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Apolipoprotein M gene single nucleotide polymorphisms discovery in patients with chronic obstructive pulmonary disease and determined by the base-quenched probe technique.
Abstract 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 quic...
Source: Gene - September 16, 2017 Category: Genetics & Stem Cells Authors: Yu Y, Zhang J, Qiao Y, Pan L, Li J, Mao H, Wei J, Zhang X, Xu N, Luo G Tags: Gene Source Type: research

miR-101-1 expression pattern in Qinchuan cattle and its role in the regulation of cell differentiation.
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. Transfected the exogenous miR-101-1 into the C2C12 myoblast could decrease myotube formation, and the mRNA expression levels of the myogenic marker genes MyOD, MyOG and MyHC were up-regulated. The protein level of MyOD, MyOG and MyHC were also u...
Source: Gene - September 14, 2017 Category: Genetics & Stem Cells Authors: Wu J, He D, Yue B, Zhang C, Fang X, Chen H Tags: Gene Source Type: research

Multiplex PCR and NGS-based identification of mRNA splicing variants: Analysis of BRCA1 splicing pattern as a model.
Abstract 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. To identify ASVs in a gene of interest, we h...
Source: Gene - September 14, 2017 Category: Genetics & Stem Cells Authors: Hojny J, Zemankova P, Lhota F, Sevcik J, Stranecky V, Hartmannova H, Hodanova K, Mestak O, Pavlista D, Janatova M, Soukupova J, Vocka M, Kleibl Z, Kleiblova P Tags: Gene Source Type: research

Integrated analysis of microRNA and gene expression profiles reveals a functional regulatory module associated with liver fibrosis.
Abstract 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. Differentially expressed miRNAs (DEMs) a...
Source: Gene - September 14, 2017 Category: Genetics & Stem Cells Authors: Chen W, Zhao W, Yang A, Xu A, Wang H, Cong M, Liu T, Wang P, You H Tags: Gene Source Type: research

Associations of cholesteryl ester transfer protein (CETP) gene variants with predisposition to age-related macular degeneration.
CONCLUSION: Our study identified two polymorphisms with a higher risk of AMD development (rs5882 and rs708272) and a protective polymorphism for AMD (rs3764261). PMID: 28918250 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - September 13, 2017 Category: Genetics & Stem Cells Authors: Liutkeviciene R, Vilkeviciute A, Streleckiene G, Kriauciuniene L, Chaleckis R, Deltuva VP Tags: Gene Source Type: research

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.
Abstract 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. This f...
Source: Gene - September 13, 2017 Category: Genetics & Stem Cells Authors: Martynova NY, Eroshkin FM, Оrlov EE, Zaraisky AG Tags: Gene Source Type: research

A PDGF/VEGF homologue provides new insights into the nucleus grafting operation and immune response in the pearl oyster Pinctada fucata.
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. Comparative phylogenetic analysis revealed that PfPVF shows relatively high identity with other invertebrate PVF homologues. Furthermore, gene expression analysis revealed that PfPVF is involved in not only the nucleus grafting operation and but also the response to immune stimulation. The st...
Source: Gene - September 13, 2017 Category: Genetics & Stem Cells Authors: Huang XD, Zhang H, He MX Tags: Gene Source Type: research

Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia).
Abstract 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 ki...
Source: Gene - September 12, 2017 Category: Genetics & Stem Cells Authors: Brouchkov A, Kabilov M, Filippova S, Baturina O, Rogov V, Galchenko V, Mulyukin A, Fursova O, Pogorelko G Tags: Gene Source Type: research

Transcriptome profiling of the Plutella xylostella (Lepidoptera: Plutellidae) ovary reveals genes involved in oogenesis.
CONCLUSIONS: Our newly developed P. xylostella ovary transcriptome provides an overview of the gene expression profiling in this specialized tissue and the functional gene network closely related to the ovary development and oogenesis. This is the first genome-wide transcriptome dataset of P. xylostella ovary that includes a subset of functionally activated genes. This global approach will be the basis for further studies on molecular mechanisms of P. xylostella reproduction aimed at screening potential molecular targets for integrated pest management. PMID: 28916376 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - September 12, 2017 Category: Genetics & Stem Cells Authors: Peng L, Wang L, Yang YF, Zou MM, He WY, Wang Y, Wang Q, Vasseur L, You MS Tags: Gene Source Type: research

Clinical and molecular characterization of two Chinese patients with Type 2 congenital generalized lipodystrophy.
CONCLUSION: We describe two patients with classic clinical manifestations of CGL2 confirmed by genetic sequence analysis. A novel variant in BSCL2 gene was detected in one patient (c.713G>A/p.Gly238Asp). PMID: 28916377 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - September 12, 2017 Category: Genetics & Stem Cells Authors: Chen R, Yuan X, Wang J, Zhang Y Tags: Gene Source Type: research

Differential expression by chromatin modifications of alcohol dehydrogenase 1 of Chorispora bungeana in cold stress.
This study expands our understanding of the regulation of gene expression by epigenetic modifications in response to environmental cues. PMID: 28912063 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - September 11, 2017 Category: Genetics & Stem Cells Authors: Liu L, Song Y, Xu J, Li D, Li G, An L Tags: Gene Source Type: research

Cell cycle and histone modification genes were decreased in placenta tissue from unexplained early miscarriage.
Abstract 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 pr...
Source: Gene - September 11, 2017 Category: Genetics & Stem Cells Authors: Zhu Y, Li B, Wu T, Ye L, Zeng Y, Zhang Y Tags: Gene Source Type: research

Taino and African maternal heritage in the Greater Antilles.
Abstract 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 referenc...
Source: Gene - September 11, 2017 Category: Genetics & Stem Cells Authors: Bukhari A, Luis JR, Alfonso-Sanchez MA, Garcia-Bertrand R, Herrera RJ Tags: Gene Source Type: research

Cooperative regulation of Gja1 expression by members of the AP-1 family cJun and cFos in TM3 Leydig and TM4 Sertoli cells.
Abstract 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. Thus, we performed cotransfections of AP-1 expression plasmids wi...
Source: Gene - September 10, 2017 Category: Genetics & Stem Cells Authors: Ghouili F, Martin LJ Tags: Gene Source Type: research

Isolation and characterization of peroxiredoxin 1 gene of Dunaliella salina.
In this study, a suppression subtractive hybridization cDNA library of D. salina was constructed, and 6 flagellum-associated genes including D. salina Prdx1 (DsPrdx1) were isolated and identified. A 956bp full-length cDNA of DsPrdx1 was cloned using rapid amplification of cDNA end (RACE). The open reading frame (ORF) of this DNA sequence encodes a polypeptide of 201 amino acids with a predicted molecular weight of 22kDa and a theoretical isoelectric point (pI) of 5.27. Sequence comparison showed that Prdx1 is highly evolutionarily conserved from the unicellular green alga D. salina to human. To our knowledge, this is the f...
Source: Gene - September 10, 2017 Category: Genetics & Stem Cells Authors: Gong F, Wang J, Li J Tags: Gene Source Type: research

Inflammation polymorphisms and prostate cancer risk in Jamaican men: Role of obesity/body size.
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
Source: Gene - September 10, 2017 Category: Genetics & Stem Cells Authors: Dubey B, Jackson M, Zeigler-Johnson C, Devarajan K, Flores-Obando RE, McFarlane-Anderson N, Tulloch-Reid M, Aiken W, Kimbro K, Jones D, Kidd LR, Ragin C Tags: Gene Source Type: research

Single cell transcriptome analysis of muscle satellite cells reveals widespread transcriptional heterogeneity.
Abstract Tissue specific stem cells are indispensable contributors to adult tissue maintenance, repair, and regeneration. In skeletal muscle, satellite cells (SCs) are the resident muscle stem cell population and are required to maintain skeletal muscle homeostasis throughout life. Increasing evidence suggests that SCs are a heterogeneous cell population with substantial biochemical and functional diversity. A major limitation in the field is an incomplete understanding of the nature and extent of this cellular heterogeneity. Single cell analyses are well suited to addressing this issue, especially when coupled to...
Source: Gene - September 8, 2017 Category: Genetics & Stem Cells Authors: Cho DS, Doles JD Tags: Gene Source Type: research

Molecular characterization and functional analysis of chalcone synthase from Syringa oblata Lindl. in the flavonoid biosynthetic pathway.
In conclusion, these results suggest that SoCHS1 plays an essential role in flavonoid biosynthesis in S. oblata, and could be used to modify flavonoid components in other plant species. PMID: 28890377 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - September 7, 2017 Category: Genetics & Stem Cells Authors: Wang Y, Dou Y, Wang R, Guan X, Hu Z, Zheng J Tags: Gene Source Type: research

MicroRNA-219-5p inhibits the proliferation, migration, and invasion of epithelial ovarian cancer cells by targeting the Twist/Wnt/ β-catenin signaling pathway.
In this study, we sought to explore the potential functions of miR-219-5p in epithelial ovarian cancer. Herein, we found that miR-219-5p levels were significantly decreased in epithelial ovarian cancer tissues and cell lines. Further experiments showed that overexpression of miR-219-5p inhibited epithelial ovarian cancer cell proliferation, migration, and invasion, and suppressed the Wnt/β-catenin signaling pathway. By contrast, suppression of miR-219-5p exhibited the opposite effects. Twist was identified as a downstream target of miR-219-5p, and its expression was directly regulated by miR-219-5p. Restoration of Twi...
Source: Gene - September 7, 2017 Category: Genetics & Stem Cells Authors: Wei C, Zhang X, He S, Liu B, Han H, Sun X Tags: Gene Source Type: research

Characterization of conserved and novel miRNAs using deep sequencing and prediction of miRNA targets in Crucian carp (Carassius auratus).
This study represents a first large-scale identification and characterization of C. auratus miRNAs and their potential target genes. Taken together, our results add new information to existing data on C. auratus miRNAs and should be useful for investigating the biological functions of miRNAs in fishes and other aquatic species. PMID: 28890379 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - September 7, 2017 Category: Genetics & Stem Cells Authors: Huang Y, Gao XC, Ren HT, Xiong JL, Sun XH Tags: Gene Source Type: research

Fascaplysin inhibit ovarian cancer cell proliferation and metastasis through inhibiting CDK4.
CONCLUSIONS: Above all, our results showed that fascaplysin has anti-tumor activity against ovarian cancer cell lines through inhibiting CDK4, and may be a therapeutic target for the treatment of ovarian carcinomas. PMID: 28888575 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - September 6, 2017 Category: Genetics & Stem Cells Authors: Chen S, Guan X, Wang LL, Li B, Sang XB, Liu Y, Zhao Y Tags: Gene Source Type: research

Association of vitamin D and vitamin D binding protein (DBP) gene polymorphism with susceptibility of type 2 diabetes mellitus in Bangladesh.
Abstract AIMS: Polymorphism in vitamin D binding protein gene may have an impact on serum vitamin D transport and thus may have relation with type 2 diabetes mellitus. In our study, we investigated the association of serum vitamin D level and vitamin D-binding protein gene polymorphism with the onset of type 2 diabetes mellitus. MATERIALS AND METHODS: Blood samples were collected from 104 type 2 diabetic patients and 107 healthy volunteers. Serum vitamin D was measured by high-performance liquid chromatography. Genetic analysis of vitamin D-binging protein gene was carried out by polymerase chain reaction - r...
Source: Gene - September 6, 2017 Category: Genetics & Stem Cells Authors: Rahman MM, Hosen MB, Faruk MO, Hasan MM, Kabir Y, Howlader MZH Tags: Gene Source Type: research

CRISPR knock out CTLA-4 enhances the anti-tumor activity of cytotoxic T lymphocytes.
In this study, we use CRISPR-Cas9 system to knock out (KO) CTLA-4 from cytotoxic T lymphocytes (CTLs) and evaluate its effect on the anti-tumor activity of the CTLs. CTLA-4 KO CTLs robustly enhanced tumor cell death by 40% compared to the control and facilitated apoptosis and caspase activities in tumor cells. The knockout of CTLA-4 also increased TNF-α and IFN-γ secretion of the CTLs by approximately 2-fold. The effectiveness of CTLA-4 KO in enhancing anti-tumor activity of the CTLs was verified in vivo using mouse xenograft model. The xenografted mice treated with CTLA-4 KO CTLs demonstrated repressed tumor g...
Source: Gene - September 6, 2017 Category: Genetics & Stem Cells Authors: Shi L, Meng T, Zhao Z, Han J, Zhang W, Gao F, Cai J Tags: Gene Source Type: research

When figures and data contradict text: MiR346 is apparently reduced in breast cancer tissue, contrary to claims by a paper's author.
Abstract A recent article in Gene highlighted potential function of miR-346 in human breast cancer (Yang et al., 2017). We request an explanation or correction of the report. In its current state, the text will certainly create confusion in the field and lead to incorrect assumptions. The authors made several critical errors. The abstract stated "we found that the expression of miR-346 was higher in breast cancer tissues than in their paired corresponding non-cancerous tissues" and the main text and legend for Fig. 1A stated "miR-346 expression was significantly higher in breast cancer tissues than ...
Source: Gene - September 6, 2017 Category: Genetics & Stem Cells Authors: Lahiri DK, Maloney B, Sambamurti K Tags: Gene Source Type: research

The association between FOXP3 gene variations and autism: True or false positive?
PMID: 28887156 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - September 5, 2017 Category: Genetics & Stem Cells Authors: Mirfakhraie R Tags: Gene Source Type: research

Effect of a single nucleotide polymorphism in the growth hormone secretagogue receptor (GHSR) gene on growth rate in pigs.
In this study, we examined the possible role of GHSR in the growth traits of four pig breeds, namely Tibetan pigs (n=45), Diannan small-eared pigs (n=40), Yorkshire pigs (n=45), and New Huai pigs (n=122). Single nucleotide polymorphisms (SNPs) in these pigs were identified by polymerase chain reaction (PCR) sequencing and genotyping was performed using PCR-restriction fragment length polymorphisms (PCR-RFLPs). A SNP (C/A) named C-1595A (the "C" allele), which is located 1595bp upstream of the initiation codon of the GHSR gene, was found at a higher frequency in the fast-growing Yorkshire pigs than in the slow-gro...
Source: Gene - September 5, 2017 Category: Genetics & Stem Cells Authors: Zhang B, Shang P, Tao Z, Qiangba Y, Wang Z, Zhang H Tags: Gene Source Type: research

Lack of association of CASC8 rs1447295 with colorectal cancer in Iranian population: A multicenter case-control study.
In conclusion, it is unlikely that the rs1447295 polymorphism is a risk variant for the development of CRC in Iranian population. PMID: 28887158 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - September 5, 2017 Category: Genetics & Stem Cells Authors: Haerian MS, Haerian BS, Molanaei S, Kosari F, Sabeti S, Bidari-Zerehpoosh F, Abdolali E Tags: Gene Source Type: research

Integrative analysis of DNA methylation and mRNA expression during differentiation of umbilical cord blood derived mononuclear cells to endothelial cells.
Abstract Differentiation of umbilical cord blood derived mononuclear cells to endothelial cells is accompanied by massive changes in gene expression. Although methylation and demethylation of DNA likely play crucial roles in regulating gene expression, their interplay during differentiation remains elusive. To address this question, we performed deep sequencing of DNA methylation and mRNA expression to profile global changes in promoter methylation and gene expression during differentiation from mononuclear cells to outgrowing cells. We identified 61 downregulated genes with hypermethylation, including CD74, VAV1,...
Source: Gene - September 5, 2017 Category: Genetics & Stem Cells Authors: Jeong Y, Jun Y, Kim J, Park H, Choi KS, Zhang H, Park JA, Kwon JY, Kim YM, Lee S, Kwon YG Tags: Gene Source Type: research

Silencing of the pentose phosphate pathway genes influences DNA replication in human fibroblasts.
Abstract Previous reports and our recently published data indicated that some enzymes of glycolysis and the tricarboxylic acid cycle can affect the genome replication process by changing either the efficiency or timing of DNA synthesis in human normal cells. Both these pathways are connected with the pentose phosphate pathway (PPP pathway). The PPP pathway supports cell growth by generating energy and precursors for nucleotides and amino acids. Therefore, we asked if silencing of genes coding for enzymes involved in the pentose phosphate pathway may also affect the control of DNA replication in human fibroblasts. ...
Source: Gene - September 5, 2017 Category: Genetics & Stem Cells Authors: Fornalewicz K, Wieczorek A, Węgrzyn G, Łyżeń R Tags: Gene Source Type: research

Loss of discoidin domain receptor 1 (DDR1) via CpG methylation during EMT in epithelial ovarian cancer.
Abstract Epithelial ovarian cancer (EOC) can be stratified according to the stages of epithelial-mesenchymal transition (EMT). Here, we aim to identify tyrosine kinases (TKs) in EOC that correlate with the EMT subtypes. By gene expression microarray, we analyzed the expression levels of tyrosine kinases in EOC cell lines in correlation with EMT. Among the candidate TKs identified, DDR1 was expressed mainly in EOC cells with an Epithelial phenotype. Its expression was validated by qPCR, ELISA and western blotting. Using Infinium HumanMethylation27K BeadChip array and pyrosequencing, we further analyzed the CpG meth...
Source: Gene - September 5, 2017 Category: Genetics & Stem Cells Authors: Chung VY, Tan TZ, Huang RL, Lai HC, Huang RY Tags: Gene Source Type: research

Genetic variations in UGT2B28, UGT2B17, UGT2B15 genes and the risk of prostate cancer: A case-control study.
Abstract Glucuronidation is a major pathway for elimination of exogenous and endogenous compounds such as environmental carcinogens and androgens from the body. This biochemical pathway is mediated by enzymes called uridine diphosphoglucuronosyltransferases (UGTs). Null (del/del) genes polymorphisms in UGT2B17, and UGT2B28 and D85Y single-nucleotide polymorphism (SNP) of UGT2B15 have been reported to increase the risk of prostate cancer. The goal of this study was to determine the association of mentioned genetic variants with the risk of prostate cancer. We investigated the copy number variations (CNVs) of UGT2B1...
Source: Gene - September 4, 2017 Category: Genetics & Stem Cells Authors: Habibi M, Mirfakhraie R, Khani M, Rakhshan A, Azargashb E, Pouresmaeili F Tags: Gene Source Type: research

Anaerobic sulfatase maturase AslB from Escherichia coli activates human recombinant iduronate-2-sulfate sulfatase (IDS) and N-acetylgalactosamine-6-sulfate sulfatase (GALNS).
In conclusion, our results suggest that AslB is involve in the maturation of heterologous human sulfatases in E. coli BL21(DE3), and that it can have important implications in the production of recombinant sulfatases for therapeutic purposes and research. PMID: 28882567 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - September 4, 2017 Category: Genetics & Stem Cells Authors: Alméciga-Díaz CJ, Tolosa-Díaz AD, Pimentel LN, Bonilla YA, Rodríguez-López A, Espejo-Mojica AJ, Patiño JD, Sánchez OF, Gonzalez-Santos J Tags: Gene Source Type: research

Identification of pathogenic genes related to rheumatoid arthritis through integrated analysis of DNA methylation and gene expression profiling.
Abstract The purpose of our study was to identify new pathogenic genes used for exploring the pathogenesis of rheumatoid arthritis (RA). To screen pathogenic genes of RA, an integrated analysis was performed by using the microarray datasets in RA derived from the Gene Expression Omnibus (GEO) database. The functional annotation and potential pathways of differentially expressed genes (DEGs) were further discovered by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Afterwards, the integrated analysis of DNA methylation and gene expression profiling was used to screen cruci...
Source: Gene - September 4, 2017 Category: Genetics & Stem Cells Authors: Zhang L, Ma S, Wang H, Su H, Su K, Li L Tags: Gene Source Type: research

miR-130a regulates differential lipid accumulation between intramuscular and subcutaneous adipose tissues of pigs via suppressing PPARG expression.
In conclusion, tissue variance of miR-130a levels results in the diverse of PPARG, and might be the reason for differential fat deposition between IM and SC fat tissues in pigs. Our study would provide the molecular foundation for IM fat deposition increase and therefore contribute to pork quality improvement. PMID: 28882569 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - September 4, 2017 Category: Genetics & Stem Cells Authors: Wei W, Sun W, Han H, Chu W, Zhang L, Chen J Tags: Gene Source Type: research

Use of targeted sequence capture and high-throughput sequencing identifies a novel PKD1 mutation involved in adult polycystic kidney disease.
Abstract Polycystic kidney disease (PKD) is a common inherited disease that is characterized by a progressive development of renal cysts. Approximately 85% of PKD cases are due to mutations in the polycystin 1 (PKD1) gene. Here, we report a pedigree containing nine patients with autosomal dominant PKD (ADPKD). Using targeted exome sequencing of PKD1 and PKD2 genes, we identified a novel heterozygous frameshift mutation c.3976_3977insCT (p.F1326Sfs*21) in the PKD1 gene that segregated between affected and unaffected family members. This mutation is currently not present in the 1000 Genomes Project nor ExAC database...
Source: Gene - September 1, 2017 Category: Genetics & Stem Cells Authors: Sha YK, Sha YW, Mei LB, Huang XJ, Wang X, Lin SB, Li L, Li P Tags: Gene Source Type: research

Counter regulation of ECRG4 gene expression by hypermethylation-dependent inhibition and the Sp1 transcription factor-dependent stimulation of the c2orf40 promoter.
Abstract The human cytokine precursor ECRG4 has been associated with multiple physiological, developmental and pathophysiological processes involving cell proliferation, cell migration, innate immunity, inflammation, cancer progression and metastases. Although down-regulation of ECRG4 gene expression has been largely attributed to hypermethylation of CpG islands in the 5'untranslated region of the ECRG4 promoter, the mechanisms that underlie the dynamics of its regulation have never been systematically described. Here we show that the ECRG4 gene is widely expressed in human tissues and report that its core promote...
Source: Gene - September 1, 2017 Category: Genetics & Stem Cells Authors: Dang X, Zeng X, Coimbra R, Eliceiri BP, Baird A Tags: Gene Source Type: research

Expression and activation of Daphnia pulex Caspase-3 are involved in regulation of aging.
Abstract Death-mediating proteases such as Caspases have been implicated in aging. Remarkably, active Caspase-3 can trigger widespread damage and degeneration, playing a key role in causing cell death. In order to explore the relationship between Caspase-3 and aging in Daphnia pulex, we cloned and analyzed the full-length cDNA sequence of its Caspase-3 gene. Both mRNA expression and activity of D. pulex Caspase-3 increased with age. Moreover, different forms of Caspase-3 appeared with aging. The expression of casp3-L was higher and decreased with age, while that of casp3-S was weak and increased with age, consiste...
Source: Gene - August 31, 2017 Category: Genetics & Stem Cells Authors: Tong Q, Zhang M, Cao X, Xu S, Wang D, Zhao Y Tags: Gene Source Type: research

Different histories of two highly variable LTR retrotransposons in sunflower species.
Abstract In the Helianthus genus, very large intra- and interspecific variability related to two specific retrotransposons of Helianthus annuus (Helicopia and SURE) exists. When comparing these two sequences to sunflower sequence databases recently produced by our lab, the Helicopia family was shown to belong to the Maximus/SIRE lineage of the Sirevirus genus of the Copia superfamily, whereas the SURE element (whose superfamily was not even previously identified) was classified as a Gypsy element of the Ogre/Tat lineage of the Metavirus genus. Bioinformatic analysis of the two retrotransposon families revealed the...
Source: Gene - August 31, 2017 Category: Genetics & Stem Cells Authors: Mascagni F, Cavallini A, Giordani T, Natali L Tags: Gene Source Type: research

Molecular mapping and genetic analysis of a QTL controlling spike formation rate and tiller number in wheat.
Abstract Spike formation rate (SR), which is based on maximum tiller number per unit area and spike number per unit area, is an important yield-related trait in wheat. Increasing the spike formation rate reduces growth competition and wastage of photosynthate from ineffective tillers. Unfortunately, research studies involving quantitative trait locus (QTL) mapping for wheat spike formation rate are limited. In the present study, a set of 371 recombinant inbreed line (RIL) population, which were derived from 1BL/LRS wheat-rye translocation lines CN18 and T1208, was analysed by simple sequence repeat (SSR) markers. ...
Source: Gene - August 31, 2017 Category: Genetics & Stem Cells Authors: Hu YS, Ren TH, Li Z, Tang YZ, Ren ZL, Yan BJ Tags: Gene Source Type: research

Activity analysis of LTR12C as an effective regulatory element of the RAE1 gene.
We examined the transcriptional activity of LTR12C by using the luciferase assay, and showed that the tandem repeat region (TRR) located within LTR12C was required for its regulatory function. A bioinformatics analysis revealed that the LTR12C element had multiple transcription factor binding sites specific for nuclear transcription factor Y (NF-Y), and the promoter activity of LTR12C was significantly decreased after NF-Y knockdown. Additionally, we discovered novel data indicating that LTR12C was initially inserted into the gorilla genome. Taken together, our results reveal that the TRR of LTR12C has powerful regulatory ...
Source: Gene - August 31, 2017 Category: Genetics & Stem Cells Authors: Jung YD, Lee HE, Jo A, Hiroo I, Cha HJ, Kim HS Tags: Gene Source Type: research

The developmental transcriptome landscape of receptive endometrium during embryo implantation in dairy goats.
In this study, the endometrium from gestational day 5 (D5, PE) and gestational day 15 (D15, RE) dairy goats were selected to systematically analyze the transcriptome using strand-specific Ribo-Zero RNA-Seq,>120 million high-quality paired-end reads were generated and 47,616 transcripts were identified in the endometrium of dairy goats. A total of 810 mRNAs were differentially expressed genes (DEGs) between the RE and PE meeting the criteria of P-values
Source: Gene - August 30, 2017 Category: Genetics & Stem Cells Authors: Zhang L, Liu X, Liu J, Ma L, Zhou Z, Song Y, Cao B Tags: Gene Source Type: research

A homozygous CEP135 mutation is associated with multiple morphological abnormalities of the sperm flagella (MMAF).
Abstract Multiple morphological abnormalities of the sperm flagella (MMAF) is a rare disease associated with primary infertility; however, ~50% of the genetic alterations associated with MMAF remain unclear. Here, we reported the case of a 30-year-old infertile male from a consanguineous family. Whole-exome sequencing identified a homozygous mutation in the CEP135 gene (c.A1364T:p.D455V), with CEP135 previously reported to play a role in centriole biogenesis and specifically central pair assembly. D455V-mutated proteins formed protein aggregates in the centrosome and the flagella, which might potentially affect th...
Source: Gene - August 30, 2017 Category: Genetics & Stem Cells Authors: Sha YW, Xu X, Mei LB, Li P, Su ZY, He XQ, Li L Tags: Gene Source Type: research

Comparative profiling of microRNAs and their association with sexual dimorphism in the fig wasp Ceratosolen solmsi.
In this study, we constructed six small RNA libraries from female and male wasps in three different developmental stages, i.e., larvae, early pupae, and late pupae. We detected known miRNAs and predicted novel miRNAs, and compared their expression patterns in both sexes and among different developmental stages. We focused mainly on the miRNAs with significantly different expression patterns between sexes and among different life stages, as well as their putative associations with metamorphosis and the formation of sexual dimorphism. PMID: 28866085 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - August 30, 2017 Category: Genetics & Stem Cells Authors: Wang YK, Li JP, Li TT, Liu R, Jia LY, Wei XQ, Xiao JH, Huang DW Tags: Gene Source Type: research

Evaluation of the relationship between CD36 and MARCO single-nucleotide polymorphisms and susceptibility to carotid atherosclerosis in a Chinese Han population.
CONCLUSIONS: CD36 and MARCO are associated with the susceptibility of Chinese Han females to carotid atherosclerosis. Menopausal status may affect the association between gene polymorphisms and carotid atherosclerosis in the female Chinese Han population. PMID: 28866086 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - August 30, 2017 Category: Genetics & Stem Cells Authors: Chu Y, Lao W, Jin G, Dai D, Chen L, Kang H Tags: Gene Source Type: research

Identification, structural characterization and expression analysis of a novel carbonic anhydrase from freshwater mussel Hyriopsis cumingii.
In this study, an α-carbonic anhydrase (α-CA), HcCA3, from Hyriopsis cumingii was characterized. The full-length cDNA of HcCA3 was 1628bp, including a CA domain and an ORF of 1053bp which encoded 350 amino acids. Its predicted molecular weight was 39.69kDa and the pI was 5.92. qRT-PCR was used to determine the expression of the gene in various tissues at 0h, 3h, 6h, 12h, 24h, 48h, 96h, 7d, 14d, 21d, 28d and 35d after inserting the pearl nucleus. The results showed that the HcCA3 was highly expressed in the mantle, whereas its expression was low in other tissues. Expression in the posterior mantle pallial (pMP) ...
Source: Gene - August 30, 2017 Category: Genetics & Stem Cells Authors: Wang GL, Wang Q, Xu ZC, Wang YY, Li JL Tags: Gene Source Type: research

Identification of apoptosis-related genes Bcl2 and Bax from yellow catfish Pelteobagrus fulvidraco and their transcriptional responses to waterborne and dietborne zinc exposure.
Abstract Apoptosis plays a key role in the physiology of multicellular organisms, and has been well studied in mammals, but not in teleosts. Zinc (Zn) has been shown to be an important regulator of apoptosis and apoptosis involves in the regulation of lipid metabolism. Moreover, our recent study indicated that waterborne and dietborne Zn exposure differently influenced lipid metabolism in Pelteobagrus fulvidraco, but further mechanism remained unknown. The hypothesis of the present study is that apoptosis mediated the Zn-induced changes of lipid metabolism of P. fulvidraco subjected to different exposure pathways....
Source: Gene - August 29, 2017 Category: Genetics & Stem Cells Authors: Li DD, Luo Z, Chen GH, Song YF, Wei CC, Pan YX Tags: Gene Source Type: research

Leptin siRNA promotes ovarian granulosa cell apoptosis and affects steroidogenesis by increasing NPY2 receptor expression.
In conclusion, knockdown of leptin significantly affected ovarian steroidogenesis and ovarian function through NPY. siLeptin transfection impaired the activation of JAK2/STAT3 and contributed to ovarian granulosa cell apoptosis partially through up-regulating NPY2R expression. PMID: 28864114 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - August 29, 2017 Category: Genetics & Stem Cells Authors: Ding X, Kou X, Zhang Y, Zhang X, Cheng G, Jia T Tags: Gene Source Type: research

RasGRP3 controls cell proliferation and migration in papillary thyroid cancer by regulating the Akt-MDM2 pathway.
In this study, we demonstrate that RasGRP3 was overexpressed in PTC tissues and cell lines. Downregulation of RasGRP3 using small interfering (si) RNA significantly inhibited PTC cell proliferation and migration in vitro, and tumor growth in vivo, reflecting an oncogenic role of RasGRP3 in PTC. We subsequently identified that the expression of mouse double minute 2 homolog (MDM2) and phosphorylated Akt (p-Akt) was significantly decreased in RasGRP3-downregulated PTC cells. Overexpression of MDM2 attenuated the function of si-RasGRP3. Taken together, our data show that RasGRP3 exerts its oncogenic effect in PTC through Akt-...
Source: Gene - August 29, 2017 Category: Genetics & Stem Cells Authors: Qiu W, Xia X, Qiu Z, Guo M, Yang Z Tags: Gene Source Type: research

The role of long non-coding RNA PCA3 in epithelial ovarian carcinoma tumorigenesis and progression.
CONCLUSIONS: Research results show that lncRNA PCA3 may coordinate EOC tumorigenesis through disrupting miR-106b regulated gene expression. PCA3 may be a novel and important diagnostic biomarker and a valuable marker for prediction in the clinical care of epithelial ovarian carcinoma. PMID: 28864116 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - August 29, 2017 Category: Genetics & Stem Cells Authors: Liu Y, Zong ZH, Guan X, Wang LL, Zhao Y Tags: Gene Source Type: research

Genotype-dependent regulation of drought-responsive genes in tolerant and sensitive sugarcane cultivars.
Abstract Drought is the most damaging among the major abiotic stresses. Transcriptomic studies allow a global overview of expressed genes, providing the basis for molecular markers development. Here, the HT-SuperSAGE technique allowed the evaluation of four drought-tolerant cultivars and four-sensitive cultivars, after 24h of irrigation suppression. We identified 9831 induced unitags from roots of the tolerant cultivars with different regulations by the -sensitive cultivars after the applied stress. These unitags allowed a proposal of 15 genes, whose expressed profiles were validated by RT-qPCR, evaluating each cu...
Source: Gene - August 27, 2017 Category: Genetics & Stem Cells Authors: da Silva MD, de Oliveira Silva RL, Neto JRCF, Benko-Iseppon AM, Kido EA Tags: Gene Source Type: research