Identification of Scolopendra Dispensing Granules by Allele-specific PCR / 中国实验方剂学杂志

ObjectiveTo establish an allele-specific polymerase chain reaction （PCR） method for identifying Scolopendra dispensing granules， so as to ensure the quality and therapeutic effects of Scolopendra and its preparations. MethodThe primer interval suitable for the PCR was selected based on the cytochrome c oxidase subunit 3（COX-3） gene sequence of Scolopendra， and the single nucleotide polymorphism （SNP） loci of Scolopendra and its adulterants were mined from the interval for the design of specific primers. The samples of Scolopendra and its adulterants were collected. The PCR system was established and optimized regarding the annealing temperature， cycles， Taq enzymes， DNA template amount， PCR instruments， and primer concentrations， and the specificity and applicability of this method were evaluated. ResultThe PCR system was composed of 12.5 μL 2×M5 PCR Mix， 0.4 μL forward primer （10 μmol·L-1）， 0.4 μL reverse primer （10 μmol·L-1）， 2.5 μL DNA template， and 9.2 μL sterile double distilled water. PCR parameters： Pre-denaturation at 94 ℃ for 3 min， 30 cycles （94 ℃ for 20 s， 62 ℃ for 20 s， 72 ℃ for 45 s）， and extension at 72 ℃ for 5 min. After PCR amplification with the system and parameters above， the electrophoresis revealed a bright band at about 135 bp for Scolopendra and no band for the adulterants. ConclusionThe established allele-specific PCR method can accurately identify the medicinal materials， decoction pieces， and standard decoction freeze-dried powder of Scolopendra， as well as the intermediates and final products of Scolopendra dispensing granules， which is of great significance for ensuring the quality and clinical efficacy of Scolopendra and its preparations.

The importance of deep genotyping in crop breeding / La importancia de la genotipificación profunda en el mejoramiento genético

ABSTRACT One of the greatest challenges facing humanity is the development of sustainable strategies to ensure food availability in response to population growth and climate change. One approach that can contribute to increase food security is to close yield gaps and enhancing genetic gain; to such end, what is known as "molecular breeding" plays a fundamental role. Since a crop breeding program is mainly based on the quality of the germplasm, its detailed genetic characterization is mandatory to ensure the efficient use of genetic resources and accelerating development of superior varieties. Deep genotyping is an essential tool for a comprehensive characterization of the germplasm of interest and, fortunately, the technology is now accessible at a reasonable cost. What must be ensured is the correct interpretation of the genotypic information and on that basis develop efficient practical molecular crop breeding strategies that respond to the real needs of the breeding program.

RESUMEN Uno de los mayores desafíos que enfrenta la humanidad es el desarrollo de estrategias sostenibles para asegurar la disponibilidad de alimentos en respuesta al crecimiento de la población y el cambio climático. Un enfoque que puede contribuir a aumentar la seguridad alimentaria es cerrar las brechas de rendimiento y mejorar la ganancia genética; para tal fin, lo que se conoce como "mejoramiento molecular" juega un papel fundamental. Dado que un programa de mejoramiento de cultivos se basa principalmente en la calidad del germoplasma, su caracterización genética detallada es fundamental para garantizar el uso eficiente de los recursos genéticos y acelerar el desarrollo de variedades superiores. La genotipificación profunda es una herramienta esencial para una caracterización integral del germoplasma de interés y, afortunadamente, en la actualidad se puede acceder a la tecnología a un costo razonable. Lo que debe asegurarse es la interpretación correcta de la información genotípica y sobre esa base desarrollar estrategias eficientes y prácticas de mejoramiento molecular de cultivos que respondan a las necesidades reales del programa de mejoramiento.

Performance of the tetra-primer PCR technique compared to PCR-RFLP in the search for rs12979860 (C/T) and rs8099917 (T/G) single nucleotide polymorphisms (SNPs) in the IFNL4 gene / Desempenho da técnica tetra-primer PCR em relação a PCR-RFLP na pesquisa de polimorfismos de nucleotídeos únicos (SNPs) rs12979860 (C/T) e rs8099917 (T/G) no gene IFNL4

Single nucleotide polymorphisms (SNPs, rs12979860 e rs8099917) in the Interferon Lambda 4 gene (IFNL4, formerly IFNL3and/or IL28B) has been associated with failure in the innate immune response, sustained virological response in hepatitis C, and HTLV-1-associated myelopathy (HAM) development. To search for these polymorphisms several methodologies can be employed, such as sequencing, real-time or quantitative polymerase chain reaction (qPCR), restriction fragment length polymorphism analysis in PCR products (PCR-RFLP), and tetra-primer PCR. The present study compared the performance of the tetra-primer PCR in relation to the PCR-RFLP, both optimized in the Research HTLV Laboratory of the Center of Immunology of Instituto Adolfo Lutz in São Paulo. One hundred DNA samples obtained from patients of STD/Aids Reference Centre in São Paulo, previously analyzed for IL28B SNPs by PCR-RFLP were selected for analysis, after confirming that they represent all IL28B SNPs patterns described in the literature. The results obtained showed concordance between the PCR-RFLP and the tetra-primer PCR SNPs results, and because of the low cost, easy to perform, and minor employment of biological specimen and reagents, the tetra-primer PCR is of choice to be used in routine. (AU)

Polimorfismos de nucleotídeos únicos (single nucleotide polymorphisms, SNPs rs12979860 e rs8099917) no gene que codifica o Interferon Lambda 4 (IFNL4, antigamente IFNL3 e/ou IL28B) têm sido associados às falhas na resposta imune inata e resposta virológica sustentada na hepatite C, e a mielopatia associada ao HTLV-1 (HTLV-1-associated myelopathy, HAM). A pesquisa destes polimorfismos pode empregar diversas metodologias: sequenciamento, reação em cadeia da polimerase em tempo real ou quantitativa (quantitative polymerase chain reaction, qPCR), análise de fragmentos de restrição enzimática em produtos de PCR (restriction fragment length polymorphism in PCR products, PCR-RFLP) e a tetra-primer PCR. Este estudo comparou o desempenho da tetra-primer PCR em relação a PCR-RFLP, ambas otimizadas no Laboratório de Pesquisa em HTLV do Centro de Imunologia do Instituto Adolfo Lutz de São Paulo. Foram selecionadas 100 amostras de DNA obtidas de pacientes do Centro de Referência e Treinamento em DST/Aids de São Paulo cujos SNPs na IL28B foram anteriormente determinados por PCR-RFLP e representaram todos os perfis descritos em literatura. Os resultados obtidos mostraram concordância entre elas, e pelo fato da tetra-primer PCR ter menor custo, ser de fácil execução, empregar menos tempo, insumos e material biológico, é a técnica de escolha para uso em rotina. (AU)

Role of melatonin receptor 1B gene polymorphism and its effect on the regulation of glucose transport in gestational diabetes mellitus / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Melatonin receptor 1B (MT2, encoded by the MTNR1B gene), a high-affinity receptor for melatonin, is associated with glucose homeostasis including glucose uptake and transport. The rs10830963 variant in the MTNR1B gene is linked to glucose metabolism disorders including gestational diabetes mellitus (GDM); however, the relationship between MT2-mediated melatonin signaling and a high birth weight of GDM infants from maternal glucose abnormality remains poorly understood. This article aims to investigate the relationship between rs10830963 variants and GDM development, as well as the effects of MT2 receptor on glucose uptake and transport in trophoblasts. TaqMan-MGB (minor groove binder) probe quantitative real-time polymerase chain reaction (qPCR) assays were used for rs10930963 genotyping. MT2 expression in the placenta of GDM and normal pregnant women was detected by immunofluorescence, western blot, and qPCR. The relationship between MT2 and glucose transporters (GLUTs) or peroxisome proliferator-activated receptor γ (PPARγ) was established by western blot, and glucose consumption of trophoblasts was measured by a glucose assay kit. The results showed that the genotype and allele frequencies of rs10830963 were significantly different between GDM and normal pregnant women (P<0.05). The fasting, 1-h and 2-h plasma glucose levels of G-allele carriers were significantly higher than those of C-allele carriers (P<0.05). Besides, the protein and messenger RNA (mRNA) expression of MT2 in the placenta of GDM was significantly higher than that of normal pregnant women (P<0.05). Melatonin could stimulate glucose uptake and GLUT4 and PPARγ protein expression in trophoblasts, which could be attenuated by MT2 receptor knockdown. In conclusion, the rs10830963 variant was associated with an increased risk of GDM. The MT2 receptor is essential for melatonin to raise glucose uptake and transport, which may be mediated by PPARγ.

Research progress on emerging biomarkers in kidney transplantation / 器官移植

The hosts could show complex and diverse immune responses to the allografts. Whether biomarkers can be employed to explain the complexity of graft immune responses and the degree of disease damage are of significance. Conventional biomarkers, such as estimated glomerular filtration rate and blood concenrtation of immunosuppressant, lack of sensitivity and specificity in accurately identifying between immune and non-immune renal allograft injuries. Although renal biopsy is the "gold standard" for the diagnosis of postoperative complications, it still has disadvantages, such as invasiveness and high price, etc. Emerging biomarkers have potential advantages in the non-invasive diagnosis of subclinical injury of renal allograft, prediction of treatment response and individualized adjustment of immunosuppressive regimen. In this article, emerging biomarkers including blood, urine and tissue biomarkers that have been applied and are expected to be applied in clinical practice in the field of kidney transplantation were reviewed, and the range of application and effect of these biomarkers were evaluated, aiming to promote appropriate and rational application of these promising emerging biomarkers in clinical practice.

Rapid Screening of Gastrodia elata with High Purity by PCR-RFLP Identification / 中国实验方剂学杂志

ObjectiveTo establish a rapid screening method for germplasm materials of Gastrodia elata with high purity， and lay a foundation for pure line breeding and cross breeding. MethodBased on the whole genome sequencing and population resequencing of G. elata， 20 restriction fragment length polymorphism (RFLP) markers were developed by single nucleotide polymorphism (SNP) sites. The polymerase chain reaction (PCR)-RFLP method was used to carry out restriction endonuclease experiments on 20 RFLP markers of 15 G. elata germplasms. According to the number of enzymatic bands at 20 RFLP marker sites, the purity of 15 germplasms was calculated and evaluated. On this basis, genome resequencing technology was used to verify the assessment results. ResultTen germplasm materials with purity greater than 95% were screened out by PCR-RFLP method， 3 of which had 95% purity and 7 had 100% purity. Nine germplasm materials with purity greater than 95% were screened out by genome resequencing methods, and 8 of them were consistent with the results of PCR-RFLP. ConclusionThe PCR-RFLP method established in this study for screening G. elata germplasms with high purity precision of RFLP markers has 80% precision and 89% accuracy. The method is simple， efficient， and significantly less expensive than genome resequencing method, which provides technical support for pure line breeding of G. elata and references for breeding of other Chinese medicinal materials.

Bovine TMEM95 gene: Polymorphisms detecting in five Chinese indigenous cattle breeds and their association with growth traits

BACKGROUND: Transmembrane protein 95 (TMEM95) plays a role in male fertility. Previous studies showed that genes with a significant impact on reproductive traits can also affect the growth traits of livestock. Thus, we speculated that the genetic variation of TMEM95 gene may have effects on growth traits of cattle. RESULTS: Two SNPs were genotyped. The rs136174626 and rs41904693 were in the intron 4 and 30 -untranslated region, respectively. The linkage disequilibrium analysis illustrated that these two loci were not linked. The rs136174626 was associated with six growth traits of Nanyang cattle, four traits of Luxi cattle, and three traits of Ji'an cattle. For rs41904693 locus, the GG individuals had greater body height and abdominal girth in Ji' an cattle than TT and TG individuals. In Jinnan cattle, GG and TT individuals had greater body height, height at hip cross, body length, and heart girth than TG individuals. The potential splice site prediction results suggest that the rs136174626 may influence the splicing efficiency of TMEM95, and the miRNA binding site prediction results showed that the rs41904693 may influence the expression of TMEM95 by affecting the binding efficiency of Bta-miR-1584 and TMEM95 30 -UTR. CONCLUSIONS: The findings of the study suggested that the two SNPs in TMEM95 could be a reliable basis for molecular breeding in cattle.

Diseño y validación de un ensayo de minisecuenciación múltiple para detectar polimorfismos asociados con Síndrome Metabólico / Design and validation of a multiple minisequencing assay to detect polymorphisms associated with Metabolic Syndrome

Resumen Introducción: Es importante identificar los polimorfismos de interés clínico en patologías complejas como el Síndrome Metabólico. Por esto, las metodologías para su evaluación deben estar diseñadas y validadas correctamente, esto permite optimizar recursos y tiempo en la genotipificación y detección correcta de los alelos presentes en los individuos. Objetivo: Diseñar y validar una PCR múltiple, seguida de detección por minisecuenciación, para la genotipificación de ocho polimorfismos de nucleótido simple ubicados en el gen del Receptor Beta 3-Adrenérgico (rs4994 y rs4998), gen de la Apolipoproteina A5 (rs3135506 y rs2075291), gen de la Adiponectina (rs1501299 y rs2241766) y gen del Receptor Activador de la Proliferación de los Peroxisomas tipo gamma (rs1801282 y rs1800571), asociados con el síndrome metabólico. Materiales y métodos: Se diseñaron 24 cebadores para la amplificación y detección de ocho polimorfismos de nucleótido sencillo ubicados en cuatro genes candidatos a estar asociados con el síndrome metabólico, usando el software Primer3®. Dieciséis fueron diseñados para amplificar los polimorfismos y ocho para detectarlos por minisecuenciación. Las estructuras secundarias entre los cebadores se verificaron con el software Autodimer. Los polimorfismos se amplificaron simultáneamente y los fragmentos amplificados se acoplaron a las sondas diseñadas para detectar por minisecuenciación el alelo presente, por medio de bases marcadas con fluorocromos. Finalmente, los alelos fueron detectados por electroforesis capilar en un analizador genético ABI 310 y se interpretaron con el software GeneMapper®. La validación del multiplex se realizó genotipando 20 muestras de individuos, cada uno de ellos autorizó este procedimiento por medio del consentimiento informado. Resultados: Se obtuvieron los perfiles genéticos de los 20 controles genotipados, a partir de la amplificación múltiple, seguida de minisecuenciación, diseñada y validada para detectar los ocho polimorfismos. Conclusión: Se diseñó y validó un ensayo para la detección simultánea de los polimorfismos, ubicados en cuatro genes asociados con el Síndrome metabólico. Los cuales pueden ser empleados como referencia para futuros estudios poblacionales.

Abstract Introduction: It is important to identify the polymorphisms of clinical interest in complex pathologies such as Metabolic Syndrome. Therefore, the methodologies for its evaluation must be designed and validated correctly, this permits optimization of resources and time in genotyping and correct detection of the alleles present in individuals. Objective: To design and validate a multiplex PCR, followed by detection by minisequencing, for the genotyping of eight single nucleotide polymorphisms located in the Beta 3-Adrenergic Receptor gene (rs4994 and rs4998), Apolipoprotein A5 gene (rs3135506 and rs2075291), Adiponectin gene (rs1501299 and rs2241766) and gamma-type Peroxisome Proliferation Activating Receptor gene (rs1801282 and rs1800571), associated with metabolic syndrome. Materials and methods: Twenty-four primers were designed for the amplification and detection of eight single nucleotide polymorphisms located in four candidate genes to be associated with the metabolic syndrome, using the Primer3® software. Sixteen were designed to amplify the polymorphisms and eight to detect them by minisequencing. The secondary structures between the primers were verified with Autodimer software. The polymorphisms were simultaneously amplified, and the amplified fragments were coupled to probes designed to minisequence the present allele using fluorochrome-labeled bases. Finally, the alleles were detected by capillary electrophoresis using an ABI 310 genetic analyzer and analyzed with the GeneMapper® software. The validation of the multiplex was performed by genotyping 20 individual samples, each of them authorized this procedure through informed consent. Results: The genetic profiles of the 20 genotyped controls were obtained, from multiple amplification, followed by minisequencing, designed and validated to detect the eight polymorphisms. Conclusion: An essay was designed and validated for the simultaneous detection of polymorphisms, located in four genes associated with metabolic syndrome, and can used as a reference for future population studies.

Molecular cloning, characterization and expression analysis of three key starch synthesis-related genes from the bulb of a rare lily germplasm, / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Starch is the predominant compound in bulb scales, and previous studies have shown that bulblet development is closely associated with starch enrichment. However, how starch synthesis affects bulbification at the molecular level is unclear. In this study, we demonstrate that

Identification of Armeniacae Semen Amarum Adulterated in Persicae Semen by Allele-specific Polymerase Chain Reaction / 中国实验方剂学杂志

Objective:Due to the limitation of traditional identification methods of Chinese medicinal materials， the study established a rapid method to identify Persicae Semen mixed with Armeniacae Semen Amarum by allele-specific polymerase chain reaction （PCR）. Method:By comparing the ribosomal DNA internal transcribed spacer （ITS） gene sequences of Persicae Semen and Armeniacae Semen Amarum， single nucleotide polymorphism （SNP） sites were searched and specific primers were designed. Different Persicae Semen and Armeniacae Semen Amarum samples were amplified by PCR， the effects of annealing temperature， primer concentration and cycle number on the PCR reaction system were optimized， and the specificity and detection limit of this method were investigated. In addition， the established PCR method was used to detect the samples of Persicae Semen mixed with different proportion of Armeniacae Semen Amarum from different sources and producing areas. Result:A specific PCR method for identifying Persicae Semen mixed with Armeniacae Semen Amarum was established. When the annealing temperature was 63 ℃ and the number of primer cycles was 30， only Armeniacae Semen Amarum could be amplified with 432 bp specific band， while Persicae Semen samples did not have this band. The minimum detection limit of this method for Armeniacae Semen Amarum was 0.2 ng， and the detection limit for Armeniacae Semen Amarum adulterated in Persicae Semen was 1%. Conclusion:The established allele-specific PCR method can accurately detect whether there is Armeniacae Semen Amarum in Persicae Semen， which can provide experimental basis for the quality control of Persicae Semen and guarantee the safety of its clinical use.

Molecular Mechanism of Salvia miltiorrhiza Quality Formation Based on Single Nucleotide Polymorphism of Functional Genes / 中国实验方剂学杂志

Objective:To investigate the relationship between the single nucleotide polymorphism（SNP）of function genes and effective components of <italic>Salvia miltiorrhiza</italic> and the molecular mechanism of specific quality formation of <italic>S. miltiorrhiza</italic>. Method:The fingerprints of components in <italic>S. miltiorrhiza</italic> from eight different habitats and varieties were obtained by high-performance liquid chromatography （HPLC）. The full-length cDNA of three functional genes<italic> </italic>acetyl-CoA C-acetyltransferase（<italic>SmAACT</italic>），4-diphosphocytidyl-2-C-methyl-<italic>D</italic>-erythritol kinase（<italic>SmCMK</italic>） and isopentenyl diphosphate isomerase（<italic>SmIPPI</italic>） in tanshinone metabolic pathway were amplified by polymerase chain reaction（PCR），cloned， and sequenced，followed by bioinformatics analysis. Result:The full-length cDNA sequences of three functional genes <italic>SmAACT</italic>，<italic>SmCMK</italic>， and <italic>SmIPPI</italic> in tanshinone metabolic pathway were obtained from 23 strains of <italic>S. miltiorrhiza</italic> from eight different habitats and varieties. As revealed by the analysis of SNP and amino acid polymorphisms of three functional genes，18，16， and 14 SNP sites were found respectively. HPLC results showed the samples from Beijing，Hubei，Shandong （No. SDB），Shanxi，Henan， and Shandong （No. SDZ） were clustered into one branch，and those from Hebei and Inner Mongolia were clustered into another branch， which suggested that the variation trend of <italic>S. miltiorrhiza</italic> components had little correlation with geographical distance，but the variety was a critical factor for the quality. Conclusion:There was an obvious genetic differentiation trend in <italic>S. miltiorrhiza</italic> from different habitats，and different origin-specific genotypes were formed. The molecular mechanism of the formation of the specific quality of <italic>S. miltiorrhiza</italic> from different habitats was discussed，which laid a foundation for the stability and effectiveness of clinical medication，and guided the breeding of excellent varieties of <italic>S. miltiorrhiza</italic>.

SNP Panel Analysis of Ancestry Inference in East Asian Populations / 法医学杂志

Objective To develop an SNP Panel for East Asian population, which has a high individual identification rate and the capability of ancestry analysis. Methods The 55 SNP Panel by Professor KIDD of Yale University and the 128 SNP Panel by Professor SELDIN of Davis School of California University, 170 SNP Panel in total was used as the basis and its test data in the East Asian population was collected. The genetic parameters of SNP loci were calculated and combined with the results of heatmap analysis to screen SNP loci suitable for East Asian population. Some Tibetan and Han samples were tested. The possibility of using the SNP loci in ancestry inference was analyzed by means of STRUCTURE analysis, principal component analysis and heatmap analysis. Results A Panel with 45 SNPs （45 SNP Panel） was screened out, and the average genetic parameters of each SNP were better than 170 SNP Panel, with the same ancestry analysis and inference ability. Conclusion In terms of ancestry inference information, the 45 SNP Panel can completely replace the 170 SNP Panel and achieve the same ancestry analysis and inference ability. In genetic parameters, 45 SNP Panel is better than 170 SNP Panel in the East Asian population, which shows its important potential forensic application value.

Bibliometric Analysis of Forensic Genetics Literatures in SCIE from 1989 to 2019 / 法医学杂志

Objective To conduct bibliometric analysis of forensic genetics literatures published by Chinese mainland scholars in SCIE journals from 1989 to 2019, to show the research achievements of the past three decades and predict future research fields and directions. Methods Microsoft Office Excel 2019 was utilized to analyze the general situation, research institutions, authors, funds, author keywords, etc. of the literatures. The status of research in forensic genetics in Chinese mainland was visualized by PlotDB, Gephi 0.9.2 software and literature interpretation. Results During the last three decades, 1 126 forensic genetics literatures were published by scholars from Chinese mainland on SCIE journals, mostly articles. The quantity and quality of the literatures were both on the increase. The number of literatures published in Forensic Science International-Genetics was the highest, and 60.83% of the literatures were funded, mainly by the National Natural Science Foundation of China （498 literatures）. The current research hotspots were STR, SNP, InDel polymorphisms, linkage genetic markers, mtDNA genetic markers, epigenetic markers, RNA genetic markers, chip technology and omics research method. Conclusion The forensic genetics in China has developed rapidly along with the promotion of forensic science in universities. The SCIE literatures on forensic genetics published by Chinese mainland scholars increased rapidly with the funding from the National Natural Science Foundation of China and Ministry of Science and Technology of the People's Republic of China, which positively contributes to the development of basic research and the improvement of overall level in forensic genetics in China.

Serum mir-195-5p exhibits clinical significance in the diagnosis of essential hypertension with type 2 diabetes

OBJECTIVES: Diagnosis and management of essential hypertension (EH) or type 2 diabetes mellitus (T2DM) by combining comprehensive treatment and classificatory diagnosis have been continuously improved. However, understanding the pathogenesis of EH patients with concomitant T2DM and subsequent treatment remain the major challenges owing to the lack of non-invasive biomarkers and information regarding the underlying mechanisms. METHODS: Herein, we collected 200 serum samples from EH and/or T2DM patients and healthy donors (N). Gene-expression profiling was conducted to identify candidate microRNAs with clinical significance. Then, a larger cohort of the aforementioned patients and 50 N were used to identify the correlation between the tumor suppressor miR-195-5p and EH and/or T2DM. The dual-luciferase reporter assay was used to explore the target genes of miR-195-5p. The suppressive effects of miR-195-5p on the 3′-UTR of the dopamine receptor D1 (DRD1) transcript in EH patients with concomitant T2DM were verified as well. RESULTS: Compared with that in other groups, serum miR-195-5p was highly downregulated in EH patients with concomitant T2DM. miR-195-5p overexpression efficiently suppressed DRD1 expression by binding to the two 3′-UTRs. Additionally, two single nucleotide polymorphisms, including 231T-A and 233C-G, in the miR-195-5p binding sites of the DRD1 3′-UTR were further identified. Collectively, we identified the potential clinical significance of DRD1 regulation by miR-195-5p in EH patients with concomitant T2DM. CONCLUSIONS: Our data suggested that miR-195-5p circulating in the peripheral blood served as a novel biomarker and therapeutic target for EH and T2DM, which could eventually help address major challenges during the diagnosis and treatment of EH and T2DM.

Association between lncRNAH19 polymorphisms and susceptibility to gastric carcinoma and EBV-associated gastric carcinoma in Han population in Qingdao / 中国肿瘤生物治疗杂志

@# Objective: To evaluate the potential associations between the single nucleotide polymorphisms (SNPs) of lncRNA H19 genes and the susceptibility to gastric cancer (GC), especially to EBV-associated gastric cancer (EBVaGC) in Han population in Qingdao. Methods: 225 cases of pathologically confirmed fresh gastric cancer tissues or paraffin embedded gastric cancer tissues during January 2015 and October 2018 were collected from Affiliated Hospital of Qingdao University, as GC group; in the meanwhile, 200 healthy people underwent physical examination at Outpatient were collected as control. The 225 cases of cancer tissues were assigned into two groups according to the transcription result of EBV-encoded small molecule non-polyadenylation (EBER 1) by In situ hybridization: EBVaGC group (70 cases) and EBVnGC group (155 cases). DNA was extracted from the tissues of two groups and peripheral blood of healthy participants.According to the general setting of HaploView software (MAF>0.05, r2>0.8), four TagSNPs (rs217727, rs2735971, rs2839698 and rs3741216) of H19 were screened. Genotyping of each SNP locus was carried out by using Taq-Man MGB allele typing kit, and the gene polymorphisms were examined. Results: H19 SNPs of collected tissue samples were in accordance with the HardyWeinberg equilibrium. Compared with control group, patients carrying TT genotype of H19 rs217727 loci had significantly increased susceptibility to gastric cancer (χ2=9.073, P=0.003, OR=1.999, 95% CI=1.271-3.143), so did the T allele (χ2=13.475, P=0.001, OR= 1.661, 95% CI=1.266-2.180). In contrast, patients carrying TC and CC genotype of rs2839698 loci had significantly increased susceptibility to gastric cancer (χ2=9.407, P=0.002; χ2=6.517, P=0.011), and patients carrying C allele had obviously increased susceptibility to GC (χ2=6.163, P=0.013, OR=1.417, 95%CI=1.076-1.867; χ2=9.542, P=0.02, OR=2.070, 95%CI=1.298-3.302).As for the rs2735971 and rs3741216, there was no significant difference between the GC group and the control group (all P>0.05). The distribution of 4 H19 SNPs showed no statistical difference in both EBVaGC group and EBVnGC group (all P>0.05). Conclusion: There was an association between H19 gene polymorphism (rs217727 and rs2839698) and gastric carcinoma; patients carrying the TT genotype of rs217727 and C allele of rs2839698 may increase the risk of gastric carcinoma. No significant association was observed between H19 SNP polymorphism and risk of EBVaGC.

Correlation between single nucleotide polymorphism of TET2 gene and susceptibility and prognosis of sepsis / 中华急诊医学杂志

Objective@#To investigate the association of SNPs in TET2 gene with the susceptibility and prognosis of sepsis.@*Methods@#Ninety-nine patients diagnosed with sepsis and 107 controls were enrolled in the study. The septic patients were further divided into survivors (56 cases) and non-survivors (43 cases) according to the outcome of 28-day hospitalization. Patients without sepsis after major surgery were enrolled as the controls. The genotypes of the five loci (rs6839705, rs7670522, rs7679673, rs7698522 and rs10010325) with high minor allele frequency in the TET2 were screened according to the existing research reports and the SNP database of the NCBI website. The five loci were detected by TaqMan probe based allelic discrimination assays using real-time polymerase chain reaction (PCR). The data were calculated for genetic association study through χ2 test and Fisher’s exact probability method.@*Results@#There was no significant difference in genotype frequencies of the five tested SNPs in TET2 gene between septic patients and controls or between survivors and non-survivors in septic patients (P > 0.05). Furthermore, the allelic frequencies of the five SNPs between septic patients and controls or between survivors and non-survivors in septic patients also had no significant difference (P > 0.05).@*Conclusions@#This study showed that the five SNPs in TET2 gene (rs6839705, rs7670522, rs7679673, rs7698522, and rs10010325) were not associated with the susceptibility and prognosis of sepsis, which needs to be further confirmed by large-sample studies.

Correlation between single nucleotide polymorphism of TET2 gene and susceptibility and prognosis of sepsis / 中华急诊医学杂志

Objective To investigate the association of SNPs in TET2 gene with the susceptibility and prognosis of sepsis.Methods Ninety-nine patients diagnosed with sepsis and 107 controls were enrolled in the study.The septic patients were further divided into survivors (56 cases) and non-survivors (43 cases) according to the outcome of 28-day hospitalization.Patients without sepsis after major surgery were enrolled as the controls.The genotypes of the five loci (rs6839705,rs7670522,rs7679673,rs7698522 and rs10010325) with high minor allele frequency in the TET2 were screened according to the existing research reports and the SNP database of the NCBI website.The five loci were detected by TaqMan probe based allelic discrimination assays using real-time polymerase chain reaction (PCR).The data were calculated for genetic association study through x2 test and Fisher's exact probability method.Results There was no significant difference in genotype frequencies of the five tested SNPs in TET2 gene between septic patients and controls or between survivors and non-survivors in septic patients (P ＞ 0.05).Furthermore,the allelic frequencies of the five SNPs between septic patients and controls or between survivors and non-survivors in septic patients also had no significant difference (P ＞ 0.05).Conclusions This study showed that the five SNPs in TET2 gene (rs6839705,rs7670522,rs7679673,rs7698522,and rs10010325) were not associated with the susceptibility and prognosis of sepsis,which needs to be further confirmed by large-sample studies.

Association analysis of FOS gene rs1063169 polymorphism and Alzheimer's disease in Han Chinese people / 上海交通大学学报（医学版）

Objective: To investigate the relation between FOS gene and Alzheimer's disease (AD), and the relation between tag single nucleotide polymorphism (SNP) in rs1063169 and AD in Han Chinese people. Methods: The difference in FOS gene expression in various brain regions between AD patients and healthy people was studied using Alzdata website, and protein-protein interaction (PPI) network among FOS protein and 28 proteins encoded by AD-related susceptibility genes was constructed through String database in order to explore whether FOS gene was associated with AD in these known database. Then, 715 AD patients and 760 healthy controls from Southwest and East China were collected to analyze tag SNP rs1063169 by SNaPshot assay. Results: The cross-platform normalized expression data on Alzdata showed that FOS gene in AD patients expressed differently in entorhinal cortex (P=0.003) and hippocampus (P=0.001) compared with healthy people. PPI network found out that FOS protein had interactions with 4 proteins encoded by AD-related susceptibility genes, which were apolipoprotein E (APOE), clusterin (CLU), β-amyloid precursor protein (APP), and protein-tyrosine kinase 2β (PTK2B). However, there was no significant difference in the frequencies of genotypes and alleles in rs1063169 between the AD cases and the healthy controls (P>0.05). Conclusion: There is differential expression of FOS in the entorhinal cortex and hippocampus of AD patients and healthy people, and FOS protein may have effects on the development of AD through the interaction with proteins encoded by AD-related susceptibility genes, but no relation was found between rs1063169 polymorphism and AD in the collected Han Chinese people.

Genetic Diversity and Drug Susceptibility of Mycobacterium tuberculosis Isolates in a Remote Mountain Area of China / 生物医学与环境科学（英文）

<p><b>OBJECTIVE</b>We determined the genetic diversity of Mycobacterium tuberculosis (MTB) in a remote mountainous area of southwest China and evaluated the resolving ability of single nucleotide polymorphism (SNP) genotyping combined with variable number tandem repeat (VNTR) genotyping for Beijing family strains in association with drug resistance status.</p><p><b>METHODS</b>Three hundred thirty-one MTB strains were isolated from patients living in mountainous regions of southwest China, and 8-loci SNP, VNTR-15 genotyping assays, and drug susceptibility testing of 9 drugs were performed.</p><p><b>RESULTS</b>A total of 183 [55.29% (183/331)] strains were classified into the Beijing family. Of the 183 strains, 111 (60.66%) were defined as modern Beijing strains. The most predominant modern Beijing sub-lineage and ancient Beijing sub-lineage were Bmyc10 [39.34% (72/183)] and Bmyc25 [20.77% (38/183)], respectively. Of the isolates, 19.64% (65/331) were resistant to at least 1 of the 9 anti-TB drugs and 17 [4.98% (17/331)] MTB isolates were multi-drug resistant tuberculosis (MDR-TB). Two hundred sixty-one isolates showed a clustering rate of 14.18% (37/261) and a discriminatory index of 0.9990. The Beijing lineage exhibited a significantly higher prevalence of MDR-TB, as well as resistance to isoniazid (INH), rifampin (RIF), and para-aminosalicylic acid (PAS) when analyzed independently (P = 0.005, P = 0.017, P = 0.014, and P = 0.006 respectively). The Beijing lineage was not associated with genetic clustering or resistance to any drug. In addition, genetic clustering was not associated with drug resistance.</p><p><b>CONCLUSION</b>MTB strains demonstrate high genetic diversity in remote mountainous areas of southwest China. Beijing strains, especially modern Beijing strains, are predominant in remote mountainous area of China. The combination of 8-loci SNPs and VNTR-15 genotyping is a useful tool to study the molecular epidemiology of MTB strains in this area.</p>

Genetic analysis of a case of 46, XX, SRY－ male syndrome / 中华男科学杂志

<p><b>Objective</b>To identify the etiology of chromosome abnormality in an infertile man and analyze the correlation between the genotype and phenotype.</p><p><b>METHODS</b>We analyzed the karyotype of an infertile male using the routine G-banding technique and then the chromosome abnormality of the patient by Illumina Human CytoSNP-12 Beadchip array.</p><p><b>RESULTS</b>Negative results were found in the examination of the sex-determining region Y (SRY) gene and the STR locus in the AZF zone of the patient. The karyotype of the patient was 46, XX. SNP array showed a 1.05 Mb 19p12 duplication and a 0.93 Mb Xq27.1 duplication.</p><p><b>CONCLUSIONS</b>The patient was confirmed as a case of 46,XX male syndrome. The increased copies of the FGF13 gene may be the major causes of abnormal sex determination and testis development.</p>