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https://www.readbyqxmd.com/read/29231922/gene-expression-profiling-in-the-intestinal-mucosa-of-obese-rats-administered-probiotic-bacteria
#1
Julio Plaza-Díaz, Cándido Robles-Sánchez, Francisco Abadía-Molina, María José Sáez-Lara, Laura María Vilchez-Padial, Ángel Gil, Carolina Gómez-Llorente, Luis Fontana
We investigated whether the administration of Lactobacillus paracasei CNCM I-4034, Bifidobacterium breve CNCM I-4035 and Lactobacillus rhamnosus CNCM I-4036 modulate the expression of genes in the intestinal mucosa of obese Zucker rats. Forty-eight Zucker-Leprfa/fa and 16 Zucker lean Lepr+/fa rats were used. Eight Zucker lean Lepr+/fa and 8 Zucker-Leprfa/fa rats were euthanized as a reference. The remaining 40 Zucker-Leprfa/fa rats were then assigned to receive 1010 colony forming units (CFU) of one of the three probiotic strains, a mixture of L...
December 12, 2017: Scientific Data
https://www.readbyqxmd.com/read/29231860/predicting-the-functional-impact-of-cdh1-missense-mutations-in-hereditary-diffuse-gastric-cancer
#2
REVIEW
Soraia Melo, Joana Figueiredo, Maria Sofia Fernandes, Margarida Gonçalves, Eurico Morais-de-Sá, João Miguel Sanches, Raquel Seruca
The role of E-cadherin in Hereditary Diffuse Gastric Cancer (HDGC) is unequivocal. Germline alterations in its encoding gene (CDH1) are causative of HDGC and occur in about 40% of patients. Importantly, while in most cases CDH1 alterations result in the complete loss of E-cadherin associated with a well-established clinical impact, in about 20% of cases the mutations are of the missense type. The latter are of particular concern in terms of genetic counselling and clinical management, as the effect of the sequence variants in E-cadherin function is not predictable...
December 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29230367/a-novel-approach-for-human-whole-transcriptome-analysis-based-on-absolute-gene-expression-of-microarray-data
#3
Shirley Bikel, Leonor Jacobo-Albavera, Fausto Sánchez-Muñoz, Fernanda Cornejo-Granados, Samuel Canizales-Quinteros, Xavier Soberón, Rogerio R Sotelo-Mundo, Blanca E Del Río-Navarro, Alfredo Mendoza-Vargas, Filiberto Sánchez, Adrian Ochoa-Leyva
Background: In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays...
2017: PeerJ
https://www.readbyqxmd.com/read/29230233/whole-genome-sequencing-of-fusarium-fujikuroi-provides-insight-into-the-role-of-secretory-proteins-and-cell-wall-degrading-enzymes-in-causing-bakanae-disease-of-rice
#4
Bishnu M Bashyal, Kirti Rawat, Sapna Sharma, Deepika Kulshreshtha, S Gopala Krishnan, Ashok K Singh, Himanshu Dubey, Amolkumar U Solanke, T R Sharma, Rashmi Aggarwal
Fusarium fujikuroi causing bakanae disease has emerged as one of the major pathogen of rice across the world. The study aims to comparative genomic analysis of Fusarium fujikuroi isolates and identification of the secretary proteins of the fungus involved in rice pathogenesis. In the present study, F. fujikuroi isolate "F250" was sequenced with an assembly size of 42.47 Mb providing coverage of 96.89% on reference IMI58289 genome. A total of 13,603 protein-coding genes were predicted from genome assembly. The average gene density in the F...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29230204/a-comprehensive-overview-of-online-resources-to-identify-and-predict-bacterial-essential-genes
#5
REVIEW
Chong Peng, Yan Lin, Hao Luo, Feng Gao
Genes critical for the survival or reproduction of an organism in certain circumstances are classified as essential genes. Essential genes play a significant role in deciphering the survival mechanism of life. They may be greatly applied to pharmaceutics and synthetic biology. The continuous progress of experimental method for essential gene identification has accelerated the accumulation of gene essentiality data which facilitates the study of essential genes in silico. In this article, we present some available online resources related to gene essentiality, including bioinformatic software tools for transposon sequencing (Tn-seq) analysis, essential gene databases and online services to predict bacterial essential genes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29230105/growth-characteristics-of-methanomassiliicoccus-luminyensis-and-expression-of-methyltransferase-encoding-genes
#6
Lena Kröninger, Jacqueline Gottschling, Uwe Deppenmeier
DNA sequence analysis of the human gut revealed the presence a seventh order of methanogens referred to as Methanomassiliicoccales. Methanomassiliicoccus luminyensis is the only member of this order that grows in pure culture. Here, we show that the organism has a doubling time of 1.8 d with methanol + H2 and a growth yield of 2.4 g dry weight/mol CH4. M. luminyensis also uses methylamines + H2 (monomethylamine, dimethylamine, and trimethylamine) with doubling times of 2.1-2.3 d. Similar cell yields were obtained with equimolar concentrations of methanol and methylamines with respect to their methyl group contents...
2017: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/29230012/estimation-of-immune-cell-content-in-tumour-tissue-using-single-cell-rna-seq-data
#7
Max Schelker, Sonia Feau, Jinyan Du, Nav Ranu, Edda Klipp, Gavin MacBeath, Birgit Schoeberl, Andreas Raue
As interactions between the immune system and tumour cells are governed by a complex network of cell-cell interactions, knowing the specific immune cell composition of a solid tumour may be essential to predict a patient's response to immunotherapy. Here, we analyse in depth how to derive the cellular composition of a solid tumour from bulk gene expression data by mathematical deconvolution, using indication-specific and cell type-specific reference gene expression profiles (RGEPs) from tumour-derived single-cell RNA sequencing data...
December 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/29229946/find_tfsbp-find-thermodynamics-feasible-and-smallest-balanced-pathways-with-high-yield-from-large-scale-metabolic-networks
#8
Zixiang Xu, Jibin Sun, Qiaqing Wu, Dunming Zhu
Biologically meaningful metabolic pathways are important references in the design of industrial bacterium. At present, constraint-based method is the only way to model and simulate a genome-scale metabolic network under steady-state criteria. Due to the inadequate assumption of the relationship in gene-enzyme-reaction as one-to-one unique association, computational difficulty or ignoring the yield from substrate to product, previous pathway finding approaches can't be effectively applied to find out the high yield pathways that are mass balanced in stoichiometry...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229634/genomic-insights-into-colistin-resistant-klebsiella-pneumoniae-from-a-tunisian-teaching-hospital
#9
Nadia Jaidane, Rémy A Bonnin, Wejdene Mansour, Delphine Girlich, Elodie Creton, Garance Colleton, Cherifa Chaouch, Noureddine Boujaafar, Olfa Bouallegue, Thierry Naas
The emergence of colistin-resistant Klebsiella pneumoniae (CoRKp) is a public health concern since this antibiotic has become the last line of treatment for infections caused by multidrug-resistant (MDR) gram-negatives. In this study, we have investigated the molecular basis of colistin-resistance in 13 MDR Kp isolated from 12 patients in a teaching hospital in Sousse, Tunisia. Whole-genome sequencing (WGS) was used to decipher the molecular mechanism of colistin-resistance and to identify the resistome of these CoRKp It revealed a genome of ca...
December 11, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29229320/vaccine-mismatched-influenza-b-yamagata-lineage-viruses-in-cuba-2012-2013-season
#10
Amely Arencibia, Alexander Piñón, Belsy Acosta, Leandro Fernandez, Mayra Muné, Odalys Valdés, Clara Savón, Suset Oropesa, Grehete Gonzalez, Rosmery Roque, Guelsys Gonzalez, Bárbara Hernández, Javier Martínez Alfonso
Annual trivalent influenza vaccines contain one of influenza B lineages; influenza B/Victoria-lineage or influenza B/Yamagata viruses. Theoretically, these vaccines should protect against viruses expected to circulate in the next influenza season. The National Influenza Centers, based on surveillance data from National Reference Laboratories, selects the strains composing each annual trivalent or tetravalent vaccine. Nevertheless, in some epidemics, vaccine strains do not match genetically with circulating strains...
December 8, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29228836/complete-mtdna-sequencing-reveals-mutations-m-9185t-c-and-m-13513g-a-in-three-patients-with-leigh-syndrome
#11
Dita Pelnena, Birute Burnyte, Eriks Jankevics, Baiba Lace, Evelina Dagyte, Kristina Grigalioniene, Algirdas Utkus, Zita Krumina, Jolanta Rozentale, Irina Adomaitiene, Janis Stavusis, Liana Pliss, Inna Inashkina
The most common mitochondrial disorder in children is Leigh syndrome, which is a progressive and genetically heterogeneous neurodegenerative disorder caused by mutations in nuclear genes or mitochondrial DNA (mtDNA). In the present study, a novel and robust method of complete mtDNA sequencing, which allows amplification of the whole mitochondrial genome, was tested. Complete mtDNA sequencing was performed in a cohort of patients with suspected mitochondrial mutations. Patients from Latvia and Lithuania (n = 92 and n = 57, respectively) referred by clinical geneticists were included...
December 12, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29228601/genome-wide-analysis-of-circular-rnas-in-prenatal-and-postnatal-muscle-of-sheep
#12
Cunyuan Li, Xiaoyue Li, Yang Yao, Qiman Ma, Wei Ni, Xiangyu Zhang, Yang Cao, Wureli Hazi, Dawei Wang, Renzhe Quan, Xiaoxu Hou, Zhijin Liu, Qianqian Zhan, Li Liu, Mengdan Zhang, Shuting Yu, Shengwei Hu
Circular RNAs (circRNAs), a type of non-coding RNA with circular structure, were generated by back splicing and widely expressed in animals and plants. Recent studies have shown that circRNAs extensively participate in cell proliferation, cell differentiation, cell autophagy and other biological processes. However, the role and expression of circRNAs in the development and growth of muscle have not been studied in sheep. In our study, we first used RNA-seq to study the circRNAs in prenatal and postnatal longissimus dorsi muscle of sheep...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228366/genotype-influences-day-to-day-variability-in-sleep-in-drosophila-melanogaster
#13
Katherine J Wu, Shailesh Kumar, Yazmin L Serrano Negron, Susan T Harbison
Patterns of sleep often vary among individuals. But sleep and activity may also vary within an individual, fluctuating in pattern across time. One possibility is that these daily fluctuations in sleep are caused by the underlying genotype of the individual. However, differences attributable to genetic causes are difficult to distinguish from environmental factors in outbred populations such as humans. We therefore employed Drosophila as a model of intra-individual variability in sleep using previously collected sleep and activity data from the Drosophila Genetic Reference Panel, a collection of wild-derived inbred lines...
December 8, 2017: Sleep
https://www.readbyqxmd.com/read/29228361/identification-of-clinical-isolates-of-aspergillus-including-cryptic-species-by-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-maldi-tof-ms
#14
M Reyes Vidal-Acuña, Maite Ruiz-Pérez de Pipaón, María José Torres-Sánchez, Javier Aznar
An expanded library of matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been constructed using the spectra generated from 42 clinical isolates and 11 reference strains, including 23 different species from 8 sections (16 cryptic plus 7 noncryptic species). Out of a total of 379 strains of Aspergillus isolated from clinical samples, 179 strains were selected to be identified by sequencing of beta-tubulin or calmodulin genes. Protein spectra of 53 strains, cultured in liquid medium, were used to construct an in-house reference database in the MALDI-TOF MS...
December 8, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29228314/demodifying-rna-for-transcriptomic-analyses-of-archival-formalin-fixed-paraffin-embedded-samples
#15
Leah C Wehmas, Charles E Wood, Remi Gagne, Andrew Williams, Carole Yauk, Mark M Gosink, Deidre Dalmas, Ruixin Hao, Raegan O'Lone, Susan Hester
Archival formalin-fixed paraffin-embedded (FFPE) tissue samples offer a vast but largely untapped resource for genomic research. The primary technical issues limiting use of FFPE samples are RNA yield and quality. In this study, we evaluated methods to demodify RNA highly fragmented and crosslinked by formalin fixation. Primary endpoints were RNA recovery, RNA-sequencing quality metrics, and transcriptional responses to a reference chemical (phenobarbital, PB). Frozen mouse liver samples from control and PB groups (n = 6/group) were divided and preserved for 3 months as follows: frozen (FR); 70% ethanol (OH); 10% buffered formalin for 18 hours followed by ethanol (18F); or 10% buffered formalin (3F)...
December 7, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29228202/activity-of-ceftazidime-avibactam-against-problem-enterobacteriaceae-and-pseudomonas-aeruginosa-in-the-uk-2015-16
#16
David M Livermore, Danièle Meunier, Katie L Hopkins, Michel Doumith, Robert Hill, Rachel Pike, Peter Staves, Neil Woodford
Background: Ceftazidime/avibactam combines an established oxyimino-cephalosporin with the first diazabicyclooctane β-lactamase inhibitor to enter clinical use. We reviewed its activity against Gram-negative isolates, predominantly from the UK, referred for resistance investigation in the first year of routine testing, beginning in July 2015. Methods: Isolates were as received from referring laboratories; there is a bias to submit those with suspected carbapenem resistance...
December 8, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29228005/rna-seq-reveals-transcriptome-changes-in-goats-following-myostatin-gene-knockout
#17
Lamei Wang, Bei Cai, Shiwei Zhou, Haijing Zhu, Lei Qu, Xiaolong Wang, Yulin Chen
Myostatin (MSTN) is a powerful negative regulator of skeletal muscle mass in mammalian species that is primarily expressed in skeletal muscles, and mutations of its encoding gene can result in the double-muscling trait. In this study, the CRISPR/Cas9 technique was used to edit MSTN in Shaanbei Cashmere goats and generate knockout animals. RNA sequencing was used to determine and compare the transcriptome profiles of the muscles from three wild-type (WT) goats, three fibroblast growth factor 5 (FGF5) knockout goats (FGF5+/- group) and three goats with disrupted expression of both the FGF5 and MSTN genes (FM+/- group)...
2017: PloS One
https://www.readbyqxmd.com/read/29227892/effects-of-rare-earth-and-acid-rain-pollution-on-plant-chloroplast-atp-synthase-and-element-contents-at-different-growth-stages
#18
Fan Zhang, Huiqing Hu, Lihong Wang, Qing Zhou, Xiaohua Huang
Combined rare earth and acid rain pollution has become a new environmental problem, seriously affecting plant survival. The effects of these two kinds of pollutants on plant photosynthesis have been reported, but the micro mechanisms are not very clear. In this research, we studied the effects of lanthanum [La(III), 0.08, 1.20 and 2.40 mM] and acid rain (pH value = 2.5, 3.5 and 4.5) on the ATPase activity and gene transcription level and the functional element contents in rice leaf chloroplasts. The results showed that the combined 0...
December 1, 2017: Chemosphere
https://www.readbyqxmd.com/read/29226593/the-face-in-marfan-syndrome-a-3d-quantitative-approach-for-a-better-definition-of-dysmorphic-features
#19
Claudia Dolci, Valentina Pucciarelli, Daniele M Gibelli, Marina Codari, Susan Marelli, Giuliana Trifirò, Alessandro Pini, Chiarella Sforza
INTRODUCTION: Marfan syndrome (MFS) is a rare hereditable disorder of connective tissue caused by mutations in the fibrillin-1 gene FBN1. Timely diagnosis of MFS is essential to prevent life-threatening cardiovascular complications; nevertheless it can be difficult owing to the phenotypic variability of the syndrome. No clear quantitative definition of facial abnormalities associated with MFS is available. The aim of this study was to improve the definition of the facial phenotype associated with MFS and to verify the usefulness of a 3D noninvasive quantitative approach for its early recognition...
December 11, 2017: Clinical Anatomy
https://www.readbyqxmd.com/read/29226580/a-novel-truncating-variant-within-exon-7-of-kat6b-associated-with-features-of-both-say-barber-bieseker-young-simpson-syndrome-and-genitopatellar-syndrome-further-evidence-of-a-continuum-in-the-clinical-spectrum-of-kat6b-related-disorders
#20
Giuseppe Marangi, Marilena C Di Giacomo, Serena Lattante, Daniela Orteschi, Sara Patrizi, Paolo N Doronzio, Francesco N Riviello, Alessandro Vaisfeld, Silvia Frangella, Marcella Zollino
KAT6B sequence variants have been identified in both patients with the Say-Barber-Biesecker-Young-Simpson syndrome (SBBYSS) and in the genitopatellar syndrome (GPS). In SBBYSS, they were reported to affect mostly exons 16-18 of KAT6B, and the predicted mechanism of pathogenesis was haploinsufficiency or a partial loss of protein function. Truncating variants in KAT6B leading to GPS appear to cluster within the proximal portion of exon 18, associated with a dominant-negative effect of the mutated protein, most likely...
December 11, 2017: American Journal of Medical Genetics. Part A
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