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George Nysia I - - 2014
Next-generation sequencing (NGS) has advanced the application of high-throughput sequencing technologies in genetic and genomic variation analysis. Due to the large dynamic range of expression levels, RNA-seq is more prone to detect transcripts with low expression. It is clear that genes with no mapped reads are not expressed; however, there ...
Torricelli André Augusto Miranda AA Division of Ophthalmology and the Laboratory for Investigation in Ophthalmology (LIM-33), University of São Paulo Medical School, Av. Dr. Arnaldo 455, 5th floor, 01246-903 São Paulo, Brazil. Electronic address: - - 2014
To quantify ocular symptoms, goblet cells (GC) and mucin 5AC (MUC5AC) gene expression on the conjunctiva of healthy subjects exposed to ambient levels of traffic-derived air pollution and to estimate its correlation with NO2 and particulate matter smaller than 2.5μm (PM2.5) levels. Twenty-one taxi drivers or traffic controllers were assessed ...
Lim Jong Gyu JG National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Seoul National University, Seoul, 151-921, Republic of - - 2014
IscR is a global transcriptional regulator that contributes to the pathogenesis of Vibrio vulnificus, a food-borne pathogen. In the present study, the regulatory mechanism for the iscR expression of V. vulnificus was evaluated. The expression of iscR was found to be upregulated by a transcriptional regulator AphA, a homologue of ...
Rizzo Gaia G Department of Information Engineering, University of Padova, Padova, - - 2014
Substantial efforts are being spent on postmortem mRNA transcription mapping on the assumption that in vivo protein distribution can be predicted from such data. We tested this assumption by comparing mRNA transcription maps from the Allen Human Brain Atlas with reference protein concentration maps acquired with positron emission tomography (PET) ...
Yamagata Kazuo K Laboratory of Molecular Health Science of Food, Department of Food Bioscience and Biotechnology, College of Bioresourse Science, Nihon University (NUBS), Japan; Advance Research Center on Food Function, College of Bioresourse Science, Nihon University (NUBS), Japan. Electronic address: - - 2014
Docosahexaenoic acid (DHA) prevents atherosclerosis and may decrease monocyte/macrophage activation by tumor necrosis factor (TNF)-α. Here, we sought to determine the protective effects of DHA against TNF-α-induced stimulation of lectin-like oxidized low-density lipoprotein (LDL) receptor-1 (LOX-1) expression, which is associated with atherosclerosis. Using reverse transcription polymerase chain reaction, we found ...
Caraballo Juan Carlos JC Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of - - 2014
Paraoxonase 1 (PON1) is a protein found associated with high density lipoprotein (HDL), thought to prevent oxidative modification of low-density lipoprotein (LDL). This enzyme has been implicated in lowering the risk of cardiovascular disease. Anoxia-reoxygenation and oxidative stress are important elements in cardiovascular and cerebrovascular disease. However, the role of ...
Gibb Ewan A EA Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, - - 2014
5'RLM-RACE is a PCR-based technique used to map the 5' termini of transcripts in both eukaryotic and prokaryotic organisms. Free-standing homing endonuclease promoters often lack recognizable promoters making predicting the transcriptional start site challenging. Furthermore, homing endonucleases are often expressed at very low levels making transcript mapping a challenge. Here, ...
Ramachandran Vinoy K VK Department of Plant Sciences, University of Oxford, Oxford, United - - 2014
We have used differential RNA-seq (dRNA-seq) to characterise the transcriptomic architecture of S. Typhimurium SL1344, and its dependence on the bacterial alarmone, guanosine tetraphosphate (ppGpp) during late stationary phase, (LSP). Under LSP conditions we were able to identify the transcriptional start sites (TSSs) for 53% of the S. Typhimurium open ...
Liu Lei L Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, Jilin, 130062, - - 2013
High serum concentrations of nonesterified fatty acids (NEFA), which may affect the synthesis and assembly of very low density lipoproteins (VLDL), are associated with fatty liver during the early lactation period. Therefore, the objective of this study was to investigate the effects of NEFA on the synthesis and assembly of ...
Bennett M R - - 2013
Chronic restraint stress leads to increases in Brain Derived Neurotrophic Factor (BDNF), mRNA and protein in some regions of the brain, e.g. the basal lateral amygdala (BLA) but decreases in, other regions such as the CA3 region of the hippocampus and dendritic spine density increases or, decreases in line with ...
Kim Hyung Jun - - 2013
Cilostazol, a selective phosphodiesterase 3 (PDE3) inhibitor, is a vasodilator and an anti-thrombotic agent. The mechanism whereby cilostazol reduces plasma triglyceride is not completely understood. Here we investigated the effect of cilostazol on a remnant lipoprotein receptor, low-density lipoprotein receptor-related protein 1 (LRP1), which has been reported to play an ...
Xu Yi-Hui - - 2013
C-type lectins (CTLs) are pattern-recognition receptors (PRRs) that play important roles in immune response. In this study, two new CTLs containing a low-density lipoprotein receptor class A domain (LDLR) and a carbohydrate recognition domain (CRD) were identified in Marsupenaeus japonicas and designated as LdlrLec1 and LdlrLec2. The two CTLs expressed ...
Oh Seo Jin SJ Department of Obstetrics and Gynecology & Reproductive Biology, Michigan State University, College of Human Medicine, Grand Rapids, MI 49503, United States; Major in Biomodulation, Seoul National University, Seoul, Republic of - - 2013
Progesterone (P4) and progesterone receptor (PR) have important functions in uterine environment. In previous studies, using high density DNA microarray analysis, we identified low density lipoprotein receptor-related protein 2 (Lrp2) is one of the genes upregulated by P4 and PR. In present studies, we examined the expression of Lrp2 through ...
Houston Kelly - - 2013
Within the cereal grasses, variation in inflorescence architecture results in a conspicuous morphological diversity that in crop species influences the yield of cereal grains. Although significant progress has been made in identifying some of the genes underlying this variation in maize and rice, in the temperate cereals, a group that ...
Iannone Camilla - - 2013
Intron removal (pre-mRNA splicing) is a necessary step for expression of most genes in higher eukaryotes. Alternative splice site selection is a prevalent mechanism that diversifies genome outputs and offers ample opportunities for gene regulation in these organisms. Pre-mRNA splicing occurs co-transcriptionally and is influenced by features in chromatin structure, ...
Ramachandran Revathy - - 2013
The proteobacterium Pantoea stewartii subsp. stewartii causes Stewart's wilt disease in maize when it colonizes the xylem and secretes large amounts of an exopolysaccharide, stewartan. The success of disease pathogenesis lies in the timing of bacterial virulence factor expression through the different stages of infection. Regulation is achieved through a ...
Zhou Dongsheng - - 2013
Vibrio parahaemolyticus AphA and OpaR are the two master regulators of quorum sensing (QS) that are abundantly produced and operate at low cell density (LCD) and high cell density (HCD), respectively, with an outcome of reciprocally gradient production of these two proteins with transition between LCD and HCD. The cpsQ-mfpABC ...
Luo Wenshu - - 2013
Teleost fish eggs contain a substantial yolk mass consisting of lipids and proteins that provides essential nutrients for embryonic and larval development. The polar lipid and protein components of the yolk are delivered to oocytes by circulating vitellogenins, however the source(s) of the neutral lipid remains unknown. We cloned a ...
Arribere Joshua A JA Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, - - 2013
Transcript leaders (TLs) can have profound effects on mRNA translation and stability. To map TL boundaries genome-wide, we developed TL-sequencing (TL-seq), a technique combining enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. TL-seq identified mRNA start sites for the majority of yeast genes and revealed many examples of ...
Li Mei-Ling ML Department of Biochemistry & Molecular Biology, Robert Wood Johnson Medical School-University of Medicine and Dentistry of New Jersey, Piscataway, NJ, - - 2013
Activation of the mitogen-activated protein (MAP) pathway kinases p38 and MK2 induces phosphorylation of the chaperone Hsp27 and stabilization of mRNAs containing AU-rich elements (AREs) (ARE-mRNAs). Likewise, expression of phosphomimetic mutant forms of Hsp27 also stabilizes ARE-mRNAs. It appears to perform this function by promoting degradation of the ARE-mRNA decay ...
Whiteley Marvin - - 2013
Pseudomonas aeruginosa is a Gram-negative, opportunistic pathogen that causes infections in the lungs of individuals with the genetic disease cystic fibrosis. Density-dependent production of toxic factors regulated by the Pseudomonas Quinolone Signal (2-heptyl-3-hydroxy-4-quinolone; PQS) have been proposed to be involved in P. aeruginosa virulence. PQS biosynthesis requires conversion of the ...
Slaby Ondrej - - 2013
Sporadic colorectal cancer (CRC) is a typical multifactorial disease. Isothiocyanates (ITC) have been recently shown to inhibit development of CRC in many experimental models. MicroRNAs (miRNAs) are short noncoding RNAs that posttranscriptionally regulate gene expression through binding to 3' untranslated regions (3'UTR) of target mRNAs. MiRNAs are regulated by natural ...
Yuan Yang - - 2013
δ-Catenin is a component of the cadherin-catenin cell adhesion complex and its loss has been implicated in the mental retardation associated with the Cri du chat syndrome. We have previously demonstrated that loss of δ-catenin in a murine model during development results in excessive spine and synaptic density and function. ...
Britto-Kido Suzana de Aragão Sde - - 2013
Natural antisense ranscripts (NAT) are RNA molecules complementary to other endogenous RNAs. They are capable of regulating the expression of target genes at different levels (transcription, mRNA stability, translation, etc.). Such a property makes them ideal for interventions in organisms' metabolism. The present study reviewed plant NAT aspects, including features, ...
Wang Li - - 2013
Vibrio parahaemolyticus AphA and OpaR are the two master quorum sensing (QS) regulators that are abundantly expressed at low cell density (LCD) and high cell density (HCD), respectively, with a feature of reciprocally gradient production of them with transition between LCD and HCD. The type VI secretion system 2 (T6SS2) ...
Hausser Jean - - 2013
MiRNAs are post-transcriptional regulators that contribute to the establishment and maintenance of gene expression patterns. Although their biogenesis and decay appear to be under complex control, the implications of miRNA expression dynamics for the processes that they regulate are not well understood. We derived a mathematical model of miRNA-mediated gene ...
Sharma Amit - - 2012
To develop a rapid and sensitive tool for determining gene expression profiles of peripheral blood lymphocytes (PBL) as a surrogate for predicting toxicity associated with environmental exposures, studies were initiated using Taqman Low Density Array (TLDA), a medium throughput method for real time PCR (RT-PCR), for selected genes involved in ...
Blum Roy R Department of Pathology, New York University School of Medicine, New York, New York 10016, - - 2012
To identify the compendium of distal regulatory elements that govern myogenic differentiation, we generated chromatin state maps based on histone modifications and recruitment of factors that typify enhancers in myoblasts and myotubes. We found a striking concordance between the locations of these newly defined enhancers, MyoD1-binding events, and noncoding RNA ...
Tadesse Tizeta T Neuroscience Institute, Department of Biology, Graduate Program in Neurobiology & Behavior, Georgia State University, Atlanta, Georgia, - - 2013
Retinotopic maps can undergo compression and expansion in response to changes in target size, but the mechanism underlying this compensatory process has remained a mystery. The discovery of ephrins as molecular mediators of Sperry's chemoaffinity process allows a mechanistic approach to this important issue. In Syrian hamsters, neonatal, partial (PT) ...
Tomson Brett N - - 2013
Across diverse eukaryotes, the Paf1 complex (Paf1C) plays critical roles in RNA polymerase II transcription elongation and regulation of histone modifications. Beyond these roles, the human and Saccharomyces cerevisiae Paf1 complexes also interact with RNA 3'-end processing components to affect transcript 3'-end formation. Specifically, the Saccharomyces cerevisiae Paf1C functions with ...
Yashiro Takuya - - 2012
OBJECTIVE: 5-Aminoimidazole-4-carboxamide ribonucleoside (AICAR) has pleiotropic and beneficial effects on metabolic disorders. However, the effects of AICAR on low density lipoprotein (LDL) metabolism are poorly understood. METHODS AND RESULTS: AICAR induces increased LDLR mRNA levels and increased LDLR protein production in hepatocytes. The AICAR-dependent LDLR mRNA increase was partially mediated ...
Jiang Tao - - 2012
The aim of this study was to investigate the effects of transcranial direct current stimulation (TDCS) on hemichannel pannexin-1 (PX1) in cortical neurons and neural plasticity, and explore the optimal time window of TDCS therapy after stroke. Adult male Sprague-Dawley rats (n=90) were randomly assigned to sham operation, middle cerebral ...
Ding Zufeng - - 2012
Lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) has been identified as a major receptor for oxidatively modified low density lipoprotein (ox-LDL) in endothelial cells and smooth muscle cells (SMCs). MicroRNAs are small non-coding RNAs that regulate gene expression. Very few studies have reported regulation of LOX-1 expression by microRNAs in SMCs. ...
Dahabreh Diala F - - 2012
Insulin resistance is linked to dyslipidemia, characterized by a decrease in high density lipoproteins and an increase in low density lipoproteins. Thiazolidinediones (TZDs) are insulin-sensitizing agents used to improve glycemic control in patients with type 2 diabetes. Recently, the safety of certain TZD regimens has been questioned because of associated ...
Kadota Kana - - 2012
Some anesthetics can affect gene expression. Previously, we reported that sevoflurane anesthesia drastically and reversibly repressed the expression of mouse Per2 (mPer2), a core clock gene in the suprachiasmatic nucleus (SCN). In the current study, we examined the time-dependent effect of sevoflurane on mPer2 expression and its interactions with the ...
Gao Zhengquan - - 2012
The green alga Haematococcus pluvialis can produce large amounts of pink carotenoid astaxanthin which is a high value ketocarotenoid. In our study, transcriptional expression patterns of eight carotenoid genes in H. pluvialis in response to SA were measured using qRT-PCR. Results indicated that both 25 and 50mg/L salicylic acid (SA) ...
Kaneda Teruo - - 2012
Studies of meso-endoderm and neural induction and subsequent body plan formation have been analyzed using mainly amphibians as the experimental model. Xenopus is currently the predominant model, because it best enables molecular analysis of these induction processes. However, much of the embryological information on these inductions (e.g. those of the ...
Cao Lin - - 2012
A prior exposure to isoflurane, a common volatile anesthetic, provides neuroprotection (isoflurane preconditioning). To determine the role of microRNAs in this protection, we performed microRNA array assay on cerebral cortex harvested from rats exposed to isoflurane or isoflurane-exposed rat B35 neuron-like cells. We showed that isoflurane significantly increased microRNA-203 expression ...
Porri Aimone - - 2012
The plant growth regulator gibberellin (GA) contributes to many developmental processes, including the transition to flowering. In Arabidopsis, GA promotes this transition most strongly under environmental conditions such as short days (SDs) when other regulatory pathways that promote flowering are not active. Under SDs, GAs activate transcription of SUPPRESSOR OF ...
Ye Zhi - - 2012
Administration of sevoflurane at the onset of reperfusion has been confirmed to provide a cerebral protection. However, little is known about the mechanism. In this study, we tested the hypothesis that sevoflurane postconditioning induces neuroprotection through the up-regulation hypoxia inducible factor-1α (HIF-1α) and heme oxygenase-1 (HO-1) involving phosphatidylinositol-3-kinase (PI3K)/Akt pathway. ...
Matsumoto Shinya - - 2012
The mitochondrial oxidative phosphorylation (OXPHOS) proteins are encoded by both nuclear and mitochondrial DNA. The nuclear-encoded OXPHOS mRNAs have specific subcellular localizations, but little is known about which localize near mitochondria. Here, we compared mRNAs in mitochondria-bound polysome fractions with those in cytosolic, free polysome fractions. mRNAs encoding hydrophobic OXPHOS ...
Steventon Ben B Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, - - 2012
Neural crest (NC) induction is a long process that continues through gastrula and neurula stages. In order to reveal additional stages of NC induction we performed a series of explants where different known inducing tissues were taken along with the prospective NC. Interestingly the dorso-lateral marginal zone (DLMZ) is only ...
Xuereb Benoit - - 2012
The present study aimed to develop a method of quantification of heat shock protein transcript levels in the estuarine copepod Eurytemora affinis. For that, the full-length cDNA of the 78-kDa glucose-regulated protein (Ea-grp78) and the cytosolic 90-kDa heat shock protein (Ea-hsp90A) from this species have been cloned. These cDNA revealed, ...
Bentaya Souhila - - 2012
The maternal-zygotic transition (MZT) is an embryonic event that overlaps with and plays key roles in primary germ layer specification in vertebrates. During MZT, maternally supplied mRNAs are degraded while zygotic transcripts are synthesized to either reinforce the already specified cell fate or to trigger new cell identity. Here, we ...
Ito Takuya - - 2012
Maternal undernutrition during pregnancy is a risk factor for cerebrovascular and cardiovascular diseases in adulthood. Hypoxia-inducible factor 1 alpha (HIF1α) plays an essential role in cellular hypoxic responses, and its increased expression is associated with cerebrovascular and cardiovascular diseases. However, it is not known whether maternal undernutrition influences HIF1α expression ...
Geisinger Max T - - 2012
Ets-1 controls osteoblast differentiation and bone development; however, its downstream mechanism of action in osteoblasts remains largely undetermined. CCN2 acts as an anabolic growth factor to regulate osteoblast differentiation and function. CCN2 is induced by TGF-β1 and acts as a mediator of TGF-β1 induced matrix production in osteoblasts; however, the ...
Picard Flora - - 2012
In bacteria, the weak correlations at the genome scale between mRNA and protein levels suggest that not all mRNAs are translated with the same efficiency. To experimentally explore mRNA translational level regulation at the systemic level, the detailed translational status (translatome) of all mRNAs was measured in the model bacterium ...
Bhattacharjee M - - 2012
mRNA-Seq is a precise and highly reproducible technique for measurement of transcripts levels and yields sequence information of a transcriptome at a single nucleotide base-level thus enabling us to determine splice junctions and alternative splicing events with high confidence. Often analysis of mRNA-Seq data does not attempt to quantify the ...
Roszak Pawel - - 2011
Seed development in flowering plants is initiated after a double fertilization event leading to the formation of zygotic embryo and endosperm tissues surrounded by the maternally derived seed coat. Although the seed coat does not take part in the fertilization process it develops immediately after fertilization, implicating a signaling mechanism ...
Lu Fu-I - - 2011
In vertebrates, the animal-vegetal axis is determined during oogenesis and at ovulation, the egg is radially symmetric. In anamniotes, following fertilization, a microtubule-dependent movement leads to the displacement of maternal dorsal determinants from the vegetal pole to the future dorsal side of the embryo, providing the initial breaking of radial ...
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