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Acta Biochimica et Biophysica Sinica 2005年第8期37卷 573-579页

作者： Xian LI Shi-Cui ZHANG~* Zhen-Hui LIU Hong-Yan LI Department of Marine Biology,Ocean University of China,Qingdao 266003,China Department of Marine Biology Ocean University of ChinaQingdao 266003 China

The complete cDNA and deduced amino acid sequences of the ribosomal proteins S23(AmphiS23)and L35(AmphiL35)from amphioxus Branchiostoma belcheri tsingtauense were identified inthis ***23 cDNA is 546 bp long and encodes a protein of 143 amino *** has a predictedmolecular mass of 15,851 Da and a pI of ***35 cDNA comprises 473 bp,and codes for a proteinof 123 amino acids with a predicted molecular mass of 14,543 Da and a pI of ***23 shares morethan 83% identity with its homologues in the vertebrates and more than 84% identity with those in ***35 is more than 63% identical to its counterparts in the vertebrates and more than52% identical to those in the *** blot analysis demonstrated the existence of 1-2 copiesof the S23 gene and 2-3 copies of the L35 gene in the genome of amphioxus *** *** in sharp contrast to the presence of 6-13 copies of the S23 gene and 15-17 copies of the L35 gene in therat *** is clear that the housekeeping genes like S23 and L35 underwent a large-scale duplication inthe vertebrate lineage,reinforcing the gene/genome duplication hypothesis.

关键词： amphioxus ribosomal protein S23 L35 copy number

The completed macronuclear genome of a model ciliate Tetrahymena thermophila and its application in genome scrambling and copy number analyses

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Science China(Life Sciences) 2020年第10期63卷 1534-1542页

作者： Yalan Sheng Lili Duan Ting Cheng Yu Qiao Naomi AStover Shan Gao Institute of Evolution&Marine Biodiversity Ocean University of ChinaQingdao 266003China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao 266003China Department of Biology Bradley UniversityPeoriaIllinois 61625USA

The ciliate Tetrahymena thermophila has been a powerful model system for molecular and cellular ***,some investigations have been limited due to the incomplete closure and sequencing of the macronuclear genome assembly,which for many years has been stalled at 1,158 scaffolds,with large sections of unknown sequences(available in Tetrahymena Genome Database,TGD,http://***/).Here we completed the first chromosome-level Tetrahymena macronuclear genome assembly,with approximately 300×long Single Molecule,Real-Time reads of the wild-type SB210 cells—the reference strain for the initial macronuclear genome sequencing *** 181 chromosomes were capped with two telomeres and gaps were entirely *** completed genome shows significant improvements over the current assembly(TGD 2014)in both chromosome structure and sequence *** majority of previously identified gene models shown in TGD were retained,with the addition of 36 new genes and 883 genes with modified gene *** new genome and annotation were incorporated into *** new genome allows for pursuit in some underexplored areas that were far more challenging previously;two of them,genome scrambling and chromosomal copy number,were investigated in this *** expect that the completed macronuclear genome will facilitate many studies in Tetrahymena biology,as well as multiple lines of research in other eukaryotes.

关键词： Tetrahymena thermophila macronuclear genome 181 chromosomes DNA scrambling copy number

Establishment of Real-Time Quantitative PCR Method for the Determination of Transposon copy number in Cronobacter sakazakii

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Agricultural Biotechnology 2012年第1期1卷 40-43页

作者： Fei WANG Xinjun DU Rong ZHANG Guixiang XU Shuo WANG Key Laboratory of Food Nutrition and Safety Ministry of EducationTianjin University of Science&Technology

[Objective] This study aimed to establish a Real-Time quantitative PCR method for the determination of transposon copy number in C. sakazakii. [ Method ] With single-copy housekeeping gene atpD as the reference gene, recombinant plasmid containing both single-copy housekeeping gene atpD and EZ-TN5 transposon was constructed; based on the established standard curves for real-time quantitative detection of atpD gene and EZ-TN5 transposon, copy number of atpD gene and EZ-TN5 transpason in three C. sakazakii mutants was detected and the ratio was calculated. [ Result] Correlation coefficients of the standard curves for real-time quantitative detection of atpD gene and EZ-TN5 transposon were 0. 999 and 0.998, respectively ; the ratios of copy number of atpD gene and EZ-TN5 transposon in three C. sakazakii mutants were 0.98, 1.17 and 0.91, respectively, which indicates that EZ-TN5 transpeson in C. sakakii mutants is a single-copy. [ Conclusion] Real-time quantitative PCR method established in this study had high availability and could replace the Southern blot method to detect the copy num- ber of EZ-TN5 transposon in different bacteria.

关键词： Transposon copy number Real-time quantitative PCR Cronobacter sakazakii

Combination of SMN2 copy number and NAIP deletion predicts disease severity of spinal muscular atrophy in Northern China

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Combination of SMN2 copy number and NAIP deletion predicts d...

Selection of endogenous reference genes for copy number detection in transgenic sugarcane

第八次全国医学遗传学学术会议(中华医学会2009年医学遗传学年会)

作者： ZHANG Yang~1,LUO Yang~1,MA Hong-Wei~2,CAO Li-Hua~1,LIU Fang~2,WANG Shu-Seng~1 1.Research Center for Medical Ge- nomics,China Medical University,Shenyang,110001 2.Shengjing Hospital of China Medical University,Shenyang,110001

Objective Spinal muscular atrophy(SMA)is an autosomal recessive neuromuscular disorder caused by decreased levels of survival motor neuron protein(SMN).In the majority of cases,this decrease is due to absence of the SMN1 *** SMN2 gene is liighly homologous to SMN1 and has been reported to be correlated with severity of the *** clinical presentation of SMA varies from severe to mild,with four clinical subtypes(typeⅠ,typeⅡ,typeⅢand typeⅣ)that are assigned according to age of onset and severity of the *** this study,we aim to investigate the potential association between the number of copies of SMN2 and the deletion in the NAIP gene with the clinical severity of SMA in patients of Northern Chinese *** Multiplex ligation-de-pendent probe amplification(MLPA)is a modem quantitative molecular *** in SMA cases,it improves diagnostics by simultaneously identifying the number of copies of several target sequences in the SMN1 gene and in nearby ***-one probable SMA cases were examined by MLPA and those carrying deletions of the SMN1 gene were enrolled in the *** thirty-one SMA patients(3 of typeⅠ,24 typeⅡ,3 typeⅢand 1 typeⅣ)were ***2 and NAIP copy number were determined by MLPA. Results One typeⅠpatient carried one copy of SMN2,while the other two carried 1.5 *** the typeⅡSMA patients, 8 percent(2/24)of cases carried 1.5 copies of the gene,while 92 percent(22/24)carried 2 or 2.5 copies of *** the typeⅢpatients carried drree copies and the asymptomatic typeⅣpatient carried four *** analysis of NAIP showed that two typeⅠSMA patients had a homozygous deletion of this gene,while the other one had a heterozygous *** one out of 24 typeⅡSMA cases carried a homozygous deletion,while all the other typeⅡpatients had a heterozygous *** typeⅢpatients carried intact copies of the NAIP *** There exists a close relationship between SMN2 copy number and SMA disease

关键词： Spinal muscular atrophy Survival motor neuron Neuronal apoptosis inhibitory protein copy number Multiplex ligation-dependent probe amplification

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Selection of endogenous reference genes for copy number dete...

Comparing Genetic Characteristics of Retrotransposon TOS17 During Different Tissue Culture Processes in the Rice Cultivars Nipponbare and Shishoubaimao

中国作物学会2013年学术年会

作者： Bantong Xue Jinlong Guo Youxiong Que Zhiwei Fu Wu Lu-guang Liping Xu Key Laboratory of Sugarcane Biology and Genetic Breeding Fujian Agriculture and Forestry UniversityMinistry of Agriculture School of Agriculture and Food Sciences University of Queensland

Transgene copy number has a great impact on the expression level and stability of exogenous gene in transgenic *** real-time PCR technique,which depends on the use of appropriate endogenous reference genes,has been widely accepted as an accurate and time-saved method in the copy number detection of transgenic plants and GM detection to meet the regulatory and legislative *** date,most transgene crops have been developed corresponding endogenous reference genes,some species have multiple applicable endogenous reference genes,but limited in ***,further development of exogenous reference genes for polyploid and aneuploid sugarcane is very *** this study,we evaluated a set of potential ’single copy’ genes including P4H,APRT,ENOL,CYC,TST and PRR,through qualitative PCR and absolute quantitative PCR. On the basis of copy number comparison in different sugarcane genotypes,including 5 Saccharum officinarum, one *** and two ***,the copy number of these endogenous genes fell into three groups:a high copy number group with only ENOL③,a medium copy number group containing TST①and PRR①,and a low copy number group with P4H③,APRT②and CYC②.Besides,the most stable reference genes were P4H, APRT and CYC,while the least stable genes were ENOL and TST in different sugarcane ***, primer pairs P4H③,APRT②and CYC②were selected as the suitable reference gene prime pairs in sugarcane. The test of multi-target reference genes plasmid on revealed that the APRT gene was a specific amplicon within the detection using the primers APRT②,and thus this gene was assumed to be the most suitable endogenous reference gene in *** results should be helpful for the analyses of the copy number of exogenous genes in transgenic sugarcane,and are also of vital significance for sugarcane transgenic breeding and its commercial application.

关键词： Sugarcane Endogenous reference genes qRT-PCR copy number

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Agricultural Sciences in China 2010年第2期9卷 157-162页

作者： LI Kuan, WANG Chuang, YING Shan and SHOU Hui-xia State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, P.R.China State Key Laboratory of Plant Physiology and Biochemistry College of Life Sciences Zhejiang University Hangzhou 310058 P.R. China

As a retrotransposon, TOS17 was a useful tool for rice genetic and functional genomic research. To ascertain the feasibility of constructing a TOS17 insertion mutation library in the rice cultivar Shishoubaimao, the genetic and expression characteristics of TOS17 were analyzed. We made solid and suspension tissue cultures and confirmed the copy numbers of TOS17 at different time points in both tissue culture processes by real-time quantitative PCR （RT-qPCR）. Three primary copies of TOS17 were detected in naturally grown Shishoubaimao. TOS17 was activated by tissue culture, and the copy numbers of TOSI7 increased along with a prolonged tissue culture time in both the Nipponbare and the Shishoubaimao cultivars. Therefore, Shishoubaimao is a potential candidate for constructing a TOS17 insertion mutant library. Compared with Nipponbare, TOS17 was more active in Shishoubaimao during tissue culture. Higher copy numbers of TOS17 were obtained with the suspension tissue culture process than with the solid tissue culture process over the same time courses. We concluded that 3-4 months of suspension tissue culture time is suitable for constructing a TOS17 insertion mutant library in Shishoubaimao.

关键词： Shishoubaimao tissue culture TOS17 copy number insertion mutant library

Chromosome organization and gene expansion in the highly fragmented genome of the ciliate Strombidium stylifer

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Journal of Genetics and Genomics 2021年第10期48卷 908-916页

作者： Chao Li Xiao Chen Weibo Zheng Thomas G.Doak Guangyi Fan Weibo Song Ying Yan Institute of Evolution&Marine Biodiversity Ocean University of ChinaQingdao 266003China Marine College Shandong UniversityWeihai 264209China School of Life Sciences Ludong UniversityYantai 264025China Department of Biology Indiana UniversityBloomingtonIN 47405USA National Center for Genome Analysis Support Indiana UniversityBloomingtonIN 47405USA BGI-Qingdao BGI-ShenzhenQingdao 266555China State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhen 518083China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao 266237China

Chromosomes are well-organized carriers of genetic information in eukaryotes and are usually quite long,carrying hundreds and thousands of ***,a clade of single-celled ciliates,Spirotrichea,feature nanochromosomes—also called“gene-sized chromosomes”.These chromosomes predominantly carry only one gene,flanked by short telomere ***,the organization and copy number variation of the chromosomes in these highly fragmented genomes remain unexplored in many groups of Spirotrichea,including the marine *** deep genome sequencing,we assembled the macronuclear genome of Strombidium stylifer into more than 18,000 nanochromosomes(~2.4 Kb long on average).Our results show that *** occupies an intermediate position during the evolutionary history of Strombidium lineage and experienced significant expansions in several gene families related to guanyl ribonucleotide *** on the nucleotide distribution bias analysis and conserved motifs search in non-genic regions,we found that the subtelomeric regions have a conserved adenine-thymine(AT)-rich sequence *** also found that the copy number of nanochromosomes lacks precise *** work sheds light on the unique features of chromosome structure in eukaryotes with highly fragmented genomes and reveals that a rather specialized evolutionary strategy at the genomic level has resulted in great diversity within the ciliated lineages.

关键词： Ciliate copy number Nanochromosome Nucleotide distribution bias Strombidium stylifer

The diverse heterogeneity of molecular alterations in prostate cancer identified through next-generation sequencing

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Asian Journal of Andrology 2013年第3期15卷 301-308页

作者： Alexander W Wyatt Fan Mo Yuzhuo Wang Colin C Collins Vancouver Prostate Centre & Department of Urologic Sciences University of British Columbia Vancouver BC V6H 3Z6 Canada Department of Experimental Therapeutics BC Cancer Agency Vancouver BC VSZ 1L3 Canada

Prostate cancer is a leading cause of global cancer-related death but attempts to improve diagnoses and develop novel therapies have been confounded by significant patient heterogeneity. In recent years, the application of next-generation sequencing to hundreds of prostate tumours has defined novel molecular subtypes and characterized extensive genomic aberration underlying disease initiation and progression. It is now clear that the heterogeneity observed in the clinic is underpinned by a molecular landscape rife with complexity, where genomic rearrangements and rare mutations combine to amplify transcriptomic diversity. This review dissects our current understanding of prostate cancer ＇omics＇, including the sentinel role of copy number variation, the growing spectrum of oncogenic fusion genes, the potential influence of chromothripsis, and breakthroughs in defining mutation-associated subtypes. Increasing evidence suggests that genomic lesions frequently converge on specific cellular functions and signalling pathways, yet recurrent gene aberration appears rare. Therefore, it is critical that we continue to define individual tumour genomes, especially in the context of their expressed transcriptome. Only through improved characterisation of tumour to tumour variability can we advance to an age of precision therapy and personalized oncology.

关键词： cancer sequencing copy number fusion gene genome genome rearrangement personalized oncology prostate cancer transcriptome

Establishment of Hamster-and Human-PRNP Transgenic Mice

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Biomedical and Environmental Sciences 2011年第6期24卷 608-616页

作者： GONG Han Shi TIAN Chan ZHANG Bao Yun WANG Zhao Yun XIE Wu Ling JING Yuan Yuan GAO Chen JIANG Hui Ying SHI Qi LIU Yong DONG Xiao Ping School of Medicine Xi＇an Jiao Tong University Xi＇an 710061 Shaanxi China State Key Laboratory for Infectious Disease Prevention and Control National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention Beijing 102206 China

Objective To create transgenic mice expressing hamster- and human-PRNP as a model tor understanding the physiological function and pathology of prion protein （PrP）, as well as the mechanism of cross-species transmission of transmissible spongiform encephalopathies （TSEs）. Methods Hamster and human-PRNP transgenic mice were established by conventional methods. The copy number of integrated PRNP in various mouse lines was mapped by real-time PCR. PRNP mRNA and protein levels were determined by semi-quantitative RT-PCR, real-time RT-PCR, and western blot analysis. Histological analyses of transgenic mice were performed by hematoxylin and eosin （H ＆ E） staining and immunohistochemical （IHC） methods. Results Integrated PRNP copy number in various mouse lines was 53 （Tg-haPrP1）, 18 （Tg-huPrP1）, 3 （Tg-huPrP2）, and 16 （Tg-huPrP5）, respectively. Exogenous PrPs were expressed at both the transcriptional and translational level. Histological assays did not detect any abnormalities in brain or other organs. Conclusion We have established one hamster-PRNP transgenic mouse line and three human-PRNP transgenic mouse lines. These four transgenic mouse lines provide ideal models for additional research.

关键词： PrP PRNP Transgenic mice copy number

DNA alterations in the tumor genome and their associations with clinical outcome in prostate cancer

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Asian Journal of Andrology 2016年第4期18卷 533-542页

作者： Wennuan Liu Program for Personalized Cancer Care Research Institute NorthShore University HealthSystem Evanston IL USA.

Although most prostate cancer （PCa） cases are not life-threatening, approximately 293 000 men worldwide die annually due to PCa. These lethal cases are thought to be caused by coordinated genomic alterations that accumulate over time. Recent genome-wide analyses of DNA from subjects with PCa have revealed most, if not all, genetic changes in both germline and PCa tumor genomes. In this article, I first review the major, somatically acquired genomic characteristics of various subtypes of PCa. I then recap key findings on the relationships between genomic alterations and clinical parameters, such as biochemical recurrence or clinical relapse, metastasis and cancer-specific mortality. Finally, I outline the need for, and challenges with, validation of recent findings in prospective studies for clinical utility. It is clearer now than ever before that the landscape of somatically acquired aberrations in PCa is highlighted by DNA copy number alterations （CNAs） and TMPRSS2-ERG fusion derived from complex rearrangements, numerous single nucleotide variations or mutations, tremendous heterogeneity, and continuously punctuated evolution. Genome-wide CNAs, PTEN loss, MYC gain in primary tumors, and TP53 loss/mutation and AR amplification/mutation in advanced metastatic PCa have consistently been associated with worse cancer prognosis. With this recently gained knowledge, it is now an opportune time to develop DNA-based tests that provide more accurate patient stratification for prediction of clinical outcome, which will ultimately lead to more personalized cancer care than is possible at present.

关键词： copy number DNA markers fusion mutation outcome prognostic prostate cancer tumor genome