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https://www.readbyqxmd.com/read/28939339/design-virtual-screening-molecular-docking-and-molecular-dynamics-studies-of-novel-urushiol-derivatives-as-potential-hdac2-selective-inhibitors
#1
Hao Zhou, Chengzhang Wang, Jianzhong Ye, Hongxia Chen, Ran Tao
Three series of novel urushiol derivatives were designed by introducing a hydroxamic acid moiety into the tail of an alkyl side chain and substituents with differing electronic properties or steric bulk onto the benzene ring and alkyl side chain. The binding affinity toward HDAC2 of the compounds was screened by Glide docking. The best scoring compounds were processed further with molecular docking, MD simulations and binding free energy studies to analyze the binding modes and mechanisms. Six compounds, 21, 23, 10, 19, 9 and 30, gave Glide scores of -7...
September 19, 2017: Gene
https://www.readbyqxmd.com/read/28939338/comparison-of-the-role-of-hhip-snps-in-susceptibility-to-chronic-obstructive-pulmonary-disease-between-chinese-han-and-mongolian-populations
#2
Guihua Xu, Xiaoyu Gao, Sainan Zhang, Yan Wang, Mingjing Ding, Wenyan Liu, Jie Shen, Dejun Sun
The contribution of risk alleles to chronic obstructive pulmonary disease (COPD) may vary between populations. This study aimed to investigate the role of single nucleotide polymorphisms (SNPs) in HHIP on COPD susceptibility in the Chinese Mongolian and Han populations from Inner Mongolia autonomous region. In this case-control study, five SNPs in HHIP gene were detected in 700 COPD patients (350 Chinese Han and 350 Chinese Mongolian) and 700 healthy controls (350 Chinese Han and 350 Chinese Mongolian). The genotype, the association with COPD, and the differences between Chinese Han and Mongolian populations were evaluated using the chi-squared (χ(2)) test, genetic models, and logistic analysis...
September 19, 2017: Gene
https://www.readbyqxmd.com/read/28935260/insights-of-lr28-mediated-wheat-leaf-rust-resistance-transcriptomic-approach
#3
Dharmendra Singh, Dhananjay Kumar, Lopamudra Satapathy, Jyoti Pathak, Saket Chandra, Adnan Riaz, Govindraj Bhaganagre, Raman Dhariwal, Manish Kumar, Kumble Vinod Prabhu, Harindra Singh Balyan, Pushpendra Kumar Gupta, Kunal Mukhopadhyay
Leaf rust is a fungal disease that causes severe yield losses in wheat. Resistant varieties with major and quantitative resistance genes are the most effective method to control the disease. However, the main problem is inadequate information for understanding resistance mechanism and its usefulness. This paper presents Lr28 mediated genome-wide response of known and unknown genes during wheat-Puccinia triticina interaction. In this study, we prepared Serial Analysis of Gene Expression (SAGE) libraries using seedling wheat mRNA for infected and mock conditions...
September 18, 2017: Gene
https://www.readbyqxmd.com/read/28935259/module-based-systematic-construction-of-plasmids-for-episomal-gene-expression-in-fission-yeast
#4
Keita Kiriya, Hayato Tsuyuzaki, Masamitsu Sato
The fission yeast Schizosaccharomyces pombe is a powerful model organism for cell biology and molecular biology, as genetic manipulation is easily achieved. Introduction of exogenous genes cloned in episomal plasmids into yeast cells can be done through well-established transformation methods. For expression of genes in S. pombe cells, the multi-copy plasmid pREP1 and its derivatives, including pREP41 and pREP81, have been widely used as vectors. Although recent advancement of technology brought a number of useful genetic elements such as new promoters, selection marker genes and fluorescent protein tags, introduction of those elements into conventional pREP1 requires a large commitment of both time and effort because cloning procedures need to be repeated until the final products are constructed...
September 18, 2017: Gene
https://www.readbyqxmd.com/read/28927745/apolipoprotein-m-gene-single-nucleotide-polymorphisms-discovery-in-patients-with-chronic-obstructive-pulmonary-disease-and-determined-by-the-base-quenched-probe-technique
#5
Yang Yu, Jun Zhang, Yingying Qiao, Lili Pan, Juzhang Li, Huihui Mao, Jiang Wei, Xiaoying Zhang, Ning Xu, Guanghua Luo
BACKGROUND: It has been reported increased serum apoM levels seen in the patients suffered from obstructive sleep apnoea and chronic obstructive pulmonary diseases. In the present, we further examine the prevalence of apoM gene SNPs in COPD patients. And a new method base-quenched probe technique is established. METHODS: In the present study, we first used the Roche 454 GS Junior high-throughput sequencer to analyze 6 COPD samples and 6 control samples, in these samples we found 3 interesting SNPs (rs805264, rs707922 and rs707921) and then we designed primers and probes to establish a simple and quick screening method that is a base-quench probe technique and the genotype was confirmed by melting curves...
September 16, 2017: Gene
https://www.readbyqxmd.com/read/28919164/integrated-analysis-of-microrna-and-gene-expression-profiles-reveals-a-functional-regulatory-module-associated-with-liver-fibrosis
#6
Wei Chen, Wenshan Zhao, Aiting Yang, Anjian Xu, Huan Wang, Min Cong, Tianhui Liu, Ping Wang, Hong You
BACKGROUND: Liver fibrosis, characterized with the excessive accumulation of extracellular matrix (ECM) proteins, represents the final common pathway of chronic liver inflammation. Ever-increasing evidence indicates microRNAs (miRNAs) dysregulation have important implications in the different stages of liver fibrosis. However, our knowledge of miRNA-gene regulation details pertaining to such disease remains unclear. METHODS: The publicly available Gene Expression Omnibus (GEO) datasets of patients suffered from cirrhosis were extracted for integrated analysis...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28919163/multiplex-pcr-and-ngs-based-identification-of-mrna-splicing-variants-analysis-of-brca1-splicing-pattern-as-a-model
#7
Jan Hojny, Petra Zemankova, Filip Lhota, Jan Sevcik, Viktor Stranecky, Hana Hartmannova, Katerina Hodanova, Ondrej Mestak, David Pavlista, Marketa Janatova, Jana Soukupova, Michal Vocka, Zdenek Kleibl, Petra Kleiblova
Alternative pre-mRNA splicing increases transcriptome plasticity by forming naturally-occurring alternative splicing variants (ASVs). Alterations of splicing processes, caused by DNA mutations, result in aberrant splicing and the formation of aberrant mRNA isoforms. Analyses of hereditary cancer predisposition genes reveal many DNA variants with unknown clinical significance (VUS) that potentially affect pre-mRNA splicing. Therefore, a comprehensive description of ASVs is an essential prerequisite for the interpretation of germline VUS in high-risk individuals...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28919162/mir-101-1-expression-pattern-in-qinchuan-cattle-and-its-role-in-the-regulation-of-cell-differentiation
#8
Jiyao Wu, Dandan He, Binglin Yue, Chunlei Zhang, Xingtang Fang, Hong Chen
MiRNAs have emerged as key regulators of skeletal muscle development, but the knowledge of miRNAs in the molecular network of muscle development remains poorly understood. In this study, we designed to examine the biological function of bovine-miR-101-1. The bovine miR-101-1 was detected in the skeletal muscle of fetal, calf and adult cattle. Its abundance was significantly higher in the skeletal muscle of calf cattle than that in fetal and adult cattle. In the course of C2C12 myoblast differentiation, the expression of miR-101-1 gradually increased...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28918252/a-pdgf-vegf-homologue-provides-new-insights-into-the-nucleus-grafting-operation-and-immune-response-in-the-pearl-oyster-pinctada-fucata
#9
Xian-De Huang, Hua Zhang, Mao-Xian He
The platelet-derived growth factor/vascular endothelial growth factor (PDGF/VEGF, PVF) family of proteins have been implicated in a wide range of biological functions in vertebrates, including cell proliferation, cell differentiation, cell migration, neural development and especially angiogenesis/vasculogenesis. In this study, a PVF gene, belonging to the PDGF/VEGF family, was cloned and characterized from Pinctada fucata. It contained an ORF of 1110bp encoding a putative protein of 369 amino acids. The deduced amino acid sequence presented the typical structural features of PDGF family members and the N-terminal signal peptide for secretion...
September 13, 2017: Gene
https://www.readbyqxmd.com/read/28918251/hmg-box-factor-soxd-sox15-and-homeodomain-containing-factor-xanf1-hesx1-directly-interact-and-regulate-the-expression-of-xanf1-hesx1-during-early-forebrain-development-in-xenopus-laevis
#10
Natalia Y Martynova, Fedor M Eroshkin, Eugeny E Оrlov, Andrey G Zaraisky
The homeodomain-containing transcription factor Anf (also known as Rpx/Hesx1 in mammals) plays an important role during the forebrain development in vertebrates. Here we demonstrate the ability of the Xenopus laevis Anf, Xanf1/Hesx1, to directly bind SRY-related HMG-box-containing transcription factor SoxD/Sox15 and to cooperate with the latter during regulating of the expression of Xanf1/Hesx1 own gene. As we have shown by GST pull-down, EMSA and the luciferase reporter assays, Xanf1/Hesx1 and SoxD/Sox15 bind the Xanf1/Hesx1 promoter region counteracting the inhibitory effect of Xanf1/Hesx1 alone...
September 13, 2017: Gene
https://www.readbyqxmd.com/read/28918250/associations-of-cholesteryl-ester-transfer-protein-cetp-gene-variants-with-predisposition-to-age-related-macular-degeneration
#11
Rasa Liutkeviciene, Alvita Vilkeviciute, Greta Streleckiene, Loresa Kriauciuniene, Romanas Chaleckis, Vytenis Pranas Deltuva
PURPOSE: To determine the frequency of the genotypes of single nucleotide polymorphisms (SNPs) in the gene encoding cholesteryl ester transfer protein (CETP) and their associations with age-related macular degeneration (AMD) in the Lithuanian population. STUDY DESIGN: A total of 1264 subjects were examined: 251 patients with early AMD, 206 patients with exudative AMD, and 807 healthy controls. METHODS: The genotyping of CETP (rs5882, rs708272, rs3764261, rs1800775, rs2303790) was carried out using the RT-PCR...
September 13, 2017: Gene
https://www.readbyqxmd.com/read/28916377/clinical-and-molecular-characterization-of-two-chinese-patients-with-type-2-congenital-generalized-lipodystrophy
#12
Ruimin Chen, Xin Yuan, Jian Wang, Ying Zhang
BACKGROUND: Type 2 congenital generalized lipodystrophy (CGL2, OMIM 269700) is a rare autosomal recessive disease, characterized by the generalized absence of adipose tissue at birth or in early infancy. Pathogenic variants in BSCL2 gene have been reported to be responsible for CGL2. The aim of this study is to analyze the clinical and genetic characteristics of two Chinese patients with CGL2, and with particular focus on the BSCL2 gene sequence variants. METHODS: Medical history, clinical manifestations, physical examination, laboratory data, and ultrasonography findings were analyzed for the two patients with CGL2...
September 12, 2017: Gene
https://www.readbyqxmd.com/read/28916376/transcriptome-profiling-of-the-plutella-xylostella-lepidoptera-plutellidae-ovary-reveals-genes-involved-in-oogenesis
#13
Lu Peng, Lei Wang, Yi-Fan Yang, Ming-Min Zou, Wei-Yi He, Yue Wang, Qing Wang, Liette Vasseur, Min-Sheng You
BACKGROUND: As a specialized organ, the insect ovary performs valuable functions by ensuring fecundity and population survival. Oogenesis is the complex physiological process resulting in the production of mature eggs, which are involved in epigenetic programming, germ cell behavior, cell cycle regulation, etc. Identification of the genes involved in ovary development and oogenesis is critical to better understand the reproductive biology and screening the potential molecular targets in Plutella xylostella, a worldwide destructive pest of economically major crops...
September 12, 2017: Gene
https://www.readbyqxmd.com/read/28916375/bacterial-community-in-ancient-permafrost-alluvium-at-the-mammoth-mountain-eastern-siberia
#14
Anatoli Brouchkov, Marsel Kabilov, Svetlana Filippova, Olga Baturina, Victor Rogov, Valery Galchenko, Andrey Mulyukin, Oksana Fursova, Gennady Pogorelko
Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa...
September 12, 2017: Gene
https://www.readbyqxmd.com/read/28912065/taino-and-african-maternal-heritage-in-the-greater-antilles
#15
Areej Bukhari, Javier Rodriguez Luis, Miguel A Alfonso-Sanchez, Ralph Garcia-Bertrand, Rene J Herrera
Notwithstanding the general interest and the geopolitical importance of the island countries in the Greater Antilles, little is known about the specific ancestral Native American and African populations that settled them. In an effort to alleviate this lacuna of information on the genetic constituents of the Greater Antilles, we comprehensively compared the mtDNA compositions of Cuba, Dominican Republic, Haiti, Jamaica and Puerto Rico. To accomplish this, the mtDNA HVRI and HVRII regions, as well as coding diagnostic sites, were assessed in the Haitian general population and compared to data from reference populations...
September 11, 2017: Gene
https://www.readbyqxmd.com/read/28912064/cell-cycle-and-histone-modification-genes-were-decreased-in-placenta-tissue-from-unexplained-early-miscarriage
#16
Yuanchang Zhu, Bing Li, Tonghua Wu, Lijun Ye, Yong Zeng, Yaou Zhang
Genetic defect is a major cause of early miscarriage, but still in many cases the etiology are not fully understood. Recent studies have shown that dysregulation of genes in placenta tissue are participated in the pathogenesis of unexplained early miscarriage. The aim of our study is to explore mRNA expression profile in placental chorionic villi and to reveal the underlying mechanism of unexplained early miscarriage. Chorionic villous were isolated and extracted from early miscarriage (n=3) and control pregnancy (n=3) placenta with normal chromosome karyotype using MLPA assay, and then mRNA expression profiles were determined by microarray...
September 11, 2017: Gene
https://www.readbyqxmd.com/read/28912063/differential-expression-by-chromatin-modifications-of-alcohol-dehydrogenase-1-of-chorispora-bungeana-in-cold-stress
#17
Lijun Liu, Yuan Song, Jun Xu, Dongming Li, Gaopeng Li, Lizhe An
Epigenetic modifications regulate plant genes to cope with a variety of environmental stresses. Chorispora bungeana is an alpine subnival plant with strong tolerance to multiple abiotic stresses, especially cold stress. In this study, we characterized the alcohol dehydrogenase 1 gene from Chorispora bungeana, CbADH1, that is up-regulated in cold conditions. Overexpression of CbADH1 in Arabidopsis thaliana improved cold tolerance, as indicated by a decreased lethal temperature (LT50). Chromatin immunoprecipitation assays showed that histone H3 is removed from the promoter region and the middle-coding region of the gene...
September 11, 2017: Gene
https://www.readbyqxmd.com/read/28903065/inflammation-polymorphisms-and-prostate-cancer-risk-in-jamaican-men-role-of-obesity-body-size
#18
Bhawna Dubey, Maria Jackson, Charnita Zeigler-Johnson, Karthik Devarajan, Rafael E Flores-Obando, Norma McFarlane-Anderson, Marshall Tulloch-Reid, William Aiken, Kevin Kimbro, Dominique Jones, LaCreis R Kidd, Camille Ragin
African ancestry and obesity are associated with higher risk of prostate cancer (PC). In a pilot study, we explored interactions between obesity (as measured by waist to hip ratio (WHR)) and inflammatory SNPs in relation to PC risk among Jamaican men. This study evaluated 87 chemokine and cytokine associated SNPs in obese and normal weight cases (N=109) and controls (N=102) using a stepwise penalized logistic regression approach in multivariable analyses. Upon stratification by WHR (normal weight (WHR<0...
September 10, 2017: Gene
https://www.readbyqxmd.com/read/28903064/isolation-and-characterization-of-peroxiredoxin-1-gene-of-dunaliella-salina
#19
Fanghua Gong, Jing Wang, Jie Li
Peroxiredoxin 1 (Prdx1) is a ubiquitously expressed protein in eukaryotic cells, and plays an important role in cell proliferation, differentiation, apoptosis, and redox signaling. Although Prdx1 has been better studied in yeasts and humans, only few Prdx1 genes have been cloned in green algae. The microalga Dunaliella salina (D. salina) is a model for the study of a variety of human cilia-related diseases. In this study, a suppression subtractive hybridization cDNA library of D. salina was constructed, and 6 flagellum-associated genes including D...
September 10, 2017: Gene
https://www.readbyqxmd.com/read/28903063/cooperative-regulation-of-gja1-expression-by-members-of-the-ap-1-family-cjun-and-cfos-in-tm3-leydig-and-tm4-sertoli-cells
#20
Firas Ghouili, Luc J Martin
Within the testis, connexin43 encoded by Gja1 plays an important role in cell-to-cell communication between Leydig cells as well as between Sertoli cells and spermatogonia. In the adult male, Leydig cells are the principal producers of testosterone sustaining spermatogenesis, while Sertoli cells nourish, protect and support the differentiating germ cells. It has been shown previously that members of the AP-1 family regulate Gja1 expression in myometrial cells, suggesting that such regulatory mechanism may also be relevant within the testis...
September 10, 2017: Gene
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