[Objective] To study the inhibition effect of berberine on cell proliferation in acute T lymphocytic leukemia cell line Molt-4,and its mechanisms.[Methods] The logarithmic growing cell lines were incubated with 0,10,100 μg/ml berberine for various hours.The apoptosis induced by berberine was detected by flow cytometry,eletrophoresis and microscopy.The protein pro-Caspase-3 and p65 were determined by Western bolt assay.[Results]Treated with berberine,Molt-4 cells were found with apoptosis bodies by microscopy.By flow cytometry,it was found that number of G2/M cells was increased and number of S cells was reduced.Necrosis band was found in DNA ladder electrophoresis.The expression of pro Caspase-3 was activated partly and p65 was down-regulated in Molt-4 cells treated with berberine.[Conclusion]Berberine can induce Molt-4 cells apoptosis, and NF-κB、Caspase-3 have been shown to regulate the apoptosis programme.

Objective To develop a simple method identifying and illustrating clustered repeats in bacterial ge-nomes, and to observe the patterns of clustered repeats in Salmonella genomes.Methods Bacterial genomes were cut to be overlapped pieces of identical size with a sliding window strategy .Each piece of genome fragment was aligned against itself with BLAT integrated in PipMaker , which was further used to build collinearity figures . Collinearity figures were analyzed to identify the clustered repeats.Results With the new pipeline CRpred ( Clustered Repeat Predicter) , Salmonella typhimurium LT2 genome was screened, and in 151 clustered repeats were disclosed.Pattern analysis on these repeats indicated that there were five categories, including low-copy simple tandem repeats, high-copy simple tandem repeats, interspaced tandem repeats, reverse-complementary re-peats, and interspaced reverse-complementary repeats.Nine repeat regions in LT2 genome were discovered which could not be simply classified into the 5 categories defined above.Conclusions A new, simple and intuitive strategy is proposed to identify and show clustered repeats in genomes , providing clues for CRISPR , VNTR and oth-er repeat-related studies .

Objective To study the distribution and evolution of yiiG, a Salmonella gene encoding a candidate type secretedsubstrate .Methods Salmonella genomes were comprehensively screened for yiiG distribution with se-quence alignment strategies .The evolutionary history of yiiG was traced .Comparative genomic analysis was per-formed to study the evolutionary mechanisms of yiiG gene acquisition , loss and duplication .RNA-seq data were combined to analyzing the correlation between yiiG and other virulence factors .A variety of bioinformatic tools were used for discovering the possible type Ⅲsecretion signals .Results yiiG distributed in S.enterica subsp.enterica but variable in other subspecies of S.enterica.No yiiG was found in S.bongori.Besides Salmonella, only a part of Shigella and E.coli strains were detected with yiiG homologs .The genomic locus of yiiG and its adjacency showed conservation among all Salmonella, E.coli and Shigella strains.In most of the serovars of S.enterica subsp.enteri-ca, there was a head-to-head tandem whole yiiG repeat sequence upstream the yiiG gene, which was renamed as yiiGRrc.RNA-seq analysis showed that yiiG gene expression level was highly correlated with T 3SS-related genes . Bioinformatic prediction also indicated the T 3SS effector signals in YiiG N-terminus.Conclusions yiiG represented an ancient genomic locus , which will be a hot spot where rearrangement events frequently happened .The function of yiiG could potentially be related with Salmonella virulence.Finally, a new protein-encoding gene (yiiGRrc) was newly identified that was closely related with yiiG, providing the target for further understanding the composition , function and function variation of yiiG gene family .

We have discovered copy number variations (CNVs) in 3,578 Korean individuals with the Affymetrix Genome-Wide SNP array 5.0, and 4,003 copy number variation regions (CNVRs) were defined in a previous study. To explore the details of the variants easily in related studies, we built a database, cataloging the CNVs and related information. This system helps researchers browsing these variants with gene and structure variant annotations. Users can easily find specific regions with search options and verify them from system-integrated genome browsers with annotations.
Asian Continental Ancestry Group ; Cataloging ; Coat Protein Complex I ; Genome ; Humans

Objective: The aim of this study was to evaluate the influence of concomitant carcinoma in situ (CCIS) on tumor survival for the upper tract urinary carcinoma (UTUC) through systematic review and meta-analysis. Methods: In the light of Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines, a systematic search of Web of Science, PubMed and EMBASE China National Knowledge Infrastructure (CNKI) and Wanfang database by key words "upper urinary tract urothelial carcinoma" "renal sputum cancer" "concomitant carcinoma in situ" , and "radical ureterectomy" were performed for all reports that included detailed results on the predictors of CCIS. The search deadline is June 2019, and the search terms are English and Chinese. Methodological quality evaluation was performed using the QUIPS tool, and statistical analysis of the relevant data was performed using Stata 12.0 and RevMan 5.3 software. Results: Sixteen articles were included in this study and all published between 2012 and 2019. A total of 11 131 patients with UTUC, including 1 774 (15.9%) patients with CCIS. According to our final results, there was a significant correlation of CCIS with worse cancer-specific survival (CSS) (HR=1.10, 95%CI 1.05-1.16, P<0.001), recurrence-free survival (RFS) (HR=1.15, 95%CI 1.09-1.21, P<0.001) and overall survival (OS) (HR=1.10, 95%CI 1.03-1.17, P=0.003). Begg′s bias analysis showed no significant publication bias in CSS (P=0.822), RFS (P=0.348), and OS (P=0.452). Conclusions This study demonstrated that CCIS was associated with poor oncological outcome and could serve as a independent prognostic factor for patient with UTUC after radical nephroureterectomy.

Amphioxus is an extant species closest to the ancestry of vertebrates.Observation of microRNA(miRNA)distribution of amphioxus would lend some hints for evolutionary research of vertebrates.In this study,using the publicly available scaffold data of the Florida amphioxus(Branchiostoma floridae)genome,we screened and characterized homologs of miRNAs that had been identified in other species.In total,68 pieces of such homologs were obtained and classified into 33 families.Most of these miRNAs were distributed as clusters in genome.Inter-species comparison showed that many miRNAs,which had been thought as vertebrate-or mammal-specific before,were also present in amphioxus,while some miRNAs that had been considered as protostome-specific before also existed in amphioxus.Compared with ciona,amphioxus had an apparent miRNA gene expansion,but phylogenetic analysis showed that the duplicated miRNAs or clusters of amphioxus had a higher homology level than those duplicated ones in vertebrates.

Together with single nucleotide polymorphism (SNP), copy number variations (CNV) are recognized to be the major component of human genetic diversity and used as a genetic marker in many disease association studies. Affymetrix Genome-wide SNP 5.0 is one of the commonly used SNP array platforms for SNP-GWAS as well as CNV analysis. However, there has been no report that validated the accuracy and reproducibility of CNVs identified by Affymetrix SNP array 5.0. In this study, we compared the characteristics of CNVs from the same set of genomic DNAs detected by three different array platforms; Affymetrix SNP array 5.0, Agilent 2X244K CNV array and NimbleGen 2.1M CNV array. In our analysis, Affymetrix SNP array 5.0 seems to detect CNVs in a reliable manner, which can be applied for association studies. However, for the purpose of defining CNVs in detail, Affymetrix Genome-wide SNP 5.0 might be relatively less ideal than NimbleGen 2.1M CNV array and Agilent 2X244K CNV array, which outperform Affymetrix array for defining the small-sized single copy variants. This result will help researchers to select a suitable array platform for CNV analysis.
Coat Protein Complex I ; DNA ; Genetic Markers ; Genetic Variation ; Humans ; Polymorphism, Single Nucleotide

Although autism spectrum disorder (ASD) has been thought to have a substantial genetic background, major contributing genes have yet to be identified or successfully replicated. Immunological dysfunction has been suggested to be associated with ASD, and T cell-mediated immunity was considered important for the development of ASD. In this study, we analyzed 163 ASD subjects and 97 normal controls by genomic quantitative PCR to evaluate the association between the copy number variation of the 7q34 locus, harboring the TCRB gene, and ASDs. As a result, there was no significant difference of the frequency distribution of TCRB copy numbers between ASD cases and normal controls. TCRB gene copy numbers ranged from 0 to 5 copies, and the frequency distribution of each copy number was similar between the two groups. The proportion of the individuals with <2 copies of TCRB was 52.8% (86/163) in ASD cases and 57.1% (52/91) in the control group (p=0.44). The proportion of individuals with >2 copies of TCRB was 11.7% (19/163) in ASD cases and 12.1% (11/91) in the control group (p=0.68). After the effects of sex were adjusted by logistic regression, ORs for individuals with <2 copies or >2 copies showed no significant difference compared with the diploid copy number as reference (n=2). Although we could not see the positive association, our results will be valuable information for mining ASD-associated genes and for exploring the role of T cell immunity further in the pathogenesis of ASD.
Autistic Disorder ; Child ; Coat Protein Complex I ; Diploidy ; Electrolytes ; Gene Dosage ; Immunity, Cellular ; Logistic Models ; Mining ; Polymerase Chain Reaction ; Autism Spectrum Disorder

Objective To systematically evaluate the expression of microvascular invasion (MVI) in predicting the clinical prognosis of patients with non-metastatic renal cell cancer (nmRCC) after surgical operation.Methods The relevant search strategy,including and excluding criteria for the relevant literature were developed by two independent researchers.Pubmed,EMBASE,China National Knowledge Infrastructure (CNKI),and Wanfang databases were searched from the inception to May 2018 for the study of tumor prognosis in the patients of nmRCC with MVI following surgical resection.The search language was English and Chinese.The methodological quality of the included studies was assessed by the NOS.Stata 12.0 software and Review Manager 5.3 were used to perform a clinical meta-analysis of relevant literature data.Results A total of 25 related clinical studies were included,published from 2004 to 2018.There were 6 741 patients with nmRCC,of which 1 768 cases of MVI,with a proportion rate of 26.2％.The results showed that the patients with MVI in pathological sections had a lower cancer-specific survival rate (CSS) [HR =1.51,95％ CI(1.41-1.62),P ＜0.001],recurrence-free survival rate(RFS) [HR =1.47,95％ CI (1.26-1.71),P＜0.001] and overall survival rate(OS) [HR=1.37,95％C1(1.19-1.57),P＜ 0.001].Egger's publication bias analysis showed no significant publication bias in terms of CSS (t =1.43,P=0.176),RFS (t =1.21,P=0.253) and OS(t =0.37,P=0.725).Conclusions MVI had a significant poor outcome in patients with surgical resection of nmRCC.It can be used as an independent risk factor to evaluate the postoperative prognosis of those patients.

Although the genetic component in the etiology of rheumatoid arthritis (RA) has been consistently suggested, many novel genetic loci remain to uncover. To identify RA risk loci, we performed a genome-wide association study (GWAS) with 100 RA cases and 600 controls using Affymetrix SNP array 5.0. The candidate risk locus (APOM gene) was re-sequenced to discover novel promoter and coding variants in a group of the subjects. Replication was performed with the independent case-control set comprising of 578 RAs and 711 controls. Through GWAS, we identified a novel SNP associated with RA at the APOM gene in the MHC class III region on 6p21.33 (rs805297, odds ratio (OR) = 2.28, P = 5.20 x 10(-7)). Three more polymorphisms were identified at the promoter region of the APOM by the re-sequencing. For the replication, we genotyped the four SNP loci in the independent case-control set. The association of rs805297 identified by GWAS was successfully replicated (OR = 1.40, P = 6.65 x 10(-5)). The association became more significant in the combined analysis of discovery and replication sets (OR = 1.56, P = 2.73 +/- 10(-10)). The individuals with the rs805297 risk allele (A) at the promoter region showed a significantly lower level of APOM expression compared with those with the protective allele (C) homozygote. In the logistic regressions by the phenotype status, the homozygote risk genotype (A/A) consistently showed higher ORs than the heterozygote one (A/C) for the phenotype-positive RAs. These results indicate that APOM promoter polymorphisms are significantly associated with the susceptibility to RA.
Apolipoproteins/*genetics ; Arthritis, Rheumatoid/*genetics ; Case-Control Studies ; DNA/genetics ; Female ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; Genotype ; Heterozygote ; Homozygote ; Humans ; Lipocalins/*genetics ; Luciferases/metabolism ; Male ; Middle Aged ; Polymorphism, Single Nucleotide/*genetics ; Promoter Regions, Genetic/*genetics ; Real-Time Polymerase Chain Reaction ; Risk Factors