从分子层面对泛癌进行研究已经得到了很大的进展,但是对宫颈鳞状细胞癌的分子分类研究仍然需要更多的探索.为了找到宫颈鳞状细胞癌潜在的子类,本文提出了一个基于多维组学数据的癌症亚型分类分析流程.通过统计学方法对癌症基因组图谱(Th...从分子层面对泛癌进行研究已经得到了很大的进展,但是对宫颈鳞状细胞癌的分子分类研究仍然需要更多的探索.为了找到宫颈鳞状细胞癌潜在的子类,本文提出了一个基于多维组学数据的癌症亚型分类分析流程.通过统计学方法对癌症基因组图谱(The Cancer Genome Atlas,TCGA)宫颈鳞状细胞癌的mRNA表达数据、小分子核糖核酸(microRNA,miRNA)表达数据、DNA甲基化数据以及拷贝数变异数据4个维度包含的分子进行筛选,然后对筛选后的分类特征进行整合聚类,进一步筛选能够区分不同子类的关键分类特征,并使用这些关键分类特征建立宫颈鳞状细胞癌分类模型.本研究为宫颈鳞状细胞癌分子层面子类的识别提供了分析流程,得到了两个临床生存水平具有显著性差异的宫颈鳞状细胞癌子类,并确定了8个宫颈鳞状细胞癌的关键分类特征.本研究中识别的宫颈鳞状细胞癌子类和关键分类特征为宫颈鳞状细胞癌早期分类及分类标志物的鉴定提供了重要参考.展开更多
The fingerprints of 27 Leymus chinensis (Trin.) Tzvel accessions from different regions in China were generated and their genomic DNA variations were assayed via amplified fragment length polymorphism (AFLP). A to...The fingerprints of 27 Leymus chinensis (Trin.) Tzvel accessions from different regions in China were generated and their genomic DNA variations were assayed via amplified fragment length polymorphism (AFLP). A total of 537 DNA fragments were amplified ranging from 75-530 bp using 8 AFLP primer combinations, among which 89 (16.6%) were monomorphic and 329 (61.3%) were polymorphic. The average number of DNA band produced by each primer combination was 66.13 and the total polymorphic rate was 78.84%. PICs (polymorphic information contents) scores for AFLP ranged from 0.0-0.5 and the mean PIC was 0.216. PIC scores were maximum (0.5) for 8.5% of the AFLP markers. All the results revealed that there was rich polymorphism in genomic DNA of L. chinensis . A DNA molecular dendrogram was established for 27 L. chinensis genotypes based on genetic variation and UPGMA cluster analysis of 537 AFLP markers amplified by 8 primer combination, suggesting that the genetic variation with high frequency showed close correlation with their ecotopes and geographical distributions. Twenty_seven L. chinensis genotypes could be divided into four groups. Among them the lower genetic relationship was shown. The reason of high genetic variation frequency in L. chinensis species and formation of varieties was discussed.展开更多
[Objective ] The study aimed to construct the AFLP molecular marking system in Mangifera indica. [ Method ] Four varieties of Mangifera indica were used to explore new ways for high-quality DNA, and AFLP analysis of 3...[Objective ] The study aimed to construct the AFLP molecular marking system in Mangifera indica. [ Method ] Four varieties of Mangifera indica were used to explore new ways for high-quality DNA, and AFLP analysis of 31 varieties of Mangifera indica was carried out to detect the varietal genetic diversity. [ Result] 14 pairs of primers with stronger polymorphism, better banding patterns and higher resolution were screened out from 64 pairs of selective amplification primers. Then they were used to analyse the fingerprint of 31 varieties of Mangifera indica, the results showed that the ratio of polymorphic bands amplificated by the 14 pairs of primers reached 97% in 31 varieties of Mangifera.[ Conclusion] It was suggested that AFLP was suitable for detecting the polymorphism of Mangifera indica resources.展开更多
The phylogenetic relationships of four species,Bufo melanostictus,Hyla chinensis,Rana limnocharis and Rana guentheri,which belong to three differrent families of Anura,were detected with RAPD technique.The genomic DNA...The phylogenetic relationships of four species,Bufo melanostictus,Hyla chinensis,Rana limnocharis and Rana guentheri,which belong to three differrent families of Anura,were detected with RAPD technique.The genomic DNA of each species was amplified with 19 random primers.16 primers given clear amplified bands were used for analysis and the genetic distances between four species were calculated.The results show that RAPD bands obtained by all 16 primers evinced different degree polymorphisms.The genetic distance between R.limnocharis and R.guentheri is the nearest,that between B.melanostictus and H.chinensis is the second nearest,and that between B.melanostictus and R.guentheri is the furthest.The different distances also indicated that the relationship between Bufoidae and Hylidae is closer than that between Bufonidae and Ranidae at genomic DNA level.In concordant with the conclusion of the morphology,chromosomal and mitochondrial DNA studies,our results provide a new evidence of the systematic evolution of the three families of Anura at DNA molecular level.展开更多
Hepatocellular carcinoma(HCC)is the sixth most common malignancy and the fourth leading cause of cancer related death worldwide.China covers over half of cases,leading HCC to be a vital threaten to public health.Despi...Hepatocellular carcinoma(HCC)is the sixth most common malignancy and the fourth leading cause of cancer related death worldwide.China covers over half of cases,leading HCC to be a vital threaten to public health.Despite advances in diagnosis and treatments,high recurrence rate remains a major obstacle in HCC management.Multi-omics currently facilitates surveillance,precise diagnosis,and personalized treatment decision making in clinical setting.Non-invasive radiomics utilizes preoperative radiological imaging to reflect subtle pixel-level pattern changes that correlate to specific clinical outcomes.Radiomics has been widely used in histopathological diagnosis prediction,treatment response evaluation,and prognosis prediction.High-throughput sequencing and gene expression profiling enabled genomics and proteomics to identify distinct transcriptomic subclasses and recurrent genetic alterations in HCC,which would reveal the complex multistep process of the pathophysiology.The accumulation of big medical data and the development of artificial intelligence techniques are providing new insights for our better understanding of the mechanism of HCC via multi-omics,and show potential to convert surgical/intervention treatment into an antitumorigenic one,which would greatly advance precision medicine in HCC management.展开更多
Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or ...Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure.In this study,a set of 155 411 expressed sequence tags(ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms(SNPs) were predicted,including 9 546 transitions,5 124 transversions and 2 481 indels.Among the 7 298 SNP substitutions located in functionally annotated contigs,58.4%(4 262) are non-synonymous SNPs capable of introducing amino acid mutations.Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding.Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous,suggesting negative selection.Distribution of non-synonymous to synonymous substitutions(Ka/Ks) ratio ranges from 0 to 4.01,(average 0.42,median 0.26),suggesting that the majority of the affected genes are under purifying selection.Enrichment analysis identified multiple gene ontology categories under positive or negative selection.Categories involved in innate immune response and male gamete generation are rich in positively selected genes,which is similar to reports in Drosophila and primates.This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species.The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.展开更多
The amplified fragment length polymorphic DNA (AFLP) technique was adopted to estimate the population genetic polymorphism among 30 sporophytes of Laminaria japonica collected from a cultivating farm in Rongcheng,Chin...The amplified fragment length polymorphic DNA (AFLP) technique was adopted to estimate the population genetic polymorphism among 30 sporophytes of Laminaria japonica collected from a cultivating farm in Rongcheng,China.Three methods were used for genomic DNA extraction from Laminaria japonica sporophyte and only the products obtained using the improved genomic DNA extraction kit method proved qualified for AFLP analysis.The parameters of the method were optimized.Samples of forty milligrams and the cell lysis time of 120 min were suggested to replace the parameters recommended by the manufacturer.Thirty individuals of Laminaria japonica from the same cultivating site were investigated using one pair of selective primers.A total of 21 loci were obtained and 17 of them were polymorphic.The mean percent age of polymorphic loci of this population was 80.95%.The Nei's gene diversity (H) within this population was 0.3028 and the average Shannon's Information index (I) was 0.4498.A genetic distance matrix among different individuals was constructed as well.Through this study,an applicable AFLP genetic analysis working system for Laminaria japonica sporophyte was established.The results of this research also revealed a high level of genetic diversity within the studied population.展开更多
AIM:To investigate the relationship between c.343A>G and c.2216A>C polymorphism sites in the CDH17 gene and colorectal carcinoma.METHODS:Ninety-three non-consanguineous colorectal carcinoma patients admitted to ...AIM:To investigate the relationship between c.343A>G and c.2216A>C polymorphism sites in the CDH17 gene and colorectal carcinoma.METHODS:Ninety-three non-consanguineous colorectal carcinoma patients admitted to the Department of Oncology at the First Affiliated Hospital of Zhengzhou University were included in this study.Ninety-three peripheral venous blood samples,of approximately one milliliter from each patient,were collected betweenDecember 2009 and August 2010.The genomic DNA of these peripheral venous blood samples were extracted and purified using a Fermentas Genomic DNA Purification Kit(Fermentas,CA) according to the manufacturer' s protocol.The single nucleotide polymorphisms(SNPs) of the liver-intestine cadherin(CDH17) gene c.343A>G and c.2216A>C were determined by the polymerase chain reaction-single strand conformation polymorphism method(PCR-SSCP) in 93 peripheral venous blood samples from patients suffering with colorectal carcinoma.Typical samples that showed different migration bands in SSCP were confirmed by sequencing.Directed DNA sequencing was used to check the correctness of the genotype results from the PCR-SSCP method.RESULTS:There was a significant association between the c.2216 A>C SNPs of the CDH17 gene and the tumor-node-metastasis(TNM) grade,as well as with lymph node status,in 93 peripheral venous blood samples from colorectal carcinoma patients.The genotype frequencies of A/C,A/A,and C/C were 12.90%,33.33% and 53.76%,respectively.There was a significant correlation between lymph node metastasis,TNM grade,and the genotype distribution(P < 0.05).The C/C genotype raised the risk of lymph node metastasis and the TNM grade.There was a significant difference in the TNM grade and lymph node metastasis between the A/A and C/C genotypes(P = 0.003 and P = 0.013,respectively).Patients with colorectal carcinoma carrying the C allele tended to have a higher risk of lymph node metastasis and have a higher TNM grade.The difference between the TNM grades,as well as the lymph node metastasis of the two alleles,was statistically significant(P < 0.01).CONCLUSION:The SNPs of the CDH17 gene c.2216 A>C might be clinically important in the prognosis of colorectal carcinoma.展开更多
AIM： To analyse the role of two common polymorphisms in genes coding for histamine metabolising enzymes as it relates to the risk to develop ulcerative colitis （UC） and the clinical course of these patients. METHOD...AIM： To analyse the role of two common polymorphisms in genes coding for histamine metabolising enzymes as it relates to the risk to develop ulcerative colitis （UC） and the clinical course of these patients. METHODS： A cohort of 229 unrelated patients with UC recruited from a single centre and 261 healthy volunteers were analysed for the presence of Thr105Ile and His645Asp amino acid substitutions at histamine N-methyltransferase （HNMT） and diamine oxidase （ABP1） enzymes, respectively, by amplification-restriction procedures. All patients were phenotyped and followed up for at least 2 years （mean time 11 years）. RESULTS： There were no significant differences in the distribution of ABP1 alleles between ulcerative colitis patients and healthy individuals [OR （95% CI） for variant alleles = 1.22 （0.91-1.61）]. However, mutated ABP1 alleles were present with higher frequency among the 58 patients that required immunosuppresive drugs [OR （95 % CI） for carriers of mutated alleles 2.41 （1.21-4.83; P=0.006）], with a significant gene-dose effect （P= 0.0038）. In agreement with the predominant role of ABP1 versus HNMT on local histamine metabolism in human bowel, the frequencies for carriers of HNMT genotypes or mutated alleles were similar among patients,regardless clinical evolution, and control individuals. CONCLUSION： The His645Asp polymorphism of the histamine metabolising enzyme ABP1 is related to severity of ulcerative colitis.展开更多
Objective： To investigate the association of XRCC4 polymorphic variants at G-1394T （rs6869366） with colorectal cancer susceptibility. Methods： In this hospital-based case-control study, the association of XRCC4 po...Objective： To investigate the association of XRCC4 polymorphic variants at G-1394T （rs6869366） with colorectal cancer susceptibility. Methods： In this hospital-based case-control study, the association of XRCC4 polymorphism with colorectal cancer risk in Chinese population was investigated. In total, 171 patients with colorectal cancer and 171 healthy individuals matched for age and gender were selected. The genomic DNAs of the patients and controls were extracted from peripheral blood and the 300 bp target DNA was amplified with Polymerase Chain Reaction. The products were then digested with restriction endonuclease HinclI, followed by agarose electrophoresis to identify the genotype. Results： We found a significant difference in the frequency of the XRCC4 G-1394T genotype between the colorectal cancer and control groups in female （1/127 vs 8/122, P〈0.05）. Those with G/T at XRCC4 G-1394T showed a decreased risk of colorectal cancer susceptibility compared with those with T/T （OR 0.113, 95%CI 0.014-0.932）. However, in overall population or in male, there was no significant difference of the distribution between the colorectal cancer and control groups. Conclusion： Our findings with decreased risk of colorectal cancer susceptibility suggested that the G allele of XRCC4 G-1394T were associated in female.展开更多
By southern hybridization with 1. 8 kb cDNA probe,a high frequency （40. 5 % ） of structural abnor- mality of p53 gene was observed in primary nasopharyngeal carcinoma （NPC） biopsies. The regions of ex- ons 1 to 4 ...By southern hybridization with 1. 8 kb cDNA probe,a high frequency （40. 5 % ） of structural abnor- mality of p53 gene was observed in primary nasopharyngeal carcinoma （NPC） biopsies. The regions of ex- ons 1 to 4 of the gene were examined by polymerase chain reaction-single strand con formation polymor- phism,no point mutation was found. Because very low rate of point mutation had been reported in exons 5 to 8, we considered that structural abnormality in the region of e-cons 1 to 8 of the gene might be uncom- mon in NPC. The spectrophotometer scanning analysis of autoradiograms and rehybridization investigation of nitrocellulose filter with exon 11 probe indicated that most of structure aberrations we observed might be rearrangement occurring in exon 11.展开更多
Trichoderma is a fungal genus of great and demonstrable biotechnological value, but its genome is poorly surveyed compared with other model microorganisms. Due to their ubiquity and rapid substrate colonization, Trich...Trichoderma is a fungal genus of great and demonstrable biotechnological value, but its genome is poorly surveyed compared with other model microorganisms. Due to their ubiquity and rapid substrate colonization, Trichoderma species have been widely used as biocontrol organisms for agriculture, and their enzyme systems are widely used in industry. Therefore, there is a clear interest to explore beyond the phenotype to exploit the underlying genetic systems using functional genomics tools. The great diversity of species within the Trichoderma genus, the absence of optimized systems for its exploration, and the great variety of genes expressed under a wide range of ambient conditions are the main challenges to consider when starting a comprehensive functional genomics study. An initial project started by three Spanish groups has been extended into the project TRICHOEST, funded by the EU (FP5, QLRT-2001-02032) to target the transcriptome analysis of selected Trichoderma strains with biocontrol potential, in conditions related to antagonism, nutrient stress and plant interactions. Once specific conditions were defined, cDNA libraries were produced and used for EST sequencing. Nine strains from seven Trichoderma species have been considered in this study and an important amount of gene sequence data has been generated, analyzed and used to compare the gene expression in different strains. In parallel to sequencing, genomic expression studies were carried out by means of macro-arrays to identify genes expressed in specific conditions. In silico analysis of DNA sequencing data together with macro-array expression results have lead to a selection based on the potential use of the gene sequences. The selected clone sequences were completed and cloned in appropriate vectors to initiate functional analysis by means of expression studies in homologous and heterologous systems.展开更多
An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot dive...An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot divergence in the genome of rice (Oryza sativa L.), as inferred from the age distribution of pairs of duplicate genes based on recent genome data for rice. Our results suggest that paleopolyploidy was widespread and played an important role in the evolution of rice.展开更多
Viruses including baculoviruses are obligatory parasites, as their genomes do not encode all the proteins required for replication. Therefore, viruses have evolved to exploit the behavior and the physiology of their h...Viruses including baculoviruses are obligatory parasites, as their genomes do not encode all the proteins required for replication. Therefore, viruses have evolved to exploit the behavior and the physiology of their hosts and olden coevolved with their hosts over millions of years. Recent comparative analyses of complete genome sequences of baculoviruses revealed the patterns of gene acquisitions and losses that have occurred during baculovirus evolution. In addition, knowledge of virus genes has also provided understanding of the mechanism of baculovirus infection including replication, species-specific virulence and host range. The Bm8 gene of Bombyx mori nucleopolyhedrovirus （NPV） and its homologues are found only in group I NPV genomes. The Autographa californica NPV Ac 16 gene is a homologue of Bm8 and, encodes a viral structural protein. It has been shown that BmS/Ac 16 interacts with baculoviral and cellular proteins. BmS/Ac 16 interacts with baculoviral IE1 that is facilitated by coiled coil domains, and the interaction with IE1 is important for Bin8 function. Acl6 also forms a complex with viral FP25 and cellular actin and associates with membranes via palmitoylation. These data suggested that this gene family encodes a multifunctional protein that accomplishes specific needs of group I NPVs.展开更多
Objective:Vitamin D receptor(VDR)mediates vitamin D activity.We examined whether VDR expression in excised melanoma tissues is associated with VDR gene(VDR)polymorphisms.Methods:We evaluated VDR protein expression(by ...Objective:Vitamin D receptor(VDR)mediates vitamin D activity.We examined whether VDR expression in excised melanoma tissues is associated with VDR gene(VDR)polymorphisms.Methods:We evaluated VDR protein expression(by monoclonal antibody immunostaining),melanoma characteristics,and carriage of VDR-Fok I-rs2228570(C>T),VDR-Bsm I-rs1544410(G>A),VDR-ApaI-rs7975232(T>G),and VDR-TaqI-rs731236(T>C)polymorphisms(by restriction fragment length polymorphism).Absence or presence of restriction site was denoted by a capital or lower letter,respectively:"F"and"f"for Fok I,"B"and"b"for Bsm I,"A"and"a"for ApaI,and "T"and"t"for TaqI endonuclease.Seventy-four Italian cutaneous primary melanomas(52.1±12.7 years old)were studied;51.4% were stage Ⅰ,21.6% stage Ⅱ ,13.5% stage Ⅲ,and 13.5% stage Ⅳ melanomas.VDR expression was categorized as follows:100% positive vs.<100%;over the median 20%(high VDR expression)vs.≤20%(low VDR expression);absence vs.presence of VDR-expressing cells.Results:Stage I melanomas,Breslow thickness of<1.00 mm,level II Clark invasion,Aa heterozygous genotype,and AaTT combined genotype were more frequent in melanomas with high vs.low VDR expression.Combined genotypes BbAA,bbAa,AATt,BbAATt,and bbAaTT were more frequent in 100%vs.<100%VDR-expressing cells.Combined genotype AATT was more frequent in melanomas lacking VDR expression(odds ratio=14.5;P=0.025).VDR expression was not associated with metastasis,ulceration,mitosis>1,regression,tumor-infiltrating lymphocytes,tumoral infiltration of vascular tissues,additional skin and non-skin cancers,and melanoma familiarity.Conclusions:We highlighted that VDR polymorphisms can affect VDR expression in excised melanoma cells.Low VDR expression in AATT carriers is a new finding that merits further study.VDR expression possibly poses implications for vitamin D supplementation against melanoma.VDR expression and VDR genotype may become precise medicinal tools for melanoma in the future.展开更多
AIM： To investigate the hepatoprotective activity of tea polyphenols （TP） and its relation with cytochrome P450 （CYP450） expression in mice. METHODS： Hepatic CYP450 and CYPbs levels were measured by UV-spectroph...AIM： To investigate the hepatoprotective activity of tea polyphenols （TP） and its relation with cytochrome P450 （CYP450） expression in mice. METHODS： Hepatic CYP450 and CYPbs levels were measured by UV-spectrophotometry in mice 2 d after intraperitoneal TP （25, 50 and 100 mg/kg per day）. Then the mice were intragastricly pre-treated with TP （100, 200 and 400 mg/kg per day） for six days before paracetamol （1000 mg/kg） was given. Their acute mortality was compared with that of control mice. The mice were pre-treated with TP （100, 200, and 400 mg/kg per day） for five days before paracetamol （500 mg/kg） was given. Hepatic CYP2E1 and CYPIA2 protein and mRNA expression levels were evaluated by Western blotting, immunohistochemical staining and transcriptase-polymerase chain reaction. RESULTS： The hepatic CYP450 and CYPb5 levels in mice of TP-treated groups （100, 200 and 400 mg/kg per day） were decreased in a dose-dependent manner compared with those in the negative control mice.TP significantly attenuated the paracetamol-induced hepatic injury and dramatically reduced the mortality of paracetamol-treated mice. Furthermore, TP reduced CYP2E1 and CYPIA2 expression at both protein and mRNA levels in a dose-dependent manner. CONCLUSION： TP possess potential hepatoprotective properties and can suppress CYP450 expression.展开更多
文摘从分子层面对泛癌进行研究已经得到了很大的进展,但是对宫颈鳞状细胞癌的分子分类研究仍然需要更多的探索.为了找到宫颈鳞状细胞癌潜在的子类,本文提出了一个基于多维组学数据的癌症亚型分类分析流程.通过统计学方法对癌症基因组图谱(The Cancer Genome Atlas,TCGA)宫颈鳞状细胞癌的mRNA表达数据、小分子核糖核酸(microRNA,miRNA)表达数据、DNA甲基化数据以及拷贝数变异数据4个维度包含的分子进行筛选,然后对筛选后的分类特征进行整合聚类,进一步筛选能够区分不同子类的关键分类特征,并使用这些关键分类特征建立宫颈鳞状细胞癌分类模型.本研究为宫颈鳞状细胞癌分子层面子类的识别提供了分析流程,得到了两个临床生存水平具有显著性差异的宫颈鳞状细胞癌子类,并确定了8个宫颈鳞状细胞癌的关键分类特征.本研究中识别的宫颈鳞状细胞癌子类和关键分类特征为宫颈鳞状细胞癌早期分类及分类标志物的鉴定提供了重要参考.
文摘The fingerprints of 27 Leymus chinensis (Trin.) Tzvel accessions from different regions in China were generated and their genomic DNA variations were assayed via amplified fragment length polymorphism (AFLP). A total of 537 DNA fragments were amplified ranging from 75-530 bp using 8 AFLP primer combinations, among which 89 (16.6%) were monomorphic and 329 (61.3%) were polymorphic. The average number of DNA band produced by each primer combination was 66.13 and the total polymorphic rate was 78.84%. PICs (polymorphic information contents) scores for AFLP ranged from 0.0-0.5 and the mean PIC was 0.216. PIC scores were maximum (0.5) for 8.5% of the AFLP markers. All the results revealed that there was rich polymorphism in genomic DNA of L. chinensis . A DNA molecular dendrogram was established for 27 L. chinensis genotypes based on genetic variation and UPGMA cluster analysis of 537 AFLP markers amplified by 8 primer combination, suggesting that the genetic variation with high frequency showed close correlation with their ecotopes and geographical distributions. Twenty_seven L. chinensis genotypes could be divided into four groups. Among them the lower genetic relationship was shown. The reason of high genetic variation frequency in L. chinensis species and formation of varieties was discussed.
基金Supported by Key Projects of Basic Platform of the National Science and Technology (2005DKA21005 )National Natural Science Foundation-funded Projects (30260086)~~
文摘[Objective ] The study aimed to construct the AFLP molecular marking system in Mangifera indica. [ Method ] Four varieties of Mangifera indica were used to explore new ways for high-quality DNA, and AFLP analysis of 31 varieties of Mangifera indica was carried out to detect the varietal genetic diversity. [ Result] 14 pairs of primers with stronger polymorphism, better banding patterns and higher resolution were screened out from 64 pairs of selective amplification primers. Then they were used to analyse the fingerprint of 31 varieties of Mangifera indica, the results showed that the ratio of polymorphic bands amplificated by the 14 pairs of primers reached 97% in 31 varieties of Mangifera.[ Conclusion] It was suggested that AFLP was suitable for detecting the polymorphism of Mangifera indica resources.
文摘The phylogenetic relationships of four species,Bufo melanostictus,Hyla chinensis,Rana limnocharis and Rana guentheri,which belong to three differrent families of Anura,were detected with RAPD technique.The genomic DNA of each species was amplified with 19 random primers.16 primers given clear amplified bands were used for analysis and the genetic distances between four species were calculated.The results show that RAPD bands obtained by all 16 primers evinced different degree polymorphisms.The genetic distance between R.limnocharis and R.guentheri is the nearest,that between B.melanostictus and H.chinensis is the second nearest,and that between B.melanostictus and R.guentheri is the furthest.The different distances also indicated that the relationship between Bufoidae and Hylidae is closer than that between Bufonidae and Ranidae at genomic DNA level.In concordant with the conclusion of the morphology,chromosomal and mitochondrial DNA studies,our results provide a new evidence of the systematic evolution of the three families of Anura at DNA molecular level.
文摘Hepatocellular carcinoma(HCC)is the sixth most common malignancy and the fourth leading cause of cancer related death worldwide.China covers over half of cases,leading HCC to be a vital threaten to public health.Despite advances in diagnosis and treatments,high recurrence rate remains a major obstacle in HCC management.Multi-omics currently facilitates surveillance,precise diagnosis,and personalized treatment decision making in clinical setting.Non-invasive radiomics utilizes preoperative radiological imaging to reflect subtle pixel-level pattern changes that correlate to specific clinical outcomes.Radiomics has been widely used in histopathological diagnosis prediction,treatment response evaluation,and prognosis prediction.High-throughput sequencing and gene expression profiling enabled genomics and proteomics to identify distinct transcriptomic subclasses and recurrent genetic alterations in HCC,which would reveal the complex multistep process of the pathophysiology.The accumulation of big medical data and the development of artificial intelligence techniques are providing new insights for our better understanding of the mechanism of HCC via multi-omics,and show potential to convert surgical/intervention treatment into an antitumorigenic one,which would greatly advance precision medicine in HCC management.
基金Supported by the Key Program of National Natural Science Foundation of China (No.30730071)the National High Technology R&D Program of China(863 Program)(No.2012AA10A404)the Agricultural Science and Technology Achievements Transformation Funds Project(No.2010GB24910700)
文摘Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure.In this study,a set of 155 411 expressed sequence tags(ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms(SNPs) were predicted,including 9 546 transitions,5 124 transversions and 2 481 indels.Among the 7 298 SNP substitutions located in functionally annotated contigs,58.4%(4 262) are non-synonymous SNPs capable of introducing amino acid mutations.Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding.Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous,suggesting negative selection.Distribution of non-synonymous to synonymous substitutions(Ka/Ks) ratio ranges from 0 to 4.01,(average 0.42,median 0.26),suggesting that the majority of the affected genes are under purifying selection.Enrichment analysis identified multiple gene ontology categories under positive or negative selection.Categories involved in innate immune response and male gamete generation are rich in positively selected genes,which is similar to reports in Drosophila and primates.This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species.The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.
基金funded by the ‘908’ Marine Survey Project of Shandong Province (SD-908-01-01-05.06)
文摘The amplified fragment length polymorphic DNA (AFLP) technique was adopted to estimate the population genetic polymorphism among 30 sporophytes of Laminaria japonica collected from a cultivating farm in Rongcheng,China.Three methods were used for genomic DNA extraction from Laminaria japonica sporophyte and only the products obtained using the improved genomic DNA extraction kit method proved qualified for AFLP analysis.The parameters of the method were optimized.Samples of forty milligrams and the cell lysis time of 120 min were suggested to replace the parameters recommended by the manufacturer.Thirty individuals of Laminaria japonica from the same cultivating site were investigated using one pair of selective primers.A total of 21 loci were obtained and 17 of them were polymorphic.The mean percent age of polymorphic loci of this population was 80.95%.The Nei's gene diversity (H) within this population was 0.3028 and the average Shannon's Information index (I) was 0.4498.A genetic distance matrix among different individuals was constructed as well.Through this study,an applicable AFLP genetic analysis working system for Laminaria japonica sporophyte was established.The results of this research also revealed a high level of genetic diversity within the studied population.
基金Supported by 2010A310011 Henan Provincial Department of Education on Natural Science Research Projects
文摘AIM:To investigate the relationship between c.343A>G and c.2216A>C polymorphism sites in the CDH17 gene and colorectal carcinoma.METHODS:Ninety-three non-consanguineous colorectal carcinoma patients admitted to the Department of Oncology at the First Affiliated Hospital of Zhengzhou University were included in this study.Ninety-three peripheral venous blood samples,of approximately one milliliter from each patient,were collected betweenDecember 2009 and August 2010.The genomic DNA of these peripheral venous blood samples were extracted and purified using a Fermentas Genomic DNA Purification Kit(Fermentas,CA) according to the manufacturer' s protocol.The single nucleotide polymorphisms(SNPs) of the liver-intestine cadherin(CDH17) gene c.343A>G and c.2216A>C were determined by the polymerase chain reaction-single strand conformation polymorphism method(PCR-SSCP) in 93 peripheral venous blood samples from patients suffering with colorectal carcinoma.Typical samples that showed different migration bands in SSCP were confirmed by sequencing.Directed DNA sequencing was used to check the correctness of the genotype results from the PCR-SSCP method.RESULTS:There was a significant association between the c.2216 A>C SNPs of the CDH17 gene and the tumor-node-metastasis(TNM) grade,as well as with lymph node status,in 93 peripheral venous blood samples from colorectal carcinoma patients.The genotype frequencies of A/C,A/A,and C/C were 12.90%,33.33% and 53.76%,respectively.There was a significant correlation between lymph node metastasis,TNM grade,and the genotype distribution(P < 0.05).The C/C genotype raised the risk of lymph node metastasis and the TNM grade.There was a significant difference in the TNM grade and lymph node metastasis between the A/A and C/C genotypes(P = 0.003 and P = 0.013,respectively).Patients with colorectal carcinoma carrying the C allele tended to have a higher risk of lymph node metastasis and have a higher TNM grade.The difference between the TNM grades,as well as the lymph node metastasis of the two alleles,was statistically significant(P < 0.01).CONCLUSION:The SNPs of the CDH17 gene c.2216 A>C might be clinically important in the prognosis of colorectal carcinoma.
基金Supported by Grants SAF 2003-00967 from Ministerio de Ciencia y Tecnología and FIS 02/0255 from Fondo de Investigación Sanitaria,Instituto de Salud Carlos Ⅲ,Madrid,Spain
文摘AIM： To analyse the role of two common polymorphisms in genes coding for histamine metabolising enzymes as it relates to the risk to develop ulcerative colitis （UC） and the clinical course of these patients. METHODS： A cohort of 229 unrelated patients with UC recruited from a single centre and 261 healthy volunteers were analysed for the presence of Thr105Ile and His645Asp amino acid substitutions at histamine N-methyltransferase （HNMT） and diamine oxidase （ABP1） enzymes, respectively, by amplification-restriction procedures. All patients were phenotyped and followed up for at least 2 years （mean time 11 years）. RESULTS： There were no significant differences in the distribution of ABP1 alleles between ulcerative colitis patients and healthy individuals [OR （95% CI） for variant alleles = 1.22 （0.91-1.61）]. However, mutated ABP1 alleles were present with higher frequency among the 58 patients that required immunosuppresive drugs [OR （95 % CI） for carriers of mutated alleles 2.41 （1.21-4.83; P=0.006）], with a significant gene-dose effect （P= 0.0038）. In agreement with the predominant role of ABP1 versus HNMT on local histamine metabolism in human bowel, the frequencies for carriers of HNMT genotypes or mutated alleles were similar among patients,regardless clinical evolution, and control individuals. CONCLUSION： The His645Asp polymorphism of the histamine metabolising enzyme ABP1 is related to severity of ulcerative colitis.
文摘Objective： To investigate the association of XRCC4 polymorphic variants at G-1394T （rs6869366） with colorectal cancer susceptibility. Methods： In this hospital-based case-control study, the association of XRCC4 polymorphism with colorectal cancer risk in Chinese population was investigated. In total, 171 patients with colorectal cancer and 171 healthy individuals matched for age and gender were selected. The genomic DNAs of the patients and controls were extracted from peripheral blood and the 300 bp target DNA was amplified with Polymerase Chain Reaction. The products were then digested with restriction endonuclease HinclI, followed by agarose electrophoresis to identify the genotype. Results： We found a significant difference in the frequency of the XRCC4 G-1394T genotype between the colorectal cancer and control groups in female （1/127 vs 8/122, P〈0.05）. Those with G/T at XRCC4 G-1394T showed a decreased risk of colorectal cancer susceptibility compared with those with T/T （OR 0.113, 95%CI 0.014-0.932）. However, in overall population or in male, there was no significant difference of the distribution between the colorectal cancer and control groups. Conclusion： Our findings with decreased risk of colorectal cancer susceptibility suggested that the G allele of XRCC4 G-1394T were associated in female.
文摘By southern hybridization with 1. 8 kb cDNA probe,a high frequency （40. 5 % ） of structural abnor- mality of p53 gene was observed in primary nasopharyngeal carcinoma （NPC） biopsies. The regions of ex- ons 1 to 4 of the gene were examined by polymerase chain reaction-single strand con formation polymor- phism,no point mutation was found. Because very low rate of point mutation had been reported in exons 5 to 8, we considered that structural abnormality in the region of e-cons 1 to 8 of the gene might be uncom- mon in NPC. The spectrophotometer scanning analysis of autoradiograms and rehybridization investigation of nitrocellulose filter with exon 11 probe indicated that most of structure aberrations we observed might be rearrangement occurring in exon 11.
文摘Trichoderma is a fungal genus of great and demonstrable biotechnological value, but its genome is poorly surveyed compared with other model microorganisms. Due to their ubiquity and rapid substrate colonization, Trichoderma species have been widely used as biocontrol organisms for agriculture, and their enzyme systems are widely used in industry. Therefore, there is a clear interest to explore beyond the phenotype to exploit the underlying genetic systems using functional genomics tools. The great diversity of species within the Trichoderma genus, the absence of optimized systems for its exploration, and the great variety of genes expressed under a wide range of ambient conditions are the main challenges to consider when starting a comprehensive functional genomics study. An initial project started by three Spanish groups has been extended into the project TRICHOEST, funded by the EU (FP5, QLRT-2001-02032) to target the transcriptome analysis of selected Trichoderma strains with biocontrol potential, in conditions related to antagonism, nutrient stress and plant interactions. Once specific conditions were defined, cDNA libraries were produced and used for EST sequencing. Nine strains from seven Trichoderma species have been considered in this study and an important amount of gene sequence data has been generated, analyzed and used to compare the gene expression in different strains. In parallel to sequencing, genomic expression studies were carried out by means of macro-arrays to identify genes expressed in specific conditions. In silico analysis of DNA sequencing data together with macro-array expression results have lead to a selection based on the potential use of the gene sequences. The selected clone sequences were completed and cloned in appropriate vectors to initiate functional analysis by means of expression studies in homologous and heterologous systems.
文摘An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot divergence in the genome of rice (Oryza sativa L.), as inferred from the age distribution of pairs of duplicate genes based on recent genome data for rice. Our results suggest that paleopolyploidy was widespread and played an important role in the evolution of rice.
文摘Viruses including baculoviruses are obligatory parasites, as their genomes do not encode all the proteins required for replication. Therefore, viruses have evolved to exploit the behavior and the physiology of their hosts and olden coevolved with their hosts over millions of years. Recent comparative analyses of complete genome sequences of baculoviruses revealed the patterns of gene acquisitions and losses that have occurred during baculovirus evolution. In addition, knowledge of virus genes has also provided understanding of the mechanism of baculovirus infection including replication, species-specific virulence and host range. The Bm8 gene of Bombyx mori nucleopolyhedrovirus （NPV） and its homologues are found only in group I NPV genomes. The Autographa californica NPV Ac 16 gene is a homologue of Bm8 and, encodes a viral structural protein. It has been shown that BmS/Ac 16 interacts with baculoviral and cellular proteins. BmS/Ac 16 interacts with baculoviral IE1 that is facilitated by coiled coil domains, and the interaction with IE1 is important for Bin8 function. Acl6 also forms a complex with viral FP25 and cellular actin and associates with membranes via palmitoylation. These data suggested that this gene family encodes a multifunctional protein that accomplishes specific needs of group I NPVs.
文摘Objective:Vitamin D receptor(VDR)mediates vitamin D activity.We examined whether VDR expression in excised melanoma tissues is associated with VDR gene(VDR)polymorphisms.Methods:We evaluated VDR protein expression(by monoclonal antibody immunostaining),melanoma characteristics,and carriage of VDR-Fok I-rs2228570(C>T),VDR-Bsm I-rs1544410(G>A),VDR-ApaI-rs7975232(T>G),and VDR-TaqI-rs731236(T>C)polymorphisms(by restriction fragment length polymorphism).Absence or presence of restriction site was denoted by a capital or lower letter,respectively:"F"and"f"for Fok I,"B"and"b"for Bsm I,"A"and"a"for ApaI,and "T"and"t"for TaqI endonuclease.Seventy-four Italian cutaneous primary melanomas(52.1±12.7 years old)were studied;51.4% were stage Ⅰ,21.6% stage Ⅱ ,13.5% stage Ⅲ,and 13.5% stage Ⅳ melanomas.VDR expression was categorized as follows:100% positive vs.<100%;over the median 20%(high VDR expression)vs.≤20%(low VDR expression);absence vs.presence of VDR-expressing cells.Results:Stage I melanomas,Breslow thickness of<1.00 mm,level II Clark invasion,Aa heterozygous genotype,and AaTT combined genotype were more frequent in melanomas with high vs.low VDR expression.Combined genotypes BbAA,bbAa,AATt,BbAATt,and bbAaTT were more frequent in 100%vs.<100%VDR-expressing cells.Combined genotype AATT was more frequent in melanomas lacking VDR expression(odds ratio=14.5;P=0.025).VDR expression was not associated with metastasis,ulceration,mitosis>1,regression,tumor-infiltrating lymphocytes,tumoral infiltration of vascular tissues,additional skin and non-skin cancers,and melanoma familiarity.Conclusions:We highlighted that VDR polymorphisms can affect VDR expression in excised melanoma cells.Low VDR expression in AATT carriers is a new finding that merits further study.VDR expression possibly poses implications for vitamin D supplementation against melanoma.VDR expression and VDR genotype may become precise medicinal tools for melanoma in the future.
基金Grant from the Science Foundation of Educational Department of Liaoning Province,05L117Dalian Science&Technology Bureau,2007J22JH012
文摘AIM： To investigate the hepatoprotective activity of tea polyphenols （TP） and its relation with cytochrome P450 （CYP450） expression in mice. METHODS： Hepatic CYP450 and CYPbs levels were measured by UV-spectrophotometry in mice 2 d after intraperitoneal TP （25, 50 and 100 mg/kg per day）. Then the mice were intragastricly pre-treated with TP （100, 200 and 400 mg/kg per day） for six days before paracetamol （1000 mg/kg） was given. Their acute mortality was compared with that of control mice. The mice were pre-treated with TP （100, 200, and 400 mg/kg per day） for five days before paracetamol （500 mg/kg） was given. Hepatic CYP2E1 and CYPIA2 protein and mRNA expression levels were evaluated by Western blotting, immunohistochemical staining and transcriptase-polymerase chain reaction. RESULTS： The hepatic CYP450 and CYPb5 levels in mice of TP-treated groups （100, 200 and 400 mg/kg per day） were decreased in a dose-dependent manner compared with those in the negative control mice.TP significantly attenuated the paracetamol-induced hepatic injury and dramatically reduced the mortality of paracetamol-treated mice. Furthermore, TP reduced CYP2E1 and CYPIA2 expression at both protein and mRNA levels in a dose-dependent manner. CONCLUSION： TP possess potential hepatoprotective properties and can suppress CYP450 expression.
