Read by QxMD icon Read

Genes and genomes

Jiayong Dong, Fei Teng, Wenyuan Guo, Jinghui Yang, Guoshan Ding, Zhiren Fu
BACKGROUND/AIMS: Long noncoding RNAs (lncRNAs) are aberrantly expressed in multiple malignant tumors involved in tumor growth and metastasis. Accumulating data show that small nucleolar RNA host gene (SNHG) 1/12/20 plays a key role in the progression of hepatocellular carcinoma (HCC). However, the molecular mechanisms by which SNHG8 contributes to HCC remain elusive and merit exploration. METHODS: The association between SNHG8 expression and the clinicopathological characteristics and prognoses in HCC patients was analysed by using qRT-PCR analysis and the data from The Cancer Genome Atlas...
2018: Cellular Physiology and Biochemistry
Joshua W Russo, Steven P Balk
In this issue of Cancer Cell, Gerhauser et al. analyze early-onset prostate cancers, showing roles for androgen receptor-driven rearrangements, an early APOBEC-driven mutational mechanism, and ESRP1 gene duplication. Through integration of whole-genome, transcriptome, and methylome data, they identify high-risk subgroups and develop an algorithm that may predict molecular evolution.
December 10, 2018: Cancer Cell
Katarina Zmajkovicova, Katalin Menyhart, Yasmina Bauer, Rolf Studer, Berengere Renault, Marie Schnoebelen, Matthias Bolinger, Oliver Nayler, John Gatfield
Idiopathic pulmonary fibrosis (IPF) is a life-threatening progressive disease characterized by loss of alveolar epithelial cells, inflammation and aberrant fibroblast activation. The two currently approved therapies do not halt or reverse tissue remodeling and therefore novel disease modifying mechanisms are needed. Our results describe YAP/TAZ inhibition through IP receptor activation as a novel mechanism that suppresses pro-fibrotic (myo)fibroblast activity. We investigated the anti-fibrotic properties of the selective prostacyclin (IP) receptor agonist ACT-333679 using primary human lung fibroblasts...
December 11, 2018: American Journal of Respiratory Cell and Molecular Biology
Yusmiati Liau, Ignatius Chua, Martin A Kennedy, Simran Maggo
Angioedema is a rare adverse effect of the commonly used angiotensin converting enzyme inhibitors (ACEi) and is reported to occur with a prevalence of 0.1 - 0.7%. Although most ACEi-induced angioedema (ACEi-A) cases are mild, severe cases requiring intensive care and even resulting in death have been reported in the literature. The mechanisms underlying ACEi-A are not yet fully understood, but bradykinin and/or substance P accumulation resulting from inhibition of ACE, is believed to play a crucial role. ACEi-A occurs at variable frequencies across different racial groups, suggesting a genetic association to the development of ACEi-A...
December 8, 2018: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
Qingyao Zhu, Hongjie Yang, Peng Cheng, Qian Han
Some lncRNAs can encode small nucleolar RNAs (snoRNAs), called small nucleolar RNA host genes (SNHGs), which exert diverse regulatory effects on cellular processes. In this study, using RNA-seq and survival data in the Cancer Genome Atlas (TCGA)-Liver Hepatocellular Carcinoma (LIHC), we examined the expression profile of some SNHG genes and explored their prognostic value in hepatocellular carcinoma (HCC). Level-3 RNA-sequencing data, the clinicopathological and survival data of patients with primary HCC were downloaded from the UCSC Xena browser (https://xenabrowser...
December 8, 2018: BioFactors
Ana Carolina Tahira, André Rocha Barbosa, Arthur Sant'Anna Feltrin, Vinicius Daguano Gastaldi, Victor Hugo Calegari de Toledo, José Geraldo de Carvalho Pereira, Bianca Cristina Garcia Lisboa, Viviane Neri de Souza Reis, Ana Cecília Feio Dos Santos, Mariana Maschietto, Helena Brentani
The male-biased prevalence of certain neurodevelopmental disorders and the sex-biased outcomes associated with stress exposure during gestation have been previously described. Here, we hypothesized that genes distinctively targeted by only one or both homologous proteins highly conserved across therian mammals, SOX3 and SRY, could induce sexual adaptive changes that result in a differential risk for neurodevelopmental disorders. ChIP-seq/chip data showed that SOX3/SRY gene targets were expressed in different brain cell types in mice...
December 9, 2018: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
Chi-Yang Chiu, Fang Yuan, Bing-Song Zhang, Ao Yuan, Xin Li, Hong-Bin Fang, Kenneth Lange, Daniel E Weeks, Alexander F Wilson, Joan E Bailey-Wilson, Anthony M Musolf, Dwight Stambolian, M'Hamed Lajmi Lakhal-Chaieb, Richard J Cook, Francis J McMahon, Christopher I Amos, Momiao Xiong, Ruzong Fan
We develop linear mixed models (LMMs) and functional linear mixed models (FLMMs) for gene-based tests of association between a quantitative trait and genetic variants on pedigrees. The effects of a major gene are modeled as a fixed effect, the contributions of polygenes are modeled as a random effect, and the correlations of pedigree members are modeled via inbreeding/kinship coefficients. <mml:math xmlns:mml=""> <mml:mi>F</mml:mi> </mml:math> -statistics and χ 2 likelihood ratio test (LRT) statistics based on the LMMs and FLMMs are constructed to test for association...
December 9, 2018: Genetic Epidemiology
Joanne Trinh, Katja Lohmann, Hauke Baumann, Alexander Balck, Max Borsche, Norbert Brüggemann, Leon Dure, Marissa Dean, Jens Volkmann, Sinem Tunc, Jannik Prasuhn, Heike Pawlack, Sophie Imhoff, Christina M Lill, Meike Kasten, Peter Bauer, Arndt Rolfs, Christine Klein
BACKGROUND: Although the genetic load is high in early-onset Parkinson's disease, thorough investigation of the genetic diagnostic yield has yet to be established. The objectives of this study were to assess variants in known genes for PD and other movement disorders and to find new candidates in 50 patients with early-onset PD. METHODS: We searched for variants either within genes listed by the International Parkinson and Movement Disorder Society Task Force on Genetic Nomenclature or rare homozygous variants in novel candidate genes...
December 10, 2018: Movement Disorders: Official Journal of the Movement Disorder Society
Genevieve M Hoopes, John P Hamilton, Joshua C Wood, Eddi Esteban, Asher Pasha, Brieanne Vaillancourt, Nicholas J Provart, C Robin Buell
Maize(Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide.The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long-read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA-sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36,207 expressed genes...
December 7, 2018: Plant Journal: for Cell and Molecular Biology
Luchen Ruan, Meng Meng, Cong Wang, Lihua Hou
BACKGROUND: The salt tolerant yeast strain C.versatilis usually is added in the high-salt liquid-state soy sauce fermentation. The genome of C.versatilis was sequenced in our previous study, but the reason of high-osmolarity ability was not clear. RESULTS: The 9.7Mbp genome of C.versatilis contained 4711 CDS. C. versatilis was the closest with another yeast Zygosaccharomyces rouxii added in the soy sauce fermentation in the evolutionary relationship. The protein sequence of the whole genome was divided into 4338 groups, accounting for 92...
December 10, 2018: Journal of the Science of Food and Agriculture
Feng Lv, Wei-Hua Jin, Xian-Lin Zhang, Zhong-Rui Wang, Ai-Jun Sun
Tamoxifen treatment is important assistant for estrogen-receptor-positive breast cancer (BRCA) after resection. This study aimed to identify signatures for predicting the prognosis of patients with BRCA after tamoxifen treatment. Data of gene-specific DNA methylation (DM), as well as the corresponding clinical data for the patients with BRCA, were obtained from The Cancer Genome Atlas and followed by systematic bioinformatics analyses. After mapping these DM CPG sites onto genes, we finally obtained 352 relapse-free survival (RFS) associated DM genes, with which 61,776 gene pairs were combined, including 1,614 gene pairs related to RFS...
December 7, 2018: Journal of Cellular Physiology
Anat Vivante, Eugene Brozgol, Irena Bronshtein, Vered Levi, Yuval Garini
During the past three decades, the study of nuclear and chromatin organization has become of great interest. The organization and dynamics of chromatin are directly responsible for many functions including gene regulation, genome replication, and maintenance. In order to better understand the details of these mechanisms, we need to understand the role of specific proteins that take part in these processes. The genome in the nucleus is organized in different length scales, ranging from the bead-like nucleosomes through topological associated domains (TADs) up to chromosome territories...
December 9, 2018: Genes, Chromosomes & Cancer
Panfeng Zhao, Qiuye You, Mingguang Lei
In vascular (Arabidopsis thaliana) and nonvascular (Physcomitrella patens) plants, PHOSPHATE 1 (PHO1) homologs play important roles in the acquisition and transfer of phosphate. The tomato genome contains six genes (SlPHO1;1-SlPHO1;6) homologous to AtPHO1. The six proteins have typical characteristics of the plant PHO1 family, such as the three SPX sub domains in the N-terminal portion and one EXS domain in the C-terminal portion. Phylogenetic analysis revealed that the SlPHO1 family is subdivided into three clusters...
December 8, 2018: Physiologia Plantarum
Eric D Salomaki, Christopher E Lane
Parasitism is a life strategy that has repeatedly evolved within the Florideophyceae. Historically, the terms adelphoparasite and alloparasite have been used to distinguish parasites based on the relative phylogenetic relationship of host and parasite. However, analyses using molecular phylogenetics indicate that nearly all red algal parasites infect within their taxonomic family, and a range of relationships exist between host and parasite. To date, all investigated adelphoparasites have lost their plastid, and instead, incorporate a host derived plastid when packaging spores...
December 9, 2018: Journal of Phycology
Aneesha Acharya, Simin Li, Xiangqiong Liu, George Pelekos, Dirk Ziebolz, Nikos Mattheos
BACKGROUND AND OBJECTIVE: Primary research concerning molecular pathways that link rheumatoid arthritis with periodontitis is limited. Biomedical literature data mining can offer insights into putative linkage mechanisms toward hypothesis development, based on information discovery. The aim of this study was to explore potential Periodontitis-Rheumatoid Arthritis biological links by analysing "overlapping" genes reported in biomedical abstracts. MATERIAL AND METHODS: PubMed abstracts for terms: (a) "Periodontitis" or "Periodontal Diseases" (PD), (b) "Rheumatoid arthritis" (RA), and (c) their combination with "AND" (RA+PD), were each text-mined to extract genes using "Human Genome Nomenclature Committee" (HGNC) symbols...
December 10, 2018: Journal of Periodontal Research
Fangyao Chen, Zhe Li, Hui Zhou
OBJECT: This study was conducted to identify the prognostic microRNA (miRNA) for the prediction of survival in colon adenocarcinoma (CA). METHODS: miRNA profiling of patients with CA was downloaded from The Cancer Genome Atlas (TCGA) database. After data processing, univariate Cox regression was performed to select potential prognostic miRNAs. Least absolute shrinkage and selection operator approach was conducted to identify the key prognostic miRNA biomarkers. Log-rank test was performed to compare survival outcome between patients with different regulation type of identified miRNAs...
December 9, 2018: Journal of Cellular Biochemistry
Tian Yang, Xue Li, Zahra Montazeri, Julian Little, Susan M Farrington, John Pa Ioannidis, Malcolm G Dunlop, Harry Campbell, Maria Timofeeva, Evropi Theodoratou
The cause of colorectal cancer (CRC) is multifactorial, involving both genetic variants and environmental risk factors. We systematically searched the MEDLINE, EMBASE, China National Knowledge Infrastructure (CNKI) and Wanfang databases from inception to December 2016, to identify systematic reviews and meta-analyses of observational studies that investigated gene-environment (G × E) interactions in CRC risk. Then, we critically evaluated the cumulative evidence for the G × E interactions using an extension of the Human Genome Epidemiology Network's Venice criteria...
December 11, 2018: International Journal of Cancer. Journal International du Cancer
Gan-Xun Li, Ze-Yang Ding, Yu-Wei Wang, Tong-Tong Liu, Wei-Xun Chen, Jing-Jing Wu, Wei-Qi Xu, Peng Zhu, Bi-Xiang Zhang
DNA methylation is a crucial regulator of gene transcription in the etiology and pathogenesis of hepatocellular carcinoma (HCC). Thus, it is reasonable to identify DNA methylation-related prognostic markers. Currently, we aimed to make an integrative epigenetic analysis of HCC to identify the effectiveness of epigenetic drivers in predicting prognosis for HCC patients. By the software pipeline TCGA-Assembler 2, RNA-seq, and methylation data were downloaded and processed from The Cancer Genome Atlas. A bioconductor package MethylMix was utilized to incorporate gene expression and methylation data on all 363 samples and identify 589 epigenetic drivers with transcriptionally predictive...
December 7, 2018: Journal of Cellular Physiology
Jeffrey L Neul, Timothy A Benke, Eric D Marsh, Steven A Skinner, Jonathan Merritt, David N Lieberman, Shannon Standridge, Timothy Feyma, Peter Heydemann, Sarika Peters, Robin Ryther, Mary Jones, Bernhard Suter, Walter E Kaufmann, Daniel G Glaze, Alan K Percy
Mutations in the X-linked gene MECP2 are associated with a severe neurodevelopmental disorder, Rett syndrome (RTT), primarily in girls. It had been suspected that mutations in Methyl-CpG-binding protein 2 (MECP2) led to embryonic lethality in males, however such males have been reported. To enhance understanding of the phenotypic spectrum present in these individuals, we identified 30 males with MECP2 mutations in the RTT Natural History Study databases. A wide phenotypic spectrum was observed, ranging from severe neonatal encephalopathy to cognitive impairment...
December 7, 2018: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
L Rajeev, M E Garber, G M Zane, M N Price, I Dubchak, J D Wall, P S Novichkov, A Mukhopadhyay, A E Kazakov
Bacterial genes for molybdenum-containing and tungsten-containing enzymes are often differentially regulated depending on the metal availability in the environment. Here, we describe a new family of transcription factors with an unusual DNA-binding domain related to excisionases of bacteriophages. These transcription factors are associated with genes for various molybdate and tungstate-specific transporting systems as well as molybdo/tungsto-enzymes in a wide range of bacterial genomes. We used a combination of computational and experimental techniques to study a member of the TF family, named TaoR (for tungsten-containing aldehyde oxidoreductase regulator)...
December 10, 2018: Environmental Microbiology
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"