investigate the codon usage of protein-encoding genes, which one fundamental questions molecular biology. The presentation, parameter learning, and decoding conditional random field (CRF) model are implemented then utilized analyze genes Escherichia coli its phages. Most E. use codons conforming weights determined by all genes. Phages like their host . Finally, study evaluates several example in context model. These results help understand