Progress of Microsatellite (GT/CA)n Repeat Polymorphisms in Non-small Cell Lung Cancer / 肿瘤防治研究

Non-small cell lung cancer (NSCLC) is the most important histological type of lung cancer. This disease affects a large number of patients, and the prognosis of advanced patients is poor. Although great progress has been achieved for existing treatment methods, challenges still exist. Cancer is a genetic disease, and its occurrence is accompanied by substantial genomic-sequence instability. (GT/CA)n repeat sequence is a common microsatellite sequence serving as transcriptional function-related regions, DNA-methylation modification sites, and other functional sites. Its polymorphism is closely related to the expression of EGFR, HO-1, and HIF-1α in NSCLC patients. (GT/CA)n repeat sequence is the breakthrough point to explore the molecular mechanism of NSCLC occurrence and development, develop molecular markers for diagnosis and prognosis and epigenetics research. This paper summarizes the studies on (GT/CA)n repeat polymorphisms in NSCLC with the aim of providing references for relevant NSCLC research.

Progress in Research on the Novel Tumor Marker circRNA / 中国医学科学院学报

Circular RNA(circRNA)is a novel type of endogenous non-coding RNA.Most circRNAs act as microRNA(miRNA)sponges to regulate the expression of functional genes.In addition,some circRNAs can be translated and interact with RNA-binding proteins to perform biological functions.The expression of circRNAs is prevalent in tissues and body fluids,and their abnormal expression is related to tumor progression.circRNAs are stable even under the treatment of RNase R because of their circular conformation.As circRNAs have construct stability,wide variety,specific regulation of tumor progression and high expression in body fluids,it is potential for circRNAs to serve as candidate diagnostic,prognostic and therapeutic targets.However,the knowledge about circRNAs remains poor.In addition to the not completely resolved functions and generation mechanisms of circRNAs,the annotations of circRNAs are also waiting for expanding.Here,we review the generation mechanisms,biological functions,and application of circRNAs in tumor research,aiming to provide integrated information for the future research.

Comparative analysis of three complete chloroplast genomes of Inula genus with phylogenetic analysis of 49 plants from Carduoideae / 药学学报

italic>Inula japonica, Inula hupehensis and Inula linaariifolia are all medicinal plants of Inula L. in the Compositae family, and Inula hupehensis is endemic to China. In order to compare their genomic sequence differences and provide scientific basis for their germplasm conservation and development, we obtained and analyzed the complete chloroplast genomes of these three species. Total DNAs were extracted from fresh leaves and subjected to next-generation DNA sequencing. NOVOPlasty was used to assemble the chloroplast genomes from the sequence reads. CPGAVAS2 was used to annotate the genes and repeats in each genome. Lastly, phylogenomics analysis was conducted using RAxML. The results showed that the total length of the chloroplast genome of Inula japonica, Inula hupehensis and Inula linaariifolia is 150 754, 150 909, and 150 812 bp respectively, each consisting of a large single copy region, a small single copy region and a pair of inverted repeat regions. In addition, the G/C content of all three chloroplast genomes was approximately 37.7% and each encoded 111 unique genes, including 79 protein-coding, 28 tRNA and 4 rRNA genes. Meanwhile, 32, 33, 34 simple repeat sequences, 18, 22, 18 tandem repeat sequences and 33, 37, 38 scattered repeat sequences were identified in three species. Phylogenomic analysis showed that all three species of Inula L. and Pluchea indica were clustered together, with the relationship between Inuleae and Senecioneae closer, suggesting that Inuleae may have originated from the Senecioneae, not the Cardueae. The data in this study not only enriches the chloroplast genome database of Inula L., but also lays the foundation for the future studies of species identification, phylogenetic relationships, evolution history and genetic diversity of Inula species.

A method to predict clustered repeats in Salmonella genomes / 基础医学与临床

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 .

Observation and analysis of STR loci mutation among 1 786 cases of paternity test in Guangxi area / 重庆医学

Objective To observe and analyze the mutation characteristics of 17 STR loci among the paternity test cases in Guangxi area .Methods Among 1 786 cases of non—exclusion parentage ,1 430 cases were parental triplet and 356 cases were uniparental diad ,1 001 persons were Han people ,2 102 persons were Zhuang people and 113 persons were other ethnic group in the parents .The genome DNA was extracted by Chelex-100 method .17 short tandem repeat (STR) loci were detected by Power Plex ? 18D System Kit .The paternity testing containing mutant STR loci were screened out from 1786 cases .The locus-specific ,specificity of paternal and maternal ,and allele-specific mutation rates were observed and analyzed ,respectively .The characteristics of the muta-tions were studied .Results In total ,75 mutations events were observed at 16 of the 17 loci .Among them ,73 (97 .34% ) times were one step mutation ,onece(1 .33% ) was two—step mutation ,and once(1 .33% ) was three—step mutation ,no mutation was found at the TPOX locus .The mutation rates ranged 0 .031 1% —0 .404 2% ,and the mean mutation rate was 0 .145 8% .The proportion of the paternal mutations and the maternal mutations was 5 .4:1 .0 ,the difference had statistical significance(P0 .05) .Conclusion STR loci mutation is common phenomenon in paternity test .The data of STR loci mutations should be constantly accumulated for selecting the genetic characteristics in line with the Guangxi population and the genetic markers of STR loci with high identification ability to ensure ac-curate and reliable identification results .

Related research of male breast cancer and CAG repeat polymorphism of AR gene / 实用肿瘤学杂志

Objectiv e To investigate the correlation between ( CAG) n repeat polymorphism of androgen receptor(AR)geneandmalebreastcancer.Methods 40casesofmalebreastcancerand40controlswerecol-lected.DNA was extracted from peripheral blood and the AR gene CAG coding exon sequences for PCR amplifica -tion,sequencing and calculated the number of CAG repeats frquency .χ2 test and Logistic regression analysis were used assess the AR gene CAG repeat length frequency affect the number of male breast cancer risk .Results There was statistically significant difference in male breast cancer cases and controls the number of CAG repeat length frequency.Man for whom the(CAG)n≥22 repeat sequence had 3.52 times risk of male breast compared (CAG)n≤22(OR=3.52,P=0.036).Conclusion AR gene CAG repeat length is a predictor of the frequency of male breast cancer risk .Longer CAG repeats can increase the risk of male breast cancer .

Genotipificación de Mycobacterium leprae colombiano para la determinación de patrones de transmisión de la enfermedad / Genotyping colombian Mycobacterium leprae for determining disease transmission patterns

Objetivo Evaluar la variabilidad de VNTR (variable-number tandem repeat) de Mycobacterium leprae de pacientes colombianos con y sin tratamiento previo para identificar posibles fuentes de infección y entender los patrones de transmisión de la enfermedad. Metodología Estudio transversal descriptivo, en donde mediante un muestreo electivo a conveniencia se tomaron 161 biopsias de pacientes multibacilares de lepra, que habían sido solicitadas para diagnóstico y seguimiento de la enfermedad, de las cuales se realizó extracción de ADN de M. leprae y usando la técnica de PCR para VNTRs de M. leprae estandarizada, se establecieron los genotipos y los diferentes clusters mediante el agrupamiento apareado UPGMA. Resultados En las 161 muestras totales se hallaron 22 genotipos VNTRs diferentes, de las cuales 100 muestras (62,1 por ciento) pertenecían al genotipo único VNTRU, y de los genotipos restantes, los mayoritarios, es decir los que dieron lugar a formación de grupos o clusters fueron VNTR17 (5,6 por ciento), VNTR20 (4,3 por ciento), VNTR18 (4,3 por ciento), VNTR14 (4,3 por ciento) y VNTR13 (3,7 por ciento). Conclusión En este estudio se evidencia por análisis de agrupamiento que se pueden detectar clones con diferente grado de virulencia/agresividad, lo cual implica la necesidad de incrementar varias de las actividades del programa de control que darán como resultado la verdadera disminución de la transmisión del microorganismo.

Objective Assessing VNTR (variable-number tandem repeat) variability of Mycobacterium leprae from Colombian patients with and without prior treatment to identify potential sources of infection and to understand the patterns of disease transmission. Methodology This was a descriptive cross-sectional study where a convenience sample of biopsies was taken from 161 multibacillary leprosy patients; diagnosis and monitoring of the disease had been requested for these patients. DNA was extracted from M. leprae and standardised using the PCR technique for M. leprae VNTR, ge­notypes were established and different clusters grouped by unweighted pair group method with arithmetic mean (UPGMA). Results 22 different VNTR genotypes were found from 161 samples, of which 100 samples (62.1 percent) had a single u-VNTR genotype and the remaining genotypes were VNTR 17 (5.6 percent), VNTR 20 (4.3 percent), VNTR 18 (4.3 percent), VNTR 14 (4.3 percent) and VNTR 13 (3.7 percent), namely those forming groups or clusters. Conclusion This study showed that clones can be detected with varying degrees of virulence / aggressiveness by cluster analysis, implying the need for more monitoring programme activities which will result in a real decline in microorganism transmission.

The association of a CA repeat polymorphism in ER? gene with unknown aetiology hypomenorrhea / 重庆医科大学学报

20. Case group SS genotype rate was 66%,control group 51%,OR=1.865(95%CI:1.055～3.298).The SS and LL allele genotypes frequency was compared in two groups and the difference was significant(?2=4.634,P=0.031). Conclusion:ER? gene CA repeat polymorphism is related to unknown aetiological hypomenorrhea. SS allele genotype may be the risk factor of unknown aetiological hypomenorrhea.

Relationship between Mutation of IR in the mtr System of Neisseria Gonorrhoeae and Multiple Antibiotic Resistance / 华中科技大学学报（医学）（英德文版）

To study the relationship between mutation of the inverted repeat sequence (IR) in the multiple transferable resistant system (mtr) of Neisseria gonorrhoeae (NG) and itsmultiple antibiotic resistance, minimal inhibitory concentrations (MICs) for the clinically isolated strains were tested by agar-dilution-method. The mtr system's IR gene of NG was sequenced after amplification by polymerase chain reaction (PCR). Either two susce ptive or five penicillin-resistant strains had no base mutation in IR gene, while all of the 13 strains with multiple-antibiotic-resistance had a singlebase deletion (A/T). The result suggests that a single-base deletion of the thirteen-base IR sequence in mtr system of NG might result in multiple antibiotic resistance but is not associated with single antibiotic resistance.

The association of a TA repeat polymorphism in ERa gene with unknown aetiology hypomenorrhea / 重庆医科大学学报

Objective:To investigate the association of a(TA)n dinucleotide repeat polymorphism with unknown aetiology hypomenorrhea.Methods:100 normal menstruation person(control group) and 100 hypomenorrhea patients(case group)were recruited.they all came from southen-western China.The(TA)n dinucleotide repeat in ERa gene upstream hypervariable region were purifed,cloned and sequence analysed.we observe the ERa gene(TA)n dinucleotide repeat polymorphism distribution in the two groups.Results:All samples exhibted 7 different alleles.The(TA)n dinucleotide repeats were 11~17,The most prevalent allele was TA14 repeat in control group.The distribution of the different alleles of the(TA)n dinucleotide repeat sequence in the group and control group has significant difference(?2=13.412,P =0.037).Fisher's exact test was applied to compare the frequency of each a1lele between two groups.The frenquency of the TA13 allele was found to be significantly greater in hypomenorrhea group(P =0.006),and the frenquency of the TA15 allele was less in the group(P =0.033).Conclusion:A(TA)n dinucleotide repeat sequence which is in ERa gene upstream hypervariable region was associated with unknown aetiology hypomenorrhea.The TA13 allele was found to be associated with unknown aetiology hypomenorrhea and may be a risk factor;whereas TA15 allele may be a protective factor for patients.