A5102769031- Genomics and Phylogenetic Studies
- Bacterial Identification and Susceptibility Testing
- Infective Endocarditis Diagnosis and Management
- SARS-CoV-2 detection and testing
- Advanced biosensing and bioanalysis techniques
- Mycobacterium research and diagnosis
- Nanopore and Nanochannel Transport Studies
- Glycogen Storage Diseases and Myoclonus
- Genetics and Neurodevelopmental Disorders
- SARS-CoV-2 and COVID-19 Research
- Chromosomal and Genetic Variations
- Genomic variations and chromosomal abnormalities
- Breast Lesions and Carcinomas
- Enzyme Catalysis and Immobilization
- Microbial Metabolic Engineering and Bioproduction
- Biosensors and Analytical Detection
- RNA modifications and cancer
- Biofuel production and bioconversion
- Gut microbiota and health
- Cancer-related molecular mechanisms research
- Ocular Infections and Treatments
- Neutropenia and Cancer Infections
- Coccidia and coccidiosis research
- Microbial Natural Products and Biosynthesis
- Peptidase Inhibition and Analysis
Wuhan University
2011-2023
Wuhan Institute of Bioengineering
2015-2019
University of South Dakota
2007
Abstract Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese HX1 by single-molecule real-time (SMRT) long-read sequencing, construct physical map NanoChannel arrays and generate 2.93 Gb (contig N50: 8.3 Mb, scaffold 22.0 including 39.3 Mb N-bases), together 206 alternative haplotypes. The fully or partially fills 274 (28.4%) N-gaps reference genome GRCh38....
Abstract Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome wild soybean accession W05, with final assembled size 1013.2 Mb and contig N50 3.3 Mb. The analytical power W05 is demonstrated by several examples. First, identify an inversion at locus determining seed coat color during domestication. Second, translocation event between chromosomes 11 13 some genotypes shown to...
The ongoing global novel coronavirus pneumonia COVID-19 outbreak has engendered numerous cases of infection and death. diagnosis relies upon nucleic acid detection; however, currently recommended methods exhibit high false-negative rates are unable to identify other respiratory virus infections, thereby resulting in patient misdiagnosis impeding epidemic containment. Combining the advantages targeted amplification long-read, real-time nanopore sequencing, herein, sequencing (NTS) is...
Testosterone deficiency can lead to depressive symptoms in humans; however, the causes of this are incompletely understood. Here, we isolated Mycobacterium neoaurum from fecal samples testosterone-deficient patients with depression and showed that strain could degrade testosterone vitro. Furthermore, gavaging rats M. reduced their serum brain levels induced depression-like behaviors. We identified gene encoding 3β-hydroxysteroid dehydrogenase (3β-HSD) as enzyme causing degradation....
PlantGDB ( http://www.plantgdb.org/ ) is a genomics database encompassing sequence data for green plants (Viridiplantae). provides annotated transcript assemblies > 100 plant species, with transcripts mapped to their cognate genomic context where available, integrated variety of analysis tools and web services. For 14 species emerging or complete genome sequence, PlantGDB's browsers (xGDB) serve as graphical interface viewing, evaluating annotating protein alignments chromosome bacterial...
Abstract Background The outbreak of COVID-2019 is becoming a global public health emergency. Although its basic clinical features have been reported, the dynamic characteristics immune system in patients, especially those critical patients with refractory hypoxemia, are not yet well understood. We aim to describe 3 and discuss relationship between hypoxemia severity cell levels, changes gut microbes patient. Methods This retrospective study from 2019-nCoV infection admitted Renmin Hospital...
A very recent outbreak of the novel coronavirus, COVID-19, in city Wuhan, China, December 2019 and its subsequent spread within across China have resulted several deaths infections. Presently, nucleic acid amplification test is essential for confirmation COVID infection. In this report, we summarized six promising methods, including whole-genome sequencing, real-time reverse transcription polymerase chain reaction, nanopore target antibody-based immunoassay techniques, use paper-based...
Pathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood valve cultures are gold standard IE pathogens detection, many cases culture-negative, especially in patients who had received long-term antibiotic treatment, has therefore become a major challenge clinic. Metagenomic sequencing can provide both information on pathogenic strain susceptibility profile patient samples without culturing, offering powerful method to...
Recent RNA-seq technology revealed thousands of splicing events that are under rapid evolution in primates, whereas the reliability these events, as well their combination on isoform level, have not been adequately addressed due to its limited sequencing length. Here, we performed comparative transcriptome analyses human and rhesus macaque cerebellum using single molecule long-read (Iso-seq) matched RNA-seq. Besides 359 million reads, 4,165,527 Iso-seq reads were generated with a mean length...
Abstract The ongoing novel coronavirus pneumonia COVID-19 outbreak in Wuhan, China, has engendered numerous cases of infection and death. diagnosis relies upon nucleic acid detection; however, current recommended methods exhibit high false-negative rates, low sensitivity, cannot identify other respiratory virus infections, thereby resulting patient misdiagnosis impeding epidemic containment. Combining the advantages target amplification long-read, real-time nanopore sequencing, we developed...
Small 2020, 16, 2002169 DOI: 10.1002/smll.202002169 In the originally published article, Data Availability paragraph of experimental section was mistakenly deleted during copyediting process. The original sequencing dataset has been submitted to China National Center for Bioinformation GSA database (http://ngdc.cncb.ac.cn/gsa/), with accession number CRA004499. This update can link research paper. editorial office apologizes any inconvenience caused.
Traditional microbiological methodology has limited sensitivity, detection range, and turnaround times in diagnosis of bloodstream infection Febrile Neutropenia (FN) patients. A more rapid sensitive technology is urgently needed. Here we used the newly developed Nanapore targeted sequencing (NTS) to diagnose pathogens blood samples. The diagnostic performance (sensitivity, specificity time) NTS 202 samples from FN patients with hematologic disease was evaluated comparison culture nested...
Cephalosporin-resistant Vibrio alginolyticus was first isolated from food products, with β-lactamases encoded by blaPER-1, blaVEB-1, and blaCMY-2 being the major mechanisms mediating their cephalosporin resistance. The complete sequence of a multidrug resistance plasmid, pVAS3-1, harboring qnrVC4 genes decoded in this study. Its backbone exhibited genetic homology to known IncA/C plasmids recoverable members family Enterobacteriaceae, suggesting its possible origin Enterobacteriaceae.
Microorganism identification is critical for the early diagnosis and management of infectious endophthalmitis, but traditional culture can yield false-negative results. Nanopore targeted sequencing (NTS) a third-generation technique with multiple advantages. This study aimed to test aqueous humour or vitreous fluid samples from presumed cases endophthalmitis using NTS evaluate feasibility in diagnosing especially culture-negative cases.This prospective enrolled patients who presented...
Quantifying the structural variants (SVs) in nonhuman primates could provide a niche to clarify genetic backgrounds underlying human-specific traits, but such resource is largely lacking. Here, we report an accurate SV map population of 562 rhesus macaques, verified by in-house benchmarks eight macaque genomes with long-read sequencing and another one genome assembly. This indicates stronger selective constrains on inversions at regulatory regions, suggesting strategy for prioritizing them...
Intronic (TTTCA)n insertions in the SAMD12, TNRC6A, and RAPGEF2 genes have been identified as causes of familial cortical myoclonic tremor with epilepsy.To identify cause epilepsy pedigrees without RAPGEF2.Repeat-primed polymerase chain reaction, long-range Sanger sequencing were performed to existence a novel (TTTGA)n insertion. Targeted long-read was confirm accurate structure insertion.We expanded intronic insertion at same site previously reported SAMD12. This cosegregated 1 Chinese...
The etiology of granulomatous lobular mastitis (GLM) remains unknown. This study aimed to detect bacteria in GLM using Nanopore sequencing and identify the relationship between Corynebacterium kroppenstedtii.The bacterial detection on fresh samples (including breast pus tissue) 50 patients nanopore culture methods. rate participants with different stages were compared analyzed. Formalin-fixed paraffin-embedded (FFPE) tissues from 39 performed Gram staining Gram-positive bacilli (GPB) within...
Abstract BACKGROUND As approximately 19% of global deaths are attributable to infectious diseases, early diagnosis infection is very important reduce mortality. Traditional detection strategies have limited sensitivity, range, and turnaround times; a technology that can simultaneously detect bacterial fungal infections within 24 h urgently need in clinical settings. METHODS We developed nanopore targeted sequencing (NTS) for same-day simultaneous Diagnosis infections. NTS was by...
The development of multivalent protein ligands for nanoparticles lags behind that multidentate polymers and small-molecule largely because a lack thorough understanding the interaction between multimeric proteins. Guided by crystal structures, we have harnessed recombinant technology to develop collection mCherry fused proteins with different spatial distributions quantum dot (QD)-binding sequence, hexahistidine tag (histag). All can behave as assemble ZnS-CdSe QDs through...
Unambiguous evidence indicates that microbes are closely linked to various human diseases, including cancer. Most prior work investigating the microbiome of breast tissue describes an association between compositional differences microbial species in benign and malignant tissues, but few studies have examined relative abundance communities within at level. In this work, a total 44 samples tissues with adjacent normal pairs were collected, Oxford Nanopore long-read sequencing was employed...
Abstract Purpose This paper aimed to assess the diagnostic utility of a newly developed gene-based technology-nanopore targeted sequencing (NTS) in suspected endophthalmitis patients. Methods retrospective study included 43 patients (44 eyes) with endophthalmitis. NTS was applied along microbiological culture detect unknown pathogens intraocular fluid samples. The mainly evaluated from three aspects, including positivity rate bacterial/fungal presence, turnaround time and frequency change...