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Infer HIV transmission dynamics from gene sequences among young men who have sex with men in China

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Infectious Disease Modelling 2021年第1期6卷 832-838页

作者： Xin Jin Jinjin Cheng Jie Lou Department of Mathematics Shanghai University99 Shangda RoadShanghai200444PR China

To investigate the transmission dynamics and temporal and spatial migration characteristics of HIV spread among men who have sex with men(MSM)in China,a total of 1012 HIV-1 partial pol sequences,including five subtypes,were *** analysis were applied for each subtype to infer its dynamic characters including the effective reproductive number(R_(e))and migration *** mean curve of each R_(e) was almost always greater than 1(even the 95%highest posterior density(HPD)lower value)along with time,which supports the necessity for a comprehensive study about risk behaviors among young MSM group in *** also should reappraise the free treatment strategy,especially the therapeutic effect during the free treatment policy.

关键词： HIV gene sequence Transmission dynamics Bayesian analysis Effective reproductive number

Effect of Different Bacterial-Feeding Nematode Species on Soil Bacterial Numbers,Activity,and Community Composition

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Pedosphere 2014年第1期24卷 116-124页

作者： XIAO Hai-Feng LI Gen LI Da-Ming HU Feng LI Hui-Xin Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences College of Resources and Environmental Sciences Nanjing Agricultural University

The effects of bacterial-feeding nematodes on bacterial number, activity, and community composition were studied through a microcosm experiment using sterilized soil inoculated with soil bacteria （soil suspension） and with bacteria and three species of bacterial-feeding nematodes （ Cephalobus persegnis, Protorhabditis filiformis, and Caenorhabditis elegans）. Catalyzed reporter deposition-fluorescence in situ hybridization, CO2 evolution, and denaturing gradient gel electrophoresis （DGGE） of PCR ampli- fied 16S rRNA gene fragments were used to investigate bacterial numbers, antivity, and community composition, respectively. Our results showed that bacterial numbers and activity significantly increased in the presence of bacterial-feeding nematodes, which indicated that bacterial-feeding nematodes had a significant positive effect on soil bacteria. The different nematode species had different effects on bacterial numbers and activity. C. persegnis and P. filiformis, isolated from native soil, increased the bacterial number and activity more than C. elegans. The DGGE analysis results showed that dominant bacterial species significantly differed among the treatments, which suggested that bacterial-feeding nematode species modified the bacterial community composition in soil. Further gene sequence analysis results showed that the dominant bacterial species in this study were gram-negative bacteria. Given the completely same conditions except nematode species, the varied selective feeding behavior of different nematode species was the most likely reason for the altered bacterial community composition. Overall, the alteration of bacterial numbers, activity and community composition resulting from the bacterial-feeding nematodes may ult!mately affect soil ecological functioning and processes.

关键词： CARD-FISH CO2 evolution DGGE gene sequence gram-negative bacteria

New Primers for Denaturing Gradient Gel Electrophoresis Analysis of Nitrate-Reducing Bacterial Community in Soil

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Pedosphere 2013年第3期23卷 340-349页

作者： R.PASTORELLI R.PICCOLO S.SIMONCINI S.LANDI Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Centro di Ricerca per l'Agrobiologia e la Pedologia CRA-ABP

The narG gene is frequently used as a molecular marker for bacterial nitrate-reducing community analysis. In this study, a new set of primers targeting the narG gene was designed and applied to semi-nested polymerase chain reaction-denaturing gradient gel electrophoresis （PCR-DGGE） assay. The potential of the new primers was verified on DNA directly extracted from soils from five different experimental sites distributed in Central and Southern Italy. Specificity of the primers was determined by excision, amplification, and sequencing of bands resolved by DGGE. A phylogenetic analysis showed the correlation between the sequences retrieved from the soils studied and the narG sequences from βand y-Proteobacteria. These primers expanded the existing molecular tools for ecological study on the size and diversity of nitrate-reducing bacterial community in soil.

关键词： DNA gene sequence narG phylogenetic analysis Proteobacteria

Malignant solitary fibrous tumor of the greater omentum: A case report and review of literature

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World Journal of Clinical Cases 2021年第2期9卷 445-456页

作者： Yu-Chen Guo Li-Yu Yao Zhi-Sen Tian Bing Shi Ying Liu Yuan-Yi Wang Department of Gastrointestinal Surgery The First Hospital of Jilin UniversityChangchun 130021Jilin ProvinceChina Department of Pediatric Surgery The First Hospital of Jilin UniversityChangchun 130021Jilin ProvinceChina Department of Spine Surgery China-Japan Union Hospital of Jilin UniversityChangchun 130021Jilin ProvinceChina Department of Gastroenterology The First Hospital of Jilin UniversityChangchun 130021Jilin ProvinceChina Department of Spine Surgery The First Hospital of Jilin UniversityChangchun 130021Jilin ProvinceChina

BACKGROUND Malignant solitary fibrous tumors(SFTs)account for 15%-20%of all SFTs,and malignant SFTs arising from the greater omentum are extremely *** malignant SFTs of the greater omentum are diagnosed via pathological examinations after *** this study,we report a case of malignant omental SFT and review the published literature on this rare *** SUMMARY A 64-year-old female presented with an abdominal mass,and underwent exploratory surgery,during which a huge tumor originating from the greater omentum and intraperitoneal implants were identified and *** results of the pathological examination,immunohistochemistry staining,and gene sequencing led to the diagnosis of malignant SFT of the greater *** patient died one and a half years later due to tumor recurrence and *** This is the first report of the application of gene sequencing in the diagnosis of malignant SFTs of the greater omentum.

关键词： Solitary fibrous tumor Omentum malignancy Peritoneal implant Hemangiopericytoma gene sequence Case report

An Approach for Searching Insertions in Bacterial genes Leading to the Phase Shift of Triplet Periodicity

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Genomics, Proteomics & Bioinformatics 2011年第4期9卷 158-170页

作者： Maria A. Korotkova Nikolay A. Kudryashov Eugene V. Korotkov Centre of Bioengineering Russian Academy of Sciences National University of Nuclear Investigations (MIFI)

The concept of the phase shift of triplet periodicity （TP） was used for searching potential DNA insertions in genes from 17 bacterial genomes. A mathematical algorithm for detection of these insertions has been developed. This approach can detect potential insertions and deletions with lengths that are not multiples of three bases, especially insertions of relatively large DNA fragments （〉 100 bases）. New similarity measure between triplet matrixes was employed to improve the sensitivity for detecting the TP phase shift. sequences of 17,220 bacterial genes with each consisting of more than 1,200 bases were analyzed, and the presence of a TP phase shift has been shown in -16% of analysed genes （2,809 genes）, which is about 4 times more than that detected in our previous work. We propose that shifts of the TP phase may indicate the shifts of reading frame in genes after insertions of the DNA fragments with lengths that are not multiples of three bases. A relationship between the phase shifts of TP and the frame shifts in genes is discussed.

关键词： triplet periodicity insertion gene sequence reading frame phase shift change-point problem

Application of gene sequencing directly to identify the pathogens in specimens

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Chinese Medical Journal 2010年第24期123卷 3534-3539页

作者： LU Xin-xin YUAN Liang WAN Xiao-hua GENG Jia-jing Department of Laboratory Medicine Beijing Tongren Hospital Capital Medical University Beijing 100730 China

Background Accurate identification of bacterial isolates is an essential task in clinical microbiology. This study compared culturing to analyzing 16S rRNA gene sequences as methods to identify bacteria in clinical samples. We developed a key technique to directly identify bacteria in clinical samples via nucleic acid sequences, thus improving the ability to confirm *** We obtained 225 samples from Beijing Tongran Hospital and examined them by conventional culture and 16S rDNA sequencing to identify pathogens. This study made use of a modified sample pre-treatment technique which came from our laboratory to extract DNA. 16S rDNA was amplified by PCR. The amplified product was sequenced on a CEQ8000 capillary sequencer. sequences were uploaded to the GenBank BLAST database for *** Among the positively cultivated bacterial strains, seven strains were identified differently by Vitek32 and by 16S rDNA sequencing. Twelve samples that were negative by standard culturing were determined to have pathogens by sequence *** The use of 16S rRNA gene sequencing can improve clinical microbiology by providing better identification of unidentified bacteria or providing reference identification of unusual strains.

关键词： pathogen gene sequence specimens

Preparation and Identification of scFv and bsFv against Transferrin Receptor

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Journal of Huazhong University of Science and Technology(Medical Sciences) 2008年第6期28卷 621-625页

作者：刘静肖代雯周小鸥文雪代红王志华沈昕代维杨道锋沈关心 Department of Immunology Tongji Medical CollegeHuazhong University of Science and Technology Clinical Laboratory Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital Department of Microbiology Jiujiang Medical College Department of Infectious Diseases Tongji HospitalTongji Medical CollegeHuazhong University of Science and Technology

To obtain single chain variable fragment （scFv） and bivalent single chain variable fragment （bsFv） against transferrin receptor, up-stream and down-stream primers were designed according to the complementary sequences of FR1 region of variable heavy （VH） and FR4 of variable light （VL）, respectively, which contained inter-linker G4S and the restriction endonuclease SfiI, AscI and NotI. Two pieces of scFv fragments were first amplified through PCR and then inserted into plasmid pAB1, which could express scFv protein once induced by IPTG in the host bacteria. To express scFv and bsFv, E. coli TG1 was cultured in LB broth and was induced by IPTG. The restriction enzyme digestion map and DNA sequencing demonstrated that scFv and bsFv genes were successfully inserted into the expression plasmid. SDS-PAGE and Western blotting revealed the protein band at 35kD and 60kD, which were consistent with the molecular weight of scFv and bsFv respectively. Flow cytometry showed that scFv and bsFv harbored the specific binding activity with TfR expressed in various tumor cells, and the avidity of bsFv was higher than that of the parent scFv.

关键词： gene sequence G4S linker scFv bsFv transferrin receptor