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next-generation sequencing of MHC Class Ⅰ Genes Reveals Trans-species Polymorphism in Eutropis multifasciata and Other Species of Scincidae

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Asian Herpetological Research 2023年第4期14卷 261-270页

作者： Shufang ZHANG Youfu LIN Yingzhi CHENG Haiyun YANG Xiaming ZHU Yu DU Longhui LIN Yanfu QU LianCHEN Hong LI College of Life Sciences Nanjing Normal UniversityNanjing 210023JiangsuChina College of Life Sciences Nanjing Forestry UniversityNanjing 210037JiangsuChina Hainan Key Laboratory of Herpetological Research College of Fisheries and Life ScienceHainan Tropical Ocean UniversitySanya 572022HainanChina Herpetological Research Center College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou 311121ZhejiangChina

The genes of the major histocompatibility complex(MHC) encode cell surface proteins that are essential for adaptive immunity. MHC genes show the most prominent genetic diversity in vertebrates,reflecting the adaptation of populations to their evolving environment, population survival and reproduction. In the present study, we used nextgeneration sequencing(NGS) to study the loci polymorphism of exon 3 of the MHC class Ⅰ genes in an ovoviviparous skink, the many-lined sun skink,Eutropis multifasciata and five other species of Scincidae, to quantify genetic variation. In addition,we genotyped the same MHC class Ⅰ genes of *** using clone sequencing, to directly compare the effectiveness of both analytical techniques for MHC genotyping. NGS detected 20MHC class Ⅰ alleles in E. multifasciata, and 2 to 15 alleles in the other five Scincidae species. However,clone sequencing detected only 15 of those MHC class Ⅰ alleles in E. multifasciata. In addition, transspecies polymorphism of MHC class Ⅰ genes was studied by constructing a phylogenetic tree using the gene sequences obtained by NGS. Phylogenetic analysis revealed that MHC class I alleles were shared among different species of Scincidae with trans-species polymorphism, and did not exhibit specific genealogical inheritance. These results have important implications for understanding polymorphism interspecies diversity in the MHC genes of Scincidae, and the evolution of the MHC more broadly.

关键词： Eutropis multifasciata major histocompatibility complex next-generation sequencing Scincidae trans-species polymorphism

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next-generation sequencing:toward an increase in the diagnostic yield in patients with apparently idiopathic spermatogenic failure

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Asian Journal of Andrology 2021年第1期23卷 24-29页

作者： Rossella Cannarella Rosita A Condorelli Stefano Paolacci Federica Barbagallo Giulia Guerri Matteo Bertelli Sandro La Vignera Aldo E Calogero Department of Clinical and Experimental Medicine University of CataniaCatania 95123Italy MAGI EUREGIO Bolzano 39100Italy

A large proportion of patients with idiopathic spermatogenic failure(SPGF;oligozoospermia or nonobstructive azoospermia[NOA])do not receive a diagnosis despite an extensive diagnostic *** evidence has shown that the etiology remains undefined in up to 75%of these patients.A number of genes involved in germ-cell proliferation,spermatocyte meiotic divisions,and spermatid development have been called into play in the pathogenesis of idiopathic oligozoospermia or ***,this evidence mainly comes from case ***,this study was undertaken to identify the molecular causes of *** accomplish this,15 genes(USP9Y,NR5A1,KLHL10,ZMYND15,PLK4,TEX15,TEX11,MEIOB,SOHLH1,HSF2,SYCP3,TAF4B,NANOS1,SYCE1,and RHOXF2)involved in idiopathic SPGF were simultaneously analyzed in a cohort of 25 patients with idiopathic oligozoospermia or NOA,accurately selected after a thorough diagnostic *** next-generation sequencing(NGS)analysis,we identified the presence of rare variants in the NR5A1 and TEX11 genes with a pathogenic role in 3/25(12.0%)*** other different variants were identified,and among them,13 have never been reported *** out of 17 variants were likely pathogenic and deserve functional or segregation *** genes most frequently mutated were MEIOB,followed by USP9Y,KLHL10,NR5A1,and *** alterations were found in the SYCP3,TAF4B,NANOS1,SYCE1,or RH0XF2 *** conclusion,NGS technology,by screening a specific custom-made panel of genes,could help increase the diagnostic rate in patients with idiopathic oligozoospermia or NOA.

关键词： azoospermia next-generation sequencing oligozoospermia spermatogenetic failure

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next-generation sequencing-based analysis of the effect of N^(6)-methyldeoxyadenosine modification on DNA replication in human cells

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Chinese Chemical Letters 2022年第4期33卷 2077-2080页

作者： Juan Wang Yuwei Sheng Ying Yang Xiaoxia Dai Changjun You Molecular Science and Biomedicine Laboratory State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan Provincial Key Laboratory of Biomacromolecular Chemical BiologyHunan UniversityChangsha 410082China

N^(6)-methyldeoxyadenosine(6 mdA) modification is considered as a new epigenetic mark that may play important roles in various biological ***,it remains unclear about the effect of 6 mdA on DNA replication in human ***,we combined next-generation sequencing with shuttle vector technology to explore how 6 mdA affects the efficiency and accuracy of DNA replication in human *** results showed that 6 mdA neither blocked DNA replication nor induced mutations in human ***,we found that the depletion of translesion synthesis DNA polymerase(Pol) κ,Pol η,Pol ι or Pol ζ did not significantly change the biological consequences of 6 mdA during replication in human *** negligible impact of 6 mdA on DNA replication is consistent with its potential role in epigenetic gene expression.

关键词： N^(6)-methyldeoxyadenosine DNA replication next-generation sequencing Shuttle vector technology Translesion synthesis DNA polymerase

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next-generation sequencing revealed specific microbial symbionts in Porites lutea with pigment abnormalities in North Sulawesi, Indonesia

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Acta Oceanologica Sinica 2018年第12期37卷 78-84页

作者： OU Danyun CHEN Bin HADI Tri Aryono SUHARSONO NIU Wentao ALFIANSAH Yustian Rovi Third Institute of Oceanography Ministry of Natural Resources Research Center for Oceanography Indonesian Institute of Sciences

Bacterial diseases affecting corals pose an enormous threat to the health of coral reefs. The relationship between certain bacterial species and coral diseases remain largely unknown. Pigment abnormalities are common in Porites lutea. Here we used Illumina 16S rRNA gene sequencing to analyze the bacterial communities associated with healthy P. lutea and P. lutea with pigment abnormalities. We observed an increase of alpha diversity of the bacterial community of P. lutea with pigment abnormalities, relative to healthy corals. We then identified changes in the abundance of individual operational taxonomic units(OTUs) between pigmented and healthy corals. We were able to identify eight OTUs associated with pigment abnormalities, which are possibly the causative agents of pigment abnormalities.

关键词： Porites lutea pigment abnormalities next-generation sequencing 16S rRNA bacterial diversity

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next-generation sequencing technology for diagnosis and efficacy evaluation of a patient with visceral leishmaniasis: A case report

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World Journal of Clinical Cases 2021年第32期9卷 9903-9910页

作者： Zhou-Ning Lin Yong-Cheng Sun Jia-Ping Wang Yan-Li Lai Li-Xia Sheng Internal Medicine School of Medicine Ningbo UniversityNingbo 315000Zhejiang ProvinceChina Department of Hematology Ningbo First HospitalNingbo 315000Zhejiang ProvinceChina

BACKGROUND Visceral leishmaniasis(VL)is a parasitic disease caused by Leishmania and transmitted by infected sand *** has a low incidence in China,and its clinical presentation is complex and *** disease is easily misdiagnosed and can become life-threatening within a short period of ***,early,rapid and accurate diagnosis and treatment of the disease are *** SUMMARY A 25-year-old male patient presented with the clinical manifestations of irregular fever,hepatosplenomegaly,increased polyclonal globulin,and *** first bone marrow puncture biopsy did not provide a clear *** order to relieve the pressure and discomfort of the organs caused by the enlarged spleen and to confirm the diagnosis,splenectomy was performed,and hemophagocytic syndrome was diagnosed by pathological examination of the spleen *** bone marrow and spleen pathological re-diagnosis and metagenomic next-generation sequencing(mNGS)technology detection,the patient was finally diagnosed with *** treatment with liposomal amphotericin B,the body temperature quickly returned to normal and the hemocytes recovered ***-treatment re-examination of the bone marrow puncture and mNGS data showed that Leishmania was not *** As a fast and accurate detection method,mNGS can diagnose and evaluate the efficacy of treatment in suspicious cases of leishmaniasis.

关键词： Visceral leishmaniasis Kala-azar next-generation sequencing Hemophagocytic lymphohistiocytosis Diagnosis Case report

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next-generation sequencing traces human induced pluripotent stem cell lines clonally generated from heterogeneous cancer tissue

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World Journal of Stem Cells 2017年第5期9卷 77-88页

作者： Tetsuya Ishikawa Cell Biology Core Facilities for Research and Innovative MedicineNational Cancer Center Research InstituteTokyo 104-0045Japan Central Animal Division Fundamental Innovative Oncology Core CenterNational Cancer Center Research InstituteTokyo 104-0045Japan

AIM To investigate genotype variation among induced pluripotent stem cell(iPSC) lines that were clonally generated from heterogeneous colon cancer tissues using next-generation sequencing. METHODS Human iPSC lines were clonally established by selecting independent single colonies expanded from heterogeneous primary cells of S-shaped colon cancer tissues by retroviral gene transfer(OCT3/4, SOX2, and KLF4). The ten iPSC lines, their starting cancer tissues, and the matched adjacent non-cancerous tissues were analyzed using nextgeneration sequencing and bioinformatics analysis using the human reference genome hg19. Non-synonymous single-nucleotide variants(SNVs)(missense, nonsense,and read-through) were identified within the target region of 612 genes related to cancer and the human kinome. All SNVs were annotated using dbS NP135, CCDS, RefSeq, GENCODE, and 1000 Genomes. The SNVs of the iPSC lines were compared with the genotypes of the cancerous and non-cancerous tissues. The putative genotypes were validated using allelic depth and genotype quality. For final confirmation, mutated genotypes were manually curated using the Integrative Genomics Viewer. RESULTS In eight of the ten iPSC lines, one or two non-synonymous SNVs in EIF2AK2, TTN, ULK4, TSSK1 B, FLT4, STK19, STK31, TRRAP, WNK1, PLK1 or PIK3R5 were identified as novel SNVs and were not identical to the genotypes found in the cancer and non-cancerous tissues. This result suggests that the SNVs were de novo or pre-existing mutations that originated from minor populations, such as multifocal pre-cancer(stem) cells or pre-metastatic cancer cells from multiple, different clonal evolutions, present within the heterogeneous cancer tissue. The genotypes of all ten iPSC lines were different from the mutated ERBB2 and MKNK2 genotypes of the cancer tissues and were identical to those of the noncancerous tissues and that found in the human reference genome hg19. Furthermore, two of the ten iPSC lines did not have any confir

关键词： Colon cancer next-generation sequencing Single-nucleotide variant Genotype Heterogeneous cancer tissue Cancer associated fibroblast Pre-cancer cell Induced pluripotent stem cell Single cell Clonal evolution

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next-generation sequencing technology for the diagnosis of Pneumocystis pneumonia in an immunocompetent female:A case report

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World Journal of Clinical Cases 2023年第18期11卷 4425-4432页

作者： Jing-Ji Huang Song-Song Zhang Man-Li Liu En-Yu Yang Yu Pan Jing Wu The Second Clinical Medical College Guizhou University of Traditional Chinese MedicineGuiyang 550000Guizhou ProvinceChina Intensive Care Unit Guizhou Provincial People's HospitalGuiyang 550000Guizhou ProvinceChina

BACKGROUND Pneumocystis pneumonia(PCP)is a serious fungal infection usually seen in patients with human immunodeficiency virus,and it is more frequently found and has a high fatality rate in immunocompromised ***,it rarely occurs in immunocompetent ***,the clinical diagnosis of this pathogen is made more difficult by the difficulty of obtaining accurate microbiological evidence with routine *** case reports a PCP patient with normal immune function who was diagnosed through next-generation sequencing(NGS).CASE SUMMARY A 23-year-old female who had no special disease in the past was admitted to the hospital with a persistent fever and *** on the initial examination results,the patient was diagnosed with bipulmonary pneumonia,and empirical broad-spectrum antibiotic therapy was ***,due to the undetermined etiology,the patient's condition continued to *** was transferred to the intensive care unit because of acute respiratory *** the diagnosis of Pneumocystis jirovecii infection through NGS in bronchoalveolar lavage fluid and treatment with trimethoprim/sulfamethoxazole and caspofungin,the patient gradually recovered and had a good *** This case emphasizes that,for patients with normal immune function the possibility of PCP infection,although rare,cannot be *** plays an important role in the diagnosis of refractory interstitial pneumonia and acute respiratory failure.

关键词： Pneumocystis pneumonia Pneumocystis jirovecii next-generation sequencing Immunocompetent Trimethoprim/Sulfamethoxazole Case report

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next-generation sequencing-Based Diagnosis of Bacteremic Listeria monocytogenes Meningitis in a Patient with Anti-Interferon Gamma Autoantibodies:A Case Report

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Infectious Microbes & Diseases 2022年第1期4卷 44-46页

作者： Fanfan Xing Derek L.L.Hung Simon K.F.Lo Shuang Chen Susanna K.P.Lau Patrick C.Y.Woo Department of Clinical Microbiology and Infection Control The University of Hong Kong–Shenzhen HospitalShenzhenGuangdongChina Department of Microbiology The University of Hong KongHong KongChina Department of Pathology The University of Hong Kong-Shenzhen HospitalShenzhenGuangdongChina

Although various opportunistic infections have been described in patients with anti-interferon gamma autoantibodies,so far there is no Listeria monocytogenes infection reported to be associated with this primary ***,we describe the first case of bacteremic *** meningitis in a 59-year-old Chinese man with anti-interferon gamma autoantibodies,who presented with acute onset of fever and severe *** culture was positive but culture of the cerebrospinal fluid was negative,although it showed features suggestive of partially treated bacterial *** presence of *** in the cerebrospinal fluid was confirmed by next-generation *** of high-risk food items in these patients is important for the prevention of *** use of antibiotic regimens that cover Listeria is crucial for empirical treatment,particularly if such patients develop acute or subacute ***-generation sequencing is becoming an important diagnostic modality for culture-negative infections.

关键词： Listeria monocytogenes meningitis anti-interferon gamma autoantibody next-generation sequencing

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Machine-learning-aided precise prediction of deletions with next-generation sequencing

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Journal of Central South University 2016年第12期23卷 3239-3247页

作者：管瑞髙敬阳 College of Information Science and Technology Beijing University of Chemical Technology

When detecting deletions in complex human genomes,split-read approaches using short reads generated with next-generation sequencing still face the challenge that either false discovery rate is high,or sensitivity is *** address the problem,an integrated strategy is *** organically combines the fundamental theories of the three mainstream methods(read-pair approaches,split-read technologies and read-depth analysis) with modern machine learning algorithms,using the recipe of feature extraction as a *** with the state-of-art split-read methods for deletion detection in both low and high sequence coverage,the machine-learning-aided strategy shows great ability in intelligently balancing sensitivity and false discovery rate and getting a both more sensitive and more precise call set at single-base-pair ***,users do not need to rely on former experience to make an unnecessary trade-off beforehand and adjust parameters over and over again any *** should be noted that modern machine learning models can play an important role in the field of structural variation prediction.

关键词： next-generation sequencing deletion prediction sensitivity false discovery rate feature extraction machine learning

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The Role of Quality Control in Targeted next-generation sequencing Library Preparation

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Genomics, Proteomics & Bioinformatics 2016年第4期14卷 200-206页

作者： Rouven Nietsch Jan Haas Alan Lai Daniel Oehler Stefan Mester Karen S. Frese Farbod Sedaghat-Hamedani Elham Kayvanpour Andreas Keller Benjamin Meder Institute for Cardiomyopathies Department of Internal Medicine IIIUniversity of Heidelberg69120 HeidelbergGermany German Centre for Cardiovascular Research(DZHK) Heidelberg/MannheimGermany Chair for Clinical Bioinformatics Medical FacultySaarland University66123 SaarbruckenGermany

next-generation sequencing （NGS） is getting routinely used in the diagnosis of hereditary diseases, such as human cardiomyopathies. Hence. it is of utter importance to secure high quality sequencing data, enabling the identification of disease-relevant mutations or the conclusion of negative test results. During the process of sample preparation, each protocol for target enrichment library preparation has its own requirements for quality control （QC）; however, there is little evi- dence on the actual impact of these guidelines on resulting data quality. In this study, we analyzed the impact of QC during the diverse library preparation steps of Agilent SureSelect XT target enrichment and lllumina sequencing. We quantified the parameters for a cohort of around 600 samples, which include starting amount of DNA, amount of sheared DNA, smallest and largest fragment size of the starting DNA; amount of DNA after the pre-PCR, and smallest and largest fragment size of the resulting DNA; as well as the amount of the final library, the corresponding smallest and largest fragment size, and the number of detected variants. Intriguingly, there is a high tolerance for variations in all QC steps, meaning that within the boundaries proposed in the current study, a considerable variance at each step of QC can be well tolerated without compromising NGS quality.

关键词： next-generation sequencing Quality control Library preparation Target enrichment Sequence variants

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