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A reliable high-density variant map of a maize synthetic population

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A reliable high-density variant map of a maize synthetic pop...

Developmental and genomic architecture of plant embryogenesis: from model plant to crops

2016年全国植物生物学大会

作者： Jingyun Luo Haijun Liu Luyao Niu Xiaqing Wang Wenyu Yang Yingjie Xiao Ruyang Zhang Chunhui Li Feng Qiao Jiuran Zhao Jianbing Yan National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Maize Research Center Beijing Academy of Agriculture & Forestry SciencesBeijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding

Maize(Zea mays) is an essential crop and a great model for plant research. However,the great genetic diversity and complex genome structure makes it ever challenging in variant calling and following genomic studies. In present study,we provided an integrated strategy in variant calling and imputation for large maize population(1404 individuals) at such low sequencing coverage(x). Over 53 M SNPs,2.8M In Dels,660 K SVs,600 M novel sequences were finally obtained,which constituted the highest density and the most diverse maize variant map to date. The SNP set was found >99% consistency compared with genotypes derived from array-and assembly-based methods,while the percent of validated large structural variants was considered as 0%. This variant map was further shown to be excellent in association mapping,taking plant height as an example,some known genes and potentially novel loci have been identified simultaneously. In brief,the variant map,together with the methodological practices,would be a great valuable resource for the plant community.

关键词： variant whole-genome-resequencing synthetic population genomics Zea mays

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Plant Communications 2021年第1期2卷 1-12页

作者： Alma Armenta-Medina C.Stewart Gillmor Peng Gao Javier Mora-Macias Leon V.Kochian Daoquan Xiang Raju Datla Global Institute for Food Security University of SaskatchewanSaskatoonSK S7N 4J8Canada Laboratorio Nacional de Genòmica para la Biodiversidad(Langebio) Unidad de Genòmica AvanzadaCentro de Investigaciòny Estudios Avanzados del IPN(CINVESTAV-IPN)IrapuatoGuanajuatoMéxico National Research Council Canada 110 Gymnasium PlaceSaskatoonSK S7N 0W9Canada

Embryonic development represents an important reproductive phase of sexually reproducing plant *** fusion of egg and sperm produces the plant zygote,a totipotent cell that,through cell division and cell identity specification in early embryogenesis,establishes the major cell lineages and tissues of the adult *** subsequent morphogenesis phase produces the full-sized embryo,while the late embryogenesis maturation process prepares the seed for dormancy and subsequent germination,ensuring continuation of the plant life *** this review on embryogenesis,we compare the model eudicot Arabidopsis thaliana with monocot crops,focusing on genome activation,paternal and maternal regulation of early zygote development,and key organizers of patterning,such as auxin and WOX transcription *** the early stages of embryo development are apparently conserved among plant species,embryo maturation programs have diversified between eudicots and *** diversification in crop species reflects the likely effects of domestication on seed quality traits that are determined during embryo maturation,and also assures seed germination in different environmental *** review describes the most important features of embryonic development in plants,and the scope and applications of genomics in plant embryo studies.

关键词： embryogenesis embryo patterning zygote genome activation transcription factors genomics transcriptomics

Toxicokinetic and genomic analysis of chronic arsenic exposure in multidrug-resistance mdr1a-1b(-/-) double knockout mice

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Toxicokinetic and genomic analysis of chronic arsenic exposu...

Determination of Quality Markers is Basis for Establishing Quality Standard and Control of Chinese Herbal Medicines

中国环境诱变剂学会抗诱变剂和抗癌剂专业委员会第三次全国学术会议、中国毒理学会生化与分子毒理专业委员会第五届学术交流会、贵州省环境诱变剂学会成立大会暨首届学术交流会

作者： Curtis D.Klaassen Michael.Waalkes University of Kansas Medical Center Kansas CityKSUSA Inorganic Carcinogenesis Section Laboratory of Comparative CarcinogenesisNational Cancer Institute at National Institute of Environmental Health SciencesResearch Triangle ParkNC

Multidrug-resistance gene knockout mdr1a/1b(-/-) mice,which are deficient in P-glycoproteins,are more sensitive than wild-type(WT) mice to acute arsenic *** study assessed toxic manifestations of chronic oral arsenic in mkr1a/1b(-/-) mice including oxidative stress and altered gene expression,and investigated altered toxicokinetics as a potential basis of enhanced arsenic ***, mdr1a/1b(-/-) and WT mice were exposed to sodium arsenite(0-80 ppm as arsenic) in the drinking water for 10 weeks at which time hepatic arsenic accumulation,lipid peroxidation(LPO),redox status and change in gene expression level were *** mice survived the arsenic exposure,but body weight gain in the highest dose group was reduced in both mdr1a/1b(-/-) than in WT *** induced pathological changes, elevated LPO levels and enhanced glutathione S-transferase(GST) activity,in the liver to a greater extent in mdr1a/1b(-/-) than in WT *** also decreased Cu-Zn superoxide dismutase activity in both mdr1a/1b(-/-) and WT *** expressions of certain genes,such as those encoding cell proliferation,GST, acute-phase proteins and metabolic enzymes,were modestly altered in arsenic-exposed *** expression of cyclin D1,a potential hepatic oncogenen,was enhanced in arsenic-exposed mdr1a/1b(-/-) mice *** the highest level of exposure,hepatic arsenic content was higher in mdr1a/1b(-/-) than in WT mice,suggesting that enhanced accumulation due to transport deficient may,in part,account for the enhanced toxicity in these mice,In summary,this study shows that chronic arsenic toxicity,including liver pathology and oxidative stress, is enhanced in mdr1a/1b(-/-) mice,possibly due to enhanced accumulation of arsenic as a result of transport system deficiency.

关键词： arsenic genomics toxicokinetics mice multidrug-resistance

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Chinese Herbal Medicines 2017年第4期9卷 299-300页

作者： Chang-xiao Liu CHM

The quality marker is a brand new concept not only for the quality assessment and control of TCMs but also for other herbal medicine systems which shares similar features of multiple *** is also worth to mention that integration of traditional Chinese medicinal theory with such modern science as natural products chemistry,chromatographic analysis,network pharmacology,systems biology,is essential for the determination and validation of reasonable,scientific,and practical quality markers.

关键词： pharmacology shares herbal medicinal paeoniflorin mention genomics validation marker gallate

Clinical applications of next-generation sequencing in colorectal cancers

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World Journal of Gastroenterology 2013年第40期19卷 6784-6793页

作者： Tae-Min Kim Sug-Hyung Lee Yeun-Jun Chung MRC Cancer Evolution Research Center College of MedicineThe Catholic University of KoreaSeoul 137-701South Korea Integrated Research Center for Genome Polymorphism Department of MicrobiologyCollege of MedicineThe Catholic University of KoreaSeoul 137-701South Korea Department of Pathology College of MedicineThe Catholic University of KoreaSeoul 137-701South Korea

Like other solid tumors,colorectal cancer(CRC) is a genomic disorder in which various types of genomic alterations,such as point mutations,genomic rearrangements,gene fusions,or chromosomal copy number alterations,can contribute to the initiation and progression of the disease. The advent of a new DNA sequencing technology known as next-generation sequencing(NGS) has revolutionized the speed and throughput of cataloguing such cancer-related genomic alterations. Now the challenge is how to exploit this advanced technology to better understand the underlying molecular mechanism of colorectal carcinogenesis and to identify clinically relevant genetic biomarkers for diagnosis and personalized therapeutics. In this review,we will introduce NGS-based cancer genomics studies focusing on those of CRC,including a recent large-scale report from the Cancer Genome Atlas. We will mainly discuss how NGS-based exome-,whole genome- and methylome-sequencing have extended our understanding of colorectal carcinogenesis. We will also introduce the unique genomic features of CRC discovered by NGS technologies,such as the relationship with bacterial pathogens and the massive genomic rearrangements of chromothripsis. Finally,we will discuss the necessary steps prior to development of a clinical application of NGS-related findings for the advanced management of patients with CRC.

关键词： Next-generation sequencing Cancer genomics Colorectal cancers Personalized medicine The cancer genome atlas

Recent updates of genetic and genomic alterations in hepatocellular carcinoma

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Hepatoma Research 2016年第1期2卷 31-35页

作者： Zhang Zhao Jian Huang Liver Research Center Experimental CenterBeijing Friendship HospitalCapital Medical UniversityBeijing 100050China

Hepatocellular carcinoma(HCC)is one of the most common malignant cancers ***,the molecular mechanisms underlining the development and progression of HCC remain *** and genomic alterations are common events in various types of cancers including *** the development and application of next generation sequencing technology,novel genetic and genomic alterations in HCC have been ***,the article reviews recent updates on the genetic and genomic alterations in HCC.

关键词： Hepatocellular carcinoma genetics genomics next generation sequencing

Addiction Research Update 2009

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Addiction Research Update 2009

INSTRUCTIONS TO AUTHORS

自主创新与持续增长第十一届中国科协年会

作者： Mark S.GOLD Lisa J.MERLO Department of psychiatry McKnight Brain Institute University of Florida

Dr. Gold has worked in this field since the early 1970s. Since that time, the United States’ leading causes of death are still related to alcohol and drug use, tobacco smoke exposure, and behavioral addictions. Each year, more than 400,000 Americans die as a result of smoking, overeating, substance use, and related accidents and suicide. There are notable advances in the treatment of addiction disorders. Animal models have improved and research is currently ongoing with addicted rats. In addition, advances in neurobiology and imaging, proteomics, nanotechnology, pharmacology, and behavioral research have impacted the addiction field. Several components of the neurological reward system (eg, the nucleus accumbens, the ventral tegmental area, and the neurotransmitters (particularly dopamine)) have been implicated in addiction. Similarly, morphine, cannabis, nicotine, and ethanol administration result in increased dopamine release in the nucleus accumbens. In addition, the brain’s endogenous opioid and cannabinoid systems, within the pathway connecting the ventral tegmental area and the nucleus accumbens, are activated by several drugs of abuse. Increased glutamate release in the pathway connecting the prelimbic cortex to the accumbens is associated with drug- seeking behavior. Research findings indicate that individual differences in sensitivity to substances of abuse may be affected by developmental factors such as when the person begins using drugs and dosage. Developmental neurobiology, genetic factors and early environmental factors, all appear critical. Several pharmacological interventions for the treatment of addiction and the prevention of relapse target these systems and their receptors. Findings from recent studies indicate that drug effects are long-lasting and recovery is slow and difficult. Drug dependence appears to be related to changes and dysregulation of the reward system and stress system. Many persons with substance abuse actually choose to change

关键词： dopamine stress behavioral addictions drug addiction neurobiology proteomics genomics

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World Journal of Stem Cells 2014年第3期6卷 371-375页

GENERAL INFORMATIONWorld Journal of Stem Cells(World J Stem Cells,WJSC,online ISSN 1948-0210,DOI:10.4252),is a peer-reviewed open access(OA)academic journal that aims to guide clinical practice and improve diagnostic and therapeutic skills of *** and scopeWJSC covers topics concerning all aspects of stem cells:embryonic,neural,hematopoietic,mesenchymal,tissue-specific,and cancer stem cells;the stem cell niche,stem cell genomics and proteomics,and stem cell techniques and their application in clinical trials.

关键词： proteomics genomics hematopoietic embryonic niche editorial concerning reviewers submitted http

Molecularly targeted therapy for advanced hepatocellular carcinoma-a drug development crisis?

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World Journal of Gastrointestinal Oncology 2016年第2期8卷 173-185页

作者： Kiruthikah Thillai Paul Ross Debashis Sarker department of medical oncology guy’s and st thomas nhs trustLondon SE1 9RTUnited Kingdom division of cancer studies king’s college londonguy’s hospitalLondon SE1 9RTUnited Kingdom institute of liver studies king’s college hospital nhs trustLondon SE5 9RSUnited Kingdom

Hepatocellular carcinoma is the fastest growing cause of cancer related death globally. Sorafenib,a multitargeted kinase inhibitor,is the only drug proven to improve outcomes in patients with advanced disease offering modest survival benefit. Although comprehensive genomic mapping has improved understanding of the genetic aberrations in hepatocellular cancer(HCC),this knowledge has not yet impacted clinical care. The last few years have seen the failure of several first and second line phase Ⅲ clinical trials of novel molecularly targeted therapies,warranting a change in the way new therapies are investigated in HCC. Potential reasons for these failures include clinical and molecular heterogeneity,trial design and a lack of biomarkers. This review discusses the current crisis in HCC drug development and how we should learn from recent trial failures to develop a more effective personalised treatment paradigm for patients with HCC.

关键词： Hepatocellular carcinoma Molecular targets genomics Sorafenib Tyrosine kinase inhibitors