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Technology-Driven and Evidence-Based genomic analysis for Integrated Pediatric and Prenatal Genetics Evaluation

Journal of Genetics and genomics 2013年第1期40卷 1-14页

作者： Yuan Wei Fang Xu Peining Li Laboratory of Molecular Cytogenetics and genomics Department of GeneticsYale University School of Medicine Department of Obstetrics and Gynecology Peking University Third Hospital

The first decade since the completion of the Human Genome Project has been marked with rapid development of genomic technologies and their immediate clinical applications. genomic analysis using oligonucleotide array comparative genomic hybridization （aCGH） or single nucleotide polymorphism （SNP） chips has been applied to pediatric patients with developmental and intellectual disabilities （DD/ ID）, multiple congenital anomalies （MCA） and autistic spectrum disorders （ASD）. Evaluation of analytical and clinical validities of aCGH showed 〉 99% sensitivity and specificity and increased analytical resolution by higher density probe coverage. Reviews of case series, multi-center comparison and large patient-control studies demonstrated a diagnostic yield of 12%--20%; approximately 60% of these abnormalities were recurrent genomic disorders. This pediatric experience has been extended toward prenatal diagnosis. A series of reports indicated approximately 10% of pregnancies with ultrasound-detected structural anomalies and normal cytogenetic findings had genomic abnormalities, and 30% of these abnormalities were syndromic genomic disorders. Evidence-based practice guidelines and standards for implementing genomic analysis and web-delivered knowledge resources for interpreting genomic findings have been established. The progress from this technology-driven and evidence-based genomic analysis provides not only opportunities to dissect disease-causing mechanisms and develop rational therapeutic interventions but also important lessons for integrating genomic sequencing into pediatric and prenatal genetic evaluation.

关键词： genomic analysis Analytical and clinical validity Evidence-based standards and guidelines Integrated genetic evaluation

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Identification of novel mammalian viruses in tree shrews(Tupaia belangeri chinensis)

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Zoological Research 2024年第2期45卷 429-438页

作者： Hong Zhou Ren-Rong Tian Xiu-Rong Wang Jin-Xuan Yang Yun-Xiao Wang Ming-Liang Zhao Xu-Dong Zhang Yu-Hua Ma Long-Bao Lv Edward CHolmes Yong-Tang Zheng Wei-Feng Shi School of Clinical and Basic Medical Sciences Shandong First Medical University&Shandong Academy of Medical SciencesJi’nanShandong 250117China Key Laboratory of Emerging Infectious Diseases in Universities of Shandong Shandong First Medical University and Shandong Academy of Medical SciencesTaianShandong 271000China Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common DiseasesCenter for Biosafety Mega-ScienceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China School of Public Health Shandong First Medical University&Shandong Academy of Medical SciencesJi’nanShandong 250117China National Resource Center for Non-Human Primates Kunming Primate Research CenterKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650107China Sydney Institute for Infectious Diseases School of Medical SciencesThe University of SydneySydneyNew South Wales 2006Australia Department of Infectious Diseases Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghai 200025China Shanghai Institute of Virology Shanghai Jiao Tong University School of MedicineShanghai 200025China

The Chinese tree shrew(Tupaia belangeri chinensis),a member of the mammalian order Scandentia,exhibits considerable similarities with primates,including humans,in aspects of its nervous,immune,and metabolic *** similarities have established the tree shrew as a promising experimental model for biomedical research on cancer,infectious diseases,metabolic disorders,and mental health ***,we used metatranscriptomic sequencing to analyze plasma,as well as oral and anal swab samples,from 105 healthy asymptomatic tree shrews to identify the presence of potential zoonotic *** total,eight mammalian viruses with complete genomes were identified,belonging to six viral families,including Flaviviridae,Hepeviridae,Parvovirinae,Picornaviridae,Sedoreoviridae,and ***,the presence of rotavirus was recorded in tree shrews for the first *** viruses-hepacivirus 1,parvovirus,and picornavirus-exhibited low genetic similarity(94%)to known viral *** analyses also revealed that the rotavirus and mammalian orthoreovirus identified in this study may be novel *** findings provide insights into the diverse viral spectrum present in captive Chinese tree shrews,highlighting the necessity for further research into their potential for crossspecies transmission.

关键词： Tree shrew(Tupaia belangeri chinensis) Meta-transcriptomic sequencing Mammalian viruses genomic analysis

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Characterization of bacteriophage BUCT631 lytic for K1 Klebsiella pneumoniae and its therapeutic efficacy in Galleria mellonella larvae

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Virologica Sinica 2023年第5期38卷 801-812页

作者： Pengjun Han Mingfang Pu Yahao Li Huahao Fan Yigang Tong College of Life Science and Technology Beijing University of Chemical TechnologyBeijing100029China Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical TechnologyBeijing100029China

Severe infections caused by multidrug-resistant Klebsiella pneumoniae(***)highlight the need for new therapeutics with activity against this *** therapy is an alternative treatment approach for multidrug-resistant *** ***,we report a novel bacteriophage(phage)BUCT631 that can specifically lyse capsule-type K1 *** characterization revealed that phage BUCT631 could rapidly adsorb to the surface of *** and form an obvious halo ring,and it had relatively favorable thermal stability(4–50C)and pH tolerance(pH?4–12).In addition,the optimal multiplicity of infection(MOI)of phage BUCT631 was 0.01,and the burst size was approximately 303 PFU/*** analysis showed that phage BUCT631 has double-stranded DNA(total length of 44,812 bp)with a G t C content of 54.1%,and the genome contains 57 open reading frames(ORFs)and no virulence or antibiotic resistance related *** on phylogenetic analysis,phage BUCT631 could be assigned to a new species in the genus Drulisvirus of the subfamily *** addition,phage BUCT631 could quickly inhibit the growth of *** within 2 h in vitro and significantly elevated the survival rate of *** infected Galleria mellonella larvae from 10%to 90%in *** studies suggest that phage BUCT631 has promising potential for development as a safe alternative for control and treatment of multidrug-resistant *** infection.

关键词： Bacteriophage BUCT631 Klebsiella pneumoniae genomic analysis Phage therapy Galleria mellonella

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Integrated genome-wide differentiation and association analyses identify causal genes underlying breeding-selected grain quality traits in japonica rice

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Molecular Plant 2023年第9期16卷 1460-1477页

作者： Hideki Yoshida Satoshi Okada Fanmiao Wang Shohei Shiota Masaki Mori Mayuko Kawamura Xue Zhao Yiqiao Wang Naho Nishigaki Asako Kobayashi Kotaro Miura Shinya Yoshida Masaru Ikegami Akitoshi Ito Lin-Tzu Huang Yue-le Caroline Hsing Yoshiyuki Yamagata Yoichi Morinaka Masanori Yamasaki Toshihisa Kotake Eiji Yamamoto Jian Sun Ko Hirano Makoto Matsuoka Institute of Fermentation Sciences Fukushima UniversityFukushima 960-1248Japan Bioscience and Biotechnology Center Nagoya UniversityNagoyaAichi 464-8601Japan Food Resources Education and Research Center Graduate School of Agricultural ScienceKobe UniversityUzuranoKasaiHyogo 675-2103Japan Research Center of Genetic Resources NARO2-1-1 KannondaiTsukubaIbaraki 305-8602Japan Rice Research Institute Shenyang Agricultural UniversityShenyangChina Division of Life Science Graduate School of Science and EngineeringSaitama University255 Shimo-okuboSakura-kuSaitamaJapan Fukui Agricultural Experiment Station Fukui 918-8215Japan Department of Bioscience and Biotechnology Fukui Prefectural UniversityFukui 910-1195Japan Hyogo Prefectural Research Center for Agriculture Forestry and FisheriesKasaiHyogo 679-0198Japan Research Insttute for Food and Agriculture Ryukoku UniversityOotsuShiga 520-2194Japan Food Research Centre Aichi Centre for Industry and Science Technology2-1-1 Shimpukuji-choNagoyaAichi 451-0083Japan institute of Plant and Microbial Biology Academia SinicaTaipeiTaiwanChina Department of Agronomy National Taiwan UniversityTaipeiTaiwanChina lant Breeding Laboratory Facultyf gricultureKyushu University744MoookaNishikuFukukaJapan Graduate School of Agiculture Meji University1-1-1 Higashi-MitaTama-kuKawasakiKanagawa 214571Japa Crop Science Laboratory Faculty of AgricultureNigata UniversityIkarashiNishi-kuNigata 950-2181Japan

Improving grain quality is a primary objective in contemporary rice *** modern rice breeding has developed two different types of rice,eating and sake-brewing rice,with different grain characteristics,indicating the selection of variant gene alleles during the breeding *** the critical importance of promptly and efficiently identifying genes selected in past breeding for future molecular breeding,we conducted genome scans for divergence,genome-wide association studies,and map-based ***,we successfully identified two genes,OsMnS and OsWOX9D,both contributing to rice grain *** encodes a mannan synthase that increases the white core frequency in the endosperm,a desirable trait for sake brewing but decreases the grain appearance ***9D encodes a grass-specific homeobox-containing transcription factor,which enhances grain width for better sake ***,haplotype analysis revealed that their defective alleles were selected in East Asia,but not Europe,during modern *** addition,our analyses indicate that a reduction in grain mannan content during African rice domestication may also be caused a defective OsMnS allele due to breeding *** study not only reveals the delicate balance between grain appearance quality and nutrition in rice but also provides a new strategy for isolating causal genes underlying complex traits,based on the concept of“breeding-assisted genomics”in plants.

关键词： rice grain quality sake brewing mannan genomic analysis

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Lactobacillus plantarum KLDS1.0386 with antioxidant capacity ameliorates the lipopolysaccharide-induced acute liver injury in mice by NF-κB and Nrf2 pathway

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Food Bioscience 2022年第3期47卷 184-196页

作者： Jiahuan Dong Lijun Ping Qinggang Xie Deyu Liu Li Zhao Smith Etareri Evivie Zhongjiang Wang Bailiang Li Guicheng Huo Key Laboratory of Dairy Science Ministry of EducationNortheast Agricultural UniversityHarbin150030China Food College Northeast Agricultural UniversityHarbin150030China Heilongjiang Feihe Dairy Co. LtdQiqihaer164800China Department of Food Science and Human Nutrition Faculty of AgricultureUniversity of BeninBenin City300001Nigeria Department of Animal Science Faculty of AgricultureUniversity of BeninBenin City300001Nigeria

The Lactobacillus is of great interest as a natural antioxidant to ameliorate liver injury for its antioxidant *** a previous experiment,Lactobacillus plantarum KLDS 1.0386 was excellent in adhesion and *** research assessed the antioxidant capacity of *** KLDS 1.0386 and how it ameliorates the LPS-induced acute liver *** vitro results showed that *** KLDS 1.0386 had potential antioxidant capacity with 27 genes,and it had better capacities in hydroxyl radicals scavenging and lipid antioxidant than the reference strain *** WCFS1 (P < 0.05).In vivo results,*** KLDS 1.0386 significantly reduced hepatic tissue injury,pro-inflammatory cytokines (TNF-α,IL-6),myeloperoxidase (MPO) activities and biochemical indicators of hepatotoxicity (ALT,AST,ALP) (P < 0.05),compared with the LPS-treated ***,*** KLDS 1.0386 increased the relative abundance of the genera,including Lachnospiraceae_NK4A136_group,Muribaculaceae and Alistipes,which significantly increased the level of acetic acid and butyric acid (P < 0.05).The results also showed *** KLDS 1.0386 significantly adjusted the expression of HO-1,NQO1,CAT,NF-κB,TLR4 and IκB-α in the liver (P < 0.05).Overall,these results indicated that *** KLDS 1.0386 had great functionality in reducing LPS-induced acute liver injury.

关键词： Lactobacillus plantarum genomic analysis Lipid antioxidant Hydroxyl radical scavenging Gut microbiota SCFAs

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An imported human case with the SARS-CoV-2 Omicron subvariant BA.2.75 in Yunnan Province,China

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Biosafety and Health 2022年第6期4卷 406-409页

作者： Meiling Zhang Zhixiao Chen Jienan Zhou Xiaonan Zhao Yaoyao Chen Yanhong Sun Zhaosheng Liu Wenpeng Gu Chunrui Luo Xiaoqing Fu Xiang Zhao Yunnan Center for Disease Control and Prevention Kunming 650022China National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and PreventionBeijing 102206China

The Omicron variants spread rapidly worldwide after being initially detected in South Africa in November *** showed increased transmissibility and immune evasion with far more amino acid mutations in the spike(S)protein than the previously circulating variants of concern(VOCs).Notably,on 15 July 2022,we monitored the first VOC/Omicron subvariant BA.2.75 in China from an imported ***,nowadays,this subvariant still is predominant in *** has nine additional mutations in the S protein compared to BA.2,three of which(W152R,G446S,and R493Q reversion)might contribute to higher transmissibility and immune *** subvariant could cause wider spread and pose a threat to the global *** timely reporting and continuous genomic analysis are essential to fully elucidate the characteristics of the subvariant BA.2.75 in the future.

关键词： SARS-CoV-2 Omicron subvariant Mutations genomic analysis

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