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Improving genomic predictions by correction of genotypes from genotyping by sequencing in livestock populations

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Journal of Animal Science and Biotechnology 2019年第2期10卷 283-292页

作者： Xiao Wang Mogens SandΦ Lund Peipei Ma Luc Janss Haja N.Kadarmideen Guosheng Su Center for Quantitative genetics and Genomics Department of Molecular Biology and GeneticsAarhus UniversityTjeleDenmark School of Agriculture and biology Shanghai Jiaotong UniversityShanghaiChina.

Background: Genotyping by sequencing(GBS) is a robust method to genotype markers. Many factors can influence the genotyping quality. One is that heterozygous genotypes could be wrongly genotyped as homozygotes,dependent on the genotyping depths. In this study, a method correcting this type of genotyping error was demonstrated. The efficiency of this correction method and its effect on genomic prediction were assessed using simulated data of livestock ***: Chip array(Chip) and four depths of GBS data was simulated. After quality control(call rate ≥ 0.8 and MAF ≥ 0.01), the remaining number of Chip and GBS SNPs were both approximately 7,000, averaged over 10 replicates. GBS genotypes were corrected with the proposed method. The reliability of genomic prediction was calculated using GBS, corrected GBS(GBSc), true genotypes for the GBS loci(GBSr) and Chip data. The results showed that GBSc had higher rates of correct genotype calls and higher correlations with true genotypes than GBS. For genomic prediction, using Chip data resulted in the highest reliability. As the depth increased to 10, the prediction reliabilities using GBS and GBSc data approached those using true GBS data. The reliabilities of genomic prediction using GBSc data were 0.604, 0.672, 0.684 and 0.704 after genomic correction, with the improved values of 0.013, 0.009, 0.006 and 0.001 at depth = 2, 4, 5 and 10, ***: The current study showed that a correction method for GBS data increased the genotype accuracies and, consequently, improved genomic predictions. These results suggest that a correction of GBS genotype is necessary, especially for the GBS data with low depths.

关键词： Genomic prediction Genotype correction Genotyping by sequencing Simulation

The heterogeneity of store-operated calcium entry in melanoma

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Science China(Life Sciences) 2016年第8期59卷 764-769页

作者： Robert Hooper M.Raza Zaidi Jonathan Soboloff Fels Institute for Cancer research and molecular biology Lewis Katz School of Medicine at Temple University Department of Medical genetics & molecular Biochemistry Lewis Katz School of Medicine at Temple University

Calcium is a key regulator of many physiological processes that are perturbed in cancer, such as migration, proliferation and apoptosis. The proteins STIM and Orai mediate store-operated calcium entry(SOCE), the main pathway for calcium entry in non-excitable cells. Changes in the expression and function of STIM and Orai have been found in a range of cancer types and thus implicated in disease progression. Here we discuss the role of STIM, Orai and the SOCE pathway in the progression of melanoma and explore how the heterogeneous nature of melanoma may explain the lack of consensus in the field regarding the role of SOCE in the progression of this disease.

关键词： melanoma STIM1 Orail metastasis

Histone Deacetylase Genes in Arabidopsis Development

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Journal of Integrative Plant biology 2008年第7期50卷 875-885页

作者： Courtney Hollende Department of Cell biology and molecular genetics University of Maryland College ParkMaryland 20742USA

Histone acetylation and deacetylation are directly connected with transcriptional activation and silencing in eukaryotes. Gene families for enzymes that accomplish these histone modifications show surprising complexity in domain organization, tissue-specific expression, and function. This review is focused on the family of histone deacetylases （HDACs） that remove the acetyl group from core histone tails, resulting in a ＂closed＂ chromatin and transcriptional repression. In Arabidopsis, 18 HDAC genes are divided into three different types - RPD3-1ike, HD-tuin and sirtuin - with two or more members in each type. The structural feature of each HDAC class, the expression profile of each HDAC gene during development and functional insights of important family members are summarized here. It is clear that HDACs are an important class of global transcriptional regulators that play crucial roles in plant development, defense, and adaptation.

关键词： chromatin epigenetic regulation gene silencing histone deacetylase plant development

Rosaceae fruit transcriptome database(ROFT)-a useful genomic resource for comparing fruits of apple,peach,strawberry,and raspberry

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Horticulture research 2023年第12期10卷 276-285页

作者： Muzi Li Stephen M.Mount Zhongchi Liu Department of Cell biology and molecular genetics University of MarylandCollege ParkMD 20742USA

Rosaceae is a large plant family consisting of many economically important fruit crops including peach,apple,pear,strawberry,raspberry,plum,and *** into their growth and development will promote both basic understanding and progress toward increasing fruit yield and *** the ever-increasing high-throughput sequencing data of Rosaceae,comparative studies are hindered by inconsistency of sample collection with regard to tissue,stage,growth conditions,and by vastly different handling of the ***,databases that enable easy access and effective utilization of directly comparable transcript data are highly ***,we describe a database for comparative analysis,ROsaceae Fruit Transcriptome database(ROFT),based on RNA-seq data generated from the same laboratory using similarly dissected and staged fruit tissues of four important Rosaceae fruit crops:apple,peach,strawberry,and red ***,the database is unique in allowing easy and robust comparisons among fruit gene expression across the four *** enables researchers to query orthologous genes and their expression patterns during different fruit developmental stages in the four species,identify tissue-specific and tissue-/stage-specific genes,visualize and compare ortholog expression in different fruit types,explore consensus co-expression networks,and download different data *** database provides users access to vast amounts of RNA-seq data across the four economically important fruits,enables investigations of fruit type specification and evolution,and facilitates the selection of genes with critical roles in fruit development for further studies.

关键词： straw crops database

ULK1 and JNK are involved in mitophagy incurred by LRRK2 G2019S expression

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Protein & Cell 2013年第9期4卷 711-721页

作者： Yuangang Zhu Chunyan Wang Mei Yu Jie Cui Liang Liu Zhiheng Xu The National Key Laboratory of molecular Developmental biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

Mutations in LR RK2(Leucine rich repeat kinase 2)are a major cause of Parkinson’s disease(PD).We and others reported recently that expression of the pathogenic gain-of-function mutant form of LRRK2,LRRK2 G2019S,induc-es mitochondrial fi ssion in neurons through *** we provide evidence that expression of LRRK2 G2019S stimulates mitochondria loss or *** have char-acterized several LRRK2 interacting proteins and found that LRRK2 interacts with ULK1 which plays an essential role in *** of either ULK1 or DLP1 expression with shRNAs suppresses LRRK2 G2019S expression-induced mitochondrial clearance,suggesting that LRRK2 G2019S expression induces mitochondrial fi ssion through DLP1 followed by mitophagy via an ULK1 dependent *** addition to ULK1,we found that LRRK2 interacts with the endogenous MKK4/7,JIP3 and coordinates with them in the activation of JNK ***,LRRK2 G2019S-induced loss of mitochon-dria can also be suppressed by 3 different JNK inhibitors,implying the involvement of the JNK pathway in the path-ogenic mechanism of mutated *** our fi ndings may provide an insight into the complicated pathogenesis of PD as well as some clues to the development of novel therapeutic strategies.

关键词： LRRK2 Parkinson’s disease mitophagy ULK1 JNK DLP1

Do not curse the darkness of the spinal cord,light TDP-43

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Neural Regeneration research 2021年第5期16卷 986-987页

作者： Kazuhide Asakawa Hiroshi Handa Koichi Kawakami Department of Chemical biology Tokyo Medical UniversityTokyoJapan Division of molecular and Developmental biology National Institute of GeneticsDepartment of GeneticsGraduate University for Advanced Studies(SOKENDAI)ShizuokaJapan

Cytoplasmic inc lus ions containing the transactivation response element(TAR)DNAbinding protein-43(TDP-43)aggregates are hallmarks of neurodegenerative disorders,such as amyotrophic lateral sclerosis(ALS)and frontotemporal dementia(Arai et al.,2006;Neumann et al.,2006).Despite the well-recognized correlation between TDP-43 aggregation and neuronal degeneration,whether this relationship is causal has remained unclear.

关键词： al. degeneration TDP

Chromosome 11 aneusomy in esophageal cancers and precancerous lesions-an early event in neoplastic transformation:An interphase fluorescence in situ hybridization study from south India

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World Journal of Gastroenterology 2007年第4期13卷 503-508页

作者： Vasavi Mohan Shivani Ponnala Hemakumar M Reddy Radha Sistla Rachel A Jesudasan Yog Raj Ahuja Qurratulain Hasan Department of genetics & molecular Medicine Kamineni Hospitals LB Nagar Hyderabad AP India Department of molecular biology Center for Cellular and Molecular Biology Uppal Road Hyderabad AP India Department of genetics & molecular Medicine Kamineni Hospitals LB Nagar Hyderabad AP IndiaDepartment of Pathology Kamineni Hospitals Hyderabad AP India Department of genetics Vasavi Hospital and Research Center Lakdi-ka-pul Hyderabad AP India Department of genetics & molecular Medicine Kamineni Hospitals LB Nagar Hyderabad AP IndiaDepartment of Genetics Bhagwan Mahavir Medical Research Center AC Guards Hyderabad AP India

AIM: To detect aneusomic changes with respect to chromosome 11 copy number in esophageal precancers and cancers wherein the generation of cancer-specific phenotypes is believed to be associated with specific chromosomal aneuploidies. METHODS: We performed fluorescence in situ hybridization (FISH) on esophageal tissue paraffin sections to analyze changes in chromosome 11 copy number using apotome-generated images by optical sectioning microscopy. Sections were prepared from esophageal tumor tissue, tissues showing preneoplastic changes and histologically normal tissues (control) obtained from patients referred to the clinic for endoscopic evaluation. RESULTS: Our results demonstrated that aneusomy was seen in all the cancers and preneoplastic tissues, while none of the controls showed aneusomic cells. There was no increase in aneusomy from precancers to cancers. CONCLUSION: Our results suggest that evaluation of chromosome 11 aneusomy in esophageal tissue using FISH with an appropriate signal capture-analysis system, can be used as an ancillary molecular marker predictive of early neoplastic changes. Future studies can be directed towards the genes on chromosome 11,which may play a role in the neoplastic transformation of esophageal precancerous lesions to cancers.

关键词： Esophageal cancer Aneusomy Chromosome11 Fluorescence in situ hybridization Early detection

Factors influencing the spinal motoneurons in development

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Neural Regeneration research 2015年第11期10卷 1773-1776页

作者： Stefan Wiese Faculty for biology and Biotechnology Group for Molecular Cell Biology Universitaetsstr.150 Ruhr University Bochum

The development of the spinal cord needs a concerted interaction of transcription factors activating diverse genes and signals from outside acting on the specification of the different cells. Signals have to act on the segments of the embryo as well as on the cranial-caudal axis and the dorso-ventral axis. Additionally the axons of the motoneurons have to cross the central nervous system barrier to connect to the periphery. Intensive anatomical studies have been followed by molecular characterization of the different subsets of transcription factors that are expressed by cells of the developing spinal cord. Here, intensive studies for the most important appearing cells, the motoneurons, have resulted in a good knowledge on the expression patterns of these proteins. Nonetheless motoneurons are by far not the only important cells and the concert activity of all cells besides them is necessary for the correct function and integrity of motoneurons within the spinal cord. This article will briefly summarize the different aspects on spinal cord development and focuses on the differentiation as well as the functionalization of motoneurons.

关键词： axon neurite synapse muscle extracellular matrix transcription factors

Protein engineering of insulin: Two novel fast-acting insulins [B16Ala]insulin and [B26Ala]insulin

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Science China(Life Sciences) 2003年第5期46卷 474-480页

作者：张舟唐月华姚矢音朱尚权冯佑民 State Key Laboratory of molecular biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biology Sciences Chinese Academy of Sciences 102 research group Institute of Biochemistry and Cell Biology Shanghai Institutes for Biology Sciences Chinese Academy of Sciences

Blood glucose lowering assay proved that [B16Ala]insulin and [B26Ala]insulin exhibit potency of acute blood glucose lowering in normal pigs, which demonstrates that they are fast- acting insulin. Single-chain precursor of [B16Ala]insulin and [B26Ala]insulin is [B16Ala]PIP and [B26Ala]PIP, respectively, which are suitable for gene expression. Secretory expression level of the precursors in methylotrophic yeast Pichia pastoris was quite high, 650 mg/L and 130 mg/L, respectively. In vivo biological assay showed that the two fast-acting insulins have full or nearly full biological activity. So both [B16Ala]insulin and [B26Ala]insulin can be well developed as fast-acting insulin for clinic use.

关键词： insulin, monomeric insulin, fast-acting insulin, Pichia pastoris.