bacterial messenger rna: Topics by WorldWideScience.org

Studying bacterial transcriptomes using RNA-seq

BackgroundSynonymous sites are freer to vary because of redundancy in genetic code. Messenger RNA secondary structure restricts this freedom, as revealed by previous findings in...Full Text Available

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A bacterial amber suppressor in Saccharomyces cerevisiae is selectively recognized by a bacterial aminoacyl-tRNA synthetase.

Genome-wide studies of bacterial gene expression are shifting from microarray technology to second generation sequencing platforms. RNA-seq has a number of advantages over hybridization-based techniques,...Full Text Available

2010-10-01

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Adenine and guanine recognition of stop codon is mediated by different N domain conformations of translation termination factor eRF1

Little is known about the conservation of determinants for the identities of tRNAs between organisms. We showed previously that Escherichia coli tyrosine tRNA synthetase can charge the Saccharomyces...Full Text Available

1990-04-01

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Improved Understanding of the Bacterial Vaginal Microbiota of Women before and after Probiotic Instillation

Positioning of release factor eRF1 toward adenines and the ribose-phosphate backbone of the UAAA stop signal in the ribosomal decoding site was studied using messenger RNA (mRNA) analogs containing...Full Text Available

2011-09-01

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Euryarchaeal ?-CASP Proteins with Homology to Bacterial RNase J Have 5?- to 3?-Exoribonuclease Activity*

The vaginal bacterial microbiota of 19 premenopausal women was examined by PCR-denaturing gradient gel electrophoresis (DGGE) and sequencing of the V2-V3 region of the 16S rRNA gene. Ten of the women...Full Text Available

2003-01-01

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Small Regulatory RNA and Legionella pneumophila

In the Archaea only a handful of ribonucleases involved in RNA processing and degradation have been characterized. One potential group of archaeal ribonucleases are homologues of the bacterial RNase...Full Text Available

2010-06-04

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Stochastic kinetics of ribosomes: single motor properties and collective behavior

Legionella pneumophila is a gram-negative bacterial species that is ubiquitous in almost any aqueous environment. It is the agent of Legionnaires’ disease, an acute and often...Full Text Available

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The ribosome and the mechanism of protein synthesis

Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the polymerization of the corresponding protein. The forward movement, however, is characterized by an alternating sequence of translocation and pause. Using a quantitative model, which captures the mechanochemical cycle of an individual ribosome, we derive an {\\it exact} analytical expression for the distribution of its dwell times at the successive positions on the mRNA track. Inverse of the average dwell time satisfies a ``Michaelis-Menten-like'' equation and is consistent with the general formula for the average velocity of a molecular motor with an unbranched mechano-chemical cycle. Extending this formula appropriately, we also derive the exact force-velocity ...

2009-01-01

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Modeling protein synthesis from a physicist's perspective: a toy model

In virtually all forms of life on earth, proteins in each cell are made according to a genetic blueprint, in the form of DNA. The translation of copies of this genetic blueprint (in the form of messenger RNA) into polypeptides is performed on the ribosome, a highly complex molecular machine composed of RNAs and proteins. To this end, special adaptor molecules called transfer RNAs are lined up by the ribosome in the sequence dictated by the genetic code, such that the amino acids carried by these molecules can be linked into a polypeptide. Several cofactors are involved in these processes, some of which require energy freed up by GTP hydrolysis. Although the ribosome was discovered more than 50 years ago, its structure has only been solved recently by X-ray crystallography. Another technique, cryo-electron microscopy, is starting to contribute toward our understanding of the ribosome's function, by portraying its conformational changes ...

2006-05-01

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Worlds within worlds: evolution of the vertebrate gut microbiota

Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called {\\it ribosome}. Although, traditionally, the experimental investigation of protein synthesis has been an active area of research in molecular cell biology, important quantitative models of this phenomenon have been reported mostly in the research journals devoted to statistical physics and related interdisciplinary topics. From the perspective of a physicist, protein synthesis is a phenomenon of {\\it classical transport of interacting ribosomes on a messenger RNA (mRNA) template} that dictates the sequence of the amino acids on the protein. Here we bring this frontier area of contemporary research into the classroom by appropriate simplification of the models and methods. In particular, we develope a simple toy model and analyze it by some elementary techniques of non-equilibrium statistical mechanics to predict the ...

2007-01-01

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Seasonal and Spatial Variability of Bacterial and Archaeal Assemblages in the Coastal Waters near Anvers Island, Antarctica

Here we use published 16S rRNA gene sequences to compare the bacterial assemblages associated with humans, other mammals, other metazoa, and free-living microbial communities spanning a range...Full Text Available

2008-10-01

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Detection of Atopobium vaginae in Postmenopausal Women by Cultivation-Independent Methods Warrants Further Investigation

A previous report of high levels of members of the domain Archaea in Antarctic coastal waters prompted us to investigate the ecology of Antarctic planktonic prokaryotes. rRNA hybridization...Full Text Available

1998-07-01

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Evolution of a molecular switch: universal bacterial GTPases regulate ribosome function.

We sequenced 16S rRNA genes from the vaginal swab contents of a postmenopausal woman with asymptomatic bacterial vaginosis (BV). Sequences from Atopobium vaginae were the most commonly...Full Text Available

2004-04-01

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Increased transcription of the c-myc oncogene in two methylcholanthrene-induced quail fibroblastic cell lines

The GTPases comprise a protein superfamily of highly conserved molecular switches adapted to many diverse functions. These proteins are found in all domains of life and often perform essential roles in fundamental cellular processes. Analysis of data from genome sequencing projects demonstrates that bacteria possess a core of 11 universally conserved GTPases (elongation factor G and Tu, initiation factor 2, LepA, Era, Obg, ThdF/TrmE, Ffh, FtsY, EngA and YchF). Investigations aimed at understanding the function of GTPases indicate that a second conserved feature of these proteins is that they elicit their function through interaction with RNA and/or ribosomes. An emerging concept suggests that the 11 universal GTPases are either necessary for ribosome function or transmitting information from the ribosome to downstream targets for the purpose of generating specific cellular responses. Furthermore, it is suggested that progenitor GTPases were early regulators of ...

2001-07-01

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Detection of Atopobium vaginae in postmenopausal women by cultivation-independent methods warrants further investigation.

The expression of three c-onc genes (c-erb, c-myc, c-myb) was investigated in five cell lines established from fibrosarcomas induced with 20-methylcholanthrene (MCA) of Japanese quails. These cell lines showed low levels of the three c-onc genes, with the exception of two cell lines that accumulated moderate (MCAQ 1-4) and large amounts (MCAQ 3-5) of c-myc RNA. Molecular cloning and restriction endonuclease analyses indicated that expression of c-myc in these two cell lines were not associated with detectable rearrangements in the c-myc locus, that the size of the c-myc transcript (2.7 kb) in MCAQ 3-5 was similar to that of the normal c-myc messenger RNAs (mRNA) and that the transcriptional activatin observed in MCAQ 3-5 was not mediated by the LTR (long terminal repeat) of a proximate ALV (avian leukosis virus) provirus. Finally, when analyzed with the restriction enzymes Msp I and Hpa II, the c-myc locus of MCAQ 3-5 and ...

1984-12-01

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Regulation by small RNAs via coupled degradation: mean-field and variational approaches

We sequenced 16S rRNA genes from the vaginal swab contents of a postmenopausal woman with asymptomatic bacterial vaginosis (BV). Sequences from Atopobium vaginae were the most commonly detected. In a survey of 35 other postmenopausal women, this organism was detected in 44% with BV but not in any subjects deemed healthy. PMID:15071062

2004-04-01

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Distinctive Responses of Metabolically Active Microbiota to Acidification in a Thermophilic Anaerobic Digester

Regulatory genes called small RNAs (sRNAs) are known to play critical roles in cellular responses to changing environments. For several sRNAs, regulation is effected by coupled stoichiometric degradation with messenger RNAs (mRNAs). The nonlinearity inherent in this regulatory scheme indicates that exact analytical solutions for the corresponding stochastic models are intractable. Here, we present a variational approach to analyze a well-studied stochastic model for regulation by sRNAs via coupled degradation. The proposed approach is efficient and provides accurate estimates of mean mRNA levels as well as higher order terms. Results from the variational ansatz are in excellent agreement with data from stochastic simulations for a wide range of parameters, including regions of parameter space where mean-field approaches break down. The proposed approach can be applied to quantitatively model stochastic gene expression in complex regulatory ...

2011-01-01

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British Library Electronic Table of Contents (United Kingdom)

Acidification is one of the most common and serious problems inducing process failure in anaerobic digesters. The production of volatile fatty acids (VFAs) mainly triggers acidic shock. However, little is known about the bacteria involved in the processes of acidogenic metabolism, such as fermentation and reductive acetogenesis. Here, the metabolic responses of a methanogenic community to the acidification and resulting process deterioration were investigated using transcriptional profiling of both the 16S rRNA and formyltetrahydrofolate synthetase (FTHFS) genes. The 16S rRNA-based analyses demonstrated that the dynamic shift of bacterial populations was closely correlated with reactor performance, especially with VFA accumulation levels. The pH drop accompanied by an increase in VFAs stim...

2011-01-01

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Bacterial conjunctivitis

Complete genome sequence of Conexibacter woesei type strain (ID131577T)

Clinical questionWhat is the best treatment for bacterial conjunctivitis?ResultsTopical antibiotics expedite recovery from bacterial conjunctivitis....Full Text Available

2010-01-01

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The expression profile of TLR9 mRNA and CpG ODNs immunostimulatory actions in the teleost gilthead seabream points to a major role of lymphocytes

The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with Conexibacter woesei as the type species of the genus. C. woesei is a representative of a deep evolutionary line of des-cent within the class Actinobacteria. Strain ID131577T was originally isolated from temperate forest soil in Gerenzano (Italy). Cells are small, short rods that are motile by peritrichous fla-gella. They may form aggregates after a longer period of growth and, then as a typical charac-teristic, an undulate structure is formed by self-aggregation of flagella with entangled bacteri-al cells. Here we describe the features of the organism, together with the complete sequence and annotation. The 6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.

2010-01-01

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British Library Electronic Table of Contents (United Kingdom)

Abstract. The potential effects of synthetic unmethylated oligodeoxynucleotides (ODN) containing CpG motifs, mimicking bacterial DNA, has never been evaluated on the immune response in the teleost fish gilthead seabream (Sparus aurata), the most important fish species in Mediterranean aquaculture. First, binding and competition studies have demonstrated that binding is saturated and promiscuous, suggesting the participation of several receptors. Moreover, leucocyte cytotoxic (NCC) activity, production of ROIs (reactive oxygen intermediates), and expression of immune-relevant genes was greatly primed by ODNs. Focusing on the mechanism, the TLR9 gene is widely distributed in seabream tissues and differently regulated in vitro by several stimuli. Moreover, and for the first time in fish, TLR9...

2008-01-01

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Methanogen community structure in the rumens of farmed sheep, cattle and red deer fed different diets

British Library Electronic Table of Contents (United Kingdom)

Abstract Development of inhibitors and vaccines that mitigate rumen-derived methane by targeting methanogens relies on knowledge of the methanogens present. We investigated the composition of archaeal communities in the rumens of farmed sheep (Ovis aries), cattle (Bos taurus) and red deer (Cervus elaphus) using denaturing gradient gel electrophoresis (DGGE) to generate fingerprints of archaeal 16S rRNA genes. The total archaeal communities were relatively constant across species and diets, and were less variable and less diverse than bacterial communities. There were diet- and ruminant-species-based differences in archaeal community structure, but the same dominant archaea were present in all rumens. These were members of three coherent clades: species related to Methanobrevibacter ruminan...

2011-01-01

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Functional adaptation of microbial communities from jet fuel-contaminated soil under bioremediation treatment: simulation of pollutant rebound

British Library Electronic Table of Contents (United Kingdom)

Abstract To investigate the link between the functionality and the diversity of microbial communities under strong selective pressure from pollutants, two types of mesocosms that simulate natural attenuation and phytoremediation were generated using soil from a site highly contaminated with jet fuel and under air-sparging treatment. An increase in the petroleum hydrocarbon concentration from 4900 to 18-500-mg-kg-1-dw soil simulated a pollutant rebound (postremediation pollutant reversal due to residual contamination). Analysis of soil bacterial communities by denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments showed stronger changes and selection for a phylogenetically diverse microbial population in the mesocosms with pollutant-tolerant willow trees. Enumerat...

2011-01-01

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Olfactomedin 4 suppresses prostate cancer cell growth and metastasis via negative interaction with cathepsin D and SDF-1.

Novel snake venom ligand dendroaspis natriuretic peptide is selective for natriuretic peptide receptor-A in human heart: downregulation of natriuretic peptide receptor-A in heart failure.

The human olfactomedin 4 gene (OLFM4) encodes an olfactomedin-related glycoprotein. OLFM4 is normally expressed in a limited number of tissues, including the prostate, but its biological functions in prostate are largely unknown. In this study, we found that OLFM4 messenger RNA was reduced or undetectable in prostate cancer tissues and prostate cancer cell lines. To study the effects of OLFM4 on prostate cancer progression, we transfected PC-3 prostate cancer cells with OLFM4 to establish OLFM4-expressing PC-3 cell clones. The OLFM4-expressing PC-3 cell clones were found to have decreased proliferation and invasiveness compared with vector-transfected control PC-3 cells in vitro. In addition, nude mice injected with OLFM4-expressing PC-3 cells demonstrated reduced tumor growth and bone invasion and metastasis compared with mice injected with vector-transfected control cells. Mechanistic studies revealed that OLFM4 may exhibit its anticancer ...

2011-04-05

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Scintillation proximity assay for measurement of RNA methylation

The natriuretic peptides are considered to be cardioprotective; however, their receptors have not been identified in human myocardium using radiolabeled analogs. Dendroaspis natriuretic peptide (DNP) has been recently identified as a new member of this peptide family and is thought to be less susceptible to enzymatic degradation. Therefore, we have developed the novel radiolabeled analog [125I]-DNP and used this to localize high-affinity (K(D)=0.2 nmol/L), saturable, specific binding sites in adult human heart (n=6) and coronary artery (n=8). In competition binding experiments, atrial natriuretic peptide and brain type natriuretic peptide had greater affinity for [125I]-DNP binding sites than C-type natriuretic peptide and the natriuretic peptide receptor (NPR)-C ligand, cANF. This rank order of potency suggested binding of [125I]-DNP was specific to NPR-A. Messenger RNA encoding NPR-A was identified in left ventricle and coronary artery smooth ...

2006-06-15

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Pteromalus puparum venom impairs host cellular immune responses by decreasing expression of its scavenger receptor gene.

Methylation of RNA by methyltransferases is a phylogenetically ubiquitous post-transcriptional modification that occurs most extensively in transfer RNA (tRNA) and ribosomal RNA (rRNA). Biochemical...Full Text Available

2009-03-01

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Quantitative evaluation of siRNA delivery in vivo

Insect host/parasitoid interactions are co-evolved systems in which host defenses are balanced by parasitoid mechanisms to disable or hide from host immune effectors. Although there is a rich literature on these systems, parasitoid immune-disabling mechanisms have not been fully elucidated. Here we report on a newly discovered immune-disabling mechanism in the Pieris rapae/Pteromalus puparum host/parasitoid system. Because venom injections and parasitization suppresses host phagocytosis, we turned attention to the P. rapae scavenger receptor (Pr-SR), posing the hypothesis that P. puparum venom suppresses expression of the host Pr-SR gene. To test our hypothesis, we cloned a full-length cDNA of the Pr-SR. Multiple sequences alignment showed the deduced amino acid sequence of Pr-SR is similar to scavenger receptors of other lepidopterans. Bacterial and bead injections induced Pr-SR mRNA and protein expression, which peaked at 4h post-bead ...

2011-07-22

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The Functional Role of Calcineurin in Hypertrophy, Regeneration, and Disorders of Skeletal Muscle

Effective small interfering RNA (siRNA)–mediated therapeutics require the siRNA to be delivered into the cellular RNA-induced silencing complex (RISC). Quantitative information of this essential...Full Text Available

2010-12-01

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Structural basis of ligand binding by a c-di-GMP riboswitch

Skeletal muscle uses calcium as a second messenger to respond and adapt to environmental stimuli. Elevations in intracellular calcium levels activate calcineurin, a serine/threonine phosphatase, resulting...Full Text Available

2010-01-01

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Cytoplasmic heat shock granules are formed from precursor particles and are associated with a specific set of mRNAs.

The second messenger signaling molecule bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) regulates many processes in bacteria, including motility, pathogenesis,...Full Text Available

2009-12-01

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Cyclic Diguanylate Signaling Proteins Control Intracellular Growth of Legionella pneumophila

In heat-shocked tomato cell cultures, cytoplasmic heat shock granules (HSGs) are tightly associated with a specific subset of mRNAs coding mainly for the untranslated control proteins. This messenger...Full Text Available

1989-03-01

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Age-dependent changes in Ca²⁺ homeostasis in peripheral neurones: implications for changes in function

Proteins that metabolize or bind the nucleotide second messenger cyclic diguanylate regulate a wide variety of important processes in bacteria. These processes include motility, biofilm formation, cell...Full Text Available

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Poncirin promotes osteoblast differentiation but inhibits adipocyte differentiation in mesenchymal stem cells.

Calcium ions represent universal second messengers within neuronal cells integrating multiple cellular functions, such as release of neurotransmitters, gene expression, proliferation, excitability,...Full Text Available

2007-06-01

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Artesunate in combination with oxacillin protect sepsis model mice challenged with lethal live methicillin-resistant Staphylococcus aureus (MRSA) via its inhibition on proinflammatory cytokines release and enhancement on antibacterial activity of oxacillin

Poncirin, flavanone glycoside, isolated from the fruit of Poncirus trifoliata, has anti-bacterial and anti-inflammatory activities. In this study, the effects of poncirin on the differentiation of mesenchymal stem cells were investigated. The C3H10T1/2 mesenchymal stem cells and primary bone marrow mesenchymal stem cells were studied. In the C3H10T1/2 cells, poncirin prevented adipocyte differentiation, as demonstrated by inhibition of cytoplasm lipid droplet accumulation and peroxisome proliferator-activating receptor-? (PPAR-?) and CCAAT-enhancer-binding protein-? (C/EBP-?) mRNA expression. By contrast, poncirin enhanced the expression of the key osteogenic transcription factors, runt-related transcription factor 2 (Runx2) and transcriptional coactivator with PDZ-binding motif (TAZ). Poncirin also enhanced expression of the osteogenic marker genes including alkaline phosphatase (ALP) and osteocalcin (OC). Poncirin increased mineral nodule ...

2011-05-01

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British Library Electronic Table of Contents (United Kingdom)

Sepsis induced by methicillin-resistant Staphylococcus aureus (MRSA) has worse outcome because of multiresistance to a large group of antibiotics, which may lead to death from septic shock. In the present study, we firstly found that artesunate in combination with oxacillin was capable of protecting mice challenged with live MRSA WHO-2 (WHO-2) and the protection was related to the reduced TNF-a and IL-6 levels and decreased bacterial load. Based on above results, artesunate was further investigated from two aspects in vitro, anti-inflammation effect and antibacterial enhancement effect on antibiotics. Artesunate not only inhibited TNF-a and IL-6 release but also inhibited mRNA and protein expressions of TLR2 and Nod2, two important receptors, in murine peritoneal macrophages stimulated wit...

2011-01-01

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Electrically triggered all-or-none Ca(2)+-liberation during action potential in the giant alga Chara.

Electrically Triggered All-or-None Ca2+-Liberation during Action Potential in the Giant Alga Chara

Electrically triggered action potentials in the giant alga Chara corallina are associated with a transient rise in the concentration of free Ca(2)+ in the cytoplasm (Ca(2)+(cyt)). The present measurements of Ca(2)+(cyt) during membrane excitation show that stimulating pulses of low magnitude (subthreshold pulse) had no perceivable effect on Ca(2)+(cyt). When the strength of a pulse exceeded a narrow threshold (suprathreshold pulse) it evoked the full extent of the Ca(2)+(cyt) elevation. This suggests an all-or-none mechanism for Ca(2)+ mobilization. A transient calcium rise could also be induced by one subthreshold pulse if it was after another subthreshold pulse of the same kind after a suitable interval, i.e., not closer than a few 100 ms and not longer than a few seconds. This dependency of Ca(2)+ mobilization on single and double pulses can be simulated by a model in which a second messenger is produced in a voltage-dependent manner. This second ...

2001-07-01

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Bunyamwera virus can repair both insertions and deletions during RNA replication

Electrically triggered action potentials in the giant alga Chara corallina are associated with a transient rise in the concentration of free Ca2+ in the cytoplasm (Ca2+cyt). The present measurements of Ca2+cyt during membrane excitation show that stimulating pulses of low magnitude (subthreshold pulse) had no perceivable effect on Ca2+cyt. When the strength of a pulse exceeded a narrow threshold (suprathreshold pulse) it evoked the full extent of the Ca2+cyt elevation. This suggests an all-or-none mechanism for Ca2+ mobilization. A transient calcium rise could also be induced by one subthreshold pulse if it was after another subthreshold pulse of the same kind after a suitable interval, i.e., not closer than a few 100 ms and not longer than a few seconds. This dependency of Ca2+ mobilization on single and double pulses can be simulated by a model in which a second messenger is produced in a voltage-dependent manner. This second messenger ...

2001-01-01

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Factors Linked to Bacterial Vaginosis in Nonpregnant Women

The genomic termini of RNA viruses contain essential cis-acting signals for such diverse functions as packaging, genome translation, mRNA transcription, and RNA replication, and thus...Full Text Available

2010-06-01

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Bacterial chemoreceptors: high-performance signaling in networked arrays

Objectives. The purposes of this study were to test the hypothesis that vaginal douching is linked to bacterial vaginosis in both symptomatic and asymptomatic women and to identify...Full Text Available

2001-10-01

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Thermal Design and Performance of the Gamma-Ray Spectrometer for the MESSENGER Spacecraft

Chemoreceptors are crucial components in the bacterial sensory systems that mediate chemotaxis. Chemotactic responses exhibit exquisite sensitivity, extensive dynamic range and precise adaptation....Full Text Available

2008-01-01

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Hepatitis C Virus RNA Replication Requires a Conserved Structural Motif within the Transmembrane Domain of the NS5B RNA-Dependent RNA Polymerase ?

A gamma-ray spectrometer (GRS) has been built and delivered to the Mercury MESSENGER spacecraft which launched on August 3, 2004, from Cape Canaveral, Florida. The GRS, a part of seven scientific instruments on board MESSENGER, is based on a coaxial high-purity germanium detector. Gamma-ray detectors based on germanium have the advantage of providing excellent energy resolution, which is critical to achieving the science goals of the mission. However, germanium has the disadvantage that it must operate at cryogenic temperatures (typically {approx}80 K). This requirement is easy to satisfy in the laboratory but difficult near Mercury, which has an extremely hot thermal radiation environment. To cool the detector, a Stirling cycle mechanical cooler is employed. In addition, radiation and conduction techniques a are used to reduce the GRS heat load. Before delivering the flight sensor, a complete thermal prototype was built and tested. The results ...

2004-10-13

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A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli.

Hepatitis C virus (HCV) nonstructural protein 5B (NS5B), the viral RNA-dependent RNA polymerase (RdRp), is a tail-anchored protein with a highly conserved C-terminal transmembrane domain (TMD) that...Full Text Available

2010-11-01

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Two and 8-azido photoaffinity probes. 1. Enzymatic synthesis, characterization, and biological properties of 2- and 8-azido photoprobes of 2-5A and photolabeling of 2-5A binding proteins

We have determined that 10Sa RNA (one of the small stable RNAs found in Escherichia coli) has an interesting structural feature: the 5' end and the 3' end of 10Sa RNA can be arranged in a structure...Full Text Available

1994-09-27

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The crystal structure of unmodified tRNA^Phe from Escherichia coli

The 2- and 8-azido trimer 5'-triphosphate photoprobes of 2-5A have been enzymatically synthesized from [#gamma#-"3"2P]2-azidoATP and [#alpha#-"3"2P]8-azidoAPT by 2-5A synthetase from rabbit reticulocyte lysates. Identification and structural determination of the 2- and 8-azido adenylate trimer 5'-triphosphates were accomplished by enzymatic hydrolyses with T2 RNase, snake venom phosphodiesterase, and bacterial alkaline phosphatase. Hydrolysis products were identified by HPLC and PEI-cellulose TLC analyses. The 8-azido photoprobe of 2-5A displaces p_3A_4["3"2P]pCp from RNase L with affinity equivalent to p_3A_3. The 8-azido photoprobe also activates RNase L to hydrolyze poly(U)["3"2P]pCp 50% at 7 /times/ 10/sup /minus/9/ M in core-cellulose assays. The 2- and 8-azido photoprobes and authentic p_3A_3 activate RNase L to cleave 28S and 18S rRNA to specific cleavage products at 10/sup /minus/9/ M in rRNA cleavage assays. The ...

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The DEXD/H-box RNA Helicase DDX19 Is Regulated by an ?-Helical Switch*S?

Post-transcriptional nucleoside modifications fine-tune the biophysical and biochemical properties of transfer RNA (tRNA) so that it is optimized for participation in cellular processes. Here we report...Full Text Available

2010-07-01

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Specific Residues of the Influenza A Virus Hemagglutinin Viral RNA Are Important for Efficient Packaging into Budding Virions?

DEXD/H-box RNA helicases couple ATP hydrolysis to RNA remodeling by an unknown mechanism. We used x-ray crystallography and biochemical analysis of the human DEXD/H-box...Full Text Available

2009-04-17

48

Purification and translation of murine mammary tumor virus mRNA's.

A final step in the influenza virus replication cycle is the assembly of the viral structural proteins and the packaging of the eight segments of viral RNA (vRNA) into a fully infectious virion. The...Full Text Available

2007-09-01

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Nucleocapsid and Matrix Protein Contributions to Selective Human Immunodeficiency Virus Type 1 Genomic RNA Packaging

We have studied the functions of the intracellular RNAs of mouse mammary tumor virus (MMTV) by purification and translation in vitro. Two major size classes of MMTV RNA, 35S and 24S RNA, were isolated...Full Text Available

1981-07-01

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Naturally occurring double-stranded RNA and immune responses. III. Immunogenicity and antigenicity in animals.

The nucleocapsid protein (NC) of retroviruses plays a major role in genomic RNA packaging, and some evidence has implicated the matrix protein (MA) of certain retroviruses in viral RNA binding. To further...Full Text Available

1998-03-01

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Mutational Analysis of cis-Acting RNA Signals in Segment 7 of Influenza A Virus?

Naturally occurring, double-stranded RNA (ds-RNA)) was immunogenic when injected into mice, rats, guinea-pigs, rabbits, dogs and baboons. The response to native material administered intravenously (i.v.)...Full Text Available

1975-12-01

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Isoform-level microRNA-155 target prediction using RNA-seq

The genomic viral RNA (vRNA) segments of influenza A virus contain specific packaging signals at their termini that overlap the coding regions. To further characterize cis-acting signals...Full Text Available

2008-12-01

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Involvement of the Matrix and Nucleocapsid Domains of the Bovine Leukemia Virus Gag Polyprotein Precursor in Viral RNA Packaging

Computational prediction of microRNA targets remains a challenging problem. The existing rule-based, data-driven and expression profiling approaches to target prediction are mostly approached from the...Full Text Available

2011-05-01

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In vitro analysis of nuclear mRNA export using molecular beacons for target detection

The RNA packaging process for retroviruses involves a recognition event of the genome-length viral RNA by the viral Gag polyprotein precursor (PrGag), an important step in particle morphogenesis. The...Full Text Available

2003-09-01

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Genomic but Not Antigenomic Hepatitis Delta Virus RNA Is Preferentially Exported from the Nucleus Immediately after Synthesis and Processing

A detailed molecular characterization of nuclear mRNA export will require an in vitro system, allowing a biochemical reconstitution of transport. To this end, an mRNA export assay has...Full Text Available

2003-06-01

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Dose Optimization for Long-term rAAV-mediated RNA Interference in the Nigrostriatal Projection Neurons

Hepatitis delta virus (HDV) contains a viroid-like circular RNA that replicates via a double rolling circle replication mechanism. It is generally assumed that HDV RNA is synthesized and remains exclusively...Full Text Available

2002-04-01

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Differential expression of microRNA-675, microRNA-139-3p and microRNA-335 in benign and malignant adrenocortical tumours

Short-hairpin RNA (shRNA)–mediated gene knockdown is a powerful tool for targeted gene silencing and an emerging novel therapeutic strategy. Recent publications, however, reported unexpected...Full Text Available

2009-09-01

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Computational Challenges in miRNA Target Predictions: To Be or Not to Be a True Target?

BackgroundFor the clinical management of adrenocortical neoplasms it is crucial to correctly distinguish between benign and malignant tumours. Even histomorphologically based scoring...Full Text Available

2011-06-01

59

A functional peptide encoded in the Escherichia coli 23S rRNA.

All microRNA (miRNA) target—finder algorithms return lists of candidate target genes. How valid is that output in a biological setting? Transcriptome analysis has proven to be a useful approach...Full Text Available

2009-01-01

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Locked nucleic acid (LNA): High affinity targeting of RNA for diagnostics and therapeutics

A pentapeptide open reading frame equipped with a canonical ribosome-binding site is present in the Escherichia coli 23S rRNA. Overexpression of 23S rRNA fragments containing the mini-gene renders cells...Full Text Available

1996-05-28

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DEFF Research Database (Denmark)

Locked nucleic acid (LNA) is a nucleic acid analogue containing one or more LNA nucleotide monomers with a bicyclic furanose unit locked in an RNA mimicking sugar conformation. This conformational restriction results in unprecedented hybridization affinity towards complementary single stranded RNA and thus, makes LNA uniquely suited for mimicking RNA structures and sequence specific targeting of RNA in vitro or in vivo. The focus of this paper is on LNAantisense, LNA-modified siRNA (siLNA), and detection and analysis of microRNAs by LNA-modified oligonucleotide probes.

2005-01-01

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Sexual intercourse association with asymptomatic bacterial vaginosis and Trichomonas vaginalis treatment in relationship to preterm birth.

Effect of Chitosan Solution on the Inhibition of Pseudomonas fluorescens Causing Bacterial Head Rot of Broccoli

PMID:12439520

2002-11-01

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Does oral metronidazole prevent preterm delivery in normal-risk pregnant women with asymptomatic bacterial vaginosis (BV)?

Full Text Available

2010-06-01

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Application of Quantitative Real-Time PCR for Enumeration of Total Bacterial, Archaeal, and Yeast Populations in Kimchi

PMID:10923545

2000-06-01

65

Inhibition of Ribonucleic Acid Synthesis by Nalidixic Acid in Escherichia coli

Full Text Available

2009-12-01

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Impregnation of silver nanoparticles into bacterial cellulose for antimicrobial wound dressing

The effect of low concentrations of nalidixic acid on ribonucleic acid (RNA) synthesis in Escherichia coli was examined. It was observed that RNA synthesis in exponentially growing...Full Text Available

1974-10-01

67

British Library Electronic Table of Contents (United Kingdom)

Bacterial cellulose was produced by Acetobacter xylinum (strain TISTR 975). Bacterial cellulose is an interesting material for using as a wound dressing since it provides moist environment to a wound resulting in a better wound healing. However, bacterial cellulose itself has no antimicrobial activity to prevent wound infection. To achieve antimicrobial activity, silver nanoparticles were impregnated into bacterial cellulose by immersing bacterial cellulose in silver nitrate solution. Sodium borohydride was then used to reduce the absorbed silver ion (Ag+) inside of bacterial cellulose to the metallic silver nanoparticles (Ag0). Silver nanoparticles displayed the optical absorption band around 420nm. The red-shift and broadening of the optical absorption band was observed when the mole rat...

2008-01-01

68

Visualization of inositol 1,4,5-trisphosphate receptors on the nuclear envelope outer membrane by deep etching electron microscopy

Discordant expression and variable numbers of neighboring GGA- and GAA-rich triplet repeats in the 3' untranslated regions of two groups of messenger RNAs encoded by the rat polymeric immunoglobulin receptor gene.

SummaryThe receptors for the second messenger InsP₃ comprise a family of closely related ion channels that release Ca²⁺ from intracellular stores, most prominently...Full Text Available

2010-09-01

69

Microbial community analysis of ambient temperature anaerobic digesters

An unusual S1-nuclease sensitive microsatellite (STMS) has been found in the single copy, rat polymeric immunoglobulin receptor gene (PIGR) terminal exon. In Fisher rats, elements within or beyond the...Full Text Available

1995-04-11

70

VEGF receptor mRNA expression by ACL fibroblasts is associated with functional healing of the ACL.

This paper reported on a study in which designs for Chinese and Indian fixed-dome anaerobic digesters were modified in an effort to produce smaller and more affordable digesters. While these types of systems are common in tropical regions of developing countries, they have not been used in colder climates because of the low biogas yield during the winter months. Although there is evidence that sufficient biogas production can be maintained in colder temperatures through design and operational changes, there is a lack of knowledge about the seasonal changes in the composition of the microbial communities in ambient temperature digesters. More knowledge is needed to design and operate systems for maximum biogas yield in temperate climates. The purpose of this study was to cultivate a microbial community that maximizes biogas production at psychrophilic temperatures. The study was conducted on a 300 gallon experimental anaerobic digester on the campus of Ohio State University. ...

2010-07-01

71

Termination of transcription by bacteriophage T3 RNA polymerase: homogeneous 3'-terminal oligonucleotide sequence of in vitro T3 RNA polymerase transcripts.

PMID:21331648

2011-02-19

72

Secondary Structure Analysis of a G-rich Sequence Recognizing RNA Aptamer with Structure Specific Enzymes

RNA was synthesized in vitro from a T3 DNA template by T3 RNA polymerase and subsequently separated into seven discrete size classes (molecular weights ranging between 0.21 x 10(6) and 6.2 x 10(6))...Full Text Available

1979-10-01

73

Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme.

Full Text Available

2011-06-01

74

G2 checkpoint siRNA screen in irradiated cancer cells: validation of candidate positive hits

Sequence-specific interactions between aminoacyl-tRNA synthetases and their cognate tRNAs both ensure accurate RNA recognition and prevent the binding of noncognate substrates. Here we show for Escherichia...Full Text Available

1996-07-09

75

Norwegian Open Research Archives (NORA)

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76

Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing

Cleavage of tRNA within the mature tRNA sequence by the catalytic RNA of RNase P: implication for the formation of the primer tRNA fragment for reverse transcription in copia retrovirus-like particles.

No abstract prepared.

2001-04-01

77

Arginine aminoacylation identity is context-dependent and ensured by alternate recognition sets in the anticodon loop of accepting tRNA transcripts.

The retrovirus-like particles of Drosophila are intermediates of retrotransposition of the transposable element copia. In these particles, a 39-nucleotide-long fragment from the 5' region of Drosophila...Full Text Available

1990-10-01

78

The nucleotide sequence and organization of nuclear 5S rRNA genes in yellow lupine

Yeast arginyl-tRNA synthetase recognizes the non-modified wild-type transcripts derived from both yeast tRNA(Arg) and tRNA(Asp) with equal efficiency. It discriminates its cognate natural substrate,...Full Text Available

1996-09-16

79

Toll-like receptor 2 polymorphism and gram-positive bacterial infections after liver transplantation

We have isolated a genomic clone containing 'Lupinus luteus' 5S ribosomal RNA genes by screening with 5S rDNA probe clones that were hybridized previously with the initiator methionine tRNA preparation (contaminated) with traces of rRNA or its degradation products). The clone isolated contains ten repeat units of 342 bp with 119 bp fragment showing 100% homology to the 5S rRNA from yellow lupine. Sequence analysis indicates only point heterogeneities among the flanking regions of the genes. (author). 6 refs, 3 figs.

1993-01-01

80

British Library Electronic Table of Contents (United Kingdom)

Abstract Toll-like receptor 2 (TLR2) is an immune sensor for gram-positive bacterial cell wall components. Single-nucleotide polymorphisms (SNPs) in the TLR2 gene that impair its function may, therefore, influence the risk and outcomes of gram-positive bacterial infections. In a cohort of 694 liver transplant recipients, we assessed the TLR2 SNP that is translated into an amino acid substitution of arginine for glutamine at position 753 (R753Q), and we found that its presence was associated with the clinical characteristics and outcomes of gram-positive bacterial infections. The proportions of patients with the TLR2 R753Q SNP did not significantly differ between those with gram-positive bacterial infections and those without gram-positive bacterial infections (9.6% versus 9.6%, P = 0.999)....

2011-01-01

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

81

The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation

The Mammalian Neuroendocrine Hormone Norepinephrine Supplies Iron for Bacterial Growth in the Presence of Transferrin or Lactoferrin

Interkingdom signaling is established in the gastrointestinal tract in that human hormones trigger responses in bacteria; here, we show that the corollary is true, that a specific bacterial signal,...Full Text Available

2010-01-05

82

Stable-Carbon-Isotope Composition of Fatty Acids in Hydrothermal Vent Mussels Containing Methanotrophic and Thiotrophic Bacterial Endosymbionts

Norepinephrine stimulates the growth of a range of bacterial species in nutritionally poor SAPI minimal salts medium containing 30% serum. Addition of size-fractionated serum components to SAPI...Full Text Available

2000-11-01

83

Separation of the bacterial species, Escherichia coli, from mixed-species microbial communities for transcriptome analysis

Fatty acid biomarker analysis coupled with gas chromatography-isotope ratio mass spectrometry was used to confirm the presence of methanotrophic and thiotrophic bacterial endosymbionts in the tissues...Full Text Available

1998-01-01

84

Sensitivity of Freshly Isolated Bacterial Pathogens to Certain Antibiotics and Nitrofurazone

BackgroundThe study of bacterial species interactions in a mixed-species community can be facilitated by transcriptome analysis of one species in the community using cDNA microarray...Full Text Available

85

Racial differences in cervical cytokine concentrations between pregnant women with and without bacterial vaginosis

The results of antibiotic tests on bacterial pathogens freshly isolated from avian tissues and bovine milk are presented. Coliform isolates from the avian species showed an increased resistance to...Full Text Available

1969-01-01

86

Pretreatment with the gram-positive bacterial cell wall molecule peptidoglycan improves bacterial clearance and decreases inflammation and mortality in mice challenged with Pseudomonas aeruginosa

We have examined the association between cytokine, chemokine and growth factor concentrations with bacterial vaginosis (BV) in pregnant white and black women. A nested case-control analysis...Full Text Available

2008-07-01

87

Persistence of Free-Living Protozoan Communities across Rearing Cycles in Commercial Poultry Houses ?

The objective of this study was to determine if inflammatory tolerance and enhancement of innate immune function could be induced by the gram-positive cell wall component peptidoglycan (PGN)....Full Text Available

2008-10-01

88

Pericardiectomy for Pleuropericardial Effusion Complicating Bacterial Pneumonia

The introduction and survival of zoonotic bacterial pathogens in poultry farming have been linked to bacterial association with free-living protozoa. To date, however, no information is available on...Full Text Available

2011-03-01

89

Nonlinearity in bacterial population dynamics: Proposal for experiments for the observation of abrupt transitions in patches

Severe pericardial effusion is a rare complication of bacterial pneumonia and it usually disappears under medical treatment. Herein we report a case of a girl with a congenital immunodeficient syndrome...Full Text Available

2010-01-01

90

Neonatal E. coli infection alters glial, cytokine, and neuronal gene expression in response to acute amphetamine in adolescent rats

An explicit proposal for experiments leading to abrupt transitions in spatially extended bacterial populations in a Petri dish is presented on the basis of an exact formula obtained through an analytic...Full Text Available

2008-12-02

91

Lethal protein produced in response to competition between sibling bacterial colonies

Neonatal bacterial infection in rats alters the responses to a variety of subsequent challenges later in life. Here we explored the effects of neonatal bacterial infection on a subsequent drug...Full Text Available

2010-04-19

92

Interactions of Antibiotics and Methanolic Crude Extracts of Afzelia Africana (Smith.) Against Drug Resistance Bacterial Isolates

Sibling Paenibacillus dendritiformis bacterial colonies grown on low-nutrient agar medium mutually inhibit growth through secretion of a lethal factor. Analysis of secretions reveals...Full Text Available

2010-04-06

93

IL-6-Dependent Mucosal Protection Prevents Establishment of a Microbial Niche for Attaching/Effacing Lesion-Forming Enteric Bacterial Pathogens1

Infection due to multidrug resistance pathogens is difficult to manage due to bacterial virulence factors and because of a relatively limited choice of antimicrobial agents. Thus, it is imperative to...Full Text Available

94

Generation of Novel Bacterial Regulatory Proteins That Detect Priority Pollutant Phenols

Enteric infections with attaching/effacing lesion-inducing bacterial pathogens are a worldwide health problem. A murine infection model with one such pathogen, Citrobacter rodentium,...Full Text Available

2008-05-15

95

FIRST TRIMESTER BACTERIAL VAGINOSIS, INDIVIDUAL MICROORGANISM LEVELS AND RISK OF SECOND TRIMESTER PREGNANCY LOSS AMONG URBAN WOMEN

The genetic systems of bacteria that have the ability to use organic pollutants as carbon and energy sources can be adapted to create bacterial biosensors for the detection of industrial pollution....Full Text Available

2000-01-01

96

Evaluations of bacterial contaminated full thickness burn wound healing in Sprague Dawley rats Treated with Tualang honey

ObjectiveTo examine the role of first trimester bacterial vaginosis (BV) and level of BV-associated microorganisms diagnosed using the Nugent’s Gram stain...Full Text Available

2007-11-01

97

Comparison of oral and vaginal metronidazole for treatment of bacterial vaginosis in pregnancy: impact on fastidious bacteria

Aim:The effect of Tualang honey on wound healing in bacterial contaminated full-thickness burn wounds was evaluated in 36 male Sprague Dawley rats.Materials...Full Text Available

2011-01-01

98

Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

BackgroundBacterial vaginosis (BV) is a common condition that is associated with preterm birth and acquisition of complex communities of vaginal bacteria that include several fastidious...Full Text Available

99

Bacterial Particle Endocytosis by Epithelial Cells Is Selective and Enhanced by Tumor Necrosis Factor Receptor Ligands?

BackgroundThe bacterial genus Listeria contains pathogenic and non-pathogenic species, including the pathogens L. monocytogenes and L. ivanovii,...Full Text Available

100

Bacterial Oxidation of Sulfide Minerals in Column Leaching Experiments at Suboptimal Temperatures

Bacterial pathogens use virulence strategies to invade epithelial barriers, but active processes of epithelial cells may also contribute to the endocytosis of microbial particles. To focus on the latter,...Full Text Available

2009-03-01

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

101

Bacterial Fouling in a Model Core System

The purpose of the work was to quantitatively characterize temperature effects on the bacterial leaching of sulfide ore material containing several sulfide minerals. The leaching was tested at eight...Full Text Available

1992-02-01

102

Bacterial Competition for Human Nasal Cavity Colonization: Role of Staphylococcal agr Alleles

We have used a sintered glass bead core to simulate the spaces and surfaces of reservoir rock in studies of the bacterial plugging phenomenon that affects waterflood oil recovery operations. The passage...Full Text Available

1985-03-01

103

Bacterial Artificial Chromosome Mutagenesis Using Recombineering

We examined the bacterial aerobic nasal flora of 216 healthy volunteers to identify potential competitive interactions among different species, with special emphasis on the influence of staphylococcal...Full Text Available

2003-01-01

104

Association between bacterial vaginosis or chlamydial infection and miscarriage before 16 weeks' gestation: prospective community based cohort study

Gene expression from bacterial artificial chromosome (BAC) clones has been demonstrated to facilitate physiologically relevant levels compared to viral and nonviral cDNA vectors. BACs are large enough...Full Text Available

2011-01-01

105

Application of tumor, bacterial and parasite susceptibility assays to study immune alterations induced by environmental chemicals

ObjectivesTo assess whether bacterial vaginosis or chlamydial infection before 10 weeks' gestation is associated with miscarriage before 16 weeks.DesignProspective...Full Text Available

2002-12-07

106

ACCEPTABILITY OF A SELF-SAMPLING TECHNIQUE TO COLLECT VAGINAL SMEARS FOR GRAM STAIN DIAGNOSIS OF BACTERIAL VAGINOSIS

Model systems to study the effects of chemicals of environmental concern on bacterial and parasitic diseases as well as the immunosurveillance and destruction of transplantable tumor cells were described...Full Text Available

1982-02-01

107

Regulation of human ribosomal RNA transcription.

To diagnose asymptomatic bacterial vaginosis (BV), self-sampled vaginal smears were collected during a study of risk factors for preterm birth in African American women. More than 90% of those...Full Text Available

2004-01-01

108

Removal of Organic Load from Olive Washing Water by an Aerated Submerged Biofilter and Profiling of the Bacterial Community Involved in the Process

We have used a cell-free polymerase I transcription system derived from HeLa cells to study the regulation of human rRNA synthesis. Analysis of deletion mutants spanning the start site of transcription at nucleotide +1 indicates that the control region affecting initiation of human rRNA synthesis is contained within sequences from nucleotides -158 to +18. This promoter region can be subdivided into (i) a central segment of approximately 40 base pair that is required for transcription and (ii) flanking sequences that influence the efficiency of transcription in vitro. We have examined the in vitro transcriptional activity of the human extract under various conditions that are thought to modulate rRNA synthesis in vivo. Cell-free extracts prepared from HeLa cells infected with adenovirus 2 synthesize human rRNA at levels greatly decreased relative to uninfected cell extracts. By contrast, in vitro ...

1983-06-01

109

Prediction of Bacterial Proteins Carrying A Nuclear Localization Signal and Nuclear Targeting of HsdM from Klebsiella pneumoniae

Full Text Available

2007-05-01

110

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

Full Text Available

2009-10-01

111

Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects

Computational methods for determining the secondary structure of RNA sequences from given alignments are currently either based on thermodynamic folding, compensatory base pair substitutions or both....Full Text Available

2008-11-01

112

Ubiquitin over-expression phenotypes and ubiquitin gene molecular misreading during aging in Drosophila melanogaster

For an enzyme functioning predominantly in a seemingly housekeeping role of 5′ tRNA maturation, RNase P displays a remarkable diversity in subunit make-up across the three domains of...Full Text Available

2010-01-21

113

Therapeutic potential of RNA interference in pain medicine

Molecular Misreading (MM) is the inaccurate conversion of genomic information into aberrant proteins. For example, when RNA polymerase II transcribes a GAGAG motif it synthesizes at low frequency RNA...Full Text Available

114

The viroid and viroid-like RNA database.

In recent years RNA interference (RNAi) has rapidly become the most widely used tool for gene knockdown due to its high specificity and potency. RNAi is an evolutionarily conserved mechanism...Full Text Available

2009-01-01

115

The RNA Chaperone Hfq Is Important for Growth and Stress Tolerance in Francisella novicida

The viroid and viroid-like RNA database is a compilation of all natural sequences published in journals or available from the GenBank and EMBL nucleotide sequence libraries. Several information regarding...Full Text Available

1998-01-01

116

Subunits of the Drosophila CCR4-NOT complex and their roles in mRNA deadenylation

The RNA-binding protein Hfq is recognized as an important regulatory factor in a variety of cellular processes, including stress resistance and pathogenesis. Hfq has been shown in several bacteria to...Full Text Available

117

Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus

The CCR4-NOT complex is the main enzyme catalyzing the deadenylation of mRNA. We have investigated the composition of this complex in Drosophila melanogaster by immunoprecipitation...Full Text Available

2010-07-01

118

Rapid in situ hybridization technique using 16S rRNA segments for detecting and differentiating the closely related gram-positive organisms Bacillus polymyxa and Bacillus macerans

BackgroundRNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome...Full Text Available

2010-01-01

119

RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription

A rapid, sensitive, inexpensive in situ hybridization technique, using 30-mer 16S rRNA probes, can

1992-01-01

120

Purification of mRNA guanylyltransferase from calf thymus.

A structurally conserved element, the trigger loop, has been suggested to play a key role in substrate selection and catalysis of RNA polymerase II (pol II) transcription elongation. Recently resolved...Full Text Available

2010-09-07

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121

Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin

mRNA guanylyltransferase has been extensively purified from calf thymus. A GTP-binding assay was used based on the observations by Shuman and Hurwitz (1981) and Venkatesan and Moss (1982) that vaccinia...Full Text Available

1982-01-01

122

Palindromic Sequence Plays a Critical Role in Human Foamy Virus Dimerization

The T-loop motif is an important recurrent RNA structural building block consisting of a U-turn sub-motif and a UA trans Watson–Crick/Hoogsteen base pair. In the presence of...Full Text Available

2007-11-01

123

Nuclear Organization and Dynamics of 7SK RNA in Regulating Gene Expression

The retroviral RNA genome is dimeric, consisting of two identical strands of RNA linked near their 5′ ends by a dimer linkage structure. Previously it was shown that human foamy virus (HFV)...Full Text Available

2001-04-01

124

Naturally occurring double-stranded RNA and immune responses. Effects on plaque-forming cells and antibody formation.

Noncoding RNAs play important roles in various aspects of gene regulation. We have identified 7SK RNA to be enriched in nuclear speckles or interchromatin granule clusters (IGCs), a subnuclear domain...Full Text Available

2010-12-01

125

Mode of Action of RNase BN/RNase Z on tRNA Precursors

A highly purified preparation of double-stranded RNA, obtained from virus-like particles in Penicillium cultures, was found to affert humoral immune responses in mice differentially depending on its...Full Text Available

1975-03-01

126

MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms

RNase BN, the Escherichia coli homolog of RNase Z, was previously shown to act as both a distributive exoribonuclease and an endoribonuclease on model RNA substrates and to be inhibited...Full Text Available

2010-07-23

127

Making the message clear: visualizing mRNA localization

MicroRNAs (miRNAs) are endogenously encoded small noncoding RNAs, derived by processing of short RNA hairpins, that can inhibit the translation of mRNAs bearing partially complementary target sequences....Full Text Available

2003-08-19

128

Long-term impact of acyclovir suppressive therapy on genital and plasma HIV RNA in Tanzanian women: a randomised controlled trial

Localized mRNA provides spatial and temporal protein expression essential to cell development and physiology. To explore the mechanisms involved, considerable effort has been spent in establishing new...Full Text Available

2010-07-01

129

In vitro dimerization of human immunodeficiency virus type 1 (HIV-1) spliced RNAs

BackgroundHerpes simplex virus (HSV) suppressive therapy reduces genital and plasma HIV-1 RNA over periods up to three months but the longer-term effect is unknown.Full Text Available

2010-05-01

130

Improved free-energy parameters for predictions of RNA duplex stability.

The human immunodeficiency virus type 1 (HIV-1) packages its genomic RNA as a dimer of homologous RNA molecules that has to be selected among a multitude of cellular and viral RNAs. Interestingly, spliced...Full Text Available

2007-12-01

131

Heat Stress Enhances the Accumulation of Polyadenylated Mitochondrial Transcripts in Arabidopsis thaliana

Thermodynamic parameters for prediction of RNA duplex stability are reported. One parameter for duplex initiation and 10 parameters for helix propagation are derived from enthalpy and free-energy changes...Full Text Available

1986-12-01

132

Emergence of Klebsiella pneumoniae Coproducing KPC-2 and 16S rRNA Methylase ArmA in Poland ?

BackgroundPolyadenylation of RNA has a decisive influence on RNA stability. Depending on the organisms or subcellular compartment, it either enhances transcript stability or targets...Full Text Available

133

Efficient use of accessibility in microRNA target prediction

A Klebsiella pneumoniae epidemic strain that coproduced carbapenemase KPC-2 (K. pneumoniae carbapenemase 2) and 16S rRNA methylase ArmA has emerged in Poland. Four...Full Text Available

2011-01-01

134

Differential targeting of Tetrahymena ORC to ribosomal DNA and non-rDNA replication origins

Considering accessibility of the 3′UTR is believed to increase the precision of microRNA target predictions. We show that, contrary to common belief, ranking by the hybridization energy or by...Full Text Available

2011-01-01

135

Detection of Ockelbo virus RNA in skin biopsies by polymerase chain reaction.

The Tetrahymena thermophila origin recognition complex (ORC) contains an integral RNA subunit, 26T RNA, which confers specificity to the amplified ribosomal DNA (rDNA) origin by base...Full Text Available

2009-02-04

136

Confocal microscopy for the analysis of siRNA delivery by polymeric nanoparticles

A sensitive assay based on the polymerase chain reaction for the detection of Ockelbo virus RNA was developed. Two primer pairs from the gene coding for the E2 glycoprotein were chosen. By use of a...Full Text Available

1993-08-01

137

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

Clinical applications of genetic therapies, including delivery of short, interfering RNAs (siRNAs) for RNA interference (RNAi), are limited due to the difficulty of delivering nucleic acids...Full Text Available

2010-09-01

138

Characterization of the 5'-terminal cap structures of early simian virus 40 mRNA.

An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according...Full Text Available

139

Centromere-encoded RNAs are integral components of the maize kinetochore

Early simian virus 40-specific mRNA was isolated from lytically infected and stably transformed cells and analyzed with respect to the 5'-terminal cap content. An analogous diversity of capped structures...Full Text Available

1980-09-01

140

An Efficient Fungal RNA-Silencing System Using the DsRed Reporter Gene?

RNA is involved in a variety of chromatin modification events, ranging from large-scale structural rearrangements to subtle local affects. Here, we extend the evidence for RNA–chromatin interactions...Full Text Available

2004-11-09

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141

A structural determinant required for RNA editing

In filamentous fungi, RNA silencing is an attractive alternative to disruption experiments for the functional analysis of genes. We adapted the gene encoding the autofluorescent DsRed protein as a reporter...Full Text Available

2007-02-01

142

Wide cross-species aminoacyl-tRNA synthetase replacement in vivo: yeast cytoplasmic alanine enzyme replaced by human polymyositis serum antigen.

RNA editing by adenosine deaminases acting on RNAs (ADARs) can be both specific and non-specific, depending on the substrate. Specific editing of particular adenosines may depend on the overall sequence...Full Text Available

2011-07-01

143

The Acidic Domain of Hepatitis C Virus NS4A Contributes to RNA Replication and Virus Particle Assembly?

Because of variations in tRNA sequences in evolution, tRNA synthetases either do not acylate their cognate tRNAs from other organisms or execute misacylations which can be deleterious in vivo. We report...Full Text Available

1995-05-23

144

Targeted suppression of Has2 mRNA in mouse cumulus cell-oocyte complexes by adenovirus-mediated short-hairpin RNA expression

Hepatitis C virus NS3-4A is a membrane-bound enzyme complex that exhibits serine protease, RNA helicase, and RNA-stimulated ATPase activities. This enzyme complex is essential for viral genome replication...Full Text Available

2011-02-01

145

Nucleotide sequence of a Euglena gracilis chloroplast gene coding for the 16S rRNA: homologies to E. coli and Zea mays chloroplast 16S rRNA.

RNA interference (RNAi) is an effective tool for studying gene function in oocytes, but no studies have targeted somatic cells of primary cultured cumulus cell-oocyte complexes (COCs). This...Full Text Available

2009-06-01

146

Isolation and sequence determination of 5'-terminal oligonucleotide fragments of RNA transcripts synthesized by bacteriophage T3-induced RNA polymerase from T3 DNA.

The nucleotide sequence of 16S rDNA from Euglena gracilis chloroplasts has been determined representing the first complete sequence of an algal chloroplast rRNA gene. The structural part of the 16S...Full Text Available

1982-10-25

147

Cloning of rice DNA and identification of tRNA gene clones

The nucleotide sequence of the 5'-terminal oligonucleotides produced by pancreatic RNase digestion of bacteriophage T3 RNA polymerase (EC 2.7.7.6) transcripts of T3 DNA has been determined. The sequence...Full Text Available

1980-07-01

148

Characterization and engineering of sequences controlling in vivo synthesis of brome mosaic virus subgenomic RNA.

DNA from 48 hr germinated rice embryos was cut with restriction endonuclease Bam H1 and cloned to the Bam H1 site on plasmid pBR 322. The clones containing recombinant DNA were selected by their sensitivity to tetracycline and resistance to ampicillin. Using /sup 32/P-labelled rice embryos tRNA as a probe two clones were identified to contain tRNA genes by colony hybridization.

1981-10-20

149

Molecular environment of the IIId subdomain of the IRES element of hepatitits C virus RNA on the human 40S ribosomal subunit

Expression of brome mosaic virus (BMV) coat protein and internal genes of many other positive-strand RNA viruses requires initiation of subgenomic mRNA synthesis from specific internal sites on minus-strand...Full Text Available

1988-07-01

150

British Library Electronic Table of Contents (United Kingdom)

The molecular environment of the key subdomain IIId of the internal ribosome entry site (IRES) element of hepatitis C virus (HCV) RNA in the binary complex with the human 40S ribosomal subunit was studied. To this end, HCV IRES derivatives bearing perfluorophenylazido groups activatable by mild UV at nucleotides G263 or A275 in the subdomain IIId stem were used. They were prepared by the complementary addressed modification of the corresponding RNA transcript with alkylating oligodeoxyribonucleotide derivatives. None of the RNA derivatives were shown to be crosslinked to the 18S rRNA. It was found that the photoreactive groups of the IRES G263 and A275 nucleotides are crosslinked to ribosomal proteins S3a, S14, and S16. For the IRES derivative with the photoreactive group in nucleotide G26...

2009-01-01

151

Effect of Diaporthe RNA virus 1 (DRV1) on growth and pathogenicity of different Diaporthe species

British Library Electronic Table of Contents (United Kingdom)

A 4.1?kbp positive-strand RNA virus known as Diaporthe RNA virus 1 (DRV1) occurs in hypovirulent, non-sporulating isolates of the fungal pathogen Diaporthe perjuncta. A full-length cDNA clone of DRV1 was developed and RNA transcribed from the cDNA clone used to transfect different Diaporthe spp. The transfected species included three D. ambigua isolates and an unidentified Phomopsis asexual state of a Diaporthe sp. Successful transfections were confirmed using RT-PCR. Although the in vitro-transcribed positive sense single-stranded RNA used for transfection included vector sequences at both ends, the genomes of progeny virus from DRV1-transfected isolates were free of the vector sequences. Transfection resulted in morphological changes in these fungal pathogens. However, the presence of DR...

2011-01-01

152

The vasopressin mRNA poly(A) tract is unusually long and increases during stimulation of vasopressin gene expression in vivo

Quantitative variations in the vaginal bacterial population associated with asymptomatic infections: a real-time polymerase chain reaction study.

The authors developed a method, termed an H-blot, by which the poly(A) tract of any specific mRNA may be detected by RNA filter hybridization after its removal from the body of the mRNA by a RNase H-catalyzed endonucleolytic cleavage in the 3' untranslated region. Using this method, they studied the modulation of the length of the poly(A) tract of rat vasopressin mRNA in vivo during changes in the levels of this mRNA resulting from a physiologic stimulus, osmotic stress. The poly(A) tract of hypothalamic vasopressin mRNA in hydrated rats was, quite remarkably, --250 nucleotides in length, in contrast to that of somatostatin mRNA, which was --30 nucleotides long. Vasopressin mRNA poly(A) tail length increased progressively from --250 to --400 nucleotides with the application of the hyperosmotic stimulus and ...

1988-06-01

153

Quantitative variations in the vaginal bacterial population associated with asymptomatic infections: a real-time polymerase chain reaction study

The real-time polymerase chain reaction (PCR) quantification of several vaginal bacterial groups in healthy women and patients developing asymptomatic bacterial vaginosis (BV) and candidiasis (CA) was performed. Statistical analysis revealed that the BV condition is characterised by a great variability among subjects and that it is associated with a significant increase of Prevotella, Atopobium, Veillonella and Gardnerella vaginalis, and a drop in Lactobacillus. On the contrary, the vaginal microflora of healthy women and patients developing CA was found to be homogeneous and stable over time. PMID:18762999

2008-09-02

154

British Library Electronic Table of Contents (United Kingdom)

The real-time polymerase chain reaction (PCR) quantification of several vaginal bacterial groups in healthy women and patients developing asymptomatic bacterial vaginosis (BV) and candidiasis (CA) was performed. Statistical analysis revealed that the BV condition is characterised by a great variability among subjects and that it is associated with a significant increase of Prevotella, Atopobium, Veillonella and Gardnerella vaginalis, and a drop in Lactobacillus. On the contrary, the vaginal microflora of healthy women and patients developing CA was found to be homogeneous and stable over time.

2009-01-01

155

Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments.

Metronidazole to prevent preterm delivery in pregnant women with asymptomatic bacterial vaginosis. National Institute of Child Health and Human Development Network of Maternal-Fetal Medicine Units.

The emergence of bacterial antibiotic resistance is a growing problem, yet the variables that influence the rate of emergence of resistance are not well understood. In a microfluidic device designed to mimic naturally occurring bacterial niches, resistance of Escherichia coli to the antibiotic ciprofloxacin developed within 10 hours. Resistance emerged with as few as 100 bacteria in the initial inoculation. Whole-genome sequencing of the resistant organisms revealed that four functional single-nucleotide polymorphisms attained fixation. Knowledge about the rapid emergence of antibiotic resistance in the heterogeneous conditions within the mammalian body may be helpful in understanding the emergence of drug resistance during cancer chemotherapy. PMID:21940899

2011-09-23

156

J ji Y - NASA Technical Reports Server

PMID:10684911

2000-02-24

157

Interaction of legionella pneumophila and helicobacter pylori with bacterial species isolated from drinking water biofilms

could be attributed either to removal of bacterial competition. (the reason for adding antibiotics before adding additional carbon and ...

158

Expression and regulation of the NALP3 inflammasome complex in periodontal diseases

BackgroundIt is well established that Legionella pneumophila is a waterborne pathogen; by contrast, the mode of Helicobacter pylori transmission...Full Text Available

159

Effect of Photosynthetic Bacterial Addition to Chlorella or ${\\omega}-Yeast$ on Growth of Rotifer, Brachionus plicatilis, and its Dietary Value for Flounder, Paralichthys olivaceus, Larvae

Periodontitis is an infectious process characterized by inflammation affecting the supporting structures of the teeth. Porphyromonas gingivalis is a major oral bacterial species implicated...Full Text Available

2009-09-01

160

Diversity of Dominant Bacterial Taxa in Activated Sludge Promotes Functional Resistance following Toxic Shock Loading

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2000-03-01

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British Library Electronic Table of Contents (United Kingdom)

Examining the relationship between biodiversity and functional stability (resistance and resilience) of activated sludge bacterial communities following disturbance is an important first step towards developing strategies for the design of robust biological wastewater treatment systems. This study investigates the relationship between functional resistance and biodiversity of dominant bacterial taxa by subjecting activated sludge samples, with different levels of biodiversity, to toxic shock loading with cupric sulfate (Cu[II]), 3,5-dichlorophenol (3,5-DCP), or 4-nitrophenol (4-NP). Respirometric batch experiments were performed to determine the functional resistance of activated sludge bacterial community to the three toxicants. Functional resistance was estimated as the 30?min IC50 or th...

2011-01-01

162

CURRICULUM VITAE

Bacterial flora-typing with targeted, chip-based Pyrosequencing

... 84. Fields BS, Haupt T, Davis JP, Arduino MJ, Butler JC. Pontiac fever due to Legionella micdadei from a whirlpool spa: Possible role of bacterial endotoxin. ...

163

BackgroundThe metagenomic analysis of microbial communities holds the potential to improve our understanding of the role of microbes in clinical conditions. Recent, dramatic improvements...Full Text Available

164

Bacterial body plans

Antimicrobial activity and mechanism of action of Nu-3, a protonated modified nucleotide

The bacterium Serratia marcescens produces a plethora of multicellular shapes of different colorations on solid substrates, allowing immediate visual detection of varieties. Such a...Full Text Available

2008-07-01

165

Alpha-toxin of Staphylococcus aureus.

Background"Nubiotics" are synthetic oligonucleotides and nucleotides with nuclease-resistant backbones, and are fully protonated for enhanced ability to be taken up by bacterial...Full Text Available

166

9902631 - Lysozyme - NASA

Alpha-toxin, the major cytotoxic agent elaborated by Staphylococcus aureus, was the first bacterial exotoxin to be identified as a pore former. The protein is secreted as a single-chain, water-soluble...Full Text Available

1991-12-01

167

Tungsten Effects on Phosphate-Dependent Biochemical Pathways are Species and Liver Cell Line Dependent

Protein isolated from hen egg-white and functions as a bacteriostatic enzyme by degrading bacterial cell walls. First enzyme ever characterized by protein ...

168

British Library Electronic Table of Contents (United Kingdom)

Tungsten, in the form of tungstate, polymerizes with phosphate, and as extensive polymerization occurs, cellular phosphorylation and dephosphorylation reactions may be disrupted, resulting in negative effects on cellular functions. A series of studies were conducted to evaluate the effect of tungsten on several phosphate-dependent intracellular functions, including energy cycling (ATP), regulation of enzyme activity (cytosolic protein tyrosine kinase [cytPTK] and tyrosine phosphatase), and intracellular secondary messengers (cyclic adenosine monophosphate [cAMP]). Rat noncancerous hepatocyte (Clone-9), rat cancerous hepatocyte (H4IIE), and human cancerous hepatocyte (HepG2) cells were exposed to 1-1000 mg/l tungsten (in the form of sodium tungstate) for 24 h, lysed, and analyzed for the ab...

2010-01-01

169

High Energy Neutrino Telescopes

Boron-Dependent Degradation of NIP5;1 mRNA for Acclimation to Excess Boron Conditions in Arabidopsis.

This paper presents a review of the history, motivation and current status of high energy neutrino telescopes. Many years after these detectors were first conceived, the operation of kilometer-cubed scale detectors is finally on the horizon at both the South Pole and in the Mediterranean Sea. These new detectors will perhaps provide us the first view of high energy astrophysical objects with a new messenger particle and provide us with our first real glimpse of the distant universe at energies above those accessible by gamma-ray instruments. Some of the topics that can be addressed by these new instruments include the origin of cosmic rays, the nature of dark matter, and the mechanisms at work in high energy astrophysical objects such as gamma-ray bursts, active galactic nuclei, pulsar wind nebula and supernova remnants.

2008-01-01

170

Newer systems for bacterial resistances to toxic heavy metals.

Boron (B) is an essential plant micronutrient that is toxic at higher levels. NIP5;1 is a boric acid channel required for B uptake and growth under B deficiency. Accumulation of the NIP5;1 transcript is upregulated under B deficiency in Arabidopsis thaliana roots. To elucidate the mechanism of regulation, the 5' untranslated region (UTR) of NIP5;1 was tested for its ability to confer B-dependent regulation using ?-glucuronidase and green fluorescent protein as reporters. This analysis showed that the 5' UTR was involved in NIP5;1 transcript accumulation in response to B conditions. We also found that high-B conditions trigger NIP5;1 mRNA degradation and that the sequence from +182 to +200 bp in the 5' UTR is required for this mRNA destabilization. In the nip5;1-1 mutant background, a NIP5;1 complementation construct without the 5' UTR produced high levels of mRNA accumulation, increased B concentrations in tissues, and ...

2011-09-01

171

Nature of plant stimulators in the production of Acetobacter xylinum ({open_quotes}Tea fungas{close_quotes}) biofilm used in skin therapy

Bacterial plasmids contain specific genes for resistances to toxic heavy metal ions including Ag+, AsO2-, AsO4(3-), Cd2+, Co2+, CrO4(2-), Cu2+, Hg2+, Ni2+, Pb2+, Sb3+, and Zn2+. Recent progress with...Full Text Available

1994-09-01

172

Crystal Structure of the Mycobacterium fortuitum Class A ?-Lactamase: Structural Basis for Broad Substrate Specificity

Caffeine and related xanthines were identified as potent stimulators for the bacterial cellulose production in A. xylinum. These compounds are present in several plants whose infusions are useful as culture-medium supplements for this acetobacterium. The proposed target for these native purine-like inhibitory substances is the novel diguanyl nucleotide phosphodiesterase(s) that participates in the bacterial cellulogenic complex.

1991-12-31

173

[Molecular analysis of cytoplasmic male sterility]. Progress report, June 1, 1989--June 15, 1991

β-Lactamases are the main cause of bacterial resistance to penicillins and cephalosporins. Class A β-lactamases, the largest group of β-lactamases, have been found in many bacterial...Full Text Available

2006-07-01

174

Stochastic gene expression and its consequences

We have determined the actual RNA sequence of four mitochondrial genes: pcf, nad3, rps12, and coxII. Because plant mitochondrial proteins cannot be predicted from DNA sequences, the actual primary structures of the encoded proteins were unknown. We have gained information concerning the process of RNA editing. Editing can occur before splicing. Our data is consistent with the hypothesis that RNA editing is not simultaneous with transcription. Unlike other systems, the process of editing in plant does not exhibit a discernable direction. As a result of our RNA editing studies, we have produced a number of clones of the proper coding regions tube used for incorporating these mitochondrial genes into the nucleus. 6 refs., 4 figs.

1991-12-31

175

Separation of oligo-RNA by reverse-phase HPLC.

Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to significant cell-to-cell variations in mRNA and protein levels. This variation...Full Text Available

2008-10-17

176

Mutations in RNA Binding Protein Gene Cause Familial Dilated Cardiomyopathy

A rapid and highly reproducible chromatographic technique has been developed for analysis and purification of complex mixtures of oligoribonucleotides. The method utilizes a column of microparticulate...Full Text Available

1979-10-25

177

Isolation of full-length putative rat lysophospholipase cDNA using improved methods for mRNA isolation and cDNA cloning

ObjectivesWe sought to identify a novel gene for dilated cardiomyopathy (DCM).BackgroundDCM is a heritable, genetically...Full Text Available

2009-09-01

178

Induced Expression of Doublesex-and mab-3-related Transcription Factor-1 (DMRT-1) mRNA by Testosterone in the Olive Flounder, Paralichthys olivaceus ovary

The authors have cloned a full-length putative rat pancreatic lysophospholipase cDNA by an improved mRNA isolation method and cDNA cloning strategy using (/sup 32/P)-labelled nucleotides. These new methods allow the construction of a cDNA library from the adult rat pancreas in which the majority of recombinant clones contained complete sequences for the corresponding mRNAs. A previously recognized but unidentified long and relatively rare cDNA clone containing the entire sequence from the cap site at the 5' end to the poly(A) tail at the 3' end of the mRNA was isolated by single-step screening of the library. The size, amino acid composition, and the activity of the protein expressed in heterologous cells strongly suggest this mRNA codes for lysophospholipase.

1987-03-24

179

Identification of pork derivatives in food products by species-specific polymerase chain reaction (PCR) for halal verification

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2007-08-01

180

British Library Electronic Table of Contents (United Kingdom)

Pork identification in four types of food products, which are sausages and the casings, bread and biscuits, using species-specific polymerase chain reaction (PCR) detection of a conserved region in the mitochondrial (mt) 12S ribosomal RNA (rRNA) gene was developed. Genomic DNA of the food products were successfully extracted except for the casing samples, where no genomic DNA was detected. The extracted genomic DNA was then subjected to PCR amplification targeting the specific regions of the 12S rRNA gene. The genomic DNA from the food products were found to be of good quality and produced clear PCR products on the amplification of 12S rRNA gene of 387 base pairs (bp) from pork species. The species-specific PCR identification yielded excellent results for identification of pork derivatives...

2007-01-01

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Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity

Norwegian Open Research Archives (NORA)

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182

Curcumin Binding to DNA and RNA

British Library Electronic Table of Contents (United Kingdom)

Curcumin, the yellow pigment from the rhizoma of Curcuma longa, is a widely studied phytochemical with a variety of biological activities. The ongoing research and clinical trials have proved that this natural phenolic compound has great and diverse pharmacological potencies. Beside its effective antioxidant, antiinflammatory, and antimicrobial/antiviral properties, curcumin is also considered as a cancer chemopreventive agent. While the antioxidant activity of curcumin is well documented, its interaction with DNA and RNA is not fully investigated. This study was designed to examine the interactions of curcumin with calf thymus DNA and yeast RNA in aqueous solution at physiological conditions, using constant DNA and RNA concentration (6.25?mM) and various curcumin/polynucleotide (phosphate...

2009-01-01

183

Introduction of microbial nutrients in a nuclear fuel waste disposal vault as a result of excavation and operation activities

Bacterial Pili exploit integrin machinery to promote immune activation and efficient blood-brain barrier penetration.

A nuclear fuel waste disposal vault would not likely be a sterile environment. Bacterial activity would be expected in those areas of the vault conducive to bacterial life, i.e., where effects of heat, moisture content, radiation and compaction would not prevent or severely restrict bacterial life and where suitable and sufficient nutrients would be present. An inventory of bacterial nutrients that would be emplaced 'intentionally' with vault materials (fuel waste, waste containers, buffer and backfill materials) has been made previously. This report assesses bacterial nutrients that would be added 'inadvertently' to a vault in the form of residues of materials used to excavate and operate a vault. Measurements of blasting material residues in the various water supplies, excavated broken rock (muck) and in cores drilled in old and new tunnel walls were made at AECL's Underground ...

1987-08-27

184

Nature and distribution of mucosal lesions associated with enteropathogenic and enterohemorrhagic Escherichia coli in piglets and the role of plasmid-mediated factors.

Group B Streptococcus (GBS) is the leading cause of meningitis in newborn infants. Bacterial cell surface appendages, known as pili, have been recently described in streptococcal pathogens, including GBS. The pilus tip adhesin, PilA, contributes to GBS adherence to blood-brain barrier (BBB) endothelium; however, the host receptor and the contribution of PilA in central nervous system (CNS) disease pathogenesis are unknown. Here we show that PilA binds collagen, which promotes GBS interaction with the ?(2)?(1) integrin resulting in activation of host chemokine expression and neutrophil recruitment during infection. Mice infected with the PilA-deficient mutant exhibit delayed mortality, a decrease in neutrophil infiltration and bacterial CNS dissemination. We find that PilA-mediated virulence is dependent on neutrophil influx as neutrophil depletion results in a decrease in BBB permeability and GBS-BBB penetration. Our results suggest that the ...

2011-09-06

185

Effect of Lactobacillus supplementation with and without arginine on liver damage and bacterial translocation in an acute liver injury model in the rat.

Bacterial attachment-effacement (att-eff) is emerging as an important virulence characteristic common to both enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC). The contribution of the plasmid-encoded EPEC adherence factor to the production of mucosal lesions and diarrhea was investigated in gnotobiotic piglets. Bacterial att-aff in the intestinal mucosa of piglets infected with plasmid-cured EPEC strain E2348/69 (O127) was indistinguishable from that in piglets infected with the parent strain, but the distribution of lesions was different; it occurred in the small intestines of 6 of 7 piglets infected with the parent strain compared with only 2 of 11 (P = 0.006) infected with the plasmid-cured strain. Plasmid-encoded factors in EPEC and EHEC strains did not appear to contribute to bacterial competition with normal gut microflora. Of 13 strains belonging to five EPEC serogroups, O55, O142, O26, ...

1989-04-01

186

Yeast ribosomal protein L1 is required for the stability of newly synthesized 5S rRNA and the assembly of 60S ribosomal subunits.

In acute liver failure following hepatitis, toxic insults, or after major liver surgery, there is an increased bacterial translocation from the gut. This may explain some of the infectious complications seen in these conditions. To elucidate mechanisms and find possible preventive measures, we investigated the effect of rectal administration of arginine and probiotic bacteria (Lactobacillus spp.) on bacterial translocation and the extent of liver failure. Sprague-Dawley rats were used and five different Lactobacillus strains (Lb. reuteri R2LC, Lb. rhamnosus DSM 6594 (= strain 271), Lb. plantarum DSM 9843 (= strain 299v), Lb. fermentum 8704:3 (= strain 245), and Lb. reuteri (= strain 108) were administered rectally once daily for 8 days with and without 2% arginine. Acute liver injury (ALI) was induced on the eighth day by intraperitoneal injection of D-galactosamine (1.1 g/kg body weight), and samples were collected after 24 and 48 hours. ...

1997-03-01

187

Unusual heterogeneity of the 5'-termini of human adenovirus type 2 early region E2 mRNA.

Ribosomal protein L1 from Saccharomyces cerevisiae binds 5S rRNA and can be released from intact 60S ribosomal subunits as an L1-5S ribonucleoprotein (RNP) particle. To understand the nature of the...Full Text Available

1993-05-01

188

The human U1-70K snRNP protein: cDNA cloning, chromosomal localization, expression, alternative splicing and RNA-binding.

The 5'-terminal structures of human adenovirus type 2 (Ad2) early region 2 (E2) mRNA were investigated. The E2 transcription unit has several interesting properties, including the presence of a TATA-like...Full Text Available

1984-12-11

189

The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors

We have isolated and sequenced cDNA clones encoding the human U1-70K snRNP protein, and have mapped this locus (U1AP1) to human chromosome 19. The gene produces two size classes of RNA, a major 1.7-kb...Full Text Available

1987-12-23

190

The complete sequence of a full length cDNA for human liver glyceraldehyde-3-phosphate dehydrogenase: evidence for multiple mRNA species.

In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3′- and 5′-ends of 261 yeast genes by...Full Text Available

2010-08-01

191

The Me31B DEAD-Box Helicase Localizes to Postsynaptic Foci and Regulates Expression of a CaMKII Reporter mRNA in Dendrites of Drosophila Olfactory Projection Neurons

A recombinant M13 clone (O42) containing a 65 b.p. cDNA fragment from human fetal liver mRNA coding for glyceraldehyde-3-phosphate dehydrogenase has been identified and it has been used to isolate from...Full Text Available

1984-12-11

192

The DNA and RNA specificity of eilatin Ru(II) complexes as compared to eilatin and ethidium bromide

mRNP granules at adult central synapses are postulated to regulate local mRNA translation and synapse plasticity. However, they are very poorly characterized in vivo. Here, in Drosophila...Full Text Available

193

Simultaneous Detection of Multiplex-Amplified Human Immunodeficiency Virus Type 1 RNA, Hepatitis C Virus RNA, and Hepatitis B Virus DNA Using a Flow Cytometer Microsphere-Based Hybridization Assay

Eilatin-containing ruthenium complexes bind to a broad range of different nucleic acids including: calf thymus (CT) DNA, tRNA^Phe, polymeric RNAs and DNAs, and viral RNAs including the HIV-1...Full Text Available

2003-10-01

194

Regulation of the mRNA for monocyte-derived neutrophil-activating peptide in differentiating HL60 promyelocytes.

The feasibility of performing a multiplex assay for the detection of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) RNAs and hepatitis B virus (HBV) DNA is demonstrated. This...Full Text Available

2000-03-01

195

Mutations at the accommodation gate of the ribosome impair RF2-dependent translation termination

A cDNA library was constructed from HL60 human promyelocyte poly(A)+ RNA harvested 3 h after induction of macrophage differentiation with 12-O-tetradecanoyl phorbol-13-acetate in the presence of cycloheximide....Full Text Available

1989-05-01

196

Individual products of the adenovirus 12S and 13S EIa mRNAs stimulate viral EIIa and EIII expression at the transcriptional level.

During protein synthesis, aminoacyl-tRNA (aa-tRNA) and release factors 1 and 2 (RF1 and RF2) have to bind at the catalytic center of the ribosome on the 50S subunit where they take part in peptide bond...Full Text Available

2010-09-01

197

Identification of physochemical factors controlling the capacity of nano-particles to penetrate cells of the respiratory epithelium

Recombinant plasmids containing mutant or wild-type adenovirus serotype 2 EIa genes that produce the 12S mRNA alone, the 13S mRNA alone, or both mRNAs were cotransfected into HeLa cells with plasmids...Full Text Available

1984-07-01

198

Environmental Research Database

Objectives1) To establish a protocol for transfection of immortalised type I cells with SiRNA and its effect on cell viability; 2) To optimise silencing of genes involved in endocystosis using SiRNA and confirm successful transfection with western blotting; 3) To investigate the effect of gene silencing on uptake of flourescently-labelled latex nanoparticles.DescriptionTo investigate the mechanisms of particle uptake.

2009-01-31

199

Highly efficient gene silencing using perfect complementary artificial miRNA targeting AP1 or heteromeric artificial miRNA targeting AP1 and CAL genes

Green tea increases anti-inflammatory tristetraprolin and decreases pro-inflammatory tumor necrosis factor mRNA levels in rats

Gene silencing is a useful technique for elucidating biological function of genes by knocking down their expression. A recently developed artificial microRNAs (amiRNAs) exploits an endogenous...Full Text Available

2009-03-01

200

Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)

BackgroundTristetraprolin (TTP/ZFP36) family proteins have anti-inflammatory activity by binding to and destabilizing pro-inflammatory mRNAs such as Tnf mRNA, and represent a potential...Full Text Available

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201

Evolutionary Constraints Acting on DDX3X Protein Potentially Interferes with Rev-Mediated Nuclear Export of HIV-1 RNA

BackgroundCotton fiber development undergoes rapid and dynamic changes in a single cell type, from fiber initiation, elongation, primary and secondary wall biosynthesis, to fiber...Full Text Available

2009-01-01

202

Enhanced anti-tumor effects of combined MDR1 RNA interference and human sodium/iodide symporter (NIS) radioiodine gene therapy using an adenoviral system in a colon cancer model

Differential host-pathogen interactions direct viral replication in infected cells. In HIV-1 infected cells, nuclear export of viral RNA transcripts into cellular cytoplasm is governed by interaction...Full Text Available

203

Elimination of L-A double-stranded RNA virus of Saccharomyces cerevisiae by expression of gag and gag-pol from an L-A cDNA clone.

Using an adenoviral system as a delivery mediator of therapeutic gene, we investigated the therapeutic effects of the use of combined MDR1 shRNA and human NIS (hNIS)...Full Text Available

2010-07-01

204

Distribution and threshold expression of the tRNA(Lys) mutation in skeletal muscle of patients with myoclonic epilepsy and ragged-red fibers (MERRF).

We report that expression of a nearly full-length cDNA clone of the L-A double-stranded RNA virus causes virus loss in a wild-type strain of Saccharomyces cerevisiae. We show that in this system exclusion...Full Text Available

1993-05-01

205

Different genetic requirements for anterior RNA localization revealed by the distribution of Adducin-like transcripts during Drosophila oogenesis.

We investigated the distribution and expression of mutant mtDNAs carrying the A-to-G mutation at position 8344 in the tRNA(Lys) gene in the skeletal muscle of four patients with myoclonus epilepsy and...Full Text Available

1992-12-01

206

Deriving four functional anti-HIV siRNAs from a single Pol III-generated transcript comprising two adjacent long hairpin RNA precursors

The proteins encoded by polar-localized mRNAs play an important role in cell fate specification along the anteroposterior axis of the Drosophila embryo. The only maternally synthesized mRNA known previously...Full Text Available

1993-03-15

207

Attenuation of oxidant-induced lung injury by 21-aminosteroids (lazaroids): correlation with the mRNA expression for E-selectin, P-selectin, ICAM-1, and VCAM-1.

Several different approaches exist to generate expressed RNA interference (RNAi) precursors for multiple target inhibition, a strategy referred to as combinatorial (co)RNAi. One such approach makes...Full Text Available

2010-10-01

208

Affinity labelling of ribosomes from the livers of different vertebrates by 2-nitro-4-azidobenzoyl-Phe-tRNA

We compared the effects of treatment with methylprednisolone or the 21-aminosteroids, U-74389 and U-74006F (Tirilizad mesylate), on hyperoxic lung injury and the associated expression of mRNA for several...Full Text Available

1994-12-01

209

A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions

Ribosomal protein L 10 from the livers of trout, hen, and rat was found to be the main target for 2-nitro-4-azidobenzoyl-Phe-tRNA in affinity labelling experiments. Therefore, despite somewhat different electrophoretic mobilities, this protein seems to be involved in the organization of the peptidyl transferase centre in ribosomes of various vertebrates. (author).

210

4.5S RNA is encoded by hundreds of tandemly linked genes, has a short half-life, and is hydrogen bonded in vivo to poly(A)-terminated RNAs in the cytoplasm of cultured mouse cells.

MicroRNAs are short (∼22 nucleotides) noncoding RNAs that regulate the stability and translation of mRNA targets. A number of computational algorithms have been developed to help predict which...Full Text Available

2008-11-01

211

The mammalian neuroendocrine hormone norepinephrine supplies iron for bacterial growth in the presence of transferrin or lactoferrin.

4.5S RNA is a group of RNAs 90 to 94 nucleotides long (length polymorphism due to a varying number of UMP residues at the 3' end) that form hydrogen bonds with poly(A)-terminated RNAs isolated from...Full Text Available

1986-05-01

212

Stability and cations coordination of DNA and RNA 14-mer G-quadruplexes: a multiscale computational approach.

Norepinephrine stimulates the growth of a range of bacterial species in nutritionally poor SAPI minimal salts medium containing 30% serum. Addition of size-fractionated serum components to SAPI medium indicated that transferrin was required for norepinephrine stimulation of growth of Escherichia coli. Since bacteriostasis by serum is primarily due to the iron-withholding capacity of transferrin, we considered the possibility that norepinephrine can overcome this effect by supplying transferrin-bound iron for growth. Incubation with concentrations of norepinephrine that stimulated bacterial growth in serum-SAPI medium resulted in loss of bound iron from iron-saturated transferrin, as indicated by the appearance of monoferric and apo- isoforms upon electrophoresis in denaturing gels. Norepinephrine also caused the loss of iron from lactoferrin. The pharmacologically inactive metabolite norepinephrine 3-O-sulfate, by contrast, did not result in ...

2000-11-01

213

Inhibition of glypican-3 expression via RNA interference influences the growth and invasive ability of the MHCC97-H human hepatocellular carcinoma cell line.

Molecular dynamics simulations have been used to study the differences between two DNA and RNA 14-mer quadruplexes of analogous sequences. Their structures present a completely different fold: DNA forms a bimolecular quadruplex containing antiparallel strands and diagonal loops; RNA forms an intrastrand parallel quadruplex containing a G-tetrad and an hexad, which dimerizes by hexad stacking. We used a multiscale computational approach combining classical Molecular dynamics simulations and density functional theory calculations to elucidate the difference in stability of the 2-folds and their ability in coordinating cations. The presence of 2'-OH groups in the RNA promotes the formation of a large number of intramolecular hydrogen bonds that account for the difference in fold and stability of the two 14-mers. We observe that the adenines in the RNA quadruplex play a key role in conserving the geometry ...

2008-09-03

214

Cotton plants expressing CYP6AE14 double-stranded RNA show enhanced resistance to bollworms

Glypican-3 (GPC3), a membrane-bound heparan sulfate proteoglycan, is found to be overexpressed in hepatocellular carcinoma (HCC). The purpose of the present study was to investigate the possible role of GPC3 in the development of HCC. In this study, RNA interference (RNAi) with a GPC3 small hairpin RNA (GPC3 shRNA) was used to identify the effects of GPC3 on the regulation of malignant behaviors of HCC. MHCC97-H, a highly metastatic human HCC cell line in which GPC3 mRNA and protein levels were detected as the highest among the 4 HCC cell lines assessed in this study, and was thus selected as a cell model for in vitro and in vivo experiments. The results showed that down-regulation of GPC3 can significantly inhibit the proliferative and invasive ability of MHCC97-H. Compared with the parental HCC cells, GPC3-silenced cells exhibited attenuated capacities in developing tumors in nude mice, while the ...

2011-05-20

215

British Library Electronic Table of Contents (United Kingdom)

RNA interference (RNAi) plays an important role in regulating gene expression in eukaryotes. Previously, we generated Arabidopsis and tobacco plants expressing double-stranded RNA (dsRNA) targeting a cotton bollworm (Helicoverpa armigera) P450 gene, CYP6AE14. Bollworms fed on transgenic dsCYP6AE14 plants showed suppressed CYP6AE14 expression and reduced growth on gossypol-containing diet (Mao et?al., in Nat Biotechnol 25: 1307?1313, 2007). Here we report generation and analysis of dsRNA-expressing cotton (Gossypium hirsutum) plants. Bollworm larvae reared on T2 plants of the ds6-3 line exhibited drastically retarded growth, and the transgenic plants were less damaged by bollworms than the control. Quantitative reverse-transcription polymerase chain reaction (RT-PCR) showed that the CYP6AE1...

2011-01-01

216

Thermokinetic investigation of effects of carbon source on petroleum bacterial growth

The utilization of polysaccharides by heterotrophic bacterioplankton in the Bay of Biscay (North Atlantic Ocean)

The growth power-time curves of a strain of petroleum bacteria, B-2, in various kinds of cultures containing different kinds of carbon sources, glucose, n-tetradecane, n-hexadecane and n-octadecane, and different kinds of microemulsions have been determined by using a 2277 Thermal Activity Monitor. The curves showed a single peak for cultures containing a single carbon source, glucose, and two peaks for cultures containing two kinds of carbon sources, glucose and one of the n-alkanes. The first peak indicated that bacteria grew by consuming glucose and the second peak indicated that bacteria grew by consuming n-alkane. The curves were complex when the bacterium grows in a microemulsion culture. According to a kinetic equation of bacterial growth under limited conditions, the rate constants of bacterial growth were obtained. The results showed that the microemulsion culture was more appropriate to bacteria to grow on n-alkanes.

2002-02-07

217

British Library Electronic Table of Contents (United Kingdom)

This study investigates the turnover of polysaccharides by heterotrophic bacterioplankton in the northern Bay of Biscay, a productive marine system on the continental margin of the temperate Atlantic Ocean. Bacterial biomass production (BBP) near the surface ranged from 0.5 to 25.7 nmol C L?1 h?1 during small phytoplankton blooms in May and June that occurred after the main spring bloom. A direct relationship between BBP and total polysaccharides strongly suggests the dependence of bacterial growth on the availability of semi-labile organic matter. Concentrations of combined glucose as well as rate constants of extracellular glucosidase activity and glucose uptake were determined to estimate the actual carbon fluxes from bacterial polysaccharide turnover. Results reveal that ...

2011-01-01

218

Bacterial vaginosis and other asymptomatic vaginal infections in pregnancy.

Bacterial adhesion reduction on a biocompatible Si^+ ion implanted austenitic stainless steel

Preterm birth is a common cause of neonatal morbidity and mortality. Many asymptomatic genital infections have been associated with preterm birth, but attempts to determine a causal relationship between specific infections and preterm birth have been disappointing. Treatment trials of specific infections have generally failed to show a positive effect, and in some trials have shown a deleterious effect. Although there is a strong association between the presence of bacterial vaginosis and Trichomonas vaginalis in pregnancy and preterm birth, randomized treatment trials have failed to show a benefit of treatment of these organisms. Treatment of asymptomatic bacterial vaginosis or T. vaginalis to prevent preterm birth is not warranted. PMID:12112946

2001-08-01

219

British Library Electronic Table of Contents (United Kingdom)

The colonization of an implant surface by bacteria is an extremely important medical problem, which often leads to the failure of medical devices. Modern surface modification techniques, such as ion implantation, can confer to the surfaces very different properties from those of the bulk underlying material. In this work, austenitic stainless steel 316 LVM has been superficially modified by Si^+ ion implantation. The effect of surface modification on the biocompatibility and bacterial adhesion to 316 LVM stainless steel has been investigated. To this aim, human mesenchymal stem cells (hMSCs), as precursor of osteoblastic cells, and bacterial strains relevant in infections related to orthopedic implants, i.e., Staphylococcus aureus and Staphylococcus epidermidis, have been assayed. For the ...

2011-01-01

220

Allelochemicals produced by Caribbean macroalgae and cyanobacteria have species-specific effects on reef coral microorganisms

British Library Electronic Table of Contents (United Kingdom)

Coral populations have precipitously declined on Caribbean reefs while algal abundance has increased, leading to enhanced competitive damage to corals, which likely is mediated by the potent allelochemicals produced by both macroalgae and benthic cyanobacteria. Allelochemicals may affect the composition and abundance of coral-associated microorganisms that control host responses and adaptations to environmental change, including susceptibility to bacterial diseases. Here, we demonstrate that extracts of six Caribbean macroalgae and two benthic cyanobacteria have both inhibitory and stimulatory effects on bacterial taxa cultured from the surfaces of Caribbean corals, macroalgae, and corals exposed to macroalgal extracts. The growth of 54 bacterial isolates was monitored in the presence of l...

2011-01-01

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221

Transcriptome Profiling of a Toxic Dinoflagellate Reveals a Gene-Rich Protist and a Potential Impact on Gene Expression Due to Bacterial Presence

The inhibition of staphylococcus epidermidis biofilm formation by vancomycin-modified titanium alloy and implications for the treatment of periprosthetic infection

BackgroundDinoflagellates are unicellular, often photosynthetic protists that play a major role in the dynamics of the Earth's oceans and climate. Sequencing of dinoflagellate nuclear...Full Text Available

222

The antimicrobial resistance patterns and associated determinants in Streptococcus suis isolated from humans in southern Vietnam, 1997-2008

Peri-prosthetic infections are notoriously difficult to treat as the biomaterial implant is ideal for bacterial adhesion and biofilm formation, resulting in decreased antibiotic sensitivity....Full Text Available

2008-12-01

223

The Subtilisin-Like Protease AprV2 Is Required for Virulence and Uses a Novel Disulphide-Tethered Exosite to Bind Substrates

BackgroundStreptococcus suis is an emerging zoonotic pathogen and is the leading cause of bacterial meningitis in adults in Vietnam. Systematic data on the antimicrobial...Full Text Available

224

Single-Step Production of a Recyclable Nanobiocatalyst for Organophosphate Pesticides Biodegradation Using Functionalized Bacterial Magnetosomes

Many bacterial pathogens produce extracellular proteases that degrade the extracellular matrix of the host and therefore are involved in disease pathogenesis. Dichelobacter nodosus...Full Text Available

2010-11-01

225

Relationship between Hydroxy Fatty Acids and Prostaglandin E₂ in Gingival Tissue

Enzymes are versatile catalysts in laboratories and on an industrial scale; improving their immobilization would be beneficial to broadening their applicability and ensuring their (re)use. Lipid-coated...Full Text Available

226

Pseudomonas aeruginosa selective adherence to and entry into human endothelial cells.

Bacterial hydroxy fatty acids and alpha-hydroxy fatty acids have been demonstrated in complex lipid extracts of subgingival plaque and gingival tissue. However, little is known about the relationship...Full Text Available

1998-12-01

227

Plant and algal interference in bacterial beta-D-galactosidase and beta-D-glucuronidase assays.

The pathogenesis of Pseudomonas aeruginosa disseminated infections depends on bacterial interaction with blood vessels. We have hypothesized that in order to traverse the endothelial barrier, bacteria...Full Text Available

1994-12-01

228

Parallel Evolution of a Type IV Secretion System in Radiating Lineages of the Host-Restricted Bacterial Pathogen Bartonella

Several commonly occurring freshwater and marine plants and algae were screened for beta-D-galactosidase and beta-D-glucuronidase activities by using a 60-min enzyme assay based on the hydrolysis by...Full Text Available

1994-11-01

229

Overexpression of bacterial ethylene-forming enzyme gene in Trichoderma reesei enhanced the production of ethylene

Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered...Full Text Available

2011-02-01

230

OmpA of Uropathogenic Escherichia coli Promotes Postinvasion Pathogenesis of Cystitis?

In order to efficiently utilize natural cellulose materials to produce ethylene, three expression vectors containing the ethylene-forming enzyme (efe) gene from Pseudomonas...Full Text Available

231

Occurrence and distribution of bacterial indicators and pathogens in canal communities along the Texas coast.

Type 1 pilus directs bladder epithelial binding and invasion by uropathogenic Escherichia coli (UPEC) in the initial stage of cystitis, but the bacterial determinants of postinvasion...Full Text Available

2009-12-01

232

Nuclear receptor ERR? and coactivator PGC-1? are effectors of IFN-?-induced host defense

Increased construction of residential canal communities along the southern coastline of the United States has led to a concern about their impact on water quality. Pollution of such dead-end canals...Full Text Available

1977-08-01

233

Molecular Evidence of Bartonella Infection in Domestic Dogs from Algeria, North Africa, by Polymerase Chain Reaction (PCR)

Macrophage activation by the proinflammatory cytokine interferon-γ (IFN-γ) is a critical component of the host innate response to bacterial pathogenesis. However, the precise nature...Full Text Available

2007-08-01

234

Modification of Spatial Distribution of 2,4-Dichlorophenoxyacetic Acid Degrader Microhabitats during Growth in Soil Columns

Bartonella species are being recognized as important bacterial human and canine pathogens, and are associated with multiple arthropod vectors. Bartonella DNA extracted...Full Text Available

2010-08-05

235

Measurement of the Water Potential of Stored Potato Tubers ¹

Bacterial processes in soil, including biodegradation, require contact between bacteria and substrates. Knowledge of the three-dimensional spatial distribution of bacteria at the microscale is necessary...Full Text Available

2004-05-01

236

LOUSE-BORNE BACTERIAL PATHOGENS IN LICE (PHTHIRAPTERA) OF RODENTS AND CATTLE FROM EGYPT

A method of measuring the water potential of stored potato tubers (Solanum tuberosum L.) was needed to investigate the relationship of bacterial soft rot in tubers to water potential....Full Text Available

1985-11-01

237

Intragenomic conflict in populations infected by Parthenogenesis Inducing Wolbachia ends with irreversible loss of sexual reproduction

... were erroneous. The oriental rat flea, Xenopsylla cheopis Rothschild, is considered to be the primary vector of ... laboratory and production of Weigl's exanthematous typhus vaccine. In Maintenance of hum...

238

Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence

BackgroundThe maternally inherited, bacterial symbiont, parthenogenesis inducing (PI) Wolbachia, causes females in some haplodiploid insects to produce daughters...Full Text Available

239

Induction of nonspecific tolerance to endotoxins reduces the alveolar bone resorption in ligature-treated rats.

The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically...Full Text Available

2005-11-01

240

In vivo expression and mitochondrial targeting of yeast apoiso-1-cytochrome c fusion proteins.

Previous experimental data from various laboratories indicate that endotoxin of gram-negative oral microorganisms might be one of the most important bacterial products involved in bone resorption during...Full Text Available

1983-02-01

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241

Identification of plasmid and Bacillus subtilis chromosomal recombination sites used for pE194 integration.

To define the import pathway for apoiso-1-cytochrome c in vivo, the coding region for bacterial chloramphenicol acetyltransferase (CAT) or yeast copper metallothionein (CuMT) was fused to the carboxy...Full Text Available

1990-11-01

242

Identification of genomic differences between Campylobacter jejuni subsp. jejuni and C. jejuni subsp. doylei at the nap locus leads to the development of a C. jejuni subspeciation multiplex PCR method

The plasmid pE194 (3.7 kilobases) is capable of integrating into the genome of the bacterial host Bacillus subtilis in the absence of the major homology-dependent RecE recombination system. Multiple...Full Text Available

1989-05-01

243

Heavy metals alter the electrokinetic properties of bacteria, yeasts, and clay minerals.

BackgroundThe human bacterial pathogen Campylobacter jejuni contains two subspecies: C. jejuni subsp. jejuni (Cjj)...Full Text Available

244

Gingival crevicular fluid levels of clindamycin compared with its minimal inhibitory concentrations for periodontal bacteria.

The electrokinetic patterns of four bacterial species (Bacillus subtilis, Bacillus megaterium, Pseudomonas aeruginosa, and Agrobacterium radiobacter), two yeasts (Saccharomyces cerevisiae and Candida...Full Text Available

1992-05-01

245

Genomic Evidence for the Evolution of Streptococcus equi: Host Restriction, Increased Virulence, and Genetic Exchange with Human Pathogens

Clindamycin concentrations in gingival crevicular fluid and in blood were determined over a 7-h period and were related to the minimal inhibitory concentrations of this agent for 340 bacterial strains...Full Text Available

1981-05-01

246

Genome-Wide Transcriptional Response of Chemostat-Cultured Escherichia coli to Zinc

The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered....Full Text Available

2009-03-01

247

Genetic Heterogeneity in Severe Congenital Neutropenia: How Many Aberrant Pathways Can Kill a Neutrophil?

Zinc is an essential trace metal ion for growth, but an excess of Zn is toxic and microorganisms express diverse resistance mechanisms. To understand global bacterial responses to excess Zn, we conducted...Full Text Available

2005-02-01

248

Genetic Evidence for Inhibition of Bacterial Division Protein FtsZ by Berberine

Purpose of reviewSevere congenital neutropenia (SCN) is a primary immunodeficiency in which lack of neutrophils causes inadequate innate immune host response to bacterial...Full Text Available

2007-12-01

249

Factors Affecting Daughter Cells' Arrangement during the Early Bacterial Divisions

BackgroundBerberine is a plant alkaloid that is widely used as an anti-infective in traditional medicine. Escherichia coli exposed to berberine form filaments, suggesting...Full Text Available

250

Evaluating the Involvement of Alternative Sigma Factors SigF and SigG in Clostridium perfringens Sporulation and Enterotoxin Synthesis?

On agar plates, daughter cells of Escherichia coli mutually slide and align side-by-side in parallel during the first round of binary fission. This phenomenon has been previously attributed...Full Text Available

251

Endometrial biopsy in Holstein-Friesian dairy cows. III. Bacteriological analysis and correlations with histological findings.

Clostridium perfringens type A food poisoning is the second most commonly identified bacterial food-borne illness. Sporulation contributes to this disease in two ways: (i) most food-poisoning...Full Text Available

2010-10-01

252

Endogenous Nitric Oxide Protects Bacteria Against a Wide Spectrum of Antibiotics

This study examines the results of bacterial culture from 159 endometrial biopsy samples from 97 commercial dairy cows and correlations between bacteriological and histological findings. Bacteria were...Full Text Available

1991-04-01

253

Effect of Wastewater Treatment Plant Effluent on Microbial Function and Community Structure in the Sediment of a Freshwater Stream with Variable Seasonal Flow?

Bacterial nitric oxide synthases (bNOS) are present in many Gram-positive species and have been demonstrated to synthesize NO from arginine in vitro and in vivo. However, the physiological role...Full Text Available

2009-09-11

254

Effect of Feeding Cows Genetically Modified Maize on the Bacterial Community in the Bovine Rumen?

We investigated the effects of wastewater treatment plant (WWTP) discharge on the ecology of bacterial communities in the sediment of a small, low-gradient stream in South Australia. The quantification...Full Text Available

2008-05-01

255

Distribution Frequency of Pathogenic Bacteria Isolated from Cutaneus Leishmaniasis Lesions

Rumen-cannulated cows (n = 4) were fed successively silage made from either conventional or genetically modified (GM) maize. Results revealed no effects of GM maize on the dynamics...Full Text Available

2007-12-01

256

Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations

Cutaneous leishmaniasis (CL) is a parasitic disease characterized by single or multiple ulcerations. Secondary bacterial infections are one of the complications that can increase the tissue destruction...Full Text Available

2008-09-01

257

Display of Recombinant Proteins on Bacillus subtilis Spores, Using a Coat-Associated Enzyme as the Carrier?

Many pathogens colonize different anatomical sites, but the selective pressures contributing to survival in the diverse niches are poorly understood. Group A Streptococcus (GAS) is...Full Text Available

2011-03-22

258

Detection of Streptococcus mutans Genomic DNA in Human DNA Samples Extracted from Saliva and Blood

The display of proteins such as feed enzymes at the surface of bacterial spore systems has a great potential use for animal feed. Feed enzymes increase the digestibility of nutrients, leading to greater...Full Text Available

2010-09-01

259

Delineating Bacteriostatic and Bactericidal Targets in Mycobacteria Using IPTG Inducible Antisense Expression

Caries is a multifactorial disease, and studies aiming to unravel the factors modulating its etiology must consider all known predisposing factors. One major factor is bacterial colonization,...Full Text Available

2011-01-01

260

Biotransformation of Explosives by the Old Yellow Enzyme Family of Flavoproteins

In order to identify novel high value antibacterial targets it is desirable to delineate whether the inactivation of the target enzyme will lead to bacterial death or stasis. This knowledge is particularly...Full Text Available

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261

Biological processing and interactions with coal: Summary of activities for the period January 1, 1988--March 31, 1988

Several independent studies of bacterial degradation of nitrate ester explosives have demonstrated the involvement of flavin-dependent oxidoreductases related to the old yellow enzyme (OYE) of yeast....Full Text Available

2004-06-01

262

Binary Bacterial Toxins: Biochemistry, Biology, and Applications of Common Clostridium and Bacillus Proteins

Biodegradation/solubilization of coal is described. The degradation of dibenzothiophene by two bacterial strains is reported. The effects of adding salicylate to the treatments was also investigated. 2 figs., 5 tabs. (CBS)

1988-01-01

263

Bacterial response to siderophore and quorum-sensing chemical signals in the seawater microbial community

Certain pathogenic species of Bacillus and Clostridium have developed unique methods for intoxicating cells that employ the classic enzymatic “A-B” paradigm for protein toxins. The binary...Full Text Available

2004-09-01

264

Bacterial lipopolysaccharide induces an endocrine switch from prostaglandin F_2? to prostaglandin E₂ in bovine endometrium

BackgroundOceans are iron-deficient and nutrient-poor environments. These conditions impart limitations on our understanding of and our ability to identify microorganisms from the...Full Text Available

265

Bacterial infections in suspected cutaneous leishmaniasis lesions.

Escherichia coli infection of the endometrium causes uterine disease after parturition and is associated with prolonged luteal phases of the ovarian cycle in cattle. Termination...Full Text Available

2009-04-01

266

Bacterial indicators of risk of diarrhoeal disease from drinking-water in the Philippines.

In Iran, microscopic examination of skin scrapings from 2202 individuals with clinically diagnosed cutaneous leishmaniasis (CL) lesions revealed the presence of amastigotes in 1123 cases (51.0%). Bacteriological...Full Text Available

1990-01-01

267

Bacterial glycolipids and analogs as antigens for CD1d-restricted NKT cells

Inadequate measures of water quality have been used in many studies of the health effects associated with water supplies in developing countries. The present 1-year epidemiological-microbiological study...Full Text Available

1991-01-01

268

Association of Nasophyaryngeal Bacterial Colonization during Upper Respiratory Tract Infection and the Development of Acute Otitis Media

The CD1 family of proteins binds self and foreign glycolipids for presentation to CD1-restricted T cells. To identify previously uncharacterized active CD1 ligands, especially those of microbial origin,...Full Text Available

2005-02-01

269

Association between skin diseases and severe bacterial infections in children: case-control study

Acute Otitis Media occurs mostly after upper respiratory tract infection; the causative bacteria are those colonized in the nasopharynx. We studied 709 URI episodes and found that children with...Full Text Available

2008-02-15

270

Antimicrobial susceptibilities of bacteria associated with periodontal disease.

BackgroundSepsis or bacteraemia, however rare, is a significant cause of high mortality and serious complications in children. In previous studies skin disease or skin infections...Full Text Available

271

Analysis of the Sulfate-Reducing Bacterial and Methanogenic Archaeal Populations in Contrasting Antarctic Sediments

A total of 193 bacterial strains were tested for their susceptibilities to 14 antimicrobial agents. Penicillin G was active at 2 U/ml against 98% of the oral isolates. Other antibiotics with good activity...Full Text Available

1983-03-01

272

Allosteric regulation of glycerol kinase by enzyme IIIglc of the phosphotransferase system in Escherichia coli and Salmonella typhimurium.

The distribution and activity of communities of sulfate-reducing bacteria (SRB) and methanogenic archaea in two contrasting Antarctic sediments were investigated. Methanogenesis dominated in freshwater...Full Text Available

2003-06-01

273

Adrenaline modulates the global transcriptional profile of Salmonella revealing a role in the antimicrobial peptide and oxidative stress resistance responses

The mechanism by which enzyme IIIglc of the bacterial phosphotransferase system regulates the activity of crystalline glycerol kinase from Escherichia coli has been studied, and the inhibitory effects...Full Text Available

1985-05-01

274

Actinobacillus actinomycetemcomitans Lipopolysaccharide-Mediated Experimental Bone Loss Model for Aggressive Periodontitis

BackgroundThe successful interaction of bacterial pathogens with host tissues requires the sensing of specific chemical and physical cues. The human gut contains a huge number of...Full Text Available

275

Acetic Acid Bacterial Biota of the Pink Sugar Cane Mealybug, Saccharococcus sacchari, and Its Environs

BackgroundBacterial constituents, such as Gram-negative derived lipopolysaccharide (LPS), can initiate inflammatory bone loss through induction of host-derived inflammatory...Full Text Available

2007-03-01

276

ADP-Glucose Pyrophosphorylase, a Regulatory Enzyme for Bacterial Glycogen Synthesis

Saccharococcus sacchari is the primary colonizer of the developing “sterile” tissue between the leaf sheath and stem of sugar cane. The honeydew secreted by the mealybugs...Full Text Available

1990-03-01

277

A report of clinical trial conducted on Toto ointment and soap products.

The accumulation of α-1,4-polyglucans is an important strategy to cope with transient starvation conditions in the environment. In bacteria and plants, the synthesis of glycogen and starch occurs...Full Text Available

2003-06-01

278

A Marker-Dense Physical Map of the Bradyrhizobium japonicum Genome

OBJECTIVE: The efficacy of Toto ointment and soap on common skin disorders was tested. METHODOLOGY: A cohort of Nigerians with common skin conditions such as fungal and bacterial skin infections, scabies,...Full Text Available

2003-01-01

279

A Coxiella burnetti repeated DNA element resembling a bacterial insertion sequence.

Bacterial artificial chromosome (BAC) clones are effective mapping and sequencing reagents for use with a wide variety of small and large genomes. This report describes the development of a physical...Full Text Available

2001-08-01

280

Evolution of Hox Post-Transcriptional Regulation by Alternative Polyadenylation and MicroRNA Modulation Within 12 Drosophila Genomes.

A DNA fragment located on the 3' side of the Coxiella burnetii htpAB operon was determined by Southern blotting to exist in approximately 19 copies in the Nine Mile I genome. The DNA sequences of this...Full Text Available

1992-09-01

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281

Effect of tetracycline hydrochloride treatment on the critical thermal maximum of common shiners

Hox genes encode a family of transcriptional regulators that operate differential developmental programs along the anteroposterior axis of bilateral animals. Regulatory changes affecting Hox gene expression are believed to have been crucial for the evolution of animal body plans. In Drosophila melanogaster, Hox expression is post-transcriptionally regulated by microRNAs (miRNAs) acting on target sites located in the 3' untranslated regions (3'UTRs) of Hox mRNAs. Notably, recent work has shown that during D. melanogaster development Hox genes produce mRNAs with variable 3'UTRs (short and long forms) in different sets of tissues as a result of alternative polyadenylation; importantly, Hox short and long 3'UTRs contain very different target sites for miRNAs. Here, we use a computational approach to explore the evolution of Hox 3'UTRs treated with especial regard to miRNA regulation. Our work is focused on the 12 Drosophila species for which genomic sequences are ...

2011-03-24

282

Isotope labeling strategies for NMR studies of RNA

The transfer of fish from field to laboratory facilities or their propagation in closed or restricted systems frequently results in bacterial infection and ultimately large-scale mortality. In attemps to alleviate this problem, we have added tetracycline hydrochloride to the water prophylactically (pretreating tanks before wild fish were added) and therapeutically (treating tanks after bacterial outbreaks were detected.) In the present study, we examined the effect of tetracyline hydrochloride on the critical thermal maximum (CTM) of the common shiner (Notropis cornutus).

1980-01-01

283

High-energy cosmic-ray nuclei from high- and low-luminosity gamma-ray bursts and implications for multi-messenger astronomy

The known biological functions of RNA have expanded in recent years and now include gene regulation, maintenance of sub-cellular structure, and catalysis, in addition to propagation of genetic information. As for proteins, RNA function is tightly correlated with structure. Unlike proteins, structural information for larger, biologically functional RNAs is relatively limited. NMR signal degeneracy, relaxation problems, and a paucity of long-range {sup 1}H-{sup 1}H dipolar contacts have limited the utility of traditional NMR approaches. Selective isotope labeling, including nucleotide-specific and segmental labeling strategies, may provide the best opportunities for obtaining structural information by NMR. Here we review methods that have been developed for preparing and purifying isotopically labeled RNAs, as well as NMR strategies that have been employed for signal assignment and structure determination.

2010-01-15

284

YAPI, a New Yersinia pseudotuberculosis Pathogenicity Island

Gamma-ray burst (GRB) is one of the candidates of high-energy cosmic-ray acceleration sites. They may be also ultra-high-energy (above 3 EeV) cosmic-ray (UHECR) sources. In this paper, we discuss possibilities and implications of high-energy cosmic-ray acceleration in GRBs. (1) First, we show that not only protons but also heavier nuclei can be accelerated up to ultra-high energies in both usual high-luminosity (HL) and low-luminosity (LL) GRBs by using the Geant4. LL GRBs may also make a significant contribution to the observed UHECR flux if they form a distinct population, and we investigate cosmic-ray acceleration in LL GRBs in detail. (2) Second, we discuss implications of the GRB-UHECR hypothesis (and Hypernova-UHECR hypothesis) to cosmic-ray astronomy. HL GRBs and LL GRBs will lead to different source number densities as UHECR sources, so that the determination of the number density of UHECR sources and strength of the mean extragalactic magnetic field (EGMF) will give us useful ...

2008-01-01

285

Use of synthetic oligoribonucleotides to probe RNA-protein interactions in the MS2 translational operator complex.

Pathogenicity islands (PAIs) are chromosomal clusters of pathogen-specific virulence genes often found at tRNA loci. In the Yersinia pseudotuberculosis 32777 chromosome, we characterized...Full Text Available

2004-08-01

286

Use of synthetic oligonucleotide DNA probes for identification and direct detection of Bacteroides forsythus in plaque samples.

Synthetic oligoribonucleotides have been used to probe the interaction of MS2 coat protein with the translational operator of the MS2 replicase gene. We have investigated the possible formation of a...Full Text Available

1990-06-25

287

Two separate domains within vesicular stomatitis virus phosphoprotein support transcription when added in trans.

Oligonucleotide DNA probes complementary to the hypervariable region of the 16S rRNA of Bacteroides forsythus were tested for their specificity and sensitivity against reference and clinical isolates...Full Text Available

1991-10-01

288

Two Proline-Rich Nuclear Localization Signals in the Amino- and Carboxyl-Terminal Regions of the Borna Disease Virus Phosphoprotein

The structural phosphoprotein NS of vesicular stomatitis virus, in association with the virion-associated RNA polymerase L protein, transcribes the genome ribonucleoprotein template in vitro. It contains...Full Text Available

1987-12-01

289

Translation Elongation Factor 1A Facilitates the Assembly of the Tombusvirus Replicase and Stimulates Minus-Strand Synthesis

Borna disease virus (BDV) uses a unique strategy of replication and transcription which takes place in the nucleus, unlike other known, nonsegmented, negative-stranded RNA viruses of animal origin....Full Text Available

1998-12-01

290

Towards computational prediction of microRNA function and activity

Replication of plus-strand RNA viruses depends on host factors that are recruited into viral replicase complexes. Previous studies showed that eukaryotic translation elongation factor (eEF1A) is one...Full Text Available

2010-11-01

291

Time course profiling of the retinal transcriptome after optic nerve transection and optic nerve crush

While it has been established that microRNAs (miRNAs) play key roles throughout development and are dysregulated in many human pathologies, the specific processes and pathways regulated by individual...Full Text Available

2010-08-01

292

Synaptic Signaling and Aberrant RNA Splicing in Autism Spectrum Disorders

PurposeA time-course analysis of gene regulation in the adult rat retina after intraorbital nerve crush (IONC) and intraorbital nerve transection (IONT).MethodsRNA...Full Text Available

293

Subcellular Localization of Expansin mRNA in Xylem Cells12

Interactions between presynaptic and postsynaptic cellular adhesion molecules (CAMs) drive synapse maturation during development. These trans-synaptic interactions are regulated by alternative splicing...Full Text Available

294

Species-specific microRNA roles elucidated following astrocyte activation

Terminal differentiation of many vascular cells involves cell wall changes. Cells first elongate their primary wall, then lay down a lignified secondary wall, which is often followed by digestion of...Full Text Available

2000-06-01

295

Slug down-regulation by RNA interference inhibits invasion growth in human esophageal squamous cell carcinoma

MicroRNAs (miRNAs) are short non-coding RNAs that play a central role in regulation of gene expression by binding to target genes. Many miRNAs were associated with the function of the central nervous...Full Text Available

2011-05-01

296

Selective Degradation of Newly Synthesized Nonmessenger Simian Virus 40 Transcripts

BackgroundEsophageal squamous cell carcinoma (ESCC) is one of the most aggressive carcinomas of the gastrointestinal tract. We assessed the relevance of Slug in measuring the invasive...Full Text Available

297

SWISS MADE: Standardized WithIn Class Sum of Squares to Evaluate Methodologies and Dataset Elements

By pretreating simian virus 40-infected BSC-1 cells with glucosamine, [³H]uridine labeling of both cellular and viral RNA can be halted instantaneously by addition of cold uridine. We have...Full Text Available

1978-11-01

298

Role of microRNA-23b in flow-regulation of Rb phosphorylation and endothelial cell growth

Contemporary high dimensional biological assays, such as mRNA expression microarrays, regularly involve multiple data processing steps, such as experimental processing, computational processing, sample...Full Text Available

299

RNA:DNA Ratio and Other Nucleic Acid Derived Indices in Marine Ecology

MicroRNAs (miRs) can regulate many cellular functions, but their roles in regulating responses of vascular endothelial cells (ECs) to mechanical stimuli remain unexplored. We hypothesize that the physiological...Full Text Available

2010-02-16

300

RNA recognition by the embryonic cell fate determinant and germline totipotency factor MEX-3

Some of most used indicators in marine ecology are nucleic acid-derived indices. They can be divided by target levels in three groups: 1) at the organism level as ecophysiologic indicators, indicators...Full Text Available

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301

RNA expression in a cartilaginous fish cell line reveals ancient 3? noncoding regions highly conserved in vertebrates

Totipotent stem cells have the potential to differentiate into every cell type. Renewal of totipotent stem cells in the germline and cellular differentiation during early embryogenesis rely upon posttranscriptional...Full Text Available

2009-12-01

302

Profiling highly conserved microrna expression in recombinant IgG-producing and parental Chinese hamster ovary cells

We have established a cartilaginous fish cell line [Squalus acanthias embryo cell line (SAE)], a mesenchymal stem cell line derived from the embryo of an elasmobranch, the spiny dogfish...Full Text Available

2007-01-23

303

British Library Electronic Table of Contents (United Kingdom)

Abstract MicroRNAs (miRNAs) play important roles in global gene regulation. Researchers in recombinant protein production have proposed miRNAs as biomarkers and cell engineering targets. However, miRNA expression remains understudied in Chinese Hamster Ovary cells, one of the most commonly used host cell systems for therapeutic protein production. To profile highly conserved miRNA expression, we used the miRCURY- miRNA array for screening miRNAs in CHO cells. The selection criteria for further miRNA profiling included positive hybridization signals and experimentally validated predicted regulatory targets. On the basis of screening, we selected 16 miRNAs for quantitative RT-PCR profiling. We profiled miR expression in parental CHO DG44 and CHO K1 cell lines as well as four recombinant DG44...

2011-01-01

304

Production of dissolved DNA, RNA, and protein by microbial populations in a Florida reservoir.

Polymorphisms in IRF7 reduce IFN? responses of pDCs to HIV-1

Production of dissolved macromolecules by ambient autotrophic and heterotrophic microbial populations was measured in a eutrophic Florida reservoir by in situ labeling with various radioactive substrates....Full Text Available

1990-10-01

305

Perinuclear P granules are the principal sites of mRNA export in adult C. elegans germ cells

Recognition of HIV-1 ssRNA by TLR7 induces the production of the pro-inflammatory cytokines that may contribute to the systemic immune activation associated with HIV-1 disease progression. Here...Full Text Available

2011-03-13

306

PCR-based method for targeting 16S-23S rRNA intergenic spacer regions among Vibrio species

Germline-specific granules of unknown function are found in a wide variety of organisms, including C. elegans, where they are called P granules. P granules are cytoplasmic bodies...Full Text Available

2010-04-15

307

Northern blotting analysis of microRNAs, their precursors and RNA interference triggers

BackgroundThe genus Vibrio is a diverse group of Gram-negative bacteria comprised of 74 species. Furthermore, the genus has and is expected to continue expanding...Full Text Available

308

NASA/CR--- _'j_.,- 207636 - NASA Technical Report Server (NTRS)

BackgroundNumerous microRNAs (miRNAs) have heterogeneous ends resulting from imprecise cleavages by processing nucleases and from various non-templated nucleotide additions. The...Full Text Available

309

Modulation of the human hair follicle pigmentary unit by corticotropin-releasing hormone and urocortin peptides

adenines, like adenine itself, may fllerefore have played an important role in the. RNA world. Griffin, B.E., Haslam, W.J., Reese, C. B.: 1964, J. Mo/. ...

310

Modeling RNA polymerase competition: the effect of ?-subunit knockout and heat shock on gene transcription level

Human skin is a local source of corticotropin-releasing hormone (CRH) and expresses CRH and CRH receptors (CRH-R) at mRNA and protein levels. Epidermal melanocytes respond to CRH by induction...Full Text Available

2006-05-01

311

Miranda as a multidomain adapter linking apically localized Inscuteable and basally localized Staufen and Prospero during asymmetric cell division in Drosophila

BackgroundModeling of a complex biological process can explain the results of experimental studies and help predict its characteristics. Among such processes is transcription in...Full Text Available

312

MAPPING THE INITIATOR BINDING TAF2 SUBUNIT IN THE STRUCTURE OF HYDRATED YEAST TFIID

Neuroblasts in the developing Drosophila CNS asymmetrically localize the cell fate determinants Numb and Prospero as well as prospero RNA to the basal cortex during...Full Text Available

1998-06-15

313

Intact A?-fibers up-regulate TRPA1 and contribute to cold hypersensitivity in neuropathic rats

SummaryThe general transcription factor TFIID is a large multi-subunit complex required for the transcription of most protein-encoding genes by RNA polymerase II. Taking advantage...Full Text Available

2009-03-11

314

Insertion in the mRNA of a metachromatic leukodystrophy patient with sphingolipid activator protein-1 deficiency.

Mechanisms underlying cold hypersensitivity in neuropathic states are unclear. Recent data indicate both TRPM8 and TRPA1 play a role. In relation to TRPA1, there are reported increases in mRNA....Full Text Available

2008-06-26

315

In vitro selection of RNA molecules that displace cocaine from the membrane-bound nicotinic acetylcholine receptor

The lysosomal catabolism of sulfatide requires arylsulfatase A and a specific sphingolipid activator protein, SAP-1. While most patients with metachromatic leukodystrophy have mutations in the gene...Full Text Available

1990-02-01

316

Hyperoxia enhances VEGF release from A549 cells via post-transcriptional processes

The nicotinic acetylcholine receptor (AChR) controls signal transmission between cells in the nervous system. Abused drugs such as cocaine inhibit this receptor. Transient kinetic investigations indicate...Full Text Available

1998-11-24

317

Human Immunodeficiency Virus type-1 reverse transcriptase exists as post-translationally modified forms in virions and cells

Exposure of animals to hyperoxia decreases lung VEGF mRNA expression concomitant with an acute increase in VEGF protein within the epithelial lining fluid (ELF). The VEGF concentration in ELF...Full Text Available

2007-09-01

318

General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq

BackgroundHIV-1 reverse transcriptase (RT) is a heterodimer composed of p66 and p51 subunits and is responsible for reverse transcription of the viral RNA genome into DNA. RT can...Full Text Available

319

Gene expression analysis of interferon ? in laser capture microdissected cervical epithelium

BackgroundSpecies with heteromorphic sex chromosomes face the challenge of large-scale imbalance in gene dose. Microarray-based studies in several independent male heterogametic...Full Text Available

320

Expression profiles of precursor and mature microRNAs under dehydration and high salinity shock in Populus euphratica

Optimal sample handling techniques for tissue preparation and storage, RNA extraction and quantification, and target gene detection are crucial for reliable gene expression analysis. Methods...Full Text Available

2008-10-01

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321

British Library Electronic Table of Contents (United Kingdom)

MicroRNAs (miRNAs) are small non-coding RNAs that play vital roles in plant abiotic stress responses via cleavage or translational inhibition of their target mRNAs. Populus euphratica is a typical stress-resistant sessile organism that grows in desert areas. Here, we identified sequences of 12 miRNA precursors from 11 families and 13 mature miRNAs from 12 families by PCR amplification in P. euphratica. To detect expression differences in mature miRNAs and their precursors under dehydration and high salinity shock in P. euphratica, we examined 14 miRNA precursors from 13 miRNA families and 17 mature miRNAs from 17 miRNA families using the SYBR Green RT?PCR assay. This is the first report of expression profiles for both precursor and mature miRNAs in P. euphratica. By profiling both the matu...

2011-01-01

322

Engineering ligand-responsive RNA controllers in yeast through the assembly of RNase III tuning modules

Effect of hypophysectomy on liver nuclear ribonucleic acid synthesis in aging rats.

The programming of cellular networks to achieve new biological functions depends on the development of genetic tools that link the presence of a molecular signal to gene-regulatory activity. Recently,...Full Text Available

2011-07-01

323

Ectopic Expression of Constitutively Activated RACB in Barley Enhances Susceptibility to Powdery Mildew and Abiotic Stress1

Changes in RNA synthesis in liver nuclei were observed at different ages and after hypophysectomy and hormone replacement in female Sprague-Dawley rats. As determined by the incorporation of [3H]UMP...Full Text Available

1979-12-15

324

Direct Evidence for Postmeiotic Transcription During Drosophila melanogaster Spermatogenesis

Small RAC/ROP-family G proteins regulate development and stress responses in plants. Transient overexpression and RNA interference experiments suggested that the barley (Hordeum vulgare)...Full Text Available

2005-09-01

325

Differential recognition of viral RNA by RIG-I

Extensive gene expression during meiosis is a hallmark of spermatogenesis. Although it was generally accepted that RNA transcription ceases during meiosis, recent observations suggest that some transcription...Full Text Available

2010-09-01

326

Defects in the Secretory Pathway and High Ca²⁺ Induce Multiple P-bodies

Retinoic acid inducible gene I (RIG-I) is a pattern recognition receptor (PRR) responsible for detection of nucleic acids from pathogens in the cytoplasm of infected cells and induction of type I interferon...Full Text Available

2011-03-01

327

Defective hepatitis B virus particles are generated by packaging and reverse transcription of spliced viral RNAs in vivo.

mRNA is sequestered and turned over in cytoplasmic processing bodies (PBs), which are induced by various cellular stresses. Unexpectedly, in Saccharomyces cerevisiae, mutants of the...Full Text Available

2010-08-01

328

Conserved Alternative Splicing and Expression Patterns of Arthropod N-Cadherin

Generation of replicative defective viruses is frequently observed during viral infections. We now report that encapsidation and reverse transcription of spliced viral RNA is an additional mechanism...Full Text Available

1991-10-01

329

Complexity of the microRNA repertoire revealed by next-generation sequencing

Metazoan development requires complex mechanisms to generate cells with diverse function. Alternative splicing of pre-mRNA not only expands proteomic diversity but also provides a means to regulate...Full Text Available

2009-04-01

330

Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA

MicroRNAs (miRNAs) have been implicated to play key roles in normal physiological functions, and altered expression of specific miRNAs has been associated with a number of diseases. It is of great interest...Full Text Available

2010-11-01

331

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

RNAs transcribed from the mitochondrial genome of Physarum polycephalum are heavily edited. The most prevalent editing event is the insertion of single Cs, with Us and dinucleotides...Full Text Available

2011-08-01

332

Coat protein gene duplication in a filamentous RNA virus of plants.

BackgroundStructured noncoding RNAs perform many functions that are essential for protein synthesis, RNA processing, and gene regulation. Structured RNAs can be detected by comparative...Full Text Available

2010-01-01

333

Characterization of the Molecular Mechanism of Defective Interfering RNA-Mediated Symptom Attenuation in Tombusvirus-Infected Plants

Computer-assisted analysis revealed a striking sequence similarity between the putative 24-kDa protein (p24) encoded by open reading frame (ORF) 5 of beet yellows closterovirus and the coat protein...Full Text Available

1992-10-01

334

Cbk1 regulation of the RNA binding protein Ssd1 integrates cell fate with translational control

Different tombusviruses were able to support the replication of either homologous or heterologous defective interfering (DI) RNAs, and those infected plants usually developed typical attenuated symptoms....Full Text Available

1998-07-01

335

Avian Nephritis Virus (ANV) as a New Member of the Family Astroviridae and Construction of Infectious ANV cDNA

SummarySpatial control of gene expression, at the level of both transcription and translation, is critical for cellular differentiation [1-Full Text Available

2009-12-29

336

Association of Unique, Isolated Treponemes with Bovine Digital Dermatitis Lesions?

The complete RNA genome of the avian nephritis virus (ANV) associated with acute nephritis in chickens has been molecularly cloned and sequenced. Excluding the poly(A) tail, the genome comprises 6,927...Full Text Available

2000-09-01

337

Assessing phytoremediation potentials of selected tropical plants for acrylamide

This study used a PCR-based approach targeting 16S rRNA gene fragments to determine the occurrence and association of the three bovine digital dermatitis (BDD) treponeme phylogroups within lesions found...Full Text Available

2009-03-01

338

Amber suppression in Escherichia coli by unusual mitochondria-like?transfer?RNAs

In biotechnology, acrylamide is being used in DNA and RNA analysis using the polyacrylamide gel electrophoreses procedure. Polymerized acrylamide is degraded into acrylamide through time; it is converted into a hazardous contaminant that is carcinogenic and neurotoxic to animals and humans. Because ...

339

A small RNA promotes siderophore production through transcriptional and metabolic remodeling

The “cloverleaf” base-pairing pattern was established as the structural paradigm of active tRNA species some 30 years ago. Nevertheless, this pattern does not accommodate the folding...Full Text Available

1998-02-17

340

A retinoid responsive cytokine gene, MK, is preferentially expressed in the proximal tubules of the kidney and human tumor cell lines.

Siderophores are essential factors for iron (Fe) acquisition in bacteria during colonization and infection of eukaryotic hosts, which restrain iron access through iron-binding protein, such as lactoferrin...Full Text Available

2010-08-24

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341

A T to A base substitution and small deletions in the conalbumin TATA box drastically decrease specific in vitro transcription.

The aim of this study was to survey the expression of an embryonic cytokine gene, MK, in the normal organs and neoplastic tissues of adults. Northern analysis showed that MK mRNA was exclusively expressed...Full Text Available

1993-02-01

342

A Curated Database of miRNA Mediated Feed-Forward Loops Involving MYC as Master Regulator

We have previously shown that a T to G transversion at the second T of the conalbumin "TATA" box drastically decreases specific initiation of transcription by RNA polymerase B (1). We now report that...Full Text Available

1981-04-24

343

A Cellular J-Domain Protein Modulates Polyprotein Processing and Cytopathogenicity of a Pestivirus

BackgroundThe MYC transcription factors are known to be involved in the biology of many human cancer types. But little is known about the Myc/microRNAs cooperation in the regulation...Full Text Available

344

The nucleotide sequence of a major species of leucine tRNA from bovine liver.

Pestiviruses are positive-strand RNA viruses closely related to human hepatitis C virus. Gene expression of these viruses occurs via translation of a polyprotein, which is further processed by cellular...Full Text Available

2001-10-01

345

The effect of mitochondrial dysfunction on cytosolic nucleotide metabolism

Through the use of a variety of post-labeling techniques, the nucleotide sequence of a major species of leucine tRNA from bovine liver was determined to be pG-G-U-A-G-C-G-U-G-m-G-C-ac-C-G-A-G-C-G-G-D-C-psi-A-A-G-G-C-m-G-C-U-G-G-A-psim-...Full Text Available

1980-02-25

346

DEFF Research Database (Denmark)

Several enzymes of the metabolic pathways responsible for metabolism of cytosolic ribonucleotides and deoxyribonucleotides are located in mitochondria. Studies described in this paper suggest dysfunction of the mitochondria to affect these metabolic pathways and limit the available levels of cytosolic ribonucleotides and deoxyribonucleotides, which in turn can result in aberrant RNA and DNA synthesis. Mitochondrial dysfunction has been linked to genomic instability, and it is possible that the limiting effect of mitochondrial dysfunction on the levels of nucleotides and resulting aberrant RNA and DNA synthesis in part can be responsible for this link. This paper summarizes the parts of the metabolic pathways responsible for nucleotide metabolism that can be affected by mitochondrial dysfunction.

2010-01-01

347

Ionization and fragmentation of DNA, RNA bases induced by proton impact

An experimental investigation of the Hahn-Noll revenue neutral auction for emissions licenses

We present recent results obtained in the Toulouse's group that deal with proton to base and nucleoside interactions. We stress the weakness of the sugar part in the nucleoside, i.e. the uridine molecule under scrutiny. Since some parts of the fragmentation spectrum correspond to the fragmentation of a 'pure' uracil molecule, i.e. the RNA base, an 'additivity rule' seems to prevail for the nucleoside, something that still has to be confirmed. Moreover, some results that deal with the secondary electronic emission from uracil are also displayed.

2008-02-01

348

[mRNA level and cytochrome P450 1A activity in the liver of C57BL mice induced by various xenobiotics].

This paper reports on three series of laboratory experiments designed to test the performance of the Hahn-Noll revenue neutral auction (RNA). An alternative institution, a no-rebate uniform price auction (UPA), is also examined as a benchmark. In these experiments, the RNA markets were little different from UPA markets in terms of either prices or market efficiencies. The two institutions did differ in terms of the distribution of the gains from exchange and of the propensity of bidders to engage in a certain type of overbidding. 25 refs., 13 figs., 3 tabs.

1993-01-01

349

Effects of low-intensity prolonged exercise on PGC-1 mRNA expression in rat epitrochlearis muscle.

The rate of hepatic cytochrome P450 Cypla1 and Cyp1a2 induction was investigated in C57BL male mice during induction with o-aminoazotoluene (OAT), benzo[a]pyrene (BP) and 1,4-dihydroxyanthraquinone (AQ). The Cypla1 mPNA level determined by quantitative RT-competitive PCR increased more than three orders of magnitude during induction with OAT and BP compared with untreated animals and remained unchanged during induction with AQ. The Cypla2 mRNA level was only 8.5, 18.7 and 1.9 times higher during induction with OAT, BP and AQ respectively than in untreated mice. At the same time 7-Ethoxyresorufin-O-deethylase (EROD) and 7-Methoxyresorufin-O-demethylase (MROD) activities of Cypla were also investigated in liver. The increase of Cypla1 mRNA level correlated with the increase of EROD activity. This suggests involvement of the transcriptional mechanism of the inducibility of this enzyme. In the case of Cypla2 there was insignificant increase of its ...

350

Expression of bacterial luciferase in eukaryotic cells

We previously reported that the peroxisome proliferator-activated receptor gamma coactivator-1 (PGC-1) mRNA in rat epitrochlearis muscle was increased after swimming exercise training. In the present study, we demonstrated further that PGC-1 mRNA expression in the epitrochlearis muscle of 4-5-week-old male Sprague-Dawley rats was increased after a 6-h acute bout of low-intensity swimming exercise. With this increase, the expression level was approximately 8-fold of control and immersion group rats that stayed for 6-h in warm water, maintained at the identical temperature of the swimming barrel (35 degrees C) (p<0.01). Second, PGC-1 mRNA expression in the muscle was found to have increased 6-h after 30 10-s tetani contractions were induced by in vitro electrical stimulation. Finally, PGC-1 mRNA expression in the muscle incubated for 18-h with 0.5mM 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR: ...

2002-08-16

351

Steady-state levels of G-protein beta-subunit expression are regulated by treatment of cells with bacterial toxins

Expression of Bacterial luciferase enzyme (lux) in mammalian cells would be a powerful bioreporter protein system for in vivo imaging because eukaryotic luciferases need expensive substrates. However, only a few efforts have been made to express bacterial luciferase enzyme in mammalian cells. As the result of this, we attempted to construct bicistronic vector including two bacterial luciferase genes (LuxA and LuxB) for assessing the potential to be visualized in vitro or in vivo by optical imaging system after transfection to mammalian cells. We designed and synthesized luxA and luxB genes from Photorhabdus Luminescens. To co-express both luxA and luxB genes from a single promoter, we cloned as a bicistronic transcript fused with an internal ribosomal entry site (IRES). This bicistronic transcript was transfected by Superfect to HEK 293T cell line. We also transfected lux A and lux B vector to HEK 293T cells separately. To ...

2005-11-18

352

Quantification of antibiotic drug potency by a two-compartment radioassay of bacterial growth

Cultures of 3T3-L1 cells were incubated with either 10 ng/ml cholera toxin or 10 ng/ml pertussis toxin from 4 days prior to the initiation of differentiation and throughout the subsequent incubation. Toxin concentrations were sufficient to completely prevent the labelling of alpha-subunits with ["3"2P]NAD"+ and pertussis toxin and to prevent by more than 90% the labelling with ["3"2P]NAD"+ and cholera toxin in membranes prepared from these cells. Neither toxin prevented the differentiation to the adipocyte phenotype. Neither toxin prevented the increases in the relative amounts of G-proteins which occur upon differentiation. Both toxins dramatically decreased the amount of beta-subunits. As measured by quantitative immunoblotting with antisera specific for both the 35 kDa and 36 kDa beta-subunits, levels of beta-subunit were decreased by more than 50% of steady-state level of control cells. Thus, bacterial toxins which modifies G-protein alpha-subunits are capable ...

1987-06-07

353

Comparison of newer synthetic and biological wound dressings.

The two-compartment radioassay for microbial kinetics based on continuous measurement of the {sup 14}CO{sub 2} released by bacterial metabolism of 14C-labeled substrate offers a valuable approach to testing the potency of antimicrobial drugs. By using a previously validated radioassay with gram-positive and gram-negative bacteria, a group of protein synthesis inhibitors was evaluated for their effect on microbial growth kinetics. All tested drugs induced changes in both the slopes and intercepts of the growth curves. An exponential growth model was applied to quantify the drug effect on the processes of bacterial {sup 14}CO{sub 2} liberation and cell generation. The response was measured in terms of a generation rate constant. A linear dependence of the generation rate constant on the dose of spectinomycin was observed with Escherichia coli. Sigmoidal-shaped curves were found in the assays of chloramphenicol and tetracycline. The implications ...

1990-06-01

354

Analysis of S-adenosylmethionine and related sulfur metabolites in bacterial isolates of Pseudomonas aeruginosa (BAA-47) by liquid chromatography/electrospray ionization coupled to a hybrid linear quadrupole ion trap and Fourier transform ion cyclotron resonance mass spectrometry

In 18 piglets, weighing 10-15 kg, third-degree burns or full-thickness skin excisions of 4 X 4 cm were inflicted. The effect of five dressing materials on adhesiveness to the wounds, appearance, conformability, wound contraction, bacterial count, and morphology of the wound was studied at the end of the seventh and fourteenth days without dressing changes. In 11 piglets with a burn wound, the most adherent dressing was collagen sponge(CS), followed by polyurethane sponge (PU), pigskin xenograph (PS), and xeroform. CS more effectively debrided the wound from coagulated necrotic tissue than the other dressings. Wound contraction was maximal with CS dressing (52%), followed by PU (44%), xeroform (32%), and PS (27%). In another seven piglets with full-thickness excised wounds, a velour dressing made of polytetrafluoroethylene (PTFE) or PU adhered significantly more than CS or PS. Wound contraction was greater with CS (37%) or PTFE (35%) than with PS (23%) or PU (18%). ...

1981-06-01

355

British Library Electronic Table of Contents (United Kingdom)

A comprehensive and highly selective method for detecting in bacterial supernatants a modified sulfur nucleoside, S-adenosyl-L-methionine (SAM), and its metabolites, i.e., S-adenosylhomocysteine (SAH), adenosine (Ado), 5prime-deoxy-5prime-methylthioadenosine (MTA), adenine (Ade), S-adenosyl-methioninamine (dcSAM), homocysteine (Hcy) and methionine (Met), was developed. The method is based on reversed-phase liquid chromatography with positive electrospray ionization (ESI+) coupled to a hybrid linear quadrupole ion trap (LTQ) and 7-T Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). A gradient elution was employed with a binary solvent of 0.05 M ammonium formate at pH 4 and acetonitrile. The assay involves a simultaneous cleanup of cell-free bacterial broths by solid-pha...

2009-01-01

356

Effects of human serum on bacterial competition with neutrophils for molecular oxygen.

Vaginal Matrix Metalloproteinase Levels in Pregnant Women With Bacterial Vaginosis

A dialyzable factor(s) in human serum is known to stimulate gonococcal oxygen consumption. Its effect on other human pathogens was investigated. A 10% serum solution increased peak O2 consumption for Escherichia coli and Staphylococcus aureus to 157% (P less than 0.05) and 199% (P less than 0.02), respectively, of their O2 consumption when suspended in Hanks balanced salt solution, compared with a 356% increase for Neisseria gonorrhoeae with serum. Dialyzed serum lacked stimulatory capacity. Bacteria, serum, and neutrophils are often incubated to evaluate neutrophil bactericidal activity. Samples of 10(8) N. gonorrhoeae, S. aureus, and E. coli turned resazurin colorless (anaerobic conditions, Eh less than -42 mV) after 7.4, 13.3, and 15.1 min, respectively. Because neutrophil formation of reactive oxygen intermediates requires ambient O2, the effect of live bacteria and serum on this process was explored. After 5 min of incubation of 10(8) N. gonorrhoeae or S. aureus in 10% normal or ...

1986-06-01

357

British Library Electronic Table of Contents (United Kingdom)

Objective To compare matrix metalloproteinase (MMP)-8 and MMP-9 levels in the vaginal secretions of pregnant women with or without asymptomatic bacterial vaginosis (BV). Methods In this study, vaginal levels and molecular forms of MMP-8 and MMP-9 were studied in 36 pregnant women between 28 and 34 weeks of gestation with asymptomatic BV and 41 pregnant women, matched for gestational age, without BV. Results Vaginal MMP-8 concentrations were significantly higher (P = .023) in BV-positive women. There was no significant difference in MMP-9 levels between healthy pregnant controls and BV-positive pregnant women. The presence of MMP-8 was confirmed by a 38-kd band on Western blots. Conclusions Our findings show that BV is associated with increased levels of MMP-8 in vaginal fluid. Increased pr...

2006-01-01

358

Testing an agent-based model of bacterial cell motility: How nutrient concentration affects speed distribution

British Library Electronic Table of Contents (United Kingdom)

We revisit a recently proposed agent-based model of active biological motion and compare its predictions with own experimental findings for the speed distribution of bacterial cells, Salmonella typhimurium. Agents move according to a stochastic dynamics and use energy stored in an internal depot for metabolism and active motion. We discuss different assumptions of how the conversion from internal to kinetic energy d(v) may depend on the actual speed, to conclude that d 2 v ? with either ? = 2 or 1 ? < 2 are promising hypotheses. To test these, we compare the model?s prediction with the speed distribution of bacteria which were obtained in media of different nutrient concentration and at different times. We find that both hypotheses are in line with the experimental observations, with ? bet...

2011-01-01

359

Synergistic interaction of eugenol with antibiotics against Gram negative bacteria

British Library Electronic Table of Contents (United Kingdom)

Eugenol, the principal chemical component of clove oil from Eugenia aromatica has been long known for its analgesic, local anesthetic, anti-inflammatory, and antibacterial effects. The interaction of the eugenol with ten different hydrophobic and hydrophilic antibiotics was studied against five different Gram negative bacteria. The MIC of the combination was found to decrease by a factor of 5-1000 with respect to their individual MIC. This synergy is because of the membrane damaging nature of eugenol, where 1mM of its concentration is able to damage nearly 50% of the bacterial membrane. Eugenol was also able to enhance the activities of lysozyme, Triton X-100 and SDS in damaging the bacterial cell membrane. The hydrophilic antibiotics such as vancomycin and b-lactam antibiotics which have ...

2009-01-01

360

Susceptibility to invasive bacterial infections in children with sickle cell disease

British Library Electronic Table of Contents (United Kingdom)

Individuals with sickle cell disease (SCD) demonstrate an increased susceptibility to invasive bacterial infections (IBI). The most common organisms causing IBI are Streptococcus pneumoniae, nontyphi Salmonella species and Haemophilus influenzae type b (Hib). IBI are the most common causes of death in children below 5 years of age with SCD. Increased susceptibility to IBI is because of several factors including dysfunctional antibody production and opsonophagocytosis as well as defective splenic clearance. Early diagnosis of Hib and pneumococcal infections combined with antibiotic prophylaxis and immunization programs, could lead to significant improvements in mortality, especially in Africa. Pediatr Blood Cancer. 2010;55:401-406. Copyright 2010 Wiley-Liss, Inc.

2010-01-01

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361

Regulation and secretion of Xanthomonas virulence factors

British Library Electronic Table of Contents (United Kingdom)

Abstract Plant pathogenic bacteria of the genus Xanthomonas cause a variety of diseases in economically important monocotyledonous and dicotyledonous crop plants worldwide. Successful infection and bacterial multiplication in the host tissue often depend on the virulence factors secreted including adhesins, polysaccharides, LPS and degradative enzymes. One of the key pathogenicity factors is the type III secretion system, which injects effector proteins into the host cell cytosol to manipulate plant cellular processes such as basal defense to the benefit of the pathogen. The coordinated expression of bacterial virulence factors is orchestrated by quorum-sensing pathways, multiple two-component systems and transcriptional regulators such as Clp, Zur, FhrR, HrpX and HpaR. Furthermore, virule...

2010-01-01

362

Nationwide surveillance of bacterial respiratory pathogens conducted by the Japanese Society of Chemotherapy in 2008: general view of the pathogens? antibacterial susceptibility

British Library Electronic Table of Contents (United Kingdom)

For the purpose of nationwide surveillance of the antimicrobial susceptibility of bacterial respiratory pathogens collected from patients in Japan, the Japanese Society of Chemotherapy conducted a third year of nationwide surveillance during the period from January to April 2008. A total of 1,097 strains were collected from clinical specimens obtained from well-diagnosed adult patients with respiratory tract infections. Susceptibility testing was evaluable with 987 strains (189 Staphylococcus aureus, 211 Streptococcus pneumoniae, 6 Streptococcus pyogenes, 187 Haemophilus influenzae, 106 Moraxella catarrhalis, 126 Klebsiella pneumoniae, and 162 Pseudomonas aeruginosa). A total of 44 antibacterial agents, including 26 ?-lactams (four penicillins, three penicillins in combination with ?-lacta...

2011-01-01

363

Leaching of zinc sulfide by Thiobacillus ferrooxidans: Bacterial oxidation of the sulfur product layer increases the rate of zinc sulfide dissolution at high concentrations of ferrous ions

In situ synthesis of silver chloride nanoparticles into bacterial cellulose membranes

This paper reports the results of leaching experiments conducted with and without Thiobacillus ferroxidans at the same conditions in solution. The extent of leaching of ZnS with Bacteria is significantly higher than that without bacteria at high concentrations of ferrous ions. A porous layer of elemental sulfur is present on the surfaces of the chemically leached particles, which no sulfur is present on the surfaces of the bacterially leached particles. The analysis of the data using the shrinking-core model shows that the chemical leaching of ZnS is limited by the diffusion of ferrous ions through the sulfur product layer at high concentrations of ferrous ions. The analysis of the data shows that diffusion through the product layer does not limit the rate of dissolution when bacteria are present. This suggests that the action of T.ferroxidans in oxidizing the sulfur formed on the particle surface is to remove the barrier to diffusion by ferrous ions.

1999-12-01

364

British Library Electronic Table of Contents (United Kingdom)

In situ synthesis of silver chloride (AgCl) nanoparticles was carried out under ambient conditions in nanoporous bacterial cellulose (BC) membranes as nanoreactors. The growth of the nanoparticles was readily obtained by alternating dipping of BC membranes in the solution of silver nitrate or sodium chloride followed by a rinse step. X-ray diffraction (XRD) patterns indicated the existence of AgCl nanoparticles in the BC and scanning electron microscopy (SEM) images showed that the AgCl nanoparticles well dispersed on the surface of BC and penetrated into the BC network. The AgCl nanoparticle-impregnated BC membranes exhibited high hydrophilic ability and strong antimicrobial activity against Escherichia coli (Gram-negative) and Staphylococcus aureus (Gram-positive). The preparative proced...

2009-01-01

365

Comparison of iodine and glutaraldehyde as surface disinfectants for red porgy (Pagrus pagrus) and white sea bream (Diplodus sargus sargus) eggs

British Library Electronic Table of Contents (United Kingdom)

Abstract The efficacy of iodine and glutaraldehyde as fish egg surface disinfectants were assessed in red porgy (Pagrus pagrus) and white sea bream (Diplodus sargus sargus) eggs, two species of interest for Mediterranean aquaculture. Iodine was effective in reducing the bacterial load of the 1-day-old eggs when applied at 50 mg L-1 for 5 min. The same concentration did not cause any significant change in hatching success or survival of the larvae for the first 5 days. Glutaraldehyde failed to reduce the bacterial load of the fish eggs at concentrations that were safe for the eggs (100 mg L-1 for 5 min), as it had a significant effect in preventing hatching of the developed embryo. Disinfecting 0-day-old eggs with iodine resulted in a significant reduction of hatching percentage, while larv...

2007-01-01

366

Biosorption of lead from aqueous solutions by Bacillus strains possessing heavy-metal resistance

British Library Electronic Table of Contents (United Kingdom)

In this study, bacterial strains were investigated in order to determine their heavy metal tolerance. The bacterial strains were identified as Bacillus cereus and Bacillus pumilus. In the batch system, the effects of operating variables such as solution pH, initial metal concentration, contact time, and adsorbent dosage were investigated. Both isolates were highly resistance to copper and lead in comparison with the control strain examined. The adsorption capacities of B. cereus and B. pumilus were found to be 22.1mg/g and 28.06mg/g, respectively. The biosorption follows pseudo-second order kinetics and the isotherm fits well to the Langmuir isotherm model. In column experiments, the biosorption was fitted well by the Thomas model. The breakthrough and exhaustion capacity of each biosorben...

2011-01-01

367

Aerogels from Unaltered Bacterial Cellulose: Application of scCO2 Drying for the Preparation of Shaped, Ultra-Lightweight Cellulosic Aerogels

British Library Electronic Table of Contents (United Kingdom)

Bacterial cellulose produced by the gram-negative bacterium Gluconacetobacter xylinum was found to be an excellent native starting material for preparing shaped ultra-lightweight cellulose aerogels. The procedure comprises thorough washing and sterilization of the aquogel, quantitative solvent exchange and subsequent drying with supercritical carbon dioxide at 40 degreeC and 100 bar. The average density of the obtained dry cellulose aerogels is only about 8 mg cm-3 which is comparable to the most lightweight silica aerogels and distinctly lower than all values for cellulosic aerogels obtained from plant cellulose so far. SEM, ESEM and nitrogen adsorption experiments at 77 K reveal an open-porous network structure that consists of a comparatively high percentage of large mesopores and small...

2010-01-01

368

Ability of a ?minimum?? microbial food web model to reproduce response patterns observed in mesocosms manipulated with N and P, glucose, and Si

British Library Electronic Table of Contents (United Kingdom)

We compared an idealised mathematical model of the lower part of the pelagic food web to experimental data from a mesocosm experiment in which the supplies of mineral nutrients (nitrogen and phosphorous), bioavailable dissolved organic carbon (BDOC, as glucose), and silicate were manipulated. The central hypothesis of the experiment was that bacterial consumption of BDOC depends on whether the growth rate of heterotrophic bacteria is limited by organic-C or by mineral nutrients. In previous work, this hypothesis was examined qualitatively using a conceptual food web model. Here we explore the extent to which a ?simplest possible?? mathematical version of this conceptual model can reproduce the observed dynamics. The model combines algal?bacterial competition for mineral nutrients (phosphor...

2007-01-01

369

Mapping a nucleolar targeting sequence of an RNA binding nucleolar protein, Nop25

cDNA Cloning and mRNA analysis of PGC-1 in epitrochlearis muscle in swimming-exercised rats.

Nop25 is a putative RNA binding nucleolar protein associated with rRNA transcription. The present study was undertaken to determine the mechanism of Nop25 localization in the nucleolus. Deletion experiments of Nop25 amino acid sequence showed Nop25 to contain a nuclear targeting sequence in the N-terminal and a nucleolar targeting sequence in the C-terminal. By expressing derivative peptides from the C-terminal as GFP-fusion proteins in the cells, a lysine and arginine residue-enriched peptide (KRKHPRRAQDSTKKPPSATRTSKTQRRRR) allowed a GFP-fusion protein to be transported and fully retained in the nucleolus. When the peptide was fused with cMyc epitope and expressed in the cells, a cMyc epitope was then detected in the nucleolus. Nop25 did not localize in the nucleolus by deletion of the peptide from Nop25. Furthermore, deletion of a subdomain (KRKHPRRAQ) in the peptide or amino acid substitution of lysine and arginine residues in the subdomain ...

2006-06-10

370

Probiotics inhibit enteropathogenic E. coli adherence in vitro by inducing intestinal mucin gene expression.

Peroxisome proliferator-activated receptor gamma coactivator-1 (PGC-1), a cold-inducible coactivator of nuclear receptors, stimulates mitochondrial biogenesis and respiration in muscle cells. In the present study, we first cloned a rat PGC-1 gene from a brown adipose tissue cDNA library which encodes a predicted 796-amino-acid protein and exhibits respectively 98% and 95% identity with the mouse and human homologues. Next, we examined the effect of swimming exercise training on the level of expression of the PGC-1 gene in rat epitrochlearis (Epi) muscle. PGC-1 mRNA level in Epi muscle in rats that swam 2 h a day for 3 and 7 days increased dramatically by 154% and 163%, respectively, compared to the non-exercised control group. PGC-1 mRNA up-regulation was not observed in an immersion group treated at 35 degrees C during the training program but without swimming exercise. These results demonstrate that expression of the PGC-1 gene in Epi muscle ...

2000-08-01

371

Modulation of gene expression in differentiating 3T3 - L1 preadipocytes

Probiotic agents, live microorganisms with beneficial effects for the host, may offer an alternative to conventional antimicrobials in the treatment and prevention of enteric infections. The probiotic agents Lactobacillus plantarum 299v and Lactobacillus rhamnosus GG quantitatively inhibited the adherence of an attaching and effacing pathogenic Escherichia coli to HT-29 intestinal epithelial cells but did not inhibit adherence to nonintestinal HEp-2 cells. HT-29 cells were grown under conditions that induced high levels of either MUC2 or MUC3 mRNA, but HEp-2 cells expressed only minimal levels of MUC2 and no MUC3 mRNA. Media enriched for MUC2 and MUC3 mucin were added exogenously to binding assays and were shown to be capable of inhibiting enteropathogen adherence to HEp-2 cells. Incubation of L. plantarum 299v with HT-29 cells increased MUC2 and MUC3 mRNA expression levels. From these in vitro studies, we propose the ...

1999-04-01

372

INDUCIBLE RNAi-MEDIATED GENE SILENCING USING NANOSTRUCTURED GENE DELIVERY ARRAYS

3T3 - L1 cells can be induced to differentiate by exposing cell culture to a medium containing 3-isobutyl-1-methyl-xanthine together with insulin and dexamethasone. They have observed that oxalomalate (OMA) which inhibits aconitase thus blocking the citric cycle, also favours differentiation to adipocytes leading to fatty acids accumulation and increased synthesis of specific proteins. They compared the effects of 3-isobutyl-1-methyl-xanthine-insulin-dexamethasone and OMA on the steady-state levels of mRNA of c / EBP, H-ferritin and aconitase / IRE-BP. OMA does not affect the steady-state mRNA amount of C / EBP, H-ferritin and aconitase / IRE-BP but the 3-isobutyl-1-methyl-xanthine-insulin-dexamethasone mixture is able to induce a five-fold increase of mRNA levels for aconitase / IRE-BP. This is the first finding correlating iron metabolism to adipocyte differentiation. Further studies will clarify a possible role for the ...

1997-12-31

373

Human cytoplasmic actin proteins are encoded by a multigene family

RNA interference has become a powerful biological tool over the last decade. In this study, a tetracycline-inducible shRNA vector system was designed for silencing CFP expression and delivered alongside the yfp marker gene into Chinese hamster ovary cells using impalefection on spatially indexed vertically aligned carbon nanofiber arrays (VACNFs). The VACNF architecture provided simultaneous delivery of multiple genes, subsequent adherence and proliferation of interfaced cells, and repeated monitoring of single cells over time. Following impalefection and tetracycline induction, 53.1% 10.4% of impalefected cells were fully silenced by the inducible CFP-silencing shRNA vector. Additionally, efficient CFP-silencing was observed in single cells among a population of cells that remained CFP-expressing. This effective transient expression system enables rapid analysis of gene silencing effects using RNAi in single cells and cell ...

2008-01-01

374

[Intraspecies antagonism of Sh. flexneri in an HEp-2 cell line model].

The authors characterized nine human actin genes that they isolated from a library of cloned human DNA. Measurements of the thermal stability of hybrids formed between each cloned actin gene and ..cap alpha..-, ..beta..-, and ..gamma..-actin mRNA demonstrated that only one of the clones is most homologous to sarcomeric actin mRNA, whereas the remaining eight clones are most homologous to cytoplasmic actin mRNA. By the following criteria they show that these nine clones represent nine different actin gene loci rather than different alleles or different parts of a single gene: (i) the restriction enzyme maps of the coding regions are dissimilar; (ii) each clone contains sufficient coding region to encode all or most of an entire actin gene; and (iii) each clone contains sequences homologous to both the 5' and 3' ends of the coding region of a cloned chicken ..beta..-actin cDNA. They conclude, therefore, that ...

1982-06-01

375

Vertical and Horizontal Variations in the Physiological Diversity of the Aerobic Chemoheterotrophic Bacterial Microflora in Deep Southeast Coastal Plain Subsurface Sediments

The authors describe an effect of suppression of invasion of the guinea pig eye conjunctiva and the HEp-2 epithelial cells by virulent Sh. flexneri bacilli, with a simultaneous administration of the same dose of avirulent shigella mutants, genetically connected with them. The data of morphological study and experiments with 3H-glucose labeled shigellae carried out on the cell species model indicated that the bacterial competition for the specific sites for absorption on the epithelial cells underlay the observed phenomenon. PMID:331774

1977-06-01

376

The hrpK Operon of Pseudomonas syringae pv. tomato DC3000 Encodes Two Proteins Secreted by the Type III (Hrp) Protein Secretion System: HopB1 and HrpK, a Putative Type III Translocator

Aerobic chemoheterotrophic bacteria were isolated from surface soils and coastal plain subsurface (including deep aquifer) sediments (depths to 265 m) at a study site near Aiken, S.C., by plating on...Full Text Available

1989-05-01

377

The ecological role of bacteriocins in bacterial competition.

Pseudomonas syringae is a gram-negative bacterial plant pathogen that is dependent on a type III protein secretion system (TTSS) and the effector proteins it translocates into plant...Full Text Available

2005-01-01

378

Stabilization of Plutonium in Subsursface Environments via Microbial Reduction and Biofilm Formation

Bacteriocins are an abundant class of antimicrobial molecules that appear to mediate population dynamics within species. The bacteriocins of Escherichia coli have served as a model for exploring the ecological role of these potent toxins. Studies suggest that colicins provide a competitive edge in nutrient-poor environments and that there might be a trade-off between the costs and benefits of colicin production. PMID:10203843

1999-03-01

379

Prevalence of Actinobacillus pleuropneumoniae, Actinobacillus suis, Haemophilus parasuis, Pasteurella multocida, and Streptococcus suis in representative Ontario swine herds

Our work is towards mechanistically understanding interactions of unsaturated bacterial biofilms and their extracellular polymeric substances (EPS) with actinide metals and metal surrogates under vadose zone conditions. Because metal contaminants in the vadose zone co-occur with organic pollutants, some of our work has included experiments with organic pollutants.

2005-06-01

380

Phase transitions in multiplicative competitive processes

Tonsillar and nasal swabs were collected from weanling pigs in 50 representative Ontario swine herds and tested for the presence of 5 important bacterial upper respiratory tract pathogens. All but 1...Full Text Available

2008-04-01

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381

Nod2 sensing of lysozyme-digested peptidoglycan promotes macrophage recruitment and clearance of S. pneumoniae colonization in mice.

We introduce a discrete multiplicative process as a generic model of competition. Players with different abilities successively join the game and compete for finite resources. Emergence of dominant players and evolutionary development occur as a phase transition. The competitive dynamics underlying this transition is understood from a formal analogy to statistical mechanics. The theory is applicable to bacterial competition, predicting novel population dynamics near criticality.

2005-07-01

382

Mutations Affecting Motifs of Unknown Function in the Central Domain of Nitrogen Regulatory Protein C

Streptococcus pneumoniae colonizes the mucosal surface of the human upper respiratory tract. A colonization event is gradually cleared through phagocytosis by monocytes/macrophages that are recruited to the airway lumen. Here, we sought to define the bacterial and host factors that promote monocyte/macrophage influx and S. pneumoniae clearance using intranasal bacterial challenge in mice. We found that the recruitment of monocytes/macrophages required their expression of the chemokine receptor CCR2 and correlated with expression of the CCR2 ligand CCL2. Production of CCL2 and monocyte/macrophage recruitment were deficient in mice lacking digestion of peptidoglycan by lysozyme (LysM) and cytosolic sensing of the products of digestion by Nod2. Ex vivo macrophages produced CCL2 following bacterial uptake, digestion by LysM, and sensing of peptidoglycan by Nod2. Sensing of digested peptidoglycan by Nod2 also required the ...

2011-08-15

383

Isolation of a bacterial host selective for bacteriophage T4 containing cytosine in its DNA.

The positive control function of the bacterial enhancer-binding protein NtrC resides in its central domain, which is highly conserved among activators of ς⁵⁴ holoenzyme. Previous...Full Text Available

1999-09-01

384

Intrahepatic cholangiocarcinoma presenting as liver abscess: report of two cases

An Escherichia coli B strain, B834 galU56, has been isolated which supports growth of bacteriophage T4 with cytosine in its DNA while restricting growth of T4 with hydroxymethylcytosine. This host is...Full Text Available

1978-09-01

385

Intracellular activity of the peptide antibiotic NZ2114: studies with Staphylococcus aureus and human THP-1 monocytes, and comparison with daptomycin and vancomycin

Intrahepatic cholangiocarcinoma is the second most common primary malignant hepatic neoplasm. We describe two cases of intrahepatic cholangiocarcinoma which initially presented as liver abscess both clinically and radiologically. Mucin-hypersecretion from the tumor cells and extensive necrosis or secondary bacterial infection was responsible for the radiologic appearance of a liver abscess.=20

1998-10-01

386

DEFF Research Database (Denmark)

Staphylococcus aureus survives inside eukaryotic cells. Our objective was to assess the activity of NZ2114, a novel peptidic antibiotic, against intracellular S. aureus in comparison with established antistaphylococcal agents acting on the bacterial envelope with a distinct mechanism.

2010-01-01

387

First Outbreak of Multidrug-Resistant Klebsiella pneumoniae Producing both SHV-12-Type Extended-Spectrum ?-Lactamase and DHA-1-Type AmpC ?-Lactamase at a Korean Hospital

Campylobacter jejuni, C. coli, and C. lari naturally present in Leghorn laying hens and the antibiotic resistance profiles of these organisms

PurposeCoexistence of different classes of β-lactamases in a single bacterial isolate may pose diagnostic and therapeutic challenges. We investigated a spread of Klebsiella...Full Text Available

2008-02-29

388

Blockade of catecholamine-induced growth by adrenergic and dopaminergic receptor antagonists in Escherichia coli O157:H7, Salmonella enterica and Yersinia enterocolitica

Campylobacter spp. are present in the intestinal tract and internal tissues of broiler breeder and broiler chickens. Campylobacter spp. are known to cause acute bacterial gastroenteritis in humans and raw poultry products have been implicated as a significant source of these infections. The object...

389

A modeling study by response surface methodology and artificial neural network on culture parameters optimization for thermostable lipase production from a newly isolated thermophilic Geobacillus sp. strain ARM

BackgroundThe ability of catecholamines to stimulate bacterial growth was first demonstrated just over a decade ago. Little is still known however, concerning the nature of the putative...Full Text Available

390

The Morphology, Ontogeny, and Small Subunit rRNA Gene Sequence Analysis of Diophrys parappendiculata n. sp. (Protozoa, Ciliophora, Euplotida), a New Marine Ciliate from Coastal Waters of Southern China

BackgroundThermostable bacterial lipases occupy a place of prominence among biocatalysts owing to their novel, multifold applications and resistance to high temperature and other...Full Text Available

391

British Library Electronic Table of Contents (United Kingdom)

ABSTRACT. The morphology, morphogenesis, and phylogeny of Diophrys parappendiculata n. sp., a large marine ciliate isolated from the coastal waters of Daya Bay, southern China, were investigated. This new species is characterized by a combination of its large size, appendiculata-pattern of ciliature, and bipartite adoral zone of membranelles. The main stages of morphogenesis during binary fission were also recorded and described. Comparisons of morphological characteristics with similar congeners support the validity of the new species. The small subunit rRNA gene sequence of D. parappendiculata is 96.3-99.94% similar to those of four other congeners; it differs in four nucleotides from that of Diophrys appendiculata (i.e. structural similarity was 99.94%). Phylogenetic analysis indicates ...

2011-01-01

392

Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure

British Library Electronic Table of Contents (United Kingdom)

Abstract Elevated temperatures resulting from climate change pose a clear threat to reef-building corals; however, the traits that might influence corals- survival and dispersal during climate change remain poorly understood. Global gene expression profiling is a powerful hypothesis-forming tool that can help elucidate these traits. Here, we applied a novel RNA-Seq protocol to study molecular responses to heat and settlement inducers in aposymbiotic larvae of the reef-building coral Acropora millepora. This analysis of a single full-sibling family revealed contrasting responses between short- (4-h) and long-term (5-day) exposures to elevated temperatures. Heat shock proteins were up-regulated only in the short-term treatment, while the long-term treatment induced the down-regulation of rib...

2011-01-01

393

Oxidation of Elemental Sulfur by Fusarium solani Strain THIF01 Harboring Endobacterium Bradyrhizobium sp.

British Library Electronic Table of Contents (United Kingdom)

Nineteen fungal strains having an ability to oxidize elemental sulfur in mineral salts medium were isolated from deteriorated sandstones of Angkor monuments. These fungi formed clearing zone on agar medium supplemented with powder sulfur due to the dissolution of sulfur. Representative of the isolates, strain THIF01, was identified as Fusarium solani on the basis of morphological characteristics and phylogenetic analyses. PCR amplification targeting 16S rRNA gene and analyses of full 16S rRNA gene sequence indicated strain THIF01 harbors an endobacterium Bradyrhizobium sp.; however, involvement of the bacterium in the sulfur oxidation is still unclear. Strain THIF01 oxidized elemental sulfur to thiosulfate and then sulfate. Germination of the spores of strain THIF01 was observed in a liqui...

2010-01-01

394

One-step RNA pathogen detection with reverse transcriptase activity of a mutated thermostable Thermus aquaticus DNA polymerase

British Library Electronic Table of Contents (United Kingdom)

We describe the cloning and characterization of a mutated thermostable DNA polymerase from Thermus aquaticus (Taq) that exhibits an increased reverse transcriptase activity and is therefore designated for one-step PCR pathogen detection using established real-time detection methods. We demonstrate that this Taq polymerase mutant (Taq M1) has similar PCR sensitivity and nuclease activity as the respective Taq wild-type DNA polymerase. In addition, and in marked contrast to the wild-type, Taq M1 exhibits a significantly increased reverse transcriptase activity especially at high temperatures (>60degreeC). RNA generally hosts highly stable secondary structure motifs, such as hairpins and G-quadruplexes, which complicate, or in the worst case obviate, reverse transcription (RT). Thus, RT at hi...

2010-01-01

395

Clostridiaceae and Enterobacteriaceae as active fermenters in earthworm gut content

British Library Electronic Table of Contents (United Kingdom)

The earthworm gut provides ideal in situ conditions for ingested heterotrophic soil bacteria capable of anaerobiosis. High amounts of mucus- and plant-derived saccharides such as glucose are abundant in the earthworm alimentary canal, and high concentrations of molecular hydrogen (H2) and organic acids in the alimentary canal are indicative of ongoing fermentations. Thus, the central objective of this study was to resolve potential links between fermentations and active fermenters in gut content of the anecic earthworm Lumbricus terrestris by 16S ribosomal RNA (rRNA)-based stable isotope probing, with [13C]glucose as a model substrate. Glucose consumption in anoxic gut content microcosms was rapid and yielded soluble organic compounds (acetate, butyrate, formate, lactate, propionate, succi...

2011-01-01

396

The Differentially Expressed Genes by Radiotherapy in the Patients with Uterine Cervix Cancer

Regulation of the phosphoinositide pathway in cultured Sertoli cells from immature rats: effects of follicle-stimulating hormone and fluoride

Purpose : To detect differentially expressed genes in the patients with uterine cervical cancer during the radiation therapy. Materials and Methods : In patients with biopsy proven uterine cervical cancer, we took a tumor tissue just before radiation therapy and at 40 minutes after external irradiation of 1.8 Gy. Total RNAs isolated from non-irradiated and irradiated tumor tissue samples were analyzed using the differential-display reverse transcription-polymerase chain reaction (DDRT-PCR). Complementary DNA (cDNA) fragments corresponding to differentially expressed messenger RNAs(mRNAs) were eluted, and cloned. The differential expression of the corresponding mRNAs was confirmed by reverse northern blot. Differentially expressed cDNA bands were sequenced. Nucleotide sequence data were analyzed in the Gene Bank and EMBL databases via the BLAST network server to identify homologies to known genes or cDNA fragments. Expression pattern of down-regulated clone was ...

2001-12-15

397

High resolution sequence stratigraphy of Miocene deep-water clastic outcrops, Taranaki coast, New Zealand

Many hormones elicit effects on target cells by stimulating the enzyme phospholipase-C, which catalyzes the hydrolysis of phosphoinositides to the intracellular second messengers diacylglycerol and inositol phosphates. The present study examined the roles of FSH and guanine nucleotide-binding proteins (G-proteins) in regulating the hydrolysis of phosphoinositides in Sertoli cells. Sertoli cell cultures prepared from 16- to 18-day-old rats were incubated for 24 h with myo-[2-3H] inositol to label endogenous phospholipids. Treatment of cells from 0.5-20 min with preparations of ovine FSH ranging in potency from 1-60 times that of NIH FSH S1 did not affect accumulation of inositol phosphates. Levels of total [3H]inositol phosphates [[3H]inositol mono-, di-, and triphosphates (IP, IP2, and IP3)] in FSH-treated cultures was 75-120% the levels in control cultures over the various time intervals studied. Addition of testosterone and the combination of testosterone plus ...

398

Transcription of the E2F-1 gene is rendered cell cycle dependent by E2F DNA-binding sites within its promoter.

Approximately 700m of deep water clastic deposits of Mt. Messenger Formation are superbly exposed along the Taranaki coast of North Island, New Zealand. Biostratigraphy indicates the interval was deposited during the time span 10.5-9.2m.y. in water depths grading upward from lower bathyal to middle-upper bathyal. This interval is considered part of a 3rd order depositional sequence deposited under conditions of fluctuating relative sea-level, concomitant with high sedimentation rates. Several 4th order depositional sequences, reflecting successive sea-level falls, are recognized within the interval. Sequence boundaries display a range of erosive morphologies from metre-wide canyons to scours several hundred metres across. All components of a generic lowstand systems tract--basin floor fan, channel-levee complex and progading complex--are present in logical and temporal order. They are repetitive through the interval, with the relatively shallower-water components ...

1995-08-01

399

The YTH Domain Is a Novel RNA Binding Domain*

The cell cycle-regulatory transcription factor E2F-1 is regulated by interactions with proteins such as the retinoblastoma gene product and by cell cycle-dependent alterations in E2F-1 mRNA abundance....Full Text Available

1994-10-01

400

The CYP2A3 gene product catalyzes coumarin 7-hydroxylation in human liver microsomes

The YTH (YT521-B homology) domain was identified by sequence comparison and is found in 174 different proteins expressed in eukaryotes. It is characterized by 14 invariant residues within an α-helix/β-sheet...Full Text Available

2010-05-07

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401

The CYP2A3 gene product catalyzes coumarin 7-hydroxylation in human liver microsomes

Three cDNAs, designated IIA3, IIA3v, and IIA4, coding for P450s in the CYP2A gene subfamily were isolated from a {lambda}gt11 library prepared from human hepatic mRNA. Only three nucleotide differences and a single amino acid difference, Leu{sup 160}{yields}His, were found between IIA3 and IIA3v, indicating that they are probably allelic variants. IIA4 displayed 94% amino acid similarity with IIA3 and IIA3v. The three cDNAs were inserted into vaccinia virus, and recombinant viruses were used to infect human hepatoma Hep G2 cells. Only IIA3 was able to produce an enzyme that had a reduced CO-bound spectrum with a {lambda}{sub max} at 450 nm. This expressed enzyme was able to carry out coumarin 7-hydroxylation and ethoxycoumarin O-deethylation. cDNA-expressed IIA3v and IIA4 failed to incorporate heme and were enzymatically inactive. Analysis of IIA proteins in human liver microsomes, using antibody against rat IIA2, revealed two proteins of 49 and 50 kDa, the former ...

1990-02-06

402

TGFB1-Induced Extracellular Expression of TGFBIp and Inhibition of TGFBIp Expression by RNA Interference in a Human Corneal Epithelial Cell Line

Three cDNAs, designated IIA3, IIA3v, and IIA4, coding for P450s in the CYP2A gene subfamily were isolated from a #lambda#gt11 library prepared from human hepatic mRNA. Only three nucleotide differences and a single amino acid difference, Leu"1"6"0#->#His, were found between IIA3 and IIA3v, indicating that they are probably allelic variants. IIA4 displayed 94% amino acid similarity with IIA3 and IIA3v. The three cDNAs were inserted into vaccinia virus, and recombinant viruses were used to infect human hepatoma Hep G2 cells. Only IIA3 was able to produce an enzyme that had a reduced CO-bound spectrum with a #lambda#_m_a_x at 450 nm. This expressed enzyme was able to carry out coumarin 7-hydroxylation and ethoxycoumarin O-deethylation. cDNA-expressed IIA3v and IIA4 failed to incorporate heme and were enzymatically inactive. Analysis of IIA proteins in human liver microsomes, using antibody against rat IIA2, revealed two proteins of 49 and 50 kDa, the former of ...

1990-02-01

403

Specific in vitro initiation of transcription on the adenovirus type 2 early and late EII transcription units.

Purpose.To report the increased production of extracellular transforming growth factor β-induced protein (TGFBIp) by human corneal epithelial cells (HCECs) after induction...Full Text Available

2011-02-01

404

Silencing of SARS-CoV spike gene by small interfering RNA in HEK 293T cells

Three transcription units are present in the adenovirus type 2 region EII. Transcription units EIIaE and EIIaL encode the mRNA for the 72,000-dalton DNA binding protein, early and late in the lytic...Full Text Available

1981-12-01

405

Scyl1 Facilitates Nuclear tRNA Export in Mammalian Cells by Acting at the Nuclear Pore Complex

Two candidate small interfering RNAs (siRNAs) corresponding to severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike gene were designed and in vitro transcribed to explore the possibility of silencing SARS-CoV S gene. The plasmid pEGFP-optS, which contains the codon-optimized SARS-CoV S gene and expresses spike-EGFP fusion protein (S-EGFP) as silencing target and expressing reporter, was transfected with siRNAs into HEK 293T cells. At various time points of posttransfection, the levels of S-EGFP expression and amounts of spike mRNA transcript were detected by fluorescence microscopy, flow cytometry, Western blot, and real-time quantitative PCR, respectively. The results showed that the cells transfected with pEGFP-optS expressed S-EGFP fusion protein at a higher level compared with those transfected with pEGFP-S, which contains wildtype SARS-CoV spike gene sequence. The green fluorescence, mean fluorescence intensity, and SARS-CoV S ...

2004-11-26

406

Regulation of expression of a soybean storage protein subunit gene. Progress report

Scyl1 is an evolutionarily conserved N-terminal protein kinase-like domain protein that plays a role in COP1-mediated retrograde protein trafficking in mammalian cells. Furthermore, loss of Scyl1 function...Full Text Available

2010-07-15

407

Polyadenylated H3 histone transcripts and H3 histone variants in alfalfa.

We have found that the methionine repression of the ..beta..-subunit gene expression is not due to degradation of the ..beta..-subunit but is due to an effect on synthesis of the ..beta..-subunit. The effect of methionine on the synthesis of the ..beta..-is due to an inhibition of ..beta..-subunit mRNA synthesis. 3 references, 1 figure.

1984-04-23

408

One-step RNA pathogen detection with reverse transcriptase activity of a mutated thermostable Thermus aquaticus DNA polymerase.

Histone H3 mRNAs were found in polyA(+) fractions of total RNA prepared from alfalfa plants, calli and somatic embryos. The sequence analysis of cDNAs revealed the presence of a polyA tail on independent...Full Text Available

1989-04-25

409

Molecular cloning of chicken metallothionein. Deduction of the complete amino acid sequence and analysis of expression using cloned cDNA

We describe the cloning and characterization of a mutated thermostable DNA polymerase from Thermus aquaticus (Taq) that exhibits an increased reverse transcriptase activity and is therefore designated for one-step PCR pathogen detection using established real-time detection methods. We demonstrate that this Taq polymerase mutant (Taq M1) has similar PCR sensitivity and nuclease activity as the respective Taq wild-type DNA polymerase. In addition, and in marked contrast to the wild-type, Taq M1 exhibits a significantly increased reverse transcriptase activity especially at high temperatures (>60 degrees C). RNA generally hosts highly stable secondary structure motifs, such as hairpins and G-quadruplexes, which complicate, or in the worst case obviate, reverse transcription (RT). Thus, RT at high temperatures is desired to weaken or melt secondary structure motifs. To demonstrate the ability of Taq M1 for RNA detection of pathogens, we ...

2010-02-01

410

MicroRNA Let-7f Inhibits Tumor Invasion and Metastasis by Targeting MYH9 in Human Gastric Cancer

A cDNA library was constructed using RNA isolated from the livers of chickens which had been treated with zinc. This library was screened with a RNA probe complementary to mouse metallothionein-I (MT), and eight chicken MT cDNA clones were obtained. All of the cDNA clones contained nucleotide sequences homologous to regions of the longest (375 bp) cDNA clone. The latter contained an open reading frame of 189 bp, and the deduced amino acid sequence indicates a protein of 63 amino acids of which 20 are cysteine residues. Amino acid composition and partial amino acid sequence analyses of purified chicken MT protein agreed with the amino acid composition and sequence deduced from the cloned cDNA. Amino acid sequence comparison establish that chicken MT shares extensive homology with mammalian MTs. Southern blot analysis of chicken DNA indicates that the chicken MT gene is not a part of a large family of related sequences, but rather is likely to be ...

1988-01-25

411

MMP-9 Gene Ablation and TIMP-4 Mitigate PAR-1-Mediated Cardiomyocyte Dysfunction: A Plausible Role of Dicer and miRNA

BackgroundMicroRNAs (miRNAs) are important regulators that play key roles in tumorigenesis and tumor progression. A previous report has shown that let-7 family members can act as...Full Text Available

412

Large T1 oligonucleotides of Moloney leukemia virus missing in an env gene recombinant, HIX, are present on an intracellular 21S Moloney viral RNA species.

Although matrix metalloproteinase-9 (MMP-9) is involved in cardiomyocytes contractility dysfunction, tissue inhibitor of metalloproteinase-4 (TIMP-4) mitigates the effect of MMP-9, and proteinase-activated...Full Text Available

2010-07-01

413

Isolation and characterization of cDNA clones for human skeletal muscle alpha actin.

HIX, a recombinant derived from Moloney leukemia virus, has an envelope glycoprotein different from that of the Moloney virus. HIX and Moloney viruses share the majority of the large T1 oligonucleotides...Full Text Available

1978-06-01

414

Intragenic rearrangements of a mycoreovirus induced by the multifunctional protein p29 encoded by the prototypic hypovirus CHV1-EP713

Two cDNA libraries corresponding to polyA+ RNA from human adult skeletal muscle have been constructed by cloning in the PstI site of pBR322. Skeletal alpha actin cDNA clones have been isolated and characterized....Full Text Available

1983-06-11

415

Insulin regulation of protein biosynthesis in differentiated 3T3 adipocytes. Regulation of glyceraldehyde-3-phosphate dehydrogenase

Mycoreovirus 1 (MyRV1), a member of the Reoviridae family possessing a genome consisting of 11 dsRNA segments (S1–S11), and the prototype hypovirus (CHV1-EP713)...Full Text Available

2008-12-01

416

Identification of a nucleoside triphosphate binding site on calf thymus RNA polymerase II

The effect of insulin on protein biosynthesis was examined in differentiated 3T3-L1 and 3T3-F442A adipocytes. Insulin altered the relative rate of synthesis of specific proteins independent of its ability to hasten conversion of the fibroblast (preadipocyte) phenotype to the adipocyte phenotype. Although more than one pattern of response to insulin was observed, the authors focused on the induction of a Mr 33,000 protein which was identified as the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Exposure of 3T3 adipocytes to insulin throughout differentiation specifically increased GAPDH activity and protein content by 2- to 3-fold as compared to 3T3 adipocytes differentiated in the absence of insulin. These changes in enzyme activity and content could be accounted for by a 4-fold increase in the relative rate of synthesis of GAPDH and a 9-fold increase in hybridizable mRNA levels. Within 2 h of insulin addition to 3T3 adipocytes differentiated ...

1985-10-05

417

Hypoxia down-regulates sFlt-1 (sVEGFR-1) expression in human microvascular endothelial cells by a mechanism involving mRNA alternative processing

A nucleoside triphosphate binding site on calf thymus RNA polymerase II was identified by using photoaffinity analogues of adenosine 5'-triphosphate and guanosine 5'-triphosphate. Both radiolabeled 8-azidoadenosine 5'-triphosphate (8-N3ATP) and radiolabeled 8-azidoguanosine 5'-triphosphate (8-N3GTP) bound to a single polypeptide of this enzyme. This polypeptide has a molecular mass of 37 kilodaltons and an isoelectric point of 5.4. Ultraviolet (UV) irradiation was necessary for photolabeling to occur. In addition, no labeling occurred when the probe was prephotolyzed or when the enzyme was inactivated. Furthermore, photolabeling of the enzyme could be decreased by preincubation with natural substrates. To provide evidence that the radiolabeled polypeptide forms a part of the domain of the nucleoside triphosphate binding site, experiments were performed using unlabeled 8-N3ATP. Although this unlabeled analogue was not a substrate ...

1986-01-14

418

Highly Ordered Spatial Organization of the Structural Long Noncoding NEAT1 RNAs within Paraspeckle Nuclear Bodies

sFlt-1 (soluble Flt-1) potently inhibits angiogenesis by binding extracellularly to VEGF (vascular endothelial growth factor). In the present paper, we report that hypoxia down-regulates sFlt-1 expression...Full Text Available

2011-06-01

419

Extraribosomal functions associated with the C terminus of the 37/67?kDa laminin receptor are required for maintaining cell viability

Paraspeckles (PSPs) are nuclear bodies associated with the retention in the nucleus of specific mRNAs. Two isoforms of a long noncoding RNA (NEAT1_v1/Menε and NEAT1_v2/Menβ)...Full Text Available

2010-11-15

420

Expression of alternatively spliced human T-lymphotropic virus type I pX mRNA in infected cell lines and in primary uncultured cells from patients with adult T-cell leukemia/lymphoma and healthy carriers.

The 37/67 kDa laminin receptor (LAMR) is a multifunctional protein, acting as an extracellular receptor, localizing to the nucleus, and playing roles in rRNA processing and ribosome assembly....Full Text Available

2010-05-01

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421

Dissecting toxin immunity in virus-infected killer yeast uncovers an intrinsic strategy of self-protection

Although human T-cell lymphotropic virus type I (HTLV-I) is the etiologic agent of adult T-cell leukemia/lymphoma (ATL), the role of viral gene expression in the progression to and maintenance of the...Full Text Available

1992-04-01

422

Discrimination of Listeria monocytogenes from other Listeria species by ligase chain reaction.

Toxin-secreting “killer” yeasts were initially identified >40 years ago in Saccharomyces cerevisiae strains infected with a double-stranded RNA “killer”...Full Text Available

2006-03-07

423

Differentiation associated regulation of microRNA expression in vivo in human CD8⁺T cell subsets

A ligase chain reaction assay based on a single-base-pair difference in the V9 region of the 16S rRNA gene (16S rDNA) was developed to distinguish between Listeria monocytogenes and other Listeria species....Full Text Available

1992-11-01

424

Differential expression of human Fas mRNA species upon peripheral blood mononuclear cell activation.

BackgroundThe differentiation of CD8⁺T lymphocytes following priming of naïve cells is central in the establishment of the adaptive immune response. Yet, the...Full Text Available

425

Cumulus expansion, nuclear maturation and connexin 43, cyclooxygenase-2 and FSH receptor mRNA expression in equine cumulus-oocyte complexes cultured in vitro in the presence of FSH and precursors for hyaluronic acid synthesis

Human Fas/Apo-1 is a cell-surface protein that mediates apoptosis upon ligation with Fas ligand. The gene lies on the long arm of chromosome 10, consists of nine exons, and spans more than 26 kb of...Full Text Available

1995-09-15

426

Cordycepin Blocks Lung Injury-Associated Inflammation and Promotes BRCA1-Deficient Breast Cancer Cell Killing by Effectively Inhibiting PARP

The aim of this study was to investigate cumulus expansion, nuclear maturation and expression of connexin 43, cyclooxygenase-2 and FSH receptor transcripts in equine cumuli oophori during in vivo and...Full Text Available

427

Comparison of the NucliSens easyMAG and Qiagen BioRobot 9604 Nucleic Acid Extraction Systems for Detection of RNA and DNA Respiratory Viruses in Nasopharyngeal Aspirate Samples?

Cordycepin has been shown to interfere with a myriad of molecular processes from RNA elongation to kinase activity, and prevents numerous inflammatory processes in animal models. Here we show in a mouse...Full Text Available

2011-09-01

428

Cloning, chromosomal assignment, and regulation of the rat thyrotropin receptor: Expression of the gene is regulated by thyrotropin, agents that increase cAMP levels, and thyroid autoantibodies

The NucliSens easyMAG and BioRot 9604 automated nucleic acid extraction systems were evaluated and compared with the manual QIAamp (Qiagen) extraction method for their abilities to extract nucleic acid...Full Text Available

2008-07-01

429

Cadmium down-regulation of kidney Sp1 binding to mouse SGLT1 and SGLT2 gene promoters: Possible reaction of cadmium with the zinc finger domain of Sp1

A rat thyrotropin (thyroid-stimulating hormone, TSH) receptor cDNA was isolated that encoded a protein of 764 amino acids, M_r 86,528. Transfection of the cDNA caused COS-7 cells to develop a TSH-sensitive adenylate cyclase response and the ability to bind "1"2"5I-labeled TSH; both activities were similar to those of rat FRTL-5 thyroid cells and not duplicated by lutropin. The gene represented by the cDNA was assigned to mouse chromosome 12 and human chromosome 14. Northern analyses identified two species of mRNA, 5.6 and 3.3 kilobases, in FRTL-5 thyroid cells; the transcripts appeared to differ only in the extent of their 3' noncoding sequences. There were minimal amounts of the two mRNAs in rat ovary, and neither was detected in RNA preparations from rat testis, liver, lung, brain, spleen, and FRT thyroid cells, which do not have a functional TSH receptor. TSH decreased both mRNA species 3- to 4-fold within 8 hr in FRTL-5 ...

1990-01-01

430

Arc/Arg3.1 mRNA Global Expression Patterns Elicited by Memory Recall in Cerebral Cortex Differ for Remote Versus Recent Spatial Memories

Cadmium (Cd) exposure causes glucosuria (glucose in the urine). Previously, it was shown that Cd exposure of primary cultures of mouse kidney cells (PMKC) decreased mRNA levels of the glucose...Full Text Available

2010-05-01

431

Application of a Newly Developed ARB Software-Integrated Tool for In Silico Terminal Restriction Fragment Length Polymorphism Analysis Reveals the Dominance of a Novel pmoA Cluster in a Forest Soil

The neocortex plays a critical role in the gradual formation and storage of remote declarative memories. Because the circuitry mechanisms of systems-level consolidation are not well understood, the...Full Text Available

432

An ultraviolet-inducible adenosine-adenosine cross-link reflects the catalytic structure of the Tetrahymena ribozyme

TRF-CUT, an ARB-implemented tool, was developed to predict in silico the terminal restriction fragments of aligned small-subunit rRNA gene or functional gene sequences. Application of this new tool...Full Text Available

2005-03-01

433

Alternative mRNA Splicing Produces a Novel Biologically Active Short Isoform of PGC-1?*

When a shortened enzymatic version of the Tetrahymena self-splicing intervening sequence (IVS) RNA is placed under catalytic conditions and irradiated at 254 nm, a covalent cross-link forms with high efficiency. The position of the cross-link was mapped by using three independent methods: RNase H digestion, primer extension with reverse transcriptase, and partial hydrolysis of end-labeled RNA. The cross-link is chemically unusual in that it joins two adenosines, A57 and A95. Formation of this cross-link depends upon the identity and concentration of divalent cations present and upon heat-cool renaturation of the IVS in a manner that parallels conditions required for optimal catalytic activity. Furthermore, cross-linking requires the presence of sequences within the core structure, which is conserved among group I intervening sequences and necessary for catalytic activity. Together these correlations suggest that a common folded structure ...

1990-06-12

434

A Targeted Bypass Screen Identifies Ynl187p, Prp42p, Snu71p, and Cbp80p for Stable U1 snRNP/Pre-mRNA Interaction?

The transcriptional co-activator PGC-1α regulates functional plasticity in adipose tissue by linking sympathetic input to the transcriptional program of adaptive thermogenesis. We report here...Full Text Available

2009-11-20

435

Epitope mapping and functional analysis of sigma A and sigma NS proteins of avian reovirus

To understand how DEXD/H-box proteins recognize and interact with their cellular substrates, we have been studying Prp28p, a DEXD/H-box splicing factor required for switching the U1 snRNP with the U6...Full Text Available

2009-07-01

436

Temperature and controlled atmosphere effects on efficacy of Muscodor albus as a biofumigant

We have previously shown that avian reovirus (ARV) #sigma#A and #sigma#NS proteins possess dsRNA and ssRNA binding activity and suggested that there are two epitopes on #sigma#A (I and II) and three epitopes (A, B, and C) on #sigma#NS. To further define the location of epitopes on #sigma#A and #sigma#NS proteins and to further elucidate the biological functions of these epitopes by using monoclonal antibodies (MAbs) 62, 1F9, H1E1, and 4A123 against the ARV S1133 strain, the full-length and deletion fragments of S2 and S4 genes of ARV generated by polymerase chain reaction (PCR) were cloned into pET32 expression vectors and the fusion proteins were overexpressed in Escherichia coli BL21 strain. Epitope mapping using MAbs and E. coli-expressed deletion fragments of #sigma#A and #sigma#NS of the ARV S1133 strain, synthetic peptides, and the cross reactivity of MAbs to heterologous ARV strains demonstrated that epitope II on #sigma#A was located at ...

2005-02-20

437

British Library Electronic Table of Contents (United Kingdom)

Biofumigation with Muscodor albus was investigated to control four fungal decay pathogens (Phytophthora erythroseptica, Sclerotinia sclerotiorum, Botrytis cinerea and Penicillium expansum) and four bacterial pathogens (Erwinia carotovora pv. carotovora, Pseudomonas fluorescens, Escherichia coli, Listeria innocua) in controlled atmosphere conditions (regular air (20.8% O2+0.03% CO2), high CO2 (20.8% O2+15% CO2) or low O2 (1% O2+0.03% CO2)). In vitro experiments involved 48h exposure to M. albus at 3degreeC or 20degreeC, in vivo experiments involved 72h exposure to M. albus at 3degreeC. In vitro biofumigation with M. albus in regular air at 20degreeC killed all the pathogens. Bacterial growth was best controlled by M. albus at 20degreeC regardless of atmospheric conditions whereas fungal gro...

2008-01-01

438

Sulfur and carbon cycling in a flue gas desulfurization sludge disposal site.

Impact of Bifidobacterium animalis subsp. lactis BB-12 and, Lactobacillus acidophilus LA-5-containing yoghurt, on fecal bacterial counts of healthy adults

Products of a power plant flue gas desulfurization scrubber are discharged into a pond as sludge consisting of calcite (initial delta13C 3.2-3.8 per thousand), gypsum (initial delta34S 7.6-8.6 per thousand), and aqueous solution. Reducing conditions exist below a boundary that appears to move vertically as a function of changes in pond water level. Under reducing conditions, bacteria partially reduce aqueous sulfate to low-delta34S sulfide, consuming organic carbon and generating low-delta13C bicarbonate. Under oxidizing conditions, sulfide is converted to sulfate, leading to calcite dissolution, gypsum precipitation, and isotopic re-equilibration of remaining calcite with dissolved bicarbonate near the pond surface. The gypsum has delta34S near 6 per thousand, and calcite has delta13C as low as -1.7 per thousand; the changes from initial values correspond to predictions based on isotopic balance and reaction stoichiometry. The pond largely contains the products of ...

2003-04-01

439

British Library Electronic Table of Contents (United Kingdom)

This randomized, placebo-controlled, double blind, parallel dose-response study investigated the impact of 4-week commercial yoghurt consumption supplemented with Bifidobacterium animalis subsp. lactis (BB-12) and Lactobacillus acidophilus (LA-5) on fecal bacterial counts of healthy adults. Fifty-eight volunteers were randomly assigned to three different groups: 1. placebo (no probiotic, no starter and no green tea extract); 2. Yoptimal (10^9cfu/100g of BB-12 and LA-5 and 40mg of green tea extract) and 3. Yoptimal-10 (10^1^0cfu/100g of BB-12, 10^9cfu/100g of LA-5 and 40mg of green tea extract). These yoghurt products also contained Lactobacillus delbrueckii subsp. bulgaricus (10^7cfu/100g) and Streptococcus thermophilus (10^1^0cfu/100g). The quantitative PCR (qPCR) results showed that ther...

2011-01-01

440

Geochemical study on origin of natural gases in Japanese oil and gas fields

Effect of clindamycin treatment on vaginal inflammatory markers in pregnant women with bacterial vaginosis and a positive fetal fibronectin test

The origin of natural gas in the Japanese oil and gas fields are geochemically studied. Samples are taken from structural natural gas, surface gas seepage, water-dissolved natural gas and coal-field gas of the Japan Sea coast area. The origins of primary hydrocarbons are classified into bacteria gas and thermogenic gas, the latter being subclassified into gas in oil production zone with the per million deviation of the carbon isotope (/sup 13/C/sup 1/) of methane less than -35 and those gases with maturity higher than this. Surface gas seepage is subjected to migration and bacterial oxidation. Coal gas is similar to oil gas. The CO/sub 2/ concentration is 0 - 2% and /sup 13/CO/sub 2/ deviations from -30 - +30. The origin can be barely estimated from the isotopic composition because of the wide secondary change in the composition. The origin and migration of gas from the gas field of northern Niigata are not similar to those in the southern area, which consist of a ...

1988-05-01

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

441

British Library Electronic Table of Contents (United Kingdom)

Objective To compare the levels of interleukin (IL)-1?, IL-6, and matrix metalloproteinase (MMP)-8 in the vaginal secretions of pregnant women with a positive fetal fibronectin (fFN) test result with or without asymptomatic bacterial vaginosis (BV) before and after treatment with oral clindamycin. Methods A prospective cohort study was conducted among 43 pregnant women with a positive fFN test result. All patients were treated with clindamycin, and the pre- and post-treatment levels of IL-1?, IL-6, and MMP-8 were compared. Results Before treatment, levels of IL-1? and MMP-8 were significantly higher in women with BV compared with women without BV (P<0.05). Vaginal levels of IL-1? and IL-6, but not MMP-8, decreased after treatment in pregnant women with BV. Conclusions The inability of clin...

2009-01-01

442

Use of the K88 antigen for in vivo bacterial competition with porcine strains of enteropathogenic Escherichia coli.

The wavelength dependence of ultraviolet enhanced reactivation in a mammalian cell-virus system

Infant mice were used to measure the amount of fluid accumulation (enterosorption) in the intestinal tract after oral inoculation of a porcine strain of enteropathogenic Escherichia coli (K88-+, Ent-+). Significant reduction in the amount of fluid found in the intestinal tract was observed if the mice were first inoculated with a K88-possessing, non-enterotoxigenic strain of E. coli. The protection provided is thought to be due to specific competition for attachment sites on cells of the small intestine. PMID:1095492

1975-07-01

443

Mineral biotechnology. Microbial aspects of mineral beneficiation, metal extraction, and environmental control

The effect of UV radiation in the wavelength region 230 nm to 302 nm on the ability of an irradiated mammalian cell to reactivate UV-irradiated mammalian virus was tested. An action spectrum for radiation enhanced reactivation (RER) is presented. The shape of the action spectrum points to a combined nucleic acid-protein target for UV radiation effects on this cellular parameter. An analysis of the results of others involving the biochemical and photobiological events involved in RER does not allow us to distinguish which macromolecule is the major contributor to this effect. Studies involving an analogous phenomenon in bacteris (Weigle reactivation) imply that RER and WR amy involve similar mechanisms. (author).

444

Effect of microwaves on microorganisms in foods

Papers in this book illustrate the utility of mineral biotechnology with respect to biobeneficiation, bioleaching, bioremediation and biomineralization. Papers of particular interest to the coal industry include: depression of pyrite flotation by yeast and bacteris (S.K. Kawatra and T.C. Eisele); desulfurization of coal by microbial flotation in a semicontinuous system (T. Nagaoka and others); biochemical removal of HAP precursors from coal - INEEL slurry column testing (K.S. Noah and G.J. Olson); microorganisms, biotechnology and acid rock drainage - emphasis on passive-biological control and treatment methods (N. Kuyucak); and utility of bioreagents in mineral processing (P. Somasundaran and others).

2001-07-01

445

Dipyrone-induced changes in DNA repair and other cell membrane associated processes in Escherichia coli

The microbial safety of foods cooked in microwave ovens was investigated. The mechanisms of microwave destruction of microorganisms were examined. Effects of time and temperature on microorganisms in different food systems were described. Studies showed that: microwave heating of food is more ''''food dependent'' than conventional heating; recommended microwave treatment time for some foods may not destroy high levels of bacteria; use of microwaves in combination with conventional heating methods results in more uniform heating of foods and destruction of bacteria; and microwaves exert different killing effects on individual bacterial species. (78 references, 2 tables)

1980-08-01

446

Dipyrone-induced changes in DNA repair and other cell membrane associated processes in Escherichia coli

The analgesic, dipyrone (1,phenyl-2,3-dimethyl-5-pyrazolone-4-methylamino methane sulphonate sodium), at 20 mM concentration, inhibited the rejoining of single-strand scissions in DNA of Escherichia coli B/r cells induced by 20 krad gamma-radiation. The chemical altered the cell membrane structure as evidenced from the uptake of acriflavin, the efflux of potassium ions from the bacterial cells and the inhibition of alkaline phosphatase-a cell membrane associated enzyme. (author). 18 refs., 6 figures.

1982-09-01

447

Characterisation of anti-Staphylococcus aureus activity of quercetin

The analgesic, dipyrone (1,phenyl-2,3-dimethyl-5-pyrazolone-4-methylamino methane sulphonate sodium), at 20 mM concentration, inhibited the rejoining of single-strand scissions in DNA of Escherichia coli B/r cells induced by 20 krad gamma-radiation. The chemical altered the cell membrane structure as evidenced from the uptake of acriflavin, the efflux of potassium ions from the bacterial cells and the inhibition of alkaline phosphatase-a cell membrane associated enzyme. (author).

448

British Library Electronic Table of Contents (United Kingdom)

Summary Although many antibiotics are available for the treatment of bacterial infections, the emergence and global spread of antibiotic-resistant bacteria is a community-wide problem. To overcome this problem, we must explore alternative antimicrobials. This study investigated the antibacterial properties of quercetin, a flavonoid present in vegetables and fruits. Quercetin was tested against gram-positive and gram-negative bacteria and was found to exert selective antibacterial activity against Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), and Staphylococcus epidermidis. Some clinical MRSA strains showed remarkable susceptibility to quercetin. In combination with antibiotics, such as oxacillin, ampicillin, vancomycin, gentamicin, and erythromycin, quercetin sho...

2010-01-01

449

X-ray absorption spectroscopy of bacterial sulfur globules

The association of asymptomatic bacterial vaginosis with upper genital tract infection.

Sulfur K-edge X-ray absorption spectroscopy is a powerful in situ probe of sulfur biochemistry in intact cells and tissues. Under favorable circumstances the technique can provide quantitative information on the chemical identify of the sulfur species that are present in a sample. Prange et al. have recently reported an X-ray absorption spectroscopic study of bacterial sulfur storage globules. Unfortunately there are substantial problems with the experimental technique employed that, they contend, lead to completely erroneous conclusions. In the more recent of their two papers Prange et al. employed a curve-fitting method similar to that used by us (for more than 10 years). In essence, the method employs simply fitting a linear combination of the spectra of standard compounds to that of the unknown, in this case cultures of bacterial cells. This type of analysis can provide quantitative estimates of the individual sulfur types in the sample, ...

2002-08-01

450

Nonphotochemical Hole-Burning Studies of Energy Transfer Dynamics in Antenna Complexes of Photosynthetic Bacteria

Objective: To determine whether asymptomatic bacterial vaginosis (BV) is associated with upper genital tract inflammation or bacterial colonization.Methods: Fifty nonpregnant women with intact uteri who planned to undergo gynecologic surgery and had no recent symptoms of vaginal infection were enrolled. We obtained a vaginal swab for Gram stain, endocervical swab for chlamydia and gonorrhea DNA probe testing, and Pipelle endometrial biopsy for aerobic and anaerobic cultures and histology. We correlated surgical findings and histology of available surgical specimens with the microbiologic results. The diagnosis of BV was made according to Speigel's criteria. Bacteria isolated from the uterus were classified as high virulence versus low virulence. Contingency tables were analyzed using the chi-square or Fisher Exact tests.Results: Twenty-one of 50 patients had BV on Gram stain, 3 had intermediate BV, and 3 had unreadable slides. Eleven patients ...

1998-07-01

451

Isolation of imidacloprid degrading bacteria from industrial sites

This thesis contains the candidate's original work on excitonic structure and energy transfer dynamics of two bacterial antenna complexes as studied using spectral hole-burning spectroscopy. The general introduction is divided into two chapters (1 and 2). Chapter 1 provides background material on photosynthesis and bacterial antenna complexes with emphasis on the two bacterial antenna systems related to the thesis research. Chapter 2 reviews the underlying principles and mechanism of persistent nonphotochemical hole-burning (NPHB) spectroscopy. Relevant energy transfer theories are also discussed. Chapters 3 and 4 are papers by the candidate that have been published. Chapter 3 describes the application of NPHB spectroscopy to the Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Prosthecochloris aestuarii; emphasis is on determination of the low energy vibrational structure that is important for ...

2002-06-27

452

Bacterial radiosensitization by using radiation processing in combination with essential oil: Mechanism of action

Immidacloprid is a cyclodiene organochlorine used as an insecticide all over the world and possessing a serous environmental threat. It is mostly used for cotton insects (bollworm, aphid and white fly). For isolation of imidacloprid degrading bacteria, two soil samples were collected from industrial contaminated sites of Kala Shah Kahu district sheikupura, having ten year history of use. Soil samples were analyzed by measuring pH and electric conductivity. The isolation of imidacroprid degrading bacteria was performed by enrichment technique. Eight bacterial strains, S/sub 1-a/ S/2-2-b/ S/2-c/ S/2-d/ S/2-e/ S/sub 2-f/ and S/sub 2-g/ and S/sub e-a/ were isolated on the basis of their colony morphologies. The purified colonies were characterized morphologically, physiologically and biochemically. Gram staining was done and Gram negative strain were confirmed on MacConkey agar and Eosin Methylene Blue. Bacterial strains were also checked for ...

453

cDNA cloning, sequence analysis and organ distribution of horse preproendothelin-2.

Spice extracts under the form of essential oils were tested for their efficiency to increase the relative radiosensitivity of Listeria monocytogenes and Escherichia coli O157H7 in culture media. The two pathogens were treated by gamma-irradiation alone or in combination with oregano essential oil to evaluate their mechanism of action. The membrane murein composition, and the intracellular and extracellular concentration of ATP was determined. The bacterial strains were treated with two irradiation doses: 1.2 kGy to induce cell damage and 3.5 kGy to cause cell death for L. monocytogenes. A dose of 0.4 kGy to induce cell damages, 1.1 kGy to obtain viable but nonculturable (VBNC) state and 1.3 kGy to obtain a lethal dose was also applied on E. coli O157H7. Oregano essential oil was used at 0.020% and 0.025% (w/v), which is the minimum inhibitory concentration (MIC) for L. monocytogenes. For E. coli O157H7, a concentration of 0.006% and 0.025% (w/v) which is the ...

2009-07-15

454

The mitochondrial genome of the entomophagous endoparasite Xenosvesparum (Insecta: Strepsiptera)

We cloned and characterized horse preproendothelin-2 (PPET-2) cDNA from intestinal tissue. The cDNA encoded 178 amino acids of the PPET-2 polypeptide, in which a 21-amino-acid mature endothelin-2 peptide and a 16-amino acid endothelin-2-like peptide were found. For the open reading frame the correspondence of horse PPET-2 cDNA with those of the ferret, human, dog, mouse and rat was 85.1%, 84.9%, 82.1%, 77.8% and 77.2%, respectively. Analysis of the organ distribution of PPET-2 mRNA by reverse transcription-polymerase chain reaction demonstrated that the kidney, stomach and small intestine are major sites of expression of the PPET-2 gene. Surprisingly, the mRNA is not detected in the large intestine, where high expression is demonstrated in the mouse and rat. This difference may result from the underlying functional differences of the large intestine between a herbivore (horse) and an omnivore (mouse and rat). PMID:15838341

2004-11-01

455

Systems Biology Approach in Chlamydomonas Reveals Connections between Copper Nutrition and Multiple Metabolic Steps[C][W][OA

In this study, the nearly complete sequence (14,519 bp) of the mitochondrial DNA (mtDNA) of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera) is described. All protein coding genes (PCGs) are in the arrangement known to be ancestral for insects, but three tRNA genes (trnA, trnS(gcu), and trnL(uag)) have transposed to derived positions and there are three tandem copies of trnH, each of which is potentially functional. All of these rearrangements except for that of trnL(uag) is within the short span between nad3 and nad4 and there are numerous blocks of unassignable sequence in this region, perhaps as remnants of larger scale predisposing rearrangements. X. vesparum mtDNA nucleotide composition is strongly biased toward As and Ts, as is typical for insect mtDNAs. There is also significant strand skew in the distribution of these nucleotides, with the J-strand being richer in A than T and in C than G, and the N-strand showing an opposite skew for ...

2005-12-01

456

Purification and analysis of RNA polymerase II transcription factors by using wheat germ agglutinin affinity chromatography.

In this work, we query the Chlamydomonas reinhardtii copper regulon at a whole-genome level. Our RNA-Seq data simulation and analysis pipeline validated a 2-fold cutoff and 10 RPKM (reads per kilobase of mappable length per million mapped reads) (~1 mRNA per cell) to reveal 63 CRR1 targets plus another 86 copper-responsive genes. Proteomic and immunoblot analyses captured 25% of the corresponding proteins, whose abundance was also dependent on copper nutrition, validating transcriptional regulation as a major control mechanism for copper signaling in Chlamydomonas. The impact of copper deficiency on the expression of several O2-dependent enzymes included steps in lipid modification pathways. Quantitative lipid profiles indicated increased polyunsaturation of fatty acids on thylakoid membrane digalactosyldiglycerides, indicating a global impact of copper deficiency on the photosynthetic apparatus. Discovery of a putative plastid copper chaperone ...

2011-04-01

457

Nuclear factor of activated T cell (NFAT) transcription proteins regulate genes involved in adipocyte metabolism and lipolysis

We recently found that many RNA polymerase II transcription factors are modified with N-acetylglucosamine residues. These sugar moieties confer upon transcription factors an ability to bind the lectin wheat germ agglutinin. We have taken advantage of this interaction to devise a purification procedure for the "GC-box" binding transcription factor Sp1. Crude nuclear extracts are first subjected to wheat germ agglutinin affinity chromatography and then subjected to sequence-specific DNA affinity chromatography. The Sp1 protein purified by this procedure is at least 95% pure, and the overall recovery is greater than 80%. In addition to yielding larger quantities of Sp1 than conventional schemes, the new purification procedure is also simpler and more rapid. We show that wheat germ agglutinin affinity chromatography can also be used to purify the glycosylated forms of the CCAAT-binding transcription factor. Thus, wheat germ agglutinin affinity chromatography may aid ...

1989-03-01

458

Human T-cell lymphotropic virus type III infection of the central nervous system: a preliminary in situ analysis

NFAT involvement in adipocyte physiological processes was examined by treatment with CsA and/or GSK3{beta} inhibitors (Li{sup +} or TZDZ-8), which prevent or increase NFAT nuclear translocation, respectively. CsA treatment reduced basal and TNF{alpha}-induced rates of lipolysis by 50%. Adipocytes preincubated with Li{sup +} or TZDZ-8 prior to CsA and/or TNF{alpha}, exhibited enhanced basal rates of lipolysis and complete inhibition of CsA-mediated decreased rates of lipolysis. CsA treatment dramatically reduced the mRNA levels of adipocyte-specific genes (aP2, HSL, PPAR{gamma}, ACS and Adn), compared with control or TNF{alpha}-treatment, whereas Li{sup +} pretreatment blocked the inhibitory effects of CsA, and mRNA levels of aP2, HSL, PPAR{gamma}, and ACS were found at or above control levels. NFAT nuclear localization, assessed by EMSA, confirmed that CsA or Li{sup +} treatments inhibited or increased NFAT nuclear translocation, respectively. ...

2007-09-21

459

Hsp22 (HspB8/H11) knockdown induces sam68 expression and stimulates proliferation of glioblastoma cells

Patients with acquired immunodeficiency syndrome (AIDS) are subject to a spectrum of central nervous system (CNS) disorders. Recent evidence implicates the human T-cell lymphotropic virus type III (HTLV-III) in the pathogenesis of some of these illnesses, although the cells infected by the virus have yet to be identified. Using in situ hybridization, the authors examined brain tissue from two patients with AIDS encephalopathy for the presence of HTLV-III RNA. In both cases, viral RNA was detected and concentrated in, though not limited to, the white matter. The CNS cells most frequently infected included macrophages, pleomorphic microglia, and multinucleated giant cells. Less frequently, cells morphologically consistent with astrocytes, oligodendroglia, and rarely neurons were also infected. The findings strengthen the association of HTLV-III with the pathogenesis of AIDS encephalopathy. In situ hybridization can be applied to routinely ...

1986-11-07

460

British Library Electronic Table of Contents (United Kingdom)

Abstract Sam68 (Src-associated protein in mitosis 68-kDa) is a multifunctional protein, known to govern cellular signal transduction, transcription, RNA metabolism, proliferation, apoptosis, and HIV-1 replication. Although intrinsic mechanisms that modulate Sam68 function are beginning to emerge, the regulatory events contributing to its expression remain elusive. We previously reported that heat shock protein-22 (Hsp22) antagonizes Sam68 function in rev-response element (RRE)-mediated gene expression. We now demonstrate that Sam68 levels correlate inversely with Hsp22 in a variety of cells, including U87, Jurkat, 293T, and U-937. In U87 glioblastoma cells, which contained high levels of Hsp22 than other cell lines tested, Hsp22 knockdown dramatically increased both Sam68 mRNA and protein,...

2011-01-01

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

461

Heat shock factor binds to heat shock elements upstream of heat shock protein 70a and Samui genes to confer transcriptional activity in Bombyx mori diapause eggs exposed to 5^oC

British Library Electronic Table of Contents (United Kingdom)

To understand the molecular mechanisms of how 5^oC-incubation activates mRNA expression of Hsp70a and Samui genes in Bombyx mori diapause eggs, we first searched the 5'-upstream regions of the Hsp70a and Samui genes for heat shock elements (HSEs) and found two regions [Hsp70aHSE-1 (-95 to -58) and -2 (-145 to -121), and SamuiHSE-1 (-84 to -55) and -2 (-304 to -290)] corresponding to HSEs (repeats of nGAAn and/or nTTCn). We cloned four cDNAs encoding heat shock factor (HSF)-a2 (627 amino acids), -b (685 aa), -c (682 aa) and -d (705 aa), which were produced by alternative splicing. When we exposed diapause eggs to 5^oC beginning at 2 day post-oviposition to break diapause, HSFd mRNA only increased after chilling for 6-8 days, a pattern very similar to those of Hsp70a and Samui mRNAs. To exam...

2011-01-01

462

HSP70, the earliest-induced gene in the zebrafish retina during optic nerve regeneration: Its role in cell survival

British Library Electronic Table of Contents (United Kingdom)

Fish retinal ganglion cells (RGCs) can survive and regrow their axons after optic nerve injury. Injured RGCs express anti-apoptotic proteins, such as Bcl-2, after nerve injury; however, upstream effectors of this anti-apoptotic protein are not yet fully understood. Heat shock proteins (HSPs) play a crucial role in cell survival against various stress conditions. In this study, we focused on HSP70 expression in the zebrafish retina after optic nerve injury. HSP70 mRNA and protein levels increased rapidly 2.3-fold in RGCs by 1-6 h after injury and returned to control levels by 1-3 days. HSP70 transcription is regulated by heat shock factor 1 (HSF1). HSF1 mRNA and phosphorylated-HSF1 protein rapidly increased by 2.2-fold in RGCs 0.5-6 h after injury. Intraocular injection of HSP inhibitor I s...

2011-01-01

463

Four small puzzles that Rosetta doesn't solve

Magnetic silica extraction for low-viremia human immunodeficiency virus type 1 genotyping.

A complete macromolecule modeling package must be able to solve the simplest structure prediction problems. Despite recent successes in high resolution structure modeling and design, the Rosetta software suite fares poorly on deceptively small protein and RNA puzzles, some as small as four residues. To illustrate these problems, this manuscript presents extensive Rosetta results for four well-defined test cases: the 20-residue mini-protein Trp cage, an even smaller disulfide-stabilized conotoxin, the reactive loop of a serine protease inhibitor, and a UUCG RNA tetraloop. In contrast to previous Rosetta studies, several lines of evidence indicate that conformational sampling is not the major bottleneck in modeling these small systems. Instead, approximations and omissions in the Rosetta all-atom energy function currently preclude discriminating experimentally observed conformations from de novo models at atomic resolution. These molecular ...

2011-01-01

464

Influence of chromatin molecular changes on RNA synthesis during embryonic development

Nucleic acid extraction and human immunodeficiency virus type 1 (HIV-1) genotyping using the NucliSens miniMAG platform and the TruGene HIV-1 genotyping kit gave HIV-1 sequence data from HIV-1-negative plasma spiked with 100 copies/ml reference HIV-1 RNA and from low-viremia clinical samples (<500 copies/ml) without the need for ultracentrifugation or nested second-round PCR. PMID:17122019

2006-11-22

465

Acute gastric erosions in the rat. II. Viability of the gastric mucosa

Two aspects of the chromatin repeat length (r_l) are discussed: (i) Why is r_l longer for slowly dividing cells than in rapidly dividing cells?, and (ii) Why is the temporal evolution of r_l a decreasing function of time (t) in mammalian cortical neurons whereas it is an increasing function of t for granule cells around the time of birth? These questions are discussed in terms of a hypothesis which assumes a correlation between deoxyribonucleic acid (DNA) packaging, transcription, and replication. (author). 27 refs.

466

Viral RNA testing and automation on the bead-based CBNE detection microsystem.

The autoradiographic appearance of the gastric mucosa, 5 hours after administration of indomethacin, was investigated in 29 adult rats. Indomethacin induced superficial gastric erosions. Autoradiography demonstrated the presence of viable gastric cells (as deduced by their ability to incorporate 3H-cytidin, an RNA precursor) not only in the mucosa without erosions, but also in the mucosa underneath the superficial erosions. The results indicate that indomethacin induced gastric erosions are not the superficial expression of a necrotic process taking place in the full thickness of the gastric mucosa at a particular site. A lumen-borne mechanism appears to be responsible for the formation of erosive areas in the mucosa.

1981-01-01

467

Two and 8-azido photoaffinity probes. 2. Studies on the binding process of 2-5A synthetase by photosensitive ATP analogues

We developed prototype chemistry for nucleic acid hybridization on our bead-based diagnostics platform and we established an automatable bead handling protocol capable of 50 part-per-billion (ppb) sensitivity. We are working towards a platform capable of parallel, rapid (10 minute), raw sample testing for orthogonal (in this case nucleic acid and immunoassays) identification of biological (and other) threats in a single sensor microsystem. In this LDRD we developed the nucleic acid chemistry required for nucleic acid hybridization. Our goal is to place a non-cell associated RNA virus (Bovine Viral Diarrhea, BVD) on the beads for raw sample testing. This key pre-requisite to showing orthogonality (nucleic acid measurements can be performed in parallel with immunoassay measurements). Orthogonal detection dramatically reduces false positives. We chose BVD because our collaborators (UC-Davis) can supply samples from persistently infected animals; and because ...

2008-09-01

468

Protein-coding and non-coding gene expression analysis in differentiating human keratinocytes using a three-dimensional epidermal equivalent.

The photoaffinity probes [#gamma#-"3"2P]2-azidoATP (2-N_3ATP) and [#alpha#-"3"2P]8-azido-ATP (8-N_3ATP) were used to investigate the binding of ATP to highly purified 2-5A synthetase. 2-N_3APT and 8-N_3ATP are substrates for 2-5A synthetase. In this study the authors show that 2- and 8-N_3ATP are competitive inhibitors of the enzymatic conversion of ATP to 2-5A. Ultraviolet irradiation results in the photoinsertion of 2-N_3ATP and 8-N_3ATP into the enzyme. The covalent photoinsertion of [#alpha#-"3"2P]8-N_3ATP into the 2-5A synthetase is proportional to the inactivation of the enzyme as UV irradiation is increased. Photolabeling of 2-5A synthetase is saturated at 1.5 mM 2-N_3ATP and 2.0 mM 8-N_3ATP. Computer analysis of the curvilinear Scatchard plots of the 2-5A synthetase suggest the presence of high-affinity and low-affinity binding sites that may correspond to the acceptor and the 2'-adenylation sites of the enzyme. The competition of nucleotides for the covalent photoinsertion of ...

469

Localisation of the neuropeptide PACAP and its receptors in the rat parathyroid and thyroid glands.

The epidermal compartment is complex and organized into several strata composed of keratinocytes (KCs), including basal, spinous, granular, and cornified layers. The continuous process of self-renewal and barrier formation is dependent on a homeostatic balance achieved amongst KCs involving proliferation, differentiation, and cell death. To determine genes responsible for initiating and maintaining a cornified epidermis, organotypic cultures comprised entirely of stratified KCs creating epidermal equivalents (EE) were raised from a submerged state to an air/liquid (A/L) interface. Compared to the array profile of submerged cultures containing KCs predominantly in a proliferative (relatively undifferentiated) state, EEs raised to an A/L interface displayed a remarkably consistent and distinct profile of mRNAs. Cultures lifted to an A/L interface triggered the induction of gene groups that regulate proliferation, differentiation, and cell death. Next, differentially expressed microRNAs ...

2010-05-25

470

Gene rearrangement and radiation carcinogenesis

PACAP (pituitary adenylate cyclase activating polypeptide) is widely distributed neuropeptide acting via three subtypes of receptors, PAC(1), VPAC(1) and VPAC(2). Here we examined the localisation and nature of PACAP-immunoreactive nerves in the rat thyroid and parathyroid glands and defined the distribution of PAC(1), VPAC(1) and VPAC(2) receptor mRNA's. In the parathyroid gland a large number of nerve fibres displaying PACAP-immunoreactivity were distributed beneath the capsule, around blood vessels and close to glandular cells. Most of the PACAP-nerves were sensory, since they co-stored CGRP (calcitonin-gene-related peptide) and were sensitive to capsaicin-treatment. mRNA's for PAC(1) and VPAC(2) receptors occurred in the parathyroid gland, mainly located in the glandular cells. In the thyroid gland PACAP-immunoreactive nerve fibres were associated with blood vessels, thyroid follicles and parafollicular C-cells. A high degree of ...

2010-12-19

471

Hydration of swelling clay and bacteria interaction. An experimental in situ reaction study; Hydratation des argiles gonflantes et influence des bacteries. Etude experimentale de reaction in situ

The development of leukemia and thyroid cancer is characterized by activation of the abl oncogene and ret oncogene, respectively. In order to clarify the relationship between these gene aberrations and radiation, the pro-myelogenous leukemia-derived cell line HL60 and the thyroid cancer-derived cell line 8505C, were irradiated in vitro with 100Gy of X-rays. RNA was then extracted from 10"8 cells of the respective cell lines and examined by the reverse transcription PCR method for rearrangements of abl and ret genes. Five kinds of positive bands were observed in the HL-60 cells irradiated with 100Gy of X-ray. Similarly, six positive bands were also observed in the 8505C cells irradiated with 100Gy. In vitro X-irradiation activation of oncogenes found in radiation induced cancers imply that gene rearrangement by X-rays is involved in the development of malignant tumors. Furthermore, in an experiment to detect radiation effects in A-bomb survivors, ...

1993-11-01

472

[Study on denitrification characteristics of dynamic membrane based on nitrate liquid-membrane microelectrodes].

This study reports on the physical-chemical behaviour of swelling di-octahedral clays (smectites) and their interaction with aqueous solutions and bacteria (Shewanella putrefaciens). Experimental results are presented for compacted clays, hydrated under confined volume conditions, using a new type of reaction-cell (the 'wet-cell' of Warr and Hoffman, 2004) that was designed for in situ X-ray diffraction (XRD) measurement. For comparison, dispersed clay systems were studied using standard batch solutions subjected to varying degrees of agitation. The combination of time-dependent in situ XRD measurements with gravimetric measurements and calculated diffraction patterns using the CALCMIX software (Plancon and Drits, 1999) allowed to successful quantification of the dynamics of water uptake and storage. This analytical procedure combined with published water vapour adsorption data enabled determination of the abundance of structured water layers, developed in the ...

2008-01-15

473

[Dysspermia due to inflammation. The evaluation of sperm cultures].

Nitrate microelectrodes and ORP microelectrodes were fabricated to study the denitrification characteristics of dynamic membrane at different COD loadings. The denitrification process was found at 0.6-1 mm depth beneath the interface of biofilm/bulk. The results of ORP microelectrode also demonstrated that the ORP value in the range of denitrification area was between 88.6 approximately -128.4 mV which was appropriate to denitrification. When the COD loading was 0.45 kg/(m3 x d), the denitrification rate (NO3- -N) was the maximum of 0.6347 x 10(-6 mol/(L x s). With the increase of COD loading, the denitrification area was increasing and two layers with different denitrification rates emerged in the dynamic membrane. The phenomenon implied the effect of organic concentration, oxygen concentration and bacterial competition on the denitrification rate. PMID:17117632

2006-09-01

474

Use of flow cytometry to compare the antimicrobial efficacy of silver-containing wound dressings against planktonic Staphylococcus aureus and Pseudomonas aeruginosa

The study evaluates 160 cases of positive spermioculture taken from 522 sterile individuals examined by the authors at the Couple Sterility Outpatient unit in Department A of the Institute of Gynecology and Obstetrics at Turin University during the period between January 1984 and December 1993. The germs responsible for infection were assayed in order to evaluate the strains which showed the highest incidence every year. Whereas there was no significant change in the absolute number of cases of sterility over the period, the number of cases caused by infection increased significantly during the second five-year period. It was found that the germs predominantly implicated in the genesis of male sterility formed part of the so-called mixed flora group, responsible in women for syndromes of often asymptomatic bacterial vaginosis which are not identified and consequently not treated. PMID:8559444

475

British Library Electronic Table of Contents (United Kingdom)

Abstract Silver-impregnated wound dressings continue to be routinely used for the management of infected wounds, or wounds that are at risk of becoming infected. The ability of antimicrobials that have been incorporated into wound dressings to kill microorganisms within the dressing requires appropriate evaluation using in vitro models. In vitro models that have been exploited for this purpose have included the corrected zone of inhibition and the log reduction assay. However, these and other related culturable-based assays are purported to have poor correlation with the overall microbicidal barrier activity of an antimicrobial wound dressing. This is because culturable-based methods only retrospectively indicate bacterial cell death and do not take into account viable but nonculturable st...

2011-01-01

476

The type III secretion system is involved in Escherichia coli K1 interactions with Acanthamoeba

British Library Electronic Table of Contents (United Kingdom)

The type III secretion system among Gram-negative bacteria is known to deliver effectors into host cell to interfere with host cellular processes. The type III secretion system in Yersina, Pseudomonas and Enterohemorrhagic Escherichia coli have been well documented to be involved in the bacterial pathogenicity. The existence of type III secretion system has been demonstrated in neuropathogenic E. coli K1 strains. Here, it is observed that the deletion mutant of type III secretion system in E. coli strain EC10 exhibited defects in the invasion and intracellular survival in Acanthamoeba castellanii (a keratitis isolate) compared to its parent strain. Next, it was determined whether type III secretion system plays a role in E. coli K1 survival inside Acanthamoeba during the encystment process...

2011-01-01

477

The influence of ultrasound on the fluoroquinolones antibacterial activity

British Library Electronic Table of Contents (United Kingdom)

In this work, the antibacterial effect of fluoroquinolones (FQs) upon Escherichia coli (E.coli) was measured with and without application of 40kHz ultrasound (US) stimulation. The research results demonstrated that simultaneous application of 40kHz US apparently enhanced the antibacterial effectiveness of FQs. That is, the synergistic effect was observed and the bacterial viability was reduced when FQs and US were combined. In addition, various influencing factors, such as FQs drug concentration, US irradiation time and solution temperature, on the inhibition of E.coli were also investigated. The antibacterial activity was enhanced apparently with increasing of FQs drug concentration, US irradiation time and solution temperature. Furthermore, we discussed preliminarily the mechanism of US ...

2011-01-01

478

Synthesis, Characterization and Biological Properties of Anions of Bivalent Transition Metal [Co(II) and Ni(II)] Complexes With Acylhydrazine Derived ONO Donor Schiff Bases.

Sodium-driven motor of the polar flagellum in marine bacteria Vibrio

Some acylhydrazine derived ONO donor Schiff bases and their Co(II) and Ni(II) complexes have been prepared having the same metal ion (cation) but different anions. These synthesized metal(II) complexes have been characterized on the basis of their elemental analyses, magnetic moment, molar conductance, and IR and electronic spectral data. All of the Schiff base ligands function as tridentates and the deprotonated enolic form is preferred for coordination. In order to evaluate the effect of anions on the bactericidal activity, these synthesized complexes, in comparison to the uncomplexed Schiff bases have been screened against bacterial species., Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa and the results are reported. PMID:18475936

2000-01-01

479

British Library Electronic Table of Contents (United Kingdom)

The Na+-driven bacterial flagellar motor is a molecular machine powered by an electrochemical potential gradient of sodium ions across the cytoplasmic membrane. The marine bacterium Vibrio alginolyticus has a single polar flagellum that enables it to swim in liquid. The flagellar motor contains a basal body and a stator complexes, which are composed of several proteins. PomA, PomB, MotX, and MotY are thought to be essential components of the stator that are required to generate the torque of the rotation. Several mutations have been investigated to understand the characteristics and function of the ion channel in the stator and the mechanism of its assembly around the rotor to complete the motor. In this review, we summarize recent results of the Na+-driven motor in the polar flagellum of ...

2011-01-01

480

Root Hairs Play a Key Role in the Endophytic Colonization of Olive Roots by Pseudomonas spp. with Biocontrol Activity

British Library Electronic Table of Contents (United Kingdom)

The use of indigenous bacterial root endophytes with biocontrol activity against soil-borne phytopathogens is an environmentally-friendly and ecologically-efficient action within an integrated disease management framework. The earliest steps of olive root colonization by Pseudomonas fluorescens PICF7 and Pseudomonas putida PICP2, effective biocontrol agents (BCAs) against Verticillium wilt of olive (Olea europaea L.) caused by the fungus Verticillium dahliae Kleb., are here described. A gnotobiotic study system using in vitro propagated olive plants, differential fluorescent-protein tagging of bacteria, and confocal laser scanning microscopy analysis have been successfully used to examine olive roots?Pseudomonas spp. interactions at the single-cell level. In vivo simultaneous visualization...

2011-01-01

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481

R46 and pKM101 plasmid-mediated resistance to ionizing radiation in Escherichia coli

Practical applications and feasibility of efflux pump inhibitors in the clinic-A vision for applied use

The ability of the R46 R factor and its derivative pKM101 to modify sensitivity to "6"0Co #gamma# radiation was studied. In Escherichia coli K12 both plasmids enhanced bacterial survival after "6"0Co #gamma# irradiation. This effect was dependent on recA"+ genotype but not on recB"+, recB"+recC"+, and recF"+ genotypes. 5-Fluorouracil eliminated the R46 R factor from the parent and its rec"- mutant strains. These strains lost not only the antibiotic resistance coded for R46 R factor but their radioresistance as well.

482

British Library Electronic Table of Contents (United Kingdom)

The world of antibiotic drug discovery and development is driven by the necessity to overcome antibiotic resistance in common Gram-positive and Gram-negative pathogens. However, the lack of Gram-negative activity among both recently approved antibiotics and compounds in the developmental pipeline is a general trend despite the fact that the plethora of covered drug targets are well-conserved across the bacterial kingdom. Such intrinsic resistance in Gram-negative bacteria is largely attributed to the activity of multidrug resistance (MDR) efflux pumps. Moreover, these pumps also play a significant role in acquired clinical resistance. Together, these considerations make efflux pumps attractive targets for inhibition in that the resultant efflux pump inhibitor (EPI)/antibiotic combination d...

2006-01-01

483

Novel Techniques and Their Wide Applications to Health Foods, Medical and Agricultural Biotechnology in Relation to Policy Making on Genetically Modified Crops and Foods

Non-toxigenic Clostridium sordellii: Clinical and microbiological features of a case of cholangitis-associated bacteremia

Selected applications of novel techniques in Agricultural Biotechnology, Health Food formulations and Medical Biotechnology are being reviewed with the aim of unraveling future developments and policy changes that are likely to open new markets for Biotechnology and prevent the shrinking or closing of existing ones. Amongst the selected novel techniques with applications in both Agricultural and Medical Biotechnology are: immobilized bacterial cells and enzymes, microencapsulation and liposome production, genetic manipulation of microorganisms, development of novel vaccines from plants, epigenomics of mammalian cells and organisms, and biocomputational tools for molecular modeling related to disease and Bioinformatics. Both fundamental and applied aspects of the emerging new techniques are being discussed in relation to their anticipated, marked impact on future markets and present policy changes that are needed for success in either Agricultural or Medical ...

2004-01-01

484

British Library Electronic Table of Contents (United Kingdom)

Toxigenic Clostridium sordellii strains are increasingly recognized to cause highly lethal infections in humans that are typified by a toxic shock syndrome (TSS). Two glucosylating toxins, lethal toxin (TcsL) and hemorrhagic toxin (TcsH) are believed to be important in the pathogenesis of TSS. While non-toxigenic strains of C. sordellii demonstrate reduced cytotoxicity in vitro and lower virulence in animal models of infection, there are few data regarding their behavior in humans. Here we report a non-TSS C. sordellii infection in the context of a polymicrobial bacterial cholangitis. The C. sordellii strain associated with this infection did not carry either the TcsL-encoding tcsL gene or the tcsH gene for TcsH. In addition, the strain was neither cytotoxic in vitro nor lethal in a murine...

2011-01-01

485

N-acetoxy-N-2-acetylaminofluorene induced frameshift mutations: a comparison between the DNA modification spectrum and the mutation spectrum

In vitro diffusion bed, 3-day repeat challenge `capacity' test for antimicrobial wound dressings:

We describe the analysis of forward mutations induced in the tetracycline resistance gene of the plasmid pBR322 by directing the reaction of the carcinogen N-acetoxy-N-2-acetylaminofluorene (N-AcO-AAF) to a small restriction fragment (BamHI, SalI) that is located in the proximal part of the antibiotic-resistance gene. Mutant plasmids obtained both in wild type and excision repair deficient (uvrA) bacterial cells are compared. Preliminary data showing the distribution of the -AAF adducts along this restriction fragments are discussed in relation to the observed spectrum of mutations. 20 references, 4 figures.

486

British Library Electronic Table of Contents (United Kingdom)

Greenman J, Thorn RMS, Saad S, Austin AJ. In vitro diffusion bed, 3-day repeat challenge `capacity' test for antimicrobial wound dressings. Int Wound J 2006;3:322-329. Abstract The aim of this study was to develop an in vitro wound infection model that allows the comparison of the bacterial kill rate of antimicrobial wound dressings over the course of 3 days, with renewed microbial challenges each day, under realistic wound-like conditions. A test bed model of a moderately exuding wound was constructed from a hydrogel containing releasable foetal calf serum (FCS), and cellulose discs dosed with test microbes (Methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa) suspended in 50% FCS applied at the interface between the test dressing and the hydrogel test bed. Freshly prep...

2006-01-01

487

How microcystin-degrading bacteria express microcystin degradation activity

British Library Electronic Table of Contents (United Kingdom)

Abstract Alkali tolerance and the mechanism of microcystin (MC) degradation were investigated in the MC-degrading bacterial species, Sphingopyxis sp. C-1, to better understand the increased MC degradation under the alkaline conditions that arise during the disappearance of water blooms. MC-degrading bacteria harbour mlrA, mlrB and mlrC that encode MC-degrading enzymes. Sphingopyxis sp. C-1 also possesses these genes, as well as the mlrD gene that has been assumed to encode MC and its degradation transporter. This study demonstrated that MC degradation activity was promoted by the intermittent addition of microcystin-LR (MCLR) to cultures of strain C-1. That the expression of mlrA, mlrB and mlrC is induced by MCLR also was indicated, whereas that of mlrA and mlrB is induced by the MCLR degr...

2011-01-01

488

Growth promotion and induction of resistance in tomato plant against Xanthomonas euvesicatoria and Alternaria solani by Trichoderma spp.

British Library Electronic Table of Contents (United Kingdom)

In tomato crop, the induction of resistance emerges as an important alternative for achieving the reduction of chemicals in disease control. This study aimed to evaluate the ability of 28 Trichoderma isolates to promote the growth of tomato seedlings and to induce systemic resistance (ISR) against Xanthomonas euvesicatoria and Alternaria solani, the causal agents of bacterial spot and early blight, respectively. Twelve isolates promoted the increase of plant dry matter mass (DMM) above 100%, showing the great potential of these strains. All isolates were able to colonize the root system of tomato plants. The plant growth-promoting isolates were further evaluated for potential elicitation of ISR. Treatment of the soil with all Trichoderma isolates provided protection in tomato plants from 2...

2011-01-01

489

Enhanced antibacterial activity of bifunctional Fe3O4-Ag core-shell nanostructures

British Library Electronic Table of Contents (United Kingdom)

We describe a simple one-pot thermal decomposition method for the production of a stable colloidal suspension of narrowly dispersed superparamagnetic Fe3O4-Ag core-shell nanostructures. These biocompatible nanostructures are highly toxic to microorganisms. Antimicrobial activity studies were carried out on both Gram negative (Escherichia coli and Proteus vulgaris) and Gram positive (Bacillus megaterium and Staphylococcus aureus) bacterial strains. Efforts have been made to understand the underlying molecular mechanism of such antibacterial actions. The effect of the core-shell nanostructures on Gram negative strains was found to be better than that observed for silver nanoparticles. The minimum inhibitory concentration (MIC) values of these nanostructures were found to be considerably lowe...

2009-01-01

490

Electrochemistry of a semiconductor chalcopyrite concentrate leaching by Thiobacillus ferrooxidans

Effects of Scutellaria baicalensis on chronic cerebral hypoperfusion-induced memory impairments and chronic lipopolysaccharide infusion-induced memory impairments

Using carbon-paste-CuFeS{sub 2} electrodes and a cyclic voltammetric technique, it was found that a large number of intermediate electrochemical oxidation reactions were associated with the dissolution of chalcopyrite in presence and absence of bacteria. The effects of concentrations of copper, ferrous and ferric ions, as well as of agitation on the peaks of cyclic voltammograms were measured. It was established that chalcopyrite oxidation was solid-state controlled as suggested by the data of chronopotentiometric and chronoamperometric measurements. The activation energy of solid state diffusion of chalcopyrite leaching was determined by the Sand's method to be {triangle}E{sub a} = 20.5 kJ. The leaching mechanism is discussed in terms of solid-state properties (energy bonding) of the n-type semiconductor chalcopyrite and energy density states of redox systems of acidic bacterial leach media. A generalized model for the mechanism of chalcopyrite leaching ...

1991-01-01

491

British Library Electronic Table of Contents (United Kingdom)

Ethnopharmacological relevance: Extracts of the roots of Scutellaria baicalensis Georgi (Labiatae) have been widely used to relieve fever related to bacterial infection and inflammatory diseases in traditional Korean medicine and have been reported to be effective in brain diseases. These experiments were conducted to examine the effects of oral administration of Scutellaria baicalensis extracts on the rescue of memory impairments induced by chronic cerebral hypoperfusion or chronic lipopolysaccharide (LPS) infusion. In addition, the underlying mechanisms of these effects were investigated. Materials and methods: In the first experiment, chronic cerebral hypoperfusion was induced in male Wister rats by bilateral common carotid artery occlusion (BCCAo). Daily administration of Scutellaria b...

2011-01-01

492

Effect of carbon dioxide on the performance of biogas/diesel dual-fuel engine

Complexation of nitrogen and sulphur donor Schiff's base ligand to Cr(III) and Ni(II) metal ions: Synthesis, spectroscopic and antipathogenic studies

Methane and carbon dioxide are the two main constituents of biogas. Biogas also contains traces of nitrogen, hydrogen, oxygen and hydrogen sulphide. When diesel engine runs on biogas, the combustion is poor as compared to diesel fuel. One of the reasons of poor combustion is the presence of carbon dioxide in the biogas. Percentage of methane and carbon dioxide in biogas varies with maturities of feed stock, temperature, water content, loading rate of raw material and bacterial actions. This paper examines the effect of variations of carbon dioxide in biogas on the performance of the engine to simulate the performance of the engine running with biogas from different sources (varying proportion of methane and carbon dioxide). (Author)

1996-09-01

493

British Library Electronic Table of Contents (United Kingdom)

2,6-Diacetyl pyridine based ligand was synthesized by the reaction of 2,6-diacetyl pyridine with thiocarbohydrazide in presence of acetic acid. The coordination compounds with Cr(III) and Ni(II) metal ions having [Cr(L)X]X2 and [Ni(L)X]X compositions (where L=ligand and X=NO3^-, Cl^- and CH3COO^-) were synthesized and characterized by physicochemical and spectral studies. The studies like elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, UV-Vis, NMR, mass and EPR reveal that the complexes are octahedral. The compounds were examined against the pathogenic fungal and bacterial strains like Alternaria brassicae, Aspergillus niger, Fusarium oxysporum, Xanthomonas compestris and Pseudomonas aeruginosa. A. niger causes the diseases Apergillosis and Oto...

2011-01-01

494

Chitinolytic enzyme production and genetic improvement of a new isolate belonging to Streptomyces anulatus

British Library Electronic Table of Contents (United Kingdom)

Thirty bacterial isolates were obtained from different sources and sites at Jeddah, Saudi Arabia, on chitin agar medium; 9 of the 30 isolates were cultured in liquid medium containing chitin as sole carbon and nitrogen sources. Isolate SM21, which was isolated from shrimp shells, showed the best growth and chitinase production in liquid medium. According to its morphological, physiological and biochemical characteristics, SM21 belongs to the genus Streptomyces and was identified as Streptomyces anulatus SM21. Identification was confirmed using 16S rDNA analysis. The chitinase enzyme was precipitated with 80% NH4SO4 and purified using DEAE-cellulose ion exchange chromatography followed by Sephadex G-100 gel filtration. The molecular weight determined using sodium dodecyl sulfate polyacrylam...

2011-01-01

495

Bottom-up carbon subsidies and top-down predation pressure interact to affect aquatic food web structure

British Library Electronic Table of Contents (United Kingdom)

Human impacts such as eutrophication, overexploitation and climate change currently threaten future global food and drinking water supplies. Consequently, it is important that we understand how anthropogenic resource (bottom-up) and consumer (top-down) manipulations affect aquatic food web structure and production. Future climate changes are predicted to increase the inputs of terrestrial dissolved organic carbon to lakes. These carbon subsidies can either increase or decrease total basal production in aquatic food webs, depending on bacterial competition with phytoplankton for nutrients. This study examines the effects of carbon subsidies (bottom-up) on a pelagic community exposed to different levels of top-down predation. We conducted a large scale mesocosm experiment in an oligotrophic ...

2011-01-01

496

Application of a leukocyte and nitrite urine test strip to the management of children with neurogenic bladder.