UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

Science.gov (United States)

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 ...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

Hairpin oligonucleotides were synthesized with stems ending in a double-stranded structure, which can be ligated to double-strand breaks in DNA, and with loops that contain nucleotides modified by the...Full Text Available

Energy Technology Data Exchange (ETDEWEB)

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 ...

UK PubMed Central (United Kingdom)

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

Science.gov (United States)

In a previous study, to identify genes of importance for hepatocellular carcinogenesis, and especially for processes involved in malignant transformation, the authors investigated differences in gene expression between adenomas and carcinomas by DNA microarray. In the present study, the authors investigated AW434047, one of the sequences that was upregulated in carcinomas. The investigation led to the identification of a novel gene, which the authors named hepatocyte malignant transforming factor (HMTF), of unknown function whose expression was increased in hepatocellular carcinomas. Northern blot and in situ hybridization also demonstrated high levels of HMTF in rat hepatocellular carcinoma (HCC) cell lines, lymphocytes in the spleen, colon mucosal epithelia, spermatocytes, and granule cells of the hippocampus. Reduction of HMTF by RNA interference (RNAi) in N1 cells, an HCC cell line, caused suppression of cell proliferation, invasion, and ...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

CERN Document Server

Femtocell is emerging as a key technology to secure the coverage and capacity in indoor environments. However the deployment of a new femtocell layer may originate undesired interference to the whole system. This paper investigates spectrum resource coordination and interference management for the femtocell networks. A resource coordination scheme based on broadcasting resource coordination request messages by the femto mobile is proposed to reduce the system interference.

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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.

Science.gov (United States)

PMID:21331648

KoreaScience (Korea)

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Norwegian Open Research Archives (NORA)

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UK PubMed Central (United Kingdom)

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

CERN Document Server

This paper proposes two interference mitigation strategies that adjust the maximum transmit power of femtocell users to suppress the cross-tier interference at a macrocell base station (BS). The open-loop and the closed-loop control suppress the cross-tier interference less than a fixed threshold and an adaptive threshold based on the noise and interference (NI) level at the macrocell BS, respectively. Simulation results show that both schemes effectively compensate the uplink throughput degradation of the macrocell BS due to the cross-tier interference and that the closed-loop control provides better femtocell throughput than the open-loop control at a minimal cost of macrocell throughput.

UK PubMed Central (United Kingdom)

Pain and pain-related interference with physical function have not been thoroughly studied in individuals who have undergone knee-disarticulation amputations. The principal aim of this study...Full Text Available

Science.gov (United States)

This report covers a further year's work on the development of an Interference Electron Microscope at Imperial College. The instrument is unlike others of its type which have been operated. The basic innovations are to produce the critical illumination co...

J-STORE (Japan)

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Science.gov (United States)

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 ...

Science.gov (United States)

Field surveys were conducted to assess the community annoyance potential from electromagnetic interference to television reception (TVI) and acoustic emissions associated with the operation of a Darrieus-type, vertical axis wind turbine (VAWT). The type and extent of interference to nearby television reception was evaluated using a 17 meter VAWT. A series of measurements of observed interference levels were made at a number of sites in the turbine vicinity employing the locally available VHF and UHF television signals as sources. A simple theoretical model was developed for analyzing the TVI produced by the Darrieus turbine. Using this model in conjunction with the field measurements, it was found the Darrieus/VAWT produces the same amount of interference on the lower VHF channels as a horizontal axis turbine with a comparably sized blade scattering area, but less on all other channels.

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

Energy Technology Data Exchange (ETDEWEB)

Protein motions on all timescales faster than molecular tumbling are encoded in the spectral density. The dissection of complex protein dynamics is typically performed using relaxation rates determined at high and ultra-high field. Here we expand this range of the spectral density to low fields through field cycling using the nucleocapsid protein of the SARS coronavirus as a model system. The field-cycling approach enables site-specific measurements of R{sub 1} at low fields with the sensitivity and resolution of a high-field magnet. These data, together with high-field relaxation and heteronuclear NOE, provide evidence for correlated rigid-body motions of the entire {beta}-hairpin, and corresponding motions of adjacent loops with a time constant of 0.8 ns (mesodynamics). MD simulations substantiate these findings and provide direct verification of the time scale and collective nature of these motions.

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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...

British Library Electronic Table of Contents (United Kingdom)

Resonant scattering of atoms with formation of the Feshbach resonance in the presence of a laser radiation coupling the levels of two bound atoms (a molecule) is considered. The laser field leads to a second resonance in scattering and broadening of resonances, which facilitates the possibility of experimental observation of asymmetry of the total scattering cross-section arising because of interference between resonant and potential scatterings. The effects associated with interference of the two channels of decay of a bound system of two atoms (a molecule) in the laser field are studied. An expression is obtained for the scattering length in collision of two cold atoms in the field of laser radiation.

Science.gov (United States)

... AFRL-RV-PS-TP-2010-1001 9. SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. ... (Clearance #377 ABW-2009-1628) 13. ...

UK PubMed Central (United Kingdom)

Insect growth regulators (IGRs) are a class of new chemicals that interfere with maturation and reproduction in insects. Proposed hypotheses on the biochemical mechanism of action are presented herein....Full Text Available

UK PubMed Central (United Kingdom)

Legionella causes severe pneumonia in humans. The pathogen produces an array of effectors, which interfere with host cell functions. Among them are the glucosyltransferases Lgt1, Lgt2...Full Text Available

Energy Technology Data Exchange (ETDEWEB)

Energy spectra of the Bragg reflection of the Moessbauer ..gamma..-radiation from the /sup 57/Fe/sub 3/BO/sub 6/ weakly ferromagnetic monocrystal are studied. A strong effect of the interference transitions in iron nuclei, being in non-equivalent positions, on the spectra form is revealed. The measurement results are compared with theoretical calculations.

Science.gov (United States)

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 ...

Energy Technology Data Exchange (ETDEWEB)

Electron interference in the presence of nonclassical microwaves with frequency {omega}{sub 1} and classical RF radiation with frequency {omega}{sub 2}, is studied. The relative phase factor between the two electron beams is a quantum-mechanical operator, whose expectation value with regard to the density matrix describing the nonclassical microwaves, determines the interference. It is shown that the visibility of the time-averaged intensity is a constant for all irrational values of {omega}{sub 1}/{omega}{sub 2}, and shows peaks (fractional Shapiro steps) at all rational values. These peaks can provide direct experimental evidence of the highly nonlinear processes of frequency conversion from {ital N} photons with frequency {omega}{sub 1}, to {ital M} photons with frequency {omega}{sub 2}. Results for various types of nonclassical microwaves (e.g., coherent states, squeezed states, number eigenstates, etc.) are derived and a comparison with ...

Energy Technology Data Exchange (ETDEWEB)

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.

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

Energy Technology Data Exchange (ETDEWEB)

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.

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...

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...

CERN Document Server

Zinc-fingers, which widely exist in eukaryotic cell and play crucial roles in life processes, depend on the binding of zinc ion for their proper folding. To computationally study the zinc coupled folding of the zinc-fingers, charge transfer and metal induced protonation/deprotonation effects have to be considered. Here, by attempting to implicitly account for such effects in classical molecular dynamics and performing intensive simulations with explicit solvent for the peptides with and without zinc binding, we investigate the folding of the Cys2His2 type zinc-finger motif and the coupling between the peptide folding and zinc binding. We find that zinc ion not only stabilizes the native structure, but also participates in the whole folding process. It binds to the peptide at early stage of folding, and directs or modulates the folding and stabilizations of the component beta-hairpin and alpha-helix. Such a crucial role of zinc binding is mediated by the packing of ...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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.

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

International Nuclear Information System (INIS)

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).

UK PubMed Central (United Kingdom)

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

CERN Document Server

We report on a two-photon interference experiment in a quantum relay configuration using two picosecond regime PPLN waveguide based sources emitting paired photons at 1550 nm. The results show that the picosecond regime associated with a guided-wave scheme should have important repercussions for quantum relay implementations in real conditions, essential for improving both the working distance and the efficiency of quantum cryptography and networking systems. In contrast to already reported regimes, namely femtosecond and CW, it allows achieving a 99% net visibility two-photon interference while maintaining a high effective photon pair rate using only standard telecom components and detectors.

International Nuclear Information System (INIS)

We report the observation of quantum interference in superfluid 4He. The interferometer, an analog of a dc-superconducting quantum interference device (SQUID), employs a recently reported phenomenon wherein superfluid 4He exhibits Josephson frequency oscillations in an array of submicron apertures. An interference pattern is generated by reorienting the loop of the superfluid 'SQUID' with respect to the Earth's rotation vector, thereby varying the rotation flux in the loop. The experiment is performed at 2 K, a temperature 2000 times higher than previously achieved with superfluid 3He. We find that the interference exists not only when the aperture array current-phase relation is a sinusoidal function characteristic of the Josephson effect, but also at lower temperatures where it is linear and oscillations occur by phase slips. The modest requirements for the interferometer (2 K cryogenics and ...

UK PubMed Central (United Kingdom)

While research on cognitive control has addressed the effects that different forms of cognitive interference have on behavior and the activities of certain brain regions, until recently scientific...Full Text Available

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

Patients experiencing several cancers can be a challenge, as optimal treatment options for the different cancers might interfere with each other. In this case report, we present a woman diagnosed with...Full Text Available

UK PubMed Central (United Kingdom)

ET-743 (trabectedin; Yondelis) is approved in Europe for the treatment of soft tissue sarcomas. Emerging phase 1 and 2 clinical data have shown high response rates in myxoid liposarcoma in part owing...Full Text Available

Science.gov (United States)

The previously unknown property of the optical speckle pattern reported. The interference of a speckle with the counterpropagating phase-conjugated (PC) speckle wave produces a randomly distributed ensemble of a twisted entities (ropes) surrounding optical vortex lines. These entities appear in a wide range of a randomly chosen speckle parameters inside the phase-conjugating mirrors regardless to an internal physical mechanism of the wave-front reversal. These numerically generated interference patterns are relevant to the Brillouin PC mirrors and to a four-wave mixing PC mirrors based upon laser trapped ultracold atomic cloud.

Science.gov (United States)

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 ...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

Science.gov (United States)

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/. ...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

Energy Technology Data Exchange (ETDEWEB)

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.

Science.gov (United States)

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 ...

CERN Document Server

Two dimensional Fourier spectra of near-infrared images of galaxies provide a powerful diagnostic tool for the detection of spiral arm modulation in stellar disks. Spiral arm modulation may be understood in terms of interference patterns of outgoing and incoming density wave packets or modes. The brightness along a spiral arm will be increased where two wave crests meet and constructively interfere, but will be decreased where a wave crest and a wave trough destructively interfere. Spiral arm modulation has hitherto only been detected in grand design spirals (such as Messier 81). Spiral arm amplitude variations have the potential to become a powerful constraint for the study of galactic dynamics. We illustrate our method in two galaxies: NGC 4062 and NGC 5248. In both cases, we have detected trailing and leading m=2 waves with similar pitch angles. This suggests that the amplification mechanism is the WASER type II. In this ...

Energy Technology Data Exchange (ETDEWEB)

Radio interference and TV interference are being a problem in urban and rural areas. This interference is generated by high voltage transmission lines as well as distribution lines. The radio noise can be produced by polluted or damaged insulators, and by metal parts of the distribution lines. The corona effect on the surface of the dielectric material produces high frequency electromagnetic fields during the ionization and during the recombination period. Fields of different intensity are produced by positive voltage and negative voltage. The insulator flashover (leaking current) also produces electromagnetic fields. A new technique to measure these fields was developed. This technique measures the radiated fields on time domain and on frequency domain. This permits us to characterize the radiated field and thus identify the type of the source. Several measurements were done varying the type of the RF generator, i.e., new ...

Energy Technology Data Exchange (ETDEWEB)

Eukaryotic genomes encode a zinc finger protein (ZPR1) with tandem ZPR1 domains. In response to growth stimuli, ZPR1 assembles into complexes with eukaryotic translation elongation factor 1A (eEF1A) and the survival motor neurons protein. To gain insight into the structural mechanisms underlying the essential function of ZPR1 in diverse organisms, we determined the crystal structure of a ZPR1 domain tandem and characterized the interaction with eEF1A. The ZPR1 domain consists of an elongation initiation factor 2-like zinc finger and a double-stranded {beta} helix with a helical hairpin insertion. ZPR1 binds preferentially to GDP-bound eEF1A but does not directly influence the kinetics of nucleotide exchange or GTP hydrolysis. However, ZPR1 efficiently displaces the exchange factor eEF1B from preformed nucleotide-free complexes, suggesting that it may function as a negative regulator of eEF1A activation. Structure-based mutational and complementation analyses reveal ...

Energy Technology Data Exchange (ETDEWEB)

Increase in power utility loads in industrialized countries, as well as developing countries, demands a higher level of transmission line voltage. Radio interference (RI) problems have been determined to be a limiting factor in selecting the size of transmission line conductors. Transmission line noise is primarily caused by corona discharges in the immediate vicinity of the conductor. It has been observed that discharges occur during both half-cycles of the applied voltage, but positive corona is usually predominant at AM radio frequencies range with practical high-voltage and extra high-voltage transmission lines. The corona radio noise effect is highly dependent upon the presence of particles on the surface of the conductor and the increase of the electrical gradient beyond the breakdown value of the air. Therefore, corona radio noise varies significantly with the weather and atmospheric conditions and generally increases by 10 to 30 dB in foul weather.

International Nuclear Information System (INIS)

Increase in power utility loads in industrialized countries, as well as developing countries, demands a higher level of transmission line voltage. Radio interference (RI) problems have been determined to be a limiting factor in selecting the size of transmission line conductors. Transmission line noise is primarily caused by corona discharges in the immediate vicinity of the conductor. It has been observed that discharges occur during both half-cycles of the applied voltage, but positive corona is usually predominant at AM radio frequencies range with practical high-voltage and extra high-voltage transmission lines. The corona radio noise effect is highly dependent upon the presence of particles on the surface of the conductor and the increase of the electrical gradient beyond the breakdown value of the air. Therefore, corona radio noise varies significantly with the weather and atmospheric conditions and generally increases by 10 to 30 dB in foul weather.

CERN Document Server

Solid-state single-photon sources have many desirable features that make them attractive for applications in quantum information processing. However, the phase coherence of such devices can be severely compromised by coupling to the solid-state environment. Here, we study the effects of realistic dephasing environments on a pair of solid-state single photon sources in the context of quantum interference effects such as the Hong-Ou-Mandel dip. By means of exact solutions for the non-Markovian dynamics of the sources, we show that the resulting loss of visibility depends crucially on the timing of photon detection events. Our results demonstrate that the effective visibility can be improved via temporal post-selection, and also that time-resolved interference can be a useful probe of the interaction between the emitter and its host environment.

Energy Technology Data Exchange (ETDEWEB)

We present ANAPPRES V1.0, the first version of a computerized expert system capable of analyzing constant- and variable-flowrate interference tests, in which there is one active well and an arbitrary number of observation wells, in liquid-saturated homogeneous reservoirs. ANAPPRES successfully couples mathematical models, optimization techniques, heuristic knowledge and computerized graphics, a combination not often found in published expert systems. Its main advantages are that it is user friendly, requires essentially no experience on the part of the analyst, eliminates subjectivity associated with earlier techniques of analysis, can handle complex cases and large data sets, completes the analysis of even the most complex cases (including plotting the results) in one run, and is significantly faster than a human expert.

International Nuclear Information System (INIS)

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 ...

Science.gov (United States)

The K alpha / K beta ratio of Mn KX-rays scattered by metallic samples changed remarkably with the geometry between the sample and the (55)Fe source-Si(Li) detector system. On the contrary, this intensity ratio changed little in the cases of non-metallic scatterer samples such as lucite or mylar. This difference is interpreted as due to the occurrence of strong or weak interference in the coherent scattering photons. PMID:7280291

UK PubMed Central (United Kingdom)

Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) gene polymorphisms are associated with many autoimmune diseases. The major risk allele encodes an R620W amino acid change that...Full Text Available

Energy Technology Data Exchange (ETDEWEB)

Tetracycline in solution of benzyl alcohol was used as an extracting agent to separate uranium from interfering elements in the determination of uranium and of isotopic ratio sup(235)U/sup(238)U by neutron activation analysis. Separation gives a recovery of 97% for uranium and the interferences from matrices of pitchblende and monazite are eliminated.

Energy Technology Data Exchange (ETDEWEB)

In scattering of channeled particles by point defects and in emission of gamma rays in the spontaneous-radiation spectral region conditions are attained where the momentum transferred to the defect is taken up by the crystal as a whole. This leads to coherent and interference effects in the radiation from the crystal defects. When the longitudinal momentum transferred is zero, an induced radiation effect appears in the transitions between the states of transverse motion.

Energy Technology Data Exchange (ETDEWEB)

This paper describes a simple analysis procedure that transforms a set of beamline orbit data into a set of harmonic orbits of first, second, and third order or higher. Each harmonic orbit can be studied individually to identify errors of the specific order with minimum interference from other orders. Effectively these are orbits caused by kicks, due to harmonic errors, propagated through linear lattice. Examples from accelerator study will be presented. The application and inherent limitations of this analysis procedure are discussed.

International Nuclear Information System (INIS)

A new software for neutron activation analysis was designed, built and implemented on a desktop computer using Visual Basic 6.0 program. The construction of this data analyzer computer program is described. The new software deals with peak reports resulting from Gammaplus software with minimum interference from the user in order to save time, manpower and minimize human errors. Its ability to find the concentrations of chemical elements within samples is proven to be fast, reliable and user friendly. (author)

Science.gov (United States)

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 ...

Energy Technology Data Exchange (ETDEWEB)

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 ...

Energy Technology Data Exchange (ETDEWEB)

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 and binding ...

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...

CERN Document Server

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 average rate of ...

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...

UK PubMed Central (United Kingdom)

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

International Nuclear Information System (INIS)

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 ...

International Nuclear Information System (INIS)

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 ...

Energy Technology Data Exchange (ETDEWEB)

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.

Energy Technology Data Exchange (ETDEWEB)

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 ...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

Energy Technology Data Exchange (ETDEWEB)

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 ...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

Science.gov (United States)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

International Nuclear Information System (INIS)

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 ...

CERN Document Server

This paper presents an uplink capacity analysis and interference avoidance technique for a femtocell based two-tier DS-CDMA network using shared spectrum. Assuming randomly distributed macrocell users and femtocell base stations (BS), we evaluate a network-wide area spectral efficiency metric called the operating contour (OC) defined as the feasible combinations of the average macrocell users and femtocell BS per cell-site that meet a target outage constraint $\\epsilon$. A contribution of this work is an accurate characterization of the uplink outage probability taking cross-tier power control, path-loss and shadowing effects into account. We show that a time-hopped CDMA physical layer coupled with sectorized receive antennas shows dramatic performance improvements in both light and heavily loaded two-tier networks, relative to a split spectrum two-tier network with omnidirectional femtocell antennas. These results provide insights into design of robust shared ...

CERN Document Server

Two-tier networks, comprising a conventional cellular network overlaid with shorter range hotspots (e.g. femtocells, distributed antennas, or wired relays), offer an economically viable way to improve cellular system capacity. The capacity-limiting factor in such networks is interference. The cross-tier interference between macrocells and femtocells can suffocate the capacity due to the near-far problem, so in practice hotspots should use a different frequency channel than the potentially nearby high-power macrocell users. Centralized or coordinated frequency planning, which is difficult and inefficient even in conventional cellular networks, is all but impossible in a two-tier network. This paper proposes and analyzes an optimum decentralized spectrum allocation policy for two-tier networks that employ frequency division multiple access (including OFDMA). The proposed allocation is optimal in terms of Area Spectral Efficiency (ASE), and is ...

Energy Technology Data Exchange (ETDEWEB)

The effects of the contrast of the pump field interference pattern, that is, the effectiveness of the dynamic amplitude-phase grid, and various optical arrangements on the lasing efficiency and tuning range of a dynamic distributed-feedback dye laser are investigated. It is shown that the proper choice of prism apex angle, prism material and dye solvent in a laser in the range 400-1000 microns pumped by two beams of different intensity directed through the congruent sides of an isosceles prism in contact with the active medium solution on its third side can lead to optical losses of less than 2% from the boundaries of the prism. Measurements of polymethine dye laser efficiency and tuning range as a function of the relative intensity of the two ruby-laser pump beams reveals that as the contrast of the pump beam interference pattern decreases, the tuning range remains practically constant and the efficiency increases in the nonlinear (saturation) ...

Energy Technology Data Exchange (ETDEWEB)

Interference between the crossover leg of the Reactor Coolant System(RCS) and the Pipe Whip Restraints(PWR) has brought a degradation issue of the integrity of the Reactor Coolant System in Westinghouse type Nuclear Power Plants(NPPs) of Korea. According to the gap inspection carried out during planned overhaul (year 2000), interference between the crossover leg and the PWR was found in each RCS loop. This plant has had the high vibration problem on the RC pump 'B'. The reason for the high vibration in the RC pump 'B' had been massively surveyed and it was found that the crossover leg of RCS contacted with the PWR in hot condition. Since the contact between the crossover leg and the PWR changes the dynamic characteristics of the piping system for the RCS, this is considered as one reason for the high vibration. And a possibility of overstress on the crossover leg due to the contact with the PWR should be ...

Science.gov (United States)

Through DNA methylation, histone modifications, and small regulatory RNAs the epigenome systematically controls gene expression during development, both in utero and throughout life. The epigenome is also a very reactive system; its labile nature allows it to sense and respond to environmental perturbations to ensure survival during fetal growth. This pliability can lead to aberrant epigenetic modifications that persist into later life and induce numerous disease states. Endocrine-disrupting compounds (EDCs) are ubiquitous chemicals that interfere with growth and development. Several EDCs also interfere with epigenetic programming. The investigation of the epigenotoxic effects of bisphenol A (BPA), an EDC used in the production of plastics and resins, has further raised concern over the impact of EDCs on the epigenome. Using the Agouti viable yellow (A(vy)) mouse model, dietary BPA exposure was shown to hypomethylate both the A(vy) and the ...

Energy Technology Data Exchange (ETDEWEB)

This report describes a comparison result of technical standards applied to instrumentation and control systems for nuclear power plants between in Korea and in Russia. Russia also has a state-run organization authorized to conduct approval, cancellation, and audit in use of nuclear facility or equipment. The Russian standards for nuclear instrumentation and control equipment are analogous with the Korean ones in the aspect of basic concepts and principles. However, there are some differences in document structure, design requirements, qualification test items, depth of contents between two standard systems. The biggest deviation exists in the standard documents for seismic qualification and electromagnetic interference qualification. Korean seismic qualification standard utilizing US approach, defines testing and qualification methods specifically and clearly. Russian standards however provide only conceptual definitions and requirements in the seismic related ...

International Nuclear Information System (INIS)

The possibility of providing high accuracy of absorption and albedo methods of radiometric testing due to the use of high-energy radiation component that has passed through a barrier and gone from it in the opposite direction as a reference source, is considered. It is shown that the use of high-energy component of penetrating radiation as a reference source decreases the device response to the main interference in a much larger degree than its response to the change of measured parameter. Experiments are performed using steel pipes and plates. "2"4"1Am, "1"3"7Cs and "6"0Co are used as sources.

Energy Technology Data Exchange (ETDEWEB)

Overhead, high power transmission lines have secured rights of way on agricultural lands in Minnesota. The economic impact of such utility crossings, including effects on land price, was investigated. Sale records and survey data were analyzed. Buyers, sellers, and brokers were interviewed concerning inconvenience, radio interference, appearance, and loss of irrigation possibilities due to the transmission lines. In nine affected sales, there was only one case in which less money was indicated for the farm because of the presence of a transmission line.

Energy Technology Data Exchange (ETDEWEB)

Natural radioactivity found in rocks and its evaluation been frequently used for studies of environmental geochemistry, particularly those of detection and control of pollutants and the consequent changes in environment after antropic interferences. In this work natural radioactivity in forty nine soil samples in the basin of Buquira river, at the Northeast region of Sao Paulo State, has been analysed and measured with a Ge-HP gamma ray spectrometer. A table with the most relevant results found in rocks is shown and discussed. (author)

International Nuclear Information System (INIS)

The transverse modes of a submillimetre laser cavity that contains waveguides and open parts were studied theoretically and experimentally with the purpose of finding methods for mode selection. Two methods based on the filtering of the Fourier spectra of the waveguide modes and the use of their interference were substantiated numerically and realised in experiment. Special attention was paid to the mode selection in tunable lasers. Scaling laws allowing one to use the obtained results in a wide range of the cavity parameters and wavelengths are presented. (laser applications and other topics in quantum electronics)

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When polarized electrons traverse a region where the laser light is focused their polarization varies even if their energy and direction of motion are not changed. This effect is due to interference of the incoming electron wave and an electron wave scattered at zero angle. Equations are obtained which determine the variation of the electron-density matrix, and their solutions are given. The change in the electron polarization depends not only on the Compton cross section but on the real part of the forward Compton amplitude as well. It should be taken into account, for example, in simulations of the e{yields}{gamma} conversion for future {gamma}{gamma} colliders. (orig.). 16 refs.

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The repeated use and limited lifetime of a composite tiring vessel compel a need to survey techniques for monitoring the structural integrity of the vessel in order to determine when it should be retired. Various nondestructive techniques were researched and evaluated based on their applicability to the vessel. The methods were visual inspection, liquid penetrant testing, magnetic particle testing, surface mounted strain gauges, thermal inspection, acoustic emission, ultrasonic testing, radiography, eddy current testing, and embedded fiber optic sensors. It was determined that embedded fiber optic sensor is the most promising technique due to their ability to be embedded within layers of composites and their immunity to electromagnetic interference.

International Nuclear Information System (INIS)

The long and resource intensive process of drug discovery and development is confronted with the basic challenge of providing effective and safe therapies at reasonably low costs. The better the mechanism of a disease is known, the higher the probability to find an appropriate therapy. Also, the better and earlier a disease can be diagnosed and characterized, the higher the chance to be able to interfere in this process with a chemical entity. This reasoning sets the framework for the use of imaging in drug discovery. We discuss the relevance of magnetic resonance imaging and spectroscopy to derive anatomical, functional, metabolic and target-related information in the context of pharmacological research in vivo. (author)

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Role of ballooning effect in toroidal plasmas on the transient transport problems is investigated. Due to the mode localization along the magnetic field line, a meso scale appears in a radial correlation length of fluctuating fields. This scale length introduces the interference of the gradient and flux in different radial locations. For the fluctuation which gives the gyro-Bohm-like diffusion in a stationary state, this long radial correlation of the fluctuating field causes a fast propagation of response against a rapid transient perturbation. Upper bound of transient thermal diffusivity is derived. (author)

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Determination of thermal to fast neutron flux ratio (ffast) and fast neutron flux (phi-fast) is required for fast neutron reactions, fast neutron activation analysis, and for correcting interference reactions. The ffast and subsequently phi-fast were determined using the absolute method. The ffast ranged from 48 to 155, and the phi-fast was found in the range 1.03x1010-4.89x1010 n cm-2 s-1. These values indicate an acceptable conformity and applicable for installation of the fast neutron facility at the MNA research reactor.

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Lung transplantation has become an accepted option for many patients with end-stage pulmonary diseases. Anesthesia and surgery following lung transplantation may be required for various diseases that may affect both systemic organs and the transplanted graft. When a patient with a lung transplant undergoes surgery, there is the potential for interference with lung function, depending on the type of intervention and its anatomical site. Accurate preoperative evaluation, an understanding of the physiology of the transplanted lung, proper airway instrumentation, individualized management of intraoperative ventilation, and fluid balance are essential for a positive perioperative outcome.

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This report presents information obtained during five different studies of field effects from high voltage transmission lines performed at EPRI's High Voltage Transmission Research Center. The first study is the development of a methodology for the evaluation of the expected frequency of occurrence of specific short-term effects of spark discharges and induced currents caused by overhead high voltage transmission lines. The methodology is divided into the analysis of the expected frequency of occurrence of situations in which induction effects may occur, and the analysis of the expected severity of the effect. The second study is of the electric field in the surface and on the immediate proximity of the strands of stranded conductors used for overhead high voltage lines. In particular, the cases of deformations of stranded conductors, caused by air expansion or by popped out strands, are analyzed for the purpose of determining the conditions for occurrence of corona in fair ...

Science.gov (United States)

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

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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 ...

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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. ...

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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 ...

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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...

CERN Document Server

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 ...

International Nuclear Information System (INIS)

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.

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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 ...

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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 injection. Venom injection ...

Science.gov (United States)

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 ...

Science.gov (United States)

Put in place to protect the rights of the child, the Convention on the Rights of the Child is a set of non-negotiable standards. A core principle underpinning the Convention is the child's right to participate fully in social arenas and to access sources of social support without excessive interference. Juxtaposing this is the right of the child to be shielded from harm, abuse and exploitation. Over the past several decades the Internet has emerged as a fast and easily accessible medium for people to connect and communicate. While the Internet provides children with a source of support through chat rooms, online communities and social networking sites, just as equally it can expose vulnerable children to predatory and deviant individuals exacerbating the potential for harm. Upholding the Convention in cyberspace is a challenge. The Internet is not owned or regulated by any governing body and accountability is difficult to enforce. This article discusses some of the ...

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A water trap system based on a thermoelectric cooling device is employed to remove a major fraction of the water from air samples, prior to analysis of these samples for chemical composition, by a variety of analytical techniques where water vapor interferes with the measurement process. These analytical techniques include infrared spectroscopy, mass spectrometry, ion mobility spectrometry and gas chromatography. The thermoelectric system for trapping water present in air samples can substantially improve detection sensitivity in these analytical techniques when it is necessary to measure trace analytes with concentrations in the ppm (parts per million) or ppb (parts per billion) partial pressure range. The thermoelectric trap design is compact and amenable to use in a portable gas monitoring instrumentation.

International Nuclear Information System (INIS)

As part of the general QC/QA management of the k_0-standardization, three types of 'SMELS' (synthetic multi-element standards) are being developed to check the performance of k_0-NAA when implemented in a laboratory. Phenol-formaldehyde resin is proposed in this paper as the matrix of choice. Based on previous work, this material could be prepared with sufficient purity so as to make interferences with the spiking elements negligible. The matrix was found to be adequately resistant towards high neutron flux irradiation. A selection was made of compounds, soluble in ethyl alcohol, for spiking the prepolymer ethanolic solution with the elements of interest. Finally, some prototypes were prepared and a satisfactory homogeneity of the spiked elements was found for 50 mg sample intake.

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Biosorption of elements is a little understood phenomenon exhibited by some types of even nonliving microbial biomass. A common fungus Rhizopus arrhizus has been reportd to take up uranium from adqueous solutions to the extent of 180 mg U/sup 6 +//g. The mechanism of uranium sequestering by this type of biomass was studied by using experimental techniques such as electron microscopy, x-ray energy dispersion analysis, IR spectroscopy, and supporting evidence was obtained for a biosorption mechanism consisting of at least three processes. Uranium coordination and adsorption in the cell-wall chitin structure occur simultaneously and rapidly whereas precipitation of uranylhdroxide within the chitin microcrystalline cell-wall structure takes place at a lower rate. Interference of Fe/sup 2/ and Zn/sup 2 +/ coions with uranium biosorption is indicated.

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Recently, the public has become aware of keywords like ''Quantum computer'' or ''Quantum cryptography''. Regarding their potential application in solid state based quantum information processing and their overall benefit in fundamental research quantum dots have gained more and more public interest. In this context, quantum dots are often referred to as ''artificial atoms'', a term subsuming their physical properties quite nicely and emphasizing the huge potential for further investigations. The basic mechanism to be considered is the theoretical model of a two-level system. A quantum dot itself represents this kind of system quite nicely, provided that only the presence or absence of a single exciton in the ground state of that structure is regarded. This concept can also be expanded to the presence of two excitons (bi-exciton). Transitions between the relevant levels can be ...

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Storage of thermal energy in aquifers has obvious benefits of saving energy and decreasing the consumption of fossil fuels. However, aquifer thermal energy storage (ATES), which involves groundwater aquifers as the storage medium for heat or chill, impinges on the environment. A literature review of pertinent microbiology publications (Hicks and Stewart, 1988) identified the potential for the interaction of ATES systems and microbiological processes to create a source of infectious diseases and the potential for damage to the environment. In addition, the review identified a potential for microbiological processes to develop conditions that would interfere with the operation of an ATES system. As a result of this research effort, investigators from Finland, Germany, Switzerland, and the United States have examined several ATES systems in operation and have observed that the ATES systems studied do not contribute to infectious disease transmission, do not adversely ...

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In the first paper of this series devoted to a structural analysis of a binary metallic glass model, we study a Pd/sub 80/Si/sub 20/ sample obtained by numerical relaxation. We discuss the reproducibility of the method and make a comparison with the experimental interference functions. Then we undertake a microscopic structural analysis from several point of view: we first study the number of neighbours of each type for each type of atoms; secondly, we analyse the structure by means of the radical plane method; at last, we show that it is possible to generalize the five fundamental characteristic units introduced by Bernal, so that we can define the environment of any Si atom without any ambiguity. All these methods reveal a certain tendency towards a prismatic environment for the metalloids.

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Sex differences in pain are frequently reported in the literature. However, less is known about possible sex differences in the experience of pain secondary to a disability. The current study explored these issues in persons with limb loss (n = 335, 72% men) who were recruited as part of a postal survey. Participants provided ratings of phantom limb pain (PLP), residual limb pain (RLP), and general pain intensity. Participants also completed measures of pain-related interference, catastrophizing, coping, and beliefs. Results indicated that a greater proportion of males than females (86% vs 77%, respectively) reported the presence of PLP; however, this difference was no longer prominent when cause of limb loss was controlled. No sex differences were found in the presence of RLP, or in avera...