Search results for "Housekeeping"
showing 10 items of 29 documents
Polyphasic taxonomic characterization of Lactobacillus rossiae isolates from Belgian and Italian sourdoughs reveals intraspecific heterogeneity.
2009
Abstract (GTG) 5 -PCR fingerprinting and pheS sequence analysis of 18 Lactobacillus rossiae isolates, mainly originating from Belgian and Italian artisan sourdoughs, revealed intraspecies grouping as evidenced by the delineation of three and two subgroups, respectively. On the other hand, 16S rRNA and rpoA gene sequence analysis and DNA–DNA hybridizations supported the accommodation of all isolates in a single species. No correlation between genetic and phenotypic heterogeneity was observed. Collectively, these data do not warrant taxonomic division of L. rossiae . On the other hand, the considerable differences in intraspecies sequence variation of L. rossiae isolates displayed by the pheS…
Vibrio renipiscarius sp. nov., isolated from cultured gilthead sea bream (Sparus aurata)
2015
Two strains of Gram-negative, facultatively anaerobic, slightly halophilic bacteria, isolated from healthy gilthead sea bream (Sparus aurata) cultured in Spanish Mediterranean fish farms, were different from their closest relatives,Vibrio scophthalmiandV. ichthyoenteri, by phenotypic, phylogenetic and genomic standards. The strains were negative for decarboxylase tests and lacked extracellular hydrolytic activities, but were able to fermentd-mannitol, sucrose, cellobiose andd-gluconate, among other carbohydrates. The major cellular fatty acids were C16:1and C16:0, in agreement with other species of the genusVibrio. Their 16S rRNA gene sequences were 98.4 and 97.2 % similar to those of the t…
Multilocus Sequence Analysis of the redefined clade Scophthalmi in the genus Vibrio.
2015
A Multilocus Sequence Analysis (MLSA) was performed on members of the Scophthalmi clade in the genus Vibrio, including type and reference strains of the species V. scophthalmi, V. ichthyoenteri, and 39 strains phenotypically identified as Vibrio ichthyoenteri-like, with the aim of better defining boundaries between these two closely related, fish-associated species. The type strain of V. ponticus, recently added to the clade Scophthalmi, was also included. The study was based on partial sequences of the protein-coding housekeeping genes rpoD, mreB, recA, ftsZ, and gyrB, and the 16S rRNA. While the 16S rRNA gene-based trees were unable to pull apart members of V. scophthalmi or V. ichthyoent…
Bypassing hazard of housekeeping genes: their evaluation in rat granule neurons treated with cerebrospinal fluid of multiple sclerosis subjects
2015
Gene expression studies employing real-time PCR has become an intrinsic part of biomedical research. Appropriate normalization of target gene transcript(s) based on stably expressed housekeeping genes is crucial in individual experimental conditions to obtain accurate results. In multiple sclerosis (MS), several gene expression studies have been undertaken, however, the suitability of housekeeping genes to express stably in this disease is not yet explored. Recent research suggests that their expression level may vary under different experimental conditions. Hence it is indispensible to evaluate their expression stability to accurately normalize target gene transcripts. The present study ai…
Selection of suitable housekeeping genes for expression analysis in glioblastoma using quantitative RT-PCR
2009
Abstract Background Considering the broad variation in the expression of housekeeping genes among tissues and experimental situations, studies using quantitative RT-PCR require strict definition of adequate endogenous controls. For glioblastoma, the most common type of tumor in the central nervous system, there was no previous report regarding this issue. Results Here we show that amongst seven frequently used housekeeping genes TBP and HPRT1 are adequate references for glioblastoma gene expression analysis. Evaluation of the expression levels of 12 target genes utilizing different endogenous controls revealed that the normalization method applied might introduce errors in the estimation of…
Normalization with Corresponding Naïve Tissue Minimizes Bias Caused by Commercial Reverse Transcription Kits on Quantitative Real-Time PCR Results
2016
Real-time reverse transcription polymerase chain reaction (PCR) is the gold standard for expression analysis. Designed to improve reproducibility and sensitivity, commercial kits are commonly used for the critical step of cDNA synthesis. The present study was designed to determine the impact of these kits. mRNA from mouse brains were pooled to create serial dilutions ranging from 0.0625 μg to 2 μg, which were transcribed into cDNA using four different commercial reverse-transcription kits. Next, we transcribed mRNA from brain tissue after acute brain injury and naïve mice into cDNA for qPCR. Depending on tested genes, some kits failed to show linear results in dilution series and revealed s…
Selection of endogenous control genes for normalization of gene expression analysis after experimental brain trauma in mice.
2008
Quantitative measurements of gene expression require correction for tissue sample size, RNA quantity, and reverse transcription efficiency. This can be achieved by normalization with control genes. The study was designed to identify candidates not altered after brain trauma. Male C57Bl/6 mice were anesthetized with isoflurane, and a pneumatic brain trauma was induced by controlled cortical impact (CCI) on the right parietal cortex. Brains were removed at 15 min, and 3, 6, 12 and 24 h after CCI and from naive animals (n = 6 each). Absolute copies of six control genes (beta-2-microglobin [B2M], cyclophilin A, beta-actin, hypoxanthine ribosyltransferase [HPRT], porphobilinogen deaminase [PBGD]…
Cytokine gene expression in the tunica albuginea of patients with Peyronie's disease. Pilot study with a control group.
2012
Introduction and objective Cytokines may be involved in the pathogenesis of Peyronie's disease (PD). In this case, biological drugs, acting on specific cytokines, could be adopted in the pharmacological treatment of the disease. Materials and Methods Twenty PD patients and 8 patients affected by congenital recurvatum penis (control group) who underwent corporoplasty were enrolled in the study Histological examination and measurement by Real Time PCR of the expression of the encoding genes for IL-2, IL-4, IL-6, IL-10, IL-13, TGF-β, TNF-α and IFN-γ were performed on the removed tunica albuginea (TA). For the normalization of data GAPDH (glucerldehyde-3fosfatehydrogenase) and GUSB (β-glucuroni…
Use of ATP bioluminescence for assessing the cleanliness of hospital surfaces: A review of the published literature (1990–2012)
2014
Summary: Hospital cleanliness tends to be considered by patients and the public as an important indicator of the general quality of healthcare. Tests for detecting the presence of adenosine triphosphate (ATP) as a proxy of microbial contamination are increasing in popularity, and several studies have been conducted on this topic in the last few decades. The aim of the present study was to review the published literature on this topic and summarize and discuss the available results. The review focused on relevant English-language articles that were identified through searches of two databases [PubMed and Scopus (1990–2012)] by using the keywords “ATP”, “bioluminescence”, “hospital”, and “sur…
Clustering Bacteria Species Using Neural Gas: Preliminary Study
2009
In this work a method for clustering and visualization of bacteria taxonomy is presented. A modified version of the Batch Median Neural Gas (BNG) algorithm is proposed. The BNG algorithm is able to manage non vectorial data given as a dissimilarity matrix. We tested the modified BNG on the dissimilarity matrix obtained from sequences alignment and computing distances using bacteria genotype information regarding the16S rRNA housekeeping gene, which represents a stable part of bacteria genome. The dataset used for the experiments is obtained from the Ribosomal Database Project II, and it is made of 5159 sequences of 16S rRNA genes. Preliminary results of the experiments show a promising abil…