Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems

OpenAIRE

Chen, Yvonne Y.; Jensen, Michael C.; Smolke, Christina D.

2010-01-01

RNA molecules perform diverse regulatory functions in natural biological systems, and numerous synthetic RNA-based control devices that integrate sensing and gene-regulatory functions have been demonstrated, predominantly in bacteria and yeast. Despite potential advantages of RNA-based genetic control strategies in clinical applications, there has been limited success in extending engineered RNA devices to mammalian gene-expression control and no example of their application to functional res...

An international comparability study on quantification of mRNA gene expression ratios: CCQM-P103.1

Directory of Open Access Journals (Sweden)

Alison S. Devonshire

2016-06-01

Full Text Available Measurement of RNA can be used to study and monitor a range of infectious and non-communicable diseases, with profiling of multiple gene expression mRNA transcripts being increasingly applied to cancer stratification and prognosis. An international comparison study (Consultative Committee for Amount of Substance (CCQM-P103.1 was performed in order to evaluate the comparability of measurements of RNA copy number ratio for multiple gene targets between two samples. Six exogenous synthetic targets comprising of External RNA Control Consortium (ERCC standards were measured alongside transcripts for three endogenous gene targets present in the background of human cell line RNA. The study was carried out under the auspices of the Nucleic Acids (formerly Bioanalysis Working Group of the CCQM. It was coordinated by LGC (United Kingdom with the support of National Institute of Standards and Technology (USA and results were submitted from thirteen National Metrology Institutes and Designated Institutes. The majority of laboratories performed RNA measurements using RT-qPCR, with datasets also being submitted by two laboratories based on reverse transcription digital polymerase chain reaction and one laboratory using a next-generation sequencing method. In RT-qPCR analysis, the RNA copy number ratios between the two samples were quantified using either a standard curve or a relative quantification approach. In general, good agreement was observed between the reported results of ERCC RNA copy number ratio measurements. Measurements of the RNA copy number ratios for endogenous genes between the two samples were also consistent between the majority of laboratories. Some differences in the reported values and confidence intervals (‘measurement uncertainties’ were noted which may be attributable to choice of measurement method or quantification approach. This highlights the need for standardised practices for the calculation of fold change ratios and

Combinatorial Control of mRNA Fates by RNA-Binding Proteins and Non-Coding RNAs

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Valentina Iadevaia

2015-09-01

Full Text Available Post-transcriptional control of gene expression is mediated by RNA-binding proteins (RBPs and small non-coding RNAs (e.g., microRNAs that bind to distinct elements in their mRNA targets. Here, we review recent examples describing the synergistic and/or antagonistic effects mediated by RBPs and miRNAs to determine the localisation, stability and translation of mRNAs in mammalian cells. From these studies, it is becoming increasingly apparent that dynamic rearrangements of RNA-protein complexes could have profound implications in human cancer, in synaptic plasticity, and in cellular differentiation.

Internal control reporting and accounting quality : Insight "comply-or-explain" internal control regime

OpenAIRE

Cao Thi Thanh, Huyen; Cheung, Tina

2010-01-01

Nowadays, there exist two reporting regimes, rules-based and principle-based (comply-or-explain). In the rules-based environment, researchers have studied the relationship between internal control quality and accounting quality. Prior studies have suggested that reports on internal control are an effective way for investors to evaluate the quality of the firm‟s internal control. By having a sound system of internal control, it creates reliance upon the firm‟s financial reporting. Therefore, t...

Thermodynamic control of small RNA-mediated gene silencing

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Kumiko eUi-Tei

2012-06-01

Full Text Available Small interfering RNAs (siRNAs and microRNAs (miRNAs are crucial regulators of posttranscriptional gene silencing, which is referred to as RNA interference (RNAi or RNA silencing. In RNAi, siRNA loaded onto the RNA-induced silencing complex (RISC downregulates target gene expression by cleaving mRNA whose sequence is perfectly complementary to the siRNA guide strand. We previously showed that highly functional siRNAs possessed the following characteristics: A or U residues at nucleotide position 1 measured from the 5’ terminal, four to seven A/Us in positions 1–7, and G or C residues at position 19. This finding indicated that an RNA strand with a thermodynamically unstable 5’ terminal is easily retained in the RISC and functions as a guide strand. In addition, it is clear that unintended genes with complementarities only in the seed region (positions 2–8 are also downregulated by off-target effects. siRNA efficiency is mainly determined by the Watson-Crick base-pairing stability formed between the siRNA seed region and target mRNA. siRNAs with a low seed-target duplex melting temperature (Tm have little or no seed-dependent off-target activity. Thus, important parts of the RNA silencing machinery may be regulated by nucleotide base-pairing thermodynamic stability. A mechanistic understanding of thermodynamic control may enable an efficient target gene-specific RNAi for functional genomics and safe therapeutic applications.

Simultaneous detection and identification of four cherry viruses by two step multiplex RT-PCR with an internal control of plant nad5 mRNA.

Science.gov (United States)

Noorani, Md Salik; Awasthi, Prachi; Sharma, Maheshwar Prasad; Ram, Raja; Zaidi, Aijaz Asgar; Hallan, Vipin

2013-10-01

A multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed and standardized for the simultaneous detection of four cherry viruses: Cherry virus A (CVA, Genus; Capillovirus), Cherry necrotic rusty mottle virus (CNRMV, unassigned species of the Betaflexiviridae), Little cherry virus 1 (LChV-1, Genus; Closterovirus) and Prunus necrotic ringspot virus (PNRSV, Genus; Ilarvirus) with nad5 as plant internal control. A reliable and quick method for total plant RNA extraction from pome and stone fruit trees was also developed. To minimize primer dimer formation, a single antisense primer for CVA and CNRMV was used. A mixture of random hexamer and oligo (dT) primer was used for cDNA synthesis, which was highly suited and economic for multiplexing. All four viruses were detected successfully by mRT-PCR in artificially created viral RNA mixture and field samples of sweet cherry. The identity of the viruses was confirmed by sequencing. The assay could detect above viruses in diluted cDNA (10(-4)) and RNA (10(-3), except PNRSV which was detected only till ten times lesser dilution). The developed mRT-PCR will not only be useful for the detection of viruses from single or multiple infections of sweet cherry plants but also for other stone and pome fruits. The developed method will be therefore quite helpful for virus indexing, plant quarantine and certification programs. This is the first report for the simultaneous detection of four cherry viruses by mRT-PCR. Copyright © 2013 Elsevier B.V. All rights reserved.

Defining the RNA Internal Loops Preferred by Benzimidazole Derivatives via Two-Dimensional Combinatorial Screening and Computational Analysis

Science.gov (United States)

Velagapudi, Sai Pradeep; Seedhouse, Steven J.; French, Jonathan

2011-01-01

RNA is an important therapeutic target, however, RNA targets are generally underexploited due to a lack of understanding of the small molecules that bind RNA and the RNA motifs that bind small molecules. Herein, we describe the identification of the RNA internal loops derived from a 4096-member 3×3 nucleotide loop library that are the most specific and highest affinity binders to a series of four designer, drug-like benzimidazoles. These studies establish a potentially general protocol to define the highest affinity and most specific RNA motif targets for heterocyclic small molecules. Such information could be used to target functionally important RNAs in genomic sequence. PMID:21604752

THE INTERNAL CONTROL MODELS IN ROMANIA

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TEODORESCU CRISTIAN DRAGOȘ

2015-06-01

Full Text Available Internal control is indissolubly linked to business and accounting. Throughout history, domestic and international trade has grown exponentially, which has led to an increasing complexity of internal control, to new methods and techniques to control the business. The literature has presented the first models of internal control in the Sumerian period (3600 - 3200 BC, and the emergence and development of internal control in Egypt, Persia, Greek and Roman Empire, in the Middle Ages till modern times. The purpose of this article is to present the models of internal control in Romania, starting from the principles of the classical model of internal control (COSO model. For a better understanding of the implication of internal control in terms of public and private sector, I have structured the article in the following parts: (a the definition of internal control in the literature; (b the presentation of the COSO model; (c internal control and internal audit in public institutions; (d internal control issues in accounting regulations on the individual and consolidated annual financial statements; (e internal / managerial control; (f conclusions.

Plant RNA binding proteins for control of RNA virus infection

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Sung Un eHuh

2013-12-01

Full Text Available Plant RNA viruses have effective strategies to infect host plants through either direct or indirect interactions with various host proteins, thus suppressing the host immune system. When plant RNA viruses enter host cells exposed RNAs of viruses are recognized by the host immune system through processes such as siRNA-dependent silencing. Interestingly, some host RNA binding proteins have been involved in the inhibition of RNA virus replication, movement, and translation through RNA-specific binding. Host plants intensively use RNA binding proteins for defense against viral infections in nature. In this mini review, we will summarize the function of some host RNA binding proteins which act in a sequence-specific binding manner to the infecting virus RNA. It is important to understand how plants effectively suppresses RNA virus infections via RNA binding proteins, and this defense system can be potentially developed as a synthetic virus defense strategy for use in crop engineering.

Controllable molecular motors engineered from myosin and RNA

Science.gov (United States)

Omabegho, Tosan; Gurel, Pinar S.; Cheng, Clarence Y.; Kim, Laura Y.; Ruijgrok, Paul V.; Das, Rhiju; Alushin, Gregory M.; Bryant, Zev

2018-01-01

Engineering biomolecular motors can provide direct tests of structure-function relationships and customized components for controlling molecular transport in artificial systems1 or in living cells2. Previously, synthetic nucleic acid motors3-5 and modified natural protein motors6-10 have been developed in separate complementary strategies to achieve tunable and controllable motor function. Integrating protein and nucleic-acid components to form engineered nucleoprotein motors may enable additional sophisticated functionalities. However, this potential has only begun to be explored in pioneering work harnessing DNA scaffolds to dictate the spacing, number and composition of tethered protein motors11-15. Here, we describe myosin motors that incorporate RNA lever arms, forming hybrid assemblies in which conformational changes in the protein motor domain are amplified and redirected by nucleic acid structures. The RNA lever arm geometry determines the speed and direction of motor transport and can be dynamically controlled using programmed transitions in the lever arm structure7,9. We have characterized the hybrid motors using in vitro motility assays, single-molecule tracking, cryo-electron microscopy and structural probing16. Our designs include nucleoprotein motors that reversibly change direction in response to oligonucleotides that drive strand-displacement17 reactions. In multimeric assemblies, the controllable motors walk processively along actin filaments at speeds of 10-20 nm s-1. Finally, to illustrate the potential for multiplexed addressable control, we demonstrate sequence-specific responses of RNA variants to oligonucleotide signals.

Control of Metastatic Progression by microRNA Regulatory Networks

Science.gov (United States)

Pencheva, Nora; Tavazoie, Sohail F.

2015-01-01

Aberrant microRNA (miRNA) expression is a defining feature of human malignancy. Specific miRNAs have been identified as promoters or suppressors of metastatic progression. These miRNAs control metastasis through divergent or convergent regulation of metastatic gene pathways. Some miRNA regulatory networks govern cell-autonomous cancer phenotypes, while others modulate the cell-extrinsic composition of the metastatic microenvironment. The use of small RNAs as probes into the molecular and cellular underpinnings of metastasis holds promise for the identification of candidate genes for potential therapeutic intervention. PMID:23728460

RNA expression patterns in serum microvesicles from patients with glioblastoma multiforme and controls

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Noerholm Mikkel

2012-01-01

Full Text Available Abstract Background RNA from exosomes and other microvesicles contain transcripts of tumour origin. In this study we sought to identify biomarkers of glioblastoma multiforme in microvesicle RNA from serum of affected patients. Methods Microvesicle RNA from serum from patients with de-novo primary glioblastoma multiforme (N = 9 and normal controls (N = 7 were analyzed by microarray analysis. Samples were collected according to protocols approved by the Institutional Review Board. Differential expressions were validated by qRT-PCR in a separate set of samples (N = 10 in both groups. Results Expression profiles of microvesicle RNA correctly separated individuals in two groups by unsupervised clustering. The most significant differences pertained to down-regulated genes (121 genes > 2-fold down in the glioblastoma multiforme patient microvesicle RNA, validated by qRT-PCR on several genes. Overall, yields of microvesicle RNA from patients was higher than from normal controls, but the additional RNA was primarily of size Conclusions Serum microvesicle RNA from patients with glioblastoma multiforme has significantly down-regulated levels of RNAs coding for ribosome production, compared to normal healthy controls, but a large overabundance of RNA of unknown origin with size

Cytoplasmic Control of Sense-Antisense mRNA Pairs

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Flore Sinturel

2015-09-01

Full Text Available Transcriptome analyses have revealed that convergent gene transcription can produce many 3′-overlapping mRNAs in diverse organisms. Few studies have examined the fate of 3′-complementary mRNAs in double-stranded RNA-dependent nuclear phenomena, and nothing is known about the cytoplasmic destiny of 3′-overlapping messengers or their impact on gene expression. Here, we demonstrate that the complementary tails of 3′-overlapping mRNAs can interact in the cytoplasm and promote post-transcriptional regulatory events including no-go decay (NGD in Saccharomyces cerevisiae. Genome-wide experiments confirm that these messenger-interacting mRNAs (mimRNAs form RNA duplexes in wild-type cells and thus have potential roles in modulating the mRNA levels of their convergent gene pattern under different growth conditions. We show that the post-transcriptional fate of hundreds of mimRNAs is controlled by Xrn1, revealing the extent to which this conserved 5′-3′ cytoplasmic exoribonuclease plays an unexpected but key role in the post-transcriptional control of convergent gene expression.

Cytoplasmic Control of Sense-Antisense mRNA Pairs.

Science.gov (United States)

Sinturel, Flore; Navickas, Albertas; Wery, Maxime; Descrimes, Marc; Morillon, Antonin; Torchet, Claire; Benard, Lionel

2015-09-22

Transcriptome analyses have revealed that convergent gene transcription can produce many 3'-overlapping mRNAs in diverse organisms. Few studies have examined the fate of 3'-complementary mRNAs in double-stranded RNA-dependent nuclear phenomena, and nothing is known about the cytoplasmic destiny of 3'-overlapping messengers or their impact on gene expression. Here, we demonstrate that the complementary tails of 3'-overlapping mRNAs can interact in the cytoplasm and promote post-transcriptional regulatory events including no-go decay (NGD) in Saccharomyces cerevisiae. Genome-wide experiments confirm that these messenger-interacting mRNAs (mimRNAs) form RNA duplexes in wild-type cells and thus have potential roles in modulating the mRNA levels of their convergent gene pattern under different growth conditions. We show that the post-transcriptional fate of hundreds of mimRNAs is controlled by Xrn1, revealing the extent to which this conserved 5'-3' cytoplasmic exoribonuclease plays an unexpected but key role in the post-transcriptional control of convergent gene expression. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Selective RNA targeting and regulated signaling by RIG-I is controlled by coordination of RNA and ATP binding.

Science.gov (United States)

Fitzgerald, Megan E; Rawling, David C; Potapova, Olga; Ren, Xiaoming; Kohlway, Andrew; Pyle, Anna Marie

2017-02-17

RIG-I is an innate immune receptor that detects and responds to infection by deadly RNA viruses such as influenza, and Hepatitis C. In the cytoplasm, RIG-I is faced with a difficult challenge: it must sensitively detect viral RNA while ignoring the abundance of host RNA. It has been suggested that RIG-I has a ‘proof-reading’ mechanism for rejecting host RNA targets, and that disruptions of this selectivity filter give rise to autoimmune diseases. Here, we directly monitor RNA proof-reading by RIG-I and we show that it is controlled by a set of conserved amino acids that couple RNA and ATP binding to the protein (Motif III). Mutations of this motif directly modulate proof-reading by eliminating or enhancing selectivity for viral RNA, with major implications for autoimmune disease and cancer. More broadly, the results provide a physical explanation for the ATP-gated behavior of SF2 RNA helicases and receptor proteins.

COSO internal control integrated framework 2013

CERN Document Server

American Institute of Certified Public Accountants

2013-01-01

Issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO), the 2013 Internal Control – Integrated Framework(Framework) is expected to help organizations design and implement internal control in light of many changes in business and operating environments since the issuance of the original Framework in 1992. The new Framework retains the core definition of internal control and the five components of internal control, and it continues to emphasize the importance of management judgment in designing, implementing, and conducting a system of internal control, and in assessing its effectiveness. It broadens the application of internal control in addressing operations and reporting objectives, and clarifies the requirements for determining what constitutes effective internal control.

RNA expression patterns in serum microvesicles from patients with glioblastoma multiforme and controls

International Nuclear Information System (INIS)

Noerholm, Mikkel; Balaj, Leonora; Limperg, Tobias; Salehi, Afshin; Zhu, Lin Dan; Hochberg, Fred H; Breakefield, Xandra O; Carter, Bob S; Skog, Johan

2012-01-01

RNA from exosomes and other microvesicles contain transcripts of tumour origin. In this study we sought to identify biomarkers of glioblastoma multiforme in microvesicle RNA from serum of affected patients. Microvesicle RNA from serum from patients with de-novo primary glioblastoma multiforme (N = 9) and normal controls (N = 7) were analyzed by microarray analysis. Samples were collected according to protocols approved by the Institutional Review Board. Differential expressions were validated by qRT-PCR in a separate set of samples (N = 10 in both groups). Expression profiles of microvesicle RNA correctly separated individuals in two groups by unsupervised clustering. The most significant differences pertained to down-regulated genes (121 genes > 2-fold down) in the glioblastoma multiforme patient microvesicle RNA, validated by qRT-PCR on several genes. Overall, yields of microvesicle RNA from patients was higher than from normal controls, but the additional RNA was primarily of size < 500 nt. Gene ontology of the down-regulated genes indicated these are coding for ribosomal proteins and genes related to ribosome production. Serum microvesicle RNA from patients with glioblastoma multiforme has significantly down-regulated levels of RNAs coding for ribosome production, compared to normal healthy controls, but a large overabundance of RNA of unknown origin with size < 500 nt

International control of nuclear materials

International Nuclear Information System (INIS)

Koponen, Hannu

1989-01-01

Nuclear materials are subject to both national and international safeguards control. The International Atomic Energy Agency (IAEA) takes care of the international safeguards control. The control activities, which are discussed in this article, are carried out according to the agreements between various countries and the IAEA

1st International Symposium on Stress-Associated RNA Granules in Human Disease and Viral Infection

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Bruce W. Banfield

2014-09-01

Full Text Available In recent years, important linkages have been made between RNA granules and human disease processes. On June 8-10 of this year, we hosted a new symposium, dubbed the 1st International Symposium on Stress-Associated RNA Granules in Human Disease and Viral Infection. This symposium brought together experts from diverse research disciplines ranging from cancer and neuroscience to infectious disease. This report summarizes speaker presentations and highlights current challenges in the field.

A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA.

KAUST Repository

Cesana, Marcella

2011-10-01

Recently, a new regulatory circuitry has been identified in which RNAs can crosstalk with each other by competing for shared microRNAs. Such competing endogenous RNAs (ceRNAs) regulate the distribution of miRNA molecules on their targets and thereby impose an additional level of post-transcriptional regulation. Here we identify a muscle-specific long noncoding RNA, linc-MD1, which governs the time of muscle differentiation by acting as a ceRNA in mouse and human myoblasts. Downregulation or overexpression of linc-MD1 correlate with retardation or anticipation of the muscle differentiation program, respectively. We show that linc-MD1 "sponges" miR-133 and miR-133 [corrected] to regulate the expression of MAML1 and MEF2C, transcription factors that activate muscle-specific gene expression. Finally, we demonstrate that linc-MD1 exerts the same control over differentiation timing in human myoblasts, and that its levels are strongly reduced in Duchenne muscle cells. We conclude that the ceRNA network plays an important role in muscle differentiation.

A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA.

KAUST Repository

Cesana, Marcella; Cacchiarelli, Davide; Legnini, Ivano; Santini, Tiziana; Sthandier, Olga; Chinappi, Mauro; Tramontano, Anna; Bozzoni, Irene

2011-01-01

Recently, a new regulatory circuitry has been identified in which RNAs can crosstalk with each other by competing for shared microRNAs. Such competing endogenous RNAs (ceRNAs) regulate the distribution of miRNA molecules on their targets and thereby impose an additional level of post-transcriptional regulation. Here we identify a muscle-specific long noncoding RNA, linc-MD1, which governs the time of muscle differentiation by acting as a ceRNA in mouse and human myoblasts. Downregulation or overexpression of linc-MD1 correlate with retardation or anticipation of the muscle differentiation program, respectively. We show that linc-MD1 "sponges" miR-133 and miR-133 [corrected] to regulate the expression of MAML1 and MEF2C, transcription factors that activate muscle-specific gene expression. Finally, we demonstrate that linc-MD1 exerts the same control over differentiation timing in human myoblasts, and that its levels are strongly reduced in Duchenne muscle cells. We conclude that the ceRNA network plays an important role in muscle differentiation.

Exploring valid internal-control genes in Porphyra yezoensis (Bangiaceae) during stress response conditions

Science.gov (United States)

Wang, Wenlei; Wu, Xiaojie; Wang, Chao; Jia, Zhaojun; He, Linwen; Wei, Yifan; Niu, Jianfeng; Wang, Guangce

2014-07-01

To screen the stable expression genes related to the stress (strong light, dehydration and temperature shock) we applied Absolute real-time PCR technology to determine the transcription numbers of the selected test genes in P orphyra yezoensis, which has been regarded as a potential model species responding the stress conditions in the intertidal. Absolute real-time PCR technology was applied to determine the transcription numbers of the selected test genes in P orphyra yezoensis, which has been regarded as a potential model species in stress responding. According to the results of photosynthesis parameters, we observed that Y(II) and F v/ F m were significantly affected when stress was imposed on the thalli of P orphyra yezoensis, but underwent almost completely recovered under normal conditions, which were collected for the following experiments. Then three samples, which were treated with different grade stresses combined with salinity, irradiation and temperature, were collected. The transcription numbers of seven constitutive expression genes in above samples were determined after RNA extraction and cDNA synthesis. Finally, a general insight into the selection of internal control genes during stress response was obtained. We found that there were no obvious effects in terms of salinity stress (at salinity 90) on transcription of most genes used in the study. The 18S ribosomal RNA gene had the highest expression level, varying remarkably among different tested groups. RPS8 expression showed a high irregular variance between samples. GAPDH presented comparatively stable expression and could thus be selected as the internal control. EF-1α showed stable expression during the series of multiple-stress tests. Our research provided available references for the selection of internal control genes for transcripts determination of P. yezoensis.

12 CFR 618.8430 - Internal controls.

Science.gov (United States)

2010-01-01

... 12 Banks and Banking 6 2010-01-01 2010-01-01 false Internal controls. 618.8430 Section 618.8430 Banks and Banking FARM CREDIT ADMINISTRATION FARM CREDIT SYSTEM GENERAL PROVISIONS Internal Controls § 618.8430 Internal controls. Each Farm Credit institution's board of directors must adopt an internal...

Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli.

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Hiraku Takada

Full Text Available Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3' proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons. The binding in vitro of RNAP RpoD holoenzyme to an internal promoter, referred to the promoter of riRNA (an internal RNA of the rRNA operon, within each 16S rRNA gene was confirmed by gel shift assay and AFM observation. Using this riRNA promoter within the rrnD operon as a representative, transcription in vitro was detected with use of the purified RpoD holoenzyme, confirming the presence of a constitutive promoter in this region. LacZ reporter assay indicated that this riRNA promoter is functional in vivo. The location of riRNA promoter in vivo as identified using a set of reporter plasmids agrees well with that identified in vitro. Based on transcription profile in vitro and Northern blot analysis in vivo, the majority of transcript initiated from this riRNA promoter was estimated to terminate near the beginning of 23S rRNA gene, indicating that riRNA leads to produce the spacer-coded tRNA. Under starved conditions, transcription of the rRNA operon is markedly repressed to reduce the intracellular level of ribosomes, but the levels of both riRNA and its processed tRNAGlu stayed unaffected, implying that riRNA plays a role in the continued steady-state synthesis of tRNAs from the spacers of rRNA operons. We then propose that the tRNA genes organized within the spacers of rRNA-tRNA composite operons

Efficacy of internal control and controlling business risks

Directory of Open Access Journals (Sweden)

Luminiţa IONESCU

2010-06-01

Full Text Available Companies can gain additional efficiency in designing and implementing or assessing internal control by focusing on only those financial reporting objectives directly applicable to the company’s activities and circumstances, taking a risk based approach to internal control. It is important for any organization to have reliable financial data for internal decision-making purpose. Financial information is often useful in many internal decisions such as product or service pricing. This is why the most important function of the controller is to create and maintain the corporate financial control system. Today’s corporation operates in an increasingly complex environment and the controller’s role is to advice the management of current or future problems of the business environment or to prevent the fraud.

Efficacy of internal control and controlling business risks

OpenAIRE

IONESCU, Luminiţa

2010-01-01

Companies can gain additional efficiency in designing and implementing or assessing internal control by focusing on only those financial reporting objectives directly applicable to the company’s activities and circumstances, taking a risk based approach to internal control. It is important for any organization to have reliable financial data for internal decision-making purpose. Financial information is often useful in many internal decisions such as product or service pricing. This is why th...

Employee quality, monitoring environment and internal control

Directory of Open Access Journals (Sweden)

Chunli Liu

2017-03-01

Full Text Available We investigate the effect of internal control employees (ICEs on internal control quality. Using special survey data from Chinese listed firms, we find that ICE quality has a significant positive influence on internal control quality. We examine the effect of monitoring on this result and find that the effect is more pronounced for firms with strict monitoring environments, especially when the firms implement the Chinese internal control regulation system (CSOX, have higher institutional ownership or attach greater importance to internal control. Our findings suggest that ICEs play an important role in the design and implementation of internal control systems. Our study should be of interest to both top managers who wish to improve corporate internal control quality and regulators who wish to understand the mechanisms of internal control monitoring.

Detection of small interfering RNA (siRNA) by mass spectrometry procedures in doping controls.

Science.gov (United States)

Thomas, Andreas; Walpurgis, Katja; Delahaut, Philippe; Kohler, Maxie; Schänzer, Wilhelm; Thevis, Mario

2013-01-01

Uncovering manipulation of athletic performance via small interfering (si)RNA is an emerging field in sports drug testing. Due to the potential to principally knock down every target gene in the organism by means of the RNA interference pathway, this facet of gene doping has become a realistic scenario. In the present study, two distinct model siRNAs comprising 21 nucleotides were designed as double strands which were perfect counterparts to a sequence of the respective messenger RNA coding the muscle regulator myostatin of Rattus norvegicus. Several modified nucleotides were introduced in both the sense and the antisense strand comprising phosphothioates, 2'-O-methylation, 2'-fluoro-nucleotides, locked nucleic acids and a cholesterol tag at the 3'-end. The model siRNAs were applied to rats at 1 mg/kg (i.v.) and blood as well as urine samples were collected. After isolation of the RNA by means of a RNA purification kit, the target analytes were detected by liquid chromatography - high resolution/high accuracy mass spectrometry (LC-HRMS). Analytes were detected as modified nucleotides after alkaline hydrolysis, as intact oligonucleotide strands (top-down) and by means of denaturing SDS-PAGE analysis. The gel-separated siRNA was further subjected to in-gel hydrolysis with different RNases and subsequent identification of the fragments by untargeted LC-HRMS analysis (bottom-up, 'experimental RNomics'). Combining the results of all approaches, the identification of several 3'-truncated urinary metabolites was accomplished and target analytes were detected up to 24 h after a single administration. Simultaneously collected blood samples yielded no promising results. The methods were validated and found fit-for-purpose for doping controls. Copyright © 2013 John Wiley & Sons, Ltd.

Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1 × 1 Nucleotide UU Internal Loop Conformations

Energy Technology Data Exchange (ETDEWEB)

Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W.; Disney, Matthew D. (Scripps)

2012-03-27

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[{und UU}GGGC(C{und U}G){sub 3}GUCC]{sub 2}, refined to 2.20 and 1.52 {angstrom} resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 x 1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 {angstrom} structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 x 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 x 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 {angstrom} structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 x 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 x 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

Science.gov (United States)

Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

2013-01-01

The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

The internal control of tax

OpenAIRE

E. B. Shuvalova; L. A. Butenko; Ju. A. Rudenko

2016-01-01

The aim of the research is to study the theoretical and practical issues of internal fiscal control. Internal tax control system requires the development of methodological tools, its scientific basis and practical recommendations for the application. This difficult task is now solved only in organizations, which are the largest taxpayers. For small and medium-sized businesses in the organization of internal fiscal control may improve the quality of the accounting organization of the company. ...

Internal budget control

Directory of Open Access Journals (Sweden)

MSc. Mervete Shala

2011-06-01

Generally, duties of internal control officers within ministries and institutions must be clearly divided to reduce the risk of inco-rrect behaviour. Operations of an efficient control mechanism influence and ensure conditions for rule of law, good governance, and democracy.

48 CFR 819.7112 - Internal controls.

Science.gov (United States)

2010-10-01

... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Internal controls. 819... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7112 Internal controls. (a) OSDBU... Program objectives. OSDBU will establish internal controls as checks and balances applicable to the...

[Use of the recombinant baculovirus BacVP6C for the construction of an internal positive control of rotavirus C].

Science.gov (United States)

Abid-Ayadi, I; Guix, S; Pintó, R M; Bosch, A

2011-06-01

Unlike group A, a few studies have interested other groups of the rotavirus, especially in Tunisia. The role of rotavirus C (RVC) infection is underestimated because of its sporadic nature. The aim of our study was to develop rapid diagnostic procedures of RVC by using an internal positive control of reverse transcription PCR (RT-PCR). The internal positive control (386pb) was designed from the recombinant baculovirus BacVP6C containing the full length cDNA of the Cowden strain gene 5 (1353pb). A fragment of 596pb was amplified by PCR using the BacVP6C DNA ds as template. Then, a central part of 210pb was deleted and the remaining fragment (386pb) was cloned into pGEM-3Zf(+) plasmid between SP6 and T7 RNA polymerase promoters. The obtained recombinant plasmid "pIAM1" was then used for the generation of the internal positive control by in vitro transcription. The sensibility of the RT-PCR was about 3.66×10(5) molecules of RNA/μl. The use of a shorter positive control, as compared to the wild type, allows increased specificity of the RT-PCR reaction, and could be used for efficient diagnostic and surveillance of RVC-caused diseases. Copyright © 2009 Elsevier Masson SAS. All rights reserved.

Operational Control of Internal Transport

NARCIS (Netherlands)

J.R. van der Meer (Robert)

2000-01-01

textabstractOperational Control of Internal Transport considers the control of guided vehicles in vehicle-based internal transport systems found in facilities such as warehouses, production plants, distribution centers and transshipment terminals. The author's interest of research having direct use

48 CFR 519.7014 - Internal controls.

Science.gov (United States)

2010-10-01

... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Internal controls. 519... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS GSA Mentor-Protégé Program 519.7014 Internal controls. (a) The GSA Mentor-Protégé Program Manager will manage the Program. Internal controls will be established by...

Internally controlled, generic real-time PCR for quantification and multiplex real-time PCR with serotype-specific probes for serotyping of dengue virus infections

NARCIS (Netherlands)

Menting, Sandra; Thai, Khoa T. D.; Nga, Tran T. T.; Phuong, Hoang L.; Klatser, Paul; Wolthers, Katja C.; Binh, Tran Q.; de Vries, Peter J.; Beld, Marcel

2011-01-01

Dengue has become a global public health problem and a sensitive diagnostic test for early phase detection can be life saving. An internally controlled, generic real-time PCR was developed and validated by testing serial dilutions of a DENV positive control RNA in the presence of a fixed amount of

Influenza A virus targets a cGAS-independent STING pathway that controls enveloped RNA viruses.

Science.gov (United States)

Holm, Christian K; Rahbek, Stine H; Gad, Hans Henrik; Bak, Rasmus O; Jakobsen, Martin R; Jiang, Zhaozaho; Hansen, Anne Louise; Jensen, Simon K; Sun, Chenglong; Thomsen, Martin K; Laustsen, Anders; Nielsen, Camilla G; Severinsen, Kasper; Xiong, Yingluo; Burdette, Dara L; Hornung, Veit; Lebbink, Robert Jan; Duch, Mogens; Fitzgerald, Katherine A; Bahrami, Shervin; Mikkelsen, Jakob Giehm; Hartmann, Rune; Paludan, Søren R

2016-02-19

Stimulator of interferon genes (STING) is known be involved in control of DNA viruses but has an unexplored role in control of RNA viruses. During infection with DNA viruses STING is activated downstream of cGAMP synthase (cGAS) to induce type I interferon. Here we identify a STING-dependent, cGAS-independent pathway important for full interferon production and antiviral control of enveloped RNA viruses, including influenza A virus (IAV). Further, IAV interacts with STING through its conserved hemagglutinin fusion peptide (FP). Interestingly, FP antagonizes interferon production induced by membrane fusion or IAV but not by cGAMP or DNA. Similar to the enveloped RNA viruses, membrane fusion stimulates interferon production in a STING-dependent but cGAS-independent manner. Abolishment of this pathway led to reduced interferon production and impaired control of enveloped RNA viruses. Thus, enveloped RNA viruses stimulate a cGAS-independent STING pathway, which is targeted by IAV.

Nanoparticle orientation to control RNA loading and ligand display on extracellular vesicles for cancer regression

Science.gov (United States)

Pi, Fengmei; Binzel, Daniel W.; Lee, Tae Jin; Li, Zhefeng; Sun, Meiyan; Rychahou, Piotr; Li, Hui; Haque, Farzin; Wang, Shaoying; Croce, Carlo M.; Guo, Bin; Evers, B. Mark; Guo, Peixuan

2018-01-01

Nanotechnology offers many benefits, and here we report an advantage of applying RNA nanotechnology for directional control. The orientation of arrow-shaped RNA was altered to control ligand display on extracellular vesicle membranes for specific cell targeting, or to regulate intracellular trafficking of small interfering RNA (siRNA) or microRNA (miRNA). Placing membrane-anchoring cholesterol at the tail of the arrow results in display of RNA aptamer or folate on the outer surface of the extracellular vesicle. In contrast, placing the cholesterol at the arrowhead results in partial loading of RNA nanoparticles into the extracellular vesicles. Taking advantage of the RNA ligand for specific targeting and extracellular vesicles for efficient membrane fusion, the resulting ligand-displaying extracellular vesicles were capable of specific delivery of siRNA to cells, and efficiently blocked tumour growth in three cancer models. Extracellular vesicles displaying an aptamer that binds to prostate-specific membrane antigen, and loaded with survivin siRNA, inhibited prostate cancer xenograft. The same extracellular vesicle instead displaying epidermal growth-factor receptor aptamer inhibited orthotopic breast cancer models. Likewise, survivin siRNA-loaded and folate-displaying extracellular vesicles inhibited patient-derived colorectal cancer xenograft.

Importance of Internal Audit and Internal Control in an organization - Case Study

OpenAIRE

Bubilek, Olga

2017-01-01

This research is a descriptive case study of a company. It presents concepts of the internal audit and internal control based on an example of a Finnish company. The research examines the role and importance that internal audit and internal controls have in an organization. The main research question is “What is the role and importance of internal audit and internal control in an organization” Additional sub-questions relating to the case company that will allow for better understanding of...

Argue internal audit on how to promote the nuclear power enterprise internal control

International Nuclear Information System (INIS)

Li Xiaoming

2012-01-01

In order to strengthen and standardize enterprise internal control, improve the management level and risk prevention ability, five departments jointly established the basic rules of internal control in enterprises, large and medium-sized enterprises as the national power enterprise, the enterprise internal audit executive power in strengthening and perfecting internal control, and in the enterprise internal control of play an active role. (author)

Internal Control Organization Procedure

OpenAIRE

Radu Dorin Lenghel

2013-01-01

Internal control represents the totality of policies and procedures adopted by management, which contribute: to the fulfilment of managerial objectives, to the prevention and detection of frauds or errors, to the accuracy and exhaustiveness of accounting entries, as well as to the preparation in due course of financial accounting information. Internal control represents a managerial instrument which assures the fulfilment of objectives of the entity, being an ongoing process in which administ...

Internal controls subjects at insurance companies

OpenAIRE

Прокопенко, Жанна Володимирівна

2015-01-01

The problematic issues of determining the authorities of the internal controls subjects at insurance companies have been elucidated. The list of internal controls subjects of insurer depending on the form of control as well as the purposefulness of such kind of control have been determined.

Development of a novel recombinant encapsidated RNA particle: evaluation as an internal control for diagnostic RT-PCR

DEFF Research Database (Denmark)

King, Donald P.; Montague, Nick; Ebert, Katja

2007-01-01

-and-mouth disease virus (FMDV) and a set for swine vesicular disease virus (SVDV) was engineered into a full-length cDNA clone containing the RNA-2 segment of Cowpea Mosaic Virus (CPMV). After co-inoculation with a plasmid that expressed CPMV RNA-1, recombinant virus particles were rescued from cowpea plants (Vigna...

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments.

Science.gov (United States)

Bi, Ran; Liu, Peng

2016-03-31

RNA-Sequencing (RNA-seq) experiments have been popularly applied to transcriptome studies in recent years. Such experiments are still relatively costly. As a result, RNA-seq experiments often employ a small number of replicates. Power analysis and sample size calculation are challenging in the context of differential expression analysis with RNA-seq data. One challenge is that there are no closed-form formulae to calculate power for the popularly applied tests for differential expression analysis. In addition, false discovery rate (FDR), instead of family-wise type I error rate, is controlled for the multiple testing error in RNA-seq data analysis. So far, there are very few proposals on sample size calculation for RNA-seq experiments. In this paper, we propose a procedure for sample size calculation while controlling FDR for RNA-seq experimental design. Our procedure is based on the weighted linear model analysis facilitated by the voom method which has been shown to have competitive performance in terms of power and FDR control for RNA-seq differential expression analysis. We derive a method that approximates the average power across the differentially expressed genes, and then calculate the sample size to achieve a desired average power while controlling FDR. Simulation results demonstrate that the actual power of several popularly applied tests for differential expression is achieved and is close to the desired power for RNA-seq data with sample size calculated based on our method. Our proposed method provides an efficient algorithm to calculate sample size while controlling FDR for RNA-seq experimental design. We also provide an R package ssizeRNA that implements our proposed method and can be downloaded from the Comprehensive R Archive Network ( http://cran.r-project.org ).

Human GW182 Paralogs Are the Central Organizers for RNA-Mediated Control of Transcription.

Science.gov (United States)

Hicks, Jessica A; Li, Liande; Matsui, Masayuki; Chu, Yongjun; Volkov, Oleg; Johnson, Krystal C; Corey, David R

2017-08-15

In the cytoplasm, small RNAs can control mammalian translation by regulating the stability of mRNA. In the nucleus, small RNAs can also control transcription and splicing. The mechanisms for RNA-mediated nuclear regulation are not understood and remain controversial, hindering the effective application of nuclear RNAi and investigation of its natural regulatory roles. Here, we reveal that the human GW182 paralogs TNRC6A/B/C are central organizing factors critical to RNA-mediated transcriptional activation. Mass spectrometry of purified nuclear lysates followed by experimental validation demonstrates that TNRC6A interacts with proteins involved in protein degradation, RNAi, the CCR4-NOT complex, the mediator complex, and histone-modifying complexes. Functional analysis implicates TNRC6A, NAT10, MED14, and WDR5 in RNA-mediated transcriptional activation. These findings describe protein complexes capable of bridging RNA-mediated sequence-specific recognition of noncoding RNA transcripts with the regulation of gene transcription. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Internal budget control

OpenAIRE

MSc. Mervete Shala

2011-01-01

Internal control is established by the Government to ensure effective and proper operations of ministries, institutions and generally of all public agencies, in compliance with the law, the goals and objectives stated by them, to provide protection against abuse and mismanagement or poor governance. The instrument of internal audit entails a series of mechanisms which aim at enabling budgetary policies compliance, such as: financial reporting; effective system of communication between mana...

Internal corrosion control of northern pipelines

Energy Technology Data Exchange (ETDEWEB)

Papavinasam, S.

2005-02-01

The general causes of internal corrosion in pipelines were discussed along with the methods to control them. Efficient methods are needed to determine chemical efficiency for mitigating internal corrosion in transmission pipelines, particularly those used in environmentally sensitive regions in the Arctic where harsh environmental conditions prevail. According to the Office of Pipeline Safety, 15 per cent of pipeline failures in the United States from 1994 to 2000 were caused by internal corrosion. Since pipelines in the United States are slightly older than Canadian pipelines, internal corrosion is a significant issue from a Canadian perspective. There are 306,618 km of energy-related pipelines in western Canada. Between April 2001 and March 2002 there were 808 failures, of which 425 failures resulted from internal corrosion. The approach to control internal corrosion comprises of dehydrating the gases at production facilities; controlling the quality of corrosive gases such as carbon dioxide and hydrogen sulphide; and, using internal coatings. The approaches to control internal corrosion are appropriate, when supplemented by adequate integrity management program to ensure that corrosive liquids do not collect, over the operational lifetime of the pipelines, at localized areas. It was suggested that modeling of pipeline operations may need improvement. This paper described the causes, prediction and control of internal pitting corrosion. It was concluded that carbon steel equipment can continue to be used reliably and safely as pipeline materials for northern pipelines if the causes that lead to internal corrosion are scientifically and accurately predicted, and if corrosion inhibitors are properly evaluated and applied. 5 figs.

INTERNAL CONTROL OF INVESTMENT PROJECTS

Directory of Open Access Journals (Sweden)

Yu. N. Yudenkov

2010-01-01

Full Text Available Estimation and technics of the account of expenses, efficiency, financial result should enter into the list of regular checks from service of internal control that demands corresponding vocational training of internal controlers which should own methods of an estimation of expediency of acquisition of long-term actives.

Dual function of the McaS small RNA in controlling biofilm formation

DEFF Research Database (Denmark)

Jørgensen, Mikkel Girke; Thomason, Maureen K.; Havelund, Johannes

2013-01-01

, and biofilm formation. Moreover, ectopic McaS expression leads to induction of two additional CsrA-repressed genes encoding diguanylate cyclases. Collectively, our study shows that McaS is a dual-function sRNA with roles in the two major post-transcriptional regulons controlled by the RNA-binding proteins Hfq...

Employee quality, monitoring environment and internal control

OpenAIRE

Chunli Liu; Bin Lin; Wei Shu

2017-01-01

We investigate the effect of internal control employees (ICEs) on internal control quality. Using special survey data from Chinese listed firms, we find that ICE quality has a significant positive influence on internal control quality. We examine the effect of monitoring on this result and find that the effect is more pronounced for firms with strict monitoring environments, especially when the firms implement the Chinese internal control regulation system (CSOX), have higher institutional ow...

Ni2+-binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair.

Science.gov (United States)

Hofmann, H P; Limmer, S; Hornung, V; Sprinzl, M

1997-01-01

RNA molecules with high affinity for immobilized Ni2+ were isolated from an RNA pool with 50 randomized positions by in vitro selection-amplification. The selected RNAs preferentially bind Ni2+ and Co2+ over other cations from first series transition metals. Conserved structure motifs, comprising about 15 nt, were identified that are likely to represent the Ni2+ binding sites. Two conserved motifs contain an asymmetric purine-rich internal loop and probably a mismatch G-A base pair. The structure of one of these motifs was studied with proton NMR spectroscopy and formation of the G-A pair at the junction of helix and internal loop was demonstrated. Using Ni2+ as a paramagnetic probe, a divalent metal ion binding site near this G-A base pair was identified. Ni2+ ions bound to this motif exert a specific stabilization effect. We propose that small asymmetric purine-rich loops that contain a G-A interaction may represent a divalent metal ion binding site in RNA. PMID:9409620

Dinucleotide controlled null models for comparative RNA gene prediction.

Science.gov (United States)

Gesell, Tanja; Washietl, Stefan

2008-05-27

Comparative prediction of RNA structures can be used to identify functional noncoding RNAs in genomic screens. It was shown recently by Babak et al. [BMC Bioinformatics. 8:33] that RNA gene prediction programs can be biased by the genomic dinucleotide content, in particular those programs using a thermodynamic folding model including stacking energies. As a consequence, there is need for dinucleotide-preserving control strategies to assess the significance of such predictions. While there have been randomization algorithms for single sequences for many years, the problem has remained challenging for multiple alignments and there is currently no algorithm available. We present a program called SISSIz that simulates multiple alignments of a given average dinucleotide content. Meeting additional requirements of an accurate null model, the randomized alignments are on average of the same sequence diversity and preserve local conservation and gap patterns. We make use of a phylogenetic substitution model that includes overlapping dependencies and site-specific rates. Using fast heuristics and a distance based approach, a tree is estimated under this model which is used to guide the simulations. The new algorithm is tested on vertebrate genomic alignments and the effect on RNA structure predictions is studied. In addition, we directly combined the new null model with the RNAalifold consensus folding algorithm giving a new variant of a thermodynamic structure based RNA gene finding program that is not biased by the dinucleotide content. SISSIz implements an efficient algorithm to randomize multiple alignments preserving dinucleotide content. It can be used to get more accurate estimates of false positive rates of existing programs, to produce negative controls for the training of machine learning based programs, or as standalone RNA gene finding program. Other applications in comparative genomics that require randomization of multiple alignments can be considered. SISSIz

Dinucleotide controlled null models for comparative RNA gene prediction

Directory of Open Access Journals (Sweden)

Gesell Tanja

2008-05-01

Full Text Available Abstract Background Comparative prediction of RNA structures can be used to identify functional noncoding RNAs in genomic screens. It was shown recently by Babak et al. [BMC Bioinformatics. 8:33] that RNA gene prediction programs can be biased by the genomic dinucleotide content, in particular those programs using a thermodynamic folding model including stacking energies. As a consequence, there is need for dinucleotide-preserving control strategies to assess the significance of such predictions. While there have been randomization algorithms for single sequences for many years, the problem has remained challenging for multiple alignments and there is currently no algorithm available. Results We present a program called SISSIz that simulates multiple alignments of a given average dinucleotide content. Meeting additional requirements of an accurate null model, the randomized alignments are on average of the same sequence diversity and preserve local conservation and gap patterns. We make use of a phylogenetic substitution model that includes overlapping dependencies and site-specific rates. Using fast heuristics and a distance based approach, a tree is estimated under this model which is used to guide the simulations. The new algorithm is tested on vertebrate genomic alignments and the effect on RNA structure predictions is studied. In addition, we directly combined the new null model with the RNAalifold consensus folding algorithm giving a new variant of a thermodynamic structure based RNA gene finding program that is not biased by the dinucleotide content. Conclusion SISSIz implements an efficient algorithm to randomize multiple alignments preserving dinucleotide content. It can be used to get more accurate estimates of false positive rates of existing programs, to produce negative controls for the training of machine learning based programs, or as standalone RNA gene finding program. Other applications in comparative genomics that require

Exploring the use of internal and externalcontrols for assessing microarray technical performance

Directory of Open Access Journals (Sweden)

Game Laurence

2010-12-01

Full Text Available Abstract Background The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies. Results A layered PCA modeling methodology that uses data from a number of classes of controls (spike-in hybridization, spike-in polyA+, internal RNA degradation, endogenous or "housekeeping genes" was used for the assessment of microarray data quality. The controls provide information on multiple stages of the experimental protocol (e.g., hybridization, RNA amplification. External spike-in, hybridization and RNA labeling controls provide information related to both assay and hybridization performance whereas internal endogenous controls provide quality information on the biological sample. We find that the variance of the data generated from the external and internal controls carries critical information about technical performance; the PCA dissection of this variance is consistent with whole-array quality assessment based on a number of quality assurance/quality control (QA/QC metrics. Conclusions These results provide support for the use of both external and internal RNA control data to assess the technical quality of microarray

Comparison of HIV DNA and RNA in gut-associated lymphoid tissue of HIV-infected controllers and noncontrollers.

Science.gov (United States)

Hatano, Hiroyu; Somsouk, Ma; Sinclair, Elizabeth; Harvill, Kara; Gilman, Lee; Cohen, Michelle; Hoh, Rebecca; Hunt, Peter W; Martin, Jeffrey N; Wong, Joseph K; Deeks, Steven G; Yukl, Steven A

2013-09-10

HIV-infected controllers have provided novel insights into mechanisms of viral control. We investigated the degree to which HIV DNA and RNA are present in gut-associated lymphoid tissue (GALT) of controllers. Cross-sectional cohort study. Colorectal biopsy pieces were obtained from five untreated noncontrollers, five ART-suppressed patients, and nine untreated controllers. Rectal HIV DNA was lower in controllers (median 496 copies/10(6) CD4 T cells) than in untreated noncontrollers (117483 copies/10(6) CD4+ T cells, P = 0.001) and ART-suppressed patients (6116 copies/10(6) CD4 T cells, P = 0.004). Similarly, rectal HIV RNA was lower in controllers (19 copies/10(6) CD4 T cells) than in noncontrollers (15210 copies/10(6) CD4+ T cells, P = 0.001) and ART-suppressed patients (1625 copies/10(6) CD4+ T cells, P = 0.0599). Rectal HIV RNA/DNA ratios were not statistically different between the three groups. Despite being able to maintain very low plasma HIV RNA levels in the absence of antiretroviral therapy (ART), HIV-infected controllers have readily measurable levels of HIV DNA and RNA in GALT. As expected, controllers had lower rectal HIV DNA and RNA compared with untreated noncontrollers and ART-suppressed individuals. Compared with the mechanisms of 'natural' viral control of controllers, long-term ART does not reduce the total HIV reservoir to the level of controllers.

Avian metapneumovirus RT-nested-PCR: a novel false positive reducing inactivated control virus with potential applications to other RNA viruses and real time methods.

Science.gov (United States)

Falchieri, Marco; Brown, Paul A; Catelli, Elena; Naylor, Clive J

2012-12-01

Using reverse genetics, an avian metapneumovirus (AMPV) was modified for use as a positive control for validating all stages of a popular established RT-nested PCR, used in the detection of the two major AMPV subtypes (A and B). Resultant amplicons were of increased size and clearly distinguishable from those arising from unmodified virus, thus allowing false positive bands, due to control virus contamination of test samples, to be identified readily. Absorption of the control virus onto filter paper and subsequent microwave irradiation removed all infectivity while its function as an efficient RT-nested-PCR template was unaffected. Identical amplicons were produced after storage for one year. The modified virus is likely to have application as an internal standard as well as in real time methods. Additions to AMPV of RNA from other RNA viruses, including hazardous examples such HIV and influenza, are likely to yield similar safe RT-PCR controls. Copyright © 2012 Elsevier B.V. All rights reserved.

34A, miRNA-944, miRNA-101 and miRNA-218 in cervical cancer

African Journals Online (AJOL)

RNAs (21 - 24 nucleotides in length) that are critical for many important processes such as development, ... RNA extraction and reverse transcription. Total RNA was extracted from each of the experimental groups using ... used as an endogenous control to normalize the expression of miRNA-143, miRNA-34A, miRNA-.

49 CFR 193.2631 - Internal corrosion control.

Science.gov (United States)

2010-10-01

... 49 Transportation 3 2010-10-01 2010-10-01 false Internal corrosion control. 193.2631 Section 193... GAS FACILITIES: FEDERAL SAFETY STANDARDS Maintenance § 193.2631 Internal corrosion control. Each component that is subject to internal corrosive attack must be protected from internal corrosion by— (a...

15 CFR 752.11 - Internal Control Programs.

Science.gov (United States)

2010-01-01

... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Internal Control Programs. 752.11... COMPREHENSIVE LICENSE § 752.11 Internal Control Programs. (a) Scope—(1) Introduction. It is through Internal Control Programs (ICPs) that the SCL holder and the consignee assure that exports and reexports are not...

Identification and association of novel lncRNA pouMU1 gene ...

Indian Academy of Sciences (India)

TUANHUI REN

2017-12-08

Dec 8, 2017 ... The GAPDH gene was used as an internal control: forward and ... was extracted using. Trizol, and RNA quality was assessed using electrophore- .... tistical Product and Service Solutions, IBM Corporation,. Armonk, USA).

48 CFR 719.273-10 - Internal controls.

Science.gov (United States)

2010-10-01

... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Internal controls. 719.273...égé Program 719.273-10 Internal controls. (a) OSDBU will oversee the Program and will work in... objectives. OSDBU will establish internal controls as checks and balances applicable to the Program. These...

The Principles of Organization of Internal Control of Companies

Directory of Open Access Journals (Sweden)

Panteleiev

2017-02-01

Full Text Available The question to give a convincing assessment of the Rules of the internal controls and present them in the form of principles of organization of internal control. Since the final decision in the form of an exhaustive list and universal principles of internal control is no scientific research continues these principles. It is necessary to examine the logic of the main provisions of the organization's internal control due consideration of the requirements of international practice controls and propose principles of internal control. For this purpose, conducted a critical analysis of the main provisions of internal controls contained in the publications and in the regulations on internal control proceedings. Synthesis of articles of authors of lead scientific and practical journal Ukraine "Accounting and Auditing" for the 1994-2015 biennium pointed out that despite the coverage of current journal articles provisions, principles, requirements, rules and other modern techniques. On internal control and comprehensive set of reasonable response to the organization and classification of internal control is absent. This leads to continue the search key components of the organization's internal control. The above basic concepts in publications on the organization of internal control were used in the formation of a set of principles of control. According to the requirements of the OECD field of internal control includes risk management, cost control, change in control, complete information to guarantee the effectiveness of internal control systems, providing the ability to make decisions and so on. COSO model contains an exhaustive list of five components. The results of the questionnaire trainees have provided compelling arguments for classifying and establishing relevant principles of organization and internal controls were rejected. A list of the basic principles of the organization of internal control, which consists of 25 elements that are shaped

Evaluation of external RNA controls for the standardisation of gene expression biomarker measurements

Directory of Open Access Journals (Sweden)

Elaswarapu Ramnath

2010-11-01

Full Text Available Abstract Background Gene expression profiling is an important approach for detecting diagnostic and prognostic biomarkers, and predicting drug safety. The development of a wide range of technologies and platforms for measuring mRNA expression makes the evaluation and standardization of transcriptomic data problematic due to differences in protocols, data processing and analysis methods. Thus, universal RNA standards, such as those developed by the External RNA Controls Consortium (ERCC, are proposed to aid validation of research findings from diverse platforms such as microarrays and RT-qPCR, and play a role in quality control (QC processes as transcriptomic profiling becomes more commonplace in the clinical setting. Results Panels of ERCC RNA standards were constructed in order to test the utility of these reference materials (RMs for performance characterization of two selected gene expression platforms, and for discrimination of biomarker profiles between groups. The linear range, limits of detection and reproducibility of microarray and RT-qPCR measurements were evaluated using panels of RNA standards. Transcripts of low abundance (≤ 10 copies/ng total RNA showed more than double the technical variability compared to higher copy number transcripts on both platforms. Microarray profiling of two simulated 'normal' and 'disease' panels, each consisting of eight different RNA standards, yielded robust discrimination between the panels and between standards with varying fold change ratios, showing no systematic effects due to different labelling and hybridization runs. Also, comparison of microarray and RT-qPCR data for fold changes showed agreement for the two platforms. Conclusions ERCC RNA standards provide a generic means of evaluating different aspects of platform performance, and can provide information on the technical variation associated with quantification of biomarkers expressed at different levels of physiological abundance

Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex.

Science.gov (United States)

Cukras, Anthony R; Southworth, Daniel R; Brunelle, Julie L; Culver, Gloria M; Green, Rachel

2003-08-01

Translocation of the mRNA:tRNA complex through the ribosome is promoted by elongation factor G (EF-G) during the translation cycle. Previous studies established that modification of ribosomal proteins with thiol-specific reagents promotes this event in the absence of EF-G. Here we identify two small subunit interface proteins S12 and S13 that are essential for maintenance of a pretranslocation state. Omission of these proteins using in vitro reconstitution procedures yields ribosomal particles that translate in the absence of enzymatic factors. Conversely, replacement of cysteine residues in these two proteins yields ribosomal particles that are refractive to stimulation with thiol-modifying reagents. These data support a model where S12 and S13 function as control elements for the more ancient rRNA- and tRNA-driven movements of translocation.

Pathways of cellular internalisation of liposomes delivered siRNA and effects on siRNA engagement with target mRNA and silencing in cancer cells.

Science.gov (United States)

Alshehri, Abdullah; Grabowska, Anna; Stolnik, Snow

2018-02-28

Design of an efficient delivery system is a generally recognised bottleneck in translation of siRNA technology into clinic. Despite research efforts, cellular processes that determine efficiency of siRNA silencing achieved by different delivery formulations remain unclear. Here, we investigated the mechanism(s) of cellular internalisation of a model siRNA-loaded liposome system in a correlation to the engagement of delivered siRNA with its target and consequent silencing by adopting siRNA molecular beacon technology. Probing of cellular internalisation pathways by a panel of pharmacological inhibitors indicated that clathrin-mediated (dynamin-dependent) endocytosis, macropinocytosis (dynamine independent), and cell membrane cholesterol dependent process(es) (clathrin and caveolea-independent) all play a role in the siRNA-liposomes internalization. The inhibition of either of these entry routes was, in general, mirrored by a reduction in the level of siRNA engagement with its target mRNA, as well as in a reduction of the target gene silencing. A dramatic increase in siRNA engagement with its target RNA was observed on disruption of endosomal membrane (by chloroquine), accompanied with an increased silencing. The work thus illustrates that employing molecular beacon siRNA technology one can start to assess the target RNA engagement - a stage between initial cellular internalization and final gene silencing of siRNA delivery systems.

49 CFR 192.477 - Internal corrosion control: Monitoring.

Science.gov (United States)

2010-10-01

... 49 Transportation 3 2010-10-01 2010-10-01 false Internal corrosion control: Monitoring. 192.477... Control § 192.477 Internal corrosion control: Monitoring. If corrosive gas is being transported, coupons... internal corrosion. Each coupon or other means of monitoring internal corrosion must be checked two times...

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria.

Science.gov (United States)

Sun, Eric I; Leyn, Semen A; Kazanov, Marat D; Saier, Milton H; Novichkov, Pavel S; Rodionov, Dmitry A

2013-09-02

In silico comparative genomics approaches have been efficiently used for functional prediction and reconstruction of metabolic and regulatory networks. Riboswitches are metabolite-sensing structures often found in bacterial mRNA leaders controlling gene expression on transcriptional or translational levels.An increasing number of riboswitches and other cis-regulatory RNAs have been recently classified into numerous RNA families in the Rfam database. High conservation of these RNA motifs provides a unique advantage for their genomic identification and comparative analysis. A comparative genomics approach implemented in the RegPredict tool was used for reconstruction and functional annotation of regulons controlled by RNAs from 43 Rfam families in diverse taxonomic groups of Bacteria. The inferred regulons include ~5200 cis-regulatory RNAs and more than 12000 target genes in 255 microbial genomes. All predicted RNA-regulated genes were classified into specific and overall functional categories. Analysis of taxonomic distribution of these categories allowed us to establish major functional preferences for each analyzed cis-regulatory RNA motif family. Overall, most RNA motif regulons showed predictable functional content in accordance with their experimentally established effector ligands. Our results suggest that some RNA motifs (including thiamin pyrophosphate and cobalamin riboswitches that control the cofactor metabolism) are widespread and likely originated from the last common ancestor of all bacteria. However, many more analyzed RNA motifs are restricted to a narrow taxonomic group of bacteria and likely represent more recent evolutionary innovations. The reconstructed regulatory networks for major known RNA motifs substantially expand the existing knowledge of transcriptional regulation in bacteria. The inferred regulons can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. The obtained genome

Internal combustion engine and method for control

Science.gov (United States)

Brennan, Daniel G

2013-05-21

In one exemplary embodiment of the invention an internal combustion engine includes a piston disposed in a cylinder, a valve configured to control flow of air into the cylinder and an actuator coupled to the valve to control a position of the valve. The internal combustion engine also includes a controller coupled to the actuator, wherein the controller is configured to close the valve when an uncontrolled condition for the internal engine is determined.

Influence Implementation Internal Control To Quality Audit Internal Education Consultant In Indonesian

Directory of Open Access Journals (Sweden)

Nur Zeina Maya Sari

2015-08-01

Full Text Available Abstract This research focus to quality audit internal with accountancy Inspection. Hameed 1995 found that the most important factors that affect auditing quality are auditors experience honesty and the knowledge in accounting and auditing standards. Research into this express an inspection of Intern Accountancy amp attributed to Monetary inspection an consultant education with quality. Audit quality is obtained by a process of identifying and administering the activities needed to achieve the quality objectives . Since an entityamp8223s internal control is under the purview of its audit committee Krishnan 2005 the relation between audit committee quality and internal control weaknesses is a subject to be investigated. The methodology used is a quantitative analysis by examining the relationship between variables conceptually. While some study its accounting activity. In self-supporting internal control. Internal control is defined as a process affected by an entitys board of directors management and other personnel designed to provide reasonable assurance regarding the achievement of objectives International Organization of Supreme Audit Institutions 1998 its bearing by reporting level an environment and reduction conduct in reporting result of mistake. What finally involvement by Audit Intern can be of benefit. In addition to researching into proposing Audit Intern can improve the target of consultant education going concern.

Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them.

Science.gov (United States)

Leppek, Kathrin; Das, Rhiju; Barna, Maria

2018-03-01

RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5' untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5' UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms.

The cis-acting replication signal at the 3' end of Flock House virus RNA2 is RNA3-dependent

International Nuclear Information System (INIS)

Albarino, Cesar G.; Eckerle, Lance D.; Ball, L. Andrew

2003-01-01

The nodavirus Flock House virus has a bipartite positive-sense RNA genome consisting of RNAs 1 and 2, which encode the viral RNA-dependent RNA polymerase (RdRp) and capsid protein precursor, respectively. The RdRp catalyzes replication of both genome segments and produces from RNA1 a subgenomic RNA (RNA3) that transactivates RNA2 replication. Here, we replaced internal sequences of RNAs 1 and 2 with a common heterologous core and were thereby able to test the RNA termini for compatibility in supporting the replication of chimeric RNAs. The results showed that the 3' 50 nt of RNA2 contained an RNA3-dependent cis-acting replication signal. Since covalent RNA dimers can direct the synthesis of monomeric replication products, the RdRp can evidently respond to cis-acting replication signals located internally. Accordingly, RNA templates containing the 3' termini of both RNAs 1 and 2 in tandem generated different replication products depending on the presence or absence of RNA3

The fission yeast RNA binding protein Mmi1 regulates meiotic genes by controlling intron specific splicing and polyadenylation coupled RNA turnover.

Directory of Open Access Journals (Sweden)

Huei-Mei Chen

Full Text Available The polyA tails of mRNAs are monitored by the exosome as a quality control mechanism. We find that fission yeast, Schizosaccharomyces pombe, adopts this RNA quality control mechanism to regulate a group of 30 or more meiotic genes at the level of both splicing and RNA turnover. In vegetative cells the RNA binding protein Mmi1 binds to the primary transcripts of these genes. We find the novel motif U(U/C/GAAAC highly over-represented in targets of Mmi1. Mmi1 can specifically regulate the splicing of particular introns in a transcript: it inhibits the splicing of introns that are in the vicinity of putative Mmi1 binding sites, while allowing the splicing of other introns that are far from such sites. In addition, binding of Mmi1, particularly near the 3' end, alters 3' processing to promote extremely long polyA tails of up to a kilobase. The hyperadenylated transcripts are then targeted for degradation by the nuclear exonuclease Rrp6. The nuclear polyA binding protein Pab2 assists this hyperadenylation-mediated RNA decay. Rrp6 also targets other hyperadenylated transcripts, which become hyperadenylated in an unknown, but Mmi1-independent way. Thus, hyperadenylation may be a general signal for RNA degradation. In addition, binding of Mmi1 can affect the efficiency of 3' cleavage. Inactivation of Mmi1 in meiosis allows meiotic expression, through splicing and RNA stabilization, of at least 29 target genes, which are apparently constitutively transcribed.

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

DEFF Research Database (Denmark)

Theis, Corinna; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

2013-01-01

Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general...... comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22495 3D modules in all PDB files results in 977 internal loop...

Dual RNA regulatory control of a Staphylococcus aureus virulence factor.

Science.gov (United States)

Chabelskaya, Svetlana; Bordeau, Valérie; Felden, Brice

2014-04-01

In pathogens, the accurate programming of virulence gene expression is essential for infection. It is achieved by sophisticated arrays of regulatory proteins and ribonucleic acids (sRNAs), but in many cases their contributions and connections are not yet known. Based on genetic, biochemical and structural evidence, we report that the expression pattern of a Staphylococcus aureus host immune evasion protein is enabled by the collaborative actions of RNAIII and small pathogenicity island RNA D (SprD). Their combined expression profiles during bacterial growth permit early and transient synthesis of Sbi to avoid host immune responses. Together, these two sRNAs use antisense mechanisms to monitor Sbi expression at the translational level. Deletion analysis combined with structural analysis of RNAIII in complex with its novel messenger RNA (mRNA) target indicate that three distant RNAIII domains interact with distinct sites of the sbi mRNA and that two locations are deep in the sbi coding region. Through distinct domains, RNAIII lowers production of two proteins required for avoiding innate host immunity, staphylococcal protein A and Sbi. Toeprints and in vivo mutational analysis reveal a novel regulatory module within RNAIII essential for attenuation of Sbi translation. The sophisticated translational control of mRNA by two differentially expressed sRNAs ensures supervision of host immune escape by a major pathogen.

Interactions between mRNA export commitment, 3'-end quality control, and nuclear degradation

DEFF Research Database (Denmark)

Libri, Domenico; Dower, Ken; Boulay, Jocelyne

2002-01-01

Several aspects of eukaryotic mRNA processing are linked to transcription. In Saccharomyces cerevisiae, overexpression of the mRNA export factor Sub2p suppresses the growth defect of hpr1 null cells, yet the protein Hpr1p and the associated THO protein complex are implicated in transcriptional el...... results show that several classes of defective RNPs are subject to a quality control step that impedes release from transcription site foci and suggest that suboptimal messenger ribonucleoprotein assembly leads to RNA degradation by Rrp6p....

INTERNAL CONTROL IN PUBLIC HEALTH SERVICES INSTITUTIONS

Directory of Open Access Journals (Sweden)

Ludmila FRUMUSACHI

2017-06-01

Full Text Available Internal control has a special role in the efficient organization of the entity’s management. The components of this control in the institutions of public health service are determined by the specific character of these institutions and National Standards of Internal Control in the Public Sector. The system of internal control in the institutions of public health service has the capacity to canalize the effort of the whole institution for the achievement of proposed objectives, to signalize permanently the dysfunctionalities about the quality of medical services and the deviations and to operate timely corrective measures for eliminating the noticed problems. In this regard the managers are obliged to analyse and to resize the system of internal control when in the organizational structure appear substantial changes.

MicroRNA-223 controls susceptibility to tuberculosis by regulating lung neutrophil recruitment

OpenAIRE

Dorhoi, Anca; Iannaccone, Marco; Farinacci, Maura; Faé, Kellen C.; Schreiber, Jörg; Moura-Alves, Pedro; Nouailles, Geraldine; Mollenkopf, Hans-Joachim; Oberbeck-Müller, Dagmar; Jörg, Sabine; Heinemann, Ellen; Hahnke, Karin; Löwe, Delia; Del Nonno, Franca; Goletti, Delia

2013-01-01

The molecular mechanisms that control innate immune cell trafficking during chronic infection and inflammation, such as in tuberculosis (TB), are incompletely understood. During active TB, myeloid cells infiltrate the lung and sustain local inflammation. While the chemoattractants that orchestrate these processes are increasingly recognized, the posttranscriptional events that dictate their availability are unclear. We identified microRNA-223 (miR-223) as an upregulated small noncoding RNA in...

Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III

OpenAIRE

Matsutani Sachiko

2004-01-01

Abstract Background In eukaryotes, RNA polymerase III (RNAP III) transcribes the genes for small RNAs like tRNAs, 5S rRNA, and several viral RNAs, and short interspersed repetitive elements (SINEs). The genes for these RNAs and SINEs have internal promoters that consist of two regions. These two regions are called the A and B blocks. The multisubunit transcription factor TFIIIC is required for transcription initiation of RNAP III; in transcription of tRNAs, the B-block binding subunit of TFII...

Internal control system

OpenAIRE

Pavésková, Ivana

2014-01-01

Dissertation focuse on the internal control system in the enterprises, aims to map the control system by focusing on the purchasing department. I focused on the purchasing process, because with an increasing trends of outsourcing services and the increasing interconnectedness of enterprises increases the risk of fraud currently in the purchasing process. To the research was selected the sample of companies from the banking and non-banking environment, to which were sent a questionnaire focusi...

An epidermal microRNA regulates neuronal migration through control of the cellular glycosylation state

DEFF Research Database (Denmark)

Pedersen, Mikael Egebjerg; Snieckute, Goda; Kagias, Konstantinos

2013-01-01

An appropriate balance in glycosylation of proteoglycans is crucial for their ability to regulate animal development. Here, we report that the Caenorhabditis elegans microRNA mir-79, an ortholog of mammalian miR-9, controls sugar-chain homeostasis by targeting two proteins in the proteoglycan bio...... that impinges on a LON-2/glypican pathway and disrupts neuronal migration. Our results identify a regulatory axis controlled by a conserved microRNA that maintains proteoglycan homeostasis in cells....

Real-time isothermal RNA amplification of toxic marine microalgae using preserved reagents on an integrated microfluidic platform.

Science.gov (United States)

Tsaloglou, Maria-Nefeli; Laouenan, Florian; Loukas, Christos-Moritz; Monsalve, Lisandro Gabriel; Thanner, Christine; Morgan, Hywel; Ruano-López, Jesus M; Mowlem, Matthew C

2013-01-21

Quantitation of specific RNA sequences is a useful technique in marine biology that can elucidate cell abundance, speciation and viability, especially for early detection of harmful algal blooms. We are thus developing an integrated microfluidic system for cell concentration and lysis, RNA extraction/purification and quantitative RNA detection for environmental applications. The portable system is based on a microfluidic cartridge, or "lab-card", using a low-cost injection moulded device, with a laminated lid. Here we present real-time isothermal RNA amplification using reagent master-mixes preserved on-chip in a gel at 4 °C for up to eight months. We demonstrate quantitation by reference to an internal control in a competitive assay with 500 cell equivalents of the toxic microalga Karenia brevis. Annealing of primers, amplification at 41 °C and real-time fluorescence detection of the internal control and target using sequence-specific molecular beacons were all performed on-chip.

49 CFR 192.475 - Internal corrosion control: General.

Science.gov (United States)

2010-10-01

... 49 Transportation 3 2010-10-01 2010-10-01 false Internal corrosion control: General. 192.475... Control § 192.475 Internal corrosion control: General. (a) Corrosive gas may not be transported by... taken to minimize internal corrosion. (b) Whenever any pipe is removed from a pipeline for any reason...

Enterovirus Control of Translation and RNA Granule Stress Responses.

Science.gov (United States)

Lloyd, Richard E

2016-03-30

Enteroviruses such as poliovirus (PV) and coxsackievirus B3 (CVB3) have evolved several parallel strategies to regulate cellular gene expression and stress responses to ensure efficient expression of the viral genome. Enteroviruses utilize their encoded proteinases to take over the cellular translation apparatus and direct ribosomes to viral mRNAs. In addition, viral proteinases are used to control and repress the two main types of cytoplasmic RNA granules, stress granules (SGs) and processing bodies (P-bodies, PBs), which are stress-responsive dynamic structures involved in repression of gene expression. This review discusses these processes and the current understanding of the underlying mechanisms with respect to enterovirus infections. In addition, the review discusses accumulating data suggesting linkage exists between RNA granule formation and innate immune sensing and activation.

Evidence for rRNA 2'-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes.

Science.gov (United States)

Erales, Jenny; Marchand, Virginie; Panthu, Baptiste; Gillot, Sandra; Belin, Stéphane; Ghayad, Sandra E; Garcia, Maxime; Laforêts, Florian; Marcel, Virginie; Baudin-Baillieu, Agnès; Bertin, Pierre; Couté, Yohann; Adrait, Annie; Meyer, Mélanie; Therizols, Gabriel; Yusupov, Marat; Namy, Olivier; Ohlmann, Théophile; Motorin, Yuri; Catez, Frédéric; Diaz, Jean-Jacques

2017-12-05

Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2'-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin in human cells. Using RiboMethSeq, a nonbiased quantitative mapping of 2'-O-Me, we identified a repertoire of 2'-O-Me sites subjected to variation and demonstrate that functional domains of ribosomes are targets of 2'-O-Me plasticity. Using the cricket paralysis virus internal ribosome entry site element, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through a 2'-O-Me pattern and not by nonribosomal actors of the translational machinery. Our data establish rRNA 2'-O-Me plasticity as a mechanism providing functional specificity to human ribosomes.

47 CFR 90.473 - Operation of internal transmitter control systems through licensed fixed control points.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 5 2010-10-01 2010-10-01 false Operation of internal transmitter control... Transmitter Control Internal Transmitter Control Systems § 90.473 Operation of internal transmitter control systems through licensed fixed control points. An internal transmitter control system may be operated...

A Tyrosine-Dependent Riboswitch Controls the Expression of a Tyrosyl-tRNA Synthetase from Acidithiobacillus ferrooxidans

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Paula Bustamante

2016-06-01

Full Text Available Expression of aminoacyl-tRNA synthetases is regulated by a variety of mechanisms at the level of transcription or translation. A T-box dependent transcription termination / antitermination riboswitch system that responds to charged / uncharged tRNA regulates expression of aminoacyl tRNA synthetase genes in Gram-positive bacteria. TyrZ, the gene encoding tyrosyl-tRNA synthetase from Acidithiobacillus ferrooxidans, a Gram-negative acidophilic bacterium that participates in bioleaching of minerals, resembles the gene from Bacillus subtilis including the 5´-untranslated region encoding the riboswitch. Transcription of A. ferrooxidans tyrZ is induced by the presence of tyrosine by a mechanism involving antitermination of transcription. This mechanism is probably adapted to the low supply of amino acids of acidic environments of autotrophic bioleaching microorganisms. This work is licensed under a Creative Commons Attribution 4.0 International License.

Artesunate Reduces Serum Lipopolysaccharide in Cecal Ligation/Puncture Mice via Enhanced LPS Internalization by Macrophages through Increased mRNA Expression of Scavenger Receptors

Directory of Open Access Journals (Sweden)

Bin Li

2014-01-01

Full Text Available Innate immunity is the first line of defense in human beings against pathogen infection; monocytes/macrophages are the primary cells of the innate immune system. Recently, macrophages/monocytes have been discovered to participate in LPS clearance, and the clearance efficiency determines the magnitude of the inflammatory response and subsequent organ injury. Previously, we reported that artesunate (AS protected sepsis mice against heat-killed E. coli challenge. Herein, we further confirmed that AS protected cecal ligation/puncture (CLP sepsis mice. Its protection on sepsis mice was related to not only reduction of pro-inflammatory cytokines and serum LPS levels but also improvement of liver function. Based on the fact that AS did not directly bind and neutralize LPS, we hypothesized that the reduction of serum LPS level might be related to enhancement of LPS internalization and subsequent detoxification. Our results showed that AS increased FITC-LPS internalization by peritoneal macrophage and liver Kupffer cell, but enhancement of LPS internalization by AS was not related to the clathrin-dependent pathway. However, AS induced mRNA expression of important scavenger receptors (SRs; SR-A and MARCO mRNA expression was upregulated, suggesting that AS enhancement of LPS internalization and inhibition of pro-inflammatory cytokines was related to changes in mRNA expression of SRs.

Control of Drosophila Type I and Type II central brain neuroblast proliferation by bantam microRNA

DEFF Research Database (Denmark)

Weng, Ruifen; Cohen, Stephen M

2015-01-01

Post-transcriptional regulation of stem cell self-renewal by microRNAs is emerging as an important mechanism controlling tissue homeostasis. Here, we provide evidence that bantam microRNA controls neuroblast number and proliferation in the Drosophila central brain. Bantam also supports proliferat......Post-transcriptional regulation of stem cell self-renewal by microRNAs is emerging as an important mechanism controlling tissue homeostasis. Here, we provide evidence that bantam microRNA controls neuroblast number and proliferation in the Drosophila central brain. Bantam also supports...

Lipoprotein Lipase mRNA expression in different tissues of farm ...

African Journals Online (AJOL)

Lipoprotein lipase (LPL) controls triacylglycerol partitioning between adipose tissues and muscles, so it is important enzyme for fattening of animals .The present work was planned to clarify the use of polymerase chain reaction (PCR) for detection of LPL mRNA expression in different tissues representing internal organs of ...

rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments

OpenAIRE

O?Connor, Patrick B. F.; Li, Gene-Wei; Weissman, Jonathan S.; Atkins, John F.; Baranov, Pavel V.

2013-01-01

Motivation: Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine?Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints. Results: Here, we provide...

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

Science.gov (United States)

Leppek, Kathrin; Das, Rhiju; Barna, Maria

2017-01-01

RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5′ untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5′ UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms. PMID:29165424

RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications

Science.gov (United States)

Xu, Liang; Wang, Wei; Chong, Jenny; Shin, Ji Hyun; Xu, Jun; Wang, Dong

2016-01-01

Accurate genetic information transfer is essential for life. As a key enzyme involved in the first step of gene expression, RNA polymerase II (Pol II) must maintain high transcriptional fidelity while it reads along DNA template and synthesizes RNA transcript in a stepwise manner during transcription elongation. DNA lesions or modifications may lead to significant changes in transcriptional fidelity or transcription elongation dynamics. In this review, we will summarize recent progress towards understanding the molecular basis of RNA Pol II transcriptional fidelity control and impacts of DNA lesions and modifications on Pol II transcription elongation. PMID:26392149

A Design Method of Robust Servo Internal Model Control with Control Input Saturation

OpenAIRE

山田, 功; 舩見, 洋祐

2001-01-01

In the present paper, we examine a design method of robust servo Internal Model Control with control input saturation. First of all, we clarify the condition that Internal Model Control has robust servo characteristics for the system with control input saturation. From this consideration, we propose new design method of Internal Model Control with robust servo characteristics. A numerical example to illustrate the effectiveness of the proposed method is shown.

Fragile X mental retardation protein: A paradigm for translational control by RNA-binding proteins.

Science.gov (United States)

Chen, Eileen; Joseph, Simpson

2015-07-01

Translational control is a common mechanism used to regulate gene expression and occur in bacteria to mammals. Typically in translational control, an RNA-binding protein binds to a unique sequence in the mRNA to regulate protein synthesis by the ribosomes. Alternatively, a protein may bind to or modify a translation factor to globally regulate protein synthesis by the cell. Here, we review translational control by the fragile X mental retardation protein (FMRP), the absence of which causes the neurological disease, fragile X syndrome (FXS). Copyright © 2015 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

RNA signal amplifier circuit with integrated fluorescence output.

Science.gov (United States)

Akter, Farhima; Yokobayashi, Yohei

2015-05-15

We designed an in vitro signal amplification circuit that takes a short RNA input that catalytically activates the Spinach RNA aptamer to produce a fluorescent output. The circuit consists of three RNA strands: an internally blocked Spinach aptamer, a fuel strand, and an input strand (catalyst), as well as the Spinach aptamer ligand 3,5-difluoro-4-hydroxylbenzylidene imidazolinone (DFHBI). The input strand initially displaces the internal inhibitory strand to activate the fluorescent aptamer while exposing a toehold to which the fuel strand can bind to further displace and recycle the input strand. Under a favorable condition, one input strand was able to activate up to five molecules of the internally blocked Spinach aptamer in 185 min at 30 °C. The simple RNA circuit reported here serves as a model for catalytic activation of arbitrary RNA effectors by chemical triggers.

An internal ribosome entry site directs translation of the 3'-gene from Pelargonium flower break virus genomic RNA: implications for infectivity.

Directory of Open Access Journals (Sweden)

Olga Fernández-Miragall

Full Text Available Pelargonium flower break virus (PFBV, genus Carmovirus has a single-stranded positive-sense genomic RNA (gRNA which contains five ORFs. The two 5'-proximal ORFs encode the replicases, two internal ORFs encode movement proteins, and the 3'-proximal ORF encodes a polypeptide (p37 which plays a dual role as capsid protein and as suppressor of RNA silencing. Like other members of family Tombusviridae, carmoviruses express ORFs that are not 5'-proximal from subgenomic RNAs. However, in one case, corresponding to Hisbiscus chlorotic ringspot virus, it has been reported that the 3'-proximal gene can be translated from the gRNA through an internal ribosome entry site (IRES. Here we show that PFBV also holds an IRES that mediates production of p37 from the gRNA, raising the question of whether this translation strategy may be conserved in the genus. The PFBV IRES was functional both in vitro and in vivo and either in the viral context or when inserted into synthetic bicistronic constructs. Through deletion and mutagenesis studies we have found that the IRES is contained within a 80 nt segment and have identified some structural traits that influence IRES function. Interestingly, mutations that diminish IRES activity strongly reduced the infectivity of the virus while the progress of the infection was favoured by mutations potentiating such activity. These results support the biological significance of the IRES-driven p37 translation and suggest that production of the silencing suppressor from the gRNA might allow the virus to early counteract the defence response of the host, thus facilitating pathogen multiplication and spread.

An internal ribosome entry site directs translation of the 3'-gene from Pelargonium flower break virus genomic RNA: implications for infectivity.

Science.gov (United States)

Fernández-Miragall, Olga; Hernández, Carmen

2011-01-01

Pelargonium flower break virus (PFBV, genus Carmovirus) has a single-stranded positive-sense genomic RNA (gRNA) which contains five ORFs. The two 5'-proximal ORFs encode the replicases, two internal ORFs encode movement proteins, and the 3'-proximal ORF encodes a polypeptide (p37) which plays a dual role as capsid protein and as suppressor of RNA silencing. Like other members of family Tombusviridae, carmoviruses express ORFs that are not 5'-proximal from subgenomic RNAs. However, in one case, corresponding to Hisbiscus chlorotic ringspot virus, it has been reported that the 3'-proximal gene can be translated from the gRNA through an internal ribosome entry site (IRES). Here we show that PFBV also holds an IRES that mediates production of p37 from the gRNA, raising the question of whether this translation strategy may be conserved in the genus. The PFBV IRES was functional both in vitro and in vivo and either in the viral context or when inserted into synthetic bicistronic constructs. Through deletion and mutagenesis studies we have found that the IRES is contained within a 80 nt segment and have identified some structural traits that influence IRES function. Interestingly, mutations that diminish IRES activity strongly reduced the infectivity of the virus while the progress of the infection was favoured by mutations potentiating such activity. These results support the biological significance of the IRES-driven p37 translation and suggest that production of the silencing suppressor from the gRNA might allow the virus to early counteract the defence response of the host, thus facilitating pathogen multiplication and spread.

Internal Temperature Control For Vibration Testers

Science.gov (United States)

Dean, Richard J.

1996-01-01

Vibration test fixtures with internal thermal-transfer capabilities developed. Made of aluminum for rapid thermal transfer. Small size gives rapid response to changing temperatures, with better thermal control. Setup quicker and internal ducting facilitates access to parts being tested. In addition, internal flows smaller, so less energy consumed in maintaining desired temperature settings.

5S rRNA-derived and tRNA-derived SINEs in fruit bats.

Science.gov (United States)

Gogolevsky, Konstantin P; Vassetzky, Nikita S; Kramerov, Dmitri A

2009-05-01

Most short retroposons (SINEs) descend from cellular tRNA of 7SL RNA. Here, four new SINEs were found in megabats (Megachiroptera) but neither in microbats nor in other mammals. Two of them, MEG-RS and MEG-RL, descend from another cellular RNA, 5S rRNA; one (MEG-T2) is a tRNA-derived SINE; and MEG-TR is a hybrid tRNA/5S rRNA SINE. Insertion locus analysis suggests that these SINEs were active in the recent fruit bat evolution. Analysis of MEG-RS and MEG-RL in comparison with other few 5S rRNA-derived SINEs demonstrates that the internal RNA polymerase III promoter is their most invariant region, while the secondary structure is more variable. The mechanisms underlying the modular structure of these and other SINEs as well as their variation are discussed. The scenario of evolution of MEG SINEs is proposed.

Rational Design and Tuning of Functional RNA Switch to Control an Allosteric Intermolecular Interaction.

Science.gov (United States)

Endoh, Tamaki; Sugimoto, Naoki

2015-08-04

Conformational transitions of biomolecules in response to specific stimuli control many biological processes. In natural functional RNA switches, often called riboswitches, a particular RNA structure that has a suppressive or facilitative effect on gene expression transitions to an alternative structure with the opposite effect upon binding of a specific metabolite to the aptamer region. Stability of RNA secondary structure (-ΔG°) can be predicted based on thermodynamic parameters and is easily tuned by changes in nucleobases. We envisioned that tuning of a functional RNA switch that causes an allosteric interaction between an RNA and a peptide would be possible based on a predicted switching energy (ΔΔG°) that corresponds to the energy difference between the RNA secondary structure before (-ΔG°before) and after (-ΔG°after) the RNA conformational transition. We first selected functional RNA switches responsive to neomycin with predicted ΔΔG° values ranging from 5.6 to 12.2 kcal mol(-1). We then demonstrated a simple strategy to rationally convert the functional RNA switch to switches responsive to natural metabolites thiamine pyrophosphate, S-adenosyl methionine, and adenine based on the predicted ΔΔG° values. The ΔΔG° values of the designed RNA switches proportionally correlated with interaction energy (ΔG°interaction) between the RNA and peptide, and we were able to tune the sensitivity of the RNA switches for the trigger molecule. The strategy demonstrated here will be generally applicable for construction of functional RNA switches and biosensors in which mechanisms are based on conformational transition of nucleic acids.

The RNA gene information: retroelement-microRNA entangling as the RNA quantum code.

Science.gov (United States)

Fujii, Yoichi Robertus

2013-01-01

MicroRNA (miRNA) and retroelements may be a master of regulator in our life, which are evolutionally involved in the origin of species. To support the Darwinism from the aspect of molecular evolution process, it has tremendously been interested in the molecular information of naive RNA. The RNA wave model 2000 consists of four concepts that have altered from original idea of the miRNA genes for crosstalk among embryonic stem cells, their niche cells, and retroelements as a carrier vesicle of the RNA genes. (1) the miRNA gene as a mobile genetic element induces transcriptional and posttranscriptional silencing via networking-processes (no hierarchical architecture); (2) the RNA information supplied by the miRNA genes expands to intracellular, intercellular, intraorgan, interorgan, intraspecies, and interspecies under the cycle of life into the global environment; (3) the mobile miRNAs can self-proliferate; and (4) cells contain two types information as resident and genomic miRNAs. Based on RNA wave, we have developed an interest in investigation of the transformation from RNA information to quantum bits as physicochemical characters of RNA with the measurement of RNA electron spin. When it would have been given that the fundamental bases for the acquired characters in genetics can be controlled by RNA gene information, it may be available to apply for challenging against RNA gene diseases, such as stress-induced diseases.

Application of small RNA technology for improved control of parasitic helminths.

Science.gov (United States)

Britton, Collette; Winter, Alan D; Marks, Neil D; Gu, Henry; McNeilly, Tom N; Gillan, Victoria; Devaney, Eileen

2015-08-15

Over the last decade microRNAs (miRNAs) and small interfering RNAs (siRNAs) have emerged as important regulators of post-transcriptional gene expression. miRNAs are short, non-coding RNAs that regulate a variety of processes including cancer, organ development and immune function. This class of small RNAs bind with partial complementarity to their target mRNA sequences, most often in the 3'UTR, to negatively regulate gene expression. In parasitic helminths, miRNAs are being increasingly studied for their potential roles in development and host-parasite interactions. The availability of genome data, combined with small RNA sequencing, has paved the way to profile miRNAs expressed at particular developmental stages for many parasitic helminths. While some miRNAs are conserved across species, others appear to be unique to specific parasites, suggesting important roles in adaptation and survival in the host environment. Some miRNAs are released from parasites, in exosomes or in protein complexes, and the potential effects of these on host immune function are being increasingly studied. In addition, release of miRNAs from schistosome and filarial parasites into host plasma can be exploited for the development of specific and sensitive diagnostic biomarkers of infection. Interfering with miRNA function, as well as silencing key components of the pathways they regulate, will progress our understanding of parasite development and provide a novel approach to therapeutic control. RNA interference (RNAi) by siRNAs has proven to be inconsistent in parasitic nematodes. However, the recent successes reported for schistosome and liver fluke RNAi, encourage further efforts to enhance delivery of RNA and improve in vitro culture systems and assays to monitor phenotypic effects in nematodes. These improvements are important for the establishment of reliable functional genomic platforms for novel drug and vaccine development. In this review we focus on the important roles of mi

Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA

Science.gov (United States)

Zhu, Yanglong; Stribinskis, Vilius; Ramos, Kenneth S.; Li, Yong

2006-01-01

RNase MRP is a eukaryote-specific endoribonuclease that generates RNA primers for mitochondrial DNA replication and processes precursor rRNA. RNase P is a ubiquitous endoribonuclease that cleaves precursor tRNA transcripts to produce their mature 5′ termini. We found extensive sequence homology of catalytic domains and specificity domains between their RNA subunits in many organisms. In Candida glabrata, the internal loop of helix P3 is 100% conserved between MRP and P RNAs. The helix P8 of MRP RNA from microsporidia Encephalitozoon cuniculi is identical to that of P RNA. Sequence homology can be widely spread over the whole molecule of MRP RNA and P RNA, such as those from Dictyostelium discoideum. These conserved nucleotides between the MRP and P RNAs strongly support the hypothesis that the MRP RNA is derived from the P RNA molecule in early eukaryote evolution. PMID:16540690

Improvement of internal book-keeping control at company "Balttranslaine"

OpenAIRE

Kolodinska, Aļona

2012-01-01

Master's thesis "Internal Accounting Control Improvement in Ltd."Balttranslaine"" is designed to determine the potential and directions for improving accounting controls Ltd. "Balttranslaine". The paper assesses Ltd. "Balttranslaine" internal accounting control system and develops proposals for its improvement, based on research on accounting control nature and its place in the overall company's internal control system, as well as the Latvian laws and regulations for construction and maint...

12 CFR 1731.5 - Internal controls, procedures, and training.

Science.gov (United States)

2010-01-01

... 12 Banks and Banking 7 2010-01-01 2010-01-01 false Internal controls, procedures, and training... HOUSING AND URBAN DEVELOPMENT SAFETY AND SOUNDNESS MORTGAGE FRAUD REPORTING § 1731.5 Internal controls, procedures, and training. An Enterprise shall establish adequate and efficient internal controls and...

Structures of two exonucleases involved in controlled RNA turnover in yeast

DEFF Research Database (Denmark)

Jonstrup, Anette Thyssen; Midtgaard, Søren Fuglsang; Van, Lan Bich

divalent cations. The Pop2p structure reveals that the ability of this enzyme to degrade poly(A)/(U)/(C), but not poly(G) may be determined by structural hindrance of interaction with this specific nucleotide. In Rrp6p, mutations known to confer specific RNA degradation phenotypes in yeast nuclei can now...... rid of aberrant RNAs. Here we describe the structures of two 3'-5' exonucleases involved in controlled RNA decay in yeast, Pop2p and Rrp6p. Rrp6p is associated with the nuclear exosome where it participates in the degradation of improperly processed precursor mRNAs and trimming of stable RNAs [1]. Pop...

Investigating the effective factors on management internal controls applying

Directory of Open Access Journals (Sweden)

Ahmad Ahmadkhani

2012-08-01

Full Text Available Information technology plays an important role on increasing internal control in many organizations. In this paper, we present an empirical study to measure the impact of information technology, hiring high quality skilled management team, using high quality standards and increasing employees' awareness on managing internal control. The survey uses a questionnaire based on Likert scale and distributes among the people who work in either administration or financial sectors of governmental agencies in province of Zanjan, Iran. The results of the study indicate that the implementation of information technology positively influences management team to control their system, more effectively, using more skilled and specialized managers positively influences management internal control, an organization with suitable standard positively influences management internal control and increasing employees' awareness positively influences management internal control.

Correlation between RNA Degradation Patterns of Rat's Brain and Early PMI at Different Temperatures.

Science.gov (United States)

Lü, Y H; Li, Z H; Tuo, Y; Liu, L; Li, K; Bian, J; Ma, J L; Chen, L

2016-06-01

To explore the correlation between early postmortem interval （PMI） and eight RNA markers of rat's brain at different temperatures. Total 222 SD rats were randomly divided into control group （PMI=0 h） and four experimental groups. And the rats in the experimental groups were sacrificed by cervical dislocation and respectively kept at 5 ℃, 15 ℃, 25 ℃ and 35 ℃ in a controlled environment chamber. The RNA was extracted from brain tissues, which was taken at 9 time points from 1 h to 24 h postmortem. The expression levels of eight markers, β-actin, GAPDH, RPS29, 18S rRNA, 5S rRNA, U6 snRNA, miRNA-9 and miRNA-125b, were detected using real-time fluorescent quantitative PCR, respectively. Proper internal reference was selected by geNorm software. Regression analysis of normalized RNA markers was performed by SPSS software. Mathematical model for PMI estimation was established using R software. Another 6 SD rats with known PMI were used to verify the mathematical model. 5S rRNA, miR-9 and miR-125b were suitable as internal reference markers for their stable expression. Both β-actin and GAPDH had well time-dependent degradation patterns and degraded continually with prolongation of PMI in 24 h postmortem. The mathematical model of the variation of ΔCt values with PMI and temperature was set up by R software and the model could be used for PMI estimation. The average error rates of model validation using β-actin and GAPDH were 14.1% and 22.2%, respectively. The expression levels of β-actin and GAPDH are well correlated with PMI and environmental temperature. The mathematical model established in present study can provide references for estimating early PMI under various temperature conditions. Copyright© by the Editorial Department of Journal of Forensic Medicine

INNOVATIVE ASPECTS OF DEVELOPMENT OF STATE INTERNAL FINANCIAL CONTROL AND INTERNAL FINANCIAL AUDIT

Directory of Open Access Journals (Sweden)

T. P. Voronchenko

2015-01-01

Full Text Available The article presents the innovative aspects of development of state internal fi nancial control and internal fi nancial audit in terms of the budgeting focused on result. A mechanism for implementing the functions of the Supervisory bodies in order to ensure the effi cient use of budgetary funds and eff ectiveness of budget expenditures. The main purpose of the article is justifi cation of implementing systems of internal fi nancial control and internal fi nancial audit in the structures of the major administrators and recipients of budgetary funds, with the allocation of the basic tools that ensure the functioning of the control mechanism, the combination of control procedures and sequence of their implementation. Methodological base of research is the generalization of domestic and foreign experience of internal fi nancial control and internal fi nancial audit, refl ecting an objective law and the necessity of development of state fi nancial control system in the conditions of innovative economy. The result of the implementation of the proposed mechanism and instruments for its implementation in key spending units and recipients of budget funds should be to ensure the eff ectiveness of the implementation of government programmes and projects. Signifi cance of the research contained in the article problems and their solutions is to ensure the effectiveness of the regulatory authorities at all stages of movement of budgetary funds and effective implementation of their Manager and recipient assigned to them socio-economic functions.

Aging-associated changes in microRNA expression profile of internal anal sphincter smooth muscle: Role of microRNA-133a

Science.gov (United States)

Singh, Jagmohan; Boopathi, Ettickan; Addya, Sankar; Phillips, Benjamin; Rigoutsos, Isidore; Penn, Raymond B.

2016-01-01

A comprehensive genomic and proteomic, computational, and physiological approach was employed to examine the (previously unexplored) role of microRNAs (miRNAs) as regulators of internal anal sphincter (IAS) smooth muscle contractile phenotype and basal tone. miRNA profiling, genome-wide expression, validation, and network analyses were employed to assess changes in mRNA and miRNA expression in IAS smooth muscles from young vs. aging rats. Multiple miRNAs, including rno-miR-1, rno-miR-340-5p, rno-miR-185, rno-miR-199a-3p, rno-miR-200c, rno-miR-200b, rno-miR-31, rno-miR-133a, and rno-miR-206, were found to be upregulated in aging IAS. qPCR confirmed the upregulated expression of these miRNAs and downregulation of multiple, predicted targets (Eln, Col3a1, Col1a1, Zeb2, Myocd, Srf, Smad1, Smad2, Rhoa/Rock2, Fn1, Tagln v2, Klf4, and Acta2) involved in regulation of smooth muscle contractility. Subsequent studies demonstrated an aging-associated increase in the expression of miR-133a, corresponding decreases in RhoA, ROCK2, MYOCD, SRF, and SM22α protein expression, RhoA-signaling, and a decrease in basal and agonist [U-46619 (thromboxane A2 analog)]-induced increase in the IAS tone. Moreover, in vitro transfection of miR-133a caused a dose-dependent increase of IAS tone in strips, which was reversed by anti-miR-133a. Last, in vivo perianal injection of anti-miR-133a reversed the loss of IAS tone associated with age. This work establishes the important regulatory effect of miRNA-133a on basal and agonist-stimulated IAS tone. Moreover, reversal of age-associated loss of tone via anti-miR delivery strongly implicates miR dysregulation as a causal factor in the aging-associated decrease in IAS tone and suggests that miR-133a is a feasible therapeutic target in aging-associated rectoanal incontinence. PMID:27634012

Control Techtronics International

Energy Technology Data Exchange (ETDEWEB)

West, J.

1995-12-31

Polish graded coal can be burned in existing stoker boilers and meet the 1998 Air Quality standard. This is accomplished with the Control Techtronics microprocessor-based combustion controller accurately and repeatedly: (a) matching the combustion air to the coal firing rate, with continuous stack sensor feedback; (b) continuously varying the boiler`s firing rate based on output water temperature or steam pressure; (c) continuously varying the exhaust fan`s speed to maintain minimum negative pressure in the boiler`s combustion chamber; and recirculating a portion of the flue gas, at varying amounts throughout the boiler`s firing rate. Systems for five boilers have been installed and are operating on MPEC`s Balicka plant in Krakow. Control Techtronics International has $10 million of U.S. Export-Import Bank funds available for similar projects throughout Poland.

Sequence organization and control of transcription in the bacteriophage T4 tRNA region.

Science.gov (United States)

Broida, J; Abelson, J

1985-10-05

Bacteriophage T4 contains genes for eight transfer RNAs and two stable RNAs of unknown function. These are found in two clusters at 70 X 10(3) base-pairs on the T4 genetic map. To understand the control of transcription in this region we have completed the sequencing of 5000 base-pairs in this region. The sequence contains a part of gene 3, gene 1, gene 57, internal protein I, the tRNA genes and five open reading frames which most likely code for heretofore unidentified proteins. We have used subclones of the region to investigate the kinetics of transcription in vivo. The results show that transcription in this region consists of overlapping early, middle and late transcripts. Transcription is directed from two early promoters, one or two middle promoters and perhaps two late promoters. This region contains all of the features that are seen in T4 transcription and as such is a good place to study the phenomenon in more detail.

MicroRNA-223 controls susceptibility to tuberculosis by regulating lung neutrophil recruitment.

Science.gov (United States)

Dorhoi, Anca; Iannaccone, Marco; Farinacci, Maura; Faé, Kellen C; Schreiber, Jörg; Moura-Alves, Pedro; Nouailles, Geraldine; Mollenkopf, Hans-Joachim; Oberbeck-Müller, Dagmar; Jörg, Sabine; Heinemann, Ellen; Hahnke, Karin; Löwe, Delia; Del Nonno, Franca; Goletti, Delia; Capparelli, Rosanna; Kaufmann, Stefan H E

2013-11-01

The molecular mechanisms that control innate immune cell trafficking during chronic infection and inflammation, such as in tuberculosis (TB), are incompletely understood. During active TB, myeloid cells infiltrate the lung and sustain local inflammation. While the chemoattractants that orchestrate these processes are increasingly recognized, the posttranscriptional events that dictate their availability are unclear. We identified microRNA-223 (miR-223) as an upregulated small noncoding RNA in blood and lung parenchyma of TB patients and during murine TB. Deletion of miR-223 rendered TB-resistant mice highly susceptible to acute lung infection. The lethality of miR-223(–/–) mice was apparently not due to defects in antimycobacterial T cell responses. Exacerbated TB in miR-223(–/–) animals could be partially reversed by neutralization of CXCL2, CCL3, and IL-6, by mAb depletion of neutrophils, and by genetic deletion of Cxcr2. We found that miR-223 controlled lung recruitment of myeloid cells, and consequently, neutrophil-driven lethal inflammation. We conclude that miR-223 directly targets the chemoattractants CXCL2, CCL3, and IL-6 in myeloid cells. Our study not only reveals an essential role for a single miRNA in TB, it also identifies new targets for, and assigns biological functions to, miR-223. By regulating leukocyte chemotaxis via chemoattractants, miR-223 is critical for the control of TB and potentially other chronic inflammatory diseases.

The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

International Nuclear Information System (INIS)

Kurkcuoglu, Ozge; Doruker, Pemra; Jernigan, Robert L; Sen, Taner Z; Kloczkowski, Andrzej

2008-01-01

The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs and mRNA; here, the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal structures are used to construct various model systems of the 70S complex with/without tRNA, elongation factor Tu and the ribosomal proteins. Computed motions reveal the well-known ratchet-like rotational motion of the large subunits, as well as the head rotation of the small subunit and the high flexibility of the L1 and L7/L12 stalks, even in the absence of ribosomal proteins. This result indicates that these experimentally observed motions during translocation are inherently controlled by the ribosomal shape and only partially dependent upon GTP hydrolysis. Normal mode analysis further reveals the mobility of A- and P-tRNAs to increase in the absence of the E-tRNA. In addition, the dynamics of the E-tRNA is affected by the absence of the ribosomal protein L1. The mRNA in the entrance tunnel interacts directly with helicase proteins S3 and S4, which constrain the mRNA in a clamp-like fashion, as well as with protein S5, which likely orients the mRNA to ensure correct translation. The ribosomal proteins S7, S11 and S18 may also be involved in assuring translation fidelity by constraining the mRNA at the exit site of the channel. The mRNA also interacts with the 16S 3' end forming the Shine–Dalgarno complex at the initiation step; the 3' end may act as a 'hook' to reel in the mRNA to facilitate its exit

Government Internal Control System Maturity: The Role of Internal Guidance and External Control of Local Government in Indonesia

Directory of Open Access Journals (Sweden)

Sutaryo Sutaryo

2017-12-01

Full Text Available This study discusses the Government Internal Control System (SPIP. The purpose of this study is to obtain empirical evidence of influence of guidance, external control, and the characteristics of Local Governments on Internal Control (SPIP maturity of local governments in Indonesia. The samples used in this study are 188 local governments in 2014. The variables used include the dependent variable, i.e. the SPIP maturity of local government; Independent variables, i.e. guidance frequency, the number of internal control findings, total assets, total expenditure and the number of local government units. This study uses secondary data obtained from the Financial and Development Supervisory Agency (BPKP and the Supreme Audit Agency (BPK. This study uses multiple regression analysis and the results show that the guidace frequency and total expenditure have a positive influence on maturity of SPIP, SPI finding has a negative influence, and the total assets and the number of units do not have significant influence on the maturity of SPIP.

Internal control in the management system of meat processing enterprises

Directory of Open Access Journals (Sweden)

Volodymyr Kushnir

2018-03-01

Full Text Available The article is described the theoretical basis of internal control and its practical aspects in the work of meat processing enterprises (a case in the meat processing industry in Ukraine. The purpose of the research is to establish the theoretical foundations of the internal control and its improvement in the activity of meat processing plants of various forms of management. It is proposed to use precisely internal control among other names of domestic control. Definition of internal control, its subject and purpose are improved. The subjects and objects of internal control are determined; the principles of its implementation are supplemented. Specific control tasks in meat processing plants according to the needs of this industry are outlined. Specific examples of control subjects are presented and the role of the revision commission is emphasized. The state of internal control in meat processing plants in Ukraine is investigated and it is established that it has a bad condition and unfounded approach to its implementation by managers of meat processing enterprises. To improve the situation we recommend that each meat processing enterprise have in its staff a revision commission or an apposer (auditor. It is established that internal control is more effective in joint-stock companies than in limited liability companies. The necessity of internal control as an important element in the enterprise management system is accented.

Expanding Internal Control Functionality Scope

Directory of Open Access Journals (Sweden)

Mykola M. Vuitsiv

2012-08-01

Full Text Available The article reviews the influence of «western» concepts of the information needs of management process provisions on forming and developing the up-to-date model of Internal Control. An attempt has been made to develop the approach to solve urgent management tasks by applying the ideas of controlling and management accounting via the traditional national approach to the content of control. The place of control in the enterprise management information system has also been reviewed.

THEORETICAL ASPECTS OF INTERNAL FINANCIAL CONTROL

Directory of Open Access Journals (Sweden)

Dzhamilya F. Ismailova

2013-01-01

Full Text Available The article considers the theoretical aspects of internal financial control, summarizes the definition formulated by scientists and experts, analyzed for differences between incompany and intrafarm control. The article discusses the collapse of Enron, notes the general provisions of various types of financial control.

Internal Control Good Cooperative Governance And Performance

Directory of Open Access Journals (Sweden)

Andry Arifian Rachman

2017-11-01

Full Text Available This study aims to examine the influence of internal control and good cooperative governance partially and simultaneously to the performance of cooperatives in West Java Province. The research method used in this research is descriptive and verification. The sample in this research is 22 boards as manager of cooperative in West Java Province. The data used in the research is the primary data through questionnaire collection. Validity and reliability testing is performed before hypothesis testing. This research uses multiple regression analysis technique. Based on hypothesis testing obtained 1 internal control has no significant effect on performance 2 good cooperative governance has a significant effect on performance and 3 internal control and good cooperative governance have a significant effect on performance.

13 CFR 107.506 - Safeguarding Licensee's assets/Internal controls.

Science.gov (United States)

2010-01-01

.../Internal controls. 107.506 Section 107.506 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION... Safeguarding Licensee's assets/Internal controls. You must adopt a plan to safeguard your assets and monitor... your control procedures. ...

Cis-regulatory RNA elements that regulate specialized ribosome activity.

Science.gov (United States)

Xue, Shifeng; Barna, Maria

2015-01-01

Recent evidence has shown that the ribosome itself can play a highly regulatory role in the specialized translation of specific subpools of mRNAs, in particular at the level of ribosomal proteins (RP). However, the mechanism(s) by which this selection takes place has remained poorly understood. In our recent study, we discovered a combination of unique RNA elements in the 5'UTRs of mRNAs that allows for such control by the ribosome. These mRNAs contain a Translation Inhibitory Element (TIE) that inhibits general cap-dependent translation, and an Internal Ribosome Entry Site (IRES) that relies on a specific RP for activation. The unique combination of an inhibitor of general translation and an activator of specialized translation is key to ribosome-mediated control of gene expression. Here we discuss how these RNA regulatory elements provide a new level of control to protein expression and their implications for gene expression, organismal development and evolution.

Internal Border Controls in the European Union

DEFF Research Database (Denmark)

Jørgensen, Carsten Willemoes; Sørensen, Karsten Engsig

2012-01-01

Recent events, involving inter alia France and Denmark, have stimulated renewed interest in the introduction of different forms of border controls at the internal borders within the European Union. These border control measures are aimed at checking either persons or goods or both. Against...... the background of these events, this article analyses the existing rules regulating controls of persons and goods, and explores how these rules may or may not stand in the way of introducing border controls at the European Union’s internal borders. These events have resulted in a call for reforms of the current...

Budgeting-Based Organization of Internal Control

Science.gov (United States)

Rogulenko, Tatiana; Ponomareva, Svetlana; Bodiaco, Anna; Mironenko, Valentina; Zelenov, Vladimir

2016-01-01

The article suggests methodical approaches to the budgeting-based organization of internal control, determines the tasks and subtasks of control that consist in the construction of an efficient system for the making, implementation, control, and analysis of managerial decisions. The organization of responsibility centers by means of implementing…

AUTOMATION OF THE SYSTEM OF INTERNAL LABORATORY QUALITY CONTROL

Directory of Open Access Journals (Sweden)

V. Z. Stetsyuk

2015-05-01

Full Text Available Quality control system base d on the principles of standardi zation of all phases of laboratory testing and analysis of internal laboratory quality control and external quality assessment. For the detection accuracy of the results of laboratory tests, carried out internally between the laboratory and laboratory quality control. Under internal laboratory quality control we understand measurement results of each analysis in each anal ytical series rendered directly in the lab every day. The purpose of internal laboratory control - identifying and eliminating unacceptable deviations from standard perfor mance test in the laboratory, i.e. identifying and eliminating harmful analytical errors. The solutions to these problems by implementing automated systems - software that allows you to optimize analytical laboratory research stage of the procedure by automatically creating process control charts was shown.

Cell cycle-dependent transcription factors control the expression of yeast telomerase RNA.

Science.gov (United States)

Dionne, Isabelle; Larose, Stéphanie; Dandjinou, Alain T; Abou Elela, Sherif; Wellinger, Raymund J

2013-07-01

Telomerase is a specialized ribonucleoprotein that adds repeated DNA sequences to the ends of eukaryotic chromosomes to preserve genome integrity. Some secondary structure features of the telomerase RNA are very well conserved, and it serves as a central scaffold for the binding of associated proteins. The Saccharomyces cerevisiae telomerase RNA, TLC1, is found in very low copy number in the cell and is the limiting component of the known telomerase holoenzyme constituents. The reasons for this low abundance are unclear, but given that the RNA is very stable, transcriptional control mechanisms must be extremely important. Here we define the sequences forming the TLC1 promoter and identify the elements required for its low expression level, including enhancer and repressor elements. Within an enhancer element, we found consensus sites for Mbp1/Swi4 association, and chromatin immunoprecipitation (ChIP) assays confirmed the binding of Mbp1 and Swi4 to these sites of the TLC1 promoter. Furthermore, the enhancer element conferred cell cycle-dependent regulation to a reporter gene, and mutations in the Mbp1/Swi4 binding sites affected the levels of telomerase RNA and telomere length. Finally, ChIP experiments using a TLC1 RNA-binding protein as target showed cell cycle-dependent transcription of the TLC1 gene. These results indicate that the budding yeast TLC1 RNA is transcribed in a cell cycle-dependent fashion late in G1 and may be part of the S phase-regulated group of genes involved in DNA replication.

Translational Control Protein 80 Stimulates IRES-Mediated Translation of p53 mRNA in Response to DNA Damage

Directory of Open Access Journals (Sweden)

Marie-Jo Halaby

2015-01-01

Full Text Available Synthesis of the p53 tumor suppressor increases following DNA damage. This increase and subsequent activation of p53 are essential for the protection of normal cells against tumorigenesis. We previously discovered an internal ribosome entry site (IRES that is located at the 5′-untranslated region (UTR of p53 mRNA and found that the IRES activity increases following DNA damage. However, the mechanism underlying IRES-mediated p53 translation in response to DNA damage is still poorly understood. In this study, we discovered that translational control protein 80 (TCP80 has increased binding to the p53 mRNA in vivo following DNA damage. Overexpression of TCP80 also leads to increased p53 IRES activity in response to DNA damage. TCP80 has increased association with RNA helicase A (RHA following DNA damage and overexpression of TCP80, along with RHA, leads to enhanced expression of p53. Moreover, we found that MCF-7 breast cancer cells with decreased expression of TCP80 and RHA exhibit defective p53 induction following DNA damage and diminished expression of its downstream target PUMA, a proapoptotic protein. Taken together, our discovery of the function of TCP80 and RHA in regulating p53 IRES and p53 induction following DNA damage provides a better understanding of the mechanisms that regulate IRES-mediated p53 translation in response to genotoxic stress.

Effect of internal controls on credit risk among listed Spanish banks

Directory of Open Access Journals (Sweden)

Ellis Kofi Akwaa-Sekyi

2016-02-01

Full Text Available Purpose: The paper examines the effectiveness of internal control systems, explores the exposure of Spanish banks to the dangers of default as a result of internal control systems and establishes a relationship between internal controls and credit risk. Design/Methodology/Approach: Quantitative research approach is used to test hypotheses on the relationship between internal controls and credit risk among listed banks in Spain. Data from Bankscope and company websites from 2004-2013 were used. Generalized Least Squares (random effect econometric estimation technique was used for the model. Findings: We find that internal control systems are in place but their effectiveness cannot be guaranteed. This exposes Spanish listed banks to serious default situations. There is significant effect of internal controls on credit risk especially the control environment, risk management, control activities and monitoring. The non-disclosure of material internal control weakness is a contributory factor to the ineffective internal control systems. There is however a perceived board ineffectiveness which does not augur well for effective internal control systems. Board characteristics for Spanish banks confirm the agency theory. Research Limitations and Implications: Data unavailability for certain years, variables and many inactive banks did not permit a larger sample size than expected. The use of quantitative variables lacks flexibility. Practical Implications: Bank management will find the work useful to ensure strict enforcement of internal control mechanisms and see it as both credit risk and operational risk issues. Central bank should hurry to compel banks to disclose material internal control weakness as provided in the reviewed COSO framework. Social Implications: Ineffective internal controls lead to credit risks, bank closure and loss of investments. Society suffers a lot from such losses and contagion. Disclosure of material internal control

IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions.

Science.gov (United States)

Mann, Martin; Wright, Patrick R; Backofen, Rolf

2017-07-03

The IntaRNA algorithm enables fast and accurate prediction of RNA-RNA hybrids by incorporating seed constraints and interaction site accessibility. Here, we introduce IntaRNAv2, which enables enhanced parameterization as well as fully customizable control over the prediction modes and output formats. Based on up to date benchmark data, the enhanced predictive quality is shown and further improvements due to more restrictive seed constraints are highlighted. The extended web interface provides visualizations of the new minimal energy profiles for RNA-RNA interactions. These allow a detailed investigation of interaction alternatives and can reveal potential interaction site multiplicity. IntaRNAv2 is freely available (source and binary), and distributed via the conda package manager. Furthermore, it has been included into the Galaxy workflow framework and its already established web interface enables ad hoc usage. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

AUDITING INTERNAL CONTROLS IN FINANCING PRESCHOOL PUBLIC INSTITUTION: EVIDENCE FROM SLOVENIA

Directory of Open Access Journals (Sweden)

Tatjana HORVAT

2017-12-01

Full Text Available Public preschool educational institutions in Slovenia are mostly financed by public money, it means bay state and municipalities. They are also financed by parents. So, it is important that preschool institutions are using public money transparent and responsible, for this reason public preschool institution should have internal controls in financing. The internal auditor as independent professional should verify if internal controls works. The purpose of this paper is to investigate how internal controls in financing public educational institution works it means which internal controls are important in financing the preschool institution - on the selected institution to show and check how internal controls work. For this reason we divide internal controls in the financing in two phases: (1 internal controls in the preparation of the annual financial plan and financial planning of financial resources for institution’s programs and activities, (2 internal controls in obtaining financial resources. We used methods of internal auditing and research approaches as sampling, unstructured interviews and analysis of documents. The results showed that selected preschool institution should work on rules of recovery and monitoring of claims. The findings provide useful academic insight to setting internal controls as well as practical guidance for preschool institutions.

Normalization of RNA-seq data using factor analysis of control genes or samples

Science.gov (United States)

Risso, Davide; Ngai, John; Speed, Terence P.; Dudoit, Sandrine

2015-01-01

Normalization of RNA-seq data has proven essential to ensure accurate inference of expression levels. Here we show that usual normalization approaches mostly account for sequencing depth and fail to correct for library preparation and other more-complex unwanted effects. We evaluate the performance of the External RNA Control Consortium (ERCC) spike-in controls and investigate the possibility of using them directly for normalization. We show that the spike-ins are not reliable enough to be used in standard global-scaling or regression-based normalization procedures. We propose a normalization strategy, remove unwanted variation (RUV), that adjusts for nuisance technical effects by performing factor analysis on suitable sets of control genes (e.g., ERCC spike-ins) or samples (e.g., replicate libraries). Our approach leads to more-accurate estimates of expression fold-changes and tests of differential expression compared to state-of-the-art normalization methods. In particular, RUV promises to be valuable for large collaborative projects involving multiple labs, technicians, and/or platforms. PMID:25150836

The Nuclotron internal target control and data acquisition system

Energy Technology Data Exchange (ETDEWEB)

Isupov, A.Yu., E-mail: isupov@moonhe.jinr.ru [Joint Institute for Nuclear Research, Dubna 141980 (Russian Federation); Krasnov, V.A.; Ladygin, V.P.; Piyadin, S.M.; Reznikov, S.G. [Joint Institute for Nuclear Research, Dubna 141980 (Russian Federation)

2013-01-11

The new control system of the Nuclotron (JINR, Dubna) internal target is described in both hardware and software aspects. The CAMAC hardware is based on the use of the standard CAMAC modules developed and manufactured at JINR. The internal target control and data acquisition (IntTarg CDAQ) system software is implemented using the ngdp framework under the Unix-like operating system (OS) FreeBSD to allow easy network distribution of the online data collected from internal target and accompanying detectors, as well as the internal target remote control.

Determinants of Effective Internal Control System in Nigerian Banks ...

African Journals Online (AJOL)

Determinants of Effective Internal Control System in Nigerian Banks. ... (21) chief internal auditors of selected recapitalized banks currently operating in Port Harcourt. ... can be carried out, high level ethical standards should be enshrined in Nigerian banks to make internal control more effective. ... HOW TO USE AJOL.

METHODOLOGICAL ASPECTS OF THE INTERNAL CONTROL SYSTEM FORMATION

Directory of Open Access Journals (Sweden)

Larisa I. Egorova

2014-01-01

Full Text Available The methodological aspects of the internal control system formation are stated in the article. The great attention is focused on the problems of financial statements misrepresentation. The basic principles and structure of the internal control system are discussed in this article.

Determinants of human resource investment in internal controls

Directory of Open Access Journals (Sweden)

Jong-Hag Choi

2013-09-01

Full Text Available Using the unique reporting environment in Korea, this study investigates the determinants of human resource investment in internal controls for 1352 listed firms disclosing the number of personnel who are in charge of internal control-related tasks (IC personnel from 2005 to 2008. We find that the number of IC personnel within a firm and several key departments increase with firm size, number of employees, complexity and for Chaebols, and decrease in rapidly growing firms. Additional analysis reveals that the factors influencing internal control systems have an accentuated effect on firms with relatively larger firm size.

Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites

Directory of Open Access Journals (Sweden)

Schraga Schwartz

2014-07-01

Full Text Available N6-methyladenosine (m6A is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins interacting with METTL3, a component of the methyltransferase complex, and show that three of them (WTAP, METTL14, and KIAA1429 are required for methylation. Monitoring m6A levels upon WTAP depletion allowed the definition of accurate and near single-nucleotide resolution methylation maps and their classification into WTAP-dependent and -independent sites. WTAP-dependent sites are located at internal positions in transcripts, topologically static across a variety of systems we surveyed, and inversely correlated with mRNA stability, consistent with a role in establishing “basal” degradation rates. WTAP-independent sites form at the first transcribed base as part of the cap structure and are present at thousands of sites, forming a previously unappreciated layer of transcriptome complexity. Our data shed light on the proteomic and transcriptional underpinnings of this RNA modification.

Solid nano-in-nanoparticles for potential delivery of siRNA.

Science.gov (United States)

Amsalem, Orit; Nassar, Taher; Benhamron, Sandrine; Lazarovici, Philip; Benita, Simon; Yavin, Eylon

2017-07-10

siRNA-based therapeutics possess great potential to treat a wide variety of genetic disorders. However, they suffer from low cellular uptake and short half-lives in blood circulation; issues that remain to be addressed. This work is, to the best of our knowledge, the first to report the production of solid nano-in-nanoparticles, termed double nano carriers (DNCs) by means of the innovative technology of nano spray drying. DNCs (with a median size of 580-770nm) were produced by spraying at low temperatures (50°C) to prevent damage to heat-sensitive biomacromolecules like siRNA. DNCs consisting of Poly (d,l-lactide-co-glycolide) used as a wall material, encapsulating 20% human serum albumin primary nanoparticles (PNPs) loaded with siRNA, were obtained as a dry nanoparticulate powder with smooth spherical surfaces and a unique inner morphology. Incubation of pegylated or non-pegylated DNCs under sink conditions at 37°C, elicited a controlled release profile of the siRNA for up to 12 or 24h, respectively, with a minimal burst effect. Prolonged incubation of pegylated DNCs loaded with active siRNA (anti EGFR) in an A549 epithelial cell culture monolayer did not induce any apparent cytotoxicity. A slow degradation of the internalized DNCs by the cells was also observed resulting in the progressive release of the siRNA for up to 6days, as corroborated by laser confocal microscopy. The structural integrity and silencing activity of the double encapsulated siRNA were fully preserved, as demonstrated by HPLC, gel electrophoresis, and potent RNAi activity of siRNA extracted from DNCs. These results demonstrate the potential use of DNCs as a nano drug delivery system for systemic administration and controlled release of siRNA and potentially other sensitive bioactive macromolecules. Copyright © 2016 Elsevier B.V. All rights reserved.

Internal control as part of prevention irregularities in accounting of budgetary institution

Directory of Open Access Journals (Sweden)

O.М. Bunda

2016-07-01

Full Text Available The article researches the principles of internal control, the importance, the rationale for the essence of the system of internal control and the legislative building in budgetary institution. It describes the main challenges and problems of practical application of internal control in the normal course of business in modern enterprises. It reveals the following elements of the internal control of a budget institution as: control environment, risk assessment process of a budget institution, information systems, control procedures and control monitoring. The dependence between the effectiveness of accounting and internal control of a budget institution is determined. The paper highlights the methods of evaluation of internal control of a budget institution. This method is recommended for use in the preliminary assessment of control risk budget institution. The concept of «decision» as on the whole and also in particular in internal control is covered. The essential grouping indications of internal control decisions are defined and every type of decisions is characterized. The main directions of improvement of internal control to prevent violations in accounting of a budgetary institution is examined.

RNA-Based Vaccines in Cancer Immunotherapy

Directory of Open Access Journals (Sweden)

Megan A. McNamara

2015-01-01

Full Text Available RNA vaccines traditionally consist of messenger RNA synthesized by in vitro transcription using a bacteriophage RNA polymerase and template DNA that encodes the antigen(s of interest. Once administered and internalized by host cells, the mRNA transcripts are translated directly in the cytoplasm and then the resulting antigens are presented to antigen presenting cells to stimulate an immune response. Alternatively, dendritic cells can be loaded with either tumor associated antigen mRNA or total tumor RNA and delivered to the host to elicit a specific immune response. In this review, we will explain why RNA vaccines represent an attractive platform for cancer immunotherapy, discuss modifications to RNA structure that have been developed to optimize mRNA vaccine stability and translational efficiency, and describe strategies for nonviral delivery of mRNA vaccines, highlighting key preclinical and clinical data related to cancer immunotherapy.

ENHANCING ASSETS' PROTECTION THROUGH AN ADEQUATE MONITORING OF INTERNAL CONTROL SYSTEM BY INTERNAL AUDIT

Directory of Open Access Journals (Sweden)

Dan Eugen Cosmin

2011-12-01

Full Text Available The assets are established into a company as very important and strategic resources that are contributing at the creation of the needed premises to conduct the daily-basis activity and also to reach present and future planned objectives. Recent studies like COSO's Fraudulent Financial Reporting 1998-2007 have highlighted an increasing fraudulent activity against assets therefore the efforts of fighting against fraud must be supplemented in order to preserve the existence and value of those resources. Internal controls are processes implemented in order to give a reasonable assurance that the company will not become a fraud victim. Even so, a lot of internal controls are paying a heavy tribute to their lack of efficiency and update. Thus, for a correct functioning, internal controls must be monitored and assessed permanently in order to preserve their strength and ability to fulfill their mission. This approach will deliver more added value because rather than being corrected after they have already occurred, the frauds related with the assets will be prevented, detected and reported at a timely moment, thereby the incidence and value of those criminal activities will decrease significantly. Furthermore, because not only the process of monitoring is important but even the entity conducting this activity we believe that internal audit is the most appropriate to undertake this responsibility. Thus, through this material we opened a discussion about how important permanent monitored and updated internal controls are in order to assure a proper assets protection and why internal audit, rather than the management, should be the most eligible to undertake this responsibility. Also we provided some suggestions regarding the main activities that must be taken into consideration by an internal audit professional when is being involved in a monitoring process of internal control system. We do believe that this paper will be the starting point for new

RNA 3D modules in genome-wide predictions of RNA 2D structure

DEFF Research Database (Denmark)

Theis, Corinna; Zirbel, Craig L; Zu Siederdissen, Christian Höner

2015-01-01

. These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D......Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational...... approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution...

The Environmental Action Internal Control Index.

Science.gov (United States)

Smith-Sebasto, N. J.; Fortner, Rosanne W.

1994-01-01

Reports research designed to develop a reliable and valid instrument to assess the relationship between locus of control of reinforcement and environmentally responsible behavior in (n=853) undergraduate students. Results suggest that the Environmental Action Internal Control Index can accurately predict environmentally responsible behavior.…

Methylated nucleosides in tRNA and tRNA methyltransferases

Directory of Open Access Journals (Sweden)

Hiroyuki eHori

2014-05-01

Full Text Available To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s. Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon–anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.

Plasma LncRNA-ATB, a Potential Biomarker for Diagnosis of Patients with Coal Workers’ Pneumoconiosis: A Case-Control Study

Directory of Open Access Journals (Sweden)

Jixuan Ma

2016-08-01

Full Text Available LncRNA-ATB (lncRNA was activated by transforming growth factor-β has been reported to be involved in specific physiological and pathological processes in human diseases, and could serve as biomarkers for cancers. However, the role of lncRNA-ATB in coal workers’ pneumoconiosis (CWP is still unknown. This study aimed to investigate the association between lncRNA-ATB and CWP. Quantitative real-time polymerase chain reaction was performed to detect plasma lncRNA-ATB expression in 137 CWP patients, 72 healthy coal miners and 168 healthy controls. LncRNA-ATB was significantly upregulated in CWP (p < 0.05. Compared with the healthy controls and healthy coal miners, the odds ratios (ORs (95% confidence interval (CI for CWP were 2.57 (1.52–4.33 and 2.17 (1.04–4.53, respectively. LncRNA-ATB was positively associated with transforming growth factor-β1 (TGF-β1 (r = 0.30, p = 0.003 and negative correlated with vital capacity (VC (r = −0.18, p = 0.033 and forced vital capacity (FVC (r = −0.18, p = 0.046 in CWP patients. Compared with healthy controls, the area under the curve (AUC was 0.84, resulting in a 71.17% sensitivity and 88.14% specificity. When compared with healthy coal miners, the AUC was 0.83, the sensitivity and specificity were 70.07% and 86.36%, respectively. LncRNA-ATB expression is commonly increased in CWP and significantly correlates with the TGF-β1 in CWP patients. Furthermore, elevated lncRNA-ATB was associated with CWP risk and may serve as a potential biomarker for CWP.

Non-Target Effects of Green Fluorescent Protein (GFP-Derived Double-Stranded RNA (dsRNA-GFP Used in Honey Bee RNA Interference (RNAi Assays

Directory of Open Access Journals (Sweden)

Francis M. F. Nunes

2013-01-01

Full Text Available RNA interference has been frequently applied to modulate gene function in organisms where the production and maintenance of mutants is challenging, as in our model of study, the honey bee, Apis mellifera. A green fluorescent protein (GFP-derived double-stranded RNA (dsRNA-GFP is currently commonly used as control in honey bee RNAi experiments, since its gene does not exist in the A. mellifera genome. Although dsRNA-GFP is not expected to trigger RNAi responses in treated bees, undesirable effects on gene expression, pigmentation or developmental timing are often observed. Here, we performed three independent experiments using microarrays to examine the effect of dsRNA-GFP treatment (introduced by feeding on global gene expression patterns in developing worker bees. Our data revealed that the expression of nearly 1,400 genes was altered in response to dsRNA-GFP, representing around 10% of known honey bee genes. Expression changes appear to be the result of both direct off-target effects and indirect downstream secondary effects; indeed, there were several instances of sequence similarity between putative siRNAs generated from the dsRNA-GFP construct and genes whose expression levels were altered. In general, the affected genes are involved in important developmental and metabolic processes associated with RNA processing and transport, hormone metabolism, immunity, response to external stimulus and to stress. These results suggest that multiple dsRNA controls should be employed in RNAi studies in honey bees. Furthermore, any RNAi studies involving these genes affected by dsRNA-GFP in our studies should use a different dsRNA control.

Non-Target Effects of Green Fluorescent Protein (GFP)-Derived Double-Stranded RNA (dsRNA-GFP) Used in Honey Bee RNA Interference (RNAi) Assays.

Science.gov (United States)

Nunes, Francis M F; Aleixo, Aline C; Barchuk, Angel R; Bomtorin, Ana D; Grozinger, Christina M; Simões, Zilá L P

2013-01-04

RNA interference has been frequently applied to modulate gene function in organisms where the production and maintenance of mutants is challenging, as in our model of study, the honey bee, Apis mellifera. A green fluorescent protein (GFP)-derived double-stranded RNA (dsRNA-GFP) is currently commonly used as control in honey bee RNAi experiments, since its gene does not exist in the A. mellifera genome. Although dsRNA-GFP is not expected to trigger RNAi responses in treated bees, undesirable effects on gene expression, pigmentation or developmental timing are often observed. Here, we performed three independent experiments using microarrays to examine the effect of dsRNA-GFP treatment (introduced by feeding) on global gene expression patterns in developing worker bees. Our data revealed that the expression of nearly 1,400 genes was altered in response to dsRNA-GFP, representing around 10% of known honey bee genes. Expression changes appear to be the result of both direct off-target effects and indirect downstream secondary effects; indeed, there were several instances of sequence similarity between putative siRNAs generated from the dsRNA-GFP construct and genes whose expression levels were altered. In general, the affected genes are involved in important developmental and metabolic processes associated with RNA processing and transport, hormone metabolism, immunity, response to external stimulus and to stress. These results suggest that multiple dsRNA controls should be employed in RNAi studies in honey bees. Furthermore, any RNAi studies involving these genes affected by dsRNA-GFP in our studies should use a different dsRNA control.

An Integrated Approach for RNA-seq Data Normalization.

Science.gov (United States)

Yang, Shengping; Mercante, Donald E; Zhang, Kun; Fang, Zhide

2016-01-01

DNA copy number alteration is common in many cancers. Studies have shown that insertion or deletion of DNA sequences can directly alter gene expression, and significant correlation exists between DNA copy number and gene expression. Data normalization is a critical step in the analysis of gene expression generated by RNA-seq technology. Successful normalization reduces/removes unwanted nonbiological variations in the data, while keeping meaningful information intact. However, as far as we know, no attempt has been made to adjust for the variation due to DNA copy number changes in RNA-seq data normalization. In this article, we propose an integrated approach for RNA-seq data normalization. Comparisons show that the proposed normalization can improve power for downstream differentially expressed gene detection and generate more biologically meaningful results in gene profiling. In addition, our findings show that due to the effects of copy number changes, some housekeeping genes are not always suitable internal controls for studying gene expression. Using information from DNA copy number, integrated approach is successful in reducing noises due to both biological and nonbiological causes in RNA-seq data, thus increasing the accuracy of gene profiling.

Meta-Strategies of the Internal Control Development within the Organization

OpenAIRE

Roman Voronko

2015-01-01

The article considers the problem of the influence of external and internal environment of the organization on the structure of the internal control system. A critical analysis is made on existing scientific researches and practice of setting internal control within the organizations. Determined the cause-and-effect relationship between the stages of development of the industry and business, on the one hand, and the development of the internal control structure on the other hand. It made it p...

Internal quality control in serological tests for syphilis.

OpenAIRE

Wasley, G D

1985-01-01

The importance of syphilis serological tests demands that laboratory reports are reliable. Internal quality control applied to the organisation of a syphilis serology service improves laboratory bench performance and reporting. Described here are internal quality control procedures of a department that serves a genitourinary medicine clinic and conducts 70 000 tests a year to investigate for syphilis.

INTERNAL CONTROLS IN ENSURING GOOD CORPORATE GOVERNANCE IN FINANCIAL INSTITUTIONS

Directory of Open Access Journals (Sweden)

KOSMAS NJANIKE

2011-01-01

Full Text Available This paper assessed factors that influence the internal controls in ensuring good corporate governance in financial institutions in developing economies with special reference to Zimbabwe. The research paper assessed how lack of internal controls affected good corporate governance and aimed to bring out elements of good corporate governance. It emerged that failure to effectively implement internal controls contributed significantly to poor corporate governance. The study discovered that internal control system overrides and the issue of “fact cat” directors also contributed to poor corporate governance. The study recommended that there is need for the board of directors to guarantee an organizational structure that clearly defines management responsibilities, authority and reporting relationships. There is also need to ensure that delegated responsibilities are effectively carried out to ensure compliance with internal controls of the financial institution concerned.

47 CFR 90.471 - Points of operation in internal transmitter control systems.

Science.gov (United States)

2010-10-01

...) SAFETY AND SPECIAL RADIO SERVICES PRIVATE LAND MOBILE RADIO SERVICES Transmitter Control Internal Transmitter Control Systems § 90.471 Points of operation in internal transmitter control systems. The... licensee for internal communications and transmitter control purposes. Operating positions in internal...

Microprocessor Activity Controls Differential miRNA Biogenesis In Vivo

Directory of Open Access Journals (Sweden)

Thomas Conrad

2014-10-01

Full Text Available In miRNA biogenesis, pri-miRNA transcripts are converted into pre-miRNA hairpins. The in vivo properties of this process remain enigmatic. Here, we determine in vivo transcriptome-wide pri-miRNA processing using next-generation sequencing of chromatin-associated pri-miRNAs. We identify a distinctive Microprocessor signature in the transcriptome profile from which efficiency of the endogenous processing event can be accurately quantified. This analysis reveals differential susceptibility to Microprocessor cleavage as a key regulatory step in miRNA biogenesis. Processing is highly variable among pri-miRNAs and a better predictor of miRNA abundance than primary transcription itself. Processing is also largely stable across three cell lines, suggesting a major contribution of sequence determinants. On the basis of differential processing efficiencies, we define functionality for short sequence features adjacent to the pre-miRNA hairpin. In conclusion, we identify Microprocessor as the main hub for diversified miRNA output and suggest a role for uncoupling miRNA biogenesis from host gene expression.

Thermonuclear controlled fusion: international cooperation

International Nuclear Information System (INIS)

Conscience, J.-F.

2001-01-01

This report summarizes the current worldwide status of research in the field of thermonuclear controlled fusion as well as the international research programme planed for the next decades. The two main projects will be the ITER facility (International Thermonuclear Experimental Reactor) that should produce 10 times more energy than the energy injected, and the IFMIF (International Fusion Materials Irradiation Facility) designed to study the reactions of materials under intense neutron fluxes. The future of the pioneering JET facility (Joint European Torus) is also discussed. The engagement of the various countries (USA, Japan, Germany, Russian Federation and Canada) and international organisations (EURATOM and IEA) in terms of investment and research is described. Switzerland is involved in this program through an agreement with EURATOM and is mainly dedicated to experimental studies with the TCV machine in Lausanne and numerical studies of plasma configurations. It will participate to the development of the microwave plasma heating system for the ITER machine

Evaluation of logistic regression models and effect of covariates for case-control study in RNA-Seq analysis.

Science.gov (United States)

Choi, Seung Hoan; Labadorf, Adam T; Myers, Richard H; Lunetta, Kathryn L; Dupuis, Josée; DeStefano, Anita L

2017-02-06

Next generation sequencing provides a count of RNA molecules in the form of short reads, yielding discrete, often highly non-normally distributed gene expression measurements. Although Negative Binomial (NB) regression has been generally accepted in the analysis of RNA sequencing (RNA-Seq) data, its appropriateness has not been exhaustively evaluated. We explore logistic regression as an alternative method for RNA-Seq studies designed to compare cases and controls, where disease status is modeled as a function of RNA-Seq reads using simulated and Huntington disease data. We evaluate the effect of adjusting for covariates that have an unknown relationship with gene expression. Finally, we incorporate the data adaptive method in order to compare false positive rates. When the sample size is small or the expression levels of a gene are highly dispersed, the NB regression shows inflated Type-I error rates but the Classical logistic and Bayes logistic (BL) regressions are conservative. Firth's logistic (FL) regression performs well or is slightly conservative. Large sample size and low dispersion generally make Type-I error rates of all methods close to nominal alpha levels of 0.05 and 0.01. However, Type-I error rates are controlled after applying the data adaptive method. The NB, BL, and FL regressions gain increased power with large sample size, large log2 fold-change, and low dispersion. The FL regression has comparable power to NB regression. We conclude that implementing the data adaptive method appropriately controls Type-I error rates in RNA-Seq analysis. Firth's logistic regression provides a concise statistical inference process and reduces spurious associations from inaccurately estimated dispersion parameters in the negative binomial framework.

Fast flexible modeling of RNA structure using internal coordinates.

Science.gov (United States)

Flores, Samuel Coulbourn; Sherman, Michael A; Bruns, Christopher M; Eastman, Peter; Altman, Russ Biagio

2011-01-01

Modeling the structure and dynamics of large macromolecules remains a critical challenge. Molecular dynamics (MD) simulations are expensive because they model every atom independently, and are difficult to combine with experimentally derived knowledge. Assembly of molecules using fragments from libraries relies on the database of known structures and thus may not work for novel motifs. Coarse-grained modeling methods have yielded good results on large molecules but can suffer from difficulties in creating more detailed full atomic realizations. There is therefore a need for molecular modeling algorithms that remain chemically accurate and economical for large molecules, do not rely on fragment libraries, and can incorporate experimental information. RNABuilder works in the internal coordinate space of dihedral angles and thus has time requirements proportional to the number of moving parts rather than the number of atoms. It provides accurate physics-based response to applied forces, but also allows user-specified forces for incorporating experimental information. A particular strength of RNABuilder is that all Leontis-Westhof basepairs can be specified as primitives by the user to be satisfied during model construction. We apply RNABuilder to predict the structure of an RNA molecule with 160 bases from its secondary structure, as well as experimental information. Our model matches the known structure to 10.2 Angstroms RMSD and has low computational expense.

Effect of internal controls on credit risk among listed Spanish banks

OpenAIRE

Akwaa-Sekyi, Ellis Kofi; Moreno Gené, Jordi

2016-01-01

Purpose: The paper examines the effectiveness of internal control systems, explores the exposure of Spanish banks to the dangers of default as a result of internal control systems and establishes a relationship between internal controls and credit risk. Design/Methodology/Approach: Quantitative research approach is used to test hypotheses on the relationship between internal controls and credit risk among listed banks in Spain. Data from Bankscope and company websites from 2004-2013 were used...

Wig1 prevents cellular senescence by regulating p21 mRNA decay through control of RISC recruitment.

Science.gov (United States)

Kim, Bong Cho; Lee, Hyung Chul; Lee, Je-Jung; Choi, Chang-Min; Kim, Dong-Kwan; Lee, Jae Cheol; Ko, Young-Gyu; Lee, Jae-Seon

2012-11-14

Premature senescence, a key strategy used to suppress carcinogenesis, can be driven by p53/p21 proteins in response to various stresses. Here, we demonstrate that Wig1 plays a critical role in this process through regulation of p21 mRNA stability. Wig1 controls the association of Argonaute2 (Ago2), a central component of the RNA-induced silencing complex (RISC), with target p21 mRNA via binding of the stem-loop structure near the microRNA (miRNA) target site. Depletion of Wig1 prohibited miRNA-mediated p21 mRNA decay and resulted in premature senescence. Wig1 plays an essential role in cell proliferation, as demonstrated in tumour xenografts in mice, and Wig1 and p21 mRNA levels are inversely correlated in human normal and cancer tissues. Together, our data indicate a novel role of Wig1 in RISC target accessibility, which is a key step in RNA-mediated gene silencing. In addition, these findings indicate that fine-tuning of p21 levels by Wig1 is essential for the prevention of cellular senescence.

7 CFR 4290.506 - Safeguarding the RBIC's assets/Internal controls.

Science.gov (United States)

2010-01-01

... 7 Agriculture 15 2010-01-01 2010-01-01 false Safeguarding the RBIC's assets/Internal controls... Safeguarding the RBIC's assets/Internal controls. You must adopt a plan to safeguard your assets and monitor... your control procedures. ...

A small RNA activates CFA synthase by isoform-specific mRNA stabilization.

Science.gov (United States)

Fröhlich, Kathrin Sophie; Papenfort, Kai; Fekete, Agnes; Vogel, Jörg

2013-11-13

Small RNAs use a diversity of well-characterized mechanisms to repress mRNAs, but how they activate gene expression at the mRNA level remains not well understood. The predominant activation mechanism of Hfq-associated small RNAs has been translational control whereby base pairing with the target prevents the formation of an intrinsic inhibitory structure in the mRNA and promotes translation initiation. Here, we report a translation-independent mechanism whereby the small RNA RydC selectively activates the longer of two isoforms of cfa mRNA (encoding cyclopropane fatty acid synthase) in Salmonella enterica. Target activation is achieved through seed pairing of the pseudoknot-exposed, conserved 5' end of RydC to an upstream region of the cfa mRNA. The seed pairing stabilizes the messenger, likely by interfering directly with RNase E-mediated decay in the 5' untranslated region. Intriguingly, this mechanism is generic such that the activation is equally achieved by seed pairing of unrelated small RNAs, suggesting that this mechanism may be utilized in the design of RNA-controlled synthetic circuits. Physiologically, RydC is the first small RNA known to regulate membrane stability.

International Telecommunication Control: International Law and the Ordering of Satellite and Other Forms of International Broadcasting.

Science.gov (United States)

Smith, Delbert D.

The need for and the available alternatives for international telecommunication controls are examined, and a functional approach to this area of law is offered. Information from a number of areas is collected and examined as it relates to the basic problem. These areas include general principles of international law, the activities of the…

A possible new mechanism for the control of miRNA expression in neurons.

Science.gov (United States)

Kinjo, Erika Reime; Higa, Guilherme Shigueto Vilar; de Sousa, Erica; Casado, Otávio Augusto Nocera; Damico, Marcio Vinicius; Britto, Luiz Roberto G; Kihara, Alexandre Hiroaki

2013-10-01

The control of gene expression by miRNAs has been widely investigated in different species and cell types. Following a probabilistic rather than a deterministic regimen, the action of these short nucleotide sequences on specific genes depends on intracellular concentration, which in turn reflects the balance between biosynthesis and degradation. Recent studies have described the involvement of XRN2, an exoribonuclease, in miRNA degradation and PAPD4, an atypical poly(A) polymerase, in miRNA stability. Herein, we examined the expression of XRN2 and PAPD4 in developing and adult rat hippocampi. Combining bioinformatics and real-time PCR, we demonstrated that XRN2 and PAPD4 expression is regulated by the uncorrelated action of transcription factors, resulting in distinct gene expression profiles during development. Analyses of nuclei position and nestin labeling revealed that both proteins progressively accumulated during neuronal differentiation, and that they are weakly expressed in immature neurons and absent in glial and endothelial cells. Despite the differences in subcellular localization, both genes were concurrently identified within identical neuronal subpopulations, including specific inhibitory interneurons. Thus, we cope with a singular circumstance in biology: an almost complete intersected expression of functional-opposed genes, reinforcing that their antagonistically driven actions on miRNAs "make sense" if simultaneously present at the same cells. Considering that the transcriptome in the nervous system is finely tuned to physiological processes, it was remarkable that miRNA stability-related genes were concurrently identified in neurons that play essential roles in cognitive functions such as memory and learning. In summary, this study reveals a possible new mechanism for the control of miRNA expression. © 2013 Elsevier Inc. All rights reserved.

Internal dosimetry and control

International Nuclear Information System (INIS)

Rich, B.L.

1990-05-01

This internal dosimetry and control report provides guidance for EG ampersand G Idaho, Inc., field programs in detecting, evaluating, and controlling personnel exposure resulting from uptake of radionuclides by the body. Procedures specific to each program or facility are required to define the details of guidance from this report. Fundamental principles related to philosophy, policies, monitoring guidelines, and dose evaluation are discussed. Specific numerical guides and action levels are developed to guide the programs in evaluating the significance of specific analytical results. The requirement to thoroughly document the results and provide a formal technical base for each policy and/or practice is outlined and explained. 8 refs., 3 figs., 7 tabs

Internal transport control in pot plant production

NARCIS (Netherlands)

Annevelink, E.

1999-01-01

Drawing up internal transport schedules in pot plant production is a very complex task. Scheduling internal transport at the operational level and providing control on a day-to-day or even hour-to-hour basis in particular requires a new approach. A hierarchical planning approach based on

Theranostic Niosomes for Efficient siRNA/microRNA Delivery and Activatable Near-Infrared Fluorescent Tracking of Stem Cells

DEFF Research Database (Denmark)

Yang, Chuanxu; Shan, Gao; Song, Ping

2018-01-01

RNA interference (RNAi) mediated gene regulation in stem cells offers great potential in regenerative medicine. In this study, we developed a theranostic platform for efficient delivery of small RNAs (siRNA/miRNA) to human mesenchymal stem cells (hMSCs) to promote differentiation, and meanwhile...... OFF/ON activatable fluorescence upon cellular internalization, resulting in efficient NIR labeling and the capability to dynamically monitor stem cells in mice. In addition, iSPN/siRNA achieved simultaneous long-term cell tracking and in vivo gene silencing after implantation in mice. These results...

RNA Interference: A Promising Tool in the Control of Important Vector Born Diseases Zika, Dengue Fever, and Malaria

Directory of Open Access Journals (Sweden)

Jalil Nejati

2017-05-01

Full Text Available Background and Objectives: RNA interference is a process, in which a molecule of double-stranded RNA prevents the expression of a particular gene and leads to its silencing. Application of this technology in the control of disease-carrying insects is rising in agriculture and medical sciences. Also, its application in control of insect-borne diseases could be considered as a new, important, and effective approach. In this article, it was attempted to study the mechanisms of RNA interference, routs of its delivery to insects, as well as its application in genetic control of disease vector insects. Methods: In this study, 71 indexed articles in databases, such as Pubmed, SID, Scopus, Science direct, and Google scholar, were used. Results: dsRNA could be delivered to insect body through three routes of oral, injection, and Impregnation. The mechanism of dsRNA entrance into the cells has considerable effect on the success and applicability of this technique. Identification of host-parasite relationship in the insect body is one of the important applications of RNAi in medical entomology. Conclusion: Although, there is a considerable number of researches on RNAi in the agricultural pests field, studies on insect vectors of human diseases have been mostly in-vivo. However, application of RNAi is suggested as a new, safe and applicable approach, alone or along with other methods. Certainly, further researches in this field can pave the way for enforcement measures in the control of disease vectors, especially Zika, dengue fever, and malaria in the not so distant future.

The ADAR RNA editing enzyme controls neuronal excitability in Drosophila melanogaster

Science.gov (United States)

Li, Xianghua; Overton, Ian M.; Baines, Richard A.; Keegan, Liam P.; O’Connell, Mary A.

2014-01-01

RNA editing by deamination of specific adenosine bases to inosines during pre-mRNA processing generates edited isoforms of proteins. Recoding RNA editing is more widespread in Drosophila than in vertebrates. Editing levels rise strongly at metamorphosis, and Adar5G1 null mutant flies lack editing events in hundreds of CNS transcripts; mutant flies have reduced viability, severely defective locomotion and age-dependent neurodegeneration. On the other hand, overexpressing an adult dADAR isoform with high enzymatic activity ubiquitously during larval and pupal stages is lethal. Advantage was taken of this to screen for genetic modifiers; Adar overexpression lethality is rescued by reduced dosage of the Rdl (Resistant to dieldrin), gene encoding a subunit of inhibitory GABA receptors. Reduced dosage of the Gad1 gene encoding the GABA synthetase also rescues Adar overexpression lethality. Drosophila Adar5G1 mutant phenotypes are ameliorated by feeding GABA modulators. We demonstrate that neuronal excitability is linked to dADAR expression levels in individual neurons; Adar-overexpressing larval motor neurons show reduced excitability whereas Adar5G1 null mutant or targeted Adar knockdown motor neurons exhibit increased excitability. GABA inhibitory signalling is impaired in human epileptic and autistic conditions, and vertebrate ADARs may have a relevant evolutionarily conserved control over neuronal excitability. PMID:24137011

Targeted siRNA Delivery and mRNA Knockdown Mediated by Bispecific Digoxigenin-binding Antibodies

Directory of Open Access Journals (Sweden)

Britta Schneider

2012-01-01

Full Text Available Bispecific antibodies (bsAbs that bind to cell surface antigens and to digoxigenin (Dig were used for targeted small interfering RNA (siRNA delivery. They are derivatives of immunoglobulins G (IgGs that bind tumor antigens, such as Her2, IGF1-R, CD22, and LeY, with stabilized Dig-binding variable domains fused to the C-terminal ends of the heavy chains. siRNA that was digoxigeninylated at its 3′end was bound in a 2:1 ratio to the bsAbs. These bsAb–siRNA complexes delivered siRNAs specifically to cells that express the corresponding antigen as demonstrated by flow cytometry and confocal microscopy. The complexes internalized into endosomes and Dig-siRNAs separated from bsAbs, but Dig-siRNA was not released into the cytoplasm; bsAb-targeting alone was thus not sufficient for effective mRNA knockdown. This limitation was overcome by formulating the Dig-siRNA into nanoparticles consisting of dynamic polyconjugates (DPCs or into lipid-based nanoparticles (LNPs. The resulting complexes enabled bsAb-targeted siRNA-specific messenger RNA (mRNA knockdown with IC50 siRNA values in the low nanomolar range for a variety of bsAbs, siRNAs, and target cells. Furthermore, pilot studies in mice bearing tumor xenografts indicated mRNA knockdown in endothelial cells following systemic co-administration of bsAbs and siRNA formulated in LNPs that were targeted to the tumor vasculature.

77 FR 43196 - Minimum Internal Control Standards and Technical Standards

Science.gov (United States)

2012-07-24

... NATIONAL INDIAN GAMING COMMISSION 25 CFR Parts 543 and 547 Minimum Internal Control Standards [email protected] . SUPPLEMENTARY INFORMATION: Part 543 addresses minimum internal control standards (MICS) for Class II gaming operations. The regulations require tribes to establish controls and implement...

Have the auditors closed the expectation gap concerning evaluation of internal control?

DEFF Research Database (Denmark)

Birkholm, Peter; Holm, Claus

internal controls intended for management directors, it provides a framework which explicitly deals with the interests of all parties involved (including auditors, board of directors and regulating bodies). The auditors took this into account by updating the particular auditing standard on internal control....... Realized discrepancies are identified and related to the necessary features of an integrated framework. The necessary features include (1) the definition of internal controls, (2) the components of internal control, (3) the criteria for evaluating internal control as stated by the auditors (4) the criteria...... for evaluating internal controls as stated by management, and (5) the integration of internal control evaluations from management and auditors. The paper provides evidence from an in-depth contents analysis comparing SAS No. 55 from 1988 with the COSO-report from 1992 and SAS No. 78 from 1995. The analysis...

Internal quality control of PCR-based genotyping methods

DEFF Research Database (Denmark)

Bladbjerg, Else-Marie; Gram, Jørgen; Jespersen, Jørgen

2002-01-01

Internal quality control programmes for genetic analyses are needed. We have focused on quality control aspects of selected polymorphism analyses used in thrombosis research. DNA was isolated from EDTA-blood (n = 500) and analysed for 18 polymorphisms by polymerase chain reaction (PCR), i...... because of positive reagent blanks (controls (Control of data handling revealed 0.1% reading mistakes and 0.5% entry mistakes. Based on our experiences, we propose an internal quality control programme......, electrophoresis (analytical factors), result reading and entry into a database (post-analytical factors). Furthermore, we evaluated a procedure for result confirmation. Isolated DNA was of good quality (42 micrograms/ml blood, A260/A280 ratio > 1.75, negative DNAsis tests). Occasionally, results were reanalysed...

Nuclear materials control and accountability internal audit program

International Nuclear Information System (INIS)

Barham, M.A.; Abbott, R.R.

1991-01-01

This paper reports that the Department of Energy Order (DOE) 5633.3, Control and Accountability for Nuclear Materials, includes several requirements for development and implementation of an internal audit program. Martin Marietta Energy System, Inc., manages five sites in Tennessee, Kentucky, and Ohio for the DOE Field Office, Oak Ridge and has a Central Nuclear Materials Control and Accountability (NMC and A) Manager with matrixed responsibility for the NMC and A program at the five sites. The Energy Systems Central NMC and A Manager has developed an NMC and A Internal Audit Handbook which defines the functional responsibilities, performance criteria, and reporting and documentation requirements for the Energy Systems NMC and A Internal Audit Program. The initial work to develop and implement these standards was tested at the K-25 Site when the site hired an internal auditor to meet the DOE requirements for an NMC and A Internal Audit program

Pengaruh Proporsi Komisaris Independen dan Komposisi Komite Audit terhadap Internal Control

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Makhdalena Makhdalena

2015-12-01

Full Text Available Accounting manipulation that occurred in recent years makes accounting experts to focus on internal control issues. The experts agree that internal control is an important issue through a substance that can be given by the internal control. Internal control can be effective if supported by the proportion of independent commissioners and audit committee composition are adequate. Based on that idea, the researchers interested in conducting research that aims to find out: the influence of the proportion of independent commissioners and audit committee composition of the internal control eithersimultaneously or partially. Research conducted by the survey in 48 listed companies in Jakarta Stock Exchange manufacturing drawn at random from the population. Data used in this study are primary data from the questionnaire and secondary data from the annual report. Data were analyzed using path analysis. The results showed that: the proportion of independent commissioners and audit committee composition has a significant influence on the internal control eithersimultaneously or partially.

Role of RNase MRP in viral RNA degradation and RNA recombination.

Science.gov (United States)

Jaag, Hannah M; Lu, Qiasheng; Schmitt, Mark E; Nagy, Peter D

2011-01-01

RNA degradation, together with RNA synthesis, controls the steady-state level of viral RNAs in infected cells. The endoribonucleolytic cleavage of viral RNA is important not only for viral RNA degradation but for RNA recombination as well, due to the participation of some RNA degradation products in the RNA recombination process. To identify host endoribonucleases involved in degradation of Tomato bushy stunt virus (TBSV) in a Saccharomyces cerevisiae model host, we tested eight known endoribonucleases. Here we report that downregulation of SNM1, encoding a component of the RNase MRP, and a temperature-sensitive mutation in the NME1 gene, coding for the RNA component of RNase MRP, lead to reduced production of the endoribonucleolytically cleaved TBSV RNA in yeast. We also show that the highly purified yeast RNase MRP cleaves the TBSV RNA in vitro, resulting in TBSV RNA degradation products similar in size to those observed in yeast cells. Knocking down the NME1 homolog in Nicotiana benthamiana also led to decreased production of the cleaved TBSV RNA, suggesting that in plants, RNase MRP is involved in TBSV RNA degradation. Altogether, this work suggests a role for the host endoribonuclease RNase MRP in viral RNA degradation and recombination.

RNA- and protein-mediated control of Listeria monocytogenes virulence gene expression

Science.gov (United States)

Lebreton, Alice; Cossart, Pascale

2017-01-01

ABSTRACT The model opportunistic pathogen Listeria monocytogenes has been the object of extensive research, aiming at understanding its ability to colonize diverse environmental niches and animal hosts. Bacterial transcriptomes in various conditions reflect this efficient adaptability. We review here our current knowledge of the mechanisms allowing L. monocytogenes to respond to environmental changes and trigger pathogenicity, with a special focus on RNA-mediated control of gene expression. We highlight how these studies have brought novel concepts in prokaryotic gene regulation, such as the ‘excludon’ where the 5′-UTR of a messenger also acts as an antisense regulator of an operon transcribed in opposite orientation, or the notion that riboswitches can regulate non-coding RNAs to integrate complex metabolic stimuli into regulatory networks. Overall, the Listeria model exemplifies that fine RNA tuners act together with master regulatory proteins to orchestrate appropriate transcriptional programmes. PMID:27217337

ncRNA-class Web Tool: Non-coding RNA feature extraction and pre-miRNA classification web tool

KAUST Repository

Kleftogiannis, Dimitrios A.; Theofilatos, Konstantinos A.; Papadimitriou, Stergios; Tsakalidis, Athanasios K.; Likothanassis, Spiridon D.; Mavroudi, Seferina P.

2012-01-01

Until recently, it was commonly accepted that most genetic information is transacted by proteins. Recent evidence suggests that the majority of the genomes of mammals and other complex organisms are in fact transcribed into non-coding RNAs (ncRNAs), many of which are alternatively spliced and/or processed into smaller products. Non coding RNA genes analysis requires the calculation of several sequential, thermodynamical and structural features. Many independent tools have already been developed for the efficient calculation of such features but to the best of our knowledge there does not exist any integrative approach for this task. The most significant amount of existing work is related to the miRNA class of non-coding RNAs. MicroRNAs (miRNAs) are small non-coding RNAs that play a significant role in gene regulation and their prediction is a challenging bioinformatics problem. Non-coding RNA feature extraction and pre-miRNA classification Web Tool (ncRNA-class Web Tool) is a publicly available web tool ( http://150.140.142.24:82/Default.aspx ) which provides a user friendly and efficient environment for the effective calculation of a set of 58 sequential, thermodynamical and structural features of non-coding RNAs, plus a tool for the accurate prediction of miRNAs. © 2012 IFIP International Federation for Information Processing.

Partial Internal Control Recovery on 1-D Klein-Gordon Systems

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Iwan Pranoto

2010-03-01

Full Text Available In this exposition, a technique to recover internal control on a distributed parameter system is reported. The system is described by 1-D Klein-Gordon partial differential equation with a time-varying parameter. We would like to recover the internal control applied to the system if we know some limited information about the output. We use a method called sentinel method to recover the internal control. It involves some construction of a linear functional, and we show that this construction relates closely to the exact controllability problem.

Internal control activities in small Turkish companies

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Ismail Bilgi

2017-01-01

Full Text Available The purpose of this paper is to present major outcomes from an empirical study concerning internal control activities in small Turkish companies, as to propose the improvement guidelines. Methods of analysis and synthesis, descriptive statistics, and statistical comparison were used. The collected data was processed with the help of the SPSS software. Тhe study is limited to organizations based in the European part of Turkey. Most of them operate in areas around large cities, such as Istanbul, Edirne, Kırklareli, and Tekirdağ. They employ on average 19-20 people and have a turnover of about TRY 3 million (≈€715,000, https://sdw.ecb.europa.eu on average. The survey concentrates mainly on small family businesses, which have been present on the market for more than ten years, with managers of good education and other characteristics that presuppose availability of internal control systems. The research results were used to compile main points of a SWOT analysis, as a part of the broader effort to help modernizing the internal control system in Turkish small businesses.

PLK-1 Silencing in Bladder Cancer by siRNA Delivered With Exosomes.

Science.gov (United States)

Greco, Kristin A; Franzen, Carrie A; Foreman, Kimberly E; Flanigan, Robert C; Kuo, Paul C; Gupta, Gopal N

2016-05-01

To use exosomes as a vector to deliver small interfering ribonucleic acid (siRNA) to silence the polo-like kinase 1 (PLK-1) gene in bladder cancer cells. Exosomes were isolated from both human embryonic kidney 293 (HEK293) cell and mesenchymal stem cell (MSC) conditioned media. Fluorescently labeled exosomes were co-cultured with bladder cancer and normal epithelial cells and uptake was quantified by image cytometry. PLK-1 siRNA and negative control siRNA were loaded into HEK293 and MSC exosomes using electroporation. An invasive bladder cancer cell line (UMUC3) was co-cultured with the electroporated exosomes. Quantitative reverse transcriptase polymerase chain reaction was performed. Protein analysis was performed by Western blot. Annexin V staining and MTT assays were used to investigate effects on apoptosis and viability. Bladder cancer cell lines internalize an increased percentage of HEK293 exosomes when compared to normal bladder epithelial cells. Treatment of UMUC3 cells with exosomes electroporated with PLK-1 siRNA achieved successful knockdown of PLK-1 mRNA and protein when compared to cells treated with negative control exosomes. HEK293 and MSC exosomes were effectively used as a delivery vector to transport PLK-1 siRNA to bladder cancer cells in vitro, resulting in selective gene silencing of PLK-1. The use of exosomes as a delivery vector for potential intravesical therapy is attractive. Copyright © 2016 Elsevier Inc. All rights reserved.

Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls.

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Andreas Keller

Full Text Available Multiple sclerosis (MS is a chronic inflammatory demyelinating disease of the central nervous system, which is heterogenous with respect to clinical manifestations and response to therapy. Identification of biomarkers appears desirable for an improved diagnosis of MS as well as for monitoring of disease activity and treatment response. MicroRNAs (miRNAs are short non-coding RNAs, which have been shown to have the potential to serve as biomarkers for different human diseases, most notably cancer. Here, we analyzed the expression profiles of 866 human miRNAs. In detail, we investigated the miRNA expression in blood cells of 20 patients with relapsing-remitting MS (RRMS and 19 healthy controls using a human miRNA microarray and the Geniom Real Time Analyzer (GRTA platform. We identified 165 miRNAs that were significantly up- or downregulated in patients with RRMS as compared to healthy controls. The best single miRNA marker, hsa-miR-145, allowed discriminating MS from controls with a specificity of 89.5%, a sensitivity of 90.0%, and an accuracy of 89.7%. A set of 48 miRNAs that was evaluated by radial basis function kernel support vector machines and 10-fold cross validation yielded a specificity of 95%, a sensitivity of 97.6%, and an accuracy of 96.3%. While 43 of the 165 miRNAs deregulated in patients with MS have previously been related to other human diseases, the remaining 122 miRNAs are so far exclusively associated with MS. The implications of our study are twofold. The miRNA expression profiles in blood cells may serve as a biomarker for MS, and deregulation of miRNA expression may play a role in the pathogenesis of MS.

SOME CONSIDERATIONS OVER THE INTERNAL CONTROL IN THE CONTEXT OF CURRENT ACCOUNTANCY REGULATIONS

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Lenghel Dorin Radu

2012-12-01

Full Text Available Through the hereby study we set ourselves on an analysis over the internal control and the ways of implementation of it. The final purpose of our research is represented by the characteristics of the internal control system in the context of current accountancy regulations. The accomplishment of such goal has forced us to research the current literature in the area and also the legal regulations over internal control. Of course, the accomplishment of such a research was possible only after a pertinent analysis over the opinions expressed in specialty literature regarding this area. Our research wants to be with a theoretical and applicative character. It is based on analysing the internal control system, the methodology of internal control and the steps of internal control. We express our belief that the implementation of the internal control in a very exact manner comes as an aid to the company management and lead to the accomplishment of managerial objectives and policies. In what it regards the result of our research there can be drawn the following conclusions: from the legal regulations (OMFP nr. 3055/2009, there is no clear conclusion over the procedures and policies of implementation of internal control applicable to an economical entity; also there are not presented in a detailed way the types (forms of internal control, being presented in the legal regulations only a classification of them after the time in which they are exercised (before, during or after the finishing of the operations; also in the legal regulations there is developed a certain way of internal control, represented by the financial and accounting internal control, as if the other forms of internal control do not exist; in what regards the components of internal control, these are presented in another way, but similar to already known models of internal control (Coso and Coco; also in the legal regulations there are presented the general objectives of internal control

Model tracking dual stochastic controller design under irregular internal noises

International Nuclear Information System (INIS)

Lee, Jong Bok; Heo, Hoon; Cho, Yun Hyun; Ji, Tae Young

2006-01-01

Although many methods about the control of irregular external noise have been introduced and implemented, it is still necessary to design a controller that will be more effective and efficient methods to exclude for various noises. Accumulation of errors due to model tracking, internal noises (thermal noise, shot noise and l/f noise) that come from elements such as resistor, diode and transistor etc. in the circuit system and numerical errors due to digital process often destabilize the system and reduce the system performance. New stochastic controller is adopted to remove those noises using conventional controller simultaneously. Design method of a model tracking dual controller is proposed to improve the stability of system while removing external and internal noises. In the study, design process of the model tracking dual stochastic controller is introduced that improves system performance and guarantees robustness under irregular internal noises which can be created internally. The model tracking dual stochastic controller utilizing F-P-K stochastic control technique developed earlier is implemented to reveal its performance via simulation

SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans.

Science.gov (United States)

Kel, Ivan; Chang, Zisong; Galluccio, Nadia; Romeo, Margherita; Beretta, Stefano; Diomede, Luisa; Mezzelani, Alessandra; Milanesi, Luciano; Dieterich, Christoph; Merelli, Ivan

2016-10-18

The interpretation of genome-wide association study is difficult, as it is hard to understand how polymorphisms can affect gene regulation, in particular for trans-regulatory elements located far from their controlling gene. Using RNA or protein expression data as phenotypes, it is possible to correlate their variations with specific genotypes. This technique is usually referred to as expression Quantitative Trait Loci (eQTLs) analysis and only few packages exist for the integration of genotype patterns and expression profiles. In particular, tools are needed for the analysis of next-generation sequencing (NGS) data on a genome-wide scale, which is essential to identify eQTLs able to control a large number of genes (hotspots). Here we present SPIRE (Software for Polymorphism Identification Regulating Expression), a generic, modular and functionally highly flexible pipeline for eQTL processing. SPIRE integrates different univariate and multivariate approaches for eQTL analysis, paying particular attention to the scalability of the procedure in order to support cis- as well as trans-mapping, thus allowing the identification of hotspots in NGS data. In particular, we demonstrated how SPIRE can handle big association study datasets, reproducing published results and improving the identification of trans-eQTLs. Furthermore, we employed the pipeline to analyse novel data concerning the genotypes of two different C. elegans strains (N2 and Hawaii) and related miRNA expression data, obtained using RNA-Seq. A miRNA regulatory hotspot was identified in chromosome 1, overlapping the transcription factor grh-1, known to be involved in the early phases of embryonic development of C. elegans. In a follow-up qPCR experiment we were able to verify most of the predicted eQTLs, as well as to show, for a novel miRNA, a significant difference in the sequences of the two analysed strains of C. elegans. SPIRE is publicly available as open source software at , together with some example

Signals Involved in Regulation of Hepatitis C Virus RNA Genome Translation and Replication.

Science.gov (United States)

Niepmann, Michael; Shalamova, Lyudmila A; Gerresheim, Gesche K; Rossbach, Oliver

2018-01-01

Hepatitis C virus (HCV) preferentially replicates in the human liver and frequently causes chronic infection, often leading to cirrhosis and liver cancer. HCV is an enveloped virus classified in the genus Hepacivirus in the family Flaviviridae and has a single-stranded RNA genome of positive orientation. The HCV RNA genome is translated and replicated in the cytoplasm. Translation is controlled by the Internal Ribosome Entry Site (IRES) in the 5' untranslated region (5' UTR), while also downstream elements like the cis -replication element (CRE) in the coding region and the 3' UTR are involved in translation regulation. The cis -elements controlling replication of the viral RNA genome are located mainly in the 5'- and 3'-UTRs at the genome ends but also in the protein coding region, and in part these signals overlap with the signals controlling RNA translation. Many long-range RNA-RNA interactions (LRIs) are predicted between different regions of the HCV RNA genome, and several such LRIs are actually involved in HCV translation and replication regulation. A number of RNA cis -elements recruit cellular RNA-binding proteins that are involved in the regulation of HCV translation and replication. In addition, the liver-specific microRNA-122 (miR-122) binds to two target sites at the 5' end of the viral RNA genome as well as to at least three additional target sites in the coding region and the 3' UTR. It is involved in the regulation of HCV RNA stability, translation and replication, thereby largely contributing to the hepatotropism of HCV. However, we are still far from completely understanding all interactions that regulate HCV RNA genome translation, stability, replication and encapsidation. In particular, many conclusions on the function of cis -elements in HCV replication have been obtained using full-length HCV genomes or near-full-length replicon systems. These include both genome ends, making it difficult to decide if a cis -element in question acts on HCV

VDR regulation of microRNA differs across prostate cell models suggesting extremely flexible control of transcription.

Science.gov (United States)

Singh, Prashant K; Long, Mark D; Battaglia, Sebastiano; Hu, Qiang; Liu, Song; Sucheston-Campbell, Lara E; Campbell, Moray J

2015-01-01

The Vitamin D Receptor (VDR) is a member of the nuclear receptor superfamily and is of therapeutic interest in cancer and other settings. Regulation of microRNA (miRNA) by the VDR appears to be important to mediate its actions, for example, to control cell growth. To identify if and to what extent VDR-regulated miRNA patterns change in prostate cancer progression, we undertook miRNA microarray analyses in 7 cell models representing non-malignant and malignant prostate cells (RWPE-1, RWPE-2, HPr1, HPr1AR, LNCaP, LNCaP-C4-2, and PC-3). To focus on primary VDR regulatory events, we undertook expression analyses after 30 minutes treatment with 1α,25(OH)2D3. Across all models, 111 miRNAs were significantly modulated by 1α,25(OH)2D3 treatment. Of these, only 5 miRNAs were modulated in more than one cell model, and of these, only 3 miRNAs were modulated in the same direction. The patterns of miRNA regulation, and the networks they targeted, significantly distinguished the different cell types. Integration of 1α,25(OH)2D3-regulated miRNAs with published VDR ChIP-seq data showed significant enrichment of VDR peaks in flanking regions of miRNAs. Furthermore, mRNA and miRNA expression analyses in non-malignant RWPE-1 cells revealed patterns of miRNA and mRNA co-regulation; specifically, 13 significant reciprocal patterns were identified and these patterns were also observed in TCGA prostate cancer data. Lastly, motif search analysis revealed differential motif enrichment within VDR peaks flanking mRNA compared to miRNA genes. Together, this study revealed that miRNAs are rapidly regulated in a highly cell-type specific manner, and are significantly co-integrated with mRNA regulation.

Internal control as part of prevention irregularities in accounting of budgetary institution

OpenAIRE

O.М. Bunda; E.М. Guzenko

2016-01-01

The article researches the principles of internal control, the importance, the rationale for the essence of the system of internal control and the legislative building in budgetary institution. It describes the main challenges and problems of practical application of internal control in the normal course of business in modern enterprises. It reveals the following elements of the internal control of a budget institution as: control environment, risk assessment process of a budget institu...

Specificity of continuous auditing approach on information technology internal controls

Directory of Open Access Journals (Sweden)

Kaćanski Slobodan

2012-01-01

Full Text Available Contemporary business world, can not be imagined without the use of information technology in all aspects of business. The use of information technology in manufacturing and non-production companies' activities can greatly facilitate and accelerate the process of operation and control. Because of its complexity, they possess vulnerable areas and provide space for the emergence of accidental and intentional frauds that can significantly materially affect the business decisions made by the companies' management. Implementation of internal controls can greatly reduce the level of errors that can contribute to making the wrong decisions. In order to protect the operating system, the company's management implement an internal audit to periodically examine the fundamental quality of the internal control systems. Since the internal audit, according to its character, only periodically checks quality of internal control systems and information technologies to be reported to the manager, the problem arises in the process of in wrong time reporting the management structures of the business entity. To eliminate this problem, management implements a special approach to internal audit, called continuous auditing.

An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions

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Daisy W. Leung

2015-04-01

Full Text Available During viral RNA synthesis, Ebola virus (EBOV nucleoprotein (NP alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20–48 that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.

An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions.

Science.gov (United States)

Leung, Daisy W; Borek, Dominika; Luthra, Priya; Binning, Jennifer M; Anantpadma, Manu; Liu, Gai; Harvey, Ian B; Su, Zhaoming; Endlich-Frazier, Ariel; Pan, Juanli; Shabman, Reed S; Chiu, Wah; Davey, Robert A; Otwinowski, Zbyszek; Basler, Christopher F; Amarasinghe, Gaya K

2015-04-21

During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20-48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

A Multisampling Reporter System for Monitoring MicroRNA Activity in the Same Population of Cells

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Pei-Chen Huang

2009-01-01

Full Text Available MicroRNAs (miRNAs downregulate gene expression by binding to the partially complementary sites in the 3′ untranslated region (UTR of target mRNAs. Several methods, such as Northern blot analysis, quantitative real-time RT-PCR, microarray, and the luciferase reporter system, are commonly used to quantify the relative level or activity of miRNAs. The disadvantage of these methods is the requirement for cell lysis, which means that several sets of wells/dishes of cells must be prepared to monitor changes in miRNA activity in time-course studies. In this study, we developed a multisampling reporter system in which two secretable bioluminescence-generating enzymes are employed, one as a reporter and the other as an internal control. The reporters consist of a pair of vectors containing the Metridia luciferase gene, one with and one without a duplicated miRNA targeting sequence at their 3′UTR, while the other vector coding for the secreted alkaline phosphatase gene is used as an internal control. This method allows miRNA activity to be monitored within the same population of cells over time by withdrawing aliquots of the culture medium. The practicability and benefits of this system are addressed in this report.

tRNA-like structure regulates translation of Brome mosaic virus RNA.

Science.gov (United States)

Barends, Sharief; Rudinger-Thirion, Joëlle; Florentz, Catherine; Giegé, Richard; Pleij, Cornelis W A; Kraal, Barend

2004-04-01

For various groups of plant viruses, the genomic RNAs end with a tRNA-like structure (TLS) instead of the 3' poly(A) tail of common mRNAs. The actual function of these TLSs has long been enigmatic. Recently, however, it became clear that for turnip yellow mosaic virus, a tymovirus, the valylated TLS(TYMV) of the single genomic RNA functions as a bait for host ribosomes and directs them to the internal initiation site of translation (with N-terminal valine) of the second open reading frame for the polyprotein. This discovery prompted us to investigate whether the much larger TLSs of a different genus of viruses have a comparable function in translation. Brome mosaic virus (BMV), a bromovirus, has a tripartite RNA genome with a subgenomic RNA4 for coat protein expression. All four RNAs carry a highly conserved and bulky 3' TLS(BMV) (about 200 nucleotides) with determinants for tyrosylation. We discovered TLS(BMV)-catalyzed self-tyrosylation of the tyrosyl-tRNA synthetase but could not clearly detect tyrosine incorporation into any virus-encoded protein. We established that BMV proteins do not need TLS(BMV) tyrosylation for their initiation. However, disruption of the TLSs strongly reduced the translation of genomic RNA1, RNA2, and less strongly, RNA3, whereas coat protein expression from RNA4 remained unaffected. This aberrant translation could be partially restored by providing the TLS(BMV) in trans. Intriguingly, a subdomain of the TLS(BMV) could even almost fully restore translation to the original pattern. We discuss here a model with a central and dominant role for the TLS(BMV) during the BMV infection cycle.

Internal controls and credit risk relationship among banks in Europe

Directory of Open Access Journals (Sweden)

Ellis Kofi Akwaa-Sekyi

2017-01-01

Full Text Available Purpose: The study purport to investigate the effectiveness of internal control mechanisms, investigate whether evidence of agency problem is found among banks in Europe and determine how internal controls affect credit risk. Design/methodology/approach: Panel data from 91 banks from 23 European Union countries were studied from 2008-2014. Hausman’s specification test suggest the use of fixed effects estimation technique of GLS. Quantitatively modelled data on 15 variables covering elements of internal controls, objectives of internal controls, agency problem, bank and country specific variables were used. Findings: There is still high credit risk in spite of measures being implemented by the European Central Bank. Banks have individual entity factors that increase or decrease credit risk. The study finds effective internal control systems because objectives of internal controls are achieved and significantly determine credit risk. Agency problem is confirmed due to significant positive relation with credit risk. There is significant effect of internal controls on credit risk with specific variables as risk assessment, return on average risk weighted assets, institutional ownership, bank size, inflation, interest rate and GDP. Research limitations/implications: Missing data prevented the use of strongly balanced panel. The lack of flexibility with using quantitative approach did not allow further scrutiny of the nature of variables. However, statistical tests were acceptable for the model used. The study has implications for management and owners of banks to be warry of agency problem because that provides incentive for reckless high risk transactions that may benefit the agent than the principal. Management must engage in actions that profile the company better and enhances value maximization. Rising default risk has tendency to impair corporate image leading to loss of reputational capital. Originality/value: The study provides the use of

The Glioma International Case-Control Study

DEFF Research Database (Denmark)

Amirian, E. Susan; Armstrong, Georgina N; Zhou, Renke

2016-01-01

Decades of research have established only a few etiological factors for glioma, which is a rare and highly fatal brain cancer. Common methodological challenges among glioma studies include small sample sizes, heterogeneity of tumor subtypes, and retrospective exposure assessment. Here, we briefly...... describe the Glioma International Case-Control (GICC) Study (recruitment, 2010-2013), a study being conducted by the Genetic Epidemiology of Glioma International Consortium that integrates data from multiple data collection sites, uses a common protocol and questionnaire, and includes biospecimen...

Short Hairpin RNA (shRNA): Design, Delivery, and Assessment of Gene Knockdown

Science.gov (United States)

Moore, Chris B.; Guthrie, Elizabeth H.; Huang, Max Tze-Han; Taxman, Debra J.

2013-01-01

Shortly after the cellular mechanism of RNA interference (RNAi) was first described, scientists began using this powerful technique to study gene function. This included designing better methods for the successful delivery of small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) into mammalian cells. While the simplest method for RNAi is the cytosolic delivery of siRNA oligonucleotides, this technique is limited to cells capable of transfection and is primarily utilized during transient in vitro studies. The introduction of shRNA into mammalian cells through infection with viral vectors allows for stable integration of shRNA and long-term knockdown of the targeted gene; however, several challenges exist with the implementation of this technology. Here we describe some well-tested protocols which should increase the chances of successful design, delivery, and assessment of gene knockdown by shRNA. We provide suggestions for designing shRNA targets and controls, a protocol for sequencing through the secondary structure of the shRNA hairpin structure, and protocols for packaging and delivery of shRNA lentiviral particles. Using real-time PCR and functional assays we demonstrate the successful knockdown of ASC, an inflammatory adaptor molecule. These studies demonstrate the practicality of including two shRNAs with different efficacies of knockdown to provide an additional level of control and to verify dose dependency of functional effects. Along with the methods described here, as new techniques and algorithms are designed in the future, shRNA is likely to include further promising application and continue to be a critical component of gene discovery. PMID:20387148

Signals Involved in Regulation of Hepatitis C Virus RNA Genome Translation and Replication

Directory of Open Access Journals (Sweden)

Michael Niepmann

2018-03-01

Full Text Available Hepatitis C virus (HCV preferentially replicates in the human liver and frequently causes chronic infection, often leading to cirrhosis and liver cancer. HCV is an enveloped virus classified in the genus Hepacivirus in the family Flaviviridae and has a single-stranded RNA genome of positive orientation. The HCV RNA genome is translated and replicated in the cytoplasm. Translation is controlled by the Internal Ribosome Entry Site (IRES in the 5′ untranslated region (5′ UTR, while also downstream elements like the cis-replication element (CRE in the coding region and the 3′ UTR are involved in translation regulation. The cis-elements controlling replication of the viral RNA genome are located mainly in the 5′- and 3′-UTRs at the genome ends but also in the protein coding region, and in part these signals overlap with the signals controlling RNA translation. Many long-range RNA–RNA interactions (LRIs are predicted between different regions of the HCV RNA genome, and several such LRIs are actually involved in HCV translation and replication regulation. A number of RNA cis-elements recruit cellular RNA-binding proteins that are involved in the regulation of HCV translation and replication. In addition, the liver-specific microRNA-122 (miR-122 binds to two target sites at the 5′ end of the viral RNA genome as well as to at least three additional target sites in the coding region and the 3′ UTR. It is involved in the regulation of HCV RNA stability, translation and replication, thereby largely contributing to the hepatotropism of HCV. However, we are still far from completely understanding all interactions that regulate HCV RNA genome translation, stability, replication and encapsidation. In particular, many conclusions on the function of cis-elements in HCV replication have been obtained using full-length HCV genomes or near-full-length replicon systems. These include both genome ends, making it difficult to decide if a cis-element in

[Correlation between RNA Expression Level and Early PMI in Human Brain Tissue].

Science.gov (United States)

Lü, Y H; Ma, K J; Li, Z H; Gu, J; Bao, J Y; Yang, Z F; Gao, J; Zeng, Y; Tao, L; Chen, L

2016-08-01

To explore the correlation between the expression levels of several RNA markers in human brain tissue and early postmortem interval （PMI）. Twelve individuals with known PMI （range from 4.3 to 22.5 h） were selected and total RNA was extracted from brain tissue. Eight commonly used RNA markers were chosen including β -actin, GAPDH, RPS29, 18S rRNA, 5S rRNA, U6 snRNA, miRNA-9 and miRNA-125b, and the expression levels were detected in brain tissue by real-time fluorescent quantitative PCR. The internal reference markers with stable expression in early PMI were screened using geNorm software and the relationship between its expression level and some relevant factors such as age, gender and cause of death were analyzed. RNA markers normalized by internal reference were inserted into the mathematic model established by previous research for PMI estimation using R software. Model quality was judged by the error rate calculated with estimated PMI. 5S rRNA, miRNA-9 and miRNA-125b showed quite stable expression and their expression levels had no relation with age, gender and cause of death. The error rate of estimated PMI using β -actin was 24.6%, while GAPDH was 41.0%. 5S rRNA, miRNA-9 and miRNA-125b are suitable as internal reference markers of human brain tissue owing to their stable expression in early PMI. The expression level of β -actin correlates well with PMI, which can be used as an additional index for early PMI estimation. Copyright© by the Editorial Department of Journal of Forensic Medicine

Evaluation of the miRNA-146a and miRNA-155 Expression Levels in Patients with Oral Lichen Planus.

Science.gov (United States)

Ahmadi-Motamayel, Fatemeh; Bayat, Zeynab; Hajilooi, Mehrdad; Shahryar-Hesami, Soroosh; Mahdavinezhad, Ali; Samie, Lida; Solgi, Ghasem

2017-12-01

Oral Lichen Planus (OLP) is a chronic autoimmune disease that could be considered as a potential premalignant status. To evaluate the miRNA-146a and miRNA-155 expression levels in patients with oral Lichen planus lesions compared to healthy subjects with normal oral mucosa. Forty patients with oral lichen planus and 18 healthy age and gender-matched controls were recruited in this case-control study. Oral lichen planus was diagnosed clinically and pathologically. The expression levels of two miRNAs in peripheral blood samples were determined using commercial TaqMan MicroRNA Assays. Relative quantification of gene expression was calculated by the 2-ΔΔct method. The expression levels of miRNA-146a and miRNA-155 in patients with oral Lichen planus were significantly higher than those of healthy controls. Also, a direct but insignificant correlation was found between miRNA-155 and miRNA-146a expression levels among the patient group. Our findings indicate that miRNA-146a and miRNA-155 could be potential biomarkers for the immunopathogenesis of oral lichen planus.

The stages of the international drug control system.

Science.gov (United States)

Carstairs, Catherine

2005-01-01

This paper argues that the history of the international drug control system of the League of Nations/United Nations can be divided into three cumulative stages. The first stage, the supply stage, dates back to early part of the 20th century, and aimed to reduce the supply of drugs through careful monitoring and trade regulations. This has remained the dominant control strategy. In the middle of the century, demand control, in the form of treatment and criminalization of the individual user, began to appear. This was the least successful stage. Finally, in the 1980s, the dangers of the drug traffic assumed an important place on the international agenda and measures to reduce drug-related organized crime were enacted. To date, this has been a process of proliferation of regulatory strategies. Recently, new challenges to the international drug control system have emerged, including well-funded non-governmental organizations critical of the war on drugs, and the adoption of harm reduction measures in national policies around the world.

International trade agreements: a threat to tobacco control policy.

Science.gov (United States)

Shaffer, E R; Brenner, J E; Houston, T P

2005-08-01

International covenants establish a role for governments in ensuring the conditions for human health and wellbeing, which has been recognised as a central human right. International trade agreements, conversely, prioritize the rights of corporations over health and human rights. International trade agreements are threatening existing tobacco control policies and restrict the possibility of implementing new controls. This situation is unrecognised by many tobacco control advocates in signatory nations, especially those in developing countries. Recent agreements on eliminating various trade restrictions, including those on tobacco, have expanded far beyond simply international movement of goods to include internal tobacco distribution regulations and intellectual property rules regulating advertising and labelling. Our analysis shows that to the extent trade agreements protect the tobacco industry, in itself a deadly enterprise, they erode human rights principles and contribute to ill health. The tobacco industry has used trade policy to undermine effective barriers to tobacco importation. Trade negotiations provide an unwarranted opportunity for the tobacco industry to assert its interests without public scrutiny. Trade agreements provide the industry with additional tools to obstruct control policies in both developed and developing countries and at every level. The health community should become involved in reversing these trends, and help promote additional measures to protect public health.

Determination of internal controls for quantitative gene expression of Isochrysis zhangjiangensis at nitrogen stress condition

Science.gov (United States)

Wu, Shuang; Zhou, Jiannan; Cao, Xupeng; Xue, Song

2016-02-01

Isochrysis zhangjiangensis is a potential marine microalga for biodiesel production, which accumulates lipid under nitrogen limitation conditions, but the mechanism on molecular level is veiled. Quantitative real-time polymerase chain reaction (qPCR) provides the possibility to investigate the gene expression levels, and a valid reference for data normalization is an essential prerequisite for firing up the analysis. In this study, five housekeeping genes, actin (ACT), α-tubulin (TUA), ß-tubulin (TUB), ubiquitin (UBI), 18S rRNA (18S) and one target gene, diacylglycerol acyltransferase (DGAT), were used for determining the reference. By analyzing the stabilities based on calculation of the stability index and on operating the two types of software, geNorm and bestkeeper, it showed that the reference genes widely used in higher plant and microalgae, such as UBI, TUA and 18S, were not the most stable ones in nitrogen-stressed I. zhangjiangensis, and thus are not suitable for exploring the mRNA expression levels under these experimental conditions. Our results show that ACT together with TUB is the most feasible internal control for investigating gene expression under nitrogen-stressed conditions. Our findings will contribute not only to future qPCR studies of I. zhangjiangensis, but also to verification of comparative transcriptomics studies of the microalgae under similar conditions.

National Transportation Safety Board : weak internal control impaired financial accountability

Science.gov (United States)

2001-09-28

The U. S. General Accounting Office (GAO) was asked to review the National Transportation Safety Board's (NTSB) internal controls over selected types of fiscal year expenditures. They were asked to determine whether internal control weaknesses were a...

RNA Interference Technology to Control Pest Sea Lampreys - A Proof-of-Concept

Science.gov (United States)

Heath, George; Childs, Darcy; Docker, Margaret F.; McCauley, David W.; Whyard, Steven

2014-01-01

The parasitic sea lamprey (Petromyzon marinus) has caused extensive losses to commercial fish stocks of the upper Great Lakes of North America. Methods of controlling the sea lamprey include trapping, barriers to prevent migration, and use of a chemical lampricide (3-trifluoromethyl-4-nitrophenol) to kill the filter-feeding larvae. Concerns about the non-specificity of these methods have prompted continued development of species-specific methods to control lampreys outside their native range. In this study, we considered the utility of RNA interference to develop a sea lamprey-specific lampricide. Injection of six different short interfering, double-stranded RNAs (siRNAs) into lamprey embryos first confirmed that the siRNAs could reduce the targeted transcript levels by more than 50%. Two size classes of lamprey larvae were then fed the siRNAs complexed with liposomes, and three of the siRNAs (targeting elongation factor 1α, calmodulin, and α-actinin) reduced transcript levels 2.5, 3.6, and 5.0–fold, respectively, within the lamprey midsections. This is not only the first demonstration of RNAi in lampreys, but it is also the first example of delivery of siRNAs to a non-mammalian vertebrate through feeding formulations. One of the siRNA treatments also caused increased mortality of the larvae following a single feeding of siRNAs, which suggests that prolonged or multiple feedings of siRNAs could be used to kill filter-feeding larvae within streams, following development of a slow-release formulation. The genes targeted in this study are highly conserved across many species, and only serve as a proof-of-concept demonstration that siRNAs can be used in lampreys. Given that RNA interference is a sequence-specific phenomenon, it should be possible to design siRNAs that selectively target gene sequences that are unique to sea lampreys, and thus develop a technology to control these pests without adversely affecting non-target species. PMID:24505485

RNA interference technology to control pest sea lampreys--a proof-of-concept.

Directory of Open Access Journals (Sweden)

George Heath

Full Text Available The parasitic sea lamprey (Petromyzon marinus has caused extensive losses to commercial fish stocks of the upper Great Lakes of North America. Methods of controlling the sea lamprey include trapping, barriers to prevent migration, and use of a chemical lampricide (3-trifluoromethyl-4-nitrophenol to kill the filter-feeding larvae. Concerns about the non-specificity of these methods have prompted continued development of species-specific methods to control lampreys outside their native range. In this study, we considered the utility of RNA interference to develop a sea lamprey-specific lampricide. Injection of six different short interfering, double-stranded RNAs (siRNAs into lamprey embryos first confirmed that the siRNAs could reduce the targeted transcript levels by more than 50%. Two size classes of lamprey larvae were then fed the siRNAs complexed with liposomes, and three of the siRNAs (targeting elongation factor 1α, calmodulin, and α-actinin reduced transcript levels 2.5, 3.6, and 5.0-fold, respectively, within the lamprey midsections. This is not only the first demonstration of RNAi in lampreys, but it is also the first example of delivery of siRNAs to a non-mammalian vertebrate through feeding formulations. One of the siRNA treatments also caused increased mortality of the larvae following a single feeding of siRNAs, which suggests that prolonged or multiple feedings of siRNAs could be used to kill filter-feeding larvae within streams, following development of a slow-release formulation. The genes targeted in this study are highly conserved across many species, and only serve as a proof-of-concept demonstration that siRNAs can be used in lampreys. Given that RNA interference is a sequence-specific phenomenon, it should be possible to design siRNAs that selectively target gene sequences that are unique to sea lampreys, and thus develop a technology to control these pests without adversely affecting non-target species.

RNA interference technology to control pest sea lampreys--a proof-of-concept.

Science.gov (United States)

Heath, George; Childs, Darcy; Docker, Margaret F; McCauley, David W; Whyard, Steven

2014-01-01

The parasitic sea lamprey (Petromyzon marinus) has caused extensive losses to commercial fish stocks of the upper Great Lakes of North America. Methods of controlling the sea lamprey include trapping, barriers to prevent migration, and use of a chemical lampricide (3-trifluoromethyl-4-nitrophenol) to kill the filter-feeding larvae. Concerns about the non-specificity of these methods have prompted continued development of species-specific methods to control lampreys outside their native range. In this study, we considered the utility of RNA interference to develop a sea lamprey-specific lampricide. Injection of six different short interfering, double-stranded RNAs (siRNAs) into lamprey embryos first confirmed that the siRNAs could reduce the targeted transcript levels by more than 50%. Two size classes of lamprey larvae were then fed the siRNAs complexed with liposomes, and three of the siRNAs (targeting elongation factor 1α, calmodulin, and α-actinin) reduced transcript levels 2.5, 3.6, and 5.0-fold, respectively, within the lamprey midsections. This is not only the first demonstration of RNAi in lampreys, but it is also the first example of delivery of siRNAs to a non-mammalian vertebrate through feeding formulations. One of the siRNA treatments also caused increased mortality of the larvae following a single feeding of siRNAs, which suggests that prolonged or multiple feedings of siRNAs could be used to kill filter-feeding larvae within streams, following development of a slow-release formulation. The genes targeted in this study are highly conserved across many species, and only serve as a proof-of-concept demonstration that siRNAs can be used in lampreys. Given that RNA interference is a sequence-specific phenomenon, it should be possible to design siRNAs that selectively target gene sequences that are unique to sea lampreys, and thus develop a technology to control these pests without adversely affecting non-target species.

17 CFR 229.308 - (Item 308) Internal control over financial reporting.

Science.gov (United States)

2010-04-01

... over financial reporting. 229.308 Section 229.308 Commodity and Securities Exchanges SECURITIES AND... § 229.308 (Item 308) Internal control over financial reporting. (a) Management's annual report on internal control over financial reporting. Provide a report of management on the registrant's internal...

Internal laboratory control in residue analysis of chlorinated hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

1980-01-01

The thesis contains a chapter on gaschromatographic system in which gas current, temperatures, separation system, detector system, recorder, dosing system and integrator are described. The chapter on reagents deals with standards and solvents, absorbents and other reagents. The chapter on laboratory equipment deals with general recommendations for apparatus, purification and total numerical result of blank test. The chapter ''Methods'' contains general references, aptitude for a special problem, common investigations and control by standard reference materials. The chapter on the work up of samples treats extraction, purification, concentrating the solution, internal standard, multiple determination and control samples. The chapter on measurement presents calibration, internal standard, multiple determination, securing the result and control samples. The chapter on evaluation consists of qualitative and quantitave evaluation, decision criteria and communication of the result. The chapter of documentation described routine investigations, tests and controls of internal laboratory control, preliminary works, maintenance and service works.

The importance of domestic law to international arms control

International Nuclear Information System (INIS)

Lehman, R.F. II.

1993-11-01

Studies of arms control and disarmament tend to focus on political, military, and diplomatic processes. Recently, in the context of the conversion of defense activities to civilian use, the economic aspects of arms control have also received renewed interest. The legal dimension, however, is in need of fresh examination. Both international and domestic law are sailing increasingly in uncharted waters. Recent arms control agreements and related developments in international peacekeeping have expanded the scope of international law and altered how one perceives certain fundamentals, including the principle of national sovereignty. Still, the nation state is largely unchallenged as the primary actor in international affairs. National governments retain near absolute sovereign rights and responsibilities even in an age of trans-national economic integration and codified international norms for human rights, freedom of the press, and the peaceful resolution of disputes. Indeed, the role of domestic law in arms control and disarmament may be more significant now than ever before. A brief review of relationships between arms control and domestic law should illustrate ways in which ones thinking has been underestimating the importance of domestic law. Hopefully, this survey will set the stage properly for the excellent, more detailed case studies by Elinor Hammarskjold and Alan Crawford. Toward that end, this paper will highlight a number of more general, and sometimes provocative, themes. These themes should be kept in mind when those two complementary presentations are considered

The importance of domestic law to international arms control

Energy Technology Data Exchange (ETDEWEB)

Lehman, R.F. II

1993-11-01

Studies of arms control and disarmament tend to focus on political, military, and diplomatic processes. Recently, in the context of the conversion of defense activities to civilian use, the economic aspects of arms control have also received renewed interest. The legal dimension, however, is in need of fresh examination. Both international and domestic law are sailing increasingly in uncharted waters. Recent arms control agreements and related developments in international peacekeeping have expanded the scope of international law and altered how one perceives certain fundamentals, including the principle of national sovereignty. Still, the nation state is largely unchallenged as the primary actor in international affairs. National governments retain near absolute sovereign rights and responsibilities even in an age of trans-national economic integration and codified international norms for human rights, freedom of the press, and the peaceful resolution of disputes. Indeed, the role of domestic law in arms control and disarmament may be more significant now than ever before. A brief review of relationships between arms control and domestic law should illustrate ways in which ones thinking has been underestimating the importance of domestic law. Hopefully, this survey will set the stage properly for the excellent, more detailed case studies by Elinor Hammarskjold and Alan Crawford. Toward that end, this paper will highlight a number of more general, and sometimes provocative, themes. These themes should be kept in mind when those two complementary presentations are considered.

13 CFR 108.506 - Safeguarding the NMVC Company's assets/Internal controls.

Science.gov (United States)

2010-01-01

... assets/Internal controls. 108.506 Section 108.506 Business Credit and Assistance SMALL BUSINESS... Requirements § 108.506 Safeguarding the NMVC Company's assets/Internal controls. You must adopt a plan to... document describing your control procedures. ...

miRNA-720 controls stem cell phenotype, proliferation and differentiation of human dental pulp cells.

Directory of Open Access Journals (Sweden)

Emilio Satoshi Hara

Full Text Available Dental pulp cells (DPCs are known to be enriched in stem/progenitor cells but not well characterized yet. Small non-coding microRNAs (miRNAs have been identified to control protein translation, mRNA stability and transcription, and have been reported to play important roles in stem cell biology, related to cell reprogramming, maintenance of stemness and regulation of cell differentiation. In order to characterize dental pulp stem/progenitor cells and its mechanism of differentiation, we herein sorted stem-cell-enriched side population (SP cells from human DPCs and periodontal ligament cells (PDLCs, and performed a locked nucleic acid (LNA-based miRNA array. As a result, miR-720 was highly expressed in the differentiated main population (MP cells compared to that in SP cells. In silico analysis and a reporter assay showed that miR-720 targets the stem cell marker NANOG, indicating that miR-720 could promote differentiation of dental pulp stem/progenitor cells by repressing NANOG. Indeed, gain-and loss-of-function analyses showed that miR-720 controls NANOG transcript and protein levels. Moreover, transfection of miR-720 significantly decreased the number of cells positive for the early stem cell marker SSEA-4. Concomitantly, mRNA levels of DNA methyltransferases (DNMTs, which are known to play crucial factors during stem cell differentiation, were also increased by miR-720 through unknown mechanism. Finally, miR-720 decreased DPC proliferation as determined by immunocytochemical analysis against ki-67, and promoted odontogenic differentiation as demonstrated by alizarin red staining, as well as alkaline phosphatase and osteopontin mRNA levels. Our findings identify miR-720 as a novel miRNA regulating the differentiation of DPCs.

Changes in apoptotic microRNA and mRNA expression profiling in Caenorhabditis elegans during the Shenzhou-8 mission

International Nuclear Information System (INIS)

Gao Ying; Li Shuai; Xu Dan; Wang Junjun; Sun Yeqing

2015-01-01

Radiation and microgravity exposure have been proven to induce abnormal apoptosis in microRNA (miRNA) and mRNA expression, but whether space conditions, including radiation and microgravity, activate miRNAs to regulate the apoptosis is undetermined. For that purpose, we investigated miRNome and mRNA expression in the ced-1 Caenorhabditis elegans mutant vs the wild-type, both of which underwent spaceflight, spaceflight 1g-centrifuge control and ground control conditions during the Shenzhou-8 mission. Results showed that no morphological changes in the worms were detected, but differential miRNA expression increased from 43 (ground control condition) to 57 and 91 in spaceflight and spaceflight control conditions, respectively. Microgravity altered miRNA expression profiling by decreasing the number and significance of differentially expressed miRNA compared with 1 g incubation during spaceflight. Alterations in the miRNAs were involved in alterations in apoptosis, neurogenesis larval development, ATP metabolism and GTPase-mediated signal transduction. Among these, 17 altered miRNAs potentially involved in apoptosis were screened and showed obviously different expression signatures between space conditions. By integrated analysis of miRNA and mRNA, miR-797 and miR-81 may be involved in apoptosis by targeting the genes ced-10 and both drp-1 and hsp-1, respectively. Compared with ground condition, space conditions regulated apoptosis though a different manner on transcription, by altering expression of seven core apoptotic genes in spaceflight condition, and eight in spaceflight control condition. Results indicate that, miRNA of Caenorhabditis elegans probably regulates apoptotic gene expression in response to space environmental stress, and shows different behavior under microgravity condition compared with 1 g condition in the presence of space radiation. (author)

Women's perceived internal control of future pregnancy outcomes and its related factors.

Science.gov (United States)

Maleki, Azam; Mazloomzadeh, Saeideh

2013-03-01

With regards to the importance of women's beliefs in improving pregnancy outcomes, this study was performed to determine the perceived internal control on future pregnancy outcomes and its related factors in women who participated in pre-marital counseling. In a cross-sectional study, women's perceived internal control was investigated. The study population comprised the women in reproductive age of whom 400 were selected by random sampling. Data collection instrument was a questionnaire consisting of demographic, pre-conceptional care, and internal control questions. Two categories of favorite and not favorite levels of internal control were defined based on the total score. The validity of the questionnaire was determined via content validity method by use of experts' opinion and its reliability was evaluated through the calculation of Cronbach's alpha coefficient which was 0.76. Data were analyzed through frequency tables, correlation coefficient, and Chi-square test at the confidence level of 0.95. Two hundred sixty-five (65%) women had a good perceived internal control and it was significantly associated with the age, educational level, and hearing about pre-conceptional care. The internal control score also showed a positive and significant correlation with both age and the subject knowledge about folic acid (r = 0.19 and r = 0.15, respectively). The majority of women had a favorite perceived internal control. Since age and educational level were the affecting factors on the perceived internal control of women, promoting the level of internal control in young women and those with low education in pre-marital counseling classes seems necessary.

RNA interference: a new strategy in the evolutionary arms race between human control strategies and insect pests.

Science.gov (United States)

Machado, Vilmar; Rodríguez-García, María Juliana; Sánchez-García, Francisco Javier; Galan, Jose

2014-01-01

The relationship between humans and the insect pests of cultivated plants may be considered to be an indirect coevolutionary process, i.e., an arms race. Over time, humans have developed several strategies to minimize the negative impacts of insects on agricultural production. However, insects have made adaptive responses via the evolution of resistance to insecticides, and more recently against Bacillus thuriengiensis. Thus, we need to continuously invest resources in the development of new strategies for crop protection. Recent advances in genomics have demonstrated the possibility of a new weapon or strategy in this war, i.e., gene silencing, which involves blocking the expression of specific genes via mRNA inactivation. In the last decade, several studies have demonstrated the effectiveness of this strategy in the control of different species of insects. However, several technical difficulties need to be overcome to transform this potential into reality, such as the selection of target genes, the concentration of dsRNA, the nucleotide sequence of the dsRNA, the length of dsRNA, persistence in the insect body, and the life stage of the target species where gene silencing is most efficient. This study analyzes several aspects related to the use of gene silencing in pest control and it includes an overview of the inactivation process, as well as the problems that need to be resolved to transform gene silencing into an effective pest control method.

Disease Control in Animals Using Molecular Technology by Inactivation of ASO, RNAi and ss-siRNA Genes

Directory of Open Access Journals (Sweden)

Muhamad Ali

2014-03-01

Full Text Available Globalization causes high mobility of human and livestock, hence increase the transmission of infectious diseases, including avian influenza, severe acute respiratory syndrome (SARS, and swine influenza. Therefore, prevention of those diseases is required. Vaccines are effective to prevent infectious diseases; however, their development takes a long time and they cannot provide immediate protection in pandemic cases. This paper describes several gene silencing technologies including antisense oligonucleotide (ASO, RNA interference (RNAi and single strand-small interfering RNA (ss-siRNA for controlling diseases. The primary mechanism of these technologies is inhibition of gene expression, typically by causing the destruction of specific RNA molecule of the pathogen. The use of gene silencing technologies is expected to give new alternative that is more effective in eradication of infectious diseases in animals before threaten human being.

Non-proliferation through effective international control, with particular reference to peaceful uses of nuclear material as a result of nuclear disarmament and international control of plutonium

International Nuclear Information System (INIS)

Imai, Ryukichi

1993-01-01

The role of nuclear factors in the international political situation has changed. The emphasis is now on the new circumstance of the post cold-war world. Non-proliferation is dealt with through effective international control, with particular reference to peaceful uses of nuclear material as a result of nuclear weapons dismantling and international control of plutonium

An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

Directory of Open Access Journals (Sweden)

Yih-Horng Shiao

Full Text Available BACKGROUND: Ribosomal RNA (rRNA is a central regulator of cell growth and may control cancer development. A cis noncoding rRNA (nc-rRNA upstream from the 45S rRNA transcription start site has recently been implicated in control of rRNA transcription in mouse fibroblasts. We investigated whether a similar nc-rRNA might be expressed in human cancer epithelial cells, and related to any genomic characteristics. METHODOLOGY/PRINCIPAL FINDINGS: Using quantitative rRNA measurement, we demonstrated that a nc-rRNA is transcribed in human lung epithelial and lung cancer cells, starting from approximately -1000 nucleotides upstream of the rRNA transcription start site (+1 and extending at least to +203. This nc-rRNA was significantly more abundant in the majority of lung cancer cell lines, relative to a nontransformed lung epithelial cell line. Its abundance correlated negatively with total 45S rRNA in 12 of 13 cell lines (P = 0.014. During sequence analysis from -388 to +306, we observed diverse, frequent intercopy single nucleotide polymorphisms (SNPs in rRNA, with a frequency greater than predicted by chance at 12 sites. A SNP at +139 (U/C in the 5' leader sequence varied among the cell lines and correlated negatively with level of the nc-rRNA (P = 0.014. Modelling of the secondary structure of the rRNA 5'-leader sequence indicated a small increase in structural stability due to the +139 U/C SNP and a minor shift in local configuration occurrences. CONCLUSIONS/SIGNIFICANCE: The results demonstrate occurrence of a sense nc-rRNA in human lung epithelial and cancer cells, and imply a role in regulation of the rRNA gene, which may be affected by a +139 SNP in the 5' leader sequence of the primary rRNA transcript.

32 CFR Appendix B to Part 327 - Internal Management Control Review Checklist

Science.gov (United States)

2010-07-01

... 32 National Defense 2 2010-07-01 2010-07-01 false Internal Management Control Review Checklist B... B to Part 327—Internal Management Control Review Checklist (a) Task: Personnel and/or Organization... See footnote 2 to this Appendix B. (1) I attest that the above listed internal controls provide...

An sRNA and Cold Shock Protein Homolog-Based Feedforward Loop Post-transcriptionally Controls Cell Cycle Master Regulator CtrA.

Science.gov (United States)

Robledo, Marta; Schlüter, Jan-Philip; Loehr, Lars O; Linne, Uwe; Albaum, Stefan P; Jiménez-Zurdo, José I; Becker, Anke

2018-01-01

Adjustment of cell cycle progression is crucial for bacterial survival and adaptation under adverse conditions. However, the understanding of modulation of cell cycle control in response to environmental changes is rather incomplete. In α-proteobacteria, the broadly conserved cell cycle master regulator CtrA underlies multiple levels of control, including coupling of cell cycle and cell differentiation. CtrA levels are known to be tightly controlled through diverse transcriptional and post-translational mechanisms. Here, small RNA (sRNA)-mediated post-transcriptional regulation is uncovered as an additional level of CtrA fine-tuning. Computational predictions as well as transcriptome and proteome studies consistently suggested targeting of ctrA and the putative cold shock chaperone cspA5 mRNAs by the trans- encoded sRNA ( trans- sRNA) GspR (formerly SmelC775) in several Sinorhizobium species. GspR strongly accumulated in the stationary growth phase, especially in minimal medium (MM) cultures. Lack of the gspR locus confers a fitness disadvantage in competition with the wild type, while its overproduction hampers cell growth, suggesting that this riboregulator interferes with cell cycle progression. An eGFP-based reporter in vivo assay, involving wild-type and mutant sRNA and mRNA pairs, experimentally confirmed GspR-dependent post-transcriptional down-regulation of ctrA and cspA5 expression, which most likely occurs through base-pairing to the respective mRNA. The energetically favored secondary structure of GspR is predicted to comprise three stem-loop domains, with stem-loop 1 and stem-loop 3 targeting ctrA and cspA5 mRNA, respectively. Moreover, this work reports evidence for post-transcriptional control of ctrA by CspA5. Thus, this regulation and GspR-mediated post-transcriptional repression of ctrA and cspA5 expression constitute a coherent feed-forward loop, which may enhance the negative effect of GspR on CtrA levels. This novel regulatory circuit involving

47 CFR 90.475 - Operation of internal transmitter control systems in specially equipped systems.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 5 2010-10-01 2010-10-01 false Operation of internal transmitter control... Control Internal Transmitter Control Systems § 90.475 Operation of internal transmitter control systems in specially equipped systems. (a) An internal transmitter control system need not be designed to meet the...

Programmed cell death 4 protein (Pdcd4) and homeodomain-interacting protein kinase 2 (Hipk2) antagonistically control translation of Hipk2 mRNA.

Science.gov (United States)

Ohnheiser, Johanna; Ferlemann, Eva; Haas, Astrid; Müller, Jan P; Werwein, Eugen; Fehler, Olesja; Biyanee, Abhiruchi; Klempnauer, Karl-Heinz

2015-07-01

The tumor suppressor protein programmed cell death 4 (Pdcd4) is a highly conserved RNA-binding protein that inhibits the translation of specific mRNAs. Here, we have identified the homeobox-interacting protein kinase-2 (Hipk2) mRNA as a novel translational target of Pdcd4. Unlike most other protein kinases Hipk2 is constitutively active after being synthesized by the ribosome and its expression and activity are thought to be mainly controlled by modulation of the half-life of the kinase. Our work provides the first evidence that Hipk2 expression is also controlled on the level of translation. We show that Hipk2 stimulates the translation of its own mRNA and that Pdcd4 suppresses the translation of Hipk2 mRNA by interfering with this auto-regulatory feedback mechanism. We also show that the translation of the related kinase Hipk1 is controlled by a similar feedback loop and that Hipk2 also stimulates the translation of Hipk1 mRNA. Taken together, our work describes a novel mechanism of translational suppression by Pdcd4 and shows for the first time that Hipk2 controls its own synthesis by an auto-regulatory feedback mechanism. Furthermore, the effect of Hipk2 on the translation of Hipk1 RNA suggests that Hipk2 and Pdcd4 can act in similar manner to control the translation of other mRNAs. Copyright © 2015 Elsevier B.V. All rights reserved.

Internal cost control on the ecological quality of products

Directory of Open Access Journals (Sweden)

N.P. Syroid

2018-04-01

Full Text Available To improve the environmental quality of products due attention should be paid to control the processes related to environmental quality input of the product. The results of the study help to state the purpose and objectives of the control, also to define objects for internal control of operations cost of environmental quality. So, we believe that the main purpose of internal cost control on the ecological quality of products is the establishment of the correctness and legality of business operations, prevention of violations and abuses in the expenditure of natural, labour, material and financial resources to ensure the minimization of negative impact on the health of consumers and the environment. The basic objectives of internal control of expenditure are brought forward, but it should be noted that they can vary and depend on the size, structure, spheres and types of economic activity of the enterprise, the requirements of management personnel. In the process of identifying the objects of control of environmental quality it should be noted that this list is not exhaustive, but it is most relevant to highlight objects such as genetically modified organisms and waste production. Also the subjects of cost control to environmental quality, their functions and the information base for monitoring are determined. Proper organization of the process of internal cost control on the ecological quality of products would benefit from a clear documentation of transactions, timely and complete registration of accounting data in the registers, the true reflection of information in managerial financial reporting and ensure reduction of the negative impact on the health of consumers and the environment.

Identifying microRNA/mRNA dysregulations in ovarian cancer.

Science.gov (United States)

Miles, Gregory D; Seiler, Michael; Rodriguez, Lorna; Rajagopal, Gunaretnam; Bhanot, Gyan

2012-03-27

novel microRNA/mRNA relationships that can be verified experimentally. We identify both generic microRNA/mRNA regulation mechanisms in the ovary as well as specific microRNA/mRNA controls which are turned on or off in ovarian tumours. Our results suggest that the disease process uses specific mechanisms which may be significant for their utility as early detection biomarkers or in the development of microRNA therapies in treating ovarian cancers. The positively correlated microRNA/mRNA pairs suggest the existence of novel regulatory mechanisms that proceed via intermediate states (indirect regulation) in ovarian tumorigenesis.

Biochemical characterization of a recombinant Japanese encephalitis virus RNA-dependent RNA polymerase

Directory of Open Access Journals (Sweden)

Kim Chan-Mi

2007-07-01

Full Text Available Abstract Background Japanese encephalitis virus (JEV NS5 is a viral nonstructural protein that carries both methyltransferase and RNA-dependent RNA polymerase (RdRp domains. It is a key component of the viral RNA replicase complex that presumably includes other viral nonstructural and cellular proteins. The biochemical properties of JEV NS5 have not been characterized due to the lack of a robust in vitro RdRp assay system, and the molecular mechanisms for the initiation of RNA synthesis by JEV NS5 remain to be elucidated. Results To characterize the biochemical properties of JEV RdRp, we expressed in Escherichia coli and purified an enzymatically active full-length recombinant JEV NS5 protein with a hexahistidine tag at the N-terminus. The purified NS5 protein, but not the mutant NS5 protein with an Ala substitution at the first Asp of the RdRp-conserved GDD motif, exhibited template- and primer-dependent RNA synthesis activity using a poly(A RNA template. The NS5 protein was able to use both plus- and minus-strand 3'-untranslated regions of the JEV genome as templates in the absence of a primer, with the latter RNA being a better template. Analysis of the RNA synthesis initiation site using the 3'-end 83 nucleotides of the JEV genome as a minimal RNA template revealed that the NS5 protein specifically initiates RNA synthesis from an internal site, U81, at the two nucleotides upstream of the 3'-end of the template. Conclusion As a first step toward the understanding of the molecular mechanisms for JEV RNA replication and ultimately for the in vitro reconstitution of viral RNA replicase complex, we for the first time established an in vitro JEV RdRp assay system with a functional full-length recombinant JEV NS5 protein and characterized the mechanisms of RNA synthesis from nonviral and viral RNA templates. The full-length recombinant JEV NS5 will be useful for the elucidation of the structure-function relationship of this enzyme and for the

Fuzzy Logic Based Set-Point Weighting Controller Tuning for an Internal Model Control Based PID Controller

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Maruthai Suresh

2009-10-01

Full Text Available Controller tuning is the process of adjusting the parameters of the selected controller to achieve optimum response for the controlled process. For many of the control problems, a satisfactory performance is obtained by using PID controllers. One of the main problems with mathematical models of physical systems is that the parameters used in the models cannot be determined with absolute accuracy. The values of the parameters may change with time or various effects. In these cases, conventional controller tuning methods suffer when trying a lot to produce optimum response. In order to overcome these difficulties a fuzzy logic based Set- Point weighting controller tuning method is proposed. The effectiveness of the proposed scheme is analyzed through computer simulation using SIMULINK software and the results are presented. The fuzzy logic based simulation results are compared with Cohen-Coon (CC, Ziegler- Nichols (ZN, Ziegler – Nichols with Set- Point weighting (ZN-SPW, Internal Model Control (IMC and Internal model based PID controller responses (IMC-PID. The effects of process modeling errors and the importance of controller tuning have been brought out using the proposed control scheme.

Chimira: analysis of small RNA sequencing data and microRNA modifications.

Science.gov (United States)

Vitsios, Dimitrios M; Enright, Anton J

2015-10-15

Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3'-modifications (e.g. uridylation, adenylation), 5'-modifications and also internal modifications or variation (ADAR editing or single nucleotide polymorphisms). Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material). These allow the visual study of the differential expression between two specific samples or sets of samples, the identification of the most highly expressed miRNAs within sample pairs (or sets of samples) and also the projection of the modification profile for specific miRNAs across all samples. Other tools have already been published in the past for various types of small RNA-Seq analysis, such as UEA workbench, seqBuster, MAGI, OASIS and CAP-miRSeq, CPSS for modifications identification. A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material. Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface. Chimira has been developed as a web application and it is accessible here: http://www.ebi.ac.uk/research/enright/software/chimira. aje@ebi.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Dimensional control and check of field machining parts for reactor internals installation

International Nuclear Information System (INIS)

Zhang Caifang

2010-01-01

Some key issues of dimensional control for reactor internals installation are analyzed, and important technical requirements of crucial quality control elements on the measurement, machining, and checking of reactor internals filed machining parts are discussed. Moreover, provisions on quality control and risk prevention of reactor internals filed machining parts are presented in this paper. (author)

An Analysis of Internal Controls and Procurement Fraud Deterrence

Science.gov (United States)

2013-12-01

might keep the organization from achieving its objectives and analyze risks , including fraud risk , so as to decide how the risk should be managed ( COSO ...internal control to adequately manage the risk ( COSO , 2013). Risk management involves developing the effective internal control targeted at a...structure and management . While the risk of fraud cannot be eliminated entirely, it can be greatly reduced with an appropriate procurement fraud prevention

RNA binding specificity of Ebola virus transcription factor VP30.

Science.gov (United States)

Schlereth, Julia; Grünweller, Arnold; Biedenkopf, Nadine; Becker, Stephan; Hartmann, Roland K

2016-09-01

The transcription factor VP30 of the non-segmented RNA negative strand Ebola virus balances viral transcription and replication. Here, we comprehensively studied RNA binding by VP30. Using a novel VP30:RNA electrophoretic mobility shift assay, we tested truncated variants of 2 potential natural RNA substrates of VP30 - the genomic Ebola viral 3'-leader region and its complementary antigenomic counterpart (each ∼155 nt in length) - and a series of other non-viral RNAs. Based on oligonucleotide interference, the major VP30 binding region on the genomic 3'-leader substrate was assigned to the internal expanded single-stranded region (∼ nt 125-80). Best binding to VP30 was obtained with ssRNAs of optimally ∼ 40 nt and mixed base composition; underrepresentation of purines or pyrimidines was tolerated, but homopolymeric sequences impaired binding. A stem-loop structure, particularly at the 3'-end or positioned internally, supports stable binding to VP30. In contrast, dsRNA or RNAs exposing large internal loops flanked by entirely helical arms on both sides are not bound. Introduction of a 5´-Cap(0) structure impaired VP30 binding. Also, ssDNAs bind substantially weaker than isosequential ssRNAs and heparin competes with RNA for binding to VP30, indicating that ribose 2'-hydroxyls and electrostatic contacts of the phosphate groups contribute to the formation of VP30:RNA complexes. Our results indicate a rather relaxed RNA binding specificity of filoviral VP30, which largely differs from that of the functionally related transcription factor of the Paramyxoviridae which binds to ssRNAs as short as 13 nt with a preference for oligo(A) sequences.

Climatic changes, the international control stakes

International Nuclear Information System (INIS)

Maljean-Dubois, S.

2007-01-01

The author presents a juridical and economic analysis of the control mechanism called ''observance'' of the Kyoto protocol. This political and juridical innovation in the domain of the international agreements on the environment deals with the national sovereignty and the economical development mode. (A.L.B.)

Development of Gold Nanoparticle towards Radioenhancement Therapy, Renal Clearance, siRNA Delivery and Light-Controlled Gene Silencing

Science.gov (United States)

Wang, Jianxin

Gold nanoparticles (GNPs) have been widely studied and used in research for diagnostic, prophylactic or therapeutic purposes. However, they still face many technical challenges before they can be used to effectively address unmet biomedical needs. The theme of this dissertation is focused on addressing challenges of GNPs in clinical translation, and to improve their potential for application in radioenhancement therapy and siRNA delivery. We demonstrate the facile self-assembly of micellar gold nanocapsules using zwitterionic surfactants, with hydrodynamic diameters below 10 nm, which holds promise for good renal clearance to promote the excretion of GNPs in human body. We also prepared PEI- and PEG-coated GNPs and demonstrated their uptake into HeLa cells with exposure to soft X-rays (120 kVp), based on the consideration that the proximity of GNPs to nuclear DNA may be beneficial for enhancing low-energy ionizing radiotherapy. GNP-mediated siRNA delivery may be challenged by nonspecific siRNA desorption during circulation, which can cause off-target effects and immunogenicity. The use of gold nanorods (GNRs) for siRNA delivery also faces challenges like reduced dispersion stability during siRNA functionalization. We developed an effective way to load siRNA onto GNRs at high density, using oleylsulfobetaine (OSB) as an intermediate surfactant and dithiocarbamates (DTCs) as desorption-resistant anchors for siRNA. The GNR?siRNA complexes provided excellent control for laser-triggered gene silencing.

Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process

Directory of Open Access Journals (Sweden)

Borges-Pérez Andrés

2008-12-01

Full Text Available Abstract Background The elucidation of gene expression patterns leads to a better understanding of biological processes. Real-time quantitative RT-PCR has become the standard method for in-depth studies of gene expression. A biologically meaningful reporting of target mRNA quantities requires accurate and reliable normalization in order to identify real gene-specific variation. The purpose of normalization is to control several variables such as different amounts and quality of starting material, variable enzymatic efficiencies of retrotranscription from RNA to cDNA, or differences between tissues or cells in overall transcriptional activity. The validity of a housekeeping gene as endogenous control relies on the stability of its expression level across the sample panel being analysed. In the present report we describe the first systematic evaluation of potential internal controls during tomato development process to identify which are the most reliable for transcript quantification by real-time RT-PCR. Results In this study, we assess the expression stability of 7 traditional and 4 novel housekeeping genes in a set of 27 samples representing different tissues and organs of tomato plants at different developmental stages. First, we designed, tested and optimized amplification primers for real-time RT-PCR. Then, expression data from each candidate gene were evaluated with three complementary approaches based on different statistical procedures. Our analysis suggests that SGN-U314153 (CAC, SGN-U321250 (TIP41, SGN-U346908 ("Expressed" and SGN-U316474 (SAND genes provide superior transcript normalization in tomato development studies. We recommend different combinations of these exceptionally stable housekeeping genes for suited normalization of different developmental series, including the complete tomato development process. Conclusion This work constitutes the first effort for the selection of optimal endogenous controls for quantitative real

MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies

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Pankaj Kumar

2015-01-01

Full Text Available The number of RNA-Seq studies has grown in recent years. The design of RNA-Seq studies varies from very simple (e.g., two-condition case-control to very complicated (e.g., time series involving multiple samples at each time point with separate drug treatments. Most of these publically available RNA-Seq studies are deposited in NCBI databases, but their metadata are scattered throughout four different databases: Sequence Read Archive (SRA, Biosample, Bioprojects, and Gene Expression Omnibus (GEO. Although the NCBI web interface is able to provide all of the metadata information, it often requires significant effort to retrieve study- or project-level information by traversing through multiple hyperlinks and going to another page. Moreover, project- and study-level metadata lack manual or automatic curation by categories, such as disease type, time series, case-control, or replicate type, which are vital to comprehending any RNA-Seq study. Here we describe “MetaRNA-Seq,” a new tool for interactively browsing, searching, and annotating RNA-Seq metadata with the capability of semiautomatic curation at the study level.

NCI RNA Biology 2017 symposium recap | Center for Cancer Research

Science.gov (United States)

The recent discovery of new classes of RNAs and the demonstration that alterations in RNA metabolism underlie numerous human cancers have resulted in enormous interest among CCR investigators in RNA biology. In order to share the latest research in this exciting field, the CCR Initiative in RNA Biology held its second international symposium April 23-24, 2017, in Natcher

RNA versatility, flexibility, and thermostability for practice in RNA nanotechnology and biomedical applications.

Science.gov (United States)

Haque, Farzin; Pi, Fengmei; Zhao, Zhengyi; Gu, Shanqing; Hu, Haibo; Yu, Hang; Guo, Peixuan

2018-01-01

In recent years, RNA has attracted widespread attention as a unique biomaterial with distinct biophysical properties for designing sophisticated architectures in the nanometer scale. RNA is much more versatile in structure and function with higher thermodynamic stability compared to its nucleic acid counterpart DNA. Larger RNA molecules can be viewed as a modular structure built from a combination of many 'Lego' building blocks connected via different linker sequences. By exploiting the diversity of RNA motifs and flexibility of structure, varieties of RNA architectures can be fabricated with precise control of shape, size, and stoichiometry. Many structural motifs have been discovered and characterized over the years and the crystal structures of many of these motifs are available for nanoparticle construction. For example, using the flexibility and versatility of RNA structure, RNA triangles, squares, pentagons, and hexagons can be constructed from phi29 pRNA three-way-junction (3WJ) building block. This review will focus on 2D RNA triangles, squares, and hexamers; 3D and 4D structures built from basic RNA building blocks; and their prospective applications in vivo as imaging or therapeutic agents via specific delivery and targeting. Methods for intracellular cloning and expression of RNA molecules and the in vivo assembly of RNA nanoparticles will also be reviewed. WIREs RNA 2018, 9:e1452. doi: 10.1002/wrna.1452 This article is categorized under: RNA Methods > RNA Nanotechnology RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs. © 2017 Wiley Periodicals, Inc.

25 CFR 542.7 - What are the minimum internal control standards for bingo?

Science.gov (United States)

2010-04-01

... 25 Indians 2 2010-04-01 2010-04-01 false What are the minimum internal control standards for bingo... SERVICES MINIMUM INTERNAL CONTROL STANDARDS § 542.7 What are the minimum internal control standards for... utilized, alternate documentation and/or procedures that provide at least the level of control described by...

Active Center Control of Termination by RNA Polymerase III and tRNA Gene Transcription Levels In Vivo.

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Keshab Rijal

2016-08-01

Full Text Available The ability of RNA polymerase (RNAP III to efficiently recycle from termination to reinitiation is critical for abundant tRNA production during cellular proliferation, development and cancer. Yet understanding of the unique termination mechanisms used by RNAP III is incomplete, as is its link to high transcription output. We used two tRNA-mediated suppression systems to screen for Rpc1 mutants with gain- and loss- of termination phenotypes in S. pombe. 122 point mutation mutants were mapped to a recently solved 3.9 Å structure of yeast RNAP III elongation complex (EC; they cluster in the active center bridge helix and trigger loop, as well as the pore and funnel, the latter of which indicate involvement of the RNA cleavage domain of the C11 subunit in termination. Purified RNAP III from a readthrough (RT mutant exhibits increased elongation rate. The data strongly support a kinetic coupling model in which elongation rate is inversely related to termination efficiency. The mutants exhibit good correlations of terminator RT in vitro and in vivo, and surprisingly, amounts of transcription in vivo. Because assessing in vivo transcription can be confounded by various parameters, we used a tRNA reporter with a processing defect and a strong terminator. By ruling out differences in RNA decay rates, the data indicate that mutants with the RT phenotype synthesize more RNA than wild type cells, and than can be accounted for by their increased elongation rate. Finally, increased activity by the mutants appears unrelated to the RNAP III repressor, Maf1. The results show that the mobile elements of the RNAP III active center, including C11, are key determinants of termination, and that some of the mutations activate RNAP III for overall transcription. Similar mutations in spontaneous cancer suggest this as an unforeseen mechanism of RNAP III activation in disease.

PERFORMANCE IN INTERNAL CONTROL AND RISK MANAGEMENT

OpenAIRE

JELER (POPA) IOANA; FOCŞAN ELEONORA IONELA; CORICI MARIAN CĂTĂLIN

2017-01-01

The purpose of this article is to highlight the importance of internal control and risk management. In practice, economic entities meet a variety of risks that have the origins from the internal environment or the external one. Although there are different of views on addressing the concept of risk - threats or opportunities, event or action, accordingly uncertain, proposed by specialists in risk management in this article we try to present these issues and identify techniques to ...

Electrokinetically-controlled RNA-DNA hybridization assay for foodborne pathogens

International Nuclear Information System (INIS)

Weng, X.; Jiang, H.; Li, D.

2012-01-01

We have developed a microfluidic chip for use in an RNA-DNA hybridization assay for foodborne pathogens. Automatic sequential reagent dispensing and washing was realized with a programmable DC voltage sequencer. Signal detection was achieved with a miniaturized optical detection module. Salmonella and Listeria monocytogenes bacteria in different concentrations were quantitatively determined by this RNA-DNA hybridization assay in the microfluidic chip. The detection limit for the Salmonella and Listeria monocytogenes bacteria is 10 3 to 10 4 CFU mL -1 . The method excels by a significant reduction in the consumption of sample and reagent, and a short assay time. This automatic-operating microfluidic RNA-DNA hybridization assay is promising for on-site pathogen detection. (author)

mRNA processing in yeast

International Nuclear Information System (INIS)

Stevens, A.

1982-01-01

Investigations in this laboratory center on basic enzymatic reactions of RNA. Still undefined are reactions involved in the conversion of precursors of mRA (pre-mRNA) to mRNA in eukaryotes. The pre-mRNA is called heterogeneous nuclear RNA and is 2 to 6 times larger than mRNA. The conversion, called splicing, involves a removal of internal sequences called introns by endoribonuclease action followed by a rejoining of the 3'- and 5'-end fragments, called exons, by ligating activity. It has not been possible yet to study the enzymes involved in vitro. Also undefined are reactions involved in the turnover or discarding of certain of the pre-mRNA molecules. Yeast is a simple eukaryote and may be expected to have the same, but perhaps simpler, processing reactions as the higher eukaryotes. Two enzymes involved in the processing of pre-mRNA and mRNA in yeast are under investigation. Both enzymes have been partially purified from ribonucleoprotein particles of yeast. The first is a unique decapping enzyme which cleaves [ 3 H]m 7 Gppp [ 14 C]RNA-poly (A) of yeast, yielding [ 3 H]m 7 GDP and is suggested by the finding that the diphosphate product, m 7 GpppA(G), and UDP-glucose are not hydrolyzed. The second enzyme is an endoribonuclease which converts both the [ 3 H] and [ 14 C] labels of [ 3 H]m 7 Gppp[ 14 C]RNA-poly(A) from an oligo(dT)-cellulose bound form to an unbound, acid-insoluble form. Results show that the stimulation involves an interaction of the labeled RNA with the small nuclear RNA. The inhibition of the enzyme by ethidium bromide and its stimulation by small nuclear RNA suggest that it may be a processing ribonuclease, requiring specific double-stranded features in its substrate. The characterization of the unique decapping enzyme and endoribonuclease may help to understand reactions involved in the processing of pre-mRNA and mRNA in eukaryotes

The role of a company’s internal control system in fraud prevention

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Dragomir Dimitrijevic

2016-01-01

Full Text Available The emergence of internal control over specific segments of activities has been associated with management needs for evaluation of the consistency between the actual situation and development targets. Monitoring activities should enable detection and timely reaction to possible target-related deviations. While responding to complex market needs, companies are exposed to numerous internal and external influences, some of which may cause significant damage. Companies have realized that it is safer and cheaper to establish their own internal control systems in order to prevent such influences. The aim of this work is to show how the overall quality of control and The emergence of internal control over specific segments of activities has been associated with management needs for evaluation of the consistency between the actual situation and development targets. Monitoring activities should enable detection and timely reaction to possible target-related deviations. While responding to complex market needs, companies are exposed to numerous internal and external influences, some of which may cause significant damage. Companies have realized that it is safer and cheaper to establish their own internal control systems in order to prevent such influences. The aim of this work is to show how the overall quality of control and company performance is improved through implementation of preventive methods by internal controls, and to indicate that a developed system of internal control represents a protective barrier against various kinds of data manipulation and fraud inside the companies. Special attention was paid to fraud in financial statements since it can cause the most serious damage leading to instability of the economic-financial environment.

RNA-Seq analysis of D. radiodurans find non coding RNAs expressed in response to radiation stress

International Nuclear Information System (INIS)

Gadewal, Nikhil; Mukhopadhyaya, Rita

2015-01-01

In bacteria discovery of functional RNA molecules that are not translated into protein, noncoding RNAs, became possible with advent of Next Generation Sequencing technology. Bacterial non coding RNAs are typically 50-300 nucleotides long and work as internal signals controlling various levels of gene expression. Deep sequencing of total cellular RNA captures all coding and noncoding transcripts with their differential levels of expression in the transcriptome. It provides a powerful approach to study bacterial gene expression and mechanisms of gene regulation. We subjected the 3 h transcriptome of Deinococcus radiodurans R1 cells post exposure to 6 KGy gamma radiation to 100 x 2 cycles of deep sequencing on the Illumina HiSeq 2000 to look for ncRNA transcripts. Bioinformatics pipeline for analysis and interpretation of RNA Seq data was done in house using Softwares available in public domains. Our sequence data aligned with 21 putative ncRNAs expressed in the intergenic regions of annotated genome of D radiodurans. Verification of 2 ncRNA candidates and 3 transcription factor genes by Real Time PCR confirmed presence of these transcripts in the 3 h transcriptome sequenced by us. Any relationship between ncRNAs and control of radiation induced gene expression in D radiodurans can be proved only after specific gene knock outs in future. (author)

Identifying optimal reference genes for the normalization of microRNA expression in cucumber under viral stress

Science.gov (United States)

Liang, Chaoqiong; Hao, Jianjun; Meng, Yan; Luo, Laixin; Li, Jianqiang

2018-01-01

Cucumber green mottle mosaic virus (CGMMV) is an economically important pathogen and causes significant reduction of both yield and quality of cucumber (Cucumis sativus). Currently, there were no satisfied strategies for controlling the disease. A better understanding of microRNA (miRNA) expression related to the regulation of plant-virus interactions and virus resistance would be of great assistance when developing control strategies for CGMMV. However, accurate expression analysis is highly dependent on robust and reliable reference gene used as an internal control for normalization of miRNA expression. Most commonly used reference genes involved in CGMMV-infected cucumber are not universally expressed depending on tissue types and stages of plant development. It is therefore crucial to identify suitable reference genes in investigating the role of miRNA expression. In this study, seven reference genes, including Actin, Tubulin, EF-1α, 18S rRNA, Ubiquitin, GAPDH and Cyclophilin, were evaluated for the most accurate results in analyses using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Gene expression was assayed on cucumber leaves, stems and roots that were collected at different days post inoculation with CGMMV. The expression data were analyzed using algorithms including delta-Ct, geNorm, NormFinder, and BestKeeper as well as the comparative tool RefFinder. The reference genes were subsequently validated using miR159. The results showed that EF-1α and GAPDH were the most reliable reference genes for normalizing miRNA expression in leaf, root and stem samples, while Ubiquitin and EF-1α were the most suitable combination overall. PMID:29543906

In vitro and in vivo delivery of siRNA via VIPER polymer system to lung cells.

Science.gov (United States)

Feldmann, Daniel P; Cheng, Yilong; Kandil, Rima; Xie, Yuran; Mohammadi, Mariam; Harz, Hartmann; Sharma, Akhil; Peeler, David J; Moszczynska, Anna; Leonhardt, Heinrich; Pun, Suzie H; Merkel, Olivia M

2018-04-28

The block copolymer VIPER (virus-inspired polymer for endosomal release) has been reported to be a promising novel delivery system of DNA plasmids both in vitro and in vivo. VIPER is comprised of a polycation segment for condensation of nucleic acids as well as a pH-sensitive segment that exposes the membrane lytic peptide melittin in acidic environments to facilitate endosomal escape. The objective of this study was to investigate VIPER/siRNA polyplex characteristics, and compare their in vitro and in vivo performance with commercially available transfection reagents and a control version of VIPER lacking melittin. VIPER/siRNA polyplexes were formulated and characterized at various charge ratios and shown to be efficiently internalized in cultured cells. Target mRNA knockdown was confirmed by both flow cytometry and qRT-PCR and the kinetics of knockdown was monitored by live cell spinning disk microscopy, revealing knockdown starting by 4 h post-delivery. Intratracheal instillation of VIPER particles formulated with sequence specific siRNA to the lung of mice resulted in a significantly more efficient knockdown of GAPDH compared to treatment with VIPER particles formulated with scrambled sequence siRNA. We also demonstrated using pH-sensitive labels that VIPER particles experience less acidic environments compared to control polyplexes. In summary, VIPER/siRNA polyplexes efficiently deliver siRNA in vivo resulting in robust gene silencing (>75% knockdown) within the lung. Copyright © 2018 Elsevier B.V. All rights reserved.

Investigating the Role of International Law in Controlling Communicable Diseases

Directory of Open Access Journals (Sweden)

Aliasghar Kheirkhah

2017-02-01

Full Text Available International law globally plays a key role in the surveillance and control of communicable diseases. Throughout the nineteenth century, international law played a dominant role in harmonizing the inconsistent national quarantine regulations of European nation states; facilitating the exchange of epidemiological information on infectious diseases; establishing international health organizations; and standardization of surveillance. Today, due to changed forms of infectious diseases and individuals' lifestyles as well as individuals' proximity caused by increased air travels, communicable diseases are in an international and cross-border form. In this regard, binding regulations and inconsistent rules adopted in international multilateral institutions like the World Health Organization, World Trade Organization, Food and Agriculture Organization can be of great use in surveillance and control of communicable diseases. With the globalization of public health, international law can be used as an essential tool in monitoring global health and reducing human vulnerability and mortality.

NCI RNA Biology 2017 symposium recap | Center for Cancer Research

Science.gov (United States)

The recent discovery of new classes of RNAs and the demonstration that alterations in RNA metabolism underlie numerous human cancers have resulted in enormous interest among CCR investigators in RNA biology. In order to share the latest research in this exciting field, the CCR Initiative in RNA Biology held its second international symposium April 23-24, 2017, in Natcher Auditorium. Learn more...

Increased 5S rRNA oxidation in Alzheimer's disease.

Science.gov (United States)

Ding, Qunxing; Zhu, Haiyan; Zhang, Bing; Soriano, Augusto; Burns, Roxanne; Markesbery, William R

2012-01-01

It is widely accepted that oxidative stress is involved in neurodegenerative disorders such as Alzheimer's disease (AD). Ribosomal RNA (rRNA) is one of the most abundant molecules in most cells and is affected by oxidative stress in the human brain. Previous data have indicated that total rRNA levels were decreased in the brains of subjects with AD and mild cognitive impairment concomitant with an increase in rRNA oxidation. In addition, level of 5S rRNA, one of the essential components of the ribosome complex, was significantly lower in the inferior parietal lobule (IP) brain area of subjects with AD compared with control subjects. To further evaluate the alteration of 5S rRNA in neurodegenerative human brains, multiple brain regions from both AD and age-matched control subjects were used in this study, including IP, superior and middle temporal gyro, temporal pole, and cerebellum. Different molecular pools including 5S rRNA integrated into ribosome complexes, free 5S rRNA, cytoplasmic 5S rRNA, and nuclear 5S rRNA were studied. Free 5S rRNA levels were significantly decreased in the temporal pole region of AD subjects and the oxidation of ribosome-integrated and free 5S rRNA was significantly increased in multiple brain regions in AD subjects compared with controls. Moreover, a greater amount of oxidized 5S rRNA was detected in the cytoplasm and nucleus of AD subjects compared with controls. These results suggest that the increased oxidation of 5S rRNA, especially the oxidation of free 5S rRNA, may be involved in the neurodegeneration observed in AD.

25 CFR 900.54 - Should the property management system prescribe internal controls?

Science.gov (United States)

2010-04-01

... System Standards § 900.54 Should the property management system prescribe internal controls? Yes. Effective internal controls should include procedures: (a) For the conduct of periodic inventories; (b) To... 25 Indians 2 2010-04-01 2010-04-01 false Should the property management system prescribe internal...

78 FR 68447 - Exposure Draft-Standards for Internal Control in the Federal Government

Science.gov (United States)

2013-11-14

... GOVERNMENT ACCOUNTABILITY OFFICE Exposure Draft--Standards for Internal Control in the Federal... revisions to the Standards for Internal Control in the Federal Government, known as the ``Green Book,'' to... proposed changes contained in the 2013 Exposure Draft update to the Standards for Internal Control in the...

49 CFR 192.476 - Internal corrosion control: Design and construction of transmission line.

Science.gov (United States)

2010-10-01

... 49 Transportation 3 2010-10-01 2010-10-01 false Internal corrosion control: Design and... STANDARDS Requirements for Corrosion Control § 192.476 Internal corrosion control: Design and construction... the risk of internal corrosion. At a minimum, unless it is impracticable or unnecessary to do so, each...

Chitosan/siRNA nanoparticles encapsulated in PLGA nanofibers for siRNA delivery

DEFF Research Database (Denmark)

Chen, Menglin; Gao, Shan; Dong, Mingdong

2012-01-01

Composite nanofibers of biodegradable poly(d,l-lactic-co-glycolic acid) (PLGA) encapsulating chitosan/siRNA nanoparticles (NPs) were prepared by electrospinning. Acidic/alkaline hydrolysis and a bulk/surface degradation mechanism were investigated in order to achieve an optimized release profile...... for prolonged and efficient gene silencing. Thermo-controlled AFM in situ imaging not only revealed the integrity of the encapsulated chitosan/siRNA polyplex but also shed light on the decreasing Tg of PLGA on the fiber surfaces during release. A triphasic release profile based on bulk erosion was obtained at p......RNA transfection, where the encapsulated chitosan/siRNA NPs exhibited up to 50% EGFP gene silencing activity after 48 h post-transfection on H1299 cells....

Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III

Directory of Open Access Journals (Sweden)

Matsutani Sachiko

2004-08-01

Full Text Available Abstract Background In eukaryotes, RNA polymerase III (RNAP III transcribes the genes for small RNAs like tRNAs, 5S rRNA, and several viral RNAs, and short interspersed repetitive elements (SINEs. The genes for these RNAs and SINEs have internal promoters that consist of two regions. These two regions are called the A and B blocks. The multisubunit transcription factor TFIIIC is required for transcription initiation of RNAP III; in transcription of tRNAs, the B-block binding subunit of TFIIIC recognizes a promoter. Although internal promoter sequences are conserved in eukaryotes, no evidence of homology between the B-block binding subunits of vertebrates and yeasts has been reported previously. Results Here, I reported the results of PSI-BLAST searches using the B-block binding subunits of human and Shizosacchromyces pombe as queries, showing that the same Arabidopsis proteins were hit with low E-values in both searches. Comparison of the convergent iterative alignments obtained by these PSI-BLAST searches revealed that the vertebrate, yeast, and Arabidopsis proteins have similarities in their N-terminal one-third regions. In these regions, there were three domains with conserved sequence similarities, one located in the N-terminal end region. The N-terminal end region of the B-block binding subunit of Saccharomyces cerevisiae is tentatively identified as a HMG box, which is the DNA binding motif. Although I compared the alignment of the N-terminal end regions of the B-block binding subunits, and their homologs, with that of the HMG boxes, it is not clear whether they are related. Conclusion Molecular phylogenetic analyses using the small subunit rRNA and ubiquitous proteins like actin and α-tubulin, show that fungi are more closely related to animals than either is to plants. Interestingly, the results obtained in this study show that, with respect to the B-block binding subunits of TFIIICs, animals appear to be evolutionarily closer to plants

Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III.

Science.gov (United States)

Matsutani, Sachiko

2004-08-09

In eukaryotes, RNA polymerase III (RNAP III) transcribes the genes for small RNAs like tRNAs, 5S rRNA, and several viral RNAs, and short interspersed repetitive elements (SINEs). The genes for these RNAs and SINEs have internal promoters that consist of two regions. These two regions are called the A and B blocks. The multisubunit transcription factor TFIIIC is required for transcription initiation of RNAP III; in transcription of tRNAs, the B-block binding subunit of TFIIIC recognizes a promoter. Although internal promoter sequences are conserved in eukaryotes, no evidence of homology between the B-block binding subunits of vertebrates and yeasts has been reported previously. Here, I reported the results of PSI-BLAST searches using the B-block binding subunits of human and Shizosacchromyces pombe as queries, showing that the same Arabidopsis proteins were hit with low E-values in both searches. Comparison of the convergent iterative alignments obtained by these PSI-BLAST searches revealed that the vertebrate, yeast, and Arabidopsis proteins have similarities in their N-terminal one-third regions. In these regions, there were three domains with conserved sequence similarities, one located in the N-terminal end region. The N-terminal end region of the B-block binding subunit of Saccharomyces cerevisiae is tentatively identified as a HMG box, which is the DNA binding motif. Although I compared the alignment of the N-terminal end regions of the B-block binding subunits, and their homologs, with that of the HMG boxes, it is not clear whether they are related. Molecular phylogenetic analyses using the small subunit rRNA and ubiquitous proteins like actin and alpha-tubulin, show that fungi are more closely related to animals than either is to plants. Interestingly, the results obtained in this study show that, with respect to the B-block binding subunits of TFIIICs, animals appear to be evolutionarily closer to plants than to fungi.

Nuclear reactor internals with control elements guides

International Nuclear Information System (INIS)

Baujat, J.; Chevereau, G.

1991-01-01

The internals have a lower plate, a superior plate, support columns and guide tubes for the control rods displacements. The lower section of the control rod guide tube have a base that fits into a bevelled seat in the lower plate. The guide tube is held into the seat by a spring, compressed between the base of the upper section of the tube and the lower plate

Evaluation of information technology impact on effective internal control in the University system

Energy Technology Data Exchange (ETDEWEB)

Sanusi Fasilat, A., E-mail: Fasilat17@gmail.com; Hassan, Haslinda, E-mail: lynn@uum.edu.my [School of Accountancy, College of Business, Universiti Utara Malaysia, Sintok, Kedah (Malaysia)

2015-12-11

Information Technology (IT) plays a key role in internal control system in various organizations in terms of maintaining records and other internal services. Internal control system is defined as an efficient control procedures set up by firm to safeguard resources and to assure the reliability and accuracy of both financial and non-financial records in line with applicable governance and procedure to acquire the established goal and objectives. This paper focuses on the impact of IT on internal control system in the Nigerian universities. Data are collected from three different universities via questionnaire. Descriptive statistics is used to analyze the data; Chi-square is performed to test the hypothesis. The results of the hypothesis showed that IT has a positive relationship with the effective internal control activities in the University system. It is concluded that the adoption of IT will significantly improve the effectiveness of the internal control system operations in the University in terms of quality service delivery.

Evaluation of information technology impact on effective internal control in the University system

International Nuclear Information System (INIS)

Sanusi Fasilat, A.; Hassan, Haslinda

2015-01-01

Information Technology (IT) plays a key role in internal control system in various organizations in terms of maintaining records and other internal services. Internal control system is defined as an efficient control procedures set up by firm to safeguard resources and to assure the reliability and accuracy of both financial and non-financial records in line with applicable governance and procedure to acquire the established goal and objectives. This paper focuses on the impact of IT on internal control system in the Nigerian universities. Data are collected from three different universities via questionnaire. Descriptive statistics is used to analyze the data; Chi-square is performed to test the hypothesis. The results of the hypothesis showed that IT has a positive relationship with the effective internal control activities in the University system. It is concluded that the adoption of IT will significantly improve the effectiveness of the internal control system operations in the University in terms of quality service delivery

Evaluation of information technology impact on effective internal control in the University system

Science.gov (United States)

Sanusi Fasilat, A.; Hassan, Haslinda

2015-12-01

Information Technology (IT) plays a key role in internal control system in various organizations in terms of maintaining records and other internal services. Internal control system is defined as an efficient control procedures set up by firm to safeguard resources and to assure the reliability and accuracy of both financial and non-financial records in line with applicable governance and procedure to acquire the established goal and objectives. This paper focuses on the impact of IT on internal control system in the Nigerian universities. Data are collected from three different universities via questionnaire. Descriptive statistics is used to analyze the data; Chi-square is performed to test the hypothesis. The results of the hypothesis showed that IT has a positive relationship with the effective internal control activities in the University system. It is concluded that the adoption of IT will significantly improve the effectiveness of the internal control system operations in the University in terms of quality service delivery.

dPORE-miRNA: Polymorphic regulation of microRNA genes

KAUST Repository

Schmeier, Sebastian; Schaefer, Ulf; MacPherson, Cameron R.; Bajic, Vladimir B.

2011-01-01

Background: MicroRNAs (miRNAs) are short non-coding RNA molecules that act as post-transcriptional regulators and affect the regulation of protein-coding genes. Mostly transcribed by PolII, miRNA genes are regulated at the transcriptional level similarly to protein-coding genes. In this study we focus on human miRNAs. These miRNAs are involved in a variety of pathways and can affect many diseases. Our interest is on possible deregulation of the transcription initiation of the miRNA encoding genes, which is facilitated by variations in the genomic sequence of transcriptional control regions (promoters). Methodology: Our aim is to provide an online resource to facilitate the investigation of the potential effects of single nucleotide polymorphisms (SNPs) on miRNA gene regulation. We analyzed SNPs overlapped with predicted transcription factor binding sites (TFBSs) in promoters of miRNA genes. We also accounted for the creation of novel TFBSs due to polymorphisms not present in the reference genome. The resulting changes in the original TFBSs and potential creation of new TFBSs were incorporated into the Dragon Database of Polymorphic Regulation of miRNA genes (dPORE-miRNA). Conclusions: The dPORE-miRNA database enables researchers to explore potential effects of SNPs on the regulation of miRNAs. dPORE-miRNA can be interrogated with regards to: a/miRNAs (their targets, or involvement in diseases, or biological pathways), b/SNPs, or c/transcription factors. dPORE-miRNA can be accessed at http://cbrc.kaust.edu.sa/dpore and http://apps.sanbi.ac.za/dpore/. Its use is free for academic and non-profit users. © 2011 Schmeier et al.

dPORE-miRNA: Polymorphic regulation of microRNA genes

KAUST Repository

Schmeier, Sebastian

2011-02-04

Background: MicroRNAs (miRNAs) are short non-coding RNA molecules that act as post-transcriptional regulators and affect the regulation of protein-coding genes. Mostly transcribed by PolII, miRNA genes are regulated at the transcriptional level similarly to protein-coding genes. In this study we focus on human miRNAs. These miRNAs are involved in a variety of pathways and can affect many diseases. Our interest is on possible deregulation of the transcription initiation of the miRNA encoding genes, which is facilitated by variations in the genomic sequence of transcriptional control regions (promoters). Methodology: Our aim is to provide an online resource to facilitate the investigation of the potential effects of single nucleotide polymorphisms (SNPs) on miRNA gene regulation. We analyzed SNPs overlapped with predicted transcription factor binding sites (TFBSs) in promoters of miRNA genes. We also accounted for the creation of novel TFBSs due to polymorphisms not present in the reference genome. The resulting changes in the original TFBSs and potential creation of new TFBSs were incorporated into the Dragon Database of Polymorphic Regulation of miRNA genes (dPORE-miRNA). Conclusions: The dPORE-miRNA database enables researchers to explore potential effects of SNPs on the regulation of miRNAs. dPORE-miRNA can be interrogated with regards to: a/miRNAs (their targets, or involvement in diseases, or biological pathways), b/SNPs, or c/transcription factors. dPORE-miRNA can be accessed at http://cbrc.kaust.edu.sa/dpore and http://apps.sanbi.ac.za/dpore/. Its use is free for academic and non-profit users. © 2011 Schmeier et al.

Issues of internal control during the reform period

Directory of Open Access Journals (Sweden)

O.I. Gresova

2012-12-01

Full Text Available The paper considers theoretical and methodological problems of organization and financial control activities, the main problems and reasons causing the need for a unified system of internal financial control in the State Administration of Railway Transport of Ukraine at the stage of the reform.

Modelling and Internal Fuzzy Model Power Control of a Francis Water Turbine

Directory of Open Access Journals (Sweden)

Klemen Nagode

2014-02-01

Full Text Available This paper presents dynamic modelling of a Francis turbine with a surge tank and the control of a hydro power plant (HPP. Non-linear and linear models include technical parameters and show high similarity to measurement data. Turbine power control with an internal model control (IMC is proposed, based on a turbine fuzzy model. Considering appropriate control responses in the entire area of turbine power, the model parameters of the process are determined from a fuzzy model, which are further included in the internal model controller. The results are compared to a proportional-integral (PI controller tuned with an integral absolute error (IAE objective function, and show an improved response of internal model control.

Internal control in the company in order to financial monitoring

Directory of Open Access Journals (Sweden)

Osipov A.V.

2017-04-01

Full Text Available the article explores the definition of financial monitoring, financial analysis and internal control in aspect to their correlation to fight money laundering and terrorism financing. Internal control is analyzed from the point of view of law, economics and management. The author pays much attention in the article to the work of systems of financial monitoring in organizations.

2′-O Methylation of Internal Adenosine by Flavivirus NS5 Methyltransferase

Science.gov (United States)

Dong, Hongping; Chang, David C.; Hua, Maggie Ho Chia; Lim, Siew Pheng; Chionh, Yok Hian; Hia, Fabian; Lee, Yie Hou; Kukkaro, Petra; Lok, Shee-Mei; Dedon, Peter C.; Shi, Pei-Yong

2012-01-01

RNA modification plays an important role in modulating host-pathogen interaction. Flavivirus NS5 protein encodes N-7 and 2′-O methyltransferase activities that are required for the formation of 5′ type I cap (m7GpppAm) of viral RNA genome. Here we reported, for the first time, that flavivirus NS5 has a novel internal RNA methylation activity. Recombinant NS5 proteins of West Nile virus and Dengue virus (serotype 4; DENV-4) specifically methylates polyA, but not polyG, polyC, or polyU, indicating that the methylation occurs at adenosine residue. RNAs with internal adenosines substituted with 2′-O-methyladenosines are not active substrates for internal methylation, whereas RNAs with adenosines substituted with N6-methyladenosines can be efficiently methylated, suggesting that the internal methylation occurs at the 2′-OH position of adenosine. Mass spectroscopic analysis further demonstrated that the internal methylation product is 2′-O-methyladenosine. Importantly, genomic RNA purified from DENV virion contains 2′-O-methyladenosine. The 2′-O methylation of internal adenosine does not require specific RNA sequence since recombinant methyltransferase of DENV-4 can efficiently methylate RNAs spanning different regions of viral genome, host ribosomal RNAs, and polyA. Structure-based mutagenesis results indicate that K61-D146-K181-E217 tetrad of DENV-4 methyltransferase forms the active site of internal methylation activity; in addition, distinct residues within the methyl donor (S-adenosyl-L-methionine) pocket, GTP pocket, and RNA-binding site are critical for the internal methylation activity. Functional analysis using flavivirus replicon and genome-length RNAs showed that internal methylation attenuated viral RNA translation and replication. Polymerase assay revealed that internal 2′-O-methyladenosine reduces the efficiency of RNA elongation. Collectively, our results demonstrate that flavivirus NS5 performs 2′-O methylation of internal adenosine of

Mechanisms controlling mRNA processing and translation : decoding the regulatory layers defining gene expression through RNA sequencing

NARCIS (Netherlands)

Klerk, Eleonora de

2015-01-01

The work described in this thesis focuses on the mechanisms that give rise to alternative mRNAs and their alternative translation into proteins. Each of the described studies has been based on a specific set of high-throughput RNA sequencing technologies. An overview of the available RNA sequencing

Modular arrangement of regulatory RNA elements.

Science.gov (United States)

Roßmanith, Johanna; Narberhaus, Franz

2017-03-04

Due to their simple architecture and control mechanism, regulatory RNA modules are attractive building blocks in synthetic biology. This is especially true for riboswitches, which are natural ligand-binding regulators of gene expression. The discovery of various tandem riboswitches inspired the design of combined RNA modules with activities not yet found in nature. Riboswitches were placed in tandem or in combination with a ribozyme or temperature-responsive RNA thermometer resulting in new functionalities. Here, we compare natural examples of tandem riboswitches with recently designed artificial RNA regulators suggesting substantial modularity of regulatory RNA elements. Challenges associated with modular RNA design are discussed.

Long Noncoding RNA HOTAIR Controls Cell Cycle by Functioning as a Competing Endogenous RNA in Esophageal Squamous Cell Carcinoma

Directory of Open Access Journals (Sweden)

Kewei Ren

2016-12-01

Full Text Available Recent studies have shown that long noncoding RNAs (lncRNAs play pivotal roles in the initiation and progression of cancer, including esophageal squamous cell carcinoma (ESCC. The lncRNA HOX transcript antisense RNA (HOTAIR was reported to be dysregulated and correlated with the progression of ESCC. However, the biological role and the underlying mechanism of HOTAIR in the development of ESCC remain unclear. Herein, we found that HOTAIR was aberrantly upregulated in ESCC cells and that HOTAIR depletion inhibited proliferation and led to G1 cell cycle arrest in ESCC cells. Besides, we found that HOTAIR acted as an endogenous sponge to downregulate miR-1 expression by directly binding to miR-1. Furthermore, HOTAIR overturned the effect of miR-1 on the proliferation and cell cycle profile in ESCC cells, which involved the derepression of cyclin D1 (CCND1 expression, a target of miR-1. Taken together, our study elucidated a novel HOTAIR /miR-1/CCND1 regulatory axis in which HOTAIR acted as a competing endogenous RNA by sponging miR-1 and upregulated CCND1 expression, thereby facilitating the tumorigenesis of ESCC. Investigation of this lncRNA/miRNA/mRNA pathway may contribute to a better understanding of ESCC pathogenesis and facilitate the development of lncRNA-directed therapy against this disease.

Regulation of human histone gene expression: transcriptional and posttranscriptional control in the coupling of histone messenger RNA stability with DNA replication

International Nuclear Information System (INIS)

Baumbach, L.L.; Stein, G.S.; Stein, J.L.

1987-01-01

The extent to which transcriptional and posttranscriptional regulation contributes to the coupling of histone gene expression and DNA replication was examined during the cell cycle in synchronized HeLa S3 cells. Rates of transcription were determined in vitro in isolated nuclei. A 3-5-fold increase in cell cycle dependent histone gene transcription was observed in early S phase, prior to the peak of DNA synthesis. This result is consistent with a previous determination of histone mRNA synthesis in intact cells. The transcription of these genes did not change appreciably after inhibition of DNA replication by hydroxyurea treatment, although Northern blot analysis indicated that cellular levels of histone mRNA decreased rapidly in the presence of the drug. Total cellular levels of histone mRNA closely parallel the rate of DNA synthesis as a function of cell cycle progression, reaching a maximal 20-fold increase as compared with non S phase levels. This DNA synthesis dependent accumulation of histone mRNA occurs predominantly in the cytoplasm and appears to be mediated primarily by control of histone mRNA stability. Changes in nuclear histone mRNA levels were less pronounced. These combined observations suggest that both transcriptional regulation and posttranscriptional regulation contribute toward control of the cell cycle dependent accumulation of histone mRNA during S phase, while the stability of histone mRNA throughout S phase and the selective turnover of histone mRNAs, either at the natural termination of S phase or following inhibition of DNA synthesis, are posttranscriptionally regulated

Aminoacyl-tRNA quality control is required for efficient activation of the TOR pathway regulator Gln3p.

Science.gov (United States)

Mohler, Kyle; Mann, Rebecca; Kyle, Amanda; Reynolds, Noah; Ibba, Michael

2017-09-14

The aminoacylation status of the cellular tRNA pool regulates both general amino acid control (GAAC) and target of rapamycin (TOR) stress response pathways in yeast. Consequently, fidelity of translation at the level of aminoacyl-tRNA synthesis plays a central role in determining accuracy and sensitivity of stress responses. To investigate effects of translational quality control (QC) on cell physiology under stress conditions, phenotypic microarray analyses were used to identify changes in QC deficient cells. Nitrogen source growth assays showed QC deficient yeast grew differently compared to WT. The QC deficient strain was more tolerant to caffeine treatment than wild type through altered interactions with the TOR and GAAC pathways. Increased caffeine tolerance of the QC deficient strain was consistent with the observation that the activity of Gln3p, a transcription factor controlled by the TOR pathway, is decreased in the QC deficient strain compared to WT. GCN4 translation, which is typically repressed in the absence of nutritional stress, was enhanced in the QC deficient strain through TOR inhibition. QC did not impact cell cycle regulation; however, the chronological lifespan of QC deficient yeast strains decreased compared to wild type, likely due to translational errors and alteration of the TOR-associated regulon. These findings support the idea that changes in translational fidelity provide a mechanism of cellular adaptation by modulating TOR activity. This, in turn, supports a central role for aminoacyl-tRNA synthesis QC in the integrated stress response by maintaining the proper aa-tRNA pools necessary to coordinate the GAAC and TOR.

Small RNA-Controlled Gene Regulatory Networks in Pseudomonas putida

DEFF Research Database (Denmark)

Bojanovic, Klara

evolved numerous mechanisms to controlgene expression in response to specific environmental signals. In addition to two-component systems, small regulatory RNAs (sRNAs) have emerged as major regulators of gene expression. The majority of sRNAs bind to mRNA and regulate their expression. They often have...... multiple targets and are incorporated into large regulatory networks and the RNA chaper one Hfq in many cases facilitates interactions between sRNAs and their targets. Some sRNAs also act by binding to protein targets and sequestering their function. In this PhD thesis we investigated the transcriptional....... Detailed insights into the mechanisms through which P. putida responds to different stress conditions and increased understanding of bacterial adaptation in natural and industrial settings were gained. Additionally, we identified genome-wide transcription start sites, andmany regulatory RNA elements...

Direct Regulation of tRNA and 5S rRNA Gene Transcription by Polo-like Kinase 1

NARCIS (Netherlands)

Fairley, Jennifer A.; Mitchell, Louise E.; Berg, Tracy; Kenneth, Niall S.; von Schubert, Conrad; Sillje, Herman H. W.; Medema, Rene H.; Nigg, Erich A.; White, Robert J.

2012-01-01

Polo-like kinase Plk1 controls numerous aspects of cell-cycle progression. We show that it associates with tRNA and 5S rRNA genes and regulates their transcription by RNA polymerase Ill (pol Ill) through direct binding and phosphorylation of transcription factor Brit During interphase, Plk1 promotes

Strategies for Enhancing Nonlinear Internal Model Control of pH Processes

Energy Technology Data Exchange (ETDEWEB)

Hu, Qiuping.; Rangaiah, G.P. [The National University of Singapore, Singapore (Singapore). Dept. of Chemical and Environmental Engineering

1999-02-01

Control of neutralization processes is very difficult due to nonlinear dynamics, different types of disturbances and modeling errors. The objective of the paper is to evaluate two strategies (augmented internal model control, AuIMC and adaptive internal model control, AdIMC) for enhancing pH control by nonlinear internal model control (NIMC). A NIMC controller is derived directly form input output linearization. The AuIMC is composed of NIMC and an additional loop through which the difference between the process and model outputs is fed back and added to the input of the controller. For the AdIMC, and adaptive law with two tuning parameters is proposed for estimating the unknown parameter. Both AuIMC and AdIMC are extensively tested via simulation for pH neutralization. The theoretical and simulation results show that both the proposed strategies can reduce the effect of modeling errors and disturbances, and thereby enhance the performance of NIMC for pH processes. (author)

ADAR RNA editing below the backbone.

Science.gov (United States)

Keegan, Liam; Khan, Anzer; Vukic, Dragana; O'Connell, Mary

2017-09-01

ADAR RNA editing enzymes ( a denosine d e a minases acting on R NA) that convert adenosine bases to inosines were first identified biochemically 30 years ago. Since then, studies on ADARs in genetic model organisms, and evolutionary comparisons between them, continue to reveal a surprising range of pleiotropic biological effects of ADARs. This review focuses on Drosophila melanogaster , which has a single Adar gene encoding a homolog of vertebrate ADAR2 that site-specifically edits hundreds of transcripts to change individual codons in ion channel subunits and membrane and cytoskeletal proteins. Drosophila ADAR is involved in the control of neuronal excitability and neurodegeneration and, intriguingly, in the control of neuronal plasticity and sleep. Drosophila ADAR also interacts strongly with RNA interference, a key antiviral defense mechanism in invertebrates. Recent crystal structures of human ADAR2 deaminase domain-RNA complexes help to interpret available information on Drosophila ADAR isoforms and on the evolution of ADARs from tRNA deaminase ADAT proteins. ADAR RNA editing is a paradigm for the now rapidly expanding range of RNA modifications in mRNAs and ncRNAs. Even with recent progress, much remains to be understood about these groundbreaking ADAR RNA modification systems. © 2017 Keegan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Effects of Internal Control Training on the Locus of Control of Some ...

African Journals Online (AJOL)

This study investigated the effect of internal control training on the locus of control of selected school going adolescents in Benin City. A sample size of 60 was drawn from two of the 27 co-educational schools in Oredo Local government area of Benin City. A table of random number technique was used to select subjects for ...

Inhibitory control in young children and its role in emerging internalization.

Science.gov (United States)

Kochanska, G; Murray, K; Jacques, T Y; Koenig, A L; Vandegeest, K A

1996-04-01

We examined inhibitory control as a quality of temperament that contributes to internalization. Children were assessed twice, at 26-41 months (N = 103) and at 43-56 months (N = 99), on repeated occasions, in multiple observational contexts and using parental reports. Comprehensive behavioral batteries incorporating multiple tasks were designed to measure inhibitory control at toddler and preschool age. They had good internal consistencies, corresponded with maternal ratings, and were developmentally sensitive. Individual children's performance was significantly correlated across both assessments, indicating stable individual differences. Girls surpassed boys at both ages. Children's internalization was observed while they were alone with prohibited objects, with a mundane chore, playing games that occasioned cheating, being induced to violate standards of conduct, and assessed using maternal reports. Inhibitory control was significantly associated with internalization, both contemporaneously and as a predictor in the longitudinal sense. The implications for considering children's temperament as a significant, yet often neglected contributor to developing internalization are discussed.

Specific micro RNA-regulated TetR-KRAB transcriptional control of transgene expression in viral vector-transduced cells.

Directory of Open Access Journals (Sweden)

Virginie Pichard

Full Text Available Precise control of transgene expression in a tissue-specific and temporally regulated manner is desirable for many basic and applied investigations gene therapy applications. This is important to regulate dose of transgene products and minimize unwanted effects. Previously described methods have employed tissue specific promoters, miRNA-based transgene silencing or tetR-KRAB-mediated suppression of transgene promoters. To improve on versatility of transgene expression control, we have developed expression systems that use combinations of a tetR-KRAB artificial transgene-repressor, endogenous miRNA silencing machinery and tissue specific promoters. Precise control of transgene expression was demonstrated in liver-, macrophage- and muscle-derived cells. Efficiency was also demonstrated in vivo in murine muscle. This multicomponent and modular regulatory system provides a robust and easily adaptable method for achieving regulated transgene expression in different tissue types. The improved precision of regulation will be useful for many gene therapy applications requiring specific spatiotemporal transgene regulation.

Immunoregulation by interference RNA (iRNA – mechanisms, role, perspective

Directory of Open Access Journals (Sweden)

Emilia Sikora

2011-08-01

Full Text Available The functioning of an organism depends on the precise control mechanisms, constantly adjusted to the actual state. Therefore, there is a need for efficient communication between both adjacent and distant cells, which may be executed by proteins such as hormones, neurotransmitters and cytokines. Recently another means of regulation has emerged – short regulatory RNAs (srRNAs. Although discovered only a couple of years ago, the mechanism of RNA interference has already become a topic of thousands of publications, defining its roles in both physiological and pathological processes, such as cancerogenesis and autoimmunization.RNAs regulating cell function may be coded in its genome (both exons and introns or be introduced from the external environment. In mammals microRNAs (miRNAs cooperate with proteins from the Ago/PIWI family to form effector ribonucleoprotein complexes, and owing to their complementarity to the target mRNA, control genes’ expression at the posttranscriptional level, either through the suppression of mRNA translation or through mRNA degradation.SrRNAs are crucial regulators throughout the development of immune cells, starting from hematopoietic stem cells, up to the effector cells of the adaptive immune response. Moreover, some of the regulatory cells perform their function by releasing miRNAs, which are then transported to the target cells, possibly enclosed in the exosomes.

Evaluating Internal Model Strength and Performance of Myoelectric Prosthesis Control Strategies.

Science.gov (United States)

Shehata, Ahmed W; Scheme, Erik J; Sensinger, Jonathon W

2018-05-01

On-going developments in myoelectric prosthesis control have provided prosthesis users with an assortment of control strategies that vary in reliability and performance. Many studies have focused on improving performance by providing feedback to the user but have overlooked the effect of this feedback on internal model development, which is key to improve long-term performance. In this paper, the strength of internal models developed for two commonly used myoelectric control strategies: raw control with raw feedback (using a regression-based approach) and filtered control with filtered feedback (using a classifier-based approach), were evaluated using two psychometric measures: trial-by-trial adaptation and just-noticeable difference. The performance of both strategies was also evaluated using Schmidt's style target acquisition task. Results obtained from 24 able-bodied subjects showed that although filtered control with filtered feedback had better short-term performance in path efficiency ( ), raw control with raw feedback resulted in stronger internal model development ( ), which may lead to better long-term performance. Despite inherent noise in the control signals of the regression controller, these findings suggest that rich feedback associated with regression control may be used to improve human understanding of the myoelectric control system.

Internal Interdecadal Variability in CMIP5 Control Simulations

Science.gov (United States)

Cheung, A. H.; Mann, M. E.; Frankcombe, L. M.; England, M. H.; Steinman, B. A.; Miller, S. K.

2015-12-01

Here we make use of control simulations from the CMIP5 models to quantify the amplitude of the interdecadal internal variability component in Atlantic, Pacific, and Northern Hemisphere mean surface temperature. We compare against estimates derived from observations using a semi-empirical approach wherein the forced component as estimated using CMIP5 historical simulations is removed to yield an estimate of the residual, internal variability. While the observational estimates are largely consistent with those derived from the control simulations for both basins and the Northern Hemisphere, they lie in the upper range of the model distributions, suggesting the possibility of differences between the amplitudes of observed and modeled variability. We comment on some possible reasons for the disparity.

Translational control by the DEAD Box RNA helicase belle regulates ecdysone-triggered transcriptional cascades.

Directory of Open Access Journals (Sweden)

Robert J Ihry

Full Text Available Steroid hormones act, through their respective nuclear receptors, to regulate target gene expression. Despite their critical role in development, physiology, and disease, however, it is still unclear how these systemic cues are refined into tissue-specific responses. We identified a mutation in the evolutionarily conserved DEAD box RNA helicase belle/DDX3 that disrupts a subset of responses to the steroid hormone ecdysone during Drosophila melanogaster metamorphosis. We demonstrate that belle directly regulates translation of E74A, an ets transcription factor and critical component of the ecdysone-induced transcriptional cascade. Although E74A mRNA accumulates to abnormally high levels in belle mutant tissues, no E74A protein is detectable, resulting in misregulation of E74A-dependent ecdysone response genes. The accumulation of E74A mRNA in belle mutant salivary glands is a result of auto-regulation, fulfilling a prediction made by Ashburner nearly 40 years ago. In this model, Ashburner postulates that, in addition to regulating secondary response genes, protein products of primary response genes like E74A also inhibit their own ecdysone-induced transcription. Moreover, although ecdysone-triggered transcription of E74A appears to be ubiquitous during metamorphosis, belle-dependent translation of E74A mRNA is spatially restricted. These results demonstrate that translational control plays a critical, and previously unknown, role in refining transcriptional responses to the steroid hormone ecdysone.

Control of the gut microbiome by fecal microRNA

Directory of Open Access Journals (Sweden)

Shirong Liu

2016-03-01

Full Text Available Since their discovery in the early 90s, microRNAs (miRNAs, small non-coding RNAs, have mainly been associated with posttranscriptional regulation of gene expression on a cell-autonomous level. Recent evidence has extended this role by adding inter-species communication to the manifold functional range. In our latest study [Liu S, et al., 2016, Cell Host & Microbe], we identified miRNAs in gut lumen and feces of both mice and humans. We found that intestinal epithelial cells (IEC and Hopx+ cells were the two main sources of fecal miRNA. Deficiency of IEC-miRNA resulted in gut dysbiosis and WT fecal miRNA transplantation restored the gut microbiota. We investigated potential mechanisms for this effect and found that miRNAs were able to regulate the gut microbiome. By culturing bacteria with miRNAs, we found that host miRNAs were able to enter bacteria, specifically regulate bacterial gene transcripts and affect bacterial growth. Oral administration of synthetic miRNA mimics affected specific bacteria in the gut. Our findings describe a previously unknown pathway by which the gut microbiome is regulated by the host and raises the possibility that miRNAs may be used therapeutically to manipulate the microbiome for the treatment of disease.

Clinical significance of LUNX mRNA, CK19 mRNA, CEA mRNA expression in detecting micrometastasis from lung cancer

International Nuclear Information System (INIS)

Zhu Guangying; Liu Delin; Chen Jie

2003-01-01

Objective: To evaluate the sensitivity, specificity and clinical significance of CK19 mRNA, CEA mRNA and LUNX mRNA for detecting micrometastasis by sampling the peripheral blood and regional lymph nodes of lung cancer patients. Methods: Reverse transcriptase chain reaction (RT-PCR) was used to detect LUNX mRNA, CK19 mRNA, CEA mRNA for micrometastasis by sampling the peripheral blood of 48 lung cancer patients and 44 regional lymph nodes of such patients treated by curative resection. Peripheral blood of 30 patients with pulmonary benign lesions and 10 normal healthy volunteers and lymph nodes of 6 patients with benign pulmonary diseases served as control. Results: 1) LUNX mRNA, CK19 mRNA, CEA mRNA were expressed in all (35/35) lung cancer tissues. 2) In the peripheral blood from 48 lung cancer patients, 30 (62.5%) were positive for LUNX mRNA, 24 (50.0%) positive for CK19 mRNA and 32(66.7%) positive for CEA mRNA. The positive detection rates of micrometastasis in 44 lymph nodes from lung cancer patients were 36.4% (16 out of 44) for LUNX mRNA, 27.3% (12 out of 44) for CK19 mRNA and 40.9% (18 out of 44) for CEA mRNA. 3) In the 30 blood samples from patients with pulmonary benign diseases, 2 (6.7%) expressed CK19 mRNA, but none expressed LUNX mRNA or CEA mRNA. All the 3 molecular markers were negative in the 10 blood samples from healthy volunteers. In 11 lymph nodes from patients with pulmonary benign lesions, none was positive for any of the three markers. 4) In 44 regional lymph nodes from lung cancer patients, 6 (13.6%) were positive for metastasis by histopathological examination, with a positive rate significantly lower than that of the RT-PCR (P<0.05). 5) The micrometastatic positive rate in the peripheral blood of 40 non-small cell lung cancer (NSCLC) patients was significantly related to TNM stage (P=0.01). Conclusions: LUNX mRNA, CK19 MRNA, CEA mRNA are all appropriate target genes for the detection of micrometastasis from lung cancer. LUNX mRNA and CEA mRNA

Retrospective exposure assessment and quality control in an international multi-centre case-control study

DEFF Research Database (Denmark)

Tinnerberg, H; Heikkilä, P; Huici-Montagud, A

2003-01-01

The paper presents the exposure assessment method and quality control procedure used in an international, multi-centre case-control study within a joint Nordic and Italian cohort. This study was conducted to evaluate whether occupational exposure to carcinogens influenced the predictivity of high...... was higher among the original assessors (the assessor from the same country as the subject) than the average prevalence assessed by the other four in the quality control round. The original assessors classified more job situations as exposed than the others. Several reasons for this are plausible: real...... country-specific differences, differences in information available to the home assessor and the others and misunderstandings or difficulties in translation of information. To ensure the consistency of exposure assessments in international retrospective case-control studies it is important to have a well...

Reactive arthritis in relation to internal derangements of the temporomandibular joint: a case control study.

Science.gov (United States)

Lund, Bodil; Holmlund, Anders; Wretlind, Bengt; Jalal, Shah; Rosén, Annika

2015-09-01

The aim of this study was to find out if reactive arthritis was involved in the aetiology of chronic closed lock of the temporomandibular joint (TMJ) by looking for bacterial antigens in the synovial membrane of the TMJ, and by studying the antibody serology and carriage of human leucocyte antigen (HLA) B27 in patients with chronic closed lock. Patients with reciprocal clicking and healthy subjects acted as controls. We studied a total of 43 consecutive patients, 15 with chronic closed lock, 13 with reciprocal clicking, and 15 healthy controls with no internal derangements of the TMJ. Venous blood samples were collected from all subjects for measurement of concentrations of HLA tissue antigen and serology against Chlamydia trachomatis, Yersinia enterocolitica, Salmonella spp., Campylobacter jejuni, and Mycoplasma pneumoniae. Samples of synovial tissue from patients with closed lock and reciprocal clicking were obtained during discectomy and divided into two pieces, the first of which was tested by strand displacement amplification for the presence of C trachomatis, and the second of which was analysed for the presence of species-specific bacterial DNA using 16s rRNA pan-polymerase chain reaction (PCR). There were no significant differences between the groups in the incidence of antibodies against M pneumoniae, Salmonella spp. or Y enterocolitica. No patient had antibodies towards C trachomatis or C jejuni. We found no bacterial DNA in the synovial fluid from any patient. The HLA B27 antigen was present in 2/15 subjects in both the closed lock and control groups, and none in the reciprocal clicking group. In conclusion, reactive arthritis does not seem to be the mechanism of internal derangement of the TMJ. Copyright © 2015. Published by Elsevier Ltd.

Reduced mRNA expression of PTGDS in peripheral blood mononuclear cells of rapid-cycling bipolar disorder patients compared with healthy control subjects

DEFF Research Database (Denmark)

Munkholm, Klaus; Peijs, Lone; Kessing, Lars Vedel

2015-01-01

was measured in 37 rapid-cycling bipolar disorder patients and 40 age- and gender-matched healthy control subjects using reverse transcription quantitative real-time polymerase chain reaction. Repeated measurements of PTGDS and AKR1C3 mRNA expression were obtained in various affective states during 6-12 months...... and compared with repeated measurements in healthy control subjects. RESULTS: Adjusted for age and gender, PTGDS mRNA expression was down-regulated in rapid-cycling bipolar disorder patients in a euthymic, depressive, and manic/hypomanic state compared with healthy control subjects. No difference in PTGDS m...

2013 International Conference on Mechatronics and Automatic Control Systems

CERN Document Server

2014-01-01

This book examines mechatronics and automatic control systems. The book covers important emerging topics in signal processing, control theory, sensors, mechanic manufacturing systems and automation. The book presents papers from the 2013 International Conference on Mechatronics and Automatic Control Systems held in Hangzhou, China on August 10-11, 2013. .

Theoretical grounds of internal audit in the system of state financial control in Ukraine

Directory of Open Access Journals (Sweden)

Dikan Larysa V.

2013-03-01

Full Text Available The article considers modern directions of reformation of the system of state financial control connected with introduction of the state internal financial control. It considers economic essence of the state internal financial control in the context of its components. It justifies the place of the internal audit in the system of the state internal financial control in Ukraine. It considers existing definitions of internal audit in legislative acts. It generalises views of scientists on interpretation of the “internal audit” notion. It provides definitions united in approaches. It conducts a critical analysis of generalised approaches. It offers the authors’ view on the essence of internal audit in budget institutions, which has certain positive features compared to existing ones.

Control of a Modular Multilevel Converter STATCOM under internal and external unbalances

DEFF Research Database (Denmark)

Tsolaridis, Georgios; Kontos, E.; Parikh, Harsh

2016-01-01

This paper develops a complete control scheme for the Modular Multilevel Converter (MMC) in a STATCOM application. The focus is laid on the internal balancing of the converter and its reliable operation under internal mismatches as well as under external unbalanced conditions. The leg energy...... and the simulation results verified the capability to provide maximum reactive power to the AC grid while maintaining internal balance through the individual control of each arm energy level....... controller ensures that the sum of the capacitor voltages of each phase are equal. An intuitive arm energy controller is also implemented which allows the decoupled control of the energy levels of every arm. The control performance of the STATCOM was evaluated under asymmetrical grid faults...

25 CFR 542.14 - What are the minimum internal control standards for the cage?

Science.gov (United States)

2010-04-01

... 25 Indians 2 2010-04-01 2010-04-01 false What are the minimum internal control standards for the... SERVICES MINIMUM INTERNAL CONTROL STANDARDS § 542.14 What are the minimum internal control standards for... and/or procedures that provide at least the level of control described by the standards in this...

25 CFR 542.8 - What are the minimum internal control standards for pull tabs?

Science.gov (United States)

2010-04-01

... 25 Indians 2 2010-04-01 2010-04-01 false What are the minimum internal control standards for pull... SERVICES MINIMUM INTERNAL CONTROL STANDARDS § 542.8 What are the minimum internal control standards for... and/or procedures that provide at least the level of control described by the standards in this...

Imaging of RNA in situ hybridization by atomic force microscopy

NARCIS (Netherlands)

Kalle, W.H.J.; Macville, M.V.E.; van de Corput, M.P.C.; de Grooth, B.G.; Tanke, H.J.; Raap, A.K.

In this study we investigated the possibility of imaging internal cellular molecules after cytochemical detection with atomic force microscopy (AFM). To this end, rat 9G and HeLa cells were hybridized with haptenized probes for 28S ribosomal RNA, human elongation factor mRNA and cytomegalovirus

In vivo efficacy and off-target effects of locked nucleic acid (LNA) and unlocked nucleic acid (UNA) modified siRNA and small internally segmented interfering RNA (sisiRNA) in mice bearing human tumor xenografts

NARCIS (Netherlands)

Mook, O. R. F.; Vreijling, Jeroen; Wengel, Suzy L.; Wengel, Jesper; Zhou, Chuanzheng; Chattopadhyaya, Jyoti; Baas, Frank; Fluiter, Kees

2010-01-01

The clinical use of small interfering RNA (siRNA) is hampered by poor uptake by tissues and instability in circulation. In addition, off-target effects pose a significant additional problem for therapeutic use of siRNA. Chemical modifications of siRNA have been reported to increase stability and

Viral Delivery of dsRNA for Control of Insect Agricultural Pests and Vectors of Human Disease: Prospects and Challenges

Directory of Open Access Journals (Sweden)

Anna Kolliopoulou

2017-06-01

Full Text Available RNAi is applied as a new and safe method for pest control in agriculture but efficiency and specificity of delivery of dsRNA trigger remains a critical issue. Various agents have been proposed to augment dsRNA delivery, such as engineered micro-organisms and synthetic nanoparticles, but the use of viruses has received relatively little attention. Here we present a critical view of the potential of the use of recombinant viruses for efficient and specific delivery of dsRNA. First of all, it requires the availability of plasmid-based reverse genetics systems for virus production, of which an overview is presented. For RNA viruses, their application seems to be straightforward since dsRNA is produced as an intermediate molecule during viral replication, but DNA viruses also have potential through the production of RNA hairpins after transcription. However, application of recombinant virus for dsRNA delivery may not be straightforward in many cases, since viruses can encode RNAi suppressors, and virus-induced silencing effects can be determined by the properties of the encoded RNAi suppressor. An alternative is virus-like particles that retain the efficiency and specificity determinants of natural virions but have encapsidated non-replicating RNA. Finally, the use of viruses raises important safety issues which need to be addressed before application can proceed.

Internal audit: the expert in providing comfort to the audit committee. The case of risk management and internal control

OpenAIRE

G. SARENS; I. DE BEELDE

2006-01-01

This study investigates to what extent audit committees feel uncomfortable about risk management and internal control, and focuses on how internal audit can be the expert in providing comfort in these areas, building upon the sociology of professions literature. Four case studies reveal that audit committees need comfort with respect to the control environment. Thanks to their internal position, their familiarity with the company, and their position close to people across the company, interna...

Developmental regulation of Xenopus 5S RNA genes

International Nuclear Information System (INIS)

Wormington, W.M.; Schlissel, M.; Brown, D.D.

1983-01-01

In this paper it is demonstrated that the actively transcribed fraction of somatic 5S RNA genes in somatic-cell chromatin is complexed stably with all required factors, so that the addition of only purified RNA polymerase III is needed to support somatic 5S RNA synthesis in vitro. Oocyte 5S RNA genes in somatic-cell chromatin appear to lack these factors, since their activation in salt-washed somatic-cell chromatin depends on exogeneous transciption factors in addition to RNA polymerase III. The developmental control of 5S RNA genes is established over a period beginning with the onset of 5S RNA synthesis in late blastula embryos, and this control is reproduced in vitro using chromatin templates isolated from appropriate stages. We propose that a decreasing concentration of the 5S-specific transcription factor during embryogenesis contributes to the inactivation of oocyte 5S RNA genes. 12 references, 4 figures, 1 table

How short RNAs impact the human ribonuclease Dicer activity: putative regulatory feedback-loops and other RNA-mediated mechanisms controlling microRNA processing.

Science.gov (United States)

Koralewska, Natalia; Hoffmann, Weronika; Pokornowska, Maria; Milewski, Marek; Lipinska, Andrea; Bienkowska-Szewczyk, Krystyna; Figlerowicz, Marek; Kurzynska-Kokorniak, Anna

2016-01-01

Ribonuclease Dicer plays a pivotal role in RNA interference pathways by processing long double-stranded RNAs and single-stranded hairpin RNA precursors into small interfering RNAs (siRNAs) and microRNAs (miRNAs), respectively. While details of Dicer regulation by a variety of proteins are being elucidated, less is known about non-protein factors, e.g. RNA molecules, that may influence this enzyme's activity. Therefore, we decided to investigate the question of whether the RNA molecules can function not only as Dicer substrates but also as its regulators. Our previous in vitro studies indicated that the activity of human Dicer can be influenced by short RNA molecules that either bind to Dicer or interact with its substrates, or both. Those studies were carried out with commercial Dicer preparations. Nevertheless, such preparations are usually not homogeneous enough to carry out more detailed RNA-binding studies. Therefore, we have established our own system for the production of human Dicer in insect cells. In this manuscript, we characterize the RNA-binding and RNA-cleavage properties of the obtained preparation. We demonstrate that Dicer can efficiently bind single-stranded RNAs that are longer than ~20-nucleotides. Consequently, we revisit possible scenarios of Dicer regulation by single-stranded RNA species ranging from ~10- to ~60-nucleotides, in the context of their binding to this enzyme. Finally, we show that siRNA/miRNA-sized RNAs may affect miRNA production either by binding to Dicer or by participating in regulatory feedback-loops. Altogether, our studies suggest a broad regulatory role of short RNAs in Dicer functioning.

Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding.

Science.gov (United States)

Vecerek, Branislav; Moll, Isabella; Bläsi, Udo

2007-02-21

The Fe2+-dependent Fur protein serves as a negative regulator of iron uptake in bacteria. As only metallo-Fur acts as an autogeneous repressor, Fe2+scarcity would direct fur expression when continued supply is not obviously required. We show that in Escherichia coli post-transcriptional regulatory mechanisms ensure that Fur synthesis remains steady in iron limitation. Our studies revealed that fur translation is coupled to that of an upstream open reading frame (uof), translation of which is downregulated by the non-coding RNA (ncRNA) RyhB. As RyhB transcription is negatively controlled by metallo-Fur, iron depletion creates a negative feedback loop. RyhB-mediated regulation of uof-fur provides the first example for indirect translational regulation by a trans-encoded ncRNA. In addition, we present evidence for an iron-responsive decoding mechanism of the uof-fur entity. It could serve as a backup mechanism of the RyhB circuitry, and represents the first link between iron availability and synthesis of an iron-containing protein.

ORGANIZATIONAL SYSTEMS OF INTERNAL FINANCIAL CONTROL IN THE WORLD

Directory of Open Access Journals (Sweden)

Mihaela – Lavinia CIOBĂNICĂ

2014-04-01

Full Text Available Beyond the multitude of definitions, internal control is found in the centre of managerial concerns worldwide. This amplification of interest towards internal control has its origin in a series of events, of which two can be mentioned: the growing business complexity and dispersal activity centres, which led to the growth and development of the delegation of competence, the only way which enables the responsible to exercise powers from a distance and entirely, bringing together the components needed by its delegates. Regulatory domain, which has not ceased to expand: laws, regulations, rules, professional constraints, budgetary and social – all these have increasingly limited the decision makers, through a network of rules that must be respected. Consequently, what can be done to be safe from any punishment and to ensure constant watch over the essentials? To answer these questions, and many others, experts in the field have taken initiatives that have enabled them to define with precision the specific internal control and to set goals, creating the famous models: COSO and CoCo.

Translational control of human acetyl-CoA carboxylase 1 mRNA is mediated by an internal ribosome entry site in response to ER stress, serum deprivation or hypoxia mimetic CoCl2.

Science.gov (United States)

Damiano, Fabrizio; Testini, Mariangela; Tocci, Romina; Gnoni, Gabriele V; Siculella, Luisa

2018-04-01

Acetyl-CoA carboxylase 1 (ACC1) is a cytosolic enzyme catalyzing the rate limiting step in de novo fatty acid biosynthesis. There is mounting evidence showing that ACC1 is susceptible to dysregulation and that it is over-expressed in liver diseases associated with lipid accumulation and in several cancers. In the present study, ACC1 regulation at the translational level is reported. Using several experimental approaches, the presence of an internal ribosome entry site (IRES) has been established in the 5' untranslated region (5' UTR) of the ACC1 mRNA. Transfection experiments with the ACC1 5' UTR inserted in a dicistronic reporter vector show a remarkable increase in the downstream cistron translation, through a cap-independent mechanism. The endoplasmic reticulum (ER) stress condition and the related unfolded protein response (UPR), triggered by treatment with thapsigargin and tunicamycin, cause an increase of the cap-independent translation of ACC1 mRNA in HepG2 cells, despite the overall reduction in global protein synthesis. Other stress conditions, such as serum starvation and incubation with hypoxia mimetic agent CoCl 2 , up-regulate ACC1 expression in HepG2 cells at the translational level. Overall, these findings indicate that the presence of an IRES in the ACC1 5' UTR allows ACC1 mRNA translation in conditions that are inhibitory to cap-dependent translation. A potential involvement of the cap-independent translation of ACC1 in several pathologies, such as obesity and cancer, has been discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

Control Modes in International Service Operations: The Propensity to Franchise

OpenAIRE

Karin Fladmoe-Lindquist; Laurent L. Jacque

1995-01-01

What determines a service firm's organizational choice between equity-based control and franchising? This question, which has elicited some theoretical answers and a few empirical tests in a domestic setting, has never been addressed in an international context before. This study explains the mode of control chosen in terms of a theoretical framework which borrows from agency theory and transaction cost analysis. The propensity to franchise internationally was found to be directly related to ...

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

DEFF Research Database (Denmark)

Peng, Zhiyu; Cheng, Yanbing; Tan, Bertrand Chin-Ming

2012-01-01

a computational pipeline that carefully controls for false positives while calling RNA editing events from genome and whole-transcriptome data of the same individual. We identified 22,688 RNA editing events in noncoding genes and introns, untranslated regions and coding sequences of protein-coding genes. Most......RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ∼767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed...... changes (∼93%) converted A to I(G), consistent with known editing mechanisms based on adenosine deaminase acting on RNA (ADAR). We also found evidence of other types of nucleotide changes; however, these were validated at lower rates. We found 44 editing sites in microRNAs (miRNAs), suggesting a potential...

Impact of Public Internal Financial Control on Public Administration in Croatia

Directory of Open Access Journals (Sweden)

Vesna VAŠIČEK

2010-04-01

Full Text Available The PIFC /Public Internal Financial Control/ was developed by the European Commission. PIFC is set of principles internal financial controls system established for the purpose of controlling, auditing, supervise on the use of national budget and European Union budget and funds. Also, in order to support candidate countries in their internal control system reforms in the public sector. Therefore, it is expected for the candidate countries to establish and develop the system of internal financial controls according to the concept which was in that field developed by the European Union based on International Standards and the best practice of European countries. Since the year 2003 the Republic of Croatia undertakes intensive activities on the establishment and development of the internal financial control system according with the regulation of European Union. In keeping with the set concept, the Republic of Croatia undertook numerous activities during the past six years to create all the necessary assumptions for the establishment and development of the system, including: the adoption of the initial strategic documents; drafting of laws; the creation of organisational capacities and human resources; and the implementation of the system with budget users at central government and local levels. In this paper we will present phases of implementation PIFC in Croatian Public Sector. Through this phases we will show impact that PIFC has on development of New Public Management in Croatia and changes in organizational structure and human resource that are caused during this process. Also, we will give critical opinion of that process and problems which occur during implementation. In this paper we will present approach in implementation of PIFC in Slovenia and Bosnia and Herzegovina and compare this with implementation in Croatia.

New RNA playgrounds : non-coding RNAs and RNA-binding proteins control cellular processes

NARCIS (Netherlands)

Kedde, Martijn

2009-01-01

Het eiwit Dead End noodzakelijk is voor het overleven van geslachtscellen. Het beschermt enkele genen tegen blokkades door microRNA’s. Dat stelt onderzoeker Martijn Kedde van het NKI-AVL in zijn proefschrift. Kedde promoveert donderdag 22 januari. MicroRNA’s, kleine stukjes RNA, blokkeren de

RNA secondary structure prediction using soft computing.

Science.gov (United States)

Ray, Shubhra Sankar; Pal, Sankar K

2013-01-01

Prediction of RNA structure is invaluable in creating new drugs and understanding genetic diseases. Several deterministic algorithms and soft computing-based techniques have been developed for more than a decade to determine the structure from a known RNA sequence. Soft computing gained importance with the need to get approximate solutions for RNA sequences by considering the issues related with kinetic effects, cotranscriptional folding, and estimation of certain energy parameters. A brief description of some of the soft computing-based techniques, developed for RNA secondary structure prediction, is presented along with their relevance. The basic concepts of RNA and its different structural elements like helix, bulge, hairpin loop, internal loop, and multiloop are described. These are followed by different methodologies, employing genetic algorithms, artificial neural networks, and fuzzy logic. The role of various metaheuristics, like simulated annealing, particle swarm optimization, ant colony optimization, and tabu search is also discussed. A relative comparison among different techniques, in predicting 12 known RNA secondary structures, is presented, as an example. Future challenging issues are then mentioned.

An Inverse Optimal Control Approach to Explain Human Arm Reaching Control Based on Multiple Internal Models.

Science.gov (United States)

Oguz, Ozgur S; Zhou, Zhehua; Glasauer, Stefan; Wollherr, Dirk

2018-04-03

Human motor control is highly efficient in generating accurate and appropriate motor behavior for a multitude of tasks. This paper examines how kinematic and dynamic properties of the musculoskeletal system are controlled to achieve such efficiency. Even though recent studies have shown that the human motor control relies on multiple models, how the central nervous system (CNS) controls this combination is not fully addressed. In this study, we utilize an Inverse Optimal Control (IOC) framework in order to find the combination of those internal models and how this combination changes for different reaching tasks. We conducted an experiment where participants executed a comprehensive set of free-space reaching motions. The results show that there is a trade-off between kinematics and dynamics based controllers depending on the reaching task. In addition, this trade-off depends on the initial and final arm configurations, which in turn affect the musculoskeletal load to be controlled. Given this insight, we further provide a discomfort metric to demonstrate its influence on the contribution of different inverse internal models. This formulation together with our analysis not only support the multiple internal models (MIMs) hypothesis but also suggest a hierarchical framework for the control of human reaching motions by the CNS.

Regulatory mechanisms of RNA function: emerging roles of DNA repair enzymes.

Science.gov (United States)

Jobert, Laure; Nilsen, Hilde

2014-07-01

The acquisition of an appropriate set of chemical modifications is required in order to establish correct structure of RNA molecules, and essential for their function. Modification of RNA bases affects RNA maturation, RNA processing, RNA quality control, and protein translation. Some RNA modifications are directly involved in the regulation of these processes. RNA epigenetics is emerging as a mechanism to achieve dynamic regulation of RNA function. Other modifications may prevent or be a signal for degradation. All types of RNA species are subject to processing or degradation, and numerous cellular mechanisms are involved. Unexpectedly, several studies during the last decade have established a connection between DNA and RNA surveillance mechanisms in eukaryotes. Several proteins that respond to DNA damage, either to process or to signal the presence of damaged DNA, have been shown to participate in RNA quality control, turnover or processing. Some enzymes that repair DNA damage may also process modified RNA substrates. In this review, we give an overview of the DNA repair proteins that function in RNA metabolism. We also discuss the roles of two base excision repair enzymes, SMUG1 and APE1, in RNA quality control.

17 CFR 240.17Ad-13 - Annual study and evaluation of internal accounting control.

Science.gov (United States)

2010-04-01

... internal accounting control. 240.17Ad-13 Section 240.17Ad-13 Commodity and Securities Exchanges SECURITIES... Company Rules § 240.17Ad-13 Annual study and evaluation of internal accounting control. (a) Accountant's... accountant concerning the transfer agent's system of internal accounting control and related procedures for...

Literature-based condition-specific miRNA-mRNA target prediction.

Directory of Open Access Journals (Sweden)

Minsik Oh

Full Text Available miRNAs are small non-coding RNAs that regulate gene expression by binding to the 3'-UTR of genes. Many recent studies have reported that miRNAs play important biological roles by regulating specific mRNAs or genes. Many sequence-based target prediction algorithms have been developed to predict miRNA targets. However, these methods are not designed for condition-specific target predictions and produce many false positives; thus, expression-based target prediction algorithms have been developed for condition-specific target predictions. A typical strategy to utilize expression data is to leverage the negative control roles of miRNAs on genes. To control false positives, a stringent cutoff value is typically set, but in this case, these methods tend to reject many true target relationships, i.e., false negatives. To overcome these limitations, additional information should be utilized. The literature is probably the best resource that we can utilize. Recent literature mining systems compile millions of articles with experiments designed for specific biological questions, and the systems provide a function to search for specific information. To utilize the literature information, we used a literature mining system, BEST, that automatically extracts information from the literature in PubMed and that allows the user to perform searches of the literature with any English words. By integrating omics data analysis methods and BEST, we developed Context-MMIA, a miRNA-mRNA target prediction method that combines expression data analysis results and the literature information extracted based on the user-specified context. In the pathway enrichment analysis using genes included in the top 200 miRNA-targets, Context-MMIA outperformed the four existing target prediction methods that we tested. In another test on whether prediction methods can re-produce experimentally validated target relationships, Context-MMIA outperformed the four existing target prediction

Integration of the Pokeweed miRNA and mRNA Transcriptomes Reveals Targeting of Jasmonic Acid-Responsive Genes

Directory of Open Access Journals (Sweden)

Kira C. M. Neller

2018-05-01

Full Text Available The American pokeweed plant, Phytolacca americana, displays broad-spectrum resistance to plant viruses and is a heavy metal hyperaccumulator. However, little is known about the regulation of biotic and abiotic stress responses in this non-model plant. To investigate the control of miRNAs in gene expression, we sequenced the small RNA transcriptome of pokeweed treated with jasmonic acid (JA, a hormone that mediates pathogen defense and stress tolerance. We predicted 145 miRNAs responsive to JA, most of which were unique to pokeweed. These miRNAs were low in abundance and condition-specific, with discrete expression change. Integration of paired mRNA-Seq expression data enabled us to identify correlated, novel JA-responsive targets that mediate hormone biosynthesis, signal transduction, and pathogen defense. The expression of approximately half the pairs was positively correlated, an uncommon finding that we functionally validated by mRNA cleavage. Importantly, we report that a pokeweed-specific miRNA targets the transcript of OPR3, novel evidence that a miRNA regulates a JA biosynthesis enzyme. This first large-scale small RNA study of a Phytolaccaceae family member shows that miRNA-mediated control is a significant component of the JA response, associated with widespread changes in expression of genes required for stress adaptation.

Seryl-tRNA Synthetases in Translation and Beyond

Directory of Open Access Journals (Sweden)

Marko Močibob

2016-06-01

in three cellular compartments: cytosol, mitochondria and chloroplasts. Plant cytosolic SerRSs showed broad tRNASer specificity and flexibility, unlike SerRSs from other organisms. High fidelity of SerRS dually targeted to mitochondria and chloroplasts indicated its importance in plant organellar quality control. This work is licensed under a Creative Commons Attribution 4.0 International License.

RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans.

Science.gov (United States)

Son, Heehwa G; Seo, Mihwa; Ham, Seokjin; Hwang, Wooseon; Lee, Dongyeop; An, Seon Woo A; Artan, Murat; Seo, Keunhee; Kaletsky, Rachel; Arey, Rachel N; Ryu, Youngjae; Ha, Chang Man; Kim, Yoon Ki; Murphy, Coleen T; Roh, Tae-Young; Nam, Hong Gil; Lee, Seung-Jae V

2017-03-09

Long-lived organisms often feature more stringent protein and DNA quality control. However, whether RNA quality control mechanisms, such as nonsense-mediated mRNA decay (NMD), which degrades both abnormal as well as some normal transcripts, have a role in organismal aging remains unexplored. Here we show that NMD mediates longevity in C. elegans strains with mutations in daf-2/insulin/insulin-like growth factor 1 receptor. We find that daf-2 mutants display enhanced NMD activity and reduced levels of potentially aberrant transcripts. NMD components, including smg-2/UPF1, are required to achieve the longevity of several long-lived mutants, including daf-2 mutant worms. NMD in the nervous system of the animals is particularly important for RNA quality control to promote longevity. Furthermore, we find that downregulation of yars-2/tyrosyl-tRNA synthetase, an NMD target transcript, by daf-2 mutations contributes to longevity. We propose that NMD-mediated RNA surveillance is a crucial quality control process that contributes to longevity conferred by daf-2 mutations.

Transcript levels, alternative splicing and proteolytic cleavage of TFIIIA control 5S rRNA accumulation during Arabidopsis thaliana development.

Science.gov (United States)

Layat, Elodie; Cotterell, Sylviane; Vaillant, Isabelle; Yukawa, Yasushi; Tutois, Sylvie; Tourmente, Sylvette

2012-07-01

Ribosome biogenesis is critical for eukaryotic cells and requires coordinated synthesis of the protein and rRNA moieties of the ribosome, which are therefore highly regulated. 5S ribosomal RNA, an essential component of the large ribosomal subunit, is transcribed by RNA polymerase III and specifically requires transcription factor IIIA (TFIIIA). To obtain insight into the regulation of 5S rRNA transcription, we have investigated the expression of 5S rRNA and the exon-skipped (ES) and exon-including (EI) TFIIIA transcripts, two transcript isoforms that result from alternative splicing of the TFIIIA gene, and TFIIIA protein amounts with respect to requirements for 5S rRNA during development. We show that 5S rRNA quantities are regulated through distinct but complementary mechanisms operating through transcriptional and post-transcriptional control of TFIIIA transcripts as well as at the post-translational level through proteolytic cleavage of the TFIIIA protein. During the reproductive phase, high expression of the TFIIIA gene together with low proteolytic cleavage contributes to accumulation of functional, full-length TFIIIA protein, and results in 5S rRNA accumulation in the seed. In contrast, just after germination, the levels of TFIIIA-encoding transcripts are low and stable. Full-length TFIIIA protein is undetectable, and the level of 5S rRNA stored in the embryo progressively decreases. After day 4, in correlation with the reorganization of 5S rDNA chromatin to a mature state, full-length TFIIIA protein with transcriptional activity accumulates and permits de novo transcription of 5S rRNA. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

The Pseudomonas aeruginosa catabolite repression control protein Crc is devoid of RNA binding activity.

Science.gov (United States)

Milojevic, Tetyana; Grishkovskaya, Irina; Sonnleitner, Elisabeth; Djinovic-Carugo, Kristina; Bläsi, Udo

2013-01-01

The Crc protein has been shown to mediate catabolite repression control in Pseudomonas, leading to a preferential assimilation of carbon sources. It has been suggested that Crc acts as a translational repressor of mRNAs, encoding functions involved in uptake and breakdown of different carbon sources. Moreover, the regulatory RNA CrcZ, the level of which is increased in the presence of less preferred carbon sources, was suggested to bind to and sequester Crc, resulting in a relief of catabolite repression. Here, we determined the crystal structure of Pseudomonas aeruginosa Crc, a member of apurinic/apyrimidinic (AP) endonuclease family, at 1.8 Å. Although Crc displays high sequence similarity with its orthologs, there are amino acid alterations in the area corresponding to the active site in AP proteins. Unlike typical AP endonuclease family proteins, Crc has a reduced overall positive charge and the conserved positively charged amino-acid residues of the DNA-binding surface of AP proteins are partially substituted by negatively charged, polar and hydrophobic residues. Crc protein purified to homogeneity from P. aeruginosa did neither display DNase activity, nor did it bind to previously identified RNA substrates. Rather, the RNA chaperone Hfq was identified as a contaminant in His-tagged Crc preparations purified by one step Ni-affinity chromatography from Escherichia coli, and was shown to account for the RNA binding activity observed with the His-Crc preparations. Taken together, these data challenge a role of Crc as a direct translational repressor in carbon catabolite repression in P. aeruginosa.

The internal initiation of translation in bovine viral diarrhea virus RNA depends on the presence of an RNA pseudoknot upstream of the initiation codon.

Science.gov (United States)

Moes, Lorin; Wirth, Manfred

2007-11-22

Bovine viral diarrhea virus (BVDV) is the prototype representative of the pestivirus genus in the Flaviviridae family. It has been shown that the initiation of translation of BVDV RNA occurs by an internal ribosome entry mechanism mediated by the 5' untranslated region of the viral RNA 1. The 5' and 3' boundaries of the IRES of the cytopathic BVDV NADL have been mapped and it has been suggested that the IRES extends into the coding of the BVDV polyprotein 2. A putative pseudoknot structure has been recognized in the BVDV 5'UTR in close proximity to the AUG start codon. A pseudoknot structure is characteristic for flavivirus IRESes and in the case of the closely related classical swine fever virus (CSFV) and the more distantly related Hepatitis C virus (HCV) pseudoknot function in translation has been demonstrated. To characterize the BVDV IRESes in detail, we studied the BVDV translational initiation by transfection of dicistronic expression plasmids into mammalian cells. A region coding for the amino terminus of the BVDV SD-1 polyprotein contributes considerably to efficient initiation of translation. The translation efficiency mediated by the IRES of BVDV strains NADL and SD-1 approximates the poliovirus type I IRES directed translation in BHK cells. Compared to the poliovirus IRES increased expression levels are mediated by the BVDV IRES of strain SD-1 in murine cell lines, while lower levels are observed in human cell lines. Site directed mutagenesis revealed that a RNA pseudoknot upstream of the initiator AUG is an important structural element for IRES function. Mutants with impaired ability to base pair in stem I or II lost their translational activity. In mutants with repaired base pairing either in stem 1 or in stem 2 full translational activity was restored. Thus, the BVDV IRES translation is dependent on the pseudoknot integrity. These features of the pestivirus IRES are reminiscent of those of the classical swine fever virus, a pestivirus, and the

The internal initiation of translation in bovine viral diarrhea virus RNA depends on the presence of an RNA pseudoknot upstream of the initiation codon

Directory of Open Access Journals (Sweden)

Moes Lorin

2007-11-01

Full Text Available Abstract Background Bovine viral diarrhea virus (BVDV is the prototype representative of the pestivirus genus in the Flaviviridae family. It has been shown that the initiation of translation of BVDV RNA occurs by an internal ribosome entry mechanism mediated by the 5' untranslated region of the viral RNA 1. The 5' and 3' boundaries of the IRES of the cytopathic BVDV NADL have been mapped and it has been suggested that the IRES extends into the coding of the BVDV polyprotein 2. A putative pseudoknot structure has been recognized in the BVDV 5'UTR in close proximity to the AUG start codon. A pseudoknot structure is characteristic for flavivirus IRESes and in the case of the closely related classical swine fever virus (CSFV and the more distantly related Hepatitis C virus (HCV pseudoknot function in translation has been demonstrated. Results To characterize the BVDV IRESes in detail, we studied the BVDV translational initiation by transfection of dicistronic expression plasmids into mammalian cells. A region coding for the amino terminus of the BVDV SD-1 polyprotein contributes considerably to efficient initiation of translation. The translation efficiency mediated by the IRES of BVDV strains NADL and SD-1 approximates the poliovirus type I IRES directed translation in BHK cells. Compared to the poliovirus IRES increased expression levels are mediated by the BVDV IRES of strain SD-1 in murine cell lines, while lower levels are observed in human cell lines. Site directed mutagenesis revealed that a RNA pseudoknot upstream of the initiator AUG is an important structural element for IRES function. Mutants with impaired ability to base pair in stem I or II lost their translational activity. In mutants with repaired base pairing either in stem 1 or in stem 2 full translational activity was restored. Thus, the BVDV IRES translation is dependent on the pseudoknot integrity. These features of the pestivirus IRES are reminiscent of those of the classical

Constitution of a centralised data base for the internal quality control in radiotherapy; Constitution d'une base de donnees centralisee pour le controle de qualite interne en radiotherapie

Energy Technology Data Exchange (ETDEWEB)

Fau, P.; Rodrigues, C.; Ruchaud, R.; Bravetti, J. [Centre Prive de Radiotherapie de Metz, 57 - Metz (France)

2009-10-15

The objective of this project was to implement a centralised data base of internal quality control in radiotherapy according to the criteria of the decree of A.f.s.s.a.p.s. (French agency of sanitary safety of health products on 27 july 2007, about the internal quality control of external radiotherapy facilities. The software on one year meets the objectives: compliance by comparison with A.f.s.s.a.p.s. criteria but particularly optimization of the centralisation and analysis of the internal quality controls. (N.C.)

[Correlation between five RNA markers of rat's skin and PMI at different temperatures].

Science.gov (United States)

Pan, Hui; Zhang, Heng; Lü, Ye-hui; Ma, Jian-long; Ma, Kai-jun; Chen, Long

2014-08-01

To explore the correlation between postmortem interval (PMI) and five RNA markers of rat's skin--β-actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S ribosomal RNA(18S rRNA), 5S ribosomal RNA (5S rRNA), and microRNA-203 (miR-203), at different temperatures. Eighteen SD rats were randomly divided into three environmental temperature groups: 4 °C, 15 °C and 35 °C, respectively. Skin samples were taken at 11 time points from 0 h to 120 h post-mortem. The total RNA was extracted from the skin samples and the five RNA levels were detected by real-time fluorescent quantitative PCR. Proper internal reference was selected by geNorm software. Regression analysis of the RNA markers was conducted by GraphPad software. 5S rRNA and miR-203 were most suitable internal references. A good linear relationship between PMI and RNA levels (β-actin and GAPDH) was observed in two groups (4 °C and 15 °C), whereas the S type curve relationship between the expression levels of the two markers (β-actin and GAPDH) and PMI was observed in the 35 °C group. The partial linear relationship between 18S rRNA and PMI was observed in the groups (15 °C and 35 °C). Skin could be a suitable material for extracting RNA. The RNA expression levels of β-actin and GAPDH correlate well with PMI, and these RNA markers of skin tissue could be additional indice for the estimation of PMI.

49 CFR 225.33 - Internal Control Plans.

Science.gov (United States)

2010-10-01

... official business. Each railroad shall amend its Internal Control Plan, as necessary, to reflect any..., incident, injury or illness will not be permitted or tolerated and will result in some stated disciplinary... paragraph (a)(1). Each railroad shall have procedures to process complaints from any person about the policy...

Lin28a uses distinct mechanisms of binding to RNA and affects miRNA levels positively and negatively.

Science.gov (United States)

Nowak, Jakub Stanislaw; Hobor, Fruzsina; Downie Ruiz Velasco, Angela; Choudhury, Nila Roy; Heikel, Gregory; Kerr, Alastair; Ramos, Andres; Michlewski, Gracjan

2017-03-01

Lin28a inhibits the biogenesis of let-7 miRNAs by triggering the polyuridylation and degradation of their precursors by terminal uridylyltransferases TUT4/7 and 3'-5' exoribonuclease Dis3l2, respectively. Previously, we showed that Lin28a also controls the production of neuro-specific miRNA-9 via a polyuridylation-independent mechanism. Here we reveal that the sequences and structural characteristics of pre-let-7 and pre-miRNA-9 are eliciting two distinct modes of binding to Lin28a. We present evidence that Dis3l2 controls miRNA-9 production. Finally, we show that the constitutive expression of untagged Lin28a during neuronal differentiation in vitro positively and negatively affects numerous other miRNAs. Our findings shed light on the role of Lin28a in differentiating cells and on the ways in which one RNA-binding protein can perform multiple roles in the regulation of RNA processing. © 2017 Nowak et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Methods and compositions for controlling gene expression by RNA processing

Science.gov (United States)

Doudna, Jennifer A.; Qi, Lei S.; Haurwitz, Rachel E.; Arkin, Adam P.

2017-08-29

The present disclosure provides nucleic acids encoding an RNA recognition sequence positioned proximal to an insertion site for the insertion of a sequence of interest; and host cells genetically modified with the nucleic acids. The present disclosure also provides methods of modifying the activity of a target RNA, and kits and compositions for carrying out the methods.

Detecting Internal Control Problems Based on COSO and Islamic Perspective: Case on SMEs

Directory of Open Access Journals (Sweden)

Yuniarti Hidayah Suyoso Putra

2014-03-01

Full Text Available Objective – The presence of Small Medium Enterprises (SMEs has been able to be livelihoods sources and absorb more labor, even though it has a relative smaller contribution of additional value compared to the Large-scale Enterprises. The number of economic actors of SMEs spread across area from urban to rural. However, SMEs have faced several serious problems. These problems are caused by the unique characteristics of SMEs itself. First, lack of managerial skills due to limited human resources and lack of monitoring which it is rarely conducted by the manager or the owner. Second, lack of information and technology to carry out operations. Both problems have great impacts in lack of internal controls. Third, SMEs also face problems in developing business scale, limited access to capital to the banks and financial institutions due to the lack of transparency. Therefore, this research aimed to detect to what extent of the problems arising in the application and assessment of internal controls performed by SMEs.Method – The research employs descriptive qualitative research method through direct observation, interview and business documentation owned by the company. Research materials are 29 SMEs consisting of 19 trading SMEs and 10 service SMEs. All SMEs are located in Malang city. Detection of application and assessment of internal controls in this study is based on the COSO framework and the Islamic perspective.Result – Internal control activities indicators apply the five principles of COSO framework which focused on three layers. First layer is self-assessment control area. Second layer is environment control area and the third layer is independent control area. While the Islamic perspective is focused on the internal control of business activities based on the Qur'an and Hadith. The results derive from application and assessment based on COSO framework and Islamic perspectives are complementary in improving the practice of internal

A microRNA feedback loop regulates global microRNA abundance during aging.

Science.gov (United States)

Inukai, Sachi; Pincus, Zachary; de Lencastre, Alexandre; Slack, Frank J

2018-02-01

Expression levels of many microRNAs (miRNAs) change during aging, notably declining globally in a number of organisms and tissues across taxa. However, little is known about the mechanisms or the biological relevance for this change. We investigated the network of genes that controls miRNA transcription and processing during C. elegans aging. We found that miRNA biogenesis genes are highly networked with transcription factors and aging-associated miRNAs. In particular, miR-71, known to influence life span and itself up-regulated during aging, represses alg-1 /Argonaute expression post-transcriptionally during aging. Increased ALG-1 abundance in mir-71 loss-of-function mutants led to globally increased miRNA expression. Interestingly, these mutants demonstrated widespread mRNA expression dysregulation and diminished levels of variability both in gene expression and in overall life span. Thus, the progressive molecular decline often thought to be the result of accumulated damage over an organism's life may be partially explained by a miRNA-directed mechanism of age-associated decline. © 2018 Inukai et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences.

Science.gov (United States)

Santamaria, Monica; Fosso, Bruno; Licciulli, Flavio; Balech, Bachir; Larini, Ilaria; Grillo, Giorgio; De Caro, Giorgio; Liuni, Sabino; Pesole, Graziano

2018-01-04

A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels. As metabarcoding data analysis rely on the availability of a well-curated barcode reference resource, a comprehensive collection of ITS1 sequences supplied with robust taxonomies, is highly needed. To address this issue, we created ITSoneDB (available at http://itsonedb.cloud.ba.infn.it/) which in its current version hosts 985 240 ITS1 sequences spanning over 134 000 eukaryotic species. Each ITS1 is mapped on the NCBI reference taxonomy with its start and end positions precisely annotated. ITSoneDB has been developed in agreement to the FAIR guidelines by enabling the users to query and download its content through a simple web-interface and access relevant metadata by cross-linking to European Nucleotide Archive. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

17 CFR 229.308T - (Item 308T) Internal control over financial reporting.

Science.gov (United States)

2010-04-01

... over financial reporting. 229.308T Section 229.308T Commodity and Securities Exchanges SECURITIES AND... § 229.308T (Item 308T) Internal control over financial reporting. Note to Item 308T: This is a special... internal control over financial reporting. Provide a report of management on the registrant's internal...

A novel TBP-TAF complex on RNA polymerase II-transcribed snRNA genes.

Science.gov (United States)

Zaborowska, Justyna; Taylor, Alice; Roeder, Robert G; Murphy, Shona

2012-01-01

Initiation of transcription of most human genes transcribed by RNA polymerase II (RNAP II) requires the formation of a preinitiation complex comprising TFIIA, B, D, E, F, H and RNAP II. The general transcription factor TFIID is composed of the TATA-binding protein and up to 13 TBP-associated factors. During transcription of snRNA genes, RNAP II does not appear to make the transition to long-range productive elongation, as happens during transcription of protein-coding genes. In addition, recognition of the snRNA gene-type specific 3' box RNA processing element requires initiation from an snRNA gene promoter. These characteristics may, at least in part, be driven by factors recruited to the promoter. For example, differences in the complement of TAFs might result in differential recruitment of elongation and RNA processing factors. As precedent, it already has been shown that the promoters of some protein-coding genes do not recruit all the TAFs found in TFIID. Although TAF5 has been shown to be associated with RNAP II-transcribed snRNA genes, the full complement of TAFs associated with these genes has remained unclear. Here we show, using a ChIP and siRNA-mediated approach, that the TBP/TAF complex on snRNA genes differs from that found on protein-coding genes. Interestingly, the largest TAF, TAF1, and the core TAFs, TAF10 and TAF4, are not detected on snRNA genes. We propose that this snRNA gene-specific TAF subset plays a key role in gene type-specific control of expression.

INTERMARS: User-controlled international management system

Science.gov (United States)

Schmitt, Harrison H.

1986-01-01

Existing international space law as well as the best interest of all nations are consistent with the establishment of a user-based international organization, herein called INTERMARS. INTERMARS would provide access to facilities and services at a Martian base which would be of high functional potential, quality, safety, and reliability. These opportunities would be available on an open and nondiscriminatory basis to all peaceful users and investors. INTERMARS is a model organization concept tailored to provide cooperative international management of a Martian base for the benefit of its members, users, and investors. Most importantly, INTERMARS would provide such management through a sharing of both sovereignty and opportunity rather then unilateral control by any one nation or set of competing nations. Through an Assembly of Parties, a Board of Governors, a Board of Users and Investors, and a Director General, INTERMARS would meet its primary goal as it would be in the self-interest of all members, users, and investors to do so. The internal structure and philosophy of INTERMARS would provide not only for all participants to have representation in decisions affecting its activities, but also would insure effective and responsive management. Surely this is the precedent wished for, to establish for mankind at the now not-so-distant shores of the new ocean of space.

Construction of an internal amplification control for Mycobacterium ...

African Journals Online (AJOL)

Elham

2013-07-03

Jul 3, 2013 ... million and 10 bacteria and the most suitable internal control concentration for the mix was ... But the risk of contamination is unavoidable in normal ..... Contamination Management: Implication for Broad-Range Ribosomal.

Internal control in an EDI environment.

OpenAIRE

Bae, Dal Hyeoung

1991-01-01

Approved for public release; distribution in unlimited. Electronic Data Interchange(EDI) is the electronic transmission of standard business documents in machine-readable format between parent companies and respective trading partners. As the use of EDI has grown, there have been the associated risks due to an uncontrolled environment. Accordingly, the necessity for effective internal controls in an EDI environment is on the rise. This thesis evaluates and analyzes the feasi...

International consensus principles for ethical wildlife control.

Science.gov (United States)

Dubois, Sara; Fenwick, Nicole; Ryan, Erin A; Baker, Liv; Baker, Sandra E; Beausoleil, Ngaio J; Carter, Scott; Cartwright, Barbara; Costa, Federico; Draper, Chris; Griffin, John; Grogan, Adam; Howald, Gregg; Jones, Bidda; Littin, Kate E; Lombard, Amanda T; Mellor, David J; Ramp, Daniel; Schuppli, Catherine A; Fraser, David

2017-08-01

Human-wildlife conflicts are commonly addressed by excluding, relocating, or lethally controlling animals with the goal of preserving public health and safety, protecting property, or conserving other valued wildlife. However, declining wildlife populations, a lack of efficacy of control methods in achieving desired outcomes, and changes in how people value animals have triggered widespread acknowledgment of the need for ethical and evidence-based approaches to managing such conflicts. We explored international perspectives on and experiences with human-wildlife conflicts to develop principles for ethical wildlife control. A diverse panel of 20 experts convened at a 2-day workshop and developed the principles through a facilitated engagement process and discussion. They determined that efforts to control wildlife should begin wherever possible by altering the human practices that cause human-wildlife conflict and by developing a culture of coexistence; be justified by evidence that significant harms are being caused to people, property, livelihoods, ecosystems, and/or other animals; have measurable outcome-based objectives that are clear, achievable, monitored, and adaptive; predictably minimize animal welfare harms to the fewest number of animals; be informed by community values as well as scientific, technical, and practical information; be integrated into plans for systematic long-term management; and be based on the specifics of the situation rather than negative labels (pest, overabundant) applied to the target species. We recommend that these principles guide development of international, national, and local standards and control decisions and implementation. © 2017 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Internal Capital Market Controls and Financial Performance in Multidivisional Firms.

OpenAIRE

Hill, Charles W L

1988-01-01

It is proposed that, within the population of M-form firms, the control systems necessary to realize economic benefits from interrelationships between subunits o f a firm are incompatible with the systems necessary to realize benef its from an M-form type internal capital market. This hypothesis is t ested on 156 large U.K. firms. Questionnaire data are used to classif y the firms according to their internal control characteristics. The findings provide tentative support for the hypothesis. C...

Delivery Pathway Regulation of 3′,3″-Bis-Peptide-siRNA Conjugate via Nanocarrier Architecture Engineering

Directory of Open Access Journals (Sweden)

Jing Sun

2018-03-01

Full Text Available Small interfering RNA (siRNA has been continuously explored for clinical applications. However, neither nanocarriers nor conjugates have been able to remove the obstacles. In this study, we employed a combined nanochemistry strategy to optimize its delivery dilemma, where different interactions and assembly modes were cooperatively introduced into the forming process of siRNA/lipids nanoplexes. In the nanoplexes, the 3′,3″-bis-peptide-siRNA conjugate (pp-siRNA and gemini-like cationic lipids (CLDs were employed as dual regulators to improve their bio-behavior. We demonstrated that the “cicada pupa”-shaped nanoplexes of MT-pp-siRNA/CLDs (MT represented the mixed two-phase method exhibited more compact multi-sandwich structure (∼25 layers, controllable size (∼150 nm, and lower zeta potential (∼22 mV than other comparable nanoplexes and presented an increased siRNA protection and stability. Significantly, the nanoplex was internalized into melanoma cells by almost caveolae-mediated endocytosis and macropinocytosis (∼99.46%, and later reduced/avoided lysosomal degradation. Finally, the nanoplex facilitated the silencing of mRNA of the mutant B-Raf protein (down by ∼60%. In addition, pp-siRNA had a high intracellular sustainability, a significantly prolonged circulating time, and accumulation in tumor tissues in vivo. Our results have demonstrated that the combined approach can improve the intracellular fate of siRNA, which opens up novel avenues for efficient siRNA delivery.

Accumulation of dsRNA in endosomes contributes to inefficient RNA interference in the fall armyworm, Spodoptera frugiperda.

Science.gov (United States)

Yoon, June-Sun; Gurusamy, Dhandapani; Palli, Subba Reddy

2017-11-01

RNA interference (RNAi) efficiency varies among insects studied. The barriers for successful RNAi include the presence of double-stranded ribonucleases (dsRNase) in the lumen and hemolymph that could potentially digest double-stranded RNA (dsRNA) and the variability in the transport of dsRNA into and within the cells. We recently showed that the dsRNAs are transported into lepidopteran cells, but they are not processed into small interference RNAs (siRNAs) because they are trapped in acidic bodies. In the current study, we focused on the identification of acidic bodies in which dsRNAs accumulate in Sf9 cells. Time-lapse imaging studies showed that dsRNAs enter Sf9 cells and accumulate in acidic bodies within 20 min after their addition to the medium. CypHer-5E-labeled dsRNA also accumulated in the midgut and fat body dissected from Spodoptera frugiperda larvae with similar patterns observed in Sf9 cells. Pharmacological inhibitor assays showed that the dsRNAs use clathrin mediated endocytosis pathway for transport into the cells. We investigated the potential dsRNA accumulation sites employing LysoTracker and double labeling experiments using the constructs to express a fusion of green fluorescence protein with early or late endosomal marker proteins and CypHer-5E-labeled dsRNA. Interestingly, CypHer-5E-labeled dsRNA accumulated predominantly in early and late endosomes. These data suggest that entrapment of internalized dsRNA in endosomes is one of the major factors contributing to inefficient RNAi response in lepidopteran insects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Thermoresponsive pegylated bubble liposome nanovectors for efficient siRNA delivery via endosomal escape

KAUST Repository

Alamoudi, Kholod

2017-05-19

Improving the delivery of siRNA into cancer cells via bubble liposomes. Designing a thermoresponsive pegylated liposome through the introduction of ammonium bicarbonate salt into liposomes so as to control their endosomal escape for gene therapy.A sub-200 nm nanovector was fully characterized and examined for cellular uptake, cytotoxicity, endosomal escape and gene silencing.The siRNA-liposomes were internalized into cancer cells within 5 min and then released siRNAs in the cytosol prior to lysosomal degradation upon external temperature elevation. This was confirmed by confocal bioimaging and gene silencing reaching up to 90% and further demonstrated by the protein inhibition of both target genes.The thermoresponsiveness of ammonium bicarbonate containing liposomes enabled the rapid endosomal escape of the particles and resulted in an efficient gene silencing.

Thermoresponsive pegylated bubble liposome nanovectors for efficient siRNA delivery via endosomal escape

KAUST Repository

Alamoudi, Kholod; Martins, Patricia; Croissant, Jonas G.; Patil, Sachin; Omar, Haneen; Khashab, Niveen M.

2017-01-01

Improving the delivery of siRNA into cancer cells via bubble liposomes. Designing a thermoresponsive pegylated liposome through the introduction of ammonium bicarbonate salt into liposomes so as to control their endosomal escape for gene therapy.A sub-200 nm nanovector was fully characterized and examined for cellular uptake, cytotoxicity, endosomal escape and gene silencing.The siRNA-liposomes were internalized into cancer cells within 5 min and then released siRNAs in the cytosol prior to lysosomal degradation upon external temperature elevation. This was confirmed by confocal bioimaging and gene silencing reaching up to 90% and further demonstrated by the protein inhibition of both target genes.The thermoresponsiveness of ammonium bicarbonate containing liposomes enabled the rapid endosomal escape of the particles and resulted in an efficient gene silencing.

Conference Scene: Advances in RNA nanotechnology promise to transform medicine.

Science.gov (United States)

Leontis, Neocles; Sweeney, Blake; Haque, Farzin; Guo, Peixuan

2013-07-01

The second International Conference on RNA Nanotechnology and Therapeutics was held on the 3-5 April in Lexington, (KY, USA). The focus of the conference was on leveraging the unique chemical and biological properties of RNA to promote transformative advances in medicine. The conference convened more than 200 researchers from 15 countries and many disciplines, roughly double the participants of the first conference. While many presentations focused on the design, assembly and characterization of RNA nanoparticles and their uses for in vivo and in vitro sensing, diagnosis and therapy, others covered a variety of relevant areas of RNA biology and chemistry.

Interactions between the HIV-1 Unspliced mRNA and Host mRNA Decay Machineries

Directory of Open Access Journals (Sweden)

Daniela Toro-Ascuy

2016-11-01

Full Text Available The human immunodeficiency virus type-1 (HIV-1 unspliced transcript is used both as mRNA for the synthesis of structural proteins and as the packaged genome. Given the presence of retained introns and instability AU-rich sequences, this viral transcript is normally retained and degraded in the nucleus of host cells unless the viral protein REV is present. As such, the stability of the HIV-1 unspliced mRNA must be particularly controlled in the nucleus and the cytoplasm in order to ensure proper levels of this viral mRNA for translation and viral particle formation. During its journey, the HIV-1 unspliced mRNA assembles into highly specific messenger ribonucleoproteins (mRNPs containing many different host proteins, amongst which are well-known regulators of cytoplasmic mRNA decay pathways such as up-frameshift suppressor 1 homolog (UPF1, Staufen double-stranded RNA binding protein 1/2 (STAU1/2, or components of miRNA-induced silencing complex (miRISC and processing bodies (PBs. More recently, the HIV-1 unspliced mRNA was shown to contain N6-methyladenosine (m6A, allowing the recruitment of YTH N6-methyladenosine RNA binding protein 2 (YTHDF2, an m6A reader host protein involved in mRNA decay. Interestingly, these host proteins involved in mRNA decay were shown to play positive roles in viral gene expression and viral particle assembly, suggesting that HIV-1 interacts with mRNA decay components to successfully accomplish viral replication. This review summarizes the state of the art in terms of the interactions between HIV-1 unspliced mRNA and components of different host mRNA decay machineries.

Internal and external force-based impedance control for cooperative manipulation

NARCIS (Netherlands)

Heck, D.J.F.; Kostic, D.; Denasi, A.; Nijmeijer, H.

2013-01-01

An asymptotically stable cascaded control algorithm is proposed for cooperative manipulation of a common object. This algorithm controls motion and internal forces of the object, as well as the contact forces between the object and environment. The motion of each manipulator is controlled using an

Implementation guide of internal contamination control

International Nuclear Information System (INIS)

Balter, Henia; Savio, Eduardo; Souto, Beatriz

1994-01-01

A review of current methods of contamination control for radioisotopes 131I, 125I and 99mTc, periodic control of personnel exposed to radiation.Maximum permissible body burden (Mpbb) for each radionuclide,radiotoxicity as danger of internal contamination directly related with Let, type of radiation,Ali values for various radionuclides and external irradiation as an opposed factor.Effective half life,examples, 99mTc in urine,iodine in thyroid caption, 99m Tc absorption by skin and mouth. Procedure of control and calculation by measurement of urine samples in a gamma spectrometer. Iodine thyroid caption by monitoring of thyroid with a solid NaI(TI)scintillator taking as background radiation the activity of upper leg muscle. Standard solutions are prepared to fill a thyroid phantoms.Results must not be higher than Mpbb of corresponding radionuclide.Bibliography

EVALUATING IMPLEMENTION OF GOVERNMENTAL PROVISION ON NO. 60 YEAR 2008 FOR GOVERNMENTAL INTERNAL CONTROL IN BOARD OF FINANCE AND DEVELOPMENT CONTROL OF SOUTH SULAWESI

OpenAIRE

Mediaty

2012-01-01

The purpose of this research is to evaluate Governmental Internal Control System in Board of Finance and Development Control of South Sulawesi. Governmental Internal Control System is a management control of government in achieving purpose of the state with the issuance of Governmental Provision No. 60 year 2008. List of Governmental Internal Control Test consists of five parts in accordance with the Internal Control System elements are: Control Environment, Risk Assessment, Control Activitie...

2nd International Conference on Mechatronics and Automatic Control

CERN Document Server

2015-01-01

This book examines mechatronics and automatic control systems. The book covers important emerging topics in signal processing, control theory, sensors, mechanic manufacturing systems and automation. The book presents papers from the second International Conference on Mechatronics and Automatic Control Systems held in Beijing, China on September 20-21, 2014. Examines how to improve productivity through the latest advanced technologies Covering new systems and techniques in the broad field of mechatronics and automatic control systems.

Structural imprints in vivo decode RNA regulatory mechanisms.

Science.gov (United States)

Spitale, Robert C; Flynn, Ryan A; Zhang, Qiangfeng Cliff; Crisalli, Pete; Lee, Byron; Jung, Jong-Wha; Kuchelmeister, Hannes Y; Batista, Pedro J; Torre, Eduardo A; Kool, Eric T; Chang, Howard Y

2015-03-26

Visualizing the physical basis for molecular behaviour inside living cells is a great challenge for biology. RNAs are central to biological regulation, and the ability of RNA to adopt specific structures intimately controls every step of the gene expression program. However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles include only two of the four nucleotides that make up RNA. Here we present a novel biochemical approach, in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE), which enables the first global view, to our knowledge, of RNA secondary structures in living cells for all four bases. icSHAPE of the mouse embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguish different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved from in vitro conditions, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA-binding proteins or RNA-modification sites that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N(6)-methyladenosine (m(6)A) modification genome wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.

Detection and comparison of microRNA expression in the serum of Doberman Pinschers with dilated cardiomyopathy and healthy controls.

Science.gov (United States)

Steudemann, Carola; Bauersachs, Stefan; Weber, Karin; Wess, Gerhard

2013-01-17

Dilated cardiomyopathy (DCM) is the most common heart disease in Doberman Pinschers. MicroRNAs (miRNAs) are short non-coding RNAs playing important roles in gene regulation. Different miRNA expression patterns have been described for DCM in humans and might represent potential diagnostic markers. There are no studies investigating miRNA expression profiles in canine DCM. The aims of this study were to screen the miRNA expression profile of canine serum using miRNA microarray and to compare expression patterns of a group of Doberman Pinschers with DCM and healthy controls. Eight Doberman Pinschers were examined by echocardiography and 24-hour-ECG and classified as healthy (n=4) or suffering from DCM (n=4). Total RNA was extracted from serum and hybridized on a custom-designed 8x60k miRNA microarray (Agilent) containing probes for 1368 individual miRNAs. Although total RNA concentrations were very low in serum samples, 404 different miRNAs were detectable with sufficient signal intensity on miRNA microarray. 22 miRNAs were differentially expressed in the two groups (p1.5), but did not reach statistical significance after multiple testing correction (false discovery rate adjusted p>0.05). Five miRNAs were selected for further analysis using quantitative Real-Time RT-PCR (qPCR) assays. No significant differences were found using specific miRNA qPCR assays (p>0.05). Numerous miRNAs can be detected in canine serum. Between healthy and DCM dogs, miRNA expression changes could be detected, but the results did not reach statistical significance most probably due to the small group size. miRNAs are potential new circulating biomarkers in veterinary medicine and should be investigated in larger patient groups and additional canine diseases.

Risk-oriented internal control: The essence, management methods at small enterprises

OpenAIRE

Piskunov, V. A.; Manyayeva, V. A.; Tatarovskaya, T. E.; Bychkova, E. Y.

2016-01-01

The research topic relevance is inspired by necessity to develop theoretical and methodical provisions on the internal control system, risk-based management at small enterprises and to prove application feasibility, using economic-mathematical methods its implementation. The purpose of this research is to develop theoretical and methodical approaches to internal control system formation in small businesses, generating reliable and relevant information on the commercial organization activities...

25 CFR 542.11 - What are the minimum internal control standards for pari-mutuel wagering?

Science.gov (United States)

2010-04-01

... 25 Indians 2 2010-04-01 2010-04-01 false What are the minimum internal control standards for pari... INTERIOR HUMAN SERVICES MINIMUM INTERNAL CONTROL STANDARDS § 542.11 What are the minimum internal control... documentation and/or procedures that provide at least the level of control described by the standards in this...

Internal versus External Control of Reinforcement: A Review of the Locus of Control Construct

Science.gov (United States)

Kormanik, Martin B.; Rocco, Tonette S.

2009-01-01

One aspect of personality, perceptions of internal versus external control of reinforcement, shifts under conditions of change. This review of the literature examines the relationship between planned organizational change and locus of control. The review includes literature from the disciplines of clinical and social psychology, adult development,…

Turbine Energy Evaluation by internal dimensional control

International Nuclear Information System (INIS)

Mediavilla, F.

2000-01-01

To maintain the optimum thermal performance in a high level throughout the life of the turbines requires a good testing program, proper analysis of the test data, and a steam path audit during turbine overhauls. If from operating data analysis collected during the performance test before the outage shows that the efficiency of the turbine is coming down, the steam path audit, that is an internal inspection and a dimensional control of the internals, identity and quantity causes of performance degradation like, seal leakages, excessive clearances, solid particle erosion damages, blades deposits and other losses. The steam path audit assigns the heat rate penalties associated with each of these individual losses to the total degradation. This are used to make cost-effective maintenance decisions during the course of the overhaul. After repairs, a closing steam path audit is conducted during the re assembly of the turbine in order to predict return to service condition of the machine and to provide a quality control check on outage repairs. (Author)

The Puf-family RNA-binding protein Puf2 controls sporozoite conversion to liver stages in the malaria parasite.

Directory of Open Access Journals (Sweden)

Katja Müller

Full Text Available Malaria is a vector-borne infectious disease caused by unicellular, obligate intracellular parasites of the genus Plasmodium. During host switch the malaria parasite employs specialized latent stages that colonize the new host environment. Previous work has established that gametocytes, sexually differentiated stages that are taken up by the mosquito vector, control expression of genes required for mosquito colonization by translational repression. Sexual parasite development is controlled by a DEAD-box RNA helicase of the DDX6 family, termed DOZI. Latency of sporozoites, the transmission stage injected during an infectious blood meal, is controlled by the eIF2alpha kinase IK2, a general inhibitor of protein synthesis. Whether RNA-binding proteins participate in translational regulation in sporozoites remains to be studied. Here, we investigated the roles of two RNA-binding proteins of the Puf-family, Plasmodium Puf1 and Puf2, during sporozoite stage conversion. Our data reveal that, in the rodent malaria parasite P. berghei, Puf2 participates in the regulation of IK2 and inhibits premature sporozoite transformation. Inside mosquito salivary glands puf2⁻ sporozoites transform over time to round forms resembling early intra-hepatic stages. As a result, mutant parasites display strong defects in initiating a malaria infection. In contrast, Puf1 is dispensable in vivo throughout the entire Plasmodium life cycle. Our findings support the notion of a central role for Puf2 in parasite latency during switch between the insect and mammalian hosts.

MicroRNA Implication in Cancer

Directory of Open Access Journals (Sweden)

Iker BADIOLA

2010-03-01

Full Text Available MicroRNAs (miRNA are a new class of posttranscriptional regulators. These small non-coding RNAs regulate the expression of target mRNA transcripts and are linked to several human disease such as Alzheimer, cancer or heart disease. But it has been the cancer disease which has experimented the major number of studies of miRNA linked to the disease progression. In the last years it has been reported the deregulation pattern of the miRNAs in malignant cells which have disrupted the control of the proliferation, differentiation or apoptosis. The evidence of the presence of specific miRNA deregulated in concrete cancer types has become the miRNAs like possible biomarkers and therapeutic targets. The specific miRNA patterns deregulated in concrete cancer cell types open new opportunities to the diagnosis and therapy.

El Control y la Confianza: dos rivales en las "International Joint Ventures"

Directory of Open Access Journals (Sweden)

Francisco Puig Blanco

2013-02-01

Full Text Available Las empresas conjuntas internacionales(International Joint Ventures se caracterizan pordos factores íntimamente relacionados: el control y eloportunismo. En este trabajo, trataremos de analizarla relación entre ambos factores y estudiaremos quétipos de control ayudarían a prevenir o a reducirel oportunismo en este tipo de empresas. Además,trataremos de identificar las ventajas e inconvenientesasociados al control y analizaremos el caso de unaInternational Joint Venture formada por dos empresas,una española y la otra americana, cuyo fracaso se debió,en gran parte, a la ausencia de control (confianza y aloportunismo.   ABSTRACT International Joint Ventures are distinguished bytwo closely related factors: control and opportunism.In this paper we will try to analyze the relationshipbetween both factors and we will study what controlswould help prevent or reduce opportunism in thisclass of enterprises. Besides, we will attempt to identifythe advantages and inconveniences associated withcontrol, and analyze one case of an International JointVenture comprised by two companies, a Spanish and anAmerican one whose failure was largely due to lack ofcontrol (trust and opportunism.

The Information Support of the Internal Control of Receivables and Accounts Payable

Directory of Open Access Journals (Sweden)

Akimova Natalia S.

2017-11-01

Full Text Available The article substantiates the necessity of organization of internal audit of receivables and accounts payable at the trade enterprises, which will allow the decision-makers to obtain confirmation of the validity of the accountance data. The theoretical substantiation of bases of monitoring together with necessity of its carrying out in the accountance system of accounts receivable and accounts payable was considered. The scheme on interaction of subjects of control has been proposed, in terms of which each of the examined subjects of control is in constant information interaction with other divisions. To effectively control the movement of debt, trade organizations are encouraged to use the forms of operational reporting developed as part of improving internal audit as a tool to enhance the efficiency of the internal control system.

Optimal closed-loop identification test design for internal model control

NARCIS (Netherlands)

Zhu, Y.; Bosch, van den P.P.J.

2000-01-01

In this work, optimal closed-loop test design for control is studied. Simple design formulas are derived based on the asymptotic theory of Ljung. The control scheme used is internal model control (IMC) and the design constraint is the power of the process output or that of the reference signal. The

Dynamic Blue Light-Inducible T7 RNA Polymerases (Opto-T7RNAPs) for Precise Spatiotemporal Gene Expression Control.

Science.gov (United States)

Baumschlager, Armin; Aoki, Stephanie K; Khammash, Mustafa

2017-11-17

Light has emerged as a control input for biological systems due to its precise spatiotemporal resolution. The limited toolset for light control in bacteria motivated us to develop a light-inducible transcription system that is independent from cellular regulation through the use of an orthogonal RNA polymerase. Here, we present our engineered blue light-responsive T7 RNA polymerases (Opto-T7RNAPs) that show properties such as low leakiness of gene expression in the dark state, high expression strength when induced with blue light, and an inducible range of more than 300-fold. Following optimization of the system to reduce expression variability, we created a variant that returns to the inactive dark state within minutes once the blue light is turned off. This allows for precise dynamic control of gene expression, which is a key aspect for most applications using optogenetic regulation. The regulators, which only require blue light from ordinary light-emitting diodes for induction, were developed and tested in the bacterium Escherichia coli, which is a crucial cell factory for biotechnology due to its fast and inexpensive cultivation and well understood physiology and genetics. Opto-T7RNAP, with minor alterations, should be extendable to other bacterial species as well as eukaryotes such as mammalian cells and yeast in which the T7 RNA polymerase and the light-inducible Vivid regulator have been shown to be functional. We anticipate that our approach will expand the applicability of using light as an inducer for gene expression independent from cellular regulation and allow for a more reliable dynamic control of synthetic and natural gene networks.

Detection of hepatitis G virus-RNA (HGV-RNA) in serum of patients with HBV hepatitis

International Nuclear Information System (INIS)

Zhu Jingfei; Hang Shangrong; Chen Min; Pu Xiangke; Wang Yongzhong; Zhou Guoping

2007-01-01

Objective: To investigate the incidence of HGV infection in patients with HBV hepatitis and any possible adverse effect of the superinfection. Methods: Serum HGV-RNA expression was examined with PCR in 1104 patients with HBV hepatitis and 251 controls. Results: The positive rate of HGV-RNA in HBV hepatitis patients was not significantly different from that in controls (3.17% vs 2.79%, P>0.05). Among the patients with HBV hepatitis, HGV-RNA positive rate in patients with chronic hepatitis was significantly higher than that in patients with acute hepatitis (4.78% vs 0.96, P<0.05). Conclusion: HGV infection might be presented as non-symptomatic carriers or other mild form of hepatitis. The incidence of HGV infection was not especially high in HBV hepatitis patients, however, concomitant HGV and HBV infection might predispose to development of chronicity. (authors)

The microRNA effector RNA-induced silencing complex in hidradenitis suppurativa: a significant dysregulation within active inflammatory lesions.

Science.gov (United States)

Hessam, S; Sand, M; Skrygan, M; Bechara, Falk G

2017-09-01

Recently, we could show that the expression levels of the key regulators of the microRNA (miRNA) maturation and transport were dysregulated in inflamed hidradenitis suppurativa (HS) tissue (Heyam et al. in Wiley Interdiscip Rev RNA 6:271-289, 2015). The RNA-induced silencing complex (RISC) is the central element of the miRNA pathway and regulates miRNA formation and function. We investigated the expression of the RISC components, namely transactivation-responsive RNA-binding protein-1 (TRBP1), TRBP2, protein activator (PACT) of the interferon-induced protein kinase R, Argonaute RISC Catalytic Component-1 (AGO1) and Component-2 (AGO2), metadherin, and staphylococcal nuclease and Tudor domain-containing-1 (SND1) in inflamed HS tissue compared to healthy and psoriatic controls by real-time reverse transcription polymerase chain reaction. Expression levels of all investigated components were significantly lower in lesional HS skin (n = 18) compared to healthy controls (n = 10). TRBP1, PACT, AGO1, AGO2, and SND1 expression levels were significantly down-regulated in lesional HS skin compared to healthy-appearing perilesional skin (n = 7). TRBP2 and SND1 expression levels were significantly lower in healthy-appearing perilesional skin compared to healthy controls. In lesional HS skin, expression levels of PACT, AGO1, and AGO2 were significantly lower compared to psoriatic skin (n = 10). In summary, our data showed that all investigated components of RISC are dysregulated in the skin of HS patients, providing support for the hypothesis that miRNAs may have a pathological role in the inflammatory pathogenesis of HS.

Methods of internal control in integrated management accounting system of the enterprise

Directory of Open Access Journals (Sweden)

Shevelev A.E.

2017-01-01

Full Text Available The purpose of internal control procedure of material and information flows is expression of independent opinion about accounting of material and information flows of the organization, development of recommendations about elimination of detected violations and preparing data to implement automated management accounting system, based on integrated system. Internal control procedure of material and information flows in the enterprise can solve complex of problems about identifying deficiencies in accounting, searching for reserves using information resources, identifying opportunities for implementation of automated management accounting system at the enterprise. Internal control was planned and conducted thus to argue that management statements are free of misstatement, and information flows provide required operability of the entire system. Internal control was carried out on a sample basis and included examining, on a test basis evidence supporting the amounts and disclosures in management reports. The disclosure of information about innovative activities, assessment of compliance with the principles and rules of accounting used in the preparation of management reporting, the review of key performance indicators, as well as evaluating the presentation of management reports are presented.

Constitution of a centralised data base for the internal quality control in radiotherapy

International Nuclear Information System (INIS)

Fau, P.; Rodrigues, C.; Ruchaud, R.; Bravetti, J.

2009-01-01

The objective of this project was to implement a centralised data base of internal quality control in radiotherapy according to the criteria of the decree of A.f.s.s.a.p.s. (French agency of sanitary safety of health products on 27 july 2007, about the internal quality control of external radiotherapy facilities. The software on one year meets the objectives: compliance by comparison with A.f.s.s.a.p.s. criteria but particularly optimization of the centralisation and analysis of the internal quality controls. (N.C.)

Reduce Fraud Risk in Your District with Stronger Internal Controls

Science.gov (United States)

Okrzesik, Daryl J.; Nuehring, Bert G.

2011-01-01

Internal accounts offer schools a faster, more convenient way to handle the income and expenses that result from student fees, school clubs and organizations, field trips, fund-raising, and similar activities. But this convenience also incurs the added risk of fraud. Fortunately, there are proven ways to strengthen internal controls and reduce…

Spinal motor control system incorporates an internal model of limb dynamics.

Science.gov (United States)

Shimansky, Y P

2000-10-01

The existence and utilization of an internal representation of the controlled object is one of the most important features of the functioning of neural motor control systems. This study demonstrates that this property already exists at the level of the spinal motor control system (SMCS), which is capable of generating motor patterns for reflex rhythmic movements, such as locomotion and scratching, without the aid of the peripheral afferent feedback, but substantially modifies the generated activity in response to peripheral afferent stimuli. The SMCS is presented as an optimal control system whose optimality requires that it incorporate an internal model (IM) of the controlled object's dynamics. A novel functional mechanism for the integration of peripheral sensory signals with the corresponding predictive output from the IM, the summation of information precision (SIP) is proposed. In contrast to other models in which the correction of the internal representation of the controlled object's state is based on the calculation of a mismatch between the internal and external information sources, the SIP mechanism merges the information from these sources in order to optimize the precision of the controlled object's state estimate. It is demonstrated, based on scratching in decerebrate cats as an example of the spinal control of goal-directed movements, that the results of computer modeling agree with the experimental observations related to the SMCS's reactions to phasic and tonic peripheral afferent stimuli. It is also shown that the functional requirements imposed by the mathematical model of the SMCS comply with the current knowledge about the related properties of spinal neuronal circuitry. The crucial role of the spinal presynaptic inhibition mechanism in the neuronal implementation of SIP is elucidated. Important differences between the IM and a state predictor employed for compensating for a neural reflex time delay are discussed.

MicroRNA Related Polymorphisms and Breast Cancer Risk

DEFF Research Database (Denmark)

Khan, Sofia; Greco, Dario; Michailidou, Kyriaki

2014-01-01

Genetic variations, such as single nucleotide polymorphisms (SNPs) in microRNAs (miRNA) or in the miRNA binding sites may affect the miRNA dependent gene expression regulation, which has been implicated in various cancers, including breast cancer, and may alter individual susceptibility to cancer....... We investigated associations between miRNA related SNPs and breast cancer risk. First we evaluated 2,196 SNPs in a case-control study combining nine genome wide association studies (GWAS). Second, we further investigated 42 SNPs with suggestive evidence for association using 41,785 cases and 41......,880 controls from 41 studies included in the Breast Cancer Association Consortium (BCAC). Combining the GWAS and BCAC data within a meta-analysis, we estimated main effects on breast cancer risk as well as risks for estrogen receptor (ER) and age defined subgroups. Five miRNA binding site SNPs associated...

RNA quality control in yeast - what is good and what is bad?

DEFF Research Database (Denmark)

Andersen, Kasper Røjkjær; Brodersen, Ditlev Egeskov

positions in the tRNA molecules [2]. We believe that in such cases, the tRNAs are recognized by a common structural alteration that causes part of the molecule to unfold and thereby mark the tRNA as defect. We therefore want to isolate and crystallize the RNA binding proteins Air1p or Air2p in complex...... with aberrant tRNA analogous to gain knowledge of how the cell determines which RNAs are good and bad and use this as a model system for how the cell in general recognizes aberrant RNAs. So far, Air1p and Air2p have been cloned from different yeast organisms and the first expression tests of the proteins have...

RNA-directed DNA methylation: Mechanisms and functions

KAUST Repository

Mahfouz, Magdy M.

2010-01-01

Epigenetic RNA based gene silencing mechanisms play a major role in genome stability and control of gene expression. Transcriptional gene silencing via RNA-directed DNA methylation (RdDM) guides the epigenetic regulation of the genome in response

Scavenger receptors in human airway epithelial cells: role in response to double-stranded RNA.

Directory of Open Access Journals (Sweden)

Audrey Dieudonné

Full Text Available Scavenger receptors and Toll-like receptors (TLRs cooperate in response to danger signals to adjust the host immune response. The TLR3 agonist double stranded (dsRNA is an efficient activator of innate signalling in bronchial epithelial cells. In this study, we aimed at defining the role played by scavenger receptors expressed by bronchial epithelial cells in the control of the innate response to dsRNA both in vitro and in vivo. Expression of several scavenger receptor involved in pathogen recognition was first evaluated in human bronchial epithelial cells in steady-state and inflammatory conditions. Their implication in the uptake of dsRNA and the subsequent cell activation was evaluated in vitro by competition with ligand of scavenger receptors including maleylated ovalbumin and by RNA silencing. The capacity of maleylated ovalbumin to modulate lung inflammation induced by dsRNA was also investigated in mice. Exposure to tumor necrosis factor-α increased expression of the scavenger receptors LOX-1 and CXCL16 and the capacity to internalize maleylated ovalbumin, whereas activation by TLR ligands did not. In contrast, the expression of SR-B1 was not modulated in these conditions. Interestingly, supplementation with maleylated ovalbumin limited dsRNA uptake and inhibited subsequent activation of bronchial epithelial cells. RNA silencing of LOX-1 and SR-B1 strongly blocked the dsRNA-induced cytokine production. Finally, administration of maleylated ovalbumin in mice inhibited the dsRNA-induced infiltration and activation of inflammatory cells in bronchoalveolar spaces and lung draining lymph nodes. Together, our data characterize the function of SR-B1 and LOX-1 in bronchial epithelial cells and their implication in dsRNA-induced responses, a finding that might be relevant during respiratory viral infections.