WorldWideScience

Sample records for rna privileged space

  1. 14 CFR 1261.317 - Attorney-client privilege.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Attorney-client privilege. 1261.317 Section... Injury or Death-Accruing On or After January 18, 1967 § 1261.317 Attorney-client privilege. (a) Attorneys... traditional attorney-client relationship with the employee with respect to application of the attorney-client...

  2. 14 CFR 65.43 - Rating privileges and exchange.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 2 2010-01-01 2010-01-01 false Rating privileges and exchange. 65.43... § 65.43 Rating privileges and exchange. (a) The holder of a senior rating on August 31, 1970, may at any time after that date exchange his rating for a facility rating at the same air traffic control...

  3. Awakening to White Privilege and Power in Canada

    Science.gov (United States)

    Syed, Khalida Tanvir; Hill, Anne

    2011-01-01

    In this article two narratives are used to illustrate how self-awareness of "White" as skin colour reveals associated subtle aspects of power and privilege and with that, an ethic of personal and professional responsibility. The narratives connect experience and action with the conceptual framework of a third, liminal space,…

  4. 14 CFR 61.113 - Private pilot privileges and limitations: Pilot in command.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 2 2010-01-01 2010-01-01 false Private pilot privileges and limitations: Pilot in command. 61.113 Section 61.113 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AIRMEN CERTIFICATION: PILOTS, FLIGHT INSTRUCTORS, AND GROUND...

  5. Privilege as a Social Determinant of Health in Medical Education: A Single Class Session Can Change Privilege Perspective.

    Science.gov (United States)

    Witten, Nash A K; Maskarinec, Gregory G

    2015-09-01

    Accredited medical schools are required to prepare students to recognize the social determinants of health, such as privilege, yet privilege education has been overlooked in medical school curricula. The purpose of this study is to determine whether a single class session on privilege, within a social justice elective offered to first and second year medical students, is sufficient to change the perspective of medical students concerning their own personal privilege. A pre-class survey, followed by a class session on privilege, and post-class survey were conducted. Thirteen of the 18 students enrolled in the elective completed the pre-class survey. Ten students completed the post-class survey, although only 9 completed both the pre- and post-class surveys. The demographic profile of the participants was 93% Asian and 7% White ethnicity, with 57% identifying as being culturally American. There was no significant difference between average male and female or between age groups' self-assessed privilege amounts. For all characteristics tested, except hair color, participants had an increased self-assessed privilege perspective following the class. Three participants had an overall positive difference in privilege perspective, three participants had an overall negative difference in privilege perspective, and three participants had only a minimal change in privilege perspective. The absolute total difference in privilege perspective was 25 units of change. The single class session on privilege was sufficient to change significantly the perspective of medical students on their own personal privilege; however, future studies with larger groups of medical students are needed to elucidate other findings suggested by this study.

  6. Sparse RNA folding revisited: space-efficient minimum free energy structure prediction.

    Science.gov (United States)

    Will, Sebastian; Jabbari, Hosna

    2016-01-01

    RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to improve the time efficiency of various structure prediction algorithms while guaranteeing the same result; however, for many such folding problems, space efficiency is of even greater concern, particularly for long RNA sequences. So far, space-efficient sparsified RNA folding with fold reconstruction was solved only for simple base-pair-based pseudo-energy models. Here, we revisit the problem of space-efficient free energy minimization. Whereas the space-efficient minimization of the free energy has been sketched before, the reconstruction of the optimum structure has not even been discussed. We show that this reconstruction is not possible in trivial extension of the method for simple energy models. Then, we present the time- and space-efficient sparsified free energy minimization algorithm SparseMFEFold that guarantees MFE structure prediction. In particular, this novel algorithm provides efficient fold reconstruction based on dynamically garbage-collected trace arrows. The complexity of our algorithm depends on two parameters, the number of candidates Z and the number of trace arrows T; both are bounded by [Formula: see text], but are typically much smaller. The time complexity of RNA folding is reduced from [Formula: see text] to [Formula: see text]; the space complexity, from [Formula: see text] to [Formula: see text]. Our empirical results show more than 80 % space savings over RNAfold [Vienna RNA package] on the long RNAs from the RNA STRAND database (≥2500 bases). The presented technique is intentionally generalizable to complex prediction algorithms; due to their high space demands, algorithms like pseudoknot prediction and RNA-RNA-interaction prediction are expected to profit even stronger than "standard" MFE folding. SparseMFEFold is free

  7. Pedagogy of the Privileged: Review of Deconstructing Privilege: Teaching and Learning as Allies in the Classroom.

    Science.gov (United States)

    Toporek, Rebecca L

    2014-08-11

    As scholarship and research in multicultural psychology evolves to a multilayered and complex discipline, increased attention to the role of larger structural forces of privilege has come to the forefront. Intersectionality of sociopolitical identities and the role those with privilege have in confronting oppression becomes a critical component of multicultural education. The edited volume, Deconstructing Privilege: Teaching and Learning as Allies in the Classroom (Case, 2013) provides concrete guidance and examples for educators seeking to enhance their approach to teaching privilege as a necessary mirror of oppression. This review highlights strengths of the book for educators in psychology and suggests recommendations for more complex discussion of the integration of privilege within the framework of structural oppression. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

  8. A probabilistic model of RNA conformational space

    DEFF Research Database (Denmark)

    Frellsen, Jes; Moltke, Ida; Thiim, Martin

    2009-01-01

    efficient sampling of RNA conformations in continuous space, and with associated probabilities. We show that the model captures several key features of RNA structure, such as its rotameric nature and the distribution of the helix lengths. Furthermore, the model readily generates native-like 3-D......, the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows......The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling...

  9. 76 FR 11756 - Action Affecting Export Privileges; Ali Amirnazmi; Order Denying Export Privileges

    Science.gov (United States)

    2011-03-03

    ... DEPARTMENT OF COMMERCE Bureau of Industry and Security Action Affecting Export Privileges; Ali Amirnazmi; Order Denying Export Privileges In the Matter of: Ali Amirnazmi, Register 63302-066, FCI... release and forfeit $81,277.37. Section 766.25 of the Export Administration Regulations (``EAR'' or...

  10. Immunity and privilege of international organizations in Kosovo

    Directory of Open Access Journals (Sweden)

    Arif Riza

    2016-11-01

    Full Text Available To speak for the Diplomatic Law (Immunities and Privileges in International Organizations, first, this topic briefly describes the international organizations, what are they, as established, as extinct, and finally, as a shared international organizations. They are not subject of this paper, but Immunity and Privileges in International Organizations are. This paper gives an overview of the history of the immunity and privileges in international organizations, conventions, laws of the country regarding Immunities and Privileges, where the seat of the International Organization, Immunities and privileges of diplomatic representatives in international organizations, Immunities and privileges of representatives of international organizations in the state where the seat of the Organization, immunity and privileges of members of the family, diplomatic representatives International Organizations, Immunities and Privileges in the European Union, the difference between the immunity and privileges of international organizations, and Immunity and Privileges between states. This paper analyzes also the immunity and inviolability of buildings of International Organizations, immunity and inviolability of the archives of international organizations, the immunity and privileges of goods to international organizations, the release from the obligation of tax payments, the release from the provision of the diplomatic staff of International Organizations, etc. However, the paper includes charts, respectively, some official data from countries where the headquarters of international organizations are situated and gives an overview of the number of international governmental and nongovernmental organizations.

  11. Privilege

    Directory of Open Access Journals (Sweden)

    Luciana Manfredi

    2006-01-01

    Full Text Available Privilege, es la marca con la que la familia Jaramillo se lanzó al mercado caleño, ofreciendo ropa sobre medida y talla para hombres y mujeres, con altos estándares de calidad, servicio personalizado y diseños de moda; su portafolio de productos incluye ropa formal y casual para ejecutivos(as. Esta marca, pese a no tener competidores directos, sí observaba que algunas marcas y diseñadores exclusivos se encontraban dentro del grupo de consideración de los consumidores objetivo de Privilege. La gerencia de la compañía enfrenta costos fijos elevados (ocupación de maquinaria al 50% que afectan la rentabilidad; un nuevo punto de venta que presenta promedio de ingresos inferiores a los necesarios para su autosostenibilidad; bajo reconocimiento de marca por parte del target, competidores con gran músculo financiero y marcas altamente reconocidas con trayectoria y precios competitivos.

  12. 77 FR 39617 - Confidential Treatment of Privileged Information

    Science.gov (United States)

    2012-07-05

    ... information that may be subject to one or more statutory or common law privileges, including the attorney... served by the common law privileges, in particular the attorney-client privilege. The Bureau understands... authority under existing law. The Bureau also believes that courts applying the principles of the common law...

  13. 32 CFR 634.18 - Reinstatement of driving privileges.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 4 2010-07-01 2010-07-01 true Reinstatement of driving privileges. 634.18 Section 634.18 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS MOTOR VEHICLE TRAFFIC SUPERVISION Driving Privileges § 634.18 Reinstatement of driving privileges....

  14. 14 CFR 65.107 - Repairman certificate (light-sport aircraft): Eligibility, privileges, and limits.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 2 2010-01-01 2010-01-01 false Repairman certificate (light-sport aircraft... CREWMEMBERS Repairmen § 65.107 Repairman certificate (light-sport aircraft): Eligibility, privileges, and...-sport aircraft) and appropriate rating: To be eligible for You must (1) A repairman certificate (light...

  15. 14 CFR 61.193 - Flight instructor privileges.

    Science.gov (United States)

    2010-01-01

    ... than Flight Instructors With a Sport Pilot Rating § 61.193 Flight instructor privileges. A person who...; (e) An aircraft rating; (f) An instrument rating; (g) A flight review, operating privilege, or...

  16. 42 CFR 3.204 - Privilege of patient safety work product.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 1 2010-10-01 2010-10-01 false Privilege of patient safety work product. 3.204... PROVISIONS PATIENT SAFETY ORGANIZATIONS AND PATIENT SAFETY WORK PRODUCT Confidentiality and Privilege Protections of Patient Safety Work Product § 3.204 Privilege of patient safety work product. (a) Privilege...

  17. SVOPME: A Scalable Virtual Organization Privileges Management Environment

    International Nuclear Information System (INIS)

    Garzoglio, Gabriele; Sfiligoi, Igor; Levshina, Tanya; Wang, Nanbor; Ananthan, Balamurali

    2010-01-01

    Grids enable uniform access to resources by implementing standard interfaces to resource gateways. In the Open Science Grid (OSG), privileges are granted on the basis of the user's membership to a Virtual Organization (VO). However, Grid sites are solely responsible to determine and control access privileges to resources using users' identity and personal attributes, which are available through Grid credentials. While this guarantees full control on access rights to the sites, it makes VO privileges heterogeneous throughout the Grid and hardly fits with the Grid paradigm of uniform access to resources. To address these challenges, we are developing the Scalable Virtual Organization Privileges Management Environment (SVOPME), which provides tools for VOs to define and publish desired privileges and assists sites to provide the appropriate access policies. Moreover, SVOPME provides tools for Grid sites to analyze site access policies for various resources, verify compliance with preferred VO policies, and generate directives for site administrators on how the local access policies can be amended to achieve such compliance without taking control of local configurations away from site administrators. This paper discusses what access policies are of interest to the OSG community and how SVOPME implements privilege management for OSG.

  18. Family Privilege

    Science.gov (United States)

    Seita, John R.

    2014-01-01

    Family privilege is defined as "strengths and supports gained through primary caring relationships." A generation ago, the typical family included two parents and a bevy of kids living under one roof. Now, every variation of blended caregiving qualifies as family. But over the long arc of human history, a real family was a…

  19. Stochastic sampling of the RNA structural alignment space.

    Science.gov (United States)

    Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H

    2009-07-01

    A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the 'structural alignment' space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtue of the implicit comparative analysis between the two sequences, the method offers an improvement over single sequence sampling of the Boltzmann ensemble. A cluster analysis shows that the samples obtained from joint sampling of the structural alignment space cluster more closely than samples generated by the single sequence method. On average, the representative (centroid) structure and alignment of the most populated cluster in the sample of structures and alignments generated by joint sampling are more accurate than single sequence sampling and alignment based on sequence alone, respectively. The 'best' centroid structure that is closest to the known structure among all the centroids is, on average, more accurate than structure predictions of other methods. Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc.rochester.edu.

  20. Social Class Privilege and Adolescent Women's Perceived Career Options

    Science.gov (United States)

    Lapour, Anne Scott; Heppner, Mary J.

    2009-01-01

    This qualitative study examined the perceived career options of 10 White adolescent young women who experienced social class privilege in their families of origin. The model of contextual privilege and career selection for adolescent White women emerged from the data, and it describes how social class privilege, gender, achievement expectations,…

  1. 46 CFR 5.67 - Physician-patient privilege.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false Physician-patient privilege. 5.67 Section 5.67 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY PROCEDURES APPLICABLE TO THE PUBLIC MARINE INVESTIGATION REGULATIONS-PERSONNEL ACTION Statement of Policy and Interpretation § 5.67 Physician-patient privilege. For...

  2. What Business Students Should Know about Attorney-Client Privilege

    Science.gov (United States)

    Draba, Robert; Marshall, Brent

    2012-01-01

    The case law on attorney-client privilege is extensive and can be somewhat complex. Over seven hundred articles in Westlaw, for example, have the phrase "attorney-client privilege" in the title; in the last three years alone, there have been over 3700 federal cases in which the phrase "attorney-client privilege" appears at least once. However,…

  3. Christian Privilege, History, and Trends in U.S. Religion

    Science.gov (United States)

    Fairchild, Ellen E.

    2009-01-01

    In her seminal essay on white privilege, McIntosh (1988) began a discussion on privilege that has taken hold in areas outside her original intent. In this chapter, the author discusses privilege as it pertains not only to race and gender but to religion, especially the Christian faith. The author incorporates the current state of religious flux in…

  4. Learning using privileged information: SVM+ and weighted SVM.

    Science.gov (United States)

    Lapin, Maksim; Hein, Matthias; Schiele, Bernt

    2014-05-01

    Prior knowledge can be used to improve predictive performance of learning algorithms or reduce the amount of data required for training. The same goal is pursued within the learning using privileged information paradigm which was recently introduced by Vapnik et al. and is aimed at utilizing additional information available only at training time-a framework implemented by SVM+. We relate the privileged information to importance weighting and show that the prior knowledge expressible with privileged features can also be encoded by weights associated with every training example. We show that a weighted SVM can always replicate an SVM+ solution, while the converse is not true and we construct a counterexample highlighting the limitations of SVM+. Finally, we touch on the problem of choosing weights for weighted SVMs when privileged features are not available. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Making Unseen Privilege Visible in Mathematics Education Research

    Science.gov (United States)

    Bartell, Tonya Gau; Johnson, Kate R.

    2013-01-01

    In this essay, the authors begin to "unpack the invisible knapsack" of mathematics education research privilege. They present short statements representing the multiplicity of their respective identities; acknowledging that efforts to understand privilege and oppression are often supported and constrained by identities. The authors then…

  6. Are Student Communications with School Psychologists Legally Privileged?

    Science.gov (United States)

    Kaplan, Ross; Zirkel, Perry A.

    2017-01-01

    As a trusted link between district personnel, students, and their families, school psychologists often have questions about whether their communications are privileged like those of other professionals. In some jurisdictions, state statutes and common, or case, law recognize privileged communications for certain specified paired roles, including…

  7. 14 CFR 61.315 - What are the privileges and limits of my sport pilot certificate?

    Science.gov (United States)

    2010-01-01

    ... sport pilot certificate? 61.315 Section 61.315 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION... INSTRUCTORS Sport Pilots § 61.315 What are the privileges and limits of my sport pilot certificate? (a) If you hold a sport pilot certificate you may act as pilot in command of a light-sport aircraft, except as...

  8. Changes in miRNA expression profile of space-flown Caenorhabditis elegans during Shenzhou-8 mission

    Science.gov (United States)

    Xu, Dan; Gao, Ying; Huang, Lei; Sun, Yeqing

    2014-04-01

    Recent advances in the field of molecular biology have demonstrated that small non-coding microRNAs (miRNAs) have a broad effect on gene expression networks and play a key role in biological responses to environmental stressors. However, little is known about how space radiation exposure and altered gravity affect miRNA expression. The "International Space Biological Experiments" project was carried out in November 2011 by an international collaboration between China and Germany during the Shenzhou-8 (SZ-8) mission. To study the effects of spaceflight on Caenorhabditis elegans (C. elegans), we explored the expression profile miRNA changes in space-flown C. elegans. Dauer C. elegans larvae were taken by SZ-8 spacecraft and experienced the 16.5-day shuttle spaceflight. We performed miRNA microarray analysis, and the results showed that 23 miRNAs were altered in a complex space environment and different expression patterns were observed in the space synthetic and radiation environments. Most putative target genes of the altered miRNAs in the space synthetic environment were predicted to be involved in developmental processes instead of in the regulation of transcription, and the enrichment of these genes was due to space radiation. Furthermore, integration analysis of the miRNA and mRNA expression profiles confirmed that twelve genes were differently regulated by seven miRNAs. These genes may be involved in embryonic development, reproduction, transcription factor activity, oviposition in a space synthetic environment, positive regulation of growth and body morphogenesis in a space radiation environment. Specifically, we found that cel-miR-52, -55, and -56 of the miR-51 family were sensitive to space environmental stressors and could regulate biological behavioural responses and neprilysin activity through the different isoforms of T01C4.1 and F18A12.8. These findings suggest that C. elegans responded to spaceflight by altering the expression of miRNAs and some target

  9. Development of a Novel Self-Enclosed Sample Preparation Device for DNA/RNA Isolation in Space

    Science.gov (United States)

    Zhang, Ye; Mehta, Satish K.; Pensinger, Stuart J.; Pickering, Karen D.

    2011-01-01

    Modern biology techniques present potentials for a wide range of molecular, cellular, and biochemistry applications in space, including detection of infectious pathogens and environmental contaminations, monitoring of drug-resistant microbial and dangerous mutations, identification of new phenotypes of microbial and new life species. However, one of the major technological blockades in enabling these technologies in space is a lack of devices for sample preparation in the space environment. To overcome such an obstacle, we constructed a prototype of a DNA/RNA isolation device based on our novel designs documented in the NASA New Technology Reporting System (MSC-24811-1/3-1). This device is self-enclosed and pipette free, purposely designed for use in the absence of gravity. Our design can also be modified easily for preparing samples in space for other applications, such as flowcytometry, immunostaining, cell separation, sample purification and separation according to its size and charges, sample chemical labeling, and sample purification. The prototype of our DNA/RNA isolation device was tested for efficiencies of DNA and RNA isolation from various cell types for PCR analysis. The purity and integrity of purified DNA and RNA were determined as well. Results showed that our developed DNA/RNA isolation device offers similar efficiency and quality in comparison to the samples prepared using the standard protocol in the laboratory.

  10. 19 CFR 4.94 - Yacht privileges and obligations.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Yacht privileges and obligations. 4.94 Section 4... THE TREASURY VESSELS IN FOREIGN AND DOMESTIC TRADES General § 4.94 Yacht privileges and obligations...) A cruising license may be issued to a yacht of a foreign country only if it has been made to appear...

  11. Whose University Is It, Anyway? Power and Privilege on Gendered Terrain

    Directory of Open Access Journals (Sweden)

    May Al Fartousi

    2013-07-01

    Full Text Available As a visible minority educator, I am always interested in analyzing the personal tensions, environmental barriers, and imaginative possibilities that exist when embracing equity- and diversity-conscious approaches to teaching, learning, and interacting in higher education institutions. In Whose University Is It, Anyway? Power and Privilege on Gendered Terrain, these areas of tension are treated as creative spaces to draw from the work of feminists who use this site as a site for power and new knowledge production.

  12. STUDY OF PRIVILEGE ESCALATION ATTACK ON ANDROID AND ITS COUNTERMEASURES

    OpenAIRE

    REJO MATHEW

    2012-01-01

    Android is most commonly used platform for smartphones today which boasts of an advanced security model having MAC and sandboxing. These features allow developers and users to restrict the execution of anapplication to the privileges assigned. The exploitation of vulnerabilities of the program is confined within the privilege boundaries of an applications sandbox. Privilege escalation attacks have grown manifold as the use of android systems have increased. Different kinds of mechanisms have ...

  13. Integrating social class and privilege in the community medicine curriculum.

    Science.gov (United States)

    Haymaker, Christopher; Cadick, Amber; Seavey, Allison

    2017-05-01

    Social class and privilege are hidden variables that impact the physician-patient relationship and health outcomes. This article presents a sample of activities from three programs utilized in the community health curriculum to teach resident physicians about patients within context, including how social class and privilege impact physician-patient relationships and patient health. These activities address resident physicians' resistance to discussion of privilege, social class, and race by emphasizing direct experience and active learning rather than traditional didactic sessions. The group format of these activities fosters flexible discussion and personal engagement that provide opportunities for reflection. Each activity affords opportunities to develop a vocabulary for discussing social class and privilege with compassion and to adopt therapeutic approaches that are more likely to meet patients where they are.

  14. A Response to "Social Privilege, Social Justice, and Group Counseling: An Inquiry"

    Science.gov (United States)

    Holcomb-McCoy, Cheryl

    2008-01-01

    This response discusses the importance of "privilege talk" and relates the concept of privilege to group counseling research. The impact of "colorblindness" on the dynamics of groups is discussed. The importance of understanding social privilege and its influence on counseling groups is emphasized.

  15. 19 CFR 360.108 - Loss of electronic licensing privileges.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 3 2010-04-01 2010-04-01 false Loss of electronic licensing privileges. 360.108 Section 360.108 Customs Duties INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE STEEL IMPORT MONITORING AND ANALYSIS SYSTEM § 360.108 Loss of electronic licensing privileges. Should Commerce determine...

  16. "The normative idea of queer is a white person": understanding perceptions of white privilege among lesbian, bisexual, and queer women of color in Toronto, Canada.

    Science.gov (United States)

    Logie, Carmen H; Rwigema, Marie-Jolie

    2014-01-01

    White privilege constructs whiteness as normative and central to lesbian, gay, bisexual, and queer (LGBQ) identities and is reproduced through social norms, media representations, and daily interactions. We aimed to enhance understanding of the processes by which white privilege was experienced among lesbian, bisexual, and queer (LBQ) women of color in Toronto, Canada. We conducted two focus groups with LBQ women of color, one with participants who self-identified as masculine of center (n = 8) and the second with participants who identified as feminine of center (n = 8). Findings indicate that LBQ women of color experience intersectional stigma (e.g., homophobia, racism, sexism) on a daily basis. Participant narratives revealed that white privilege shaped the representations of women of color in a particular way that promoted their exclusion from white LBQ spaces and broader society. By representing queerness as white, LBQ women of color were rendered invisible in both queer and racialized communities. LBQ women of color were further marginalized by constructions of "real" women as passive, feminine and white, and conversely perceptions of women of color as aggressive, emotional, and hypersexualized. These representations inform spatialized practices and social interactions through constructing racialized communities as discriminatory and "backwards" while maintaining the invisibility of white privilege and racism in LBQ spaces.

  17. Cultural Anarchism: The Consequences of Privileging Languages in Nepal

    Science.gov (United States)

    Giri, Ram Ashish

    2010-01-01

    Nepali, the official language of administration of Nepal, has been privileged through systematic political manoeuvres throughout its history. English also enjoys special status and privileges, and despite the fact that it is officially only a "foreign" language, in practice it is one of the most dominant languages in educational and…

  18. Transient Gene and miRNA Expression Profile Changes of Confluent Human Fibroblast Cells in Space

    Science.gov (United States)

    Zhang, Ye; Lu, Tao; Wong, Michael; Feiveson, Alan; Stodieck, Louis; Karouia, Fathi; Wang, Xiaoyu; Wu, Honglu

    2015-01-01

    Microgravity or an altered gravity environment from the static 1 gravitational constant has been shown to influence global gene expression patterns and protein levels in cultured cells. However, most of the reported studies conducted in space or using simulated microgravity on the ground have focused on the growth or differentiation of the cells. Whether non-dividing cultured cells will sense the presence of microgravity in space has not been specifically addressed. In an experiment conducted on the International Space Station, confluent human fibroblast cells were fixed after being cultured in space for 3 and 14 days for investigations of gene and miRNA (microRNA) expression profile changes in these cells. A fibroblast is a type of cell that synthesizes the extracellular matrix and collagen, the structural framework for tissues, and plays a critical role in wound healing and other functions. Results of the experiment showed that on Day 3, both the flown and ground cells were still proliferating slowly even though they were confluent, as measured by the expression of the protein Ki-67 positive cells, and the cells in space grew slightly faster. Gene and miRNA expression data indicated activation of NF(sub kappa)B (nuclear factor kappa-light-chain-enhancer of activated B cells) and other growth related pathways involving HGF and VEGF in the flown cells. On Day 14 when the cells were mostly non-dividing, the gene and miRNA expression profiles between the flight and ground samples were indistinguishable. Comparison of gene and miRNA expressions in the Day 3 samples in respect to Day 14 revealed that most of the changes observed on Day 3 were related to cell growth for both the flown and ground cells. Analysis of cytoskeleton changes by immunohistochemistry staining of the cells with antibodies for alpha-tubulin showed no difference between the flight and ground samples. Results of our study suggest that in true non-dividing human fibroblast cells, microgravity in

  19. Topological structure of the space of phenotypes: the case of RNA neutral networks.

    Directory of Open Access Journals (Sweden)

    Jacobo Aguirre

    Full Text Available The evolution and adaptation of molecular populations is constrained by the diversity accessible through mutational processes. RNA is a paradigmatic example of biopolymer where genotype (sequence and phenotype (approximated by the secondary structure fold are identified in a single molecule. The extreme redundancy of the genotype-phenotype map leads to large ensembles of RNA sequences that fold into the same secondary structure and can be connected through single-point mutations. These ensembles define neutral networks of phenotypes in sequence space. Here we analyze the topological properties of neutral networks formed by 12-nucleotides RNA sequences, obtained through the exhaustive folding of sequence space. A total of 4(12 sequences fragments into 645 subnetworks that correspond to 57 different secondary structures. The topological analysis reveals that each subnetwork is far from being random: it has a degree distribution with a well-defined average and a small dispersion, a high clustering coefficient, and an average shortest path between nodes close to its minimum possible value, i.e. the Hamming distance between sequences. RNA neutral networks are assortative due to the correlation in the composition of neighboring sequences, a feature that together with the symmetries inherent to the folding process explains the existence of communities. Several topological relationships can be analytically derived attending to structural restrictions and generic properties of the folding process. The average degree of these phenotypic networks grows logarithmically with their size, such that abundant phenotypes have the additional advantage of being more robust to mutations. This property prevents fragmentation of neutral networks and thus enhances the navigability of sequence space. In summary, RNA neutral networks show unique topological properties, unknown to other networks previously described.

  20. Tuning iteration space slicing based tiled multi-core code implementing Nussinov's RNA folding.

    Science.gov (United States)

    Palkowski, Marek; Bielecki, Wlodzimierz

    2018-01-15

    RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology. Fortunately, RNA secondary structure approaches, such as Nussinov's recurrence, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. This allows us to apply powerful polyhedral compilation techniques based on the transitive closure of dependence graphs to generate parallel tiled code implementing Nussinov's RNA folding. Such techniques are within the iteration space slicing framework - the transitive dependences are applied to the statement instances of interest to produce valid tiles. The main problem at generating parallel tiled code is defining a proper tile size and tile dimension which impact parallelism degree and code locality. To choose the best tile size and tile dimension, we first construct parallel parametric tiled code (parameters are variables defining tile size). With this purpose, we first generate two nonparametric tiled codes with different fixed tile sizes but with the same code structure and then derive a general affine model, which describes all integer factors available in expressions of those codes. Using this model and known integer factors present in the mentioned expressions (they define the left-hand side of the model), we find unknown integers in this model for each integer factor available in the same fixed tiled code position and replace in this code expressions, including integer factors, with those including parameters. Then we use this parallel parametric tiled code to implement the well-known tile size selection (TSS) technique, which allows us to discover in a given search space the best tile size and tile dimension maximizing target code performance. For a given search space, the presented approach allows us to choose the best tile size and tile dimension in

  1. Immune Privilege and Eye-Derived T-Regulatory Cells

    Directory of Open Access Journals (Sweden)

    Hiroshi Keino

    2018-01-01

    Full Text Available Certain cellular components of the eye, such as neural retina, are unable to regenerate and replicate after destructive inflammation. Ocular immune privilege provides the eye with immune protection against intraocular inflammation in order to minimize the risk to vision integrity. The eye and immune system use strategies to maintain the ocular immune privilege by regulating the innate and adaptive immune response, which includes immunological ignorance, peripheral tolerance to eye-derived antigens, and intraocular immunosuppressive microenvironment. In this review, we summarize current knowledge regarding the molecular mechanism responsible for the development and maintenance of ocular immune privilege via regulatory T cells (Tregs, which are generated by the anterior chamber-associated immune deviation (ACAID, and ocular resident cells including corneal endothelial (CE cells, ocular pigment epithelial (PE cells, and aqueous humor. Furthermore, we examined the therapeutic potential of Tregs generated by RPE cells that express transforming growth factor beta (TGF-β, cytotoxic T lymphocyte-associated antigen-2 alpha (CTLA-2α, and retinoic acid for autoimmune uveoretinitis and evaluated a new strategy using human RPE-induced Tregs for clinical application in inflammatory ocular disease. We believe that a better understanding of the ocular immune privilege associated with Tregs might offer a new approach with regard to therapeutic interventions for ocular autoimmunity.

  2. Immune Privilege and Eye-Derived T-Regulatory Cells.

    Science.gov (United States)

    Keino, Hiroshi; Horie, Shintaro; Sugita, Sunao

    2018-01-01

    Certain cellular components of the eye, such as neural retina, are unable to regenerate and replicate after destructive inflammation. Ocular immune privilege provides the eye with immune protection against intraocular inflammation in order to minimize the risk to vision integrity. The eye and immune system use strategies to maintain the ocular immune privilege by regulating the innate and adaptive immune response, which includes immunological ignorance, peripheral tolerance to eye-derived antigens, and intraocular immunosuppressive microenvironment. In this review, we summarize current knowledge regarding the molecular mechanism responsible for the development and maintenance of ocular immune privilege via regulatory T cells (Tregs), which are generated by the anterior chamber-associated immune deviation (ACAID), and ocular resident cells including corneal endothelial (CE) cells, ocular pigment epithelial (PE) cells, and aqueous humor. Furthermore, we examined the therapeutic potential of Tregs generated by RPE cells that express transforming growth factor beta (TGF- β ), cytotoxic T lymphocyte-associated antigen-2 alpha (CTLA-2 α ), and retinoic acid for autoimmune uveoretinitis and evaluated a new strategy using human RPE-induced Tregs for clinical application in inflammatory ocular disease. We believe that a better understanding of the ocular immune privilege associated with Tregs might offer a new approach with regard to therapeutic interventions for ocular autoimmunity.

  3. Reformulating the calculation of mining privileges for medium and large mining

    Directory of Open Access Journals (Sweden)

    Pedro Franco Concha

    2016-01-01

    Full Text Available Throughout this paper those technical and accounting concepts of the Law of mining privileges that generate ambiguity and incongruity for businesses has been analyzed and identified. For this reason, we have developed a proposal amending the calculation of mining privileges based on two main aspects: (i terminology used in the law and (ii establishment of income before retribution to stakholders and taxes as a basis for calculating privileges. As a result, it was established as an object of study for all mining companies paying privileges; however, for purposes of the investigation three representative mining companies of medium and large mining were selected. Later interviews were arranged with financial and tax managers of the companies mentioned above as well as experts in the field of mining privileges; it was concluded that the concepts of "cost" and "corresponding fiscal year" mentioned in the Law generated ambiguities, inconsistencies and accounting distortions. Also, mining companies and experts agreed that the current basis for the calculation of the privileges is not adequate for the mining sector since it does not reflect the financial situation of companies. Therefore, a proposal for reformulation of the applied priviously and a new basis for calculating the mining privileges based on the cost of sales is made; since, in the cost of sales is found what Kieso and Weygandt (1999 denominated as "the price paid for the right to seek and find a hidden Natural resources, or paid by a source already discovered"

  4. 14 CFR 61.413 - What are the privileges of my flight instructor certificate with a sport pilot rating?

    Science.gov (United States)

    2010-01-01

    ... instructor certificate with a sport pilot rating? 61.413 Section 61.413 Aeronautics and Space FEDERAL... INSTRUCTORS, AND GROUND INSTRUCTORS Flight Instructors With a Sport Pilot Rating § 61.413 What are the privileges of my flight instructor certificate with a sport pilot rating? If you hold a fight flight...

  5. The protection of the Furioso: Ariosto and the Italian privileges system

    Directory of Open Access Journals (Sweden)

    Erika Squassina

    2017-06-01

    Full Text Available First best seller of Italian literature, the Orlando Furioso by Ludovico Ariosto was printed at Ferrara in three editions under the same author’s superintendence (1516, 1521, 1532. The poet showed great resourcefulness in organizing the whole operation by himself: he purchased the paper, took charge of sales, and obtained privileges to protect the book from unauthorized reproduction, and to preserve his text in its integrity. Therefore, he incurred the time and expense of seeking privileges from several jurisdictions, from the Pope, the Emperor, Venice, Milan, Ferrara, Genoa, and other potentates. Despite this, the poem was reprinted many times, especially by Venetian printers that decreed its unstoppable rise. In addition, the Ariosto death (1533 nullified all privileges he had obtained with great difficulty, and led his heirs to try to remedy the situation by asking for privileges which protected the interests of the family. In particular, Ariosto’s heirs obtained (1535 from the Venetian Senate a privilege for the publication of the poet’s unpublished minor works.

  6. Using SAML for Attribution, Delegation and Least Privilege

    Directory of Open Access Journals (Sweden)

    Coimbatore S. Chandersekaran

    2011-02-01

    Full Text Available Delegation, Attribution and Least Privilege are an implicit part of information sharing. In operating systems like Windows there is no security enforcement for code running in kernel mode and therefore such code always runs with maximum privileges. The principle of least privilege therefore demands the use of a user mode solutions when given the choice between a kernel mode and user mode solution if the two solutions provide the same results. Discussions in this paper will be restricted to OSI model levels five and above. This paper describes the SAML delegation framework in the context of a large enclave-based architecture currently being implemented by the US Air Force. Benefits of the framework include increased flexibility to handle a number of different delegation business scenarios, decreased complexity of the solution, and greater accountability with only a modest amount of additional infrastructure required.

  7. Pica in pregnancy in a privileged population

    DEFF Research Database (Denmark)

    Mikkelsen, Tina Broby; Andersen, Anne-Marie Nybo; Olsen, Sjurdur Frodi

    2006-01-01

    frequency questionnaire mailed in gestation week 25. RESULTS: The response rate of the questionnaire was 70% of Danish National Birth Cohort participants. Only 14 women reported to have eaten substances that were clearly not foods, i.e. 0.02% had pica in this cohort of well nourished Danish women......BACKGROUND: In the literature pica is reported to be prevalent in pregnant women. Most studies have focused on less privileged populations, but is pica prevalent among privileged pregnant women? METHODS: 100,000 pregnant women in the Danish National Birth Cohort were asked about pica in a food...

  8. Unveiling Privilege to Broaden Participation

    Science.gov (United States)

    Scherr, Rachel E.; Robertson, Amy D.

    2017-10-01

    The underrepresentation of women and people of color in physics has been attributed to a wide variety of factors ranging from society-wide conditions such as income inequality and sparse role models, to daily interpersonal interactions that disadvantage or discourage women and people of color from pursuing physics. These factors may be seen as manifestations of White and/or male privilege: social, economic, educational, or political advantages that are made available to Whites and males on the basis of their social identity. White male privilege pervades the discipline of physics as well as the classrooms in which physics is taught and learned. For example, physics is portrayed in textbooks as the product of individual great men, independent of all social or political contexts, rather than as being shaped by the culture of the European Enlightenment (among other cultures) or the conditions during specific international conflicts.

  9. Unpacking the invisible knapsack: The invention of white privilege pedagogy

    Directory of Open Access Journals (Sweden)

    Leslie Margolin

    2015-12-01

    Full Text Available This article uses Ricoeur’s hermeneutics of suspicion, an interpretive strategy directed to the hidden or repressed meanings behind texts, to examine the origins of white privilege pedagogy, in particular their foundational technique, “unpacking the invisible knapsack.” This article’s chief finding is that this pedagogy, though designed to fight racism, has the unintended effect of supporting white privilege. Teaching whites to “unpack their invisible knapsack” does not make them more willing to take action against racial inequality. On the contrary, it makes them more complacent, more at home in an unjust world, and more comfortable with their whiteness. White privilege pedagogy does this by focusing on personal identity (whites’ personal identity over institutional structures, by paying more attention to whites’ experiences than to blacks’, by falsely claiming that the confession of white privileges leads to social action beneficial to blacks, and by restoring and expanding whites’ sense of moral rightness.

  10. MicroRNA Expression Profiles in Cultured Human Fibroblasts in Space

    Science.gov (United States)

    Wu, Honglu; Lu, Tao; Jeevarajan, John; Rohde, Larry; Zhang, Ye

    2014-01-01

    Microgravity, or an altered gravity environment from the static 1g, has been shown to influence global gene expression patterns and protein levels in living organisms. However, it is unclear how these changes in gene and protein expressions are related to each other or are related to other factors regulating such changes. A different class of RNA, the small non-coding microRNA (miRNA), can have a broad effect on gene expression networks by mainly inhibiting the translation process. Previously, we investigated changes in the expression of miRNA and related genes under simulated microgravity conditions on the ground using the NASA invented bioreactor. In comparison to static 1 g, simulated microgravity altered a number of miRNAs in human lymphoblastoid cells. Pathway analysis with the altered miRNAs and RNA expressions revealed differential involvement of cell communication and catalytic activity, as well as immune response signaling and NGF activation of NF-kB pathways under simulated microgravity condition. The network analysis also identified several projected networks with c- Rel, ETS1 and Ubiquitin C as key factors. In a flight experiment on the International Space Station (ISS), we will investigate the effects of actual spaceflight on miRNA expressions in nondividing human fibroblast cells in mostly G1 phase of the cell cycle. A fibroblast is a type of cell that synthesizes the extracellular matrix and collagen, the structural framework for tissues, and plays a critical role in wound healing and other functions. In addition to miRNA expressions, we will investigate the effects of spaceflight on the cellular response to DNA damages from bleomycin treatment.

  11. 17 CFR 240.12f-3 - Termination or suspension of unlisted trading privileges.

    Science.gov (United States)

    2010-04-01

    ... unlisted trading privileges. 240.12f-3 Section 240.12f-3 Commodity and Securities Exchanges SECURITIES AND... Regulations Under the Securities Exchange Act of 1934 Unlisted Trading § 240.12f-3 Termination or suspension of unlisted trading privileges. (a) The issuer of any security for which unlisted trading privileges...

  12. 36 CFR 1254.52 - Can NARA extend the period of revoked research privileges?

    Science.gov (United States)

    2010-07-01

    ... continue the revocation of research privileges. (b) You have 30 calendar days after the decision to extend... Research Room Rules Other Conduct Rules § 1254.52 Can NARA extend the period of revoked research privileges... with the rules of conduct for NARA facilities, we may extend the revocation of privileges for...

  13. Discriminatory Policy among the Undergraduate Students towards Racism and White Privilege in America

    Science.gov (United States)

    Sankar, G.

    2014-01-01

    This paper addresses racism and white privilege in America. Racism is generally discriminatory policy and behavior aimed at oppressing non whites whereas white privilege is the advantage gained by whites that is not due to ability or merit. It is argued that white privilege is largely invisible and that this allows the current unacceptable status…

  14. 48 CFR 1845.7101-5 - Contractor's privileged financial and business information.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true Contractor's privileged financial and business information. 1845.7101-5 Section 1845.7101-5 Federal Acquisition Regulations System... 1845.7101-5 Contractor's privileged financial and business information. If a transfer of property...

  15. Privileged Pursuits of Social Justice: Exploring Privileged College Students' Motivation for Engaging in Social Justice

    Science.gov (United States)

    Howard, Adam

    2011-01-01

    The author of this article explores the motivation factors that lead privileged college students to be involved in social justice efforts. The students participating in this study identified multiple reasons for their initial and continued involvement in social justice work, but all students identified three main sources of motivation: responding…

  16. Encountering My Privilege (and Others' Oppression)

    Science.gov (United States)

    Kirby, Erika L.

    2016-01-01

    Courses: Communication and Diversity, Intercultural Communication, Gender Communication. Objectives: After completing this semester-long activity, students should be able to (1) articulate a systems-of-oppression (privilege??oppression) approach to thinking about difference; (2) confront and "interact differently" with one social…

  17. Fas ligand exists on intervertebral disc cells: a potential molecular mechanism for immune privilege of the disc.

    Science.gov (United States)

    Takada, Toru; Nishida, Kotaro; Doita, Minoru; Kurosaka, Masahiro

    2002-07-15

    Rat and human intervertebral disc specimens were examined immunohistochemically. Reverse transcription polymerase chain reaction (RT-PCR) analysis was also performed on rat disc tissue to demonstrate the existence of Fas ligand. To clarify the existence of Fas ligand on intact intervertebral disc cells. The nucleus pulposus has been reported to be an immune-privileged site. The immune-privileged characteristic in other tissues such as the retina and testis has been attributed to the local expression of Fas ligand, which acts by inducing apoptosis of invading Fas-positive T-cells. The existence of Fas ligand in normal disc cells has not yet been addressed. Skeletally mature SD male rats were killed, and the coccygeal discs were harvested. Human disc specimens were obtained from idiopathic scoliosis patients during surgical procedures. Immunohistochemical staining for Fas ligand was performed for cross-sections of the discs by standard procedures. Reverse transcription polymerase chain reaction analysis was also carried out to demonstrate Fas ligand mRNA expression on rat intervertebral discs. Testes of the rats were used for positive controls, and muscles were used for negative controls. The sections were observed by light microscopy. The nucleus pulposus cells exhibited intense positive immune staining for Fas ligand. The outer anulus fibrosus cells and notochordal cells exhibited little immunopositivity. The positive controls exhibited positive immune staining, and the negative control showed no immunopositivity. The result of RT-PCR confirmed the existence of Fas ligand in disc cells. The human nucleus pulposus cells showed a similar predilection to rat disc cells. We demonstrated the existence of Fas ligand on disc cells, which should play a key role in the potential molecular mechanism to maintain immune privilege of the disc. Immune privilege and Fas ligand expression of the intervertebral disc may provide a new insight for basic science research as well as

  18. Civic Orientation in Cultures of Privilege: What Role Do Schools Play?

    Science.gov (United States)

    Ballard, Parissa J.; Caccavale, Laura; Buchanan, Christy M.

    2015-01-01

    The context of privilege provides unique opportunities and challenges for youth civic development. A mixed-method approach was used to examine links between school-based community service, school climate, and civic orientation among students in cultures of privilege. Surveys completed by students (N = 376) at two private high schools--one with an…

  19. 14 CFR 61.321 - How do I obtain privileges to operate an additional category or class of light-sport aircraft?

    Science.gov (United States)

    2010-01-01

    ... additional category or class of light-sport aircraft? 61.321 Section 61.321 Aeronautics and Space FEDERAL... INSTRUCTORS, AND GROUND INSTRUCTORS Sport Pilots § 61.321 How do I obtain privileges to operate an additional category or class of light-sport aircraft? If you hold a sport pilot certificate and seek to operate an...

  20. Agency privileges and immunities

    International Nuclear Information System (INIS)

    1969-01-01

    Switzerland has become the thirty-fifth Member State to be a party to the Agreement on the Privileges and Immunities of the International Atomic Energy Agency. Its Resident Representative, Ambassador Alfred Eschler, deposited his Government's instrument of acceptance on 16 September. This is the fourth such instrument to be deposited with the Agency since the beginning of this year, the others being Ecuador on 16 April, Niger on 17 June and Vietnam on 31 July. (author)

  1. Chalcone: A Privileged Structure in Medicinal Chemistry.

    Science.gov (United States)

    Zhuang, Chunlin; Zhang, Wen; Sheng, Chunquan; Zhang, Wannian; Xing, Chengguo; Miao, Zhenyuan

    2017-06-28

    Privileged structures have been widely used as an effective template in medicinal chemistry for drug discovery. Chalcone is a common simple scaffold found in many naturally occurring compounds. Many chalcone derivatives have also been prepared due to their convenient synthesis. These natural products and synthetic compounds have shown numerous interesting biological activities with clinical potentials against various diseases. This review aims to highlight the recent evidence of chalcone as a privileged scaffold in medicinal chemistry. Multiple aspects of chalcone will be summarized herein, including the isolation of novel chalcone derivatives, the development of new synthetic methodologies, the evaluation of their biological properties, and the exploration of the mechanisms of action as well as target identification. This review is expected to be a comprehensive, authoritative, and critical review of the chalcone template to the chemistry community.

  2. Stuck in the Middle with Jews: Religious Privilege and Jewish Campus Life

    Science.gov (United States)

    Goren, Seth

    2014-01-01

    Many scholars have examined religious privilege in society and on campus, evidencing the privileged place Christianity generally enjoys and the marginalization that Jews often encounter, regardless of the school they attend. That said, in considering the Jewish higher education experience, something else is at play here. When juxtaposed with…

  3. Liberal luxury: Decentering Snowden, surveillance and privilege

    Directory of Open Access Journals (Sweden)

    Piro Rexhepi

    2016-11-01

    Full Text Available This paper reflects on the continued potency of veillance theories to traverse beyond the taxonomies of surveillance inside liberal democracies. It provides a commentary on the ability of sousveillance to destabilise and disrupt suer/violence by shifting its focus from the centre to the periphery, where Big Data surveillance is tantamount to sur/violence. In these peripheral political spaces, surveillance is not framed by concerns over privacy, democracy and civil society; rather, it is a matter of life and death, a technique of both biopolitical and thanatopolitical power. I argue that the universalist, and universalizing, debates over surveillance cannot be mapped through the anxieties of privileged middle classes as they would neither transcend nor make possible alternative ways of tackling the intersection of surveillance and violence so long as they are couched in the liberal concerns for democracy. I call this phenomenon “liberal luxury,” whereby debates over surveillance have over-emphasised liberal proclivities at the expense of disengaging those peripheral populations most severely affected by sur/violence.

  4. [Does therapeutic privilege have a place in modern medicine?

    Science.gov (United States)

    Salinas, Rodrigo R; Echeverría B, Carlos; Arriagada U, Anamaría; Goic G, Alejandro; Quintana V, Carlos; Rojas O, Alberto; Serani M, Alejandro; Taboada R, Paulina; Vacarezza Y, Ricardo

    2017-09-01

    During the last years, bioethical discussion has highlighted the role of the patients' autonomy, being informed consent its particular expression, about decisions that they should make about their own health. The Hippocratic tradition, the deontological positions of the Geneva Declaration of the World Medical Association and numerous codes of ethics in various countries, require that the physician, above all, should ensure patients' health. In this context the discussion on pros and cons for the so-called "therapeutic privilege" are discussed. The "therapeutic privilege" refers to the withholding of information by the clinician during the consent process in the belief that disclosure of this information would lead to harm or suffering of the patient. The circumstances and conditions in which this privilege can become valid are discussed. Special reference is made in order to respect multiculturalism and to the possibility of obtaining advice from health care ethics committees. The role of prudence in the doctor-patient relation must be highlighted. Disclosure of information should be subordinated and oriented to the integral well-being of the patient.

  5. Perceived Discrimination and Privilege in Health Care: The Role of Socioeconomic Status and Race.

    Science.gov (United States)

    Stepanikova, Irena; Oates, Gabriela R

    2017-01-01

    This study examined how perceived racial privilege and perceived racial discrimination in health care varied with race and socioeconomic status (SES). The sample consisted of white, black, and Native American respondents to the Behavioral Risk Factor Surveillance System (2005-2013) who had sought health care in the past 12 months. Multiple logistic regression models of perceived racial privilege and perceived discrimination were estimated. Analyses were performed in 2016. Perceptions of racial privilege were less common among blacks and Native Americans compared with whites, while perceptions of racial discrimination were more common among these minorities. In whites, higher income and education contributed to increased perceptions of privileged treatment and decreased perceptions of discrimination. The pattern was reversed in blacks, who reported more discrimination and less privilege at higher income and education levels. Across racial groups, respondents who reported foregone medical care due to cost had higher risk of perceived racial discrimination. Health insurance contributed to less perceived racial discrimination and more perceived privilege only among whites. SES is an important social determinant of perceived privilege and perceived discrimination in health care, but its role varies by indicator and racial group. Whites with low education or no health insurance, well-educated blacks, and individuals who face cost-related barriers to care are at increased risk of perceived discrimination. Policies and interventions to reduce these perceptions should target structural and systemic factors, including society-wide inequalities in income, education, and healthcare access, and should be tailored to account for racially specific healthcare experiences. Copyright © 2016 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

  6. Illuminating Everyday Performances of Privilege and Oppression

    Science.gov (United States)

    Heuman, Amy N.

    2018-01-01

    Courses: Intercultural Communication, Interracial Communication, Gender and Communication, Introduction to Communication Course (within a unit on culture), and any courses encouraging critical analyses of power. Objectives: This activity will: illuminate the ways in which everyday performances of privilege and resulting oppressions connect with…

  7. Space and commodity-based society

    Directory of Open Access Journals (Sweden)

    Gvozden Vladimir

    2015-01-01

    Full Text Available The space is privileged in the commodity-based society. It is well known that the economic space in the 19th and 20th centuries rapidly managed to subordinate all other areas 'conveying and instilling in them their own meanings and goals' (G. Milatović. A new form of space that qualifies commodity society was created, marked by dualities: openness-closeness, private-public, sameness-difference. This paper is an attempt to criticize the usual analysis of the categories of commodity-space, linked to the ambivalent role of the state as a guarantor of the functioning of the commodity-based society, as well as its controlling instance. The increasing delocalisation of the political changes the nature of the space in the commodity-based society. Privileged areas are produced that create an illusion of protection of consumers (shopping malls, gated communities, theme parks, video surveillance, while at the same time social differentiation and identification are produced through the symbolic order of commodities and a sense of inclusion or exclusion from that order. At the same time, the examples of tourism and selling places demonstrate that such a commodity-space unusually easy reconciles sameness and difference. It entails uniformity to help achieve the fluctuation of goods, while insisting on the local as different, especially in terms of the role of particularity in the global trade.

  8. Inequality as ingroup privilege or outgroup disadvantage: the impact of group focus on collective guilt and interracial attitudes.

    Science.gov (United States)

    Powell, Adam A; Branscombe, Nyla R; Schmitt, Michael T

    2005-04-01

    Among members of privileged groups, social inequality is often thought of in terms of the disadvantages associated with outgroup membership. Yet inequality also can be validly framed in terms of ingroup privilege. These different framings have important psychological and social implications. In Experiment 1 (N = 110), White American participants assessed 24 statements about racial inequality framed as either White privileges or Black disadvantages. In Experiment 2 (N = 122), White participants generated examples of White privileges or Black disadvantages. In both experiments, a White privilege framing resulted in greater collective guilt and lower racism compared to a Black disadvantage framing. Collective guilt mediated the manipulation's effect on racism. In addition, in Experiment 2, a White privilege framing decreased White racial identification compared to a Black disadvantage framing. These findings suggest that representing inequality in terms of outgroup disadvantage allows privileged group members to avoid the negative psychological implications of inequality and supports prejudicial attitudes.

  9. Searle on External Realism and "Privileged Conceptual Scheme"

    Czech Academy of Sciences Publication Activity Database

    Marvan, Tomáš

    2012-01-01

    Roč. 19, Supp.2 (2012), s. 31-39 ISSN 1335-0668 Institutional support: RVO:67985955 Keywords : John Searle * external realism * constructivism * conceptual relativity * Privilege Conceptual Scheme Subject RIV: AA - Philosophy ; Religion

  10. 75 FR 25202 - Action Affecting Export Privileges; Orion Air, S.L. and Syrian Pearl Airlines; Order Renewing...

    Science.gov (United States)

    2010-05-07

    ... DEPARTMENT OF COMMERCE Bureau of Industry and Security Action Affecting Export Privileges; Orion Air, S.L. and Syrian Pearl Airlines; Order Renewing Order Temporarily Denying Export Privileges Orion... Denying the Export Privileges of Respondents Orion Air, S.L. (``Orion Air'') and Syrian Pearl Airlines...

  11. Hugo Grotius, Privileges, Fundamental Laws and Rights

    NARCIS (Netherlands)

    van Nifterik, G.

    2011-01-01

    As a result of the political developments in the young and struggling Dutch Republic, Grotius experienced the lack of, and the need for juridical protection of some basic rights against infringements by the government. The privileges, taken for fundamental laws, did not provide this protection

  12. A probabilistic model of RNA conformational space

    DEFF Research Database (Denmark)

    Frellsen, Jes; Moltke, Ida; Thiim, Martin

    2009-01-01

    , the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows...... conformations for 9 out of 10 test structures, solely using coarse-grained base-pairing information. In conclusion, the method provides a theoretical and practical solution for a major bottleneck on the way to routine prediction and simulation of RNA structure and dynamics in atomic detail.......The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling...

  13. Clinical privileges for laparoscopic surgery.

    Science.gov (United States)

    Albrink, M H; Rosemurgy, A S

    1993-06-01

    Laparoscopic cholecystectomy has undergone an explosive growth. Its benefits to patients--shortened recovery time and less pain--became immediately obvious. The procedure's development and adaptation have largely been devised and implemented by ingenious and creative private practitioners, not the typical mode of introduction. Most or many new procedures in the past evolved from academic institutions after laboratory and then clinical trials. With rapid development and acceptance has come an additional new burden among medical practitioners: credentialing and granting clinical privileges.

  14. Customers' expectations of complaint handling by airline service: privilege status and reasonability of demands from a social learning perspective.

    Science.gov (United States)

    Chiou, Wen-Bin; Chang, Ming-Hsu; Yang, Chao-Chin

    2009-04-01

    In the airline industry, membership and cabin class are noticeable servicescape features of customers' privilege status. Customers may learn that higher privilege customers are more desired and endured by the airline. From the customers' point of view, those with higher privilege may expect their demands to be complied with when they complain. The present study employed hypothetical scenarios to investigate how the privilege status of passengers and reasonability of their demands influenced their expectations toward the compliance of airline personnel. Analysis showed that higher privilege customers were more likely to expect airline personnel to comply with their demands. Moreover, participants with medium or high levels of privilege status had greater expectations of compliance even when demands were unreasonable. In sum, customer expectations toward complaint handling reflected predictions based on social learning.

  15. The functional half-life of an mRNA depends on the ribosome spacing in an early coding region

    DEFF Research Database (Denmark)

    Pedersen, Margit; Nissen, Søren; Mitarai, Namiko

    2011-01-01

    Bacterial mRNAs are translated by closely spaced ribosomes and degraded from the 5'-end, with half-lives of around 2 min at 37 °C in most cases. Ribosome-free or "naked" mRNA is known to be readily degraded, but the initial event that inactivates the mRNA functionally has not been fully described...

  16. Hidden climato-economic roots of differentially privileged cultures

    NARCIS (Netherlands)

    Van de Vliert, Evert

    This theory-based study tests the interactive impacts of the demands of thermal climate and wealth resources on variations in privileged culture represented by mental health, personal freedom, and political democracy. Multiple regression analysis of aggregated survey data covering 106 countries

  17. 17 CFR 240.12f-1 - Applications for permission to reinstate unlisted trading privileges.

    Science.gov (United States)

    2010-04-01

    ... reinstate unlisted trading privileges. 240.12f-1 Section 240.12f-1 Commodity and Securities Exchanges... Rules and Regulations Under the Securities Exchange Act of 1934 Unlisted Trading § 240.12f-1 Applications for permission to reinstate unlisted trading privileges. (a) An application to reinstate unlisted...

  18. 78 FR 37785 - Order Denying Export Privileges

    Science.gov (United States)

    2013-06-24

    ... DEPARTMENT OF COMMERCE Bureau of Industry and Security Order Denying Export Privileges In the... Order with the Under Secretary of Commerce for Industry and Security. The appeal must be filed within 45... the Internal Security Act of 1950 (50 U.S.C. 783(b)), or section 38 of the Arms Export Control Act (22...

  19. Agreement on the Privileges and Immunities of the International Atomic Energy Agency; Accord sur les Privileges et Immunites ee 'Agence

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1967-10-31

    The Agreement on the Privileges and Immunities of the International Atomic Energy Agency, the text of which is reproduced herein, was approved by the Board of Governors on 1 July 1959. As required by section 38, the Director General has transmitted a certified copy of the Agreement to the Government of each Member of the Agency, and will transmit such a copy to the Government of every State that becomes a Member hereafter [French] Le texte de l'Accord sur les privileges et immunites de l'Agence internationale de l'energie atomique, qui a ete approuve par le Conseil des gouverneurs le 1er juillet 1959, est reproduit dans le present document pour l'information de tous les Etats Membres. Conformment aux dispositions de la section 38 de l'Accord, le Directeur general a adresse au gouvernement de chaque Etat Membre une copie certifiee conforme de l'Accord et en enverra une auv gouvernement de chaque nouvel Etat Membre.

  20. The Embeddedness of White Fragility within White Pre-Service Principals' Reflections on White Privilege

    Science.gov (United States)

    Hines, Mack T., III

    2016-01-01

    This study analyzes the prevalence of white fragility within the six white, pre-service principals' online responses to readings about white privilege. Six white, pre-service principals were asked to provide commentary to class readings on the relevance of white privilege to their preparation for future positions as principals. The findings showed…

  1. 77 FR 27418 - Order Denying Export Privileges

    Science.gov (United States)

    2012-05-10

    ... DEPARTMENT OF COMMERCE Bureau of Industry and Security Order Denying Export Privileges In the..., Baniameri may file an appeal of this Order with the Under Secretary of Commerce for Industry and Security... (50 U.S.C. 1701-1706); 18 U.S.C. 793, 794 or 798; section 4(b) of the Internal Security Act of 1950...

  2. White Privilege, Psychoanalytic Ethics, and the Limitations of ...

    African Journals Online (AJOL)

    Whereas the critique of whiteness involves both philosophical and psychological scrutiny, subsequent calls for white political silence and withdrawal have yet to be ... These concepts throw a critical light on disavowals of white privilege and provide a novel means of thinking how white narcissism might be relinquished.

  3. Price or Privilege? Customer Perception on Loyalty Programs

    Directory of Open Access Journals (Sweden)

    Asnan Furinto

    2011-12-01

    Full Text Available The main purpose of the research is to understand how customers perceive loyalty programs. The author argues that types of loyalty programs could be classified into two: price based and privilege based. This research models that customer perceptions on loyalty programs, differ between these two types, and is contingent upon the relationship between customers and firm. Using settings of air-line domestic passengers and bank customers in Indonesia, the research provides evidence that price based rewards are perceived to provide higher utility perception in contractual relationships compared to non contractual relationships. However, this research failed to provide empirical support that privilege based rewards are perceived to provide higher utility perception in non contractual relation-ship compared to contractual relationship. Firms are therefore, encouraged to incorporate affective elements into their loyalty programs, on top of monetary elements, in order for the loyalty programs to be better perceived by their customers.

  4. 76 FR 22865 - Action Affecting Export Privileges; Orion Air, S.L. and Syrian Pearl Airlines

    Science.gov (United States)

    2011-04-25

    ... DEPARTMENT OF COMMERCE Bureau of Industry and Security Action Affecting Export Privileges; Orion Air, S.L. and Syrian Pearl Airlines In the Matter of: Orion Air, S.L., Canada Real de Merinas, 7... days the Order Temporarily Denying the Export Privileges of Respondents Orion Air, S.L. (``Orion Air...

  5. Topological recursion for chord diagrams, RNA complexes, and cells in moduli spaces

    DEFF Research Database (Denmark)

    Andersen, Jørgen Ellegaard; Chekhov, Leonid O.; Penner, Robert

    2013-01-01

    and free energies are convergent for small t and all s as a perturbation of the Gaussian potential, which arises for st=0. This perturbation is computed using the formalism of the topological recursion. The corresponding enumeration of chord diagrams gives at once the number of RNA complexes of a given...... topology as well as the number of cells in Riemann's moduli spaces for bordered surfaces. The free energies are computed here in principle for all genera and explicitly for genera less than four....

  6. Personal aggrandizement: an insight into Ben Enwonwu's privilege ...

    African Journals Online (AJOL)

    This paper titled Personal Aggrandizement: An Insight into Ben Enwonwu's Privilege Position in the Evolution of Nigerian Art, looks at the first trained artists. How the artists were classified by their styles either in the naturalistic, the abstract or the expressive imageries. The study examines and compares the contributions of ...

  7. Agreement on the privileges and immunities of the Agency

    International Nuclear Information System (INIS)

    1993-04-01

    The document lists the 63 Member States which by 28 February 1993 had accepted the Agreement on the Privileges and Immunities of the International Atomic Energy Agency. The list is followed by the texts of reservations made to the Agreement

  8. THE DEMAND FOR MORE/PRIVILEGED (THINGS): Leisured Women, Consumption Practices, and Gated Community

    OpenAIRE

    TALU, Nilüfer; TAŞKIN, Burcu

    2016-01-01

    The great body of people struggles for identity construction through the things and practices to live up to a lifestyle. Living in the gated community means bordering the lives from the city life. By means of privileged houses, a gated community functions for the terms as privilege, prestige, safety and hygiene. This study questions consumption practices of women of a gated community in Izmir. While the informants having different education levels, they spend their leisure times in a similar ...

  9. The costume of Shangri-La: thoughts on white privilege, cultural appropriation, and anti-asian racism.

    Science.gov (United States)

    Kleisath, C Michelle

    2014-01-01

    This piece poses cultural appropriation as an undertheorized aspect of white privilege in White Privilege Studies. By way of narrative exploration, it asserts that a paucity of scholarship on Orientalism and anti-Asian racism has created a gap in White Privilege Studies that curbs its radical transformative potential. It argues for the value of a structural and historically focused lens for understanding the issue of cultural appropriation, and extends questions of culture and race relations beyond the borders of the United States. It also explores the complex ways that interracial and transnational relationships can influence white racial identity, and illustrates the disruptive potential that queer interracial relationships can offer to dominant historical patterns of white behavior.

  10. Tachyons imply the existence of a privileged frame

    Energy Technology Data Exchange (ETDEWEB)

    Sjoedin, T.; Heylighen, F.

    1985-12-16

    It is shown that the existence of faster-than-light signals (tachyons) would imply the existence (and detectability) of a privileged inertial frame and that one can avoid all problems with reversed-time order only by using absolute synchronization instead of the standard one. The connection between these results and the EPR-paradox is discussed.

  11. Agreement on the privileges and immunities of the Agency

    International Nuclear Information System (INIS)

    1991-01-01

    The document lists the 61 Member States which by 1 January 1991, have accepted the Agreement on the Privileges and Immunities of the International Atomic Energy Agency as provided for in Section 38 thereof. This list is followed by the texts of reservations made to the Agreement

  12. Privileging Peer Review: Implications for Undergraduates

    Directory of Open Access Journals (Sweden)

    Amy E. Mark

    2011-11-01

    Full Text Available Librarians and teaching faculty privilege peer review articles out of ideals rooted in academic culture more then for pedagogical reasons. Undergraduates would find greater benefit in the opportunity to search and critique sources related to their personal and creative interests as well as relevant to academic research projects. Librarians can adopt the role of change-agents by engaging relevant teaching faculty in discussions about the goal of research assignments relative to peer review literature. Framing this discussion is Paulo Freire’s theory of banking information discussed in Pedagogy of the Oppressed (2000.

  13. Fas ligand expression in human and mouse cancer cell lines; a caveat on over-reliance on mRNA data

    Directory of Open Access Journals (Sweden)

    Ryan Aideen E

    2006-02-01

    Full Text Available Abstract Background During carcinogenesis, tumors develop multiple mechanisms for evading the immune response, including upregulation of Fas ligand (FasL/CD95L expression. Expression of FasL may help to maintain tumor cells in a state of immune privilege by inducing apoptosis of anti-tumor immune effector cells. Recently this idea has been challenged by studies reporting that tumor cells of varying origin do not express FasL. In the present study, we aimed to comprehensively characterize FasL expression in tumors of both murine and human origin over a 72 hour time period. Methods RNA and protein was extracted from six human (SW620, HT29, SW480, KM12SM, HCT116, Jurkat and three mouse (CMT93, CT26, B16F10 cancer cell lines at regular time intervals over a 72 hour time period. FasL expression was detected at the mRNA level by RT-PCR, using intron spanning primers, and at the protein level by Western Blotting and immunofluorescence, using a polyclonal FasL- specific antibody. Results Expression of FasL mRNA and protein was observed in all cell lines analysed. However, expression of FasL mRNA varied dramatically over time, with cells negative for FasL mRNA at many time points. In contrast, 8 of the 9 cell lines constitutively expressed FasL protein. Thus, cells can abundantly express FasL protein at times when FasL mRNA is absent. Conclusion These findings demonstrate the importance of complete analysis of FasL expression by tumor cells in order to fully characterize its biological function and may help to resolve the discrepancies present in the literature regarding FasL expression and tumor immune privilege.

  14. Privileged Social Identities and Diversity Leadership in Higher Education

    Science.gov (United States)

    Owen, David S.

    2009-01-01

    In this paper, I examine the desirability and effectiveness of appointing in predominantly White institutions of higher education diversity leaders who possess privileged social identities. I conclude that the desirability and effectiveness of such individuals depends on their ascribed identities (especially in terms of race, gender, class, and…

  15. 42 CFR 424.540 - Deactivation of Medicare billing privileges.

    Science.gov (United States)

    2010-10-01

    ... change in practice location, a change of any managing employee, and a change in billing services. A... 42 Public Health 3 2010-10-01 2010-10-01 false Deactivation of Medicare billing privileges. 424.540 Section 424.540 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND...

  16. Populism, Prejudice and the Rhetoric of Privilege

    Directory of Open Access Journals (Sweden)

    Alberto Giordano

    2017-08-01

    Full Text Available The paper aims to show, by means of a close look at the most recent samples of political discourse in Europe and America, how much and how frequently populists set up their narratives around a relatively small number of patterns, such as the worship of the people, a (more or less overt appeal to prejudice and the rhetoric of privilege. In so doing, it offers some useful insights into the nature of contemporary populism.

  17. 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)

  18. Toleration, Liberty and Privileges

    DEFF Research Database (Denmark)

    Simonton, Deborah

    2017-01-01

    Guilds are usually seen as the epitome of economic regulation and organization in early modern European towns. As organisations closely tied to the nominal male lifecycle, historians of women have tended to be chary of them and identified guilds as a key mechanism for restricting women’s access...... there were shifts in how the companies operated, who they could maintain control over and the effectiveness of these essentially mercantilist organisations in the face of growing pressures from population growth after the seventeenth–century wars, the rise in laissez faire ideas and increasing local...... and international commerce. Much of these battles and skirmishes were about gender: ‘outsider’ men encroaching on the privileges of guildsmen, and women encroaching on the worlds of men. This is a many-faceted discussion, but one that is fundamental to the urban world of eighteenth-century Europe where permission...

  19. 78 FR 58519 - Denial of Export Privileges; Sixing Liu

    Science.gov (United States)

    2013-09-24

    ... Powers Act (50 U.S.C. 1701, et seq. (2006 & Supp. IV 2010)). I have received notice of Liu's conviction... DEPARTMENT OF COMMERCE Bureau of Industry and Security Denial of Export Privileges; Sixing Liu In the Matter of: Sixing Liu, a/k/a Steve Liu, Inmate 43102-424, FCI Oxford, Federal Correctional...

  20. Rights versus labour privileges for ionizing radiation exposure activities

    International Nuclear Information System (INIS)

    Borges, Jose Carlos

    1996-01-01

    The present panorama of brazilian legislation concerning activities in which (may) occurs exposure to ionizing radiations, involves several incoherencies and privileges, as a consequence of legal rights generated from labor principles which have no social or scientific embasement. In this study, several legal labor topics are analysed and a new doutrinary context is proposed. (author)

  1. Agreement on the privileges and immunities of the Agency

    International Nuclear Information System (INIS)

    1987-05-01

    The document contains the list of Member States which, by 1 May 1987 had accepted the Agreement on the Privileges and Immunities of the International Atomic Energy Agency. The list is followed by the texts of reservations to the Agreement made by some of the Members in question when depositing their respective instruments of acceptance with the Director General

  2. Working against the Grain: White Privilege in Human Resource Development

    Science.gov (United States)

    Monaghan, Catherine H.

    2010-01-01

    Research demonstrates that white privilege and racism have a direct impact on the success of businesses and the economy (Updegrave, Byrd, and Leuchter, 1989). Furthermore, organizations that are effective in integrating diversity experience increased organizational viability and profitability. Employees' intentions and actions of engaging in the…

  3. 76 FR 6554 - Appeal Authority When Researcher Privileges Are Revoked

    Science.gov (United States)

    2011-02-07

    ..., aligning the two disciplinary appeal processes. Researchers retain their full right to appeal revocation... researchers' privileges under certain circumstances by following the procedures outlined in 36 CFR part 1254... NARA facility director; a process which is also described in 36 CFR part 1254. The current appeal...

  4. Perceiving social inequity: when subordinate-group positioning on one dimension of social hierarchy enhances privilege recognition on another.

    Science.gov (United States)

    Rosette, Ashleigh Shelby; Tost, Leigh Plunkett

    2013-08-01

    Researchers have suggested that viewing social inequity as dominant-group privilege (rather than subordinate-group disadvantage) enhances dominant-group members' support for social policies aimed at lessening such inequity. However, because viewing inequity as dominant-group privilege can be damaging to dominant-group members' self-images, this perspective is frequently resisted. In the research reported here, we explored the circumstances that enhance the likelihood of dominant-group members' viewing inequity as privilege. Because social hierarchies have multiple vertical dimensions, individuals may have high status on one dimension but low status on another. We predicted that occupying a subordinate position on one dimension of social hierarchy could enhance perceptions of one's own privilege on a different dimension of hierarchy, but that this tendency would be diminished among individuals who felt they had achieved a particularly high level of success. Results from three studies that considered gender-based and race-based hierarchies in organizational settings supported our hypothesis.

  5. A theory of biological relativity: no privileged level of causation.

    Science.gov (United States)

    Noble, Denis

    2012-02-06

    Must higher level biological processes always be derivable from lower level data and mechanisms, as assumed by the idea that an organism is completely defined by its genome? Or are higher level properties necessarily also causes of lower level behaviour, involving actions and interactions both ways? This article uses modelling of the heart, and its experimental basis, to show that downward causation is necessary and that this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes. These insights are then generalized. A priori, there is no privileged level of causation. The relations between this form of 'biological relativity' and forms of relativity in physics are discussed. Biological relativity can be seen as an extension of the relativity principle by avoiding the assumption that there is a privileged scale at which biological functions are determined.

  6. Let's Talk about Race, Baby: How a White Professor Teaches White Students about White Privilege and Racism

    Science.gov (United States)

    Heinze, Peter

    2008-01-01

    There are a variety of methods by which the themes of White privilege and racism can be presented to White students. By using the concept of racial identity a continuum of racism can be considered. Furthermore, addressing White privilege and racism in the context of a multicultural psychology course allows White students to have a greater…

  7. 13 CFR 114.111 - Does the attorney-client privilege apply when SBA employees are represented by the Government?

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Does the attorney-client privilege... Does the attorney-client privilege apply when SBA employees are represented by the Government? When... representational assistance for such an employee, those attorneys undertake a full and traditional attorney-client...

  8. Examining our privileges and oppressions: incorporating an intersectionality paradigm into nursing.

    Science.gov (United States)

    Van Herk, Kimberley A; Smith, Dawn; Andrew, Caroline

    2011-03-01

    An intersectionality paradigm is a means by which nurses can attend to issues of oppression and privilege within their practice and profession. Intersectionality is introduced as an essential theory to help debunk the hegemony of the 'white, middle class' perspective that often directs nursing research, practice, and education. The values and benefits of using an intersectionality paradigm in nursing are shown through recent research done with Aboriginal women. These findings contribute to an increased understanding of the importance and necessity of attending to the power relations that dominate nursing care encounters and influence the way nurses provide care. By acknowledging and responding to the presence of privilege and oppression and the associated power dynamics within the therapeutic encounter, nursing can strive further in helping to alleviate social injustices and health disparities that arise from unequal power relations. © 2011 Blackwell Publishing Ltd.

  9. Library of biphenyl privileged substructures using a safety-catch linker approach

    DEFF Research Database (Denmark)

    Severinsen, Rune; Bourne, Gregory T; Tran, Tran T

    2008-01-01

    A biphenyl privileged structure library containing three attachment points were synthesized using a catechol-based safety-catch linker strategy. The method requires the attachment of a bromo-acid to the linker, followed by a Pd-catalyzed Suzuki cross-coupling reaction. Further derivatization...

  10. 36 CFR 1254.50 - Does NARA consider reinstating research privileges?

    Science.gov (United States)

    2010-07-01

    ... Research Room Rules Other Conduct Rules § 1254.50 Does NARA consider reinstating research privileges? (a) You have 30 calendar days after the date of revocation to appeal the action in writing and seek... identification card, which we issue to you if your conduct during the probationary period follows the rules of...

  11. Systematic Analysis of mRNA and miRNA Expression of 3D-Cultured Neural Stem Cells (NSCs in Spaceflight

    Directory of Open Access Journals (Sweden)

    Yi Cui

    2018-01-01

    Full Text Available Recently, with the development of the space program there are growing concerns about the influence of spaceflight on tissue engineering. The purpose of this study was thus to determine the variations of neural stem cells (NSCs during spaceflight. RNA-Sequencing (RNA-Seq based transcriptomic profiling of NSCs identified many differentially expressed mRNAs and miRNAs between space and earth groups. Subsequently, those genes with differential expression were subjected to bioinformatic evaluation using gene ontology (GO, Kyoto Encyclopedia of Genes and Genomes pathway (KEGG and miRNA-mRNA network analyses. The results showed that NSCs maintain greater stemness ability during spaceflight although the growth rate of NSCs was slowed down. Furthermore, the results indicated that NSCs tended to differentiate into neuron in outer space conditions. Detailed genomic analyses of NSCs during spaceflight will help us to elucidate the molecular mechanisms behind their differentiation and proliferation when they are in outer space.

  12. 75 FR 66728 - Action Affecting Export Privileges; Orion Air, S.L. and Syrian Pearl Airlines: Orion Air, S.L...

    Science.gov (United States)

    2010-10-29

    ... DEPARTMENT OF COMMERCE Bureau of Industry and Security Action Affecting Export Privileges; Orion Air, S.L. and Syrian Pearl Airlines: Orion Air, S.L., Canada Real de Merinas, 7 Edificio 5, 3'A... Denying the Export Privileges of Respondents Orion Air, S.L. (``Orion Air'') and Syrian Pearl Airlines...

  13. Privilege of Witness under Ethical Perspective%伦理视野下的证人拒证权

    Institute of Scientific and Technical Information of China (English)

    李远红; 高华

    2011-01-01

    论证了证人拒证权的伦理属性,认为它表现在起源的伦理性、权利本身的功利性和权利内容的人性关怀三方面。这使得从伦理的视野审视证人拒证权成为必要。在伦理的视野下,证人拒证权是法律对效率价值的追求,是一种必要的“恶”;是宪法核心价值人性尊严原则在证据法中的体现;是对正义的守护。我国法律缺乏对证人拒证权的伦理审视,缺乏对拒证权必要的伦理规制,包括诚信规制和德性规制。%The privilege of witness has the inherent ethical attributes, which could be reflected in the ethical origin, the utilitarian of the right and right's content of human caring. As a result, it is necessary to carefully examine the privilege under ethical perspective. Under ethical perspective, witness' privilege is the pursue of law to the efficiency value, is one kind of essential wickedness; is the embodiment of principle of human dignity in the law of evidence, which is the core value of constitution; and is the guardian of justice. China's law system lacks the ethical review on privilege of witness, lacks necessary ethical regulation on privilege, including regulation of credit and regulation of morality.

  14. The Color of Supremacy: Beyond the Discourse of "White Privilege"

    Science.gov (United States)

    Leonardo, Zeus

    2004-01-01

    In the last decade, the study of white privilege has reached currency in the educational and social science literature. Concerned with the circuits and meanings of whiteness in everyday life, scholars have exposed the codes of white culture, worldview of the white imaginary, and assumptions of the invisible marker that depends on the racial other…

  15. Peeling the Onion: Teaching Critical Literacy with Students of Privilege.

    Science.gov (United States)

    Foss, Abigail

    2002-01-01

    Describes a teacher who explores her passion for critical literacy by challenging students of privilege to name their identities and disrupt the familiar. Creates a classroom founded on the philosophy that every student needs and deserves to be exposed to critical literacy--reading literature and their own lives with an awareness of systems of…

  16. Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer

    International Nuclear Information System (INIS)

    Baba, Seiki; Someya, Tatsuhiko; Kawai, Gota; Nakamura, Kouji; Kumasaka, Takashi

    2010-01-01

    The RNA-binding protein Hfq from B. subtilis was crystallized using the hanging-drop vapour-diffusion method in two crystal forms that belonged to space groups I422 and F222; diffraction data were collected to 2.2 Å resolution from both forms. The Hfq protein is a hexameric RNA-binding protein which regulates gene expression by binding to RNA under the influence of diverse environmental stresses. Its ring structure binds various types of RNA, including mRNA and sRNA. RNA-bound structures of Hfq from Escherichia coli and Staphylococcus aureus have been revealed to have poly(A) RNA at the distal site and U-rich RNA at the proximal site, respectively. Here, crystals of a complex of the Bacillus subtilis Hfq protein with an A/G-repeat 7-mer RNA (Hfq–RNA) that were prepared using the hanging-drop vapour-diffusion technique are reported. The type 1 Hfq–RNA crystals belonged to space group I422, with unit-cell parameters a = b = 123.70, c = 119.13 Å, while the type 2 Hfq–RNA crystals belonged to space group F222, with unit-cell parameters a = 91.92, b = 92.50, c = 114.92 Å. Diffraction data were collected to a resolution of 2.20 Å from both crystal forms. The hexameric structure of the Hfq protein was clearly shown by self-rotation analysis

  17. Journalists' Privilege to Withhold Information in Judicial and Other Proceedings: State Shield Statutes

    National Research Council Canada - National Science Library

    Cohen, Henry

    2007-01-01

    .... To date, 33 states and the District of Columbia have recognized a journalists' privilege through the enactment of press "shield laws," which protect the relationship between reporters, their source...

  18. 13 CFR 120.1711 - Suspension or termination of Program participation privileges.

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Suspension or termination of Program participation privileges. 120.1711 Section 120.1711 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION BUSINESS LOANS Establishment of SBA Secondary Market Guarantee Program for First Lien Position 504...

  19. 77 FR 65463 - Filing of Privileged Materials and Answers to Motions

    Science.gov (United States)

    2012-10-29

    ... Government Paperwork Elimination Act and the E-Government Act of 2002. First, the Commission establishes two... the E-Government Act of 2002. First, the Commission establishes two categories of privileged material... Used in 44 Administrative Proceedings 1. Comments 45 2. Commission Response 46 E. Procedures for...

  20. Students' Imaginings of Spaces of Learning in Outdoor and Environmental Education

    Science.gov (United States)

    Preston, Lou

    2014-01-01

    In this article, I interrogate students' stories about the spaces and places in a tertiary Outdoor and Environmental Education course that support and shape their environmental ethics. Drawing on a longitudinal qualitative study, I explore the ways in which particular sites of learning (outdoor, practical learning) are privileged and how…

  1. Client Privacy and the School Counselor: Privilege, Ethics, and Employer Policies.

    Science.gov (United States)

    Tompkins, Loren; Mehring, Teresa

    1993-01-01

    Notes that number of school counselors are confused about issues of confidentiality. Discusses issues of privileged communication, confidentiality, and employer policies. Concludes with section on law, ethics, employer policy, and the counselor. Provides six recommendations for school counselors to use in their day-to-day practice to avoid…

  2. Public Space and Plurality of Beliefs

    Directory of Open Access Journals (Sweden)

    Francesc Rovira i Llopart

    2007-06-01

    Full Text Available In this work, the author deals with how the issue of religion can be managed in the public space. For this, he wonders and argues whether or not the public space should be a homogeneous space from the point of view of convictions or if it can give room to heterogeneousexpressions, stemming from the plurality of profound convictions existing among the citizens. In addition, he lays out the concept of public space, discusses its “contaminations” and focuses fundamentally on its meaning as a place in which the supply, exchangeand debate of ideas, principles, intuitions, etc. are openly developed, although he devotes a little bit of attention to their most tangible or physical aspects. And he underscores the idea that in a context of democratically chosen public powers and a secular institutional framework, there should not exist privileges nor discriminations.

  3. Logistic Costs of Privileged Procedures in the Republic of Croatia

    Directory of Open Access Journals (Sweden)

    Čedomir Ivaković

    2006-07-01

    Full Text Available Logistic processes condition more and more the rationalizationof time required for manipulation of goods (loading,unloading, storage. The customs representation costs that arethe result of loss of time due to the customs procedures exclusivelyduring the working hours of the customs office affect alsothe total logistic costs, and may be significantly reduced by applyingthe privileged procedures in import and export.

  4. Agreement on the Privileges and Immunities of the Agency

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1959-12-21

    The text of the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, which was approved by the Board of Governors on 1 July 1959, is reproduced in this document for the information of all Members. As required by section 38 of the Agreement, the Director General is transmitting to the Government of each Member a certified copy of the Agreement in each of the Agency's four working languages.

  5. Agreement on the Privileges and Immunities of the Agency

    International Nuclear Information System (INIS)

    1959-01-01

    The text of the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, which was approved by the Board of Governors on 1 July 1959, is reproduced in this document for the information of all Members. As required by section 38 of the Agreement, the Director General is transmitting to the Government of each Member a certified copy of the Agreement in each of the Agency's four working languages [ru

  6. Agreement on the Privileges and Immunities of the Agency

    International Nuclear Information System (INIS)

    1959-01-01

    The text of the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, which was approved by the Board of Governors on 1 July 1959, is reproduced in this document for the information of all Members. As required by section 38 of the Agreement, the Director General is transmitting to the Government of each Member a certified copy of the Agreement in each of the Agency's four working languages

  7. French-Armenian Privileged Relationships: an Attempt to Use Applied Analysis

    Directory of Open Access Journals (Sweden)

    David Anatolievich Khachaturyan

    2016-12-01

    Full Text Available France takes a priority position in the foreign policy of Armenia. Bilateral relations are at high level and both countries characterize them as privileged relationships. To clarify the structure of relations between the countries, the author realizes a content analysis of the activity reports of the Ministry of Foreign Affairs of Armenia, quantitative analysis of the bilateral visits and meetings, friendship groups at the parliament of France, decentralized cooperation, as well as vote in the UN General Assembly and cooperation at the PACE are analyzed. Armenian-French privileged relationships correspond to the coincidence of more than half of the voting of the countries in the UN General Assembly. Regular visits of the President, the Minister of Foreign Affairs and the Minister of Diaspora of Armenia to France show the important French vector in foreign policy of Armenia. Due to the activities of the Armenian community of France, Armenia can rely on the group of supporters not only in the French Parliament, but, respectively, in the PACE, the European Parliament, etc., and decentralized co-operation with France develops dynamically and is not inferior to the interaction of Armenia with other countries in this area.

  8. MysiRNA-designer: a workflow for efficient siRNA design.

    Directory of Open Access Journals (Sweden)

    Mohamed Mysara

    Full Text Available The design of small interfering RNA (siRNA is a multi factorial problem that has gained the attention of many researchers in the area of therapeutic and functional genomics. MysiRNA score was previously introduced that improves the correlation of siRNA activity prediction considering state of the art algorithms. In this paper, a new program, MysiRNA-Designer, is described which integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches. It also features the MysiRNA score, a highly ranked correlated siRNA efficacy prediction score for ranking the designed siRNAs, in addition to top scoring models Biopredsi, DISR, Thermocomposition21 and i-Score, and integrates them in a unique siRNA score-filtration technique. This multi-score filtration layer filters siRNA that passes the 90% thresholds calculated from experimental dataset features. MysiRNA-Designer takes an accession, finds conserved regions among its transcript space, finds accessible regions within the mRNA, designs all possible siRNAs for these regions, filters them based on multi-scores thresholds, and then performs SNP and off-target filtration. These strict selection criteria were tested against human genes in which at least one active siRNA was designed from 95.7% of total genes. In addition, when tested against an experimental dataset, MysiRNA-Designer was found capable of rejecting 98% of the false positive siRNAs, showing superiority over three state of the art siRNA design programs. MysiRNA is a freely accessible (Microsoft Windows based desktop application that can be used to design siRNA with a high accuracy and specificity. We believe that MysiRNA-Designer has the potential to play an important role in this area.

  9. Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer.

    Science.gov (United States)

    Baba, Seiki; Someya, Tatsuhiko; Kawai, Gota; Nakamura, Kouji; Kumasaka, Takashi

    2010-05-01

    The Hfq protein is a hexameric RNA-binding protein which regulates gene expression by binding to RNA under the influence of diverse environmental stresses. Its ring structure binds various types of RNA, including mRNA and sRNA. RNA-bound structures of Hfq from Escherichia coli and Staphylococcus aureus have been revealed to have poly(A) RNA at the distal site and U-rich RNA at the proximal site, respectively. Here, crystals of a complex of the Bacillus subtilis Hfq protein with an A/G-repeat 7-mer RNA (Hfq-RNA) that were prepared using the hanging-drop vapour-diffusion technique are reported. The type 1 Hfq-RNA crystals belonged to space group I422, with unit-cell parameters a = b = 123.70, c = 119.13 A, while the type 2 Hfq-RNA crystals belonged to space group F222, with unit-cell parameters a = 91.92, b = 92.50, c = 114.92 A. Diffraction data were collected to a resolution of 2.20 A from both crystal forms. The hexameric structure of the Hfq protein was clearly shown by self-rotation analysis.

  10. Agreement on the privileges and immunities of the Agency. Acceptances by Member States

    International Nuclear Information System (INIS)

    1995-10-01

    The list of Member States shows the 65 Members which, by 30 September 1995, had accepted the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, as provided for in Section 38 thereof

  11. Agreement on the privileges and immunities of the Agency. Acceptances by Member States

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-10-01

    The list of Member States shows the 65 Members which, by 30 September 1995, had accepted the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, as provided for in Section 38 thereof.

  12. Educating the Elite: A Social Justice Education for the Privileged Class

    Science.gov (United States)

    Wheeler-Bell, Quentin

    2017-01-01

    America is witnessing a new gilded age. Since the 1970s, inequality in wealth and income has soared within the United States--and globally (Piketty, 2014; Sayer, 2016; Therborn, 2013). Such inequalities affect human flourishing because they allow the privileged class to convert their wealth into different, and unequal, lifestyles and life chances.…

  13. Therapeutic miRNA and siRNA: Moving from Bench to Clinic as Next Generation Medicine

    Directory of Open Access Journals (Sweden)

    Chiranjib Chakraborty

    2017-09-01

    Full Text Available In the past few years, therapeutic microRNA (miRNA and small interfering RNA (siRNA are some of the most important biopharmaceuticals that are in commercial space as future medicines. This review summarizes the patents of miRNA- and siRNA-based new drugs, and also provides a snapshot about significant biopharmaceutical companies that are investing for the therapeutic development of miRNA and siRNA molecules. An insightful view about individual siRNA and miRNA drugs has been depicted with their present status, which is gaining attention in the therapeutic landscape. The efforts of the biopharmaceuticals are discussed with the status of their preclinical and/or clinical trials. Here, some of the setbacks have been highlighted during the biopharmaceutical development of miRNA and siRNA as individual therapeutics. Finally, a snapshot is illustrated about pharmacokinetics, pharmacodynamics with absorption, distribution, metabolism, and excretion (ADME, which is the fundamental development process of these therapeutics, as well as the delivery system for miRNA- and siRNA-based drugs. Keywords: miRNA, siRNA, drug development

  14. Rethinking poverty, power and privilege: A feminist post-structuralist research exploration

    Directory of Open Access Journals (Sweden)

    Thérèse Hulme

    2012-11-01

    Full Text Available In this article, I described how the use of feminist methodology and post-structuralist analyses of the experiences of women in a poor ‘Coloured’ community in my research led to new understandings of the experiences of poverty and privilege. I discovered the relevance of Foucault’s historical analysis of the operation of ‘pastoral power’ through the narratives of women from the Scottsville community. Historical and current accounts of so-called ‘Coloured’ women’s subjugation and categorisation are reminders of how it came about that ‘being Coloured’ became associated in South Africa with shame and with ‘knowing one’s place’. Feminist post-structuralist analyses made visible the conditions that created practices of injustice in poor women’s lives whilst, at the same time, creating conditions of privilege for me. Justice-making in Scottsville therefore started with a radical rethinking of the terms by which people’s marginalisation took place and, consequently also of the terms of ‘just’ cross-cultural engagements.

  15. Narratives of east Asian women teachers of English where privilege meets marginalization

    CERN Document Server

    Park, Gloria

    2017-01-01

    This book is a powerful narrative of how six women experienced their lives alongside their desire to overcome the challenging and empowering nature of the English language. This book shares who they are as transnational and mobile women living in the midst of linguistic privilege and marginalization.

  16. 24 CFR 203.22 - Payment of insurance premiums or charges; prepayment privilege.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Payment of insurance premiums or... Underwriting Procedures Eligible Mortgages § 203.22 Payment of insurance premiums or charges; prepayment privilege. (a) Payment of periodic insurance premiums or charges. Except with respect to mortgages for which...

  17. PRIVILEGES AND IMMUNITIES IN SWITZERLAND - PRACTICAL GUIDE

    CERN Multimedia

    Relations with the Host States Service

    2002-01-01

    The Permanent Mission of Switzerland to the International Organisations in Geneva has just published a practical guide to the implementation of the system of privileges and immunities and other facilities on its Web site. The guide is currently available in French only but an English translation is in preparation. Comprising around ten chapters, each dealing with a different subject (insurance, real estate, customs, etc.), the guide is not exhaustive but will be regularly supplemented, expanded and updated. The Mission specifies that the information contained in the document is given only as guide and that it implies no legal commitment on the part of the Host State. Relations with the Host States Service Tel. 72848

  18. a week in space

    Science.gov (United States)

    collette, christian

    2016-04-01

    COLLETTE Christian Institut Saint Laurent Liège Belgium. I am a science teacher at a technical high school. Generally, my students don't come from a privileged social background and are not particularly motivated for studies. For 10 years, I organize, for one of my sections, a spatial (and special) school year that ends in a spatial week. Throughout this year, with the help of my colleagues, I will introduce into all themes a lot of concepts relating to space. French, history, geography, English, mathematics, technical courses, sciences, and even gymnastics will be training actors in space culture. In spring, I will accompany my class in the Euro Space Center (Redu- Belgium) where we will live one week 24 hours on "like astronauts" One third of the time is dedicated to astronaut training (moonwalk, remote manipulator system, mission simulation, weightless wall, building rockets, satellites, etc.), One third to more intellectual activities on space (lectures, research, discovery of the outside run) the last one third of time in outside visits (museums, site of ESA-Redu) or in movies about space (October sky, Apollo 13, etc.) During this year, the profits, so educational as human, are considerable!

  19. Auditing Litigation and Claims: Conflicts and the Compromise of Privilege

    Directory of Open Access Journals (Sweden)

    Harleen Kaur

    2013-12-01

    Full Text Available Auditing standards require an auditor to make various enquiries about liabilities in general this may entail consideration of potential litigations and claims that the audited entity may be facing. To perform this part of audit, the auditors will generally seek representation letters from lawyers of the company detailing an estimate prepared by management, confirmed by their lawyers through a representation letter, and then sent directly to the auditors. This paper reviews the implications for the auditing profession of a case that involved auditors seeking such representation letters. The case involves litigation between theWestpac Banking Corporation and 789TEN Pty Ltd. While theWestpac case confirmed the legal position of the auditor in their task of collecting evidence in order to form an opinion in Australia, it highlights a significant anomaly under the law and should place the issue of solicitor’s representation letters as audit evidence firmly on the agenda of policymakers. This issue of the compromise of legal privilege during the conduct of an audit is also not confined to Australia: other common law jurisdictions, such as the UK and the US, have also sought to clarify the position of auditors when issues of the integrity of legal privacy privilege arise.

  20. 75 FR 63802 - Action Affecting Export Privileges; Parto Abgardan Cooling Towers Co.

    Science.gov (United States)

    2010-10-18

    ... Abgardan Cooling Towers Co. Parto Abgardan Cooling Towers Co., P.O. Box 966, Folsom, CA 95763; and P.O. Box... Making Denial of Export Privileges of Aqua-Loop Cooling Towers, Co. Applicable to Parto Abgardan Cooling...-Loop Cooling Towers, Co. (``Aqua-Loop'') on March 25, 2010 (``Denial Order''), applicable to the...

  1. The female lower genital tract is a privileged compartment with IL-10 producing dendritic cells and poor Th1 immunity following Chlamydia trachomatis infection.

    Directory of Open Access Journals (Sweden)

    Ellen Marks

    Full Text Available While a primary genital tract infection with C. trachomatis stimulates partial-protection against re-infection, it may also result in severe inflammation and tissue destruction. Here we have dissected whether functional compartments exist in the genital tract that restrict Th1-mediated protective immunity. Apart from the Th1-subset, little is known about the role of other CD4(+ T cell subsets in response to a genital tract chlamydial infection. Therefore, we investigated CD4(+ T cell subset differentiation in the genital tract using RT-PCR for expression of critical transcription factors and cytokines in the upper (UGT and lower genital tract (LGT of female C57BL/6 mice in response to C. trachomatis serovar D infection. We found that the Th1 subset dominated the UGT, as IFN-γ and T-bet mRNA expression were high, while GATA-3 was low following genital infection with C. trachomatis serovar D. By contrast, IL-10 and GATA-3 mRNA dominated the LGT, suggesting the presence of Th2 cells. These functional compartments also attracted regulatory T cells (Tregs differently as increased FoxP3 mRNA expression was seen primarily in the UGT. Although IL-17A mRNA was somewhat up-regulated in the LGT, no significant change in RORγ-t mRNA expression was observed, suggesting no involvement of Th17 cells. The dichotomy between the LGT and UGT was maintained during infection by IL-10 because in IL-10-deficient mice the distinction between the two compartments was completely lost and a dramatic shift to the predominance of Th1 cells in the LGT occurred. Unexpectedly, the major source of IL-10 was CD11c(+ CD11b(+ DC, probably creating an anti-inflammatory privileged site in the LGT.

  2. The oldest banknotes issued by the Privileged National Bank of the Kingdom of Serbia

    Directory of Open Access Journals (Sweden)

    Pantelić Svetlana

    2014-01-01

    Full Text Available The first paper banknotes of the Privileged National Bank: 100 dinars in gold, 50 dinars in gold and 10 dinars in silver, were placed in circulation in 1884 and 1885. The 100-dinar banknote was put in circulation on 2 July 1884, when the Privileged National Bank of the Kingdom of Serbia commenced its operations. The banknotes, especially the 100- and 50-dinar ones, were issued as temporary, with the major assistance of the Belgium National Bank. Given that until then Serbia only had coins in circulation, the paper 100- and 50-dinar banknotes were met with distrust and for quite a while there were problems in respect of their usage. The shortest lifetime had the 50-dinar banknote, due to its poor quality and consequent easy counterfeiting.

  3. Does the granting of legal privileges as an indigenous people help to reduce health disparities? Evidence from New Zealand and Malaysia.

    Science.gov (United States)

    Phua, Kai-Lit

    2009-11-01

    Both the Maori of New Zealand and the Orang Asli of Malaysia are indigenous peoples who have been subjected to prejudice, discrimination and displacement in its various forms by other ethnic groups in their respective countries. However, owing to changes in the socio-political climate, they have been granted rights (including legal privileges) in more recent times. Data pertaining to the health and socio-economic status of the Maori and the Orang Asli are analysed to see if the granting of legal privileges has made any difference for the two communities. One conclusion is that legal privileges (and the granting of special status) do not appear to work well in terms of reducing health and socio-economic gaps.

  4. 7 CFR 905.148 - Reports of special purpose shipments under certificates of privilege.

    Science.gov (United States)

    2010-01-01

    ... (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements and Orders; Fruits, Vegetables, Nuts... Regulations Non-Regulated Fruit § 905.148 Reports of special purpose shipments under certificates of privilege... name and address of the shipper or shippers; name and address of the certified organic Florida citrus...

  5. Counterspaces for Women of Color in STEM Higher Education: Marginal and Central Spaces for Persistence and Success

    Science.gov (United States)

    Ong, Maria; Smith, Janet M.; Ko, Lily T.

    2018-01-01

    Counterspaces in science, technology, engineering, and mathematics (STEM) are often considered "safe spaces" at the margins for groups outside the mainstream of STEM education. The prevailing culture and structural manifestations in STEM have traditionally privileged norms of success that favor competitive, individualistic, and solitary…

  6. Building Cultural Competence for Work with Diverse Families: Strategies from the Privileged Side.

    Science.gov (United States)

    Dewees, Marty

    2001-01-01

    A model of social work education for undergraduates from primarily privileged backgrounds links postmodern perspectives of cultural competence, diversity, social constructionism, and a generalist strengths-based orientation for work with families. Four steps for helping students recognize the role of culture in generating a worldview and develop a…

  7. Heterosexual Privilege Awareness, Prejudice, and Support of Gay Marriage among Diversity Course Students

    Science.gov (United States)

    Case, Kim; Stewart, Briana

    2010-01-01

    Although most research investigating diversity courses focuses on attitudes toward racial minorities and women, these courses may also influence student attitudes toward lesbians and gay men. The current study assessed student awareness of heterosexual privilege, prejudice against lesbians and gay men, and support for same-sex marriage. Students…

  8. Educational privilege: The role of school context in the development just world beliefs among Brazilian adolescents.

    Science.gov (United States)

    Thomas, Kendra J; Napolitano, Patricia H

    2017-12-01

    The purpose of this study is to understand the development of Brazilian adolescents' justice perceptions across different contexts of educational privilege. Past research has found that, in adolescence, the belief in a just world (BJW) differentiates between personal and general and declines. However, prior research has not included adolescents from various socioeconomic statuses, samples in Latin America, or focused on the role of the educational context on the developmental trajectory. Participants were 385 adolescents from 3 schools (private, public and military) in Southern Brazil between 9th and 11th grade. Students completed the personal and general BJW survey. Results revealed a significant interaction of school and grade level of adolescents' personal BJW. Contrary to previous research, personal and general BJW was not always lower in higher grades. Among privileged educational contexts, data indicated that personal BJW may even increase, with the decrease notable in the lower resourced school. In contrast, general BJW was relatively consistent across all Brazilian adolescents. Results provide important insight into the role that privilege and education play across adolescents' development of BJW. This research questions the generalizability of previous studies on the development of BJW and indicates that the trajectory may be dependent upon educational and cultural context. © 2016 International Union of Psychological Science.

  9. PRIVILEGES AND IMMUNITIES IN SWITZERLAND: PRACTICAL GUIDE

    CERN Multimedia

    2003-01-01

    The Permanent Mission of Switzerland to the International Organisations in Geneva has informed CERN that the "Practical Manual of the regime of privileges and immunities and other facilities" is available on its Web site: - in English (http://www.dfae.admin.ch/geneva_miss/e/home/guide.html); - in French (http://www.dfae.admin.ch/geneva_miss/f/home/guide.html). Comprising around ten chapters, each dealing with a different subject (insurance, real estate, customs, etc.), the guide is not exhaustive but will be regularly supplemented, expanded and updated. The Mission specifies that the information contained in the document is given only as guide and that it implies no legal commitment on the part of the Host State. Relations with the Host States Service http://www.cern.ch/relations/ Tel. 72848

  10. Intercultural Manifestations of Racial, Language, and Class Privilege in Schooling: An Autoethnographic Tale

    Science.gov (United States)

    Marx, Sherry

    2017-01-01

    In this autoethnographic tale, I tell the story of my own family's experience with race, class, and language privilege. In particular, I focus on my children's experience with elementary schooling in the United States and Hungary. Their intercultural education experience vividly illuminates the socially and culturally constructed nature of race,…

  11. Prediction of RNA secondary structures: from theory to models and real molecules

    International Nuclear Information System (INIS)

    Schuster, Peter

    2006-01-01

    RNA secondary structures are derived from RNA sequences, which are strings built form the natural four letter nucleotide alphabet, {AUGC}. These coarse-grained structures, in turn, are tantamount to constrained strings over a three letter alphabet. Hence, the secondary structures are discrete objects and the number of sequences always exceeds the number of structures. The sequences built from two letter alphabets form perfect structures when the nucleotides can form a base pair, as is the case with {GC} or {AU}, but the relation between the sequences and structures differs strongly from the four letter alphabet. A comprehensive theory of RNA structure is presented, which is based on the concepts of sequence space and shape space, being a space of structures. It sets the stage for modelling processes in ensembles of RNA molecules like evolutionary optimization or kinetic folding as dynamical phenomena guided by mappings between the two spaces. The number of minimum free energy (mfe) structures is always smaller than the number of sequences, even for two letter alphabets. Folding of RNA molecules into mfe energy structures constitutes a non-invertible mapping from sequence space onto shape space. The preimage of a structure in sequence space is defined as its neutral network. Similarly the set of suboptimal structures is the preimage of a sequence in shape space. This set represents the conformation space of a given sequence. The evolutionary optimization of structures in populations is a process taking place in sequence space, whereas kinetic folding occurs in molecular ensembles that optimize free energy in conformation space. Efficient folding algorithms based on dynamic programming are available for the prediction of secondary structures for given sequences. The inverse problem, the computation of sequences for predefined structures, is an important tool for the design of RNA molecules with tailored properties. Simultaneous folding or cofolding of two or more RNA

  12. Purification, crystallization and preliminary X-ray diffraction analysis of the RNA-dependent RNA polymerase from Thosea asigna virus

    International Nuclear Information System (INIS)

    Ferrero, Diego; Buxaderas, Mònica; Rodriguez, José F.; Verdaguer, Núria

    2012-01-01

    The RNA-dependent RNA polymerase of Thosea asigna virus has been purified and crystallized in two different crystal forms. Preliminary characterization of P2 1 2 1 2 and C222 1 crystals is reported. Co-crystallization experiments in the presence of lutetium produced a heavy-atom derivative suitable for structure determination. Thosea asigna virus (TaV) is a positive-sense, single-stranded RNA (ssRNA) virus that belongs to the Permutotetravirus genera within the recently created Permutotetraviridae family. The genome of TaV consists of an RNA segment of about 5.700 nucleotides with two open reading frames, encoding for the replicase and capsid protein. The particular TaV replicase does not contain N7-methyl transferase and helicase domains but includes a structurally unique RNA-dependent RNA polymerase (RdRp) with a sequence permutation in the domain where the active site is anchored. This architecture is also found in double-stranded RNA viruses of the Birnaviridae family. Here we report the purification and preliminary crystallographic studies TaV RdRp. The enzyme was crystallized by the sitting-drop vapour diffusion method using PEG 8K and lithium sulfate as precipitants. Two different crystal forms were obtained: native RdRp crystallized in space group P2 1 2 1 2 and diffracts up to 2.1 Å and the RdRp-Lu 3+ derivative co-crystals belong to the C222 1 space group, diffracting to 3.0 Å resolution. The structure of TaV RdRp represents the first structure of a non-canonical RdRp from ssRNA viruses

  13. Power, privilege and disadvantage: Intersectionality theory and political representation

    Directory of Open Access Journals (Sweden)

    Eline Severs

    2017-06-01

    Full Text Available This article critically reviews the extant literature on social group representation and clarifies the advantages of intersectionality theory for studying political representation. It argues that the merit of intersectionality theory can be found in its ontology of power. Intersectionality theory is founded on a relational conception of political power that locates the constitution of power relations within social interactions, such as political representation. As such, intersectionality theory pushes scholarship beyond studying representation inequalities —that are linked to presumably stable societal positions— to also consider the ways in which political representation (recreates positions of privilege and disadvantage.

  14. Where Are "Their" Voices? Examining Power and Privilege in a Family Literacy Text

    Science.gov (United States)

    Kumar, Tracey

    2014-01-01

    The purpose of this study was to examine how a family literacy text linked to a large-scale, U.S.-based family literacy program either privileged or disprivileged dominant, Eurocentric literacy practices. More specifically, this study investigated the ways in which the family literacy text: (1) conceptualized literacy; and (2) constructed the role…

  15. The Role of Privilege as Identity in Adolescents' Beliefs about Homelessness, Opportunity, and Inequality

    Science.gov (United States)

    Seider, Scott

    2011-01-01

    This mixed methods study investigated the impact of learning about homelessness on the civic development of privileged adolescents. Pre-post surveys, classroom observations, and qualitative interviews revealed that the participating adolescents developed a more complex understanding of the factors that contribute to homelessness; however, this…

  16. Color-Blind Racial Attitudes: Microaggressions in the Context of Racism and White Privilege

    Science.gov (United States)

    Edwards, Jared F.

    2017-01-01

    Interest in institutional racism, White privilege, and microaggressions appears to be growing. We are living in times when the impact of race and racism are debated--when even the existence of racism is debated along with the appropriateness of examining the worst parts of U.S. history. This special-issue invited article includes a brief…

  17. BENTURAN ANTARA KREDITOR PRIVILEGE DENGAN KREDITOR PREFEREN PEMEGANG HIPOTEK KAPAL LAUT TERKAIT ADANYA FORCE MAJEURE

    Directory of Open Access Journals (Sweden)

    Fani Martiawan Kumara Putra

    2013-01-01

    Full Text Available Property rights will engender creditors, creditors which are produced due to the existence of zakelijke zekerheid (property guarantee are preferred creditors who has various superior characteristics, including the payment will be prioritized than other concurrent creditors. But the superior characteristics of the preferred creditors will looks weak when it crashed with privilege creditors which the existence are regulated in Law. The conflict between preferred creditors and privilege creditors makes the preferred creditors character become so weak, it is related to debt fulfillment because of force majeure and guarantee payment by the insurance company. This situation happened because when there was a force majeure, then the preferred creditors now should be just a concurrent creditors but they still hold the characters of preferred creditors because of the implication of the promises when the ship mortgage agreement made.

  18. Changes in Diversity Course Student Prejudice and Attitudes toward Heterosexual Privilege and Gay Marriage

    Science.gov (United States)

    Case, Kim A.; Stewart, Briana

    2010-01-01

    This study examined diversity course influence on student prejudice against lesbians and gay men, awareness of heterosexual privilege, and support for gay marriage. The study included heterosexual female students in psychology of women, introduction to women's studies, and nondiversity psychology courses. Students in diversity courses expressed…

  19. Safe introduction of new procedures and emerging technologies in surgery: education, credentialing, and privileging.

    Science.gov (United States)

    Sachdeva, Ajit K; Russell, Thomas R

    2007-08-01

    Ongoing horizon scanning is needed to identify new procedures and emerging technologies that should be evaluated for introduction into surgical practice. Following evidence-based evaluation, if a new modality is found ready for adoption in practice, surgeons need education in the safe and effective use of the new modality. The educational experience should include structured teaching and learning, verification of new knowledge and skills, preceptoring or proctoring, and monitoring of outcomes. Credentialing and privileging to perform a new procedure or use an emerging technology should be based on evaluation of knowledge and skills and outcomes of surgical care, and not merely on the numbers of procedures performed. Education of the surgical team is also essential. The entire process involving education, verification of knowledge and skills, credentialing, and privileging must be transparent. Patients need to play a central role in making informed decisions regarding their care that involves use of a new procedure or an emerging technology, and they should participate actively in their perioperative care.

  20. Between system maker and privileges taker: the role of China in the Greater Mekong Sub-region

    Directory of Open Access Journals (Sweden)

    Truong-Minh Vu

    2014-01-01

    Full Text Available Utilizing China's leadership projects in the Great Mekong Sub-Region (GMS as a case study, this paper aims to investigate whether China qualifies as an international leader. This work argues that its geographic position and economic rise allow China to be a "system maker and privilege taker," which is a dual role forming in economic-political relations in the GMS in the last ten years. China is among major driving forces to set up an economic zone in GMS. Growing Chinese regional power is intimately related to the creation of various hubs connecting regional transportation, communication and energy systems that foster the economic development of this region. However, China also proves dark sides of rising powers which take advantage of their privileges to gain benefits. As a "system maker" with its own position and capability, China has notably benefited from building hydropower systems. More importantly, while China is pursuing its benefits and privileges, its hydropower projects have caused some negative effects for the ecosystem in the region. The inflation of dam constructions in both China and GMS countries is raising concerns about using natural resources of the Mekong River. Our concluding part addresses the pressing need to start a serious discussion on the balance between national interests and regional solidarity within the formulation of Chinese foreign policy in GMS.

  1. Disrupting privilege, identity, and meaning: A reflexive dance of environmental education

    Science.gov (United States)

    Neilson, Alison Laurie

    By inviting educators from diverse backgrounds to participate in creative conversations, I had hoped to reflect on experiences that had helped construct our theories of environmental education, and inform practice. I sought consistency across the espoused ethics of co-participants, namely critical perspectives grounded in environmental justice. However, this quest was interrupted by a growing awareness of the interference of power dynamics between myself and the other participants, and of my own commitment to respect the stories being told. This narrative describes my "dance" of meaning making. The community dance examining privilege, identity and meaning is a study of how I may be contributing to the same oppressive situations I passionately strive to work against. Concepts of knowledge, power, and identity ebbed and flowed within stories drawn from the mountains of Tanzania to the hills of Colombia, and from the frozen shores of Kirkland Lake to the trout filled streams of Karman, Iran. Making meaning is itself an act of power and privilege, so I danced to make room for multiple understandings of these stories, of environmental education, and of research. This work offers an experience of disruption that raises questions and broadens the inclusion of people, ideas and other life into "accepted" research and pedagogical practices. Conventions embedded within research and education were disrupted throughout this reflexive process. As the author of this text, I was uncomfortable with the role of being the dominant voice, and consciously chose not to impose my interpretation on the stories shared by co-participants. The struggle to resist the very privilege in which my own education practice and this research process are so deeply steeped revealed normative forces that often threaten to undermine attempts by educators and researchers to act according to critical theories and environmental justice ethics. To accept the invitation to dance with the text is to step into

  2. Good news-bad news: the Yin and Yang of immune privilege in the eye.

    Science.gov (United States)

    Forrester, John V; Xu, Heping

    2012-01-01

    The eye and the brain are prototypical tissues manifesting immune privilege (IP) in which immune responses to foreign antigens, particularly alloantigens are suppressed, and even completely inhibited. Explanations for this phenomenon are numerous and mostly reflect our evolving understanding of the molecular and cellular processes underpinning immunological responses generally. IP is now viewed as a property of many tissues and the level of expression of IP varies not only with the tissue but with the nature of the foreign antigen and changes in the limited conditions under which privilege can operate as a mechanism of immunological tolerance. As a result, IP functions normally as a homeostatic mechanism preserving normal function in tissues, particularly those with highly specialized function and limited capacity for renewal such as the eye and brain. However, IP is relatively easily bypassed in the face of a sufficiently strong immunological response, and the privileged tissues may be at greater risk of collateral damage because its natural defenses are more easily breached than in a fully immunocompetent tissue which rapidly rejects foreign antigen and restores integrity. This two-edged sword cuts its swathe through the eye: under most circumstances, IP mechanisms such as blood-ocular barriers, intraocular immune modulators, induction of T regulatory cells, lack of lymphatics, and other properties maintain tissue integrity; however, when these are breached, various degrees of tissue damage occur from severe tissue destruction in retinal viral infections and other forms of uveoretinal inflammation, to less severe inflammatory responses in conditions such as macular degeneration. Conversely, ocular IP and tumor-related IP can combine to permit extensive tumor growth and increased risk of metastasis thus threatening the survival of the host.

  3. Agreement on the Privileges and Immunities of the International Atomic Energy Agency

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1959-08-17

    The text of the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, as approved by the Board of Governors on 1 July 1959, is re produced in this document for the information of all Members of the Agency. As required by section 38 of the Agreement, the Director General will transmit certified copies, in the Agency's four working languages, to the Government of each Member State.

  4. Agreement on the Privileges and Immunities of the International Atomic Energy Agency

    International Nuclear Information System (INIS)

    1959-01-01

    The text of the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, as approved by the Board of Governors on 1 July 1959, is re produced in this document for the information of all Members of the Agency. As required by section 38 of the Agreement, the Director General will transmit certified copies, in the Agency's four working languages, to the Government of each Member State

  5. Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression.

    Science.gov (United States)

    Denzler, Rémy; McGeary, Sean E; Title, Alexandra C; Agarwal, Vikram; Bartel, David P; Stoffel, Markus

    2016-11-03

    Expression changes of competing endogenous RNAs (ceRNAs) have been proposed to influence microRNA (miRNA) activity and thereby regulate other transcripts containing miRNA-binding sites. Here, we find that although miRNA levels define the extent of repression, they have little effect on the magnitude of the ceRNA expression change required to observe derepression. Canonical 6-nt sites, which typically mediate modest repression, can nonetheless compete for miRNA binding, with potency ∼20% of that observed for canonical 8-nt sites. In aggregate, low-affinity/background sites also contribute to competition. Sites with extensive additional complementarity can appear as more potent, but only because they induce miRNA degradation. Cooperative binding of proximal sites for the same or different miRNAs does increase potency. These results provide quantitative insights into the stoichiometric relationship between miRNAs and target abundance, target-site spacing, and affinity requirements for ceRNA-mediated gene regulation, and the unusual circumstances in which ceRNA-mediated gene regulation might be observed. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Rapid NMR screening of RNA secondary structure and binding

    International Nuclear Information System (INIS)

    Helmling, Christina; Keyhani, Sara; Sochor, Florian; Fürtig, Boris; Hengesbach, Martin; Schwalbe, Harald

    2015-01-01

    Determination of RNA secondary structures by NMR spectroscopy is a useful tool e.g. to elucidate RNA folding space or functional aspects of regulatory RNA elements. However, current approaches of RNA synthesis and preparation are usually time-consuming and do not provide analysis with single nucleotide precision when applied for a large number of different RNA sequences. Here, we significantly improve the yield and 3′ end homogeneity of RNA preparation by in vitro transcription. Further, by establishing a native purification procedure with increased throughput, we provide a shortcut to study several RNA constructs simultaneously. We show that this approach yields μmol quantities of RNA with purities comparable to PAGE purification, while avoiding denaturation of the RNA

  7. Rapid NMR screening of RNA secondary structure and binding

    Energy Technology Data Exchange (ETDEWEB)

    Helmling, Christina; Keyhani, Sara; Sochor, Florian; Fürtig, Boris; Hengesbach, Martin; Schwalbe, Harald, E-mail: schwalbe@nmr.uni-frankfurt.de [Johann Wolfgang Goethe-Universität, Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ) (Germany)

    2015-09-15

    Determination of RNA secondary structures by NMR spectroscopy is a useful tool e.g. to elucidate RNA folding space or functional aspects of regulatory RNA elements. However, current approaches of RNA synthesis and preparation are usually time-consuming and do not provide analysis with single nucleotide precision when applied for a large number of different RNA sequences. Here, we significantly improve the yield and 3′ end homogeneity of RNA preparation by in vitro transcription. Further, by establishing a native purification procedure with increased throughput, we provide a shortcut to study several RNA constructs simultaneously. We show that this approach yields μmol quantities of RNA with purities comparable to PAGE purification, while avoiding denaturation of the RNA.

  8. 1,3,5-Triazine-based analogues of purine: from isosteres to privileged scaffolds in medicinal chemistry.

    Science.gov (United States)

    Lim, Felicia Phei Lin; Dolzhenko, Anton V

    2014-10-06

    Purines can be considered as the most ubiquitous and functional N-heterocyclic compounds in nature. Structural modifications of natural purines, particularly using isosteric ring systems, have been in the focus of many drug discovery programs. Fusion of 1,3,5-triazine ring with pyrrole, pyrazole, imidazole, 1,2,3-triazole or 1,2,4-triazole results in seven bicyclic heterocyclic systems isosteric to purine. Application of the isosterism concept for the development of new compounds with therapeutic potential in areas involving purinergic regulation or purine metabolism led to significant advances in medicinal chemistry of the azolo[1,3,5]triazines. These 1,3,5-triazine-based purine-like scaffolds significantly increase level of molecular diversity and allow covering chemical space in the important areas of medicinal chemistry. Some of these azolo[1,3,5]triazine systems have become privileged scaffolds in the development of inhibitors of various kinases, phosphodiesterase, xanthine oxidase, and thymidine phosphorylase, antagonists of adenosine and corticotropin-releasing hormone receptors, anticancer and antiviral agents. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  9. 10 CFR 1703.111 - Requests for privileged treatment of documents submitted to the board.

    Science.gov (United States)

    2010-01-01

    ... file, the Board is not making a determination on any claim for privilege. The Board retains the right... whether there is a rational basis therefor; (3) Whether the information was transmitted to and received by.... (f) Notification before release. Notice of a decision by the Designated FOIA Officer to deny a claim...

  10. Agreement on the Privileges and Immunities of the International Atomic Energy Agency

    International Nuclear Information System (INIS)

    1967-01-01

    The Agreement on the Privileges and Immunities of the International Atomic Energy Agency, the text of which is reproduced herein, was approved by the Board of Governors on 1 July 1959. As required by section 38, the Director General has transmitted a certified copy of the Agreement to the Government of each Member of the Agency, and will transmit such a copy to the Government of every State that becomes a Member hereafter [fr

  11. Agreement on the Privileges and Immunities of the International Atomic Energy Agency

    International Nuclear Information System (INIS)

    1967-01-01

    The Agreement on the Privileges and Immunities of the International Atomic Energy Agency, the text of which is reproduced herein, was approved by the Board of Governors on 1 July 1959. As required by section 38, the Director General has transmitted a certified copy of the Agreement to the Government of each Member of the Agency, and will transmit such a copy to the Government of every State that becomes a Member hereafter [ru

  12. Agreement on the Privileges and Immunities of the International Atomic Energy Agency

    International Nuclear Information System (INIS)

    1967-01-01

    The Agreement on the Privileges and Immunities of the International Atomic Energy Agency, the text of which is reproduced herein, was approved by the Board of Governors on 1 July 1959. As required by section 38, the Director General has transmitted a certified copy of the Agreement to the Government of each Member of the Agency, and will transmit such a copy to the Government of every State that becomes a Member hereafter

  13. The State Secrets Privilege and Other Limits on Litigation Involving Classified Information

    Science.gov (United States)

    2009-05-28

    Privilege And Separation Of Powers , 75 FORDHAM L. REV. 1931, 1935 (Mar. 2007). 2 Editorial, Securing Lawsuits, WASH. POST, May 11, 2009, at A16...the Supreme Court invalidated a legislative enactment that required federal courts to reopen final decisions as a violation of the separation of powers principle...95 It might be argued that the retroactivity provision in H.R. 984 also reopens final judgments in violation of the separation of powers principle

  14. Agreement on the Privileges and Immunities of the International Atomic Energy Agency

    International Nuclear Information System (INIS)

    1967-01-01

    The Agreement on the Privileges and Immunities of the International Atomic Energy Agency, the text of which is reproduced herein, was approved by the Board of Governors on 1 July 1959. As required by section 38, the Director General has transmitted a certified copy of the Agreement to the Government of each Member of the Agency, and will transmit such a copy to the Government of every State that becomes a Member hereafter [es

  15. Healthcare access as a right, not a privilege: a construct of Western thought.

    Science.gov (United States)

    Papadimos, Thomas J

    2007-03-28

    Over 45 million Americans are uninsured or underinsured. Those living in poverty exhibit the worst health status. Employment, education, income, and race are important factors in a person's ability to acquire healthcare access. Having established that there are people lacking healthcare access due to multi-factorial etiologies, the question arises as to whether the intervention necessary to assist them in obtaining such access should be considered a privilege, or a right. The right to healthcare access is examined from the perspective of Western thought. Specifically through the works of Aristotle, Immanuel Kant, Thomas Hobbes, Thomas Paine, Hannah Arendt, James Rawls, and Norman Daniels, which are accompanied by a contemporary example of intervention on behalf of the medically needy by the The Johns Hopkins Urban Health Institute. As human beings we are all valuable social entities whereby, through the force of morality, through implicitly forged covenants among us as individuals and between us and our governments, and through the natural rights we maintain as individuals and those we collectively surrender to the common good, it has been determined by nature, natural laws, and natural rights that human beings have the right, not the privilege, to healthcare access.

  16. 24 CFR 100.65 - Discrimination in terms, conditions and privileges and in services and facilities.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Discrimination in terms, conditions... Discriminatory Housing Practices § 100.65 Discrimination in terms, conditions and privileges and in services and... rental of a dwelling, because a person failed or refused to provide sexual favors. ...

  17. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

    Science.gov (United States)

    Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M

    2016-04-20

    RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. The evolution of RNA viruses: A population genetics view

    Science.gov (United States)

    Moya, Andrés; Elena, Santiago F.; Bracho, Alma; Miralles, Rosario; Barrio, Eladio

    2000-01-01

    RNA viruses are excellent experimental models for studying evolution under the theoretical framework of population genetics. For a proper justification of this thesis we have introduced some properties of RNA viruses that are relevant for studying evolution. On the other hand, population genetics is a reductionistic theory of evolution. It does not consider or make simplistic assumptions on the transformation laws within and between genotypic and phenotypic spaces. However, such laws are minimized in the case of RNA viruses because the phenotypic space maps onto the genotypic space in a much more linear way than on higher DNA-based organisms. Under experimental conditions, we have tested the role of deleterious and beneficial mutations in the degree of adaptation of vesicular stomatitis virus (VSV), a nonsegmented virus of negative strand. We also have studied how effective population size, initial genetic variability in populations, and environmental heterogeneity shapes the impact of mutations in the evolution of vesicular stomatitis virus. Finally, in an integrative attempt, we discuss pros and cons of the quasispecies theory compared with classic population genetics models for haploid organisms to explain the evolution of RNA viruses. PMID:10860958

  19. Agreement on the privileges and immunities of the Agency: Acceptances by Member States

    International Nuclear Information System (INIS)

    1989-10-01

    The document lists the 61 Member States which, by 1 October 1989, had accepted the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, as provided for in Section 38 thereof. The list is followed by the texts of such reservations to the Agreement as some of the Members in question made when depositing their respective instruments of acceptance with the Director General

  20. 32 CFR 634.9 - Suspension or revocation of driving or privately owned vehicle registration privileges.

    Science.gov (United States)

    2010-07-01

    ... violations or safe vehicle operation, is not limited or restricted by this part. (a) Suspension. (1) Driving... Government vehicles. (3) Immediate suspension of installation or overseas command POV driving privileges... which the vehicle is being operated if the jurisdiction imposes a suspension solely on the basis of the...

  1. The Gift Economy of Elite Schooling: The Changing Contours and Contradictions of Privileged Benefaction

    Science.gov (United States)

    Kenway, Jane; Fahey, Johannah

    2015-01-01

    Privileged benefaction in elite schools and the moral dilemmas, contradictions and power politics involved are the focus of this paper. The notion of "the gift" provides our analytical lens. We concentrate on two girls' schools--one in South Africa and one in England. These were both built, in various ways, on the British model of public…

  2. Exploring the Dialogic Space of Public Participation in Science

    DEFF Research Database (Denmark)

    Nielsen, Kristian Hvidtfelt

    of public understanding of science and scientific literacy approaches: that scientific knowledge in some sense is privileged, that understanding the science will lead to appreciative attitudes toward science and technology in general, and that controversial issues involving science and the public are rooted...... in public misconceptions of science. This paper uses the dialogic space proposed by Callon et al. to explore relationships between public and science. The dialogic space spans collective versus scientific dimensions. The collective (or public) is constituted by aggregation (opinion polls) or by composition...... (organized groups of concerned citizens), whereas scientific research is characterized as either secluded research that is performed exclusively by expert scientists or as collaborative research that involves lay people in the production and communication of knowledge....

  3. The European Communities (Privileges of the Joint European Torus) Order 1978 (S.I. no. 1033)

    International Nuclear Information System (INIS)

    1978-01-01

    This Order confers privileges on the Joint European Torus, as required by Decision 78/472/Euratom of 30 May 1978 of the Council of the European Communities and by the Exchange of Letters of 3 May 1978 between the Government of the United Kingdom and the European Atomic Energy Community [fr

  4. Tales from the Ethnographic Field: Navigating Feelings of Guilt and Privilege in the Research Process

    Science.gov (United States)

    DeLuca, Jaime R.; Maddox, Callie Batts

    2016-01-01

    This article explores questions of reflexivity, positionality, identity, and emotion within the process of ethnographic research. We reflect on our feelings of privilege and guilt in and through our ethnographic fieldwork and discuss the ways in which these experiences encouraged reflexive thinking and a crucial interrogation of the place of the…

  5. The Development of General Principles for EU Competition Law Enforcement - The protection of legal professional privilege

    NARCIS (Netherlands)

    Frese, M.J.

    2011-01-01

    This paper discusses the scope of the EU principle of legal professional privilege ('LPP') and the mechanisms for bottom-up integration. LPP refers to the confidential nature of certain written communications between lawyer and client. Bottom-up integration is the process whereby domestic legal

  6. RNA inverse folding using Monte Carlo tree search.

    Science.gov (United States)

    Yang, Xiufeng; Yoshizoe, Kazuki; Taneda, Akito; Tsuda, Koji

    2017-11-06

    Artificially synthesized RNA molecules provide important ways for creating a variety of novel functional molecules. State-of-the-art RNA inverse folding algorithms can design simple and short RNA sequences of specific GC content, that fold into the target RNA structure. However, their performance is not satisfactory in complicated cases. We present a new inverse folding algorithm called MCTS-RNA, which uses Monte Carlo tree search (MCTS), a technique that has shown exceptional performance in Computer Go recently, to represent and discover the essential part of the sequence space. To obtain high accuracy, initial sequences generated by MCTS are further improved by a series of local updates. Our algorithm has an ability to control the GC content precisely and can deal with pseudoknot structures. Using common benchmark datasets for evaluation, MCTS-RNA showed a lot of promise as a standard method of RNA inverse folding. MCTS-RNA is available at https://github.com/tsudalab/MCTS-RNA .

  7. Nonradioactive telomerase activity assay by microchip electrophoresis: privileges to the classical gel electrophoresis assay.

    Science.gov (United States)

    Zhelev, Zhivko; Bakalova, Rumiana; Ewis, Ashraf; Ohba, Hideki; Ishikawa, Mitsuru; Baba, Yoshinobu

    2005-08-01

    The present study accents on the privileges of microchip-based electrophoresis to the conventional gel electrophoresis in separation of telomerase repeat amplification protocol/polymerase chain reaction (PCR) ladder products obtained in telomerase-catalyzed reaction in cancer cells. We try to clarify the interpretation of the results obtained by both electrophoretic procedures and to avoid misinterpretation as a result of PCR-dependent artefacts.

  8. Common 5S rRNA variants are likely to be accepted in many sequence contexts

    Science.gov (United States)

    Zhang, Zhengdong; D'Souza, Lisa M.; Lee, Youn-Hyung; Fox, George E.

    2003-01-01

    Over evolutionary time RNA sequences which are successfully fixed in a population are selected from among those that satisfy the structural and chemical requirements imposed by the function of the RNA. These sequences together comprise the structure space of the RNA. In principle, a comprehensive understanding of RNA structure and function would make it possible to enumerate which specific RNA sequences belong to a particular structure space and which do not. We are using bacterial 5S rRNA as a model system to attempt to identify principles that can be used to predict which sequences do or do not belong to the 5S rRNA structure space. One promising idea is the very intuitive notion that frequently seen sequence changes in an aligned data set of naturally occurring 5S rRNAs would be widely accepted in many other 5S rRNA sequence contexts. To test this hypothesis, we first developed well-defined operational definitions for a Vibrio region of the 5S rRNA structure space and what is meant by a highly variable position. Fourteen sequence variants (10 point changes and 4 base-pair changes) were identified in this way, which, by the hypothesis, would be expected to incorporate successfully in any of the known sequences in the Vibrio region. All 14 of these changes were constructed and separately introduced into the Vibrio proteolyticus 5S rRNA sequence where they are not normally found. Each variant was evaluated for its ability to function as a valid 5S rRNA in an E. coli cellular context. It was found that 93% (13/14) of the variants tested are likely valid 5S rRNAs in this context. In addition, seven variants were constructed that, although present in the Vibrio region, did not meet the stringent criteria for a highly variable position. In this case, 86% (6/7) are likely valid. As a control we also examined seven variants that are seldom or never seen in the Vibrio region of 5S rRNA sequence space. In this case only two of seven were found to be potentially valid. The

  9. Publication concerning the scope of the agreement concerning privileges and exemptions of the International Atomic Energy Agency

    International Nuclear Information System (INIS)

    1981-01-01

    The agreement of July 1, 1959, concerning the privileges and exemptions of the IAEA have come into force in Maroc on March 30, 1977, and in the Mongolian People's Republic on January 12, 1976, with some reservations. (HSCH) [de

  10. Healthcare access as a right, not a privilege: a construct of Western thought

    Directory of Open Access Journals (Sweden)

    Papadimos Thomas J

    2007-03-01

    Full Text Available Abstract Over 45 million Americans are uninsured or underinsured. Those living in poverty exhibit the worst health status. Employment, education, income, and race are important factors in a person's ability to acquire healthcare access. Having established that there are people lacking healthcare access due to multi-factorial etiologies, the question arises as to whether the intervention necessary to assist them in obtaining such access should be considered a privilege, or a right. The right to healthcare access is examined from the perspective of Western thought. Specifically through the works of Aristotle, Immanuel Kant, Thomas Hobbes, Thomas Paine, Hannah Arendt, James Rawls, and Norman Daniels, which are accompanied by a contemporary example of intervention on behalf of the medically needy by the The Johns Hopkins Urban Health Institute. As human beings we are all valuable social entities whereby, through the force of morality, through implicitly forged covenants among us as individuals and between us and our governments, and through the natural rights we maintain as individuals and those we collectively surrender to the common good, it has been determined by nature, natural laws, and natural rights that human beings have the right, not the privilege, to healthcare access.

  11. The incidence of the criminal policy in the conformation of the public space

    OpenAIRE

    Monroy, Carla

    2016-01-01

    Mexican Criminal Policy is distinguished by its historical repression, the strategies implemented by the current government affected directly the violence and crime index. These facts beat and modified the conformation of the public space. Recreational places, parks, streets, squares, etc., stopped having the dynamism that used to have. On the other hand, the global postmodern speech changes the conception of the city, nowadays is privileged the consumption, so the city has transform in order...

  12. Attorney work product privilege trumps mandated child abuse reporting law: The case of Elijah W. v. Superior Court.

    Science.gov (United States)

    Lareau, Craig R

    2015-01-01

    Forensic psychologists and psychiatrists are licensed in their respective professions, but they perform most of their work with attorneys in the legal arena. Both attorneys and mental health professionals place high value on confidentiality of information, reflected in the ethics of their professions and codified into laws governing their work. In psychology and psychiatry, there are some well-known exceptions to confidentiality; two primary exceptions include the mandated reporting of suspected child abuse and various "Tarasoff" duty to warn or protect laws. Generally, however, the corresponding duty for attorneys to report suspected child abuse or to warn or protect intended victims of threatened harm is not as extensive. This difference in mandated reporting responsibilities can create significant difficulties when attorneys need to retain forensic psychologists and psychiatrists to evaluate their clients, especially in criminal contexts. If the retained psychologist or psychiatrist is required to report suspected abuse or threatened harm, the attorney may be harming his or her client's legal interests by using the forensic psychologist or psychiatrist to evaluate his or her client. This article will briefly review the development of mandated reporting laws for psychologists and psychiatrists and juxtapose those with the legal and ethical requirements of confidentiality for attorneys embodied in the attorney-client privilege and attorney work product privilege. The article will then discuss the California Court of Appeals case in Elijah W. v. Superior Court, where the court addressed the issue of whether retained mental health professionals must report suspected child abuse and threatened harm to others as required by law or if they do not need to report because they come under the umbrella of the attorney work product privilege. This California court ultimately concluded that retained psychologists and psychiatrists work under the attorney work product

  13. Good news – bad news: the Yin and Yang of immune privilege in the eye

    Directory of Open Access Journals (Sweden)

    John Vincent Forrester

    2012-11-01

    Full Text Available The eye and the brain are prototypical tissues manifesting immune privilege (IP in which immune responses to foreign antigens, particularly alloantigens are suppressed, and even completely inhibited. Explanations for this phenomenon are numerous and mostly reflect our evolving understanding of the molecular and cellular processes underpinning immunological responses generally. IP is now viewed as a property of many tissues and the level of expression of IP varies not only with the tissue but with the nature of the foreign antigen and changes in the limited conditions under which privilege can operate as a mechanism of immunological tolerance. As a result, IP functions normally as a homeostatic mechanism preserving normal function in tissues, particularly those with highly specialised function and limited capacity for renewal such as the eye and brain. However, IP is relatively easily bypassed in the face of a sufficiently strong immunological response, and the privileged tissues may be at greater risk of collateral damage because of its natural defences are more easily breached than in a fully immunocompetent tissue which rapidly rejects foreign antigen and can restores integrity. This two-edged sword cuts its swathe through the eye: under most circumstances, IP mechanisms such as blood ocular barriers, intraocular immune modulators, induction of T regulatory cells, lack of lymphatics and other properties maintain tissue integrity; however, when these are breached, various degrees of tissue damage occur from severe tissue destruction in retinal viral infections and other forms of uveoretinal inflammation, to less severe inflammatory responses in conditions such as macular degeneration. Conversely, ocular IP and tumour-related IP can combine to permit extensive tumour growth and increased risk of metastasis thus threatening the survival of the host.

  14. Large scale meta-analysis of fragment-based screening campaigns: privileged fragments and complementary technologies.

    Science.gov (United States)

    Kutchukian, Peter S; Wassermann, Anne Mai; Lindvall, Mika K; Wright, S Kirk; Ottl, Johannes; Jacob, Jaison; Scheufler, Clemens; Marzinzik, Andreas; Brooijmans, Natasja; Glick, Meir

    2015-06-01

    A first step in fragment-based drug discovery (FBDD) often entails a fragment-based screen (FBS) to identify fragment "hits." However, the integration of conflicting results from orthogonal screens remains a challenge. Here we present a meta-analysis of 35 fragment-based campaigns at Novartis, which employed a generic 1400-fragment library against diverse target families using various biophysical and biochemical techniques. By statistically interrogating the multidimensional FBS data, we sought to investigate three questions: (1) What makes a fragment amenable for FBS? (2) How do hits from different fragment screening technologies and target classes compare with each other? (3) What is the best way to pair FBS assay technologies? In doing so, we identified substructures that were privileged for specific target classes, as well as fragments that were privileged for authentic activity against many targets. We also revealed some of the discrepancies between technologies. Finally, we uncovered a simple rule of thumb in screening strategy: when choosing two technologies for a campaign, pairing a biochemical and biophysical screen tends to yield the greatest coverage of authentic hits. © 2014 Society for Laboratory Automation and Screening.

  15. 76 FR 12023 - Action Affecting Export Privileges; William Chi-Wai Tsu And Cheerway Corporation; Order Denying...

    Science.gov (United States)

    2011-03-04

    ... DEPARTMENT OF COMMERCE Bureau of Industry and Security Action Affecting Export Privileges; William... Under Secretary of Commerce for Industry and Security. The appeal must be filed within 45 days from the... the Under Secretary of Commerce for Industry and Security. The appeal must be filed within 45 days...

  16. Pre-Big Bang, space-time structure, asymptotic Universe. Spinorial space-time and a new approach to Friedmann-like equations

    Science.gov (United States)

    Gonzalez-Mestres, Luis

    2014-04-01

    cosmology based on general relativity. In the new cosmology thus introduced, the contribution of the space curvature to the value of H2 is positive definite independently of the apparent sign of this curvature, and has a much larger value than the standard curvature term. Then, a cosmological constant is no longer required. The spinorial space-time also generates automatically for each comoving observer a privileged space direction that, together with parity violation, may explain the anisotropies observed in WMAP and Planck data. Contrary to frequent statements, such a signature would not be a strange phenomenon. The effect emerges directly from the use of two complex space-time coordinates instead of the conventional four real ones, and the privileged direction would correspond to the phase of the cosmic spinor. We remind here our previous work on the subject and further discuss some cosmological implications of the spinorial space-time.

  17. Can We Do That Here? Establishing the Scope of Surgical Practice at a New Safety-Net Community Hospital Through a Transparent, Collaborative Review of Physician Privileges.

    Science.gov (United States)

    O'Neill, Sean M; Seresinghe, Sarah; Sharma, Arun; Russell, Tara A; Crawford, L'Orangerie; Frencher, Stanley K

    2018-01-01

    Stewarding of physician privileges wisely is imperative, but no guidelines exist for how to incorporate system-level factors in privileging decisions. A newly opened, safety-net community hospital tailored the scope of surgical practice through review of physician privileges. Martin Luther King, Jr. Community Hospital is a public-private partnership, safety-net institution in South Los Angeles that opened in July 2015. It has 131 beds, including a 28-bed emergency department, a 20-bed ICU, and 5 operating rooms. Staff privileging decisions were initially based only on physicians' training and experience, but this resulted in several cases that tested the boundaries of what a small community hospital was prepared to handle. A collaborative, transparent process to review physician privileges was developed. This began with physician-only review of procedure lists, followed by a larger, multidisciplinary group to assess system-level factors. Specific questions were used to guide discussion, and unanimous approval from all stakeholders was required to include a procedure. An initial list of 558 procedures across 11 specialties was reduced to 321 (57.5%). No new cases that fall outside these new boundaries have arisen. An inclusive process was crucial for obtaining buy-in and establishing cultural norms. Arranging transfer agreements remains a significant challenge. Accumulation of institutional experience continues through regular performance reviews. As this hospital's capabilities mature, a blueprint has been established for expanding surgical scope of practice based explicitly on system-level factors. Copyright © 2017 The Joint Commission. Published by Elsevier Inc. All rights reserved.

  18. Medicare program; appeals of CMS or CMS contractor determinations when a provider or supplier fails to meet the requirements for Medicare billing privileges. Final rule.

    Science.gov (United States)

    2008-06-27

    This final rule implements a number of regulatory provisions that are applicable to all providers and suppliers, including durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) suppliers. This final rule establishes appeals processes for all providers and suppliers whose enrollment, reenrollment or revalidation application for Medicare billing privileges is denied and whose Medicare billing privileges are revoked. It also establishes timeframes for deciding enrollment appeals by an Administrative Law Judge (ALJ) within the Department of Health and Human Services (DHHS) or the Departmental Appeals Board (DAB), or Board, within the DHHS; and processing timeframes for CMS' Medicare fee-for-service (FFS) contractors. In addition, this final rule allows Medicare FFS contractors to revoke Medicare billing privileges when a provider or supplier submits a claim or claims for services that could not have been furnished to a beneficiary. This final rule also specifies that a Medicare contractor may establish a Medicare enrollment bar for any provider or supplier whose billing privileges have been revoked. Lastly, the final rule requires that all providers and suppliers receive Medicare payments by electronic funds transfer (EFT) if the provider or supplier, is submitting an initial enrollment application to Medicare, changing their enrollment information, revalidating or re-enrolling in the Medicare program.

  19. Therapeutic privilege: between the ethics of lying and the practice of truth.

    Science.gov (United States)

    Richard, Claude; Lajeunesse, Yvette; Lussier, Marie-Thérèse

    2010-06-01

    The 'right to the truth' involves disclosing all the pertinent facts to a patient so that an informed decision can be made. However, this concept of a 'right to the truth' entails certain ambiguities, especially since it is difficult to apply the concept in medical practice based mainly on current evidence-based data that are probabilistic in nature. Furthermore, in some situations, the doctor is confronted with a moral dilemma, caught between the necessity to inform the patient (principle of autonomy) and the desire to ensure the patient's well-being by minimising suffering (principle of beneficence). To comply with the principle of beneficence as well as the principle of non-maleficence 'to do no harm', the doctor may then feel obliged to turn to 'therapeutic privilege', using lies or deception to preserve the patient's hope, and psychological and moral integrity, as well as his self-image and dignity. There is no easy answer to such a moral dilemma. This article will propose a process that can fit into reflective practice, allowing the doctor to decide if the use of therapeutic privilege is justified when he is faced with these kinds of conflicting circumstances. We will present the conflict arising in practice in the context of the various theoretical orientations in ethics, and then we will suggest an approach for a 'practice of truth'. Last, we will situate this reflective method in the broader clinical context of medical practice viewed as a dialogic process.

  20. A methodology based on the "anterior chamber of rabbit eyes" model for noninvasively determining the biocompatibility of biomaterials in an immune privileged site.

    Science.gov (United States)

    Lu, Pei-Lin; Lai, Jui-Yang; Tabata, Yasuhiko; Hsiue, Ging-Ho

    2008-07-01

    In this study, a novel methodology based on the anterior chamber of rabbit eyes model was developed to evaluate the in vivo biocompatibility of biomaterials in an immune privileged site. The 7-mm-diameter membrane implants made from either a biological tissue material (amniotic membrane, AM group) or a biomedical polymeric material (gelatin, GM group) were inserted in rabbit anterior chamber for 36 months and characterized by biomicroscopic examinations, intraocular pressure measurements, and corneal thickness measurements. The noninvasive ophthalmic parameters were scored to provide a quantitative grading system. In this animal model, both AM and GM implants were visible in an ocular immune privileged site during clinical observations. The implants of the AM group appeared as soft tissue patches and have undergone a slow dissolution process resulting in a partial reduction of their size. Additionally, the AM implants did not induce any foreign body reaction or change in ocular tissue response for the studied period. By contrast, in the GM groups, significant corneal edema, elevated intraocular pressure, and increased corneal thickness were noted in the early postoperative phase (within 3 days), but resolved rapidly with in vivo dissolution of the gelatin. The results from the ocular grading system showed that both implants had good long-term biocompatibility in an ocular immune privileged site for up to 3 years. It is concluded that the anterior chamber of rabbit eyes model is an efficient method for noninvasively determining the immune privileged tissue/biomaterial interactions. (c) 2007 Wiley Periodicals, Inc.

  1. GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

    Science.gov (United States)

    Boudard, Mélanie; Bernauer, Julie; Barth, Dominique; Cohen, Johanne; Denise, Alain

    2015-01-01

    Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is predicting the spatial arrangement of the various structural elements of RNA. As RNA folding is generally hierarchical, methods involving coarse-grained models hold great promise for this purpose. We present here a novel coarse-grained method for sampling, based on game theory and knowledge-based potentials. This strategy, GARN (Game Algorithm for RNa sampling), is often much faster than previously described techniques and generates large sets of solutions closely resembling the native structure. GARN is thus a suitable starting point for the molecular modeling of large RNAs, particularly those with experimental constraints. GARN is available from: http://garn.lri.fr/.

  2. Quantum correlations in Newtonian space and time: arbitrarily fast communication or nonlocality

    Science.gov (United States)

    Gisin, Nicolas

    2013-03-01

    Experimental violations of Bell inequalities using space-like separated measurements precludes the explanation of quantum correlations through causal influences propagating at subluminal speed. Yet, ``everything looks as if the two parties somehow communicate behind the scene.'' We investigate the assumption that they do so at a speed faster than light, though finite. Such an assumption doesn't respect the spirit of Einstein relativity. However, it is not crystal clear that such ``communication behind the scene'' would contradict relativity. Indeed, one could imagine that this communication remains for ever hidden to humans, i.e. that it could not be controlled by humans, only Nature exploits it to produce correlations that can't be explained by usual common causes. To define faster than light hidden communication requires a universal privileged reference frame in which this faster than light speed is defined. Again, such a universal privileged frame is not in the spirit of relativity, but it is also clearly not in contradiction: for example the reference frame in which the cosmic microwave background radiation is isotropic defines such a privileged frame. Hence, a priori, a hidden communication explanation is not more surprising than nonlocality. We prove that for any finite speed, such models predict correlations that can be exploited for faster-than-light communication. This superluminal communication doesn't require access to any hidden physical quantities, but only the manipulation of measurement devices at the level of our present-day description of quantum experiments. Consequently, all possible explanations of quantum correlations that satisfy the principle of continuity, which states that everything propagates gradually and continuously through space and time, or in other words, all combination of local common causes and direct causes that reproduce quantum correlations, lead to faster than light communication. Accordingly, either there is superluminal

  3. Intermolecular RNA Recombination Occurs at Different Frequencies in Alternate Forms of Brome Mosaic Virus RNA Replication Compartments

    Directory of Open Access Journals (Sweden)

    Hernan Garcia-Ruiz

    2018-03-01

    Full Text Available Positive-strand RNA viruses replicate their genomes in membrane-bound replication compartments. Brome mosaic virus (BMV replicates in vesicular invaginations of the endoplasmic reticulum membrane. BMV has served as a productive model system to study processes like virus-host interactions, RNA replication and recombination. Here we present multiple lines of evidence showing that the structure of the viral RNA replication compartments plays a fundamental role and that recruitment of parental RNAs to a common replication compartment is a limiting step in intermolecular RNA recombination. We show that a previously defined requirement for an RNA recruitment element on both parental RNAs is not to function as a preferred crossover site, but in order for individual RNAs to be recruited into the replication compartments. Moreover, modulating the form of the replication compartments from spherular vesicles (spherules to more expansive membrane layers increased intermolecular RNA recombination frequency by 200- to 1000-fold. We propose that intermolecular RNA recombination requires parental RNAs to be recruited into replication compartments as monomers, and that recruitment of multiple RNAs into a contiguous space is much more common for layers than for spherules. These results could explain differences in recombination frequencies between viruses that replicate in association with smaller spherules versus larger double-membrane vesicles and convoluted membranes.

  4. Microgravity validation of a novel system for RNA isolation and multiplex quantitative real time PCR analysis of gene expression on the International Space Station.

    Directory of Open Access Journals (Sweden)

    Macarena Parra

    Full Text Available The International Space Station (ISS National Laboratory is dedicated to studying the effects of space on life and physical systems, and to developing new science and technologies for space exploration. A key aspect of achieving these goals is to operate the ISS National Lab more like an Earth-based laboratory, conducting complex end-to-end experimentation, not limited to simple microgravity exposure. Towards that end NASA developed a novel suite of molecular biology laboratory tools, reagents, and methods, named WetLab-2, uniquely designed to operate in microgravity, and to process biological samples for real-time gene expression analysis on-orbit. This includes a novel fluidic RNA Sample Preparation Module and fluid transfer devices, all-in-one lyophilized PCR assays, centrifuge, and a real-time PCR thermal cycler. Here we describe the results from the WetLab-2 validation experiments conducted in microgravity during ISS increment 47/SPX-8. Specifically, quantitative PCR was performed on a concentration series of DNA calibration standards, and Reverse Transcriptase-quantitative PCR was conducted on RNA extracted and purified on-orbit from frozen Escherichia coli and mouse liver tissue. Cycle threshold (Ct values and PCR efficiencies obtained on-orbit from DNA standards were similar to Earth (1 g controls. Also, on-orbit multiplex analysis of gene expression from bacterial cells and mammalian tissue RNA samples was successfully conducted in about 3 h, with data transmitted within 2 h of experiment completion. Thermal cycling in microgravity resulted in the trapping of gas bubbles inside septa cap assay tubes, causing small but measurable increases in Ct curve noise and variability. Bubble formation was successfully suppressed in a rapid follow-up on-orbit experiment using standard caps to pressurize PCR tubes and reduce gas release during heating cycles. The WetLab-2 facility now provides a novel operational on-orbit research capability for

  5. Pre-Big Bang, space-time structure, asymptotic Universe

    Directory of Open Access Journals (Sweden)

    Gonzalez-Mestres Luis

    2014-04-01

    the standard cosmology based on general relativity. In the new cosmology thus introduced, the contribution of the space curvature to the value of H2 is positive definite independently of the apparent sign of this curvature, and has a much larger value than the standard curvature term. Then, a cosmological constant is no longer required. The spinorial space-time also generates automatically for each comoving observer a privileged space direction that, together with parity violation, may explain the anisotropies observed in WMAP and Planck data. Contrary to frequent statements, such a signature would not be a strange phenomenon. The effect emerges directly from the use of two complex space-time coordinates instead of the conventional four real ones, and the privileged direction would correspond to the phase of the cosmic spinor. We remind here our previous work on the subject and further discuss some cosmological implications of the spinorial space-time.

  6. Prescribing Privileges for Psychologists: A Public Service or Hazard?

    Directory of Open Access Journals (Sweden)

    Shaheen E. Lakhan

    2007-07-01

    Full Text Available The privilege to prescribe pharmacotherapeutics has been granted in limited areas to psychologists. The psychologist's role in society may be approaching a great evolution that can dramatically impact the state of mental healthcare and the discipline of psychiatry. Opponents argue drug company funding and cheaper non-PhD psychological professionals fuel the movement for prescription rights for PhD level psychologists. However, proponents claim that this right would equip psychologists with greater psychotherapeutic modalities and the capability of having richer doctor-patient relationships to diagnose and treat underserved populations. Nonetheless, the paucity of prescribing psychologist studies cannot allow the biopsychosocial community to make firm opinions, let alone a decision on this debate. This article reviews the history of clinical psychology and highlights the potential divergence into collaborative clinical and health psychologists and autonomous prescribing psychologists.

  7. TH-B-12A-01: TG124 “A Guide for Establishing a Credentialing and Privileging Program for Users of Fluoroscopic Equipment in Healthcare Organizations”

    Energy Technology Data Exchange (ETDEWEB)

    Moore, M [Philadelphia VA Medical Ctr., Philadelphia, PA (United States)

    2014-06-15

    Fluoroscopy credentialing and privileging programs are being instituted because of recorded patient injuries and the widespread growth in fluoroscopy use by operators whose medical education did not include formal fluoroscopy training. This lack of training is recognized as a patient safety deficiency, and medical physicists and health physicists are finding themselves responsible for helping to establish fluoroscopy credentialing programs. While physicians are very knowledgeable about clinical credentials review and the privileging process, medical physicists and health physicists are not as familiar with the process and associated requirements. To assist the qualified medical physicist (QMP) and the radiation safety officer (RSO) with these new responsibilities, TG 124 provides an overview of the credentialing process, guidance for policy development and incorporating trained fluoroscopy users into a facility's established process, as well as recommendations for developing and maintaining a risk-based fluoroscopy safety training program. This lecture will review the major topics addressed in TG124 and relate them to practical situations. Learning Objectives: Understand the difference between credentialing and privileging. Understand the responsibilities, interaction and coordination among key individuals and committees. Understand options for integrating the QMP and/or RSO and Radiation Safety Committee into the credentialing and privileging process. Understand issues related to implementing the fluoroscopy safety training recommendations and with verifying and documenting successful completion.

  8. TH-B-12A-01: TG124 “A Guide for Establishing a Credentialing and Privileging Program for Users of Fluoroscopic Equipment in Healthcare Organizations”

    International Nuclear Information System (INIS)

    Moore, M

    2014-01-01

    Fluoroscopy credentialing and privileging programs are being instituted because of recorded patient injuries and the widespread growth in fluoroscopy use by operators whose medical education did not include formal fluoroscopy training. This lack of training is recognized as a patient safety deficiency, and medical physicists and health physicists are finding themselves responsible for helping to establish fluoroscopy credentialing programs. While physicians are very knowledgeable about clinical credentials review and the privileging process, medical physicists and health physicists are not as familiar with the process and associated requirements. To assist the qualified medical physicist (QMP) and the radiation safety officer (RSO) with these new responsibilities, TG 124 provides an overview of the credentialing process, guidance for policy development and incorporating trained fluoroscopy users into a facility's established process, as well as recommendations for developing and maintaining a risk-based fluoroscopy safety training program. This lecture will review the major topics addressed in TG124 and relate them to practical situations. Learning Objectives: Understand the difference between credentialing and privileging. Understand the responsibilities, interaction and coordination among key individuals and committees. Understand options for integrating the QMP and/or RSO and Radiation Safety Committee into the credentialing and privileging process. Understand issues related to implementing the fluoroscopy safety training recommendations and with verifying and documenting successful completion

  9. Diversity, Equity, and Inclusion in Independent Schools: How Silence and Privilege Hinder the Work

    OpenAIRE

    Perez del Toro, Jessica

    2017-01-01

    Most private or independent schools originated as schools of privilege, serving the offspring of a culturally and socially elite group of white American families (Cookson, 2013; Flewelling, 2013; Slaughter-Defoe & Johnson, 1988). Since the 1960s these institutions have worked to change their predominantly White, elitist image by broadening their access and striving to become diverse and inclusive institutions that prepare all students to “thrive in a global, multicultural community” (Quanti, ...

  10. Fast Arc-Annotated Subsequence Matching in Linear Space

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li

    2010-01-01

    is deleted any arc with an endpoint in that base is also deleted. Arc-annotated strings where the arcs are "nested" are a natural model of RNA molecules that captures both the primary and secondary structure of these. The arc-preserving subsequence problem for nested arc-annotated strings is basic primitive...... for investigating the function of RNA molecules. Gramm et al. [ACM Trans. Algorithms 2006] gave an algorithm for this problem using O(nm) time and space, where m and n are the lengths of P and Q, respectively. In this paper we present; a new algorithm using O(nm) time and O(n+m,) space, thereby matching...... the previous time bound while significantly reducing the space from a quadratic term to linear. This is essential to process large RNA molecules where the space is a likely to be a bottleneck. To obtain our result we introduce several novel ideas which may be of independent interest for related problems on arc...

  11. microRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity

    Data.gov (United States)

    National Aeronautics and Space Administration — In the present study we analyzed miRNA and mRNA expression profiles in human peripheral blood lymphocytes (PBLs) incubated in microgravity condition simulated by a...

  12. Crowdsourced Quantification and Visualization of Urban Mobility Space Inequality

    Directory of Open Access Journals (Sweden)

    Michael Szell

    2018-03-01

    Full Text Available Most cities are car-centric, allocating a privileged amount of urban space to cars at the expense of sustainable mobility like cycling. Simultaneously, privately owned vehicles are vastly underused, wasting valuable opportunities for accommodating more people in a livable urban environment by occupying spacious parking areas. Since a data-driven quantification and visualization of such urban mobility space inequality is lacking, here we explore how crowdsourced data can help to advance its understanding. In particular, we describe how the open-source online platform What the Street!? uses massive user-generated data from OpenStreetMap for the interactive exploration of city-wide mobility spaces. Using polygon packing and graph algorithms, the platform rearranges all parking and mobility spaces of cars, rails, and bicycles of a city to be directly comparable, making mobility space inequality accessible to a broad public. This crowdsourced method confirms a prevalent imbalance between modal share and space allocation in 23 cities worldwide, typically discriminating bicycles. Analyzing the guesses of the platform’s visitors about mobility space distributions, we find that this discrimination is consistently underestimated in the public opinion. Finally, we discuss a visualized scenario in which extensive parking areas are regained through fleets of shared, autonomous vehicles. We outline how such accessible visualization platforms can facilitate urban planners and policy makers to reclaim road and parking space for pushing forward sustainable transport solutions.

  13. Plantão social: espaço privilegiado para identificação/notificação de violência contra crianças e adolescentes Social duty: privileged space for identification/notice of violence against children and adolescents

    Directory of Open Access Journals (Sweden)

    Fernanda de Oliveira Monteiro

    2010-09-01

    Full Text Available Este artigo tem como proposta problematizar a concepção de plantão social, que vigora no interior do Serviço Social, discutindo tal estratégica como espaço privilegiado para identificação/notificação de casos de violência praticada contra crianças e adolescentes. Pretende-se ainda refletir sobre os limites e possibilidades de avanço na emancipação dos sujeitos (crianças e adolescentes vitimizados pela violência doméstica, a partir de uma prática profissional comprometida com a ampliação da cidadania e a defesa intransigente dos direitos humanos.This article proposes to question the concept of social duty inside the Social Services. It discusses such a strategy as a privileged space for identification/notice of violence cases against children and adolescents. It still intends to consider the limits and possibilities of progress in the emancipation of the subjects (children and adolescents who are the victims of domestic violence, from a professional practice committed to the enlargement of citizenship and the uncompromising defense of human rights.

  14. Agreement on the privileges and immunities of the Agency. Acceptances by Member States. Status as of 31 December 1996

    International Nuclear Information System (INIS)

    1997-01-01

    The document lists the 65 Members which have accepted the Agreement on the Privileges and Immunities of the International Atomic Energy Agency as of 31 December 1996. The list is followed by the texts of reservations made to the Agreement

  15. Complete probabilistic analysis of RNA shapes

    Directory of Open Access Journals (Sweden)

    Voß Björn

    2006-02-01

    Full Text Available Abstract Background Soon after the first algorithms for RNA folding became available, it was recognised that the prediction of only one energetically optimal structure is insufficient to achieve reliable results. An in-depth analysis of the folding space as a whole appeared necessary to deduce the structural properties of a given RNA molecule reliably. Folding space analysis comprises various methods such as suboptimal folding, computation of base pair probabilities, sampling procedures and abstract shape analysis. Common to many approaches is the idea of partitioning the folding space into classes of structures, for which certain properties can be derived. Results In this paper we extend the approach of abstract shape analysis. We show how to compute the accumulated probabilities of all structures that share the same shape. While this implies a complete (non-heuristic analysis of the folding space, the computational effort depends only on the size of the shape space, which is much smaller. This approach has been integrated into the tool RNAshapes, and we apply it to various RNAs. Conclusion Analyses of conformational switches show the existence of two shapes with probabilities approximately 23 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaadaWcaaqaaiabikdaYaqaaiabiodaZaaaaaa@2EA2@ vs. 13 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaadaWcaaqaaiabigdaXaqaaiabiodaZaaaaaa@2EA0@, whereas the analysis of a microRNA precursor reveals one shape with a probability near to 1.0. Furthermore, it is shown that a shape can outperform an energetically more favourable one by

  16. RNA structure alignment by a unit-vector approach.

    Science.gov (United States)

    Capriotti, Emidio; Marti-Renom, Marc A

    2008-08-15

    The recent discovery of tiny RNA molecules such as microRNAs and small interfering RNA are transforming the view of RNA as a simple information transfer molecule. Similar to proteins, the native three-dimensional structure of RNA determines its biological activity. Therefore, classifying the current structural space is paramount for functionally annotating RNA molecules. The increasing numbers of RNA structures deposited in the PDB requires more accurate, automatic and benchmarked methods for RNA structure comparison. In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach. The algorithm has been implemented in the SARA program, which results in RNA structure pairwise alignments and their statistical significance. The SARA program has been implemented to be of general applicability even when no secondary structure can be calculated from the RNA structures. A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in inverted approximately 6% extra alignments with at least 50% structurally superposed nucleotides and base pairs. A first attempt to perform RNA automatic functional annotation based on structure alignments indicates that SARA can correctly assign the deepest SCOR classification to >60% of the query structures. The SARA program is freely available through a World Wide Web server http://sgu.bioinfo.cipf.es/services/SARA/. Supplementary data are available at Bioinformatics online.

  17. The privileged planet how our place in the cosmos is designed for discovery

    CERN Document Server

    Gonzalez, Guillermo

    2004-01-01

    Is Earth merely an insignificant speck in a vast and meaningless universe? On the contrary. The Privileged Planet: How Our Place in the Cosmos Is Designed for Discovery shows that this cherished assumption of materialism is dead wrong. Earth is far more significant than virtually anyone has realized. Contrary to the scientific orthodoxy, it is not an average planet around an ordinary star in an unremarkable part of the Milky Way.In this provocative book, Guillermo Gonzalez and Jay W. Richards present a staggering array of evidence that exposes the hollowness of this modern

  18. Crystallization and preliminary X-ray analysis of the mRNA-binding domain of elongation factor SelB from Escherichia coli in complex with RNA

    International Nuclear Information System (INIS)

    Soler, Nicolas; Fourmy, Dominique; Yoshizawa, Satoko

    2007-01-01

    The mRNA-binding domain of E. coli selenocysteine-specific elongation factor SelB (residues 478–614; SelB-WH3/4) was overproduced in E. coli and its cognate mRNA ligand, 23 nucleotides of the SECIS RNA hairpin, was prepared by in vitro transcription. The purified SelB-WH3/4–SECIS RNA complex crystallized in space group C2 and diffracted to 2.3 Å. In bacteria, selenocysteine (the 21st amino acid) is incorporated into proteins via machinery that includes SelB, a specific translational elongation factor. SelB binds to an mRNA hairpin called the selenocysteine-insertion sequence (SECIS) and delivers selenocysteyl-tRNA Sec to the ribosomal A site. The minimum C-terminal fragment (residues 478–614) of Escherichia coli SelB (SelB-WH3/4) required for SECIS binding has been overexpressed and purified. This protein was crystallized in complex with 23 nucleotides of the SECIS hairpin at 294 K using the hanging-drop vapour-diffusion method. A data set was collected to 2.3 Å resolution from a single crystal at 100 K using ESRF beamline BM-30. The crystal belongs to space group C2, with unit-cell parameters a = 103.50, b = 56.51, c = 48.41 Å. The asymmetric unit contains one WH3/4-domain–RNA complex. The Matthews coefficient was calculated to be 3.37 Å 3 Da −1 and the solvent content was estimated to be 67.4%

  19. Distinctive Features Hold a Privileged Status in the Computation of Word Meaning: Implications for Theories of Semantic Memory

    Science.gov (United States)

    Cree, George S.; McNorgan, Chris; McRae, Ken

    2006-01-01

    The authors present data from 2 feature verification experiments designed to determine whether distinctive features have a privileged status in the computation of word meaning. They use an attractor-based connectionist model of semantic memory to derive predictions for the experiments. Contrary to central predictions of the conceptual structure…

  20. A new learning paradigm: learning using privileged information.

    Science.gov (United States)

    Vapnik, Vladimir; Vashist, Akshay

    2009-01-01

    In the Afterword to the second edition of the book "Estimation of Dependences Based on Empirical Data" by V. Vapnik, an advanced learning paradigm called Learning Using Hidden Information (LUHI) was introduced. This Afterword also suggested an extension of the SVM method (the so called SVM(gamma)+ method) to implement algorithms which address the LUHI paradigm (Vapnik, 1982-2006, Sections 2.4.2 and 2.5.3 of the Afterword). See also (Vapnik, Vashist, & Pavlovitch, 2008, 2009) for further development of the algorithms. In contrast to the existing machine learning paradigm where a teacher does not play an important role, the advanced learning paradigm considers some elements of human teaching. In the new paradigm along with examples, a teacher can provide students with hidden information that exists in explanations, comments, comparisons, and so on. This paper discusses details of the new paradigm and corresponding algorithms, introduces some new algorithms, considers several specific forms of privileged information, demonstrates superiority of the new learning paradigm over the classical learning paradigm when solving practical problems, and discusses general questions related to the new ideas.

  1. GMO conflict between patent protection and farmers' privilege : A Schmeiser v. Monsanto Case (2)

    OpenAIRE

    Hiraki, Takayuki

    2005-01-01

    In the 1990s, genetically modified (GM) crops have rapidly gained cropping area and market share. As a result, GM crops contaminated non-GM traditional crops through pollination and other natural phenomena. In addition, the governments in the USA and Canada have concluded that GM crops can be patentable as long as they can be approved as inventions with novelty and usefulness. In the meanwhile, the “farmers' privilege" provided in the UPOV (The International Union for the Protection of New Va...

  2. Situating the Discourses of Privilege and Marginalization in the Lives of Two East Asian Women Teachers of English

    Science.gov (United States)

    Park, Gloria

    2015-01-01

    Using a narrative approach (i.e., Clandinin and Connelly 2000; Dewey 1938 [1963]), this article explores the identity constructions and negotiations of two East Asian women teachers of English in MATESOL programs. The focus of this article explores the ways in which the two women's privileged experiences coexisted with issues of marginalization…

  3. The privileges and immunities of international organizations in domestic courts

    CERN Document Server

    2013-01-01

    International organizations are increasingly operating across borders and engaging in legal transactions in virtually all jurisdictions. This makes, familiarity with the applicable law and practice imperative for both international organizations and those who engage in legal relations with them. Furthermore, the issue of whether, how, and to what extent domestic courts take into account decisions of foreign and international courts and tribunals in their own decision-making has become increasingly important in recent years. This book provides a comprehensive empirical study of this transnational judicial dialogue, focusing on the law and practice of domestic jurisdictions concerning the legal personality, privileges, and immunities of international organizations. It presents a selection of detailed country-by-country studies, examining the manner of judicial dialogue across domestic jurisdictions, and between national and international courts. The approach taken in this book intersects with three highly topi...

  4. Expression of MDM2 mRNA, MDM2, P53 and P16 Proteins in Urothelial Lesions in the View of the WHO 4th Edition Guidelines as A Molecular Insight towards Personalized Medicine

    Directory of Open Access Journals (Sweden)

    Olfat Hammam

    2017-08-01

    Full Text Available AIM: Here we imposed a multimarker molecular panel composed of P53, MDM2 protein & mRNA & P16 with the identification of sensitive and specific cut offs among the Egyptian urothelial carcinomas bilharzial or not emphasize the pathological and molecular classifications, pathways and prognosis as a privilege for adjuvant therapy. METHODS: Three hundred and ten urothelial lesions were pathologically evaluated and grouped as follows: 50 chronic cystitis as benign, 240 urothelial carcinomas and 20 normal bladder tissue as a control. Immunohistochemistry for MDM Protein, P16 & p53 and In Situ Hybridization for MDM2mRNA were done. RESULTS: MDM2mRNA overexpression correlated with low grade low stage non invasive tumors, while P53 > 40% & p16 40% & P16 10% from high grade, high stage invasive urothelial carcinomas (with p53 > 40, p16 40 & p16 < 10%, together with the histopathological features can distinguish in situ urothelial lesions from dysplastic and atypical lesions.

  5. Molecular computation: RNA solutions to chess problems.

    Science.gov (United States)

    Faulhammer, D; Cukras, A R; Lipton, R J; Landweber, L F

    2000-02-15

    We have expanded the field of "DNA computers" to RNA and present a general approach for the solution of satisfiability problems. As an example, we consider a variant of the "Knight problem," which asks generally what configurations of knights can one place on an n x n chess board such that no knight is attacking any other knight on the board. Using specific ribonuclease digestion to manipulate strands of a 10-bit binary RNA library, we developed a molecular algorithm and applied it to a 3 x 3 chessboard as a 9-bit instance of this problem. Here, the nine spaces on the board correspond to nine "bits" or placeholders in a combinatorial RNA library. We recovered a set of "winning" molecules that describe solutions to this problem.

  6. ISEV position paper: extracellular vesicle RNA analysis and bioinformatics

    Directory of Open Access Journals (Sweden)

    Andrew F. Hill

    2013-12-01

    Full Text Available Extracellular vesicles (EVs are the collective term for the various vesicles that are released by cells into the extracellular space. Such vesicles include exosomes and microvesicles, which vary by their size and/or protein and genetic cargo. With the discovery that EVs contain genetic material in the form of RNA (evRNA has come the increased interest in these vesicles for their potential use as sources of disease biomarkers and potential therapeutic agents. Rapid developments in the availability of deep sequencing technologies have enabled the study of EV-related RNA in detail. In October 2012, the International Society for Extracellular Vesicles (ISEV held a workshop on “evRNA analysis and bioinformatics.” Here, we report the conclusions of one of the roundtable discussions where we discussed evRNA analysis technologies and provide some guidelines to researchers in the field to consider when performing such analysis.

  7. Levelling the Playing Fields in PAR: The Intricacies of Power, Privilege, and Participation in a University-Community-School Partnership

    Science.gov (United States)

    Wood, Lesley; McAteer, Mary

    2017-01-01

    When academics, who occupy a traditional position of power and privilege, engage with community members whose thinking, attitudes, and responses have been shaped by ongoing sociohistorical oppression and disadvantage, democratic participation is not easy to attain. Yet, unless community members feel able to participate freely, the valuable local…

  8. Raymond Andrews as Griot: Privileging Southern Black Communities through Oral Storytelling and Cultural History

    Directory of Open Access Journals (Sweden)

    Brennan Collins

    2012-01-01

    Full Text Available Raymond Andrews’ novels celebrate rural Black life by focusing on the customs and traditions of Southern African American communities. Critical to this celebration are the rhetorical strategies Andrews uses that privilege oral over literary storytelling. Using Geneva Smitherman’s discussion of the griot and Henry Louis Gates, Jr.’s concept of the speakerly text in the context of John Miles Foley’s work on comparative oral traditions, this essay explores the possibility and implications of describing Andrews’ written work as a form of oral storytelling.

  9. Probing RNA native conformational ensembles with structural constraints

    DEFF Research Database (Denmark)

    Fonseca, Rasmus; van den Bedem, Henry; Bernauer, Julie

    2016-01-01

    substates, which are difficult to characterize experimentally and computationally. Here, we present an innovative, entirely kinematic computational procedure to efficiently explore the native ensemble of RNA molecules. Our procedure projects degrees of freedom onto a subspace of conformation space defined...

  10. QSAR modeling and chemical space analysis of antimalarial compounds

    Science.gov (United States)

    Sidorov, Pavel; Viira, Birgit; Davioud-Charvet, Elisabeth; Maran, Uko; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

    2017-05-01

    Generative topographic mapping (GTM) has been used to visualize and analyze the chemical space of antimalarial compounds as well as to build predictive models linking structure of molecules with their antimalarial activity. For this, a database, including 3000 molecules tested in one or several of 17 anti- Plasmodium activity assessment protocols, has been compiled by assembling experimental data from in-house and ChEMBL databases. GTM classification models built on subsets corresponding to individual bioassays perform similarly to the earlier reported SVM models. Zones preferentially populated by active and inactive molecules, respectively, clearly emerge in the class landscapes supported by the GTM model. Their analysis resulted in identification of privileged structural motifs of potential antimalarial compounds. Projection of marketed antimalarial drugs on this map allowed us to delineate several areas in the chemical space corresponding to different mechanisms of antimalarial activity. This helped us to make a suggestion about the mode of action of the molecules populating these zones.

  11. Testing the idea of privileged awareness of self-relevant information.

    Science.gov (United States)

    Stein, Timo; Siebold, Alisha; van Zoest, Wieske

    2016-03-01

    Self-relevant information is prioritized in processing. Some have suggested the mechanism driving this advantage is akin to the automatic prioritization of physically salient stimuli in information processing (Humphreys & Sui, 2015). Here we investigate whether self-relevant information is prioritized for awareness under continuous flash suppression (CFS), as has been found for physical salience. Gabor patches with different orientations were first associated with the labels You or Other. Participants were more accurate in matching the self-relevant association, replicating previous findings of self-prioritization. However, breakthrough into awareness from CFS did not differ between self- and other-associated Gabors. These findings demonstrate that self-relevant information has no privileged access to awareness. Rather than modulating the initial visual processes that precede and lead to awareness, the advantage of self-relevant information may better be characterized as prioritization at later processing stages. (c) 2016 APA, all rights reserved).

  12. The interaction between the iron-responsive element binding protein and its cognate RNA is highly dependent upon both RNA sequence and structure.

    Science.gov (United States)

    Jaffrey, S R; Haile, D J; Klausner, R D; Harford, J B

    1993-09-25

    To assess the influence of RNA sequence/structure on the interaction RNAs with the iron-responsive element binding protein (IRE-BP), twenty eight altered RNAs were tested as competitors for an RNA corresponding to the ferritin H chain IRE. All changes in the loop of the predicted IRE hairpin and in the unpaired cytosine residue characteristically found in IRE stems significantly decreased the apparent affinity of the RNA for the IRE-BP. Similarly, alteration in the spacing and/or orientation of the loop and the unpaired cytosine of the stem by either increasing or decreasing the number of base pairs separating them significantly reduced efficacy as a competitor. It is inferred that the IRE-BP forms multiple contacts with its cognate RNA, and that these contacts, acting in concert, provide the basis for the high affinity of this interaction.

  13. Agreement on the privileges and immunities of the IAEA. Status list as of 12 September 2000. Acceptances by Member States

    International Nuclear Information System (INIS)

    2000-01-01

    The document lists the 67 Members which, by 12 September 2000, had accepted the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, as provided for in Section 38 thereof. The list is followed by the texts of declarations/reservations made to the Agreement

  14. French language space science educational outreach

    Science.gov (United States)

    Schofield, I.; Masongsong, E. V.; Connors, M. G.

    2015-12-01

    Athabasca University's AUTUMNX ground-based magnetometer array to measure and report geomagnetic conditions in eastern Canada is located in the heart of French speaking Canada. Through the course of the project, we have had the privilege to partner with schools, universities, astronomy clubs and government agencies across Quebec, all of which operate primarily in French. To acknowledge and serve the needs of our research partners, we have endeavored to produce educational and outreach (EPO) material adapted for francophone audiences with the help of UCLA's department of Earth, Planetary and Space Sciences (EPSS). Not only will this provide greater understanding and appreciation of the geospace environment unique to Quebec and surrounding regions, it strengthens our ties with our francophone, first nations (native Americans) and Inuit partners, trailblazing new paths of research collaboration and inspiring future generations of researchers.

  15. ncRNA consensus secondary structure derivation using grammar strings.

    Science.gov (United States)

    Achawanantakun, Rujira; Sun, Yanni; Takyar, Seyedeh Shohreh

    2011-04-01

    Many noncoding RNAs (ncRNAs) function through both their sequences and secondary structures. Thus, secondary structure derivation is an important issue in today's RNA research. The state-of-the-art structure annotation tools are based on comparative analysis, which derives consensus structure of homologous ncRNAs. Despite promising results from existing ncRNA aligning and consensus structure derivation tools, there is a need for more efficient and accurate ncRNA secondary structure modeling and alignment methods. In this work, we introduce a consensus structure derivation approach based on grammar string, a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar (CFG) and a full RNA grammar including pseudoknots. Being a string defined on a special alphabet constructed from a grammar, grammar string converts ncRNA alignment into sequence alignment. We derive consensus secondary structures from hundreds of ncRNA families from BraliBase 2.1 and 25 families containing pseudoknots using grammar string alignment. Our experiments have shown that grammar string-based structure derivation competes favorably in consensus structure quality with Murlet and RNASampler. Source code and experimental data are available at http://www.cse.msu.edu/~yannisun/grammar-string.

  16. "I'm Sure as Hell Not Putting Any Man on a Pedestal": Male Privilege and Accountability in Domestic and Sexual Violence Work.

    Science.gov (United States)

    Macomber, Kris

    2018-05-01

    Efforts to involve men as allies in domestic and sexual violence work are expanding, marking a shift for these historically women-led movements. Although this shift is beneficial, it also generates new challenges. From a multi-method qualitative study, this article presents descriptive findings about the internal tensions accompanying the "men as allies" development, namely the gender inequality and male privilege reproduced within movement organizations. I draw on sociological theorizing about men in female-dominated professions to explain the reproduction of gender inequality within movement spaces. I also examine how people are dealing with these tensions by developing a discourse around "men's accountability." My findings suggest that, although discourse about accountability has been successfully integrated into the culture of domestic and sexual violence work, there are key challenges that hinder effective accountability practices. I end by offering suggestions for implementing accountability practices at the organizational level. This study contributes important empirical and theoretical insights currently missing from the literature on male allies, which can be used to inform men's growing involvement in anti-violence work.

  17. Agreement on the Privileges and Immunities of the Agency. Acceptances by Member States

    International Nuclear Information System (INIS)

    1973-01-01

    The list of Member States overleaf shows the 41 Members which, by 30 November 1972, had accepted the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, as provided for in Section 38 thereof. Members are listed in alphabetical order, which is different in versions of this document in other languages. The list is followed by the texts of such reservations to the Agreement as some of the Members in question made when depositing their respective instruments of acceptance with the Director General. The reservations are reproduced in the sequence in which the instruments of acceptance to which they relate were deposited

  18. Agreement on the Privileges and Immunities of the Agency. Acceptances by Member States

    International Nuclear Information System (INIS)

    1969-01-01

    The list of Member States overleaf shows the 35 Members which, by 1 November 1969, had accepted the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, as provided for in Section 38 thereof. Members are listed in alphabetical order, which is different in versions of this document in other languages. The list is followed by the texts of such reservations to the Agreement as some of the Members in question made when depositing their respective instruments of acceptance with the Director General. The reservations are reproduced in the sequential order of the deposit of the instruments of acceptance to which they relate

  19. Agreement on the Privileges and Immunities of the Agency. Acceptances by Member States

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1969-11-27

    The list of Member States overleaf shows the 35 Members which, by 1 November 1969, had accepted the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, as provided for in Section 38 thereof. Members are listed in alphabetical order, which is different in versions of this document in other languages. The list is followed by the texts of such reservations to the Agreement as some of the Members in question made when depositing their respective instruments of acceptance with the Director General. The reservations are reproduced in the sequential order of the deposit of the instruments of acceptance to which they relate.

  20. Agreement on the Privileges and Immunities of the Agency. Acceptances by Member States

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1973-01-15

    The list of Member States overleaf shows the 41 Members which, by 30 November 1972, had accepted the Agreement on the Privileges and Immunities of the International Atomic Energy Agency, as provided for in Section 38 thereof. Members are listed in alphabetical order, which is different in versions of this document in other languages. The list is followed by the texts of such reservations to the Agreement as some of the Members in question made when depositing their respective instruments of acceptance with the Director General. The reservations are reproduced in the sequence in which the instruments of acceptance to which they relate were deposited.

  1. The factory of illusions in the ‘Third Rome’:Circus Maximus as a space of fascist simulation

    OpenAIRE

    Kallis, Aristotle

    2014-01-01

    Although the site of the ancient Circus Maximus was one of the most loaded spaces of the Fascist ‘Third Rome’, it has received limited attention as a privileged site where a dizzying array of myths and illusions were entertained, simulated, and deposited as new Fascist layers on Rome’s urban and mnemonic palimpsest. Previously a decayed, ‘unsightly’, and overcrowded hodgepodge of layers of life, history, and memory, it was substantially restored, ruthlessly emptied of its previous life, and t...

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

    Directory of Open Access Journals (Sweden)

    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

  3. Privileged Electrophile Sensors: A Resource for Covalent Drug Development.

    Science.gov (United States)

    Long, Marcus John Curtis; Aye, Yimon

    2017-07-20

    This Perspective delineates how redox signaling affects the activity of specific enzyme isoforms and how this property may be harnessed for rational drug design. Covalent drugs have resurged in recent years and several reports have extolled the general virtues of developing irreversible inhibitors. Indeed, many modern pharmaceuticals contain electrophilic appendages. Several invoke a warhead that hijacks active-site nucleophiles whereas others take advantage of spectator nucleophilic side chains that do not participate in enzymatic chemistry, but are poised to bind/react with electrophiles. The latest data suggest that innate electrophile sensing-which enables rapid reaction with an endogenous signaling electrophile-is a quintessential resource for the development of covalent drugs. For instance, based on recent work documenting isoform-specific electrophile sensing, isozyme non-specific drugs may be converted to isozyme-specific analogs by hijacking privileged first-responder electrophile-sensing cysteines. Because this approach targets functionally relevant cysteines, we can simultaneously harness previously untapped moonlighting roles of enzymes linked to redox sensing. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. 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.

  5. Damned if you do: culture, identity, privilege, and teenage childbearing in the United States.

    Science.gov (United States)

    Geronimus, Arline T

    2003-09-01

    Why is the broad American public disapproving of urban African American teen mothers and unaware that the scientific evidence on the consequences of teen childbearing, per se, is equivocal? I focus on the links between culture, identity, and privilege. I argue that the broader society is selective in its attention to the actual life chances of urban African Americans and how these chances shape fertility-timing norms, in part, because this selective focus helps maintain the core values, competencies, and privileges of the dominant group. Delayed childbearing is an adaptive practice for European Americans and an intensely salient goal they have for their children. Yet early fertility-timing patterns may constitute adaptive practice for African American residents of high-poverty urban areas, in no small measure because they contend with structural constraints that shorten healthy life expectancy. European Americans put their cultural priorities into action ahead of the needs of African Americans and employ substantial resources to disseminate the social control message meant for their youth that teenage childbearing has disastrous consequences. Their ability to develop a more nuanced understanding of early childbearing is limited by their culturally mediated perceptions. Thus, cultural dominance can be perpetuated by well-meaning people consciously dedicated to children's well-being, social justice, and the public good. The entrenched cultural interdependence of and social inequality between European and African Americans leads African Americans to be highly visible targets of moral condemnation for their fertility behavior, and also sets up African Americans to pay a particularly high political, economic, psychosocial, and health price.

  6. A Novel Microfluidic Device for Fully Automated Extraction of RNA from Cell Cultures, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Differential gene expression by RNA profiling is a universal and critical step in space biology experiments, which seek to link specific molecular events with...

  7. Selective Allosteric Antagonists for the G Protein-Coupled Receptor GPRC6A Based on the 2-Phenylindole Privileged Structure Scaffold

    DEFF Research Database (Denmark)

    Johansson, Henrik; Boesgaard, Michael Worch; Nørskov-Lauritsen, Lenea

    2015-01-01

    G protein-coupled receptors (GPCRs) represent a biological target class of fundamental importance in drug therapy. The GPRC6A receptor is a newly deorphanized class C GPCR that we recently reported for the first allosteric antagonists based on the 2-arylindole privileged structure scaffold (e.g., 1...

  8. Akt3 is a privileged first responder in isozyme-specific electrophile response.

    Science.gov (United States)

    Long, Marcus J C; Parvez, Saba; Zhao, Yi; Surya, Sanjna L; Wang, Yiran; Zhang, Sheng; Aye, Yimon

    2017-03-01

    Isozyme-specific post-translational regulation fine tunes signaling events. However, redundancy in sequence or activity renders links between isozyme-specific modifications and downstream functions uncertain. Methods to study this phenomenon are underdeveloped. Here we use a redox-targeting screen to reveal that Akt3 is a first-responding isozyme sensing native electrophilic lipids. Electrophile modification of Akt3 modulated downstream pathway responses in cells and Danio rerio (zebrafish) and markedly differed from Akt2-specific oxidative regulation. Digest MS sequencing identified Akt3 C119 as the privileged cysteine that senses 4-hydroxynonenal. A C119S Akt3 mutant was hypomorphic for all downstream phenotypes shown by wild-type Akt3. This study documents isozyme-specific and chemical redox signal-personalized physiological responses.

  9. Linguistic Privilege and Justice: What can we learn from STEM?

    Energy Technology Data Exchange (ETDEWEB)

    Pronskikh, V. [Fermilab

    2018-01-19

    The linguistic privilege of native speakers in scientific communication, both oral and written, has been widely reported to influence researchers’ publications and careers in and beyond academia. I analyze social structure and communication in the STEM field through the example of big science and attempt to answer the question of why language injustice has a less significant effect on nonnative scientists and engineers than on humanity scholars, scrutinizing the role of signs and nonlinguistic boundary objects in STEM practice and written communication and how they mitigate the emphasis on linguistic eloquence. I suggest that although big science is relatively linguistically inclusive, for collaborative publications and presentations the rhetoric component requirements nevertheless remain at a level comparable to that of the humanities. I draw on the theory of justice to argue that to increase L2 speakers’ and writers’ satisfaction, language standards for international communication must be adjusted to a level convenient for an average L2.

  10. Enumeration of RNA complexes via random matrix theory.

    Science.gov (United States)

    Andersen, Jørgen E; Chekhov, Leonid O; Penner, Robert C; Reidys, Christian M; Sułkowski, Piotr

    2013-04-01

    In the present article, we review a derivation of the numbers of RNA complexes of an arbitrary topology. These numbers are encoded in the free energy of the Hermitian matrix model with potential V(x)=x2/2-stx/(1-tx), where s and t are respective generating parameters for the number of RNA molecules and hydrogen bonds in a given complex. The free energies of this matrix model are computed using the so-called topological recursion, which is a powerful new formalism arising from random matrix theory. These numbers of RNA complexes also have profound meaning in mathematics: they provide the number of chord diagrams of fixed genus with specified numbers of backbones and chords as well as the number of cells in Riemann's moduli spaces for bordered surfaces of fixed topological type.

  11. A Novel Microfluidic Device for Fully Automated Extraction of RNA from Cell Cultures, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Obtaining high quality, intact RNA from cells is an ubiquitous need in the pursuit of space biology. Our overall objective is to develop and commercialize a...

  12. Expression of Fas (CD95/APO-1) ligand by human breast cancers: significance for tumor immune privilege.

    LENUS (Irish Health Repository)

    O'Connell, J

    2012-02-03

    Breast cancers have been shown to elicit tumor-specific immune responses. As in other types of cancer, the antitumor immune response fails to contain breast tumor growth, and a reduction in both the quantity and cytotoxic effectiveness of tumor-infiltrating lymphocytes (TILs) is associated with a poorer prognosis. Fas ligand (FasL) induces apoptotic death of activated lymphocytes that express its cell surface receptor, FasR (CD95\\/APO-1). FasL-mediated apoptosis of activated lymphocytes contributes to normal immune downregulation through its roles in tolerance acquisition, immune response termination, and maintenance of immune privilege in the eye, testis, and fetus. In this report, we demonstrate that breast carcinomas express FasL. Using in situ hybridization and immunohistochemistry, we show that breast tumors constitutively express FasL at both the mRNA and protein levels, respectively. FasL expression is prevalent in breast cancer: 100% of breast tumors (17 of 17) were found to express FasL, and expression occurred over more than 50% of the tumor area in all cases. By immunohistochemistry, FasR was found to be coexpressed with FasL throughout large areas of all the breast tumors. This suggests that the tumor cells had acquired intracellular defects in FasL-mediated apoptotic signaling. FasL and FasR expression were independent of tumor type or infiltrative capacity. FasL expressed by tumor cells has previously been shown to kill Fas-sensitive lymphoid cells in vitro and has been associated with apoptosis of TILs in vivo. We conclude that mammary carcinomas express FasL in vivo as a potential inhibitor of the antitumor immune response.

  13. Paralogs hnRNP L and hnRNP LL exhibit overlapping but distinct RNA binding constraints.

    Directory of Open Access Journals (Sweden)

    Sarah A Smith

    Full Text Available HnRNP (heterogeneous nuclear ribonucleoprotein proteins are a large family of RNA-binding proteins that regulate numerous aspects of RNA processing. Interestingly, several paralogous pairs of hnRNPs exist that exhibit similar RNA-binding specificity to one another, yet have non-redundant functional targets in vivo. In this study we systematically investigate the possibility that the paralogs hnRNP L and hnRNP LL have distinct RNA binding determinants that may underlie their lack of functional redundancy. Using a combination of RNAcompete and native gel analysis we find that while both hnRNP L and hnRNP LL preferentially bind sequences that contain repeated CA dinucleotides, these proteins differ in their requirement for the spacing of the CAs. Specifically, hnRNP LL has a more stringent requirement for a two nucleotide space between CA repeats than does hnRNP L, resulting in hnRNP L binding more promiscuously than does hnRNP LL. Importantly, this differential requirement for the spacing of CA dinucleotides explains the previously observed differences in the sensitivity of hnRNP L and LL to mutations within the CD45 gene. We suggest that overlapping but divergent RNA-binding preferences, as we show here for hnRNP L and hnRNP LL, may be commonplace among other hnRNP paralogs.

  14. Landscape and variation of RNA secondary structure across the human transcriptome.

    Science.gov (United States)

    Wan, Yue; Qu, Kun; Zhang, Qiangfeng Cliff; Flynn, Ryan A; Manor, Ohad; Ouyang, Zhengqing; Zhang, Jiajing; Spitale, Robert C; Snyder, Michael P; Segal, Eran; Chang, Howard Y

    2014-01-30

    In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. RNA structure influences practically every step in the gene expression program. However, the nature of most RNA structures or effects of sequence variation on structure are not known. Here we report the initial landscape and variation of RNA secondary structures (RSSs) in a human family trio (mother, father and their child). This provides a comprehensive RSS map of human coding and non-coding RNAs. We identify unique RSS signatures that demarcate open reading frames and splicing junctions, and define authentic microRNA-binding sites. Comparison of native deproteinized RNA isolated from cells versus refolded purified RNA suggests that the majority of the RSS information is encoded within RNA sequence. Over 1,900 transcribed single nucleotide variants (approximately 15% of all transcribed single nucleotide variants) alter local RNA structure. We discover simple sequence and spacing rules that determine the ability of point mutations to impact RSSs. Selective depletion of 'riboSNitches' versus structurally synonymous variants at precise locations suggests selection for specific RNA shapes at thousands of sites, including 3' untranslated regions, binding sites of microRNAs and RNA-binding proteins genome-wide. These results highlight the potentially broad contribution of RNA structure and its variation to gene regulation.

  15. Star Power: An Experiential Learning Exercise to Foster Ecological Perspectives on Power, Privilege, and Oppression

    Science.gov (United States)

    Nnawulezi, Nkiru; Campbell, Christina; Landstra, Kalleigh; Davis, Se'ara; Vandegrift, Cortney; Taylor, Amanda

    2014-01-01

    The purpose of this article is to describe the utility of Star Power, as an experiential learning exercise applied in a community psychology undergraduate course. This exercise simulates systems of power, privilege, and oppression while fostering an ecological perspective that raises students’ awareness and knowledge about power differentials within society. The simulation of trading and lawmaking works best with 18 to 35 students and takes approximately 80 minutes to conduct. This paper highlights three representative student perspectives concerning their participation and experience with Star Power. Strategies for facilitating class discussion are also discussed. PMID:23480288

  16. iDoRNA: An Interacting Domain-based Tool for Designing RNA-RNA Interaction Systems

    Directory of Open Access Journals (Sweden)

    Jittrawan Thaiprasit

    2016-03-01

    Full Text Available RNA-RNA interactions play a crucial role in gene regulation in living organisms. They have gained increasing interest in the field of synthetic biology because of their potential applications in medicine and biotechnology. However, few novel regulators based on RNA-RNA interactions with desired structures and functions have been developed due to the challenges of developing design tools. Recently, we proposed a novel tool, called iDoDe, for designing RNA-RNA interacting sequences by first decomposing RNA structures into interacting domains and then designing each domain using a stochastic algorithm. However, iDoDe did not provide an optimal solution because it still lacks a mechanism to optimize the design. In this work, we have further developed the tool by incorporating a genetic algorithm (GA to find an RNA solution with maximized structural similarity and minimized hybridized RNA energy, and renamed the tool iDoRNA. A set of suitable parameters for the genetic algorithm were determined and found to be a weighting factor of 0.7, a crossover rate of 0.9, a mutation rate of 0.1, and the number of individuals per population set to 8. We demonstrated the performance of iDoRNA in comparison with iDoDe by using six RNA-RNA interaction models. It was found that iDoRNA could efficiently generate all models of interacting RNAs with far more accuracy and required far less computational time than iDoDe. Moreover, we compared the design performance of our tool against existing design tools using forty-four RNA-RNA interaction models. The results showed that the performance of iDoRNA is better than RiboMaker when considering the ensemble defect, the fitness score and computation time usage. However, it appears that iDoRNA is outperformed by NUPACK and RNAiFold 2.0 when considering the ensemble defect. Nevertheless, iDoRNA can still be an useful alternative tool for designing novel RNA-RNA interactions in synthetic biology research. The source code of iDoRNA

  17. Arabicizing, Privileges, and Liturgy in Medieval Castilian Toledo: The Problems and Mutations of Mozarab Identification (1085-1436)

    OpenAIRE

    Moreno, Aaron Michael

    2012-01-01

    Most approaches to the history of Mozarabs (Christians with lineal roots in Muslim-ruled Iberia) in Castilian Toledo are framed within linear narratives of assimilation, treating the fates of their communal linguistic, legal, and liturgical traits--that is, the use of Arabic, the enjoyment of communal-specific juridical privileges, and the adherence to the traditional Spanish rite--as a metric for gauging the vitality of their identities. Having examined Arabic, Latin, and Romance documentary...

  18. 77 FR 34339 - Yufeng Wei, a/k/a Annie Wei, 165 Beech Street, Belmont, MA 02378; Order Denying Export Privileges

    Science.gov (United States)

    2012-06-11

    ... Street, Belmont, MA 02378; Order Denying Export Privileges On January 28, 2011, in the U.S. District... of the Arms Export Control Act (22 U.S.C. 2778 (2000)) (``AECA''). Specifically, Wei was convicted of... electronic components designated on the U.S. Munitions List to China through Hong Kong between 2004 and 2007...

  19. RNA-SSPT: RNA Secondary Structure Prediction Tools.

    Science.gov (United States)

    Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

    2013-01-01

    The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

  20. Combinatorics of RNA-RNA interaction

    DEFF Research Database (Denmark)

    Li, Thomas J X; Reidys, Christian

    2012-01-01

    RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure...... means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including...

  1. A parallel implementation of the Wuchty algorithm with additional experimental filters to more thoroughly explore RNA conformational space.

    Directory of Open Access Journals (Sweden)

    Jonathan W Stone

    Full Text Available We present new modifications to the Wuchty algorithm in order to better define and explore possible conformations for an RNA sequence. The new features, including parallelization, energy-independent lonely pair constraints, context-dependent chemical probing constraints, helix filters, and optional multibranch loops, provide useful tools for exploring the landscape of RNA folding. Chemical probing alone may not necessarily define a single unique structure. The helix filters and optional multibranch loops are global constraints on RNA structure that are an especially useful tool for generating models of encapsidated viral RNA for which cryoelectron microscopy or crystallography data may be available. The computations generate a combinatorially complete set of structures near a free energy minimum and thus provide data on the density and diversity of structures near the bottom of a folding funnel for an RNA sequence. The conformational landscapes for some RNA sequences may resemble a low, wide basin rather than a steep funnel that converges to a single structure.

  2. Agreement on the privileges and immunities of the ITER International Fusion Energy Organization for the Joint Implementation of the ITER Project. Latest status. Declarations/reservations

    International Nuclear Information System (INIS)

    2007-01-01

    The Agreement on the Privileges and Immunities of the ITER International Fusion Energy Organization for the Joint Implementation of the ITER Project, for which the Director General of the IAEA is depositary, was done in Paris on 21 November 2006. Pursuant to Article 25 thereof, the Agreement on the Privileges and Immunities of the ITER International Fusion Energy Organization for the Joint Implementation of the ITER Project 'shall enter into force thirty days after the deposit of instruments of ratification, acceptance or approval of this Agreement by the People's Republic of China, EURATOM, the Republic of India, Japan, the Republic of Korea and the Russian Federation.' The text of the Agreement is reproduced in the Annex hereto for the information of all Member States

  3. 14 CFR 61.419 - How do I obtain privileges to provide training in an additional category or class of light-sport...

    Science.gov (United States)

    2010-01-01

    ... training in an additional category or class of light-sport aircraft? 61.419 Section 61.419 Aeronautics and...: PILOTS, FLIGHT INSTRUCTORS, AND GROUND INSTRUCTORS Flight Instructors With a Sport Pilot Rating § 61.419 How do I obtain privileges to provide training in an additional category or class of light-sport...

  4. Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

    International Nuclear Information System (INIS)

    Henke, Paul S.; Mak, Chi H.

    2014-01-01

    The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg 2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure

  5. Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

    Energy Technology Data Exchange (ETDEWEB)

    Henke, Paul S. [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Mak, Chi H., E-mail: cmak@usc.edu [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089 (United States)

    2014-08-14

    The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg{sup 2+} that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

  6. Marginalization: A Revisitation With Integration of Scholarship on Globalization, Intersectionality, Privilege, Microaggressions, and Implicit Biases.

    Science.gov (United States)

    Hall, Joanne M; Carlson, Kelly

    2016-01-01

    In 1994, the concept of marginalization was explored in an article in Advances in Nursing Science. This is a revisitation of the concept incorporating new scholarship. This update is founded on feminism, postcolonialism, critical race theory, and discourse deconstruction, all viewpoints that have been explicated in nursing. The purpose of this analysis is to look at new scholarship and concepts useful to applying marginalization in nursing knowledge development from the standpoint of Bourdieu's macro, meso, and micro levels. New scholarship includes globalization, intersectionality, privilege, microaggressions, and implicit bias. Implications for decreasing health disparities through this new scholarship are discussed.

  7. 14 CFR 61.429 - May I exercise the privileges of a flight instructor certificate with a sport pilot rating if I...

    Science.gov (United States)

    2010-01-01

    ... instructor certificate with a sport pilot rating if I hold a flight instructor certificate with another... Instructors With a Sport Pilot Rating § 61.429 May I exercise the privileges of a flight instructor certificate with a sport pilot rating if I hold a flight instructor certificate with another rating? If you...

  8. A Cache Considering Role-Based Access Control and Trust in Privilege Management Infrastructure

    Institute of Scientific and Technical Information of China (English)

    ZHANG Shaomin; WANG Baoyi; ZHOU Lihua

    2006-01-01

    PMI(privilege management infrastructure) is used to perform access control to resource in an E-commerce or E-government system. With the ever-increasing need for secure transaction, the need for systems that offer a wide variety of QoS (quality-of-service) features is also growing. In order to improve the QoS of PMI system, a cache based on RBAC(Role-based Access Control) and trust is proposed. Our system is realized based on Web service. How to design the cache based on RBAC and trust in the access control model is described in detail. The algorithm to query role permission in cache and to add records in cache is dealt with. The policy to update cache is introduced also.

  9. Comprehensive characterization of lncRNA-mRNA related ceRNA network across 12 major cancers

    Science.gov (United States)

    Feng, Li; Li, Feng; Sun, Zeguo; Wu, Tan; Shi, Xinrui; Li, Jing; Li, Xia

    2016-01-01

    Recent studies indicate that long noncoding RNAs (lncRNAs) can act as competing endogenous RNAs (ceRNAs) to indirectly regulate mRNAs through shared microRNAs, which represents a novel layer of RNA crosstalk and plays critical roles in the development of tumor. However, the global regulation landscape and characterization of these lncRNA related ceRNA crosstalk in cancers is still largely unknown. Here, we systematically characterized the lncRNA related ceRNA interactions across 12 major cancers and the normal physiological states by integrating multidimensional molecule profiles of more than 5000 samples. Our study suggest the large difference of ceRNA regulation between normal and tumor states and the higher similarity across similar tissue origin of tumors. The ceRNA related molecules have more conserved features in tumor networks and they play critical roles in both the normal and tumorigenesis processes. Besides, lncRNAs in the pan-cancer ceRNA network may be potential biomarkers of tumor. By exploring hub lncRNAs, we found that these conserved key lncRNAs dominate variable tumor hallmark processes across pan-cancers. Network dynamic analysis highlights the critical roles of ceRNA regulation in tumorigenesis. By analyzing conserved ceRNA interactions, we found that miRNA mediate ceRNA regulation showed different patterns across pan-cancer; while analyzing the cancer specific ceRNA interactions reveal that lncRNAs synergistically regulated tumor driver genes of cancer hallmarks. Finally, we found that ceRNA modules have the potential to predict patient survival. Overall, our study systematically dissected the lncRNA related ceRNA networks in pan-cancer that shed new light on understanding the molecular mechanism of tumorigenesis. PMID:27580177

  10. Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation

    Science.gov (United States)

    Martos, Laura; Fernández-Pardo, Álvaro; Oto, Julia; Medina, Pilar; España, Francisco; Navarro, Silvia

    2017-01-01

    microRNAs are promising biomarkers in biological fluids in several diseases. Different plasma RNA isolation protocols and carriers are available, but their efficiencies have been scarcely compared. Plasma microRNAs were isolated using a phenol and column-based procedure and a column-based procedure, in the presence or absence of two RNA carriers (yeast RNA and MS2 RNA). We evaluated the presence of PCR inhibitors and the relative abundance of certain microRNAs by qRT-PCR. Furthermore, we analyzed the association between different isolation protocols, the relative abundance of the miRNAs in the sample, the GC content and the free energy of microRNAs. In all microRNAs analyzed, the addition of yeast RNA as a carrier in the different isolation protocols used gave lower raw Cq values, indicating higher microRNA recovery. Moreover, this increase in microRNAs recovery was dependent on their own relative abundance in the sample, their GC content and the free-energy of their own most stable secondary structure. Furthermore, the normalization of microRNA levels by an endogenous microRNA is more reliable than the normalization by plasma volume, as it reduced the difference in microRNA fold abundance between the different isolation protocols evaluated. Our thorough study indicates that a standardization of pre- and analytical conditions is necessary to obtain reproducible inter-laboratory results in plasma microRNA studies. PMID:29077772

  11. Diversity, fulfilment and privilege: the image of nursing.

    Science.gov (United States)

    Morris-Thompson, Trish; Shepherd, Janet; Plata, Robin; Marks-Maran, Di

    2011-07-01

    To explore the image that nurses have of nursing and the image of nursing held by the public to determine the difference between the two and the impact of this on nurse recruitment. Recruitment and retention nurses are important to the Strategic Health Authority for London (NHS London) who commissioned a study to explore the image of nursing. Qualitative survey research was used. Data were collected from nurses and from the public. Three themes emerged related to the image of nursing held by nurses. These were diversity, fulfilment and privilege. However, the public image of nursing does not reflect these. The public appear ill-informed of what nurses do, purporting to respect nursing but would not recommend nursing as a career choice for themselves, their children or their pupils. This study could have been enhanced through the use of questionnaires to gain quantitative data about the image of nursing. The public image of nursing appears positive but also has negative aspects. The public image is different from nurse's image of nursing and is based on myth, misconception and stereotype. This may influence recruitment of nurses. The results of this study offer a way forward to develop recruitment strategies that target changing the public's image of nursing. © 2011 The Authors. Journal compilation © 2011 Blackwell Publishing Ltd.

  12. Identification of Subtype Specific miRNA-mRNA Functional Regulatory Modules in Matched miRNA-mRNA Expression Data: Multiple Myeloma as a Case

    Directory of Open Access Journals (Sweden)

    Yunpeng Zhang

    2015-01-01

    Full Text Available Identification of miRNA-mRNA modules is an important step to elucidate their combinatorial effect on the pathogenesis and mechanisms underlying complex diseases. Current identification methods primarily are based upon miRNA-target information and matched miRNA and mRNA expression profiles. However, for heterogeneous diseases, the miRNA-mRNA regulatory mechanisms may differ between subtypes, leading to differences in clinical behavior. In order to explore the pathogenesis of each subtype, it is important to identify subtype specific miRNA-mRNA modules. In this study, we integrated the Ping-Pong algorithm and multiobjective genetic algorithm to identify subtype specific miRNA-mRNA functional regulatory modules (MFRMs through integrative analysis of three biological data sets: GO biological processes, miRNA target information, and matched miRNA and mRNA expression data. We applied our method on a heterogeneous disease, multiple myeloma (MM, to identify MM subtype specific MFRMs. The constructed miRNA-mRNA regulatory networks provide modular outlook at subtype specific miRNA-mRNA interactions. Furthermore, clustering analysis demonstrated that heterogeneous MFRMs were able to separate corresponding MM subtypes. These subtype specific MFRMs may aid in the further elucidation of the pathogenesis of each subtype and may serve to guide MM subtype diagnosis and treatment.

  13. Affective privilege: Asymmetric interference by emotional distracters

    Directory of Open Access Journals (Sweden)

    Crystal eReeck

    2011-09-01

    Full Text Available Numerous theories posit that affectively salient stimuli are privileged in their capacity to capture attention and disrupt ongoing cognition. Two underlying assumptions in this theoretical position are that the potency of affective stimuli transcends task boundaries (i.e., emotional distracters do not have to belong to a current task-set to disrupt processing and that there is an asymmetry between emotional and cognitive processing (i.e., emotional distracters disrupt cognitive processing, but not vice versa. These assumptions have remained largely untested, as common experimental probes of emotion-cognition interaction rarely manipulate task-relevance and only examine one side of the presumed asymmetry of interference. To test these propositions directly, a face-word Stroop protocol was adapted to independently manipulate (a the congruency between target and distracter stimulus features, (b the affective salience of distracter features, and (c the task-relevance of emotional compared to non-emotional target features. A three-way interaction revealed interdependent effects of distracter relevance, congruence, and affective salience. Compared to task-irrelevant distracters, task-relevant congruent distracters facilitated performance and task-relevant incongruent distracters impaired performance, but the latter effect depended on the nature of the target feature and task. Specifically, task-irrelevant emotional distracters resulted in equivalent performance costs as task-relevant non-emotional distracters, whereas task-irrelevant non-emotional distracters did not produce performance costs comparable to those generated by task-relevant emotional distracters. These results document asymmetric cross-task interference effects for affectively salient stimuli, supporting the notion of affective prioritization in human information processing.

  14. antaRNA: ant colony-based RNA sequence design.

    Science.gov (United States)

    Kleinkauf, Robert; Mann, Martin; Backofen, Rolf

    2015-10-01

    RNA sequence design is studied at least as long as the classical folding problem. Although for the latter the functional fold of an RNA molecule is to be found ,: inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology ,: reliable RNA sequence design becomes a crucial step to generate novel biochemical components. In this article ,: the computational tool antaRNA is presented. It is capable of compiling RNA sequences for a given structure that comply in addition with an adjustable full range objective GC-content distribution ,: specific sequence constraints and additional fuzzy structure constraints. antaRNA applies ant colony optimization meta-heuristics and its superior performance is shown on a biological datasets. http://www.bioinf.uni-freiburg.de/Software/antaRNA CONTACT: backofen@informatik.uni-freiburg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  15. Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

    Science.gov (United States)

    Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

    2010-01-01

    The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

  16. Final report for ER65039, The Role of Small RNA in Biomass Deposition

    Energy Technology Data Exchange (ETDEWEB)

    Hudson, Matthew E. [Univ. of Illinois, Urbana, IL (United States)

    2015-03-12

    Our objective in this project was to discover the role of sRNA in regulating both biomass biosynthesis and perenniality in the Andropogoneae feedstock grasses. Our central hypothesis was that there is a time-and space specific sRNA network playing a crucial role in regulating processes associated with cell wall biosynthesis, flowering time control, overwintering/juvenility, and nutrient sequestration in the feedstock grasses. To address this, we performed a large scale biological project consisting of the growth of material, generation of Illumina libraries, sequencing and analysis for small RNA, mRNA and Degradome / cmRNA. Our subsidiary objectives included analysis of the biology of small RNAs and the cell wall composition of Miscanthus. These objectives have all been completed, one publication is in print, one is submitted and several more are in progress.

  17. Pathways to Banking: Improving Access for Students from Non-Privileged Backgrounds. Research by The Boston Consulting Group for the Sutton Trust

    Science.gov (United States)

    Kelly, Gerard

    2014-01-01

    The financial services sector is a vital and vibrant part of a national economy but it recruits from a small and relatively privileged segment of society. This report, which summarises research from the Boston Consulting Group (BCG), shows for the first time the extent of the challenge. The Sutton Trust's "Pathways to Banking" programme…

  18. From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond.

    Science.gov (United States)

    Michelini, Flavia; Jalihal, Ameya P; Francia, Sofia; Meers, Chance; Neeb, Zachary T; Rossiello, Francesca; Gioia, Ubaldo; Aguado, Julio; Jones-Weinert, Corey; Luke, Brian; Biamonti, Giuseppe; Nowacki, Mariusz; Storici, Francesca; Carninci, Piero; Walter, Nils G; Fagagna, Fabrizio d'Adda di

    2018-03-30

    Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.

  19. 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-.

  20. Extracellular RNA Communication (ExRNA)

    Data.gov (United States)

    Federal Laboratory Consortium — Until recently, scientists believed RNA worked mostly inside the cell that produced it. Some types of RNA help translate genes into proteins that are necessary for...

  1. RAG-3D: a search tool for RNA 3D substructures

    Science.gov (United States)

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-01-01

    To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

  2. 14 CFR 61.323 - How do I obtain privileges to operate a make and model of light-sport aircraft in the same...

    Science.gov (United States)

    2010-01-01

    ... make and model of light-sport aircraft in the same category and class within a different set of... TRANSPORTATION (CONTINUED) AIRMEN CERTIFICATION: PILOTS, FLIGHT INSTRUCTORS, AND GROUND INSTRUCTORS Sport Pilots § 61.323 How do I obtain privileges to operate a make and model of light-sport aircraft in the same...

  3. RNA Crystallization

    Science.gov (United States)

    Golden, Barbara L.; Kundrot, Craig E.

    2003-01-01

    RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

  4. 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

    MicroRNAs are a class of noncoding RNA molecules that co-regulate the expression of multiple genes via mRNA transcript degradation or translation inhibition. Since they often target entire pathways, they may be better drug targets than genes or proteins. MicroRNAs are known to be dysregulated in many tumours and associated with aggressive or poor prognosis phenotypes. Since they regulate mRNA in a tissue specific manner, their functional mRNA targets are poorly understood. In previous work, we developed a method to identify direct mRNA targets of microRNA using patient matched microRNA/mRNA expression data using an anti-correlation signature. This method, applied to clear cell Renal Cell Carcinoma (ccRCC), revealed many new regulatory pathways compromised in ccRCC. In the present paper, we apply this method to identify dysregulated microRNA/mRNA mechanisms in ovarian cancer using data from The Cancer Genome Atlas (TCGA). TCGA Microarray data was normalized and samples whose class labels (tumour or normal) were ambiguous with respect to consensus ensemble K-Means clustering were removed. Significantly anti-correlated and correlated genes/microRNA differentially expressed between tumour and normal samples were identified. TargetScan was used to identify gene targets of microRNA. We identified novel microRNA/mRNA mechanisms in ovarian cancer. For example, the expression level of RAD51AP1 was found to be strongly anti-correlated with the expression of hsa-miR-140-3p, which was significantly down-regulated in the tumour samples. The anti-correlation signature was present separately in the tumour and normal samples, suggesting a direct causal dysregulation of RAD51AP1 by hsa-miR-140-3p in the ovary. Other pairs of potentially biological relevance include: hsa-miR-145/E2F3, hsa-miR-139-5p/TOP2A, and hsa-miR-133a/GCLC. We also identified sets of positively correlated microRNA/mRNA pairs that are most likely result from indirect regulatory mechanisms. Our findings identify

  5. Natural RNA circles function as efficient microRNA sponges

    DEFF Research Database (Denmark)

    Hansen, Thomas Birkballe; Jensen, Trine I; Clausen, Bettina Hjelm

    2013-01-01

    MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called comp......MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so......-called competing endogenous RNA in humans and target mimicry in plants. We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain. Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more...... sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA....

  6. RNA Origami

    DEFF Research Database (Denmark)

    Sparvath, Steffen Lynge

    introducerede vores gruppe den enkeltstrengede RNA-origami metode, der giver mulighed for cotranscriptional foldning af veldefinerede nanostrukturer, og er en central del af arbejdet præsenteret heri. Denne ph.d.-afhandling udforsker potentielle anvendelser af RNA-origami nanostrukturer, som nanomedicin eller...... biosensorer. Afhandlingen består af en introduktion til RNA-nanoteknologi feltet, en introduktion af enkeltstrenget RNA-origami design, og fire studier, der beskriver design, produktion og karakterisering af både strukturelle og funktionelle RNA-origamier. Flere RNA-origami designs er blevet undersøgt, og...... projekterne, der indgår i denne afhandling, inkluderer de nyeste fremskridt indenfor strukturel RNA-nanoteknologi og udvikling af funktionelle RNA-baserede enheder. Det første studie beskriver konstruktion og karakterisering af en enkeltstrenget 6-helix RNA-origami stuktur, som er den første demonstration af...

  7. Branched RNA: A New Architecture for RNA Interference

    Directory of Open Access Journals (Sweden)

    Anna Aviñó

    2011-01-01

    Full Text Available Branched RNAs with two and four strands were synthesized. These structures were used to obtain branched siRNA. The branched siRNA duplexes had similar inhibitory capacity as those of unmodified siRNA duplexes, as deduced from gene silencing experiments of the TNF-α protein. Branched RNAs are considered novel structures for siRNA technology, and they provide an innovative tool for specific gene inhibition. As the method described here is compatible with most RNA modifications described to date, these compounds may be further functionalized to obtain more potent siRNA derivatives and can be attached to suitable delivery systems.

  8. Plant RNA Regulatory Network and RNA Granules in Virus Infection

    Directory of Open Access Journals (Sweden)

    Kristiina Mäkinen

    2017-12-01

    Full Text Available Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and

  9. Plant RNA Regulatory Network and RNA Granules in Virus Infection.

    Science.gov (United States)

    Mäkinen, Kristiina; Lõhmus, Andres; Pollari, Maija

    2017-01-01

    Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and their individual

  10. Analysis of miRNA and mRNA Expression Profiles Highlights Alterations in Ionizing Radiation Response of Human Lymphocytes under Modeled Microgravity

    Science.gov (United States)

    Casara, Silvia; Sales, Gabriele; Lanfranchi, Gerolamo; Celotti, Lucia; Mognato, Maddalena

    2012-01-01

    Background Ionizing radiation (IR) can be extremely harmful for human cells since an improper DNA-damage response (DDR) to IR can contribute to carcinogenesis initiation. Perturbations in DDR pathway can originate from alteration in the functionality of the microRNA-mediated gene regulation, being microRNAs (miRNAs) small noncoding RNA that act as post-transcriptional regulators of gene expression. In this study we gained insight into the role of miRNAs in the regulation of DDR to IR under microgravity, a condition of weightlessness experienced by astronauts during space missions, which could have a synergistic action on cells, increasing the risk of radiation exposure. Methodology/Principal Findings We analyzed miRNA expression profile of human peripheral blood lymphocytes (PBL) incubated for 4 and 24 h in normal gravity (1 g) and in modeled microgravity (MMG) during the repair time after irradiation with 0.2 and 2Gy of γ-rays. Our results show that MMG alters miRNA expression signature of irradiated PBL by decreasing the number of radio-responsive miRNAs. Moreover, let-7i*, miR-7, miR-7-1*, miR-27a, miR-144, miR-200a, miR-598, miR-650 are deregulated by the combined action of radiation and MMG. Integrated analyses of miRNA and mRNA expression profiles, carried out on PBL of the same donors, identified significant miRNA-mRNA anti-correlations of DDR pathway. Gene Ontology analysis reports that the biological category of “Response to DNA damage” is enriched when PBL are incubated in 1 g but not in MMG. Moreover, some anti-correlated genes of p53-pathway show a different expression level between 1 g and MMG. Functional validation assays using luciferase reporter constructs confirmed miRNA-mRNA interactions derived from target prediction analyses. Conclusions/Significance On the whole, by integrating the transcriptome and microRNome, we provide evidence that modeled microgravity can affects the DNA-damage response to IR in human PBL. PMID:22347458

  11. 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.

  12. RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

    International Nuclear Information System (INIS)

    Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E.; Eghbalnia, Hamid R.

    2012-01-01

    The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ( 1 H– 15 N 2D HMQC) and proton–proton nuclear Overhauser enhancement spectroscopy ( 1 H– 1 H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino resonances for a

  13. RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

    Energy Technology Data Exchange (ETDEWEB)

    Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E. [National Magnetic Resonance Facility at Madison (United States); Eghbalnia, Hamid R., E-mail: eghbalhd@uc.edu [University of Cincinnati, Department of Molecular and Cellular Physiology (United States)

    2012-04-15

    The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ({sup 1}H-{sup 15}N 2D HMQC) and proton-proton nuclear Overhauser enhancement spectroscopy ({sup 1}H-{sup 1}H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino

  14. RNA binding and replication by the poliovirus RNA polymerase

    International Nuclear Information System (INIS)

    Oberste, M.S.

    1988-01-01

    RNA binding and RNA synthesis by the poliovirus RNA-dependent RNA polymerase were studied in vitro using purified polymerase. Templates for binding and RNA synthesis studies were natural RNAs, homopolymeric RNAs, or subgenomic poliovirus-specific RNAs synthesized in vitro from cDNA clones using SP6 or T7 RNA polymerases. The binding of the purified polymerase to poliovirion and other RNAs was studied using a protein-RNA nitrocellulose filter binding assay. A cellular poly(A)-binding protein was found in the viral polymerase preparations, but was easily separated from the polymerase by chromatography on poly(A) Sepharose. The binding of purified polymerase to 32 P-labeled ribohomopolymeric RNAs was examined, and the order of binding observed was poly(G) >>> poly(U) > poly(C) > poly(A). The K a for polymerase binding to poliovirion RNA and to a full-length negative strand transcript was about 1 x 10 9 M -1 . The polymerase binds to a subgenomic RNAs which contain the 3' end of the genome with a K a similar to that for virion RNA, but binds less well to 18S rRNA, globin mRNA, and subgenomic RNAs which lack portions of the 3' noncoding region

  15. RNA.

    Science.gov (United States)

    Darnell, James E., Jr.

    1985-01-01

    Ribonucleic acid (RNA) converts genetic information into protein and usually must be processed to serve its function. RNA types, chemical structure, protein synthesis, translation, manufacture, and processing are discussed. Concludes that the first genes might have been spliced RNA and that humans might be closer than bacteria to primitive…

  16. Identification of Subtype Specific miRNA-mRNA Functional Regulatory Modules in Matched miRNA-mRNA Expression Data: Multiple Myeloma as a Case

    OpenAIRE

    Zhang, Yunpeng; Liu, Wei; Xu, Yanjun; Li, Chunquan; Wang, Yingying; Yang, Haixiu; Zhang, Chunlong; Su, Fei; Li, Yixue; Li, Xia

    2015-01-01

    Identification of miRNA-mRNA modules is an important step to elucidate their combinatorial effect on the pathogenesis and mechanisms underlying complex diseases. Current identification methods primarily are based upon miRNA-target information and matched miRNA and mRNA expression profiles. However, for heterogeneous diseases, the miRNA-mRNA regulatory mechanisms may differ between subtypes, leading to differences in clinical behavior. In order to explore the pathogenesis of each subtype, it i...

  17. Van privileges tot republiek: Evolutie van de taal van de Opstand. Een woordenboek / From the Privileges to the Republic: the Evolution of the Language of the Dutch Revolt. A Dictionary

    Directory of Open Access Journals (Sweden)

    Szmytka Rafał

    2015-11-01

    Full Text Available The second half of the 16th century is regarded as the decisive moment in the history of the Low Countries. The politics of religious intolerance and financial oppression practiced by the Habsburg governors resulted in protests and, finally, in the open revolt of the Provinces under the leadership of the princes of Orange and Nassau. The aim of this work is to follow and reconstruct the ideas of political thought accompanying the events leading to the rise of a new state. In the dicussed state forming process the main emphasis was put on the issues of freedom, states, and sovereignty, as well as on the concept of the possibility of dismissing the obedience inherited from the medieval privileges. These concepts and terms created a special sort of dictionary of the Dutch political thought.

  18. microRNA-independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA-binding protein.

    Science.gov (United States)

    Pinder, Benjamin D; Smibert, Craig A

    2013-01-01

    Argonaute (Ago) proteins are typically recruited to target messenger RNAs via an associated small RNA such as a microRNA (miRNA). Here, we describe a new mechanism of Ago recruitment through the Drosophila Smaug RNA-binding protein. We show that Smaug interacts with the Ago1 protein, and that Ago1 interacts with and is required for the translational repression of the Smaug target, nanos mRNA. The Ago1/nanos mRNA interaction does not require a miRNA, but it does require Smaug. Taken together, our data suggest a model whereby Smaug directly recruits Ago1 to nanos mRNA in a miRNA-independent manner, thereby repressing translation.

  19. RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

    Directory of Open Access Journals (Sweden)

    Andronescu Mirela

    2008-08-01

    Full Text Available Abstract Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. Results In this paper we describe RNA STRAND – the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. Conclusion RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.

  20. MicroRNA from tuberculosis RNA: A bioinformatics study

    OpenAIRE

    Wiwanitkit, Somsri; Wiwanitkit, Viroj

    2012-01-01

    The role of microRNA in the pathogenesis of pulmonary tuberculosis is the interesting topic in chest medicine at present. Recently, it was proposed that the microRNA can be a useful biomarker for monitoring of pulmonary tuberculosis and might be the important part in pathogenesis of disease. Here, the authors perform a bioinformatics study to assess the microRNA within known tuberculosis RNA. The microRNA part can be detected and this can be important key information in further study of the p...

  1. Nucleolin Mediates MicroRNA-directed CSF-1 mRNA Deadenylation but Increases Translation of CSF-1 mRNA*

    Science.gov (United States)

    Woo, Ho-Hyung; Baker, Terri; Laszlo, Csaba; Chambers, Setsuko K.

    2013-01-01

    CSF-1 mRNA 3′UTR contains multiple unique motifs, including a common microRNA (miRNA) target in close proximity to a noncanonical G-quadruplex and AU-rich elements (AREs). Using a luciferase reporter system fused to CSF-1 mRNA 3′UTR, disruption of the miRNA target region, G-quadruplex, and AREs together dramatically increased reporter RNA levels, suggesting important roles for these cis-acting regulatory elements in the down-regulation of CSF-1 mRNA. We find that nucleolin, which binds both G-quadruplex and AREs, enhances deadenylation of CSF-1 mRNA, promoting CSF-1 mRNA decay, while having the capacity to increase translation of CSF-1 mRNA. Through interaction with the CSF-1 3′UTR miRNA common target, we find that miR-130a and miR-301a inhibit CSF-1 expression by enhancing mRNA decay. Silencing of nucleolin prevents the miRNA-directed mRNA decay, indicating a requirement for nucleolin in miRNA activity on CSF-1 mRNA. Downstream effects followed by miR-130a and miR-301a inhibition of directed cellular motility of ovarian cancer cells were found to be dependent on nucleolin. The paradoxical effects of nucleolin on miRNA-directed CSF-1 mRNA deadenylation and on translational activation were explored further. The nucleolin protein contains four acidic stretches, four RNA recognition motifs (RRMs), and nine RGG repeats. All three domains in nucleolin regulate CSF-1 mRNA and protein levels. RRMs increase CSF-1 mRNA, whereas the acidic and RGG domains decrease CSF-1 protein levels. This suggests that nucleolin has the capacity to differentially regulate both CSF-1 RNA and protein levels. Our finding that nucleolin interacts with Ago2 indirectly via RNA and with poly(A)-binding protein C (PABPC) directly suggests a nucleolin-Ago2-PABPC complex formation on mRNA. This complex is in keeping with our suggestion that nucleolin may work with PABPC as a double-edged sword on both mRNA deadenylation and translational activation. Our findings underscore the complexity of

  2. Studying RNA-protein interactions in vivo by RNA immunoprecipitation

    DEFF Research Database (Denmark)

    Selth, Luke A; Close, Pierre; Svejstrup, Jesper Q

    2011-01-01

    and have significant effects on gene expression. RNA immunoprecipitation (RIP) is a powerful technique used to detect direct and indirect interactions between individual proteins and specific RNA molecules in vivo. Here, we describe RIP methods for both yeast and mammalian cells.......The crucial roles played by RNA-binding proteins in all aspects of RNA metabolism, particularly in the regulation of transcription, have become increasingly evident. Moreover, other factors that do not directly interact with RNA molecules can nevertheless function proximally to RNA polymerases...

  3. RNA SURVEILLANCE– AN EMERGING ROLE FOR RNA REGULATORY NETWORKS IN AGING

    OpenAIRE

    Montano, Monty; Long, Kimberly

    2010-01-01

    In this review, we describe recent advances in the field of RNA regulatory biology and relate these advances to aging science. We introduce a new term, RNA surveillance, an RNA regulatory process that is conserved in metazoans, and describe how RNA surveillance represents molecular cross-talk between two emerging RNA regulatory systems – RNA interference and RNA editing. We discuss how RNA surveillance mechanisms influence mRNA and microRNA expression and activity during lifespan. Additionall...

  4. Rapid Generation of MicroRNA Sponges for MicroRNA Inhibition

    NARCIS (Netherlands)

    Kluiver, Joost; Gibcus, Johan H.; Hettinga, Chris; Adema, Annelies; Richter, Mareike K. S.; Halsema, Nancy; Slezak-Prochazka, Izabella; Ding, Ye; Kroesen, Bart-Jan; van den Berg, Anke

    2012-01-01

    MicroRNA (miRNA) sponges are transcripts with repeated miRNA antisense sequences that can sequester miRNAs from endogenous targets. MiRNA sponges are valuable tools for miRNA loss-of-function studies both in vitro and in vivo. We developed a fast and flexible method to generate miRNA sponges and

  5. MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans.

    Science.gov (United States)

    Corrêa, Régis L; Steiner, Florian A; Berezikov, Eugene; Ketting, René F

    2010-04-08

    RNA interference (RNAi) is a post-transcriptional silencing process, triggered by double-stranded RNA (dsRNA), leading to the destabilization of homologous mRNAs. A distinction has been made between endogenous RNAi-related pathways and the exogenous RNAi pathway, the latter being essential for the experimental use of RNAi. Previous studies have shown that, in Caenorhabditis elegans, a complex containing the enzymes Dicer and the Argonaute RDE-1 process dsRNA. Dicer is responsible for cleaving dsRNA into short interfering RNAs (siRNAs) while RDE-1 acts as the siRNA acceptor. RDE-1 then guides a multi-protein complex to homologous targets to trigger mRNA destabilization. However, endogenous role(s) for RDE-1, if any, have remained unexplored. We here show that RDE-1 functions as a scavenger protein, taking up small RNA molecules from many different sources, including the microRNA (miRNA) pathway. This is in striking contrast to Argonaute proteins functioning directly in the miRNA pathway, ALG-1 and ALG-2: these proteins exclusively bind miRNAs. While playing no significant role in the biogenesis of the main pool of miRNAs, RDE-1 binds endogenous miRNAs and triggers RdRP activity on at least one perfectly matching, endogenous miRNA target. The resulting secondary siRNAs are taken up by a set of Argonaute proteins known to act as siRNA acceptors in exogenous RNAi, resulting in strong mRNA destabilization. Our results show that RDE-1 in an endogenous setting is actively screening the transcriptome using many different small RNAs, including miRNAs, as a guide, with implications for the evolution of transcripts with a potential to be recognized by Dicer.

  6. Plant RNA binding proteins for control of RNA virus infection

    Directory of Open Access Journals (Sweden)

    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.

  7. Effective Anti-miRNA Oligonucleotides Show High Releasing Rate of MicroRNA from RNA-Induced Silencing Complex.

    Science.gov (United States)

    Ariyoshi, Jumpei; Matsuyama, Yohei; Kobori, Akio; Murakami, Akira; Sugiyama, Hiroshi; Yamayoshi, Asako

    2017-10-01

    MicroRNAs (miRNAs) regulate gene expression by forming RNA-induced silencing complexes (RISCs) and have been considered as promising therapeutic targets. MiRNA is an essential component of RISC for the modulation of gene expression. Therefore, the release of miRNA from RISC is considered as an effective method for the inhibition of miRNA functions. In our previous study, we reported that anti-miRNA oligonucleotides (AMOs), which are composed of the 2'-O-methyl (2'-OMe) RNA, could induce the release of miRNA from RISC. However, the mechanisms underlying the miRNA-releasing effects of chemically modified AMOs, which are conventionally used as anti-cancer drugs, are still unclear. In this study, we investigated the relationship between the miRNA releasing rate from RISC and the inhibitory effect on RISC activity (IC 50 ) using conventional chemically modified AMOs. We demonstrated that the miRNA-releasing effects of AMOs are directly proportional to the IC 50 values, and AMOs, which have an ability to promote the release of miRNA from RISC, can effectively inhibit RISC activity in living cells.

  8. Isolation of Microarray-Grade Total RNA, MicroRNA, and DNA from a Single PAXgene Blood RNA Tube

    DEFF Research Database (Denmark)

    Kruhøffer, Mogens; Andersen, Lars Dyrskjøt; Voss, Thorsten

    2007-01-01

    We have developed a procedure for isolation of microRNA and genomic DNA in addition to total RNA from whole blood stabilized in PAXgene Blood RNA tubes. The procedure is based on automatic extraction on a BioRobot MDx and includes isolation of DNA from a fraction of the stabilized blood...... and recovery of small RNA species that are otherwise lost. The procedure presented here is suitable for large-scale experiments and is amenable to further automation. Procured total RNA and DNA was tested using Affymetrix Expression and single-nucleotide polymorphism GeneChips, respectively, and isolated micro......RNA was tested using spotted locked nucleic acid-based microarrays. We conclude that the yield and quality of total RNA, microRNA, and DNA from a single PAXgene blood RNA tube is sufficient for downstream microarray analysis....

  9. 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.

  10. Genetic relatedness of orbiviruses by RNA-RNA blot hybridization

    International Nuclear Information System (INIS)

    Bodkin, D.K.

    1985-01-01

    RNA-RNA blot hybridization was developed in order to identify type-specific genes among double-stranded (ds) RNA viruses, to assess the genetic relatedness of dsRNA viruses and to classify new strains. Viral dsRNA segments were electrophoresed through 10% polyacrylamide gels, transferred to membranes, and hybridized to [5' 32 P]-pCp labeled genomic RNA from a related strain. Hybridization was performed at 52 0 C, 50% formamide, 5X SSC. Under these conditions heterologous RNA species must share ≥ 74% sequence homology in order to form stable dsRNA hybrids. Cognate genes of nine members of the Palyam serogroup of orbiviruses were identified and their sequence relatedness to the prototype. Palyam virus, was determined. Reciprocal blot hybridizations were performed using radiolabeled genomic RNA of all members of the Palyam serogroup. Unique and variant genes were identified by lack of cross-homology or by weak homology between segments. Since genes 2 and 6 exhibited the highest degree of sequence variability, response to the vertebrate immune system may be a major cause of sequence divergence among members of a single serogroup. Changuinola serogroup isolates were compared by dot-blot hybridization, while Colorado tick fever (CTF) serogroup isolates were compared by the RNA-RNA blot hybridization procedure described for reovirus and Palyam serogroup isolates. Preliminary blot hybridization data were also obtained on the relatedness of members of different Orbivirus serogroups

  11. A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA-based regulation of viral processes.

    Directory of Open Access Journals (Sweden)

    Baodong Wu

    2009-03-01

    Full Text Available Plus-strand RNA viruses contain RNA elements within their genomes that mediate a variety of fundamental viral processes. The traditional view of these elements is that of local RNA structures. This perspective, however, is changing due to increasing discoveries of functional viral RNA elements that are formed by long-range RNA-RNA interactions, often spanning thousands of nucleotides. The plus-strand RNA genomes of tombusviruses exemplify this concept by possessing different long-range RNA-RNA interactions that regulate both viral translation and transcription. Here we report that a third fundamental tombusvirus process, viral genome replication, requires a long-range RNA-based interaction spanning approximately 3000 nts. In vivo and in vitro analyses suggest that the discontinuous RNA platform formed by the interaction facilitates efficient assembly of the viral RNA replicase. This finding has allowed us to build an integrated model for the role of global RNA structure in regulating the reproduction of a eukaryotic RNA virus, and the insights gained have extended our understanding of the multifunctional nature of viral RNA genomes.

  12. A quantitative analysis of secondary RNA structure using domination based parameters on trees

    Directory of Open Access Journals (Sweden)

    Zou Yue

    2006-03-01

    Full Text Available Abstract Background It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants to be utilized to numerically identify secondary RNA motifs. The domination number of a graph is a graphical invariant that is sensitive to even a slight change in the structure of a tree. The invariants selected in this study are variations of the domination number of a graph. These graphical invariants are partitioned into two classes, and we define two parameters based on each of these classes. These parameters are calculated for all small order trees and a statistical analysis of the resulting data is conducted to determine if the values of these parameters can be utilized to identify which trees of orders seven and eight are RNA-like in structure. Results The statistical analysis shows that the domination based parameters correctly distinguish between the trees that represent native structures and those that are not likely candidates to represent RNA. Some of the trees previously identified as candidate structures are found to be "very" RNA like, while others are not, thereby refining the space of structures likely to be found as representing secondary RNA structure. Conclusion Search algorithms are available that mine nucleotide sequence databases. However, the number of motifs identified can be quite large, making a further search for similar motif computationally difficult. Much of the work in the bioinformatics arena is toward the development of better algorithms to address the computational problem. This work, on the other hand, uses mathematical descriptors to more clearly characterize the RNA motifs and thereby reduce the corresponding search space. These

  13. CUSTOMS PRIVILEGES CONCERNING THE VEHICLES OF STAFF MEMBERS RESIDING IN SWITZERLAND

    CERN Document Server

    Relations with the Host States Service

    2001-01-01

    The Permanent Mission of Switzerland has informed CERN that the rules relating to customs privileges for vehicles have been modified. The new arrangements, which are more favourable than those described in Weekly Bulletin N° 32/2000, are summarised below. The rates of tax and duty referred to in this summary are currently as follows: customs duty (solely for vehicles originating from countries outside the European Union and the European Free Trade Association; calculated on the basis of the vehicle's weight, 12 to 15 Swiss centimes per kilogram); car tax (4% of the value of the vehicle); value-added tax (7.6% of the value of the vehicle). 1. Holders of a B or C-type 'Carte de légitimation' Members of the personnel holding a B or C-type Carte de légitimation issued by the Swiss Federal Department of Foreign Affairs (hereinafter referred to as «DFAE») may import or purchase a first vehicle tax and duty-free. This vehicle, subject to a three-year limited res...

  14. Bifurcations in the interplay of messenger RNA, protein and nonprotein coding RNA

    International Nuclear Information System (INIS)

    Zhdanov, Vladimir P

    2008-01-01

    The interplay of messenger RNA (mRNA), protein, produced via translation of this RNA, and nonprotein coding RNA (ncRNA) may include regulation of the ncRNA production by protein and (i) ncRNA-protein association resulting in suppression of the protein regulatory activity or (ii) ncRNA-mRNA association resulting in degradation of the miRNA-mRNA complex. The kinetic models describing these two scenarios are found to predict bistability provided that protein suppresses the ncRNA formation

  15. Patriarchy, power, and privilege: a narrative/poststructural view of work with couples.

    Science.gov (United States)

    Dickerson, Victoria

    2013-03-01

    Poststructural/narrative therapists working with heterosexual couples position themselves to attend to issues of power and privilege and how these variables differentially affect each gendered member of the couple. The poststructural therapist understands patriarchy as the grand narrative that influences us all, often invisibly, and creates conditions for people to respond outside what might be their preferences for performing relationships. This article takes the reader inside the work with couples and demonstrates how the narrative/poststructural therapist attends to aspects of the conversation, asks questions, makes comments, and otherwise intervenes with couples using patriarchy as a lens for understanding. Rather than challenging patriarchy in how it influences men and women, the intention is to bring forth more preferred ways of being that are outside of or on the other side of patriarchal effects. This way of working thickens people's accounts of themselves and of their relationships so that they might live in more satisfactory ways. © FPI, Inc.

  16. How the RNA isolation method can affect microRNA microarray results

    DEFF Research Database (Denmark)

    Podolska, Agnieszka; Kaczkowski, Bogumil; Litman, Thomas

    2011-01-01

    RNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results...... that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.......The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform micro...

  17. Treatment with native heterodimeric IL-15 increases cytotoxic lymphocytes and reduces SHIV RNA in lymph nodes.

    Directory of Open Access Journals (Sweden)

    Dionysios C Watson

    2018-02-01

    Full Text Available B cell follicles in secondary lymphoid tissues represent an immune privileged sanctuary for AIDS viruses, in part because cytotoxic CD8+ T cells are mostly excluded from entering the follicles that harbor infected T follicular helper (TFH cells. We studied the effects of native heterodimeric IL-15 (hetIL-15 treatment on uninfected rhesus macaques and on macaques that had spontaneously controlled SHIV infection to low levels of chronic viremia. hetIL-15 increased effector CD8+ T lymphocytes with high granzyme B content in blood, mucosal sites and lymph nodes, including virus-specific MHC-peptide tetramer+ CD8+ cells in LN. Following hetIL-15 treatment, multiplexed quantitative image analysis (histo-cytometry of LN revealed increased numbers of granzyme B+ T cells in B cell follicles and SHIV RNA was decreased in plasma and in LN. Based on these properties, hetIL-15 shows promise as a potential component in combination immunotherapy regimens to target AIDS virus sanctuaries and reduce long-term viral reservoirs in HIV-1 infected individuals.ClinicalTrials.gov NCT02452268.

  18. The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism.

    Science.gov (United States)

    Wang, Na; Wang, Ruoqing; Wang, Renkai; Tian, Yongsheng; Shao, Changwei; Jia, Xiaodong; Chen, Songlin

    2017-01-01

    Albinism, a phenomenon characterized by pigmentation deficiency on the ocular side of Japanese flounder (Paralichthys olivaceus), has caused significant damage. Limited mRNA and microRNA (miRNA) information is available on fish pigmentation deficiency. In this study, a high-throughput sequencing strategy was employed to identify the mRNA and miRNAs involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. These genes were enriched to 81 GO terms and 9 KEGG pathways (p≤0.05). Among those, the pigmentation related pathways-Melanogenesis and tyrosine metabolism were contained. High-throughput miRNA sequencing identified a total of 475 miRNAs, including 64 novel miRNAs. Furthermore, 33 differentially expressed miRNAs containing 13 up-regulated and 20 down-regulated miRNAs were identified in albino versus normally pigmented individuals (fold change ≥1.5 or ≤0.67 and p≤0.05). The next target prediction discovered a variety of putative target genes, of which, 134 genes including Tyrosinase (TYR), Tyrosinase-related protein 1 (TYRP1), Microphthalmia-associated transcription factor (MITF) were overlapped with differentially expressed genes derived from RNA-seq. These target genes were significantly enriched to 254 GO terms and 103 KEGG pathways (p<0.001). Of those, tyrosine metabolism, lysosomes, phototransduction pathways, etc., attracted considerable attention due to their involvement in regulating skin pigmentation. Expression patterns of differentially expressed mRNA and miRNAs were validated in 10 mRNA and 10 miRNAs by qRT-PCR. With high-throughput mRNA and miRNA sequencing and analysis, a series of interested mRNA and miRNAs involved in fish

  19. Switching off small RNA regulation with trap-mRNA

    DEFF Research Database (Denmark)

    Overgaard, Martin; Johansen, Jesper; Møller-Jensen, Jakob

    2009-01-01

    to operate at the level of transcription initiation. By employing a highly sensitive genetic screen we uncovered a novel RNA-based regulatory principle in which induction of a trap-mRNA leads to selective degradation of a small regulatory RNA molecule, thereby abolishing the sRNA-based silencing of its...

  20. Functional characterization of the Drosophila MRP (mitochondrial RNA processing) RNA gene.

    Science.gov (United States)

    Schneider, Mary D; Bains, Anupinder K; Rajendra, T K; Dominski, Zbigniew; Matera, A Gregory; Simmonds, Andrew J

    2010-11-01

    MRP RNA is a noncoding RNA component of RNase mitochondrial RNA processing (MRP), a multi-protein eukaryotic endoribonuclease reported to function in multiple cellular processes, including ribosomal RNA processing, mitochondrial DNA replication, and cell cycle regulation. A recent study predicted a potential Drosophila ortholog of MRP RNA (CR33682) by computer-based genome analysis. We have confirmed the expression of this gene and characterized the phenotype associated with this locus. Flies with mutations that specifically affect MRP RNA show defects in growth and development that begin in the early larval period and end in larval death during the second instar stage. We present several lines of evidence demonstrating a role for Drosophila MRP RNA in rRNA processing. The nuclear fraction of Drosophila MRP RNA localizes to the nucleolus. Further, a mutant strain shows defects in rRNA processing that include a defect in 5.8S rRNA processing, typical of MRP RNA mutants in other species, as well as defects in early stages of rRNA processing.

  1. The drive to innovation: The privileging of science and technology knowledge production in Canada

    Science.gov (United States)

    Cauchi, Laura

    This dissertation project explored the privileging of knowledge production in science and technology as a Canadian national economic, political and social strategy. The project incorporated the relationship between nation-state knowledge production and how that knowledge is then systematically evaluated, prioritized and validated by systems of health technology assessment (HTA). The entry point into the analysis and this dissertation project was the Scientific Research and Experimental Design (SR&ED) federal tax incentive program as the cornerstone of science and technology knowledge production in Canada. The method of inquiry and analysis examined the submission documents submitted by key stakeholders across the country, representing public, private and academic standpoints, during the public consultation process conducted from 2007 to 2008 and how each of these standpoints is hooked into the public policy interests and institutional structures that produce knowledge in science and technology. Key public meetings, including the public information sessions facilitated by the Canada Revenue Agency and private industry conferences, provided context and guidance regarding the current pervasive public and policy interests that direct and drive the policy debates. Finally, the "Innovation Canada: A Call to Action Review of Federal Support to Research and Development: Expert Panel Report," commonly referred to as "The Jenkins Report" (Jenkins et al., 2011), was critically evaluated as the expected predictor of future public policy changes associated with the SR&ED program and the future implications for the production of knowledge in science and technology. The method of inquiry and analytical lens was a materialist approach that drew on the inspiring frameworks of such scholars as Dorothy Smith, Michel Foucault, Kaushik Sunder Rajan, Melinda Cooper, and, Gilles Deleuze. Ultimately, I strove to illuminate the normalizing force and power of knowledge production in science

  2. Cytoplasmic Z-RNA

    International Nuclear Information System (INIS)

    Zarling, D.A.; Calhoun, C.J.; Hardin, C.C.; Zarling, A.H.

    1987-01-01

    Specific immunochemical probes for Z-RNA were generated and characterized to search for possible Z-RNA-like double helices in cells. Z-RNA was detected in the cytoplasm of fixed protozoan cells by immunofluorescence microscopy using these anti-Z-RNA IgCs. In contrast, autoimmune or experimentally elicited anti-DNA antibodies, specifically reactive with B-DNA or Z-DNA, stained the nuclei. Pre-or nonimmune IgGs did not bind to the cells. RNase A or T1 digestion eliminated anti-Z-RNA IgG binding to cytoplasmic determinants; however, DNase I or mung bean nuclease had no effect. Doxorubicin and ethidium bromide prevented anti-Z-RNA antibody binding; however, actinomycin D, which does not bind double-stranded RNA, did not. Anti-Z-RNA immunofluorescence was specifically blocked in competition assays by synthetic Z-RNA but not Z-DNA, A-RNA, or single-stranded RNAs. Thus, some cytoplasmic sequences in fixed cells exist in the left-handed Z-RNA conformation

  3. Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

    KAUST Repository

    Ariel, Federico D.; Jé gu, Teddy; Latrasse, David; Romero-Barrios, Natali; Christ, Auré lie; Benhamed, Moussa; Crespi, Martí n D.

    2014-01-01

    The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.

  4. Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

    KAUST Repository

    Ariel, Federico D.

    2014-08-01

    The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.

  5. Building the library of RNA 3D nucleotide conformations using the clustering approach

    Directory of Open Access Journals (Sweden)

    Zok Tomasz

    2015-09-01

    Full Text Available An increasing number of known RNA 3D structures contributes to the recognition of various RNA families and identification of their features. These tasks are based on an analysis of RNA conformations conducted at different levels of detail. On the other hand, the knowledge of native nucleotide conformations is crucial for structure prediction and understanding of RNA folding. However, this knowledge is stored in structural databases in a rather distributed form. Therefore, only automated methods for sampling the space of RNA structures can reveal plausible conformational representatives useful for further analysis. Here, we present a machine learning-based approach to inspect the dataset of RNA three-dimensional structures and to create a library of nucleotide conformers. A median neural gas algorithm is applied to cluster nucleotide structures upon their trigonometric description. The clustering procedure is two-stage: (i backbone- and (ii ribose-driven. We show the resulting library that contains RNA nucleotide representatives over the entire data, and we evaluate its quality by computing normal distribution measures and average RMSD between data points as well as the prototype within each cluster.

  6. RNA Interference - Towards RNA becoming a Medicine -42 ...

    Indian Academy of Sciences (India)

    research. A brief history of the development ofRNAi is shown in. Box 2. Mechanism of ... new RNA strand using target RNA as the template and thereby converting it ... thought to excise precursor stRNA from their -70 nt stem loop precursor to ...

  7. 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.

  8. MultiSETTER: web server for multiple RNA structure comparison.

    Science.gov (United States)

    Čech, Petr; Hoksza, David; Svozil, Daniel

    2015-08-12

    Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

  9. Classifying cognitive profiles using machine learning with privileged information in Mild Cognitive Impairment

    Directory of Open Access Journals (Sweden)

    Hanin Hamdan Alahmadi

    2016-11-01

    Full Text Available Early diagnosis of dementia is critical for assessing disease progression and potential treatment. State-or-the-art machine learning techniques have been increasingly employed to take on this diagnostic task. In this study, we employed Generalised Matrix Learning Vector Quantization (GMLVQ classifiers to discriminate patients with Mild Cognitive Impairment (MCI from healthy controls based on their cognitive skills. Further, we adopted a ``Learning with privileged information'' approach to combine cognitive and fMRI data for the classification task. The resulting classifier operates solely on the cognitive data while it incorporates the fMRI data as privileged information (PI during training. This novel classifier is of practical use as the collection of brain imaging data is not always possible with patients and older participants.MCI patients and healthy age-matched controls were trained to extract structure from temporal sequences. We ask whether machine learning classifiers can be used to discriminate patients from controls based on the learning performance and whether differences between these groups relate to individual cognitive profiles. To this end, we tested participants in four cognitive tasks: working memory, cognitive inhibition, divided attention, and selective attention. We also collected fMRI data before and after training on the learning task and extracted fMRI responses and connectivity as features for machine learning classifiers. Our results show that the PI guided GMLVQ classifiers outperform the baseline classifier that only used the cognitive data. In addition, we found that for the baseline classifier, divided attention is the only relevant cognitive feature. When PI was incorporated, divided attention remained the most relevant feature while cognitive inhibition became also relevant for the task. Interestingly, this analysis for the fMRI GMLVQ classifier suggests that (1 when overall fMRI signal for structured stimuli is

  10. RNA-Binding Proteins Revisited – The Emerging Arabidopsis mRNA Interactome

    KAUST Repository

    Köster, Tino

    2017-04-13

    RNA–protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture – where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.

  11. RNA-Binding Proteins Revisited – The Emerging Arabidopsis mRNA Interactome

    KAUST Repository

    Kö ster, Tino; Marondedze, Claudius; Meyer, Katja; Staiger, Dorothee

    2017-01-01

    RNA–protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture – where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.

  12. Fast Arc-Annotated Subsequence Matching in Linear Space

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li

    2012-01-01

    for investigating the function of RNA molecules. Gramm et al. (ACM Trans. Algorithms 2(1): 44-65, 2006) gave an algorithm for this problem using O(nm) time and space, where m and n are the lengths of P and Q, respectively. In this paper we present a new algorithm using O(nm) time and O(n+m) space, thereby matching......-annotated strings. © 2010 Springer Science+Business Media, LLC....

  13. RNA-dependent RNA polymerases from cowpea mosaic virus-infected cowpea leaves

    NARCIS (Netherlands)

    Dorssers, L.

    1983-01-01

    The aim of the research described in this thesis was the purification and identification of the RNA-dependent RNA polymerase engaged in replicating viral RNA in cowpea mosaic virus (CPMV)- infected cowpea leaves.

    Previously, an RNA-dependent RNA polymerase produced upon infection of

  14. Cyclophilin B stimulates RNA synthesis by the HCV RNA dependent RNA polymerase.

    Science.gov (United States)

    Heck, Julie A; Meng, Xiao; Frick, David N

    2009-04-01

    Cyclophilins are cellular peptidyl isomerases that have been implicated in regulating hepatitis C virus (HCV) replication. Cyclophilin B (CypB) is a target of cyclosporin A (CsA), an immunosuppressive drug recently shown to suppress HCV replication in cell culture. Watashi et al. recently demonstrated that CypB is important for efficient HCV replication, and proposed that it mediates the anti-HCV effects of CsA through an interaction with NS5B [Watashi K, Ishii N, Hijikata M, Inoue D, Murata T, Miyanari Y, et al. Cyclophilin B is a functional regulator of hepatitis C virus RNA polymerase. Mol Cell 2005;19:111-22]. We examined the effects of purified CypB proteins on the enzymatic activity of NS5B. Recombinant CypB purified from insect cells directly stimulated NS5B-catalyzed RNA synthesis. CypB increased RNA synthesis by NS5B derived from genotype 1a, 1b, and 2a HCV strains. Stimulation appears to arise from an increase in productive RNA binding. NS5B residue Pro540, a previously proposed target of CypB peptidyl-prolyl isomerase activity, is not required for stimulation of RNA synthesis.

  15. tRNA's wobble decoding of the genome: 40 years of modification.

    Science.gov (United States)

    Agris, Paul F; Vendeix, Franck A P; Graham, William D

    2007-02-09

    The genetic code is degenerate, in that 20 amino acids are encoded by 61 triplet codes. In 1966, Francis Crick hypothesized that the cell's limited number of tRNAs decoded the genome by recognizing more than one codon. The ambiguity of that recognition resided in the third base-pair, giving rise to the Wobble Hypothesis. Post-transcriptional modifications at tRNA's wobble position 34, especially modifications of uridine 34, enable wobble to occur. The Modified Wobble Hypothesis proposed in 1991 that specific modifications of a tRNA wobble nucleoside shape the anticodon architecture in such a manner that interactions were restricted to the complementary base plus a single wobble pairing for amino acids with twofold degenerate codons. However, chemically different modifications at position 34 would expand the ability of a tRNA to read three or even four of the fourfold degenerate codons. One foundation of Crick's Wobble Hypothesis was that a near-constant geometry of canonical base-pairing be maintained in forming all three base-pairs between the tRNA anticodon and mRNA codon on the ribosome. In accepting an aminoacyl-tRNA, the ribosome requires maintenance of a specific geometry for the anticodon-codon base-pairing. However, it is the post-transcriptional modifications at tRNA wobble position 34 and purine 37, 3'-adjacent to the anticodon, that pre-structure the anticodon domain to ensure the correct codon binding. The modifications create both the architecture and the stability needed for decoding through restraints on anticodon stereochemistry and conformational space, and through selective hydrogen bonding. A physicochemical understanding of modified nucleoside contributions to the tRNA anticodon domain architecture and its decoding of the genome has advanced RNA world evolutionary theory, the principles of RNA chemistry, and the application of this knowledge to the introduction of new amino acids to proteins.

  16. Fast prediction of RNA-RNA interaction using heuristic algorithm.

    Science.gov (United States)

    Montaseri, Soheila

    2015-01-01

    Interaction between two RNA molecules plays a crucial role in many medical and biological processes such as gene expression regulation. In this process, an RNA molecule prohibits the translation of another RNA molecule by establishing stable interactions with it. Some algorithms have been formed to predict the structure of the RNA-RNA interaction. High computational time is a common challenge in most of the presented algorithms. In this context, a heuristic method is introduced to accurately predict the interaction between two RNAs based on minimum free energy (MFE). This algorithm uses a few dot matrices for finding the secondary structure of each RNA and binding sites between two RNAs. Furthermore, a parallel version of this method is presented. We describe the algorithm's concurrency and parallelism for a multicore chip. The proposed algorithm has been performed on some datasets including CopA-CopT, R1inv-R2inv, Tar-Tar*, DIS-DIS, and IncRNA54-RepZ in Escherichia coli bacteria. The method has high validity and efficiency, and it is run in low computational time in comparison to other approaches.

  17. The RNA synthesis machinery of negative-stranded RNA viruses

    International Nuclear Information System (INIS)

    Ortín, Juan; Martín-Benito, Jaime

    2015-01-01

    The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and function of the ribonucleoprotein components: Atomic structure of the RNA polymerase complex. • Commonalities and differences between segmented- and non-segmented NSVs. • Transcription versus replication programmes

  18. The RNA synthesis machinery of negative-stranded RNA viruses

    Energy Technology Data Exchange (ETDEWEB)

    Ortín, Juan, E-mail: jortin@cnb.csic.es [Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CSIC) and CIBER de Enfermedades Respiratorias (ISCIII), Madrid (Spain); Martín-Benito, Jaime, E-mail: jmartinb@cnb.csic.es [Department of Macromolecular Structures, Centro Nacional de Biotecnología (CSIC), Madrid (Spain)

    2015-05-15

    The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and function of the ribonucleoprotein components: Atomic structure of the RNA polymerase complex. • Commonalities and differences between segmented- and non-segmented NSVs. • Transcription versus replication programmes.

  19. Assessment of small RNA sorting into different extracellular fractions revealed by high-throughput sequencing of breast cell lines

    Science.gov (United States)

    Tosar, Juan Pablo; Gámbaro, Fabiana; Sanguinetti, Julia; Bonilla, Braulio; Witwer, Kenneth W.; Cayota, Alfonso

    2015-01-01

    Intercellular communication can be mediated by extracellular small regulatory RNAs (sRNAs). Circulating sRNAs are being intensively studied for their promising use as minimally invasive disease biomarkers. To date, most attention is centered on exosomes and microRNAs as the vectors and the secreted species, respectively. However, this field would benefit from an increased understanding of the plethora of sRNAs secreted by different cell types in different extracellular fractions. It is still not clear if specific sRNAs are selected for secretion, or if sRNA secretion is mostly passive. We sequenced the intracellular sRNA content (19–60 nt) of breast epithelial cell lines (MCF-7 and MCF-10A) and compared it with extracellular fractions enriched in microvesicles, exosomes and ribonucleoprotein complexes. Our results are consistent with a non-selective secretion model for most microRNAs, although a few showed secretion patterns consistent with preferential secretion. On the contrary, 5′ tRNA halves and 5′ RNA Y4-derived fragments of 31–33 were greatly and significantly enriched in the extracellular space (even in non-mammary cell lines), where tRNA halves were detected as part of ∼45 kDa ribonucleoprotein complexes. Overall, we show that different sRNA families have characteristic secretion patterns and open the question of the role of these sRNAs in the extracellular space. PMID:25940616

  20. 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

  1. The microRNA and messengerRNA profile of the RNA-induced silencing complex in human primary astrocyte and astrocytoma cells.

    Science.gov (United States)

    Moser, Joanna J; Fritzler, Marvin J

    2010-10-18

    GW/P bodies are cytoplasmic ribonucleoprotein-rich foci involved in microRNA (miRNA)-mediated messenger RNA (mRNA) silencing and degradation. The mRNA regulatory functions within GW/P bodies are mediated by GW182 and its binding partner hAgo2 that bind miRNA in the RNA-induced silencing complex (RISC). To date there are no published reports of the profile of miRNA and mRNA targeted to the RISC or a comparison of the RISC-specific miRNA/mRNA profile differences in malignant and non-malignant cells. RISC mRNA and miRNA components were profiled by microarray analysis of malignant human U-87 astrocytoma cells and its non-malignant counterpart, primary human astrocytes. Total cell RNA as well as RNA from immunoprecipitated RISC was analyzed. The novel findings were fourfold: (1) miRNAs were highly enriched in astrocyte RISC compared to U-87 astrocytoma RISC, (2) astrocytoma and primary astrocyte cells each contained unique RISC miRNA profiles as compared to their respective cellular miRNA profiles, (3) miR-195, 10b, 29b, 19b, 34a and 455-3p levels were increased and the miR-181b level was decreased in U-87 astrocytoma RISC as compared to astrocyte RISC, and (4) the RISC contained decreased levels of mRNAs in primary astrocyte and U-87 astrocytoma cells. The observation that miR-34a and miR-195 levels were increased in the RISC of U-87 astrocytoma cells suggests an oncogenic role for these miRNAs. Differential regulation of mRNAs by specific miRNAs is evidenced by the observation that three miR34a-targeted mRNAs and two miR-195-targeted mRNAs were downregulated while one miR-195-targeted mRNA was upregulated. Biological pathway analysis of RISC mRNA components suggests that the RISC plays a pivotal role in malignancy and other conditions. This study points to the importance of the RISC and ultimately GW/P body composition and function in miRNA and mRNA deregulation in astrocytoma cells and possibly in other malignancies.

  2. The microRNA and messengerRNA profile of the RNA-induced silencing complex in human primary astrocyte and astrocytoma cells.

    Directory of Open Access Journals (Sweden)

    Joanna J Moser

    2010-10-01

    Full Text Available GW/P bodies are cytoplasmic ribonucleoprotein-rich foci involved in microRNA (miRNA-mediated messenger RNA (mRNA silencing and degradation. The mRNA regulatory functions within GW/P bodies are mediated by GW182 and its binding partner hAgo2 that bind miRNA in the RNA-induced silencing complex (RISC. To date there are no published reports of the profile of miRNA and mRNA targeted to the RISC or a comparison of the RISC-specific miRNA/mRNA profile differences in malignant and non-malignant cells.RISC mRNA and miRNA components were profiled by microarray analysis of malignant human U-87 astrocytoma cells and its non-malignant counterpart, primary human astrocytes. Total cell RNA as well as RNA from immunoprecipitated RISC was analyzed. The novel findings were fourfold: (1 miRNAs were highly enriched in astrocyte RISC compared to U-87 astrocytoma RISC, (2 astrocytoma and primary astrocyte cells each contained unique RISC miRNA profiles as compared to their respective cellular miRNA profiles, (3 miR-195, 10b, 29b, 19b, 34a and 455-3p levels were increased and the miR-181b level was decreased in U-87 astrocytoma RISC as compared to astrocyte RISC, and (4 the RISC contained decreased levels of mRNAs in primary astrocyte and U-87 astrocytoma cells.The observation that miR-34a and miR-195 levels were increased in the RISC of U-87 astrocytoma cells suggests an oncogenic role for these miRNAs. Differential regulation of mRNAs by specific miRNAs is evidenced by the observation that three miR34a-targeted mRNAs and two miR-195-targeted mRNAs were downregulated while one miR-195-targeted mRNA was upregulated. Biological pathway analysis of RISC mRNA components suggests that the RISC plays a pivotal role in malignancy and other conditions. This study points to the importance of the RISC and ultimately GW/P body composition and function in miRNA and mRNA deregulation in astrocytoma cells and possibly in other malignancies.

  3. Cancer-Related Triplets of mRNA-lncRNA-miRNA Revealed by Integrative Network in Uterine Corpus Endometrial Carcinoma

    Directory of Open Access Journals (Sweden)

    Chenglin Liu

    2017-01-01

    Full Text Available The regulation of transcriptome expression level is a complex process involving multiple-level interactions among molecules such as protein coding RNA (mRNA, long noncoding RNA (lncRNA, and microRNA (miRNA, which are essential for the transcriptome stability and maintenance and regulation of body homeostasis. The availability of multilevel expression data enables a comprehensive view of the regulatory network. In this study, we analyzed the coding and noncoding gene expression profiles of 301 patients with uterine corpus endometrial carcinoma (UCEC. A new method was proposed to construct a genome-wide integrative network based on variance inflation factor (VIF regression method. The cross-regulation relations of mRNA, lncRNA, and miRNA were then selected based on clique-searching algorithm from the network, when any two molecules of the three were shown as interacting according to the integrative network. Such relation, which we call the mRNA-lncRNA-miRNA triplet, demonstrated the complexity in transcriptome regulation process. Finally, six UCEC-related triplets were selected in which the mRNA participates in endometrial carcinoma pathway, such as CDH1 and TP53. The multi-type RNAs are proved to be cross-regulated as to each of the six triplets according to literature. All the triplets demonstrated the association with the initiation and progression of UCEC. Our method provides a comprehensive strategy for the investigation of transcriptome regulation mechanism.

  4. Viral RNA polymerase scanning and the gymnastics of Sendai virus RNA synthesis

    International Nuclear Information System (INIS)

    Kolakofsky, Daniel; Le Mercier, Philippe; Iseni, Frederic; Garcin, Dominique

    2004-01-01

    mRNA synthesis from nonsegmented negative-strand RNA virus (NNV) genomes is unique in that the genome RNA is embedded in an N protein assembly (the nucleocapsid) and the viral RNA polymerase does not dissociate from the template after release of each mRNA, but rather scans the genome RNA for the next gene-start site. A revised model for NNV RNA synthesis is presented, in which RNA polymerase scanning plays a prominent role. Polymerase scanning of the template is known to occur as the viral transcriptase negotiates gene junctions without falling off the template

  5. On RNA-RNA interaction structures of fixed topological genus.

    Science.gov (United States)

    Fu, Benjamin M M; Han, Hillary S W; Reidys, Christian M

    2015-04-01

    Interacting RNA complexes are studied via bicellular maps using a filtration via their topological genus. Our main result is a new bijection for RNA-RNA interaction structures and a linear time uniform sampling algorithm for RNA complexes of fixed topological genus. The bijection allows to either reduce the topological genus of a bicellular map directly, or to lose connectivity by decomposing the complex into a pair of single stranded RNA structures. Our main result is proved bijectively. It provides an explicit algorithm of how to rewire the corresponding complexes and an unambiguous decomposition grammar. Using the concept of genus induction, we construct bicellular maps of fixed topological genus g uniformly in linear time. We present various statistics on these topological RNA complexes and compare our findings with biological complexes. Furthermore we show how to construct loop-energy based complexes using our decomposition grammar. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Revisiting the picture-superiority effect in symbolic comparisons: do pictures provide privileged access?

    Science.gov (United States)

    Amrhein, Paul C; McDaniel, Mark A; Waddill, Paula

    2002-09-01

    In 4 experiments, symbolic comparisons were investigated to test semantic-memory retrieval accounts espousing processing advantages for picture over word stimuli. In Experiment 1, participants judged pairs of animal names or pictures by responding to questions probing concrete or abstract attributes (texture or size, ferocity or intelligence). Per pair, attributes were salient or nonsalient concerning their prerated relevance to animals being compared. Distance (near or far) between attribute magnitudes was also varied. Pictures did not significantly speed responding relative to words across all other variables. Advantages were found forfar attribute magnitudes (i.e., the distance effect) and salient attributes. The distance effect was much less for salient than nonsalient concrete-attribute comparisons. These results were consistently found in additional experiments with increased statistical power to detect modality effects. Our findings argue against dual-coding and some common-code accounts of conceptual attribute processing, urging reexamination of the assumption that pictures confer privileged access to long-term knowledge.

  7. Changes in rRNA levels during stress invalidates results from mRNA blotting: Fluorescence in situ rRNA hybridization permits renormalization for estimation of cellular mRNA levels

    DEFF Research Database (Denmark)

    Hansen, M.C.; Nielsen, A.K.; Molin, Søren

    2001-01-01

    obtained by these techniques are compared between experiments in which differences in growth rates, strains, or stress treatments occur, the normalization procedure may have a significant impact on the results. In this report we present a solution to the normalization problem in RNA slot blotting...... the relative level of rRNA per cell, and slot blotting to rRNA probes, which estimates the level of rRNA per extracted total RNA, the amount of RNA per cell was calculated in a series of heat shock experiments with the gram-positive bacterium Lactococcus lactis. It was found that the level of rRNA per cell...... decreased to 30% in the course of the heat shock. This lowered ribosome level led to a decrease in the total RNA content, resulting in a gradually increasing overestimation of the mRNA levels throughout the experiment. Using renormalized cellular mRNA levels, the HrcA-mediated regulation of the genes...

  8. RNA-Catalyzed Polymerization and Replication of RNA

    Science.gov (United States)

    Horning, D. P.; Samantha, B.; Tjhung, K. F.; Joyce, G. F.

    2017-07-01

    In an effort to reconstruct RNA-based life, in vitro evolution was used to obtain an RNA polymerase ribozyme that can synthesize a variety of complex functional RNAs and can catalyze the exponential amplification of short RNAs.

  9. Fast, clash-free RNA conformational morphing using molecular junctions.

    Science.gov (United States)

    Héliou, Amélie; Budday, Dominik; Fonseca, Rasmus; van den Bedem, Henry

    2017-07-15

    Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. Despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groups of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation. The source code, binaries and data are available at https://simtk.org/home/kgs . amelie.heliou@polytechnique.edu or vdbedem@stanford.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  10. microRNA-independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA-binding protein

    OpenAIRE

    Pinder, Benjamin D; Smibert, Craig A

    2012-01-01

    Argonaute 1 directly interacts with the RNA binding protein Smaug in Drosophila, is thereby recruited to the Smaug target nanos mRNA and is required for Smaug-mediated translational repression of the nanos mRNA.

  11. TargetRNA: a tool for predicting targets of small RNA action in bacteria

    OpenAIRE

    Tjaden, Brian

    2008-01-01

    Many small RNA (sRNA) genes in bacteria act as posttranscriptional regulators of target messenger RNAs. Here, we present TargetRNA, a web tool for predicting mRNA targets of sRNA action in bacteria. TargetRNA takes as input a genomic sequence that may correspond to an sRNA gene. TargetRNA then uses a dynamic programming algorithm to search each annotated message in a specified genome for mRNAs that evince basepair-binding potential to the input sRNA sequence. Based on the calculated basepair-...

  12. The modification of siRNA with 3' cholesterol to increase nuclease protection and suppression of native mRNA by select siRNA polyplexes.

    Science.gov (United States)

    Ambardekar, Vishakha V; Han, Huai-Yun; Varney, Michelle L; Vinogradov, Serguei V; Singh, Rakesh K; Vetro, Joseph A

    2011-02-01

    Polymer-siRNA complexes (siRNA polyplexes) are being actively developed to improve the therapeutic application of siRNA. A major limitation for many siRNA polyplexes, however, is insufficient mRNA suppression. Given that modifying the sense strand of siRNA with 3' cholesterol (chol-siRNA) increases the activity of free nuclease-resistant siRNA in vitro and in vivo, we hypothesized that complexation of chol-siRNA can increase mRNA suppression by siRNA polyplexes. In this study, the characteristics and siRNA activity of self assembled polyplexes formed with chol-siRNA or unmodified siRNA were compared using three types of conventional, positively charged polymers: (i) biodegradable, cross-linked nanogels (BDNG) (ii) graft copolymers (PEI-PEG), and (iii) linear block copolymers (PLL10-PEG, and PLL50-PEG). Chol-siRNA did not alter complex formation or the resistance of polyplexes to siRNA displacement by heparin but increased nuclease protection by BDNG, PLL10-PEG, and PLL50-PEG polyplexes over polyplexes with unmodified siRNA. Chol-CYPB siRNA increased suppression of native CYPB mRNA in mammary microvascular endothelial cells (MVEC) by BDNG polyplexes (35%) and PLL10-PEG polyplexes (69%) over comparable CYPB siRNA polyplexes but had no effect on PEI-PEG or PLL50-PEG polyplexes. Overall, these results indicate that complexation of chol-siRNA increases nuclease protection and mRNA suppression by select siRNA polyplexes. These results also suggest that polycationic block length is an important factor in increasing mRNA suppression by PLL-PEG chol-siRNA polyplexes in mammary MVEC. Copyright © 2010 Elsevier Ltd. All rights reserved.

  13. 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.

  14. MicroRNA-target binding structures mimic microRNA duplex structures in humans.

    Directory of Open Access Journals (Sweden)

    Xi Chen

    Full Text Available Traditionally, researchers match a microRNA guide strand to mRNA sequences using sequence comparisons to predict its potential target genes. However, many of the predictions can be false positives due to limitations in sequence comparison alone. In this work, we consider the association of two related RNA structures that share a common guide strand: the microRNA duplex and the microRNA-target binding structure. We have analyzed thousands of such structure pairs and found many of them share high structural similarity. Therefore, we conclude that when predicting microRNA target genes, considering just the microRNA guide strand matches to gene sequences may not be sufficient--the microRNA duplex structure formed by the guide strand and its companion passenger strand must also be considered. We have developed software to translate RNA binding structure into encoded representations, and we have also created novel automatic comparison methods utilizing such encoded representations to determine RNA structure similarity. Our software and methods can be utilized in the other RNA secondary structure comparisons as well.

  15. TruSeq Stranded mRNA and Total RNA Sample Preparation Kits

    Science.gov (United States)

    Total RNA-Seq enabled by ribosomal RNA (rRNA) reduction is compatible with formalin-fixed paraffin embedded (FFPE) samples, which contain potentially critical biological information. The family of TruSeq Stranded Total RNA sample preparation kits provides a unique combination of unmatched data quality for both mRNA and whole-transcriptome analyses, robust interrogation of both standard and low-quality samples and workflows compatible with a wide range of study designs.

  16. Primer-dependent and primer-independent initiation of double stranded RNA synthesis by purified arabidopsis RNA-dependent RNA polymerases RDR2 and RDR6

    DEFF Research Database (Denmark)

    Devert, Anthony; Fabre, Nicolas; Floris, Maina Huguette Joséphine

    2015-01-01

    ) targeted by RNA silencing. The dsRNA is subsequently cleaved by the ribonuclease DICER-like into secondary small interfering RNAs (siRNAs) that reinforce and/or maintain the silenced state of the target RNA. Models of RNA silencing propose that RDRs could use primer-independent and primer......Cellular RNA-dependent RNA polymerases (RDRs) are fundamental components of RNA silencing in plants and many other eukaryotes. In Arabidopsis thaliana genetic studies have demonstrated that RDR2 and RDR6 are involved in the synthesis of double stranded RNA (dsRNA) from single stranded RNA (ssRNA......-dependent initiation to generate dsRNA from a transcript targeted by primary siRNA or microRNA (miRNA). However, the biochemical activities of RDR proteins are still partly understood. Here, we obtained active recombinant RDR2 and RDR6 in a purified form. We demonstrate that RDR2 and RDR6 have primer...

  17. A Method to Predict the Structure and Stability of RNA/RNA Complexes.

    Science.gov (United States)

    Xu, Xiaojun; Chen, Shi-Jie

    2016-01-01

    RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.

  18. Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.

    Science.gov (United States)

    Konevega, Andrey L; Fischer, Niels; Semenkov, Yuri P; Stark, Holger; Wintermeyer, Wolfgang; Rodnina, Marina V

    2007-04-01

    During the translocation step of protein synthesis, a complex of two transfer RNAs bound to messenger RNA (tRNA-mRNA) moves through the ribosome. The reaction is promoted by an elongation factor, called EF-G in bacteria, which, powered by GTP hydrolysis, induces an open, unlocked conformation of the ribosome that allows for spontaneous tRNA-mRNA movement. Here we show that, in the absence of EF-G, there is spontaneous backward movement, or retrotranslocation, of two tRNAs bound to mRNA. Retrotranslocation is driven by the gain in affinity when a cognate E-site tRNA moves into the P site, which compensates the affinity loss accompanying the movement of peptidyl-tRNA from the P to the A site. These results lend support to the diffusion model of tRNA movement during translocation. In the cell, tRNA movement is biased in the forward direction by EF-G, which acts as a Brownian ratchet and prevents backward movement.

  19. Initiation of translation in bacteria by a structured eukaryotic IRES RNA.

    Science.gov (United States)

    Colussi, Timothy M; Costantino, David A; Zhu, Jianyu; Donohue, John Paul; Korostelev, Andrei A; Jaafar, Zane A; Plank, Terra-Dawn M; Noller, Harry F; Kieft, Jeffrey S

    2015-03-05

    The central dogma of gene expression (DNA to RNA to protein) is universal, but in different domains of life there are fundamental mechanistic differences within this pathway. For example, the canonical molecular signals used to initiate protein synthesis in bacteria and eukaryotes are mutually exclusive. However, the core structures and conformational dynamics of ribosomes that are responsible for the translation steps that take place after initiation are ancient and conserved across the domains of life. We wanted to explore whether an undiscovered RNA-based signal might be able to use these conserved features, bypassing mechanisms specific to each domain of life, and initiate protein synthesis in both bacteria and eukaryotes. Although structured internal ribosome entry site (IRES) RNAs can manipulate ribosomes to initiate translation in eukaryotic cells, an analogous RNA structure-based mechanism has not been observed in bacteria. Here we report our discovery that a eukaryotic viral IRES can initiate translation in live bacteria. We solved the crystal structure of this IRES bound to a bacterial ribosome to 3.8 Å resolution, revealing that despite differences between bacterial and eukaryotic ribosomes this IRES binds directly to both and occupies the space normally used by transfer RNAs. Initiation in both bacteria and eukaryotes depends on the structure of the IRES RNA, but in bacteria this RNA uses a different mechanism that includes a form of ribosome repositioning after initial recruitment. This IRES RNA bridges billions of years of evolutionary divergence and provides an example of an RNA structure-based translation initiation signal capable of operating in two domains of life.

  20. RNA processing and ribonucleoprotein assembly studied in vivo by RNA transfection

    International Nuclear Information System (INIS)

    Kleinschmidt, A.M.; Pederson, T.

    1990-01-01

    The authors present a method for studying RNA processing and ribonucleoprotein assembly in vivo, by using RNA synthesized in vitro. SP6-transcribed 32 P-labeled U2 small nuclear RNA precursor molecules were introduced into cultured human 293 cells by calcium phosphate-mediated uptake, as in standard DNA transfection experiments. RNase protection mapping demonstrated that the introduced pre-U2 RNA underwent accurate 3' end processing. The introduced U2 RNA was assembled into ribonucleoprotein particles that reacted with an antibody specific for proteins known to be associated with the U2 small nuclear ribonucleoprotein particle. The 3' end-processed, ribonucleoprotein-assembled U2 RNA accumulated in the nuclear fraction. When pre-U2 RNA with a 7-methylguanosine group at the 5' end was introduced into cells, it underwent conversion to a 2,2,7-trimethylguanosine cap structure, a characteristic feature of the U-small nuclear RNAs. Pre-U2 RNA introduced with an adenosine cap (Ap-ppG) also underwent processing, small nuclear ribonucleoprotein assembly, and nuclear accumulation, establishing that a methylated guanosine cap structure is not required for these steps in U2 small nuclear ribonucleprotein biosynthesis. Beyond its demonstrated usefulness in the study of small nuclear ribonucleoprotein biosynthesis, RNA transfection may be of general applicability to the investigation of eukaryotic RNA processing in vivo and may also offer opportunities for introducing therapeutically targeted RNAs (ribozymes or antisense RNA) into cells

  1. RNA precursor pool metabolism and RNA synthesis in X-irradiated Tetrahymena

    International Nuclear Information System (INIS)

    Stephens, R.E.; Paul, I.J.; Zimmerman, A.M.

    1976-01-01

    The incorporation of a radioactive RNA precursor ( 3 H-uridine) has been used in many studies as an index for measuring the synthesis of RNA, yet there is a distinct possibility that the results so obtained were significantly influenced by radiation-induced effects on the metabolism of this precursor into UTP (the primary immediate precursor of RNA) before its incorporation into RNA. A direct examination was therefore undertaken of the effects of X-irradiation on the metabolism of 3 H-uridine and its relationship to RNA synthesis as determined by incorporation. X-irradiation of logarithmically growing Tetrahymena pyriformis caused a dose-dependent depression of total cellular RNA synthesis. Ribosomal RNA (which comprises about 80 per cent of total cellular RNA) synthesis was also depressed by X-irradiation in a dose-dependent manner. Measurements of the levels of radioactivity present in the UTP precursor pool of both irradiated and unirradiated cells were obtained by means of DEAE-cellulose column chromatography of the extracted free nucleotides. Metabolism of 3 H-uridine into UMP, UDP and UTP was depressed by 40%, 26% and 27% respectively, whereas incorporation of 3 H-uridine into RNA was depressed by 77%. The results show that about one-third of the observed (apparent) depression in RNA synthesis was due to radiation-induced effects on the precursor pool, and the remaining two-thirds due to some definite effect of radiation at the transcription level leading to depressed synthesis of RNA. (U.K.)

  2. Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes

    Directory of Open Access Journals (Sweden)

    Nicole Ludwig

    2016-03-01

    Full Text Available Wilms tumor (WT is the most common childhood renal cancer. Recent findings of mutations in microRNA (miRNA processing proteins suggest a pivotal role of miRNAs in WT genesis. We performed miRNA expression profiling of 36 WTs of different subtypes and four normal kidney tissues using microarrays. Additionally, we determined the gene expression profile of 28 of these tumors to identify potentially correlated target genes and affected pathways. We identified 85 miRNAs and 2107 messenger RNAs (mRNA differentially expressed in blastemal WT, and 266 miRNAs and 1267 mRNAs differentially expressed in regressive subtype. The hierarchical clustering of the samples, using either the miRNA or mRNA profile, showed the clear separation of WT from normal kidney samples, but the miRNA pattern yielded better separation of WT subtypes. A correlation analysis of the deregulated miRNA and mRNAs identified 13,026 miRNA/mRNA pairs with inversely correlated expression, of which 2844 are potential interactions of miRNA and their predicted mRNA targets. We found significant upregulation of miRNAs-183, -301a/b and -335 for the blastemal subtype, and miRNAs-181b, -223 and -630 for the regressive subtype. We found marked deregulation of miRNAs regulating epithelial to mesenchymal transition, especially in the blastemal subtype, and miRNAs influencing chemosensitivity, especially in regressive subtypes. Further research is needed to assess the influence of preoperative chemotherapy and tumor infiltrating lymphocytes on the miRNA and mRNA patterns in WT.

  3. 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.

  4. 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.

  5. Alterations in messenger RNA and small nuclear RNA metabolism resulting from fluorouracil incorporation

    International Nuclear Information System (INIS)

    Armstrong, R.D.; Cadman, E.C.

    1985-01-01

    Studies were completed to examine the effect of 5-fluorouracil (FUra) incorporation on messenger RNA (mRNA) and small molecular weight nuclear RNA (SnRNA) metabolism. Studies of mRNA were completed using cDNA-mRNA hybridization methods to specifically examine dihydrofolate reductase (DHFR) mRNA. C 3 -L5178Y murine leukemia cells which are gene-amplified for DHFR, were exposed to FUra for 6, 12 or 24 hr, and the nuclear and cytoplasmic levels of DHFR-mRNA determined by hybridization with 32 P-DHFR-cDNA. FUra produced a dose-dependent increase in nuclear DHFR-mRNA levels, while total cytoplasmic DHFR-mRNA levels appeared to be unchanged. To examine only mRNA synthesized during FUra exposure, cells were also treated concurrently with [ 3 H] cytidine, and the [ 3 H]mRNA-cDNA hybrids measured following S 1 -nuclease treatment. FUra produced a concentration-dependent increase in nascent nuclear DHFR-mRNA levels, and a decrease in nascent cytoplasmic DHFR-mRNAs levels. These results suggest that FUra produces either an inhibition of mRNA processing, or an inhibition of nuclear-cytoplasmic transport. Preliminary experiments to examine ATP-dependent mRNA transport were completed with isolated nuclei from cells treated with FUra for 1 or 24 hr and then pulse-labeled for 1 hr with [ 3 H] cytidine. The results demonstrate a FUra-concentration and time-dependent inhibition of ATP-mediated mRNA efflux

  6. RNA decay by messenger RNA interferases

    DEFF Research Database (Denmark)

    Christensen-Dalsgaard, Mikkel; Overgaard, Martin; Winther, Kristoffer Skovbo

    2008-01-01

    Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mR...... cleaving enzymes such as RelE of Escherichia coli and the corresponding antitoxin RelB. In particular, we describe a set of plasmid vectors useful for the detailed analysis of cleavage sites in model mRNAs.......Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mRNA...

  7. Thermal Stability of siRNA Modulates Aptamer- conjugated siRNA Inhibition

    Directory of Open Access Journals (Sweden)

    Alexey Berezhnoy

    2012-01-01

    Full Text Available Oligonucleotide aptamer-mediated in vivo cell targeting of small interfering RNAs (siRNAs is emerging as a useful approach to enhance the efficacy and reduce the adverse effects resulting from siRNA-mediated genetic interference. A current main impediment in aptamer-mediated siRNA targeting is that the activity of the siRNA is often compromised when conjugated to an aptamer, often requiring labor intensive and time consuming design and testing of multiple configurations to identify a conjugate in which the siRNA activity has not been significantly reduced. Here, we show that the thermal stability of the siRNA is an important parameter of siRNA activity in its conjugated form, and that siRNAs with lower melting temperature (Tm are not or are minimally affected when conjugated to the 3′ end of 2′F-pyrimidine-modified aptamers. In addition, the configuration of the aptamer-siRNA conjugate retains activity comparable with the free siRNA duplex when the passenger strand is co-transcribed with the aptamer and 3′ overhangs on the passenger strand are removed. The approach described in this paper significantly reduces the time and effort necessary to screening siRNA sequences that retain biological activity upon aptamer conjugation, facilitating the process of identifying candidate aptamer-siRNA conjugates suitable for in vivo testing.

  8. Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity.

    Science.gov (United States)

    Fajardo, Teodoro; Sung, Po-Yu; Roy, Polly

    2015-12-01

    Bluetongue virus (BTV) causes hemorrhagic disease in economically important livestock. The BTV genome is organized into ten discrete double-stranded RNA molecules (S1-S10) which have been suggested to follow a sequential packaging pathway from smallest to largest segment during virus capsid assembly. To substantiate and extend these studies, we have investigated the RNA sorting and packaging mechanisms with a new experimental approach using inhibitory oligonucleotides. Putative packaging signals present in the 3'untranslated regions of BTV segments were targeted by a number of nuclease resistant oligoribonucleotides (ORNs) and their effects on virus replication in cell culture were assessed. ORNs complementary to the 3' UTR of BTV RNAs significantly inhibited virus replication without affecting protein synthesis. Same ORNs were found to inhibit complex formation when added to a novel RNA-RNA interaction assay which measured the formation of supramolecular complexes between and among different RNA segments. ORNs targeting the 3'UTR of BTV segment 10, the smallest RNA segment, were shown to be the most potent and deletions or substitution mutations of the targeted sequences diminished the RNA complexes and abolished the recovery of viable viruses using reverse genetics. Cell-free capsid assembly/RNA packaging assay also confirmed that the inhibitory ORNs could interfere with RNA packaging and further substitution mutations within the putative RNA packaging sequence have identified the recognition sequence concerned. Exchange of 3'UTR between segments have further demonstrated that RNA recognition was segment specific, most likely acting as part of the secondary structure of the entire genomic segment. Our data confirm that genome packaging in this segmented dsRNA virus occurs via the formation of supramolecular complexes formed by the interaction of specific sequences located in the 3' UTRs. Additionally, the inhibition of packaging in-trans with inhibitory ORNs

  9. The Modification of siRNA with 3′ Cholesterol to Increase Nuclease Protection and Suppression of Native mRNA by Select siRNA Polyplexes

    Science.gov (United States)

    Ambardekar, Vishakha V.; Han, Huai-Yun; Varney, Michelle L.; Vinogradov, Serguei V.; Singh, Rakesh K.; Vetro, Joseph A.

    2010-01-01

    Polymer-siRNA complexes (siRNA polyplexes) are being actively developed to improve the therapeutic application of siRNA. A major limitation for many siRNA polyplexes, however, is insufficient mRNA suppression. Given that modifying the sense strand of siRNA with 3′ cholesterol (chol-siRNA) increases the activity of free nuclease-resistant siRNA in vitro and in vivo, we hypothesized that complexation of chol-siRNA can increase mRNA suppression by siRNA polyplexes. In this study, the characteristics and siRNA activity of self assembled polyplexes formed with chol-siRNA or unmodified siRNA were compared using three types of conventional, positively charged polymers: (i) biodegradable, cross-linked nanogels (BDNG) (ii) graft copolymers (PEI-PEG), and (iii) linear block copolymers (PLL10-PEG, and PLL50-PEG). Chol-siRNA did not alter complex formation or the resistance of polyplexes to siRNA displacement by heparin but increased nuclease protection by BDNG, PLL10-PEG, and PLL50-PEG polyplexes over polyplexes with unmodified siRNA. Chol-CYPB siRNA increased suppression of native CYPB mRNA in mammary microvascular endothelial cells (MVEC) by BDNG polyplexes (35%) and PLL10-PEG polyplexes (69%) over comparable CYPB siRNA polyplexes but had no effect on PEI-PEG or PLL50-PEG polyplexes. Overall, these results indicate that complexation of chol-siRNA increases nuclease protection and mRNA suppression by select siRNA polyplexes. These results also suggest that polycationic block length is an important factor in increasing mRNA suppression by PLL-PEG chol-siRNA polyplexes in mammary MVEC. PMID:21047680

  10. RAID: a comprehensive resource for human RNA-associated (RNA–RNA/RNA–protein) interaction

    Science.gov (United States)

    Zhang, Xiaomeng; Wu, Deng; Chen, Liqun; Li, Xiang; Yang, Jinxurong; Fan, Dandan; Dong, Tingting; Liu, Mingyue; Tan, Puwen; Xu, Jintian; Yi, Ying; Wang, Yuting; Zou, Hua; Hu, Yongfei; Fan, Kaili; Kang, Juanjuan; Huang, Yan; Miao, Zhengqiang; Bi, Miaoman; Jin, Nana; Li, Kongning; Li, Xia; Xu, Jianzhen; Wang, Dong

    2014-01-01

    Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (http://www.rna-society.org/raid), an RNA-associated (RNA–RNA/RNA–protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA–RNA interactions and 1619 RNA–protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA–RNA/RNA–protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA–RNA/RNA–protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network. PMID:24803509

  11. Equations of motion in phase space

    International Nuclear Information System (INIS)

    Broucke, R.

    1979-01-01

    The article gives a general review of methods of constructing equations of motion of a classical dynamical system. The emphasis is however on the linear Lagrangian in phase space and the corresponding form of Pfaff's equations of motion. A detailed examination of the problem of changes of variables in phase space is first given. It is shown that the Linear Lagrangian theory falls very naturally out of the classical quadratic Lagrangian theory; we do this with the use of the well-known Lagrange multiplier method. Another important result is obtained very naturally as a by-product of this analysis. If the most general set of 2n variables (coordinates in phase space) is used, the coefficients of the equations of motion are the Poisson Brackets of these variables. This is therefore the natural way of introducing not only Poisson Brackets in Dynamics formulations but also the associated Lie Algebras and their important properties and consequences. We give then several examples to illustrate the first-order equations of motion and their simplicity in relation to general changes of variables. The first few examples are elementary (the harmonic Oscillator) while the last one concerns the motion of a rigid body about a fixed point. In the next three sections we treat the first-order equations of motion as derived from a Linear differential form, sometimes called Birkhoff's equations. We insist on the generality of the equations and especially on the unity of the space-time concept: the time t and the coordinates are here completely identical variables, without any privilege to t. We give a brief review of Cartan's 2-form and the corresponding equations of motion. As an illustration the standard equations of aircraft flight in a vertical plane are derived from Cartan's exterior differential 2-form. Finally we mention in the last section the differential forms that were proposed by Gallissot for the derivation of equations of motion

  12. Practices of memorialization and commemoration in public space in Argentina. Artistic interventions about the desappeared and murdered people of the last civic and military dictatorship (1976-1983

    Directory of Open Access Journals (Sweden)

    Melina Jean Jean

    2017-06-01

    Full Text Available In the last years in Argentina, practices of memorialization and commemoration in public space have been adopted multiple forms and strategies. This paper proposes to analyze the artistic interventions about the desappeared and murdered people by State terrorism in the last civic and military dictatorship (1976-1983. This case study is about the artistic productions of murals in public space, made by the “Espacio de Cultura y Memoria El Rancho Urutau” and their proyect “Mosaicos por la Memoria”, performed since 2010 in Ensenada, provincia de Buenos Aires. These murals in ceramic technique and urban scale, privilege a figurative representation for the honored victim. The murals are placed in strategic spaces, in the neighborhood that the victim belonged to. These productions work out as “memory places” because create a social space of “rememoriación” and commemoration from the victims and the recent history developments in the city.

  13. A new look at immune privilege of the eye: dual role for the vision-related molecule retinoic acid.

    Science.gov (United States)

    Zhou, Ru; Horai, Reiko; Mattapallil, Mary J; Caspi, Rachel R

    2011-10-15

    The eye is an immunologically privileged and profoundly immunosuppressive environment. Early studies reported inhibition of T cell proliferation, IFN-γ production, and generation of regulatory T cells (Tregs) by aqueous humor (AH) and identified TGF-β as a critical factor. However, T cell subsets including Foxp3(+) Treg and Th17 were unknown at that time, as was the role of retinoic acid (RA) in Treg induction. Consequently, the effect of the ocular microenvironment on T cell lineage commitment and function, and the role of RA in this process, had not been explored. We now use gene-manipulated mice and highly purified T cell populations to demonstrate that AH suppresses lineage commitment and acquisition of Th1 and Th17 effector function of naive T cells, manifested as reduction of lineage-specific transcription factors and cytokines. Instead, AH promoted its massive conversion to Foxp3(+) Tregs that expressed CD25, GITR, CTLA-4, and CD103 and were functionally suppressive. TGF-β and RA were both needed and synergized for Treg conversion by AH, with TGF-β-enhancing T cell expression of RA receptor α. Newly converted Foxp3(+) Tregs were unstable, but were stabilized upon continued exposure to AH or by the DNA demethylating agent 5-aza-2'-deoxycytidine. In contrast, T cells already committed to effector function were resistant to the suppressive and Treg-inducing effects of AH. We conclude that RA in the eye plays a dual role: in vision and in immune privilege. Nevertheless, primed effector T cells are relatively insensitive to AH, helping to explain their ability to induce uveitis despite an inhibitory ocular microenvironment.

  14. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements

    OpenAIRE

    Huang, Hsi-Yuan; Chien, Chia-Hung; Jen, Kuan-Hua; Huang, Hsien-Da

    2006-01-01

    Numerous regulatory structural motifs have been identified as playing essential roles in transcriptional and post-transcriptional regulation of gene expression. RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (i) motifs in mRNA 5′-untra...

  15. Neural redundancy applied to the parity space for signal validation

    International Nuclear Information System (INIS)

    Mol, Antonio Carlos de Abreu; Pereira, Claudio Marcio Nascimento Abreu; Martinez, Aquilino Senra

    2005-01-01

    The objective of signal validation is to provide more reliable information from the plant sensor data The method presented in this work introduces the concept of neural redundancy and applies it to the space parity method [1] to overcome an inherent deficiency of this method - the determination of the best estimative of the redundant measures when they are inconsistent. The concept of neural redundancy consists on the calculation of a redundancy through neural networks based on the time series of the own state variable. Therefore, neural networks, dynamically trained with the time series, will estimate the current value of the own measure, which will be used as referee of the redundant measures in the parity space. For this purpose the neural network should have the capacity to supply the neural redundancy in real time and with maximum error corresponding to the group deviation. The historical series should be enough to allow the estimate of the next value, during transients and at the same time, it should be optimized to facilitate the retraining of the neural network to each acquisition. In order to have the capacity to reproduce the tendency of the time series even under accident condition, the dynamic training of the neural network privileges the recent points of the time series. The tests accomplished with simulated data of a nuclear plant, demonstrated that this method applied on the parity space method improves the signal validation process. (author)

  16. Neural redundancy applied to the parity space for signal validation

    Energy Technology Data Exchange (ETDEWEB)

    Mol, Antonio Carlos de Abreu; Pereira, Claudio Marcio Nascimento Abreu [Instituto de Engenharia Nuclear (IEN), Rio de Janeiro, RJ (Brazil)]. E-mail: cmnap@ien.gov.br; Martinez, Aquilino Senra [Universidade Federal, Rio de Janeiro, RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia]. E-mail: aquilino@lmp.br

    2005-07-01

    The objective of signal validation is to provide more reliable information from the plant sensor data The method presented in this work introduces the concept of neural redundancy and applies it to the space parity method [1] to overcome an inherent deficiency of this method - the determination of the best estimative of the redundant measures when they are inconsistent. The concept of neural redundancy consists on the calculation of a redundancy through neural networks based on the time series of the own state variable. Therefore, neural networks, dynamically trained with the time series, will estimate the current value of the own measure, which will be used as referee of the redundant measures in the parity space. For this purpose the neural network should have the capacity to supply the neural redundancy in real time and with maximum error corresponding to the group deviation. The historical series should be enough to allow the estimate of the next value, during transients and at the same time, it should be optimized to facilitate the retraining of the neural network to each acquisition. In order to have the capacity to reproduce the tendency of the time series even under accident condition, the dynamic training of the neural network privileges the recent points of the time series. The tests accomplished with simulated data of a nuclear plant, demonstrated that this method applied on the parity space method improves the signal validation process. (author)

  17. Strategies underlying RNA silencing suppression by negative strand RNA viruses

    NARCIS (Netherlands)

    Hemmes, J.C.

    2007-01-01

    The research described in this thesis focused on the strategies of negative strand RNA viruses to counteract antiviral RNA silencing. In plants and insects, RNA silencing has been shown to act as a sequence specific antiviral defence mechanism that is characterised by the processing of double

  18. Diverging affinity of tospovirus RNA silencing suppressor proteins, NSs, for various RNA duplex molecules.

    Science.gov (United States)

    Schnettler, Esther; Hemmes, Hans; Huismann, Rik; Goldbach, Rob; Prins, Marcel; Kormelink, Richard

    2010-11-01

    The tospovirus NSs protein was previously shown to suppress the antiviral RNA silencing mechanism in plants. Here the biochemical analysis of NSs proteins from different tospoviruses, using purified NSs or NSs containing cell extracts, is described. The results showed that all tospoviral NSs proteins analyzed exhibited affinity to small double-stranded RNA molecules, i.e., small interfering RNAs (siRNAs) and micro-RNA (miRNA)/miRNA* duplexes. Interestingly, the NSs proteins from tomato spotted wilt virus (TSWV), impatiens necrotic spot virus (INSV), and groundnut ringspot virus (GRSV) also showed affinity to long double-stranded RNA (dsRNA), whereas tomato yellow ring virus (TYRV) NSs did not. The TSWV NSs protein was shown to be capable of inhibiting Dicer-mediated cleavage of long dsRNA in vitro. In addition, it suppressed the accumulation of green fluorescent protein (GFP)-specific siRNAs during coinfiltration with an inverted-repeat-GFP RNA construct in Nicotiana benthamiana. In vivo interference of TSWV NSs in the miRNA pathway was shown by suppression of an enhanced GFP (eGFP) miRNA sensor construct. The ability to stabilize miRNA/miRNA* by different tospovirus NSs proteins in vivo was demonstrated by increased accumulation and detection of both miRNA171c and miRNA171c* in tospovirus-infected N. benthamiana. All together, these data suggest that tospoviruses interfere in the RNA silencing pathway by sequestering siRNA and miRNA/miRNA* molecules before they are uploaded into their respective RNA-induced silencing complexes. The observed affinity to long dsRNA for only a subset of the tospoviruses studied is discussed in light of evolutional divergence and their ancestral relation to the animal-infecting members of the Bunyaviridae.

  19. Crystallization of leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii

    International Nuclear Information System (INIS)

    Fukunaga, Ryuya; Ishitani, Ryuichiro; Nureki, Osamu; Yokoyama, Shigeyuki

    2004-01-01

    The leucyl-tRNA synthetase (LeuRS) from P. horikoshii has been overexpressed in Escherichia coli and purified, and cocrystallizations with each of the tRNA Leu isoacceptors have been attempted. Cocrystals were obtained by the hanging-drop vapour-diffusion method, but only when the tRNA Leu isoacceptor with the anticodon CAA was used. All five tRNA Leu isoacceptors from the archaeon Pyrococcus horikoshii have been transcribed in vitro and purified. The leucyl-tRNA synthetase (LeuRS) from P. horikoshii was overexpressed in Escherichia coli and purified, and cocrystallizations with each of the tRNA Leu isoacceptors were attempted. Cocrystals were obtained by the hanging-drop vapour-diffusion method, but only when the tRNA Leu isoacceptor with the anticodon CAA was used. Electrophoretic analyses revealed that the crystals contain both LeuRS and tRNA Leu , suggesting that they are LeuRS–tRNA Leu complex crystals. A data set diffracting to 3.3 Å resolution was collected from a single crystal at 100 K. The crystal belongs to the orthorhombic space group P2 1 2 1 2, with unit-cell parameters a = 118.18, b = 120.55, c = 231.13 Å. The asymmetric unit is expected to contain two complexes of LeuRS–tRNA Leu , with a corresponding crystal volume per protein weight of 2.9 Å 3 Da −1 and a solvent content of 57.3%

  20. Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion.

    Science.gov (United States)

    Zhao, Shanrong; Zhang, Ying; Gamini, Ramya; Zhang, Baohong; von Schack, David

    2018-03-19

    To allow efficient transcript/gene detection, highly abundant ribosomal RNAs (rRNA) are generally removed from total RNA either by positive polyA+ selection or by rRNA depletion (negative selection) before sequencing. Comparisons between the two methods have been carried out by various groups, but the assessments have relied largely on non-clinical samples. In this study, we evaluated these two RNA sequencing approaches using human blood and colon tissue samples. Our analyses showed that rRNA depletion captured more unique transcriptome features, whereas polyA+ selection outperformed rRNA depletion with higher exonic coverage and better accuracy of gene quantification. For blood- and colon-derived RNAs, we found that 220% and 50% more reads, respectively, would have to be sequenced to achieve the same level of exonic coverage in the rRNA depletion method compared with the polyA+ selection method. Therefore, in most cases we strongly recommend polyA+ selection over rRNA depletion for gene quantification in clinical RNA sequencing. Our evaluation revealed that a small number of lncRNAs and small RNAs made up a large fraction of the reads in the rRNA depletion RNA sequencing data. Thus, we recommend that these RNAs are specifically depleted to improve the sequencing depth of the remaining RNAs.

  1. Application of Live-Cell RNA Imaging Techniques to the Study of Retroviral RNA Trafficking

    Directory of Open Access Journals (Sweden)

    Darrin V. Bann

    2012-06-01

    Full Text Available Retroviruses produce full-length RNA that serves both as a genomic RNA (gRNA, which is encapsidated into virus particles, and as an mRNA, which directs the synthesis of viral structural proteins. However, we are only beginning to understand the cellular and viral factors that influence trafficking of retroviral RNA and the selection of the RNA for encapsidation or translation. Live cell imaging studies of retroviral RNA trafficking have provided important insight into many aspects of the retrovirus life cycle including transcription dynamics, nuclear export of viral RNA, translational regulation, membrane targeting, and condensation of the gRNA during virion assembly. Here, we review cutting-edge techniques to visualize single RNA molecules in live cells and discuss the application of these systems to studying retroviral RNA trafficking.

  2. RDE-4 preferentially binds long dsRNA and its dimerization is necessary for cleavage of dsRNA to siRNA.

    Science.gov (United States)

    Parker, Greg S; Eckert, Debra M; Bass, Brenda L

    2006-05-01

    In organisms ranging from Arabidopsis to humans, Dicer requires dsRNA-binding proteins (dsRBPs) to carry out its roles in RNA interference (RNAi) and micro-RNA (miRNA) processing. In Caenorhabditis elegans, the dsRBP RDE-4 acts with Dicer during the initiation of RNAi, when long dsRNA is cleaved to small interfering RNAs (siRNAs). RDE-4 is not required in subsequent steps, and how RDE-4 distinguishes between long dsRNA and short siRNA is unclear. We report the first detailed analysis of RDE-4 binding, using purified recombinant RDE-4 and various truncated proteins. We find that, similar to other dsRBPs, RDE-4 is not sequence-specific. However, consistent with its in vivo roles, RDE-4 binds with higher affinity to long dsRNA. We also observe that RDE-4 is a homodimer in solution, and that the C-terminal domain of the protein is required for dimerization. Using extracts from wild-type and rde-4 mutant C. elegans, we show that the C-terminal dimerization domain is required for the production of siRNA. Our findings suggest a model for RDE-4 function during the initiation of RNAi.

  3. Reconstruction and analysis of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in rheumatoid arthritis.

    Science.gov (United States)

    Jiang, Hui; Ma, Rong; Zou, Shubiao; Wang, Yongzhong; Li, Zhuqing; Li, Weiping

    2017-06-01

    Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology, occurring in approximately 1.0% of general population. More and more studies have suggested that long non-coding RNAs (lncRNAs) could play important roles in various biological processes and be associated with the pathogenesis of different kinds of diseases including RA. Although a large number of lncRNAs have been found, our knowledge of their function and physiological/pathological significance is still in its infancy. In order to reveal functional lncRNAs and identify the key lncRNAs in RA, we reconstructed a global triple network based on the competitive endogenous RNA (ceRNA) theory using the data from National Center for Biotechnology Information Gene Expression Omnibus and our previous paper. Meanwhile, Gene Ontology (GO) and pathway analysis were performed using Cytoscape plug-in BinGO and Database for Annotation, Visualization, and Integration Discovery (DAVID), respectively. We found that the lncRNA-miRNA-mRNA network was composed of 7 lncRNA nodes, 90 mRNA nodes, 24 miRNA nodes, and 301 edges. The functional assay showed that 147 GO terms and 23 pathways were enriched. In addition, three lncRNAs (S5645.1, XR_006437.1, J01878) were highly related to RA, and therefore, were selected as key lncRNAs. This study suggests that specific lncRNAs are associated with the development of RA, and three lncRNAs (S5645.1, XR_006437.1, J01878) could be used as potential diagnostic biomarkers and therapeutic targets.

  4. Cap-independent translation mechanism of red clover necrotic mosaic virus RNA2 differs from that of RNA1 and is linked to RNA replication.

    Science.gov (United States)

    Mizumoto, Hiroyuki; Iwakawa, Hiro-Oki; Kaido, Masanori; Mise, Kazuyuki; Okuno, Tetsuro

    2006-04-01

    The genome of Red clover necrotic mosaic virus (RCNMV) in the genus Dianthovirus is divided into two RNA molecules of RNA1 and RNA2, which have no cap structure at the 5' end and no poly(A) tail at the 3' end. The 3' untranslated region (3' UTR) of RCNMV RNA1 contains an essential RNA element (3'TE-DR1), which is required for cap-independent translation. In this study, we investigated a cap-independent translational mechanism of RNA2 using a firefly luciferase (Luc) gene expression assay system in cowpea protoplasts and a cell-free lysate (BYL) prepared from evacuolated tobacco BY2 protoplasts. We were unable to detect cis-acting RNA sequences in RNA2 that can replace the function of a cap structure, such as the 3'TE-DR1 of RNA1. However, the uncapped reporter RNA2, RNA2-Luc, in which the Luc open reading frame (ORF) was inserted between the 5' UTR and the movement protein ORF, was effectively translated in the presence of p27 and p88 in protoplasts in which RNA2-Luc was replicated. Time course experiments in protoplasts showed that the translational activity of RNA2-Luc did not reflect the amount of RNA2. Mutations in cis-acting RNA replication elements of RNA2 abolished the cap-independent translational activity of RNA2-Luc, suggesting that the translational activity of RNA2-Luc is coupled to RNA replication. Our results show that the translational mechanism differs between two segmented genomic RNAs of RCNMV. We present a model in which only RNA2 that is generated de novo through the viral RNA replication machinery functions as mRNA for translation.

  5. Analysis of RNA binding by the dengue virus NS5 RNA capping enzyme.

    Directory of Open Access Journals (Sweden)

    Brittney R Henderson

    Full Text Available Flaviviruses are small, capped positive sense RNA viruses that replicate in the cytoplasm of infected cells. Dengue virus and other related flaviviruses have evolved RNA capping enzymes to form the viral RNA cap structure that protects the viral genome and directs efficient viral polyprotein translation. The N-terminal domain of NS5 possesses the methyltransferase and guanylyltransferase activities necessary for forming mature RNA cap structures. The mechanism for flavivirus guanylyltransferase activity is currently unknown, and how the capping enzyme binds its diphosphorylated RNA substrate is important for deciphering how the flavivirus guanylyltransferase functions. In this report we examine how flavivirus NS5 N-terminal capping enzymes bind to the 5' end of the viral RNA using a fluorescence polarization-based RNA binding assay. We observed that the K(D for RNA binding is approximately 200 nM Dengue, Yellow Fever, and West Nile virus capping enzymes. Removal of one or both of the 5' phosphates reduces binding affinity, indicating that the terminal phosphates contribute significantly to binding. RNA binding affinity is negatively affected by the presence of GTP or ATP and positively affected by S-adensyl methoninine (SAM. Structural superpositioning of the dengue virus capping enzyme with the Vaccinia virus VP39 protein bound to RNA suggests how the flavivirus capping enzyme may bind RNA, and mutagenesis analysis of residues in the putative RNA binding site demonstrate that several basic residues are critical for RNA binding. Several mutants show differential binding to 5' di-, mono-, and un-phosphorylated RNAs. The mode of RNA binding appears similar to that found with other methyltransferase enzymes, and a discussion of diphosphorylated RNA binding is presented.

  6. Benzimidazoles: an ideal privileged drug scaffold for the design of multitargeted anti-inflammatory ligands.

    Science.gov (United States)

    Kaur, Gaganpreet; Kaur, Maninder; Silakari, Om

    2014-01-01

    The recent research area endeavors to discover ultimate multi-target ligands, an increasingly feasible and attractive alternative to existing mono-targeted drugs for treatment of complex, multi-factorial inflammation process which underlays plethora of debilitated health conditions. In order to improvise this option, exploration of relevant chemical core scaffold will be an utmost need. Privileged benzimidazole scaffold being historically versatile structural motif could offer a viable starting point in the search for novel multi-target ligands against multi-factorial inflammation process since, when appropriately substituted, it can selectively modulate diverse receptors, pathways and enzymes associated with the pathogenesis of inflammation. Despite this remarkable capability, the multi-target capacity of the benzimidazole scaffold remains largely unexploited. With this in focus, the present review article attempts to provide synopsis of published research to exemplify the valuable use of benzimidazole nucleus and focus on their suitability as starting scaffold to develop multi-targeted anti-inflammatory ligands.

  7. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

    Science.gov (United States)

    Hajdin, Christine E; Bellaousov, Stanislav; Huggins, Wayne; Leonard, Christopher W; Mathews, David H; Weeks, Kevin M

    2013-04-02

    A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.

  8. Overview of methods in RNA nanotechnology: synthesis, purification, and characterization of RNA nanoparticles.

    Science.gov (United States)

    Haque, Farzin; Guo, Peixuan

    2015-01-01

    RNA nanotechnology encompasses the use of RNA as a construction material to build homogeneous nanostructures by bottom-up self-assembly with defined size, structure, and stoichiometry; this pioneering concept demonstrated in 1998 (Guo et al., Molecular Cell 2:149-155, 1998; featured in Cell) has emerged as a new field that also involves materials engineering and synthetic structural biology (Guo, Nature Nanotechnology 5:833-842, 2010). The field of RNA nanotechnology has skyrocketed over the last few years, as evidenced by the burst of publications in prominent journals on RNA nanostructures and their applications in nanomedicine and nanotechnology. Rapid advances in RNA chemistry, RNA biophysics, and RNA biology have created new opportunities for translating basic science into clinical practice. RNA nanotechnology holds considerable promise in this regard. Increased evidence also suggests that substantial part of the 98.5 % of human genome (Lander et al. Nature 409:860-921, 2001) that used to be called "junk DNA" actually codes for noncoding RNA. As we understand more on how RNA structures are related to function, we can fabricate synthetic RNA nanoparticles for the diagnosis and treatment of diseases. This chapter provides a brief overview of the field regarding the design, construction, purification, and characterization of RNA nanoparticles for diverse applications in nanotechnology and nanomedicince.

  9. mRNA expression profile in DLD-1 and MOLT-4 cancer cell lines cultured under Microgravity

    Data.gov (United States)

    National Aeronautics and Space Administration — DLD-1 and MOLT-4 cell lines were cultured in a Rotating cell culture system to simulate microgravity and mRNA expression profile was observed in comparison to Static...

  10. Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl-tRNA synthetase enzymes.

    Science.gov (United States)

    Armen, Roger S; Schiller, Stefan M; Brooks, Charles L

    2010-06-01

    Orthogonal aminoacyl-tRNA synthetase/tRNA pairs from archaea have been evolved to facilitate site specific in vivo incorporation of unnatural amino acids into proteins in Escherichia coli. Using this approach, unnatural amino acids have been successfully incorporated with high translational efficiency and fidelity. In this study, CHARMM-based molecular docking and free energy calculations were used to evaluate rational design of specific protein-ligand interactions for aminoacyl-tRNA synthetases. A series of novel unnatural amino acid ligands were docked into the p-benzoyl-L-phenylalanine tRNA synthetase, which revealed that the binding pocket of the enzyme does not provide sufficient space for significantly larger ligands. Specific binding site residues were mutated to alanine to create additional space to accommodate larger target ligands, and then mutations were introduced to improve binding free energy. This approach was used to redesign binding sites for several different target ligands, which were then tested against the standard 20 amino acids to verify target specificity. Only the synthetase designed to bind Man-alpha-O-Tyr was predicted to be sufficiently selective for the target ligand and also thermodynamically stable. Our study suggests that extensive redesign of the tRNA synthatase binding pocket for large bulky ligands may be quite thermodynamically unfavorable.

  11. Access control and privilege management in electronic health record: a systematic literature review.

    Science.gov (United States)

    Jayabalan, Manoj; O'Daniel, Thomas

    2016-12-01

    This study presents a systematic literature review of access control for electronic health record systems to protect patient's privacy. Articles from 2006 to 2016 were extracted from the ACM Digital Library, IEEE Xplore Digital Library, Science Direct, MEDLINE, and MetaPress using broad eligibility criteria, and chosen for inclusion based on analysis of ISO22600. Cryptographic standards and methods were left outside the scope of this review. Three broad classes of models are being actively investigated and developed: access control for electronic health records, access control for interoperability, and access control for risk analysis. Traditional role-based access control models are extended with spatial, temporal, probabilistic, dynamic, and semantic aspects to capture contextual information and provide granular access control. Maintenance of audit trails and facilities for overriding normal roles to allow full access in emergency cases are common features. Access privilege frameworks utilizing ontology-based knowledge representation for defining the rules have attracted considerable interest, due to the higher level of abstraction that makes it possible to model domain knowledge and validate access requests efficiently.

  12. Explaining and inducing savant skills: privileged access to lower level, less-processed information

    Science.gov (United States)

    Snyder, Allan

    2009-01-01

    I argue that savant skills are latent in us all. My hypothesis is that savants have privileged access to lower level, less-processed information, before it is packaged into holistic concepts and meaningful labels. Owing to a failure in top-down inhibition, they can tap into information that exists in all of our brains, but is normally beyond conscious awareness. This suggests why savant skills might arise spontaneously in otherwise normal people, and why such skills might be artificially induced by low-frequency repetitive transcranial magnetic stimulation. It also suggests why autistic savants are atypically literal with a tendency to concentrate more on the parts than on the whole and why this offers advantages for particular classes of problem solving, such as those that necessitate breaking cognitive mindsets. A strategy of building from the parts to the whole could form the basis for the so-called autistic genius. Unlike the healthy mind, which has inbuilt expectations of the world (internal order), the autistic mind must simplify the world by adopting strict routines (external order). PMID:19528023

  13. The ViennaRNA web services.

    Science.gov (United States)

    Gruber, Andreas R; Bernhart, Stephan H; Lorenz, Ronny

    2015-01-01

    The ViennaRNA package is a widely used collection of programs for thermodynamic RNA secondary structure prediction. Over the years, many additional tools have been developed building on the core programs of the package to also address issues related to noncoding RNA detection, RNA folding kinetics, or efficient sequence design considering RNA-RNA hybridizations. The ViennaRNA web services provide easy and user-friendly web access to these tools. This chapter describes how to use this online platform to perform tasks such as prediction of minimum free energy structures, prediction of RNA-RNA hybrids, or noncoding RNA detection. The ViennaRNA web services can be used free of charge and can be accessed via http://rna.tbi.univie.ac.at.

  14. RNA-SeQC: RNA-seq metrics for quality control and process optimization.

    Science.gov (United States)

    DeLuca, David S; Levin, Joshua Z; Sivachenko, Andrey; Fennell, Timothy; Nazaire, Marc-Danie; Williams, Chris; Reich, Michael; Winckler, Wendy; Getz, Gad

    2012-06-01

    RNA-seq, the application of next-generation sequencing to RNA, provides transcriptome-wide characterization of cellular activity. Assessment of sequencing performance and library quality is critical to the interpretation of RNA-seq data, yet few tools exist to address this issue. We introduce RNA-SeQC, a program which provides key measures of data quality. These metrics include yield, alignment and duplication rates; GC bias, rRNA content, regions of alignment (exon, intron and intragenic), continuity of coverage, 3'/5' bias and count of detectable transcripts, among others. The software provides multi-sample evaluation of library construction protocols, input materials and other experimental parameters. The modularity of the software enables pipeline integration and the routine monitoring of key measures of data quality such as the number of alignable reads, duplication rates and rRNA contamination. RNA-SeQC allows investigators to make informed decisions about sample inclusion in downstream analysis. In summary, RNA-SeQC provides quality control measures critical to experiment design, process optimization and downstream computational analysis. See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.

  15. 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.

  16. Crystallization and preliminary X-ray diffraction analysis of the CRISPR-Cas RNA-silencing Cmr complex.

    Science.gov (United States)

    Osawa, Takuo; Inanaga, Hideko; Numata, Tomoyuki

    2015-06-01

    Clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNA (crRNA) and CRISPR-associated (Cas) proteins constitute a prokaryotic adaptive immune system (CRISPR-Cas system) that targets and degrades invading genetic elements. The type III-B CRISPR-Cas Cmr complex, composed of the six Cas proteins (Cmr1-Cmr6) and a crRNA, captures and cleaves RNA complementary to the crRNA guide sequence. Here, a Cmr1-deficient functional Cmr (CmrΔ1) complex composed of Pyrococcus furiosus Cmr2-Cmr3, Archaeoglobus fulgidus Cmr4-Cmr5-Cmr6 and the 39-mer P. furiosus 7.01-crRNA was prepared. The CmrΔ1 complex was cocrystallized with single-stranded DNA (ssDNA) complementary to the crRNA guide by the vapour-diffusion method. The crystals diffracted to 2.1 Å resolution using synchrotron radiation at the Photon Factory. The crystals belonged to the triclinic space group P1, with unit-cell parameters a = 75.5, b = 76.2, c = 139.2 Å, α = 90.3, β = 104.8, γ = 118.6°. The asymmetric unit of the crystals is expected to contain one CmrΔ1-ssDNA complex, with a Matthews coefficient of 2.03 Å(3) Da(-1) and a solvent content of 39.5%.

  17. Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins

    Science.gov (United States)

    de Beauchene, Isaure Chauvot; de Vries, Sjoerd J.; Zacharias, Martin

    2016-01-01

    Abstract Protein-RNA complexes are important for many biological processes. However, structural modeling of such complexes is hampered by the high flexibility of RNA. Particularly challenging is the docking of single-stranded RNA (ssRNA). We have developed a fragment-based approach to model the structure of ssRNA bound to a protein, based on only the protein structure, the RNA sequence and conserved contacts. The conformational diversity of each RNA fragment is sampled by an exhaustive library of trinucleotides extracted from all known experimental protein–RNA complexes. The method was applied to ssRNA with up to 12 nucleotides which bind to dimers of the RNA recognition motifs (RRMs), a highly abundant eukaryotic RNA-binding domain. The fragment based docking allows a precise de novo atomic modeling of protein-bound ssRNA chains. On a benchmark of seven experimental ssRNA–RRM complexes, near-native models (with a mean heavy-atom deviation of <3 Å from experiment) were generated for six out of seven bound RNA chains, and even more precise models (deviation < 2 Å) were obtained for five out of seven cases, a significant improvement compared to the state of the art. The method is not restricted to RRMs but was also successfully applied to Pumilio RNA binding proteins. PMID:27131381

  18. Deep Sequencing Insights in Therapeutic shRNA Processing and siRNA Target Cleavage Precision.

    Science.gov (United States)

    Denise, Hubert; Moschos, Sterghios A; Sidders, Benjamin; Burden, Frances; Perkins, Hannah; Carter, Nikki; Stroud, Tim; Kennedy, Michael; Fancy, Sally-Ann; Lapthorn, Cris; Lavender, Helen; Kinloch, Ross; Suhy, David; Corbau, Romu

    2014-02-04

    TT-034 (PF-05095808) is a recombinant adeno-associated virus serotype 8 (AAV8) agent expressing three short hairpin RNA (shRNA) pro-drugs that target the hepatitis C virus (HCV) RNA genome. The cytosolic enzyme Dicer cleaves each shRNA into multiple, potentially active small interfering RNA (siRNA) drugs. Using next-generation sequencing (NGS) to identify and characterize active shRNAs maturation products, we observed that each TT-034-encoded shRNA could be processed into as many as 95 separate siRNA strands. Few of these appeared active as determined by Sanger 5' RNA Ligase-Mediated Rapid Amplification of cDNA Ends (5-RACE) and through synthetic shRNA and siRNA analogue studies. Moreover, NGS scrutiny applied on 5-RACE products (RACE-seq) suggested that synthetic siRNAs could direct cleavage in not one, but up to five separate positions on targeted RNA, in a sequence-dependent manner. These data support an on-target mechanism of action for TT-034 without cytotoxicity and question the accepted precision of substrate processing by the key RNA interference (RNAi) enzymes Dicer and siRNA-induced silencing complex (siRISC).Molecular Therapy-Nucleic Acids (2014) 3, e145; doi:10.1038/mtna.2013.73; published online 4 February 2014.

  19. Lowering the quantification limit of the QubitTM RNA HS assay using RNA spike-in.

    Science.gov (United States)

    Li, Xin; Ben-Dov, Iddo Z; Mauro, Maurizio; Williams, Zev

    2015-05-06

    RNA quantification is often a prerequisite for most RNA analyses such as RNA sequencing. However, the relatively low sensitivity and large sample consumption of traditional RNA quantification methods such as UV spectrophotometry and even the much more sensitive fluorescence-based RNA quantification assays, such as the Qubit™ RNA HS Assay, are often inadequate for measuring minute levels of RNA isolated from limited cell and tissue samples and biofluids. Thus, there is a pressing need for a more sensitive method to reliably and robustly detect trace levels of RNA without interference from DNA. To improve the quantification limit of the Qubit™ RNA HS Assay, we spiked-in a known quantity of RNA to achieve the minimum reading required by the assay. Samples containing trace amounts of RNA were then added to the spike-in and measured as a reading increase over RNA spike-in baseline. We determined the accuracy and precision of reading increases between 1 and 20 pg/μL as well as RNA-specificity in this range, and compared to those of RiboGreen(®), another sensitive fluorescence-based RNA quantification assay. We then applied Qubit™ Assay with RNA spike-in to quantify plasma RNA samples. RNA spike-in improved the quantification limit of the Qubit™ RNA HS Assay 5-fold, from 25 pg/μL down to 5 pg/μL while maintaining high specificity to RNA. This enabled quantification of RNA with original concentration as low as 55.6 pg/μL compared to 250 pg/μL for the standard assay and decreased sample consumption from 5 to 1 ng. Plasma RNA samples that were not measurable by the Qubit™ RNA HS Assay were measurable by our modified method. The Qubit™ RNA HS Assay with RNA spike-in is able to quantify RNA with high specificity at 5-fold lower concentration and uses 5-fold less sample quantity than the standard Qubit™ Assay.

  20. The early history of tRNA recognition by aminoacyl-tRNA synthetases

    Indian Academy of Sciences (India)

    Madhu

    2006-10-04

    Oct 4, 2006 ... Discovery of aminoacyl-tRNA synthetases and importance ... The pioneering work of Fritz Lipmann on the high-energy ... the peculiar structural and functional relationships tRNAs ... a bulk of only 20 families of tRNA molecules in contrast ...... balance of tRNA and aminoacyl-tRNA synthetase; Science 242.

  1. Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage

    Science.gov (United States)

    Hao, Chenhui; Li, Xiang; Tian, Cheng; Jiang, Wen; Wang, Guansong; Mao, Chengde

    2014-05-01

    RNA nanotechnology promises rational design of RNA nanostructures with wide array of structural diversities and functionalities. Such nanostructures could be used in applications such as small interfering RNA delivery and organization of in vivo chemical reactions. Though having impressive development in recent years, RNA nanotechnology is still quite limited and its programmability and complexity could not rival the degree of its closely related cousin: DNA nanotechnology. Novel strategies are needed for programmed RNA self-assembly. Here, we have assembled RNA nanocages by re-engineering a natural, biological RNA motif: the packaging RNA of phi29 bacteriophage. The resulting RNA nanostructures have been thoroughly characterized by gel electrophoresis, cryogenic electron microscopy imaging and dynamic light scattering.

  2. Site-Specific Covalent Conjugation of Modified mRNA by tRNA Guanine Transglycosylase.

    Science.gov (United States)

    Ehret, Fabian; Zhou, Cun Yu; Alexander, Seth C; Zhang, Dongyang; Devaraj, Neal K

    2018-03-05

    Modified mRNA (mod-mRNA) has recently been widely studied as the form of RNA useful for therapeutic applications due to its high stability and lowered immune response. Herein, we extend the scope of the recently established RNA-TAG (transglycosylation at guanosine) methodology, a novel approach for genetically encoded site-specific labeling of large mRNA transcripts, by employing mod-mRNA as substrate. As a proof of concept, we covalently attached a fluorescent probe to mCherry encoding mod-mRNA transcripts bearing 5-methylcytidine and/or pseudouridine substitutions with high labeling efficiencies. To provide a versatile labeling methodology with a wide range of possible applications, we employed a two-step strategy for functionalization of the mod-mRNA to highlight the therapeutic potential of this new methodology. We envision that this novel and facile labeling methodology of mod-RNA will have great potential in decorating both coding and noncoding therapeutic RNAs with a variety of diagnostic and functional moieties.

  3. A path-based measurement for human miRNA functional similarities using miRNA-disease associations

    Science.gov (United States)

    Ding, Pingjian; Luo, Jiawei; Xiao, Qiu; Chen, Xiangtao

    2016-09-01

    Compared with the sequence and expression similarity, miRNA functional similarity is so important for biology researches and many applications such as miRNA clustering, miRNA function prediction, miRNA synergism identification and disease miRNA prioritization. However, the existing methods always utilized the predicted miRNA target which has high false positive and false negative to calculate the miRNA functional similarity. Meanwhile, it is difficult to achieve high reliability of miRNA functional similarity with miRNA-disease associations. Therefore, it is increasingly needed to improve the measurement of miRNA functional similarity. In this study, we develop a novel path-based calculation method of miRNA functional similarity based on miRNA-disease associations, called MFSP. Compared with other methods, our method obtains higher average functional similarity of intra-family and intra-cluster selected groups. Meanwhile, the lower average functional similarity of inter-family and inter-cluster miRNA pair is obtained. In addition, the smaller p-value is achieved, while applying Wilcoxon rank-sum test and Kruskal-Wallis test to different miRNA groups. The relationship between miRNA functional similarity and other information sources is exhibited. Furthermore, the constructed miRNA functional network based on MFSP is a scale-free and small-world network. Moreover, the higher AUC for miRNA-disease prediction indicates the ability of MFSP uncovering miRNA functional similarity.

  4. A ribonuclease coordinates siRNA amplification and mRNA cleavage during RNAi.

    Science.gov (United States)

    Tsai, Hsin-Yue; Chen, Chun-Chieh G; Conte, Darryl; Moresco, James J; Chaves, Daniel A; Mitani, Shohei; Yates, John R; Tsai, Ming-Daw; Mello, Craig C

    2015-01-29

    Effective silencing by RNA-interference (RNAi) depends on mechanisms that amplify and propagate the silencing signal. In some organisms, small-interfering RNAs (siRNAs) are amplified from target mRNAs by RNA-dependent RNA polymerase (RdRP). Both RdRP recruitment and mRNA silencing require Argonaute proteins, which are generally thought to degrade RNAi targets by directly cleaving them. However, in C. elegans, the enzymatic activity of the primary Argonaute, RDE-1, is not required for silencing activity. We show that RDE-1 can instead recruit an endoribonuclease, RDE-8, to target RNA. RDE-8 can cleave RNA in vitro and is needed for the production of 3' uridylated fragments of target mRNA in vivo. We also find that RDE-8 promotes RdRP activity, thereby ensuring amplification of siRNAs. Together, our findings suggest a model in which RDE-8 cleaves target mRNAs to mediate silencing, while generating 3' uridylated mRNA fragments to serve as templates for the RdRP-directed amplification of the silencing signal. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Improving forensic mental health care to Indigenous Australians: theorizing the intercultural space.

    Science.gov (United States)

    Durey, A; Wynaden, D; O'Kane, M

    2014-05-01

    This paper uses the 'intercultural space' as an educational strategy to prepare nurses to work respectfully with Indigenous patients in a forensic mental health context; offers an educational approach that introduces nurses to Indigenous knowledge, beliefs and values, examines power relations in colonized countries between the dominant white cultural group and the Indigenous population and encourages nurses to critically reflect on their health care practice; and explores the intercultural space as a shared space between cultures fostering open and robust inquiry where neither culture dominates and new positions, representations and understandings can emerge. Given the disproportionately high number of Indigenous people imprisoned in colonized countries, this paper responds to research from Western Australia on the need to prepare forensic mental health nurses to deliver care to Indigenous patients with mental health disorders. The paper highlights the nexus between theory, research and education that can inform the design and implementation of programmes to help nurses navigate the complex, layered and contested 'intercultural space' and deliver culturally safe care to Indigenous patients. Nurses are encouraged to critically reflect on how beliefs and values underpinning their cultural positioning impact on health care to Indigenous patients. The paper draws on intercultural theory to offer a pedagogical framework that acknowledges the negative impacts of colonization on Indigenous health and well-being, repositions and revalues Indigenous cultures and knowledges and fosters open and robust inquiry. This approach is seen as a step towards working more effectively in the intercultural space where ultimately binary oppositions that privilege one culture over another and inhibit robust inquiry are avoided, paving the way for new, more inclusive positions, representations and understandings to emerge. While the intercultural space can be a place of struggle, tension

  6. RNase-assisted RNA chromatography

    Science.gov (United States)

    Michlewski, Gracjan; Cáceres, Javier F.

    2010-01-01

    RNA chromatography combined with mass spectrometry represents a widely used experimental approach to identify RNA-binding proteins that recognize specific RNA targets. An important drawback of most of these protocols is the high background due to direct or indirect nonspecific binding of cellular proteins to the beads. In many cases this can hamper the detection of individual proteins due to their low levels and/or comigration with contaminating proteins. Increasing the salt concentration during washing steps can reduce background, but at the cost of using less physiological salt concentrations and the likely loss of important RNA-binding proteins that are less stringently bound to a given RNA, as well as the disassembly of protein or ribonucleoprotein complexes. Here, we describe an improved RNA chromatography method that relies on the use of a cocktail of RNases in the elution step. This results in the release of proteins specifically associated with the RNA ligand and almost complete elimination of background noise, allowing a more sensitive and thorough detection of RNA-binding proteins recognizing a specific RNA transcript. PMID:20571124

  7. 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

  8. The effect of dys-1 mutation on miRNA expression profile in Caenorhabditis elegans during Shenzhou-8 mission

    Science.gov (United States)

    Xu, Dan; Sun, Yeqing; Gao, Ying; Xing, Yanfang

    microRNAs (miRNAs) is reported to be sensitive to radiation exposure and altered gravity, involved in a variety of biological processes through negative regulation of gene expression. Dystrophin-like dys-1 gene is expressed and required in muscle tissue, which plays a vital role in mechanical transduction when gravity varies. In the present study, we investigated the effect of dys-1 mutation on miRNA expression profile in Caenorhabditis elegans (C. elegans) under space radiation associated with microgravity (R+M) and radiation alone (R) environment during Shenzhou-8 mission. We performed miRNA microarray analysis in dys-1 mutant and wide-type (WT) of dauer larvae and found that 27 miRNAs changed in abundance after spaceflight. Compared with WT, there was different miRNA expression pattern in different treatments in dys-1 mutant. Cel-miR-796 and miR-124 were reversely expressed under R+M and R environment in WT and dys-1 mutant, respectively, indicating they might be affected by microgravity. Mutation of dys-1 remarkably reduced the number of altered miRNAs under space environment, resulting in the decrease of genes in biological categories of “body morphogenesis”, “behavior”, “cell adhesion” and so on. Particularly, we found that those genes controlling regulation of locomotion in WT were lost in dys-1 mutant, while genes in positive regulation of developmental process only existed in dys-1 mutant. miR-796 was predicted to target genes ace-1 and dyc-1 that are functionally linked to dys-1. Integration analysis of miRNA and mRNA expression profile revealed that miR-56 and miR-124 were involved in behavior and locomotion by regulating different target genes under space environment, among which nep-11, deb-1, C07H4.1 and F11H8.2 might be associated with neuromuscular system. Our findings suggest that dys-1 could cause alteration of miRNAs and target genes, involved in regulating the response of C. elegans to space microgravity in neuromuscular system. This

  9. RNA modifications by oxidation

    DEFF Research Database (Denmark)

    Poulsen, Henrik E; Specht, Elisabeth; Broedbaek, Kasper

    2012-01-01

    to encompass various classes of novel regulatory RNAs, including, e.g., microRNAs. It is well known that DNA is constantly oxidized and repaired by complex genome maintenance mechanisms. Analogously, RNA also undergoes significant oxidation, and there are now convincing data suggesting that oxidation......The past decade has provided exciting insights into a novel class of central (small) RNA molecules intimately involved in gene regulation. Only a small percentage of our DNA is translated into proteins by mRNA, yet 80% or more of the DNA is transcribed into RNA, and this RNA has been found......, and the consequent loss of integrity of RNA, is a mechanism for disease development. Oxidized RNA is found in a large variety of diseases, and interest has been especially devoted to degenerative brain diseases such as Alzheimer disease, in which up to 50-70% of specific mRNA molecules are reported oxidized, whereas...

  10. Lysosomal putative RNA transporter SIDT2 mediates direct uptake of RNA by lysosomes.

    Science.gov (United States)

    Aizawa, Shu; Fujiwara, Yuuki; Contu, Viorica Raluca; Hase, Katsunori; Takahashi, Masayuki; Kikuchi, Hisae; Kabuta, Chihana; Wada, Keiji; Kabuta, Tomohiro

    2016-01-01

    Lysosomes are thought to be the major intracellular compartment for the degradation of macromolecules. We recently identified a novel type of autophagy, RNautophagy, where RNA is directly taken up by lysosomes in an ATP-dependent manner and degraded. However, the mechanism of RNA translocation across the lysosomal membrane and the physiological role of RNautophagy remain unclear. In the present study, we performed gain- and loss-of-function studies with isolated lysosomes, and found that SIDT2 (SID1 transmembrane family, member 2), an ortholog of the Caenorhabditis elegans putative RNA transporter SID-1 (systemic RNA interference deficient-1), mediates RNA translocation during RNautophagy. We also observed that SIDT2 is a transmembrane protein, which predominantly localizes to lysosomes. Strikingly, knockdown of Sidt2 inhibited up to ˜50% of total RNA degradation at the cellular level, independently of macroautophagy. Moreover, we showed that this impairment is mainly due to inhibition of lysosomal RNA degradation, strongly suggesting that RNautophagy plays a significant role in constitutive cellular RNA degradation. Our results provide a novel insight into the mechanisms of RNA metabolism, intracellular RNA transport, and atypical types of autophagy.

  11. 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

  12. Patterns of privilege: A total cohort analysis of admission and academic outcomes for M?ori, Pacific and non-M?ori non-Pacific health professional students

    OpenAIRE

    Wikaire, Erena; Curtis, Elana; Cormack, Donna; Jiang, Yannan; McMillan, Louise; Loto, Rob; Reid, Papaarangi

    2016-01-01

    Background Tertiary institutions are struggling to ensure equitable academic outcomes for indigenous and ethnic minority students in health professional study. This demonstrates disadvantaging of ethnic minority student groups (whereby Indigenous and ethnic minority students consistently achieve academic outcomes at a lower level when compared to non-ethnic minority students) whilst privileging non-ethnic minority students and has important implications for health workforce and health equity ...

  13. [Satellite RNA (RNA3) of tomato black ring virus is found with one of the 2 major RNAs (RNA2) in a new capsid nucleoprotein].

    Science.gov (United States)

    Doz, B; Dunez, J; Bove, J M

    1977-12-19

    Tomato Black Ring Virus (TBRV) like other NEPOviruses posseses two nucleoproteins M and B and two major RNAs, RNA1 and RNA2 respectively distributed in B and M. A new nucleoprotein has just been discovered and comprises one molecule of RNA2 associated with one molecule of RNA3. RNA3 is a small RNA of molecular weight 500,000 d considered to be a satellite RNA. Its level appears to depend on the infection stage, local or systemic. RNA3 is able to modify the relative proportions of nucleoproteins M and B and their respective RNAs. The satellite RNA, might be part of the genome and represent a monocistronic mRNA for protein capsid synthesis. However it seems perhaps more tempting to correlate TBRV-RNA3 with satellite RNA5 of certain strains of Cucumber mosaic virus.

  14. Working with RNA

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

    Working with RNA is not a special discipline in molecular biology. However, RNA is chemically and structurally different from DNA and a few simple work rules have to be implemented to maintain the integrity of the RNA. Alkaline pH, high temperatures, and heavy metal ions should be avoided when po...

  15. Selective small-molecule inhibition of an RNA structural element

    Energy Technology Data Exchange (ETDEWEB)

    Howe, John A.; Wang, Hao; Fischmann, Thierry O.; Balibar, Carl J.; Xiao, Li; Galgoci, Andrew M.; Malinverni, Juliana C.; Mayhood, Todd; Villafania, Artjohn; Nahvi, Ali; Murgolo, Nicholas; Barbieri, Christopher M.; Mann, Paul A.; Carr, Donna; Xia, Ellen; Zuck, Paul; Riley, Dan; Painter, Ronald E.; Walker, Scott S.; Sherborne, Brad; de Jesus, Reynalda; Pan, Weidong; Plotkin, Michael A.; Wu, Jin; Rindgen, Diane; Cummings, John; Garlisi, Charles G.; Zhang, Rumin; Sheth, Payal R.; Gill, Charles J.; Tang, Haifeng; Roemer , Terry (Merck)

    2015-09-30

    Riboswitches are non-coding RNA structures located in messenger RNAs that bind endogenous ligands, such as a specific metabolite or ion, to regulate gene expression. As such, riboswitches serve as a novel, yet largely unexploited, class of emerging drug targets. Demonstrating this potential, however, has proven difficult and is restricted to structurally similar antimetabolites and semi-synthetic analogues of their cognate ligand, thus greatly restricting the chemical space and selectivity sought for such inhibitors. Here we report the discovery and characterization of ribocil, a highly selective chemical modulator of bacterial riboflavin riboswitches, which was identified in a phenotypic screen and acts as a structurally distinct synthetic mimic of the natural ligand, flavin mononucleotide, to repress riboswitch-mediated ribB gene expression and inhibit bacterial cell growth. Our findings indicate that non-coding RNA structural elements may be more broadly targeted by synthetic small molecules than previously expected.

  16. Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data.

    Science.gov (United States)

    Zhao, Zheng; Bai, Jing; Wu, Aiwei; Wang, Yuan; Zhang, Jinwen; Wang, Zishan; Li, Yongsheng; Xu, Juan; Li, Xia

    2015-01-01

    Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions. To facilitate such an effort, we have developed Co-LncRNA, which is a web-based computational tool that allows users to identify GO annotations and KEGG pathways that may be affected by co-expressed protein-coding genes of a single or multiple lncRNAs. LncRNA co-expressed protein-coding genes were first identified in publicly available human RNA-Seq datasets, including 241 datasets across 6560 total individuals representing 28 tissue types/cell lines. Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis. In addition, this software provides a graphical overview of pathways that are modulated by lncRNAs, as well as a specific tool to display the relevant networks between lncRNAs and their co-expressed protein-coding genes. Co-LncRNA also supports users in uploading their own lncRNA and protein-coding gene expression profiles to investigate the lncRNA combinatorial effects. It will be continuously updated with more human RNA-Seq datasets on an annual basis. Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community. Database URL: http://www.bio-bigdata.com/Co-LncRNA/. © The Author(s) 2015. Published by Oxford University Press.

  17. Steric restrictions of RISC in RNA interference identified with size-expanded RNA nucleobases.

    Science.gov (United States)

    Hernández, Armando R; Peterson, Larryn W; Kool, Eric T

    2012-08-17

    Understanding the interactions between small interfering RNAs (siRNAs) and the RNA-induced silencing complex (RISC), the key protein complex of RNA interference (RNAi), is of great importance to the development of siRNAs with improved biological and potentially therapeutic function. Although various chemically modified siRNAs have been reported, relatively few studies with modified nucleobases exist. Here we describe the synthesis and hybridization properties of siRNAs bearing size-expanded RNA (xRNA) nucleobases and their use as a novel and systematic set of steric probes in RNAi. xRNA nucleobases are expanded by 2.4 Å using benzo-homologation and retain canonical Watson-Crick base-pairing groups. Our data show that the modified siRNA duplexes display small changes in melting temperature (+1.4 to -5.0 °C); substitutions near the center are somewhat destabilizing to the RNA duplex, while substitutions near the ends are stabilizing. RNAi studies in a dual-reporter luciferase assay in HeLa cells revealed that xRNA nucleobases in the antisense strand reduce activity at some central positions near the seed region but are generally well tolerated near the ends. Most importantly, we observed that xRNA substitutions near the 3'-end increased activity over that of wild-type siRNAs. The data are analyzed in terms of site-dependent steric effects in RISC. Circular dichroism experiments show that single xRNA substitutions do not significantly distort the native A-form helical structure of the siRNA duplex, and serum stability studies demonstrated that xRNA substitutions protect siRNAs against nuclease degradation.

  18. mRNA/microRNA gene expression profile in microsatellite unstable colorectal cancer

    Directory of Open Access Journals (Sweden)

    Calin George A

    2007-08-01

    Full Text Available Abstract Background Colorectal cancer develops through two main genetic instability pathways characterized by distinct pathologic features and clinical outcome. Results We investigated colon cancer samples (23 characterized by microsatellite stability, MSS, and 16 by high microsatellite instability, MSI-H for genome-wide expression of microRNA (miRNA and mRNA. Based on combined miRNA and mRNA gene expression, a molecular signature consisting of twenty seven differentially expressed genes, inclusive of 8 miRNAs, could correctly distinguish MSI-H versus MSS colon cancer samples. Among the differentially expressed miRNAs, various members of the oncogenic miR-17-92 family were significantly up-regulated in MSS cancers. The majority of protein coding genes were also up-regulated in MSS cancers. Their functional classification revealed that they were most frequently associated with cell cycle, DNA replication, recombination, repair, gastrointestinal disease and immune response. Conclusion This is the first report that indicates the existence of differences in miRNA expression between MSS versus MSI-H colorectal cancers. In addition, the work suggests that the combination of mRNA/miRNA expression signatures may represent a general approach for improving bio-molecular classification of human cancer.

  19. Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processing.

    Science.gov (United States)

    Goldfarb, Katherine C; Cech, Thomas R

    2017-01-01

    MRP RNA is an abundant, essential noncoding RNA whose functions have been proposed in yeast but are incompletely understood in humans. Mutations in the genomic locus for MRP RNA cause pleiotropic human diseases, including cartilage hair hypoplasia (CHH). Here we applied CRISPR-Cas9 genome editing to disrupt the endogenous human MRP RNA locus, thereby attaining what has eluded RNAi and RNase H experiments: elimination of MRP RNA in the majority of cells. The resulting accumulation of ribosomal RNA (rRNA) precursor-analyzed by RNA fluorescent in situ hybridization (FISH), Northern blots, and RNA sequencing-implicates MRP RNA in pre-rRNA processing. Amelioration of pre-rRNA imbalance is achieved through rescue of MRP RNA levels by ectopic expression. Furthermore, affinity-purified MRP ribonucleoprotein (RNP) from HeLa cells cleaves the human pre-rRNA in vitro at at least one site used in cells, while RNP isolated from cells with CRISPR-edited MRP loci loses this activity, and ectopic MRP RNA expression restores cleavage activity. Thus, a role for RNase MRP in human pre-rRNA processing is established. As demonstrated here, targeted CRISPR disruption is a valuable tool for functional studies of essential noncoding RNAs that are resistant to RNAi and RNase H-based degradation. © 2017 Goldfarb and Cech; Published by Cold Spring Harbor Laboratory Press.

  20. Mutational analysis of Sep-tRNA:Cys-tRNA synthase reveals critical residues for tRNA-dependent cysteine formation.

    Science.gov (United States)

    Helgadóttir, Sunna; Sinapah, Sylvie; Söll, Dieter; Ling, Jiqiang

    2012-01-02

    In methanogenic archaea, Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep-tRNA(Cys) to Cys-tRNA(Cys). The mechanism of tRNA-dependent cysteine formation remains unclear due to the lack of functional studies. In this work, we mutated 19 conserved residues in Methanocaldococcus jannaschii SepCysS, and employed an in vivo system to determine the activity of the resulting variants. Our results show that three active-site cysteines (Cys39, Cys42 and Cys247) are essential for SepCysS activity. In addition, combined with structural modeling, our mutational and functional analyses also reveal multiple residues that are important for the binding of PLP, Sep and tRNA. Our work thus represents the first systematic functional analysis of conserved residues in archaeal SepCysSs, providing insights into the catalytic and substrate binding mechanisms of this poorly characterized enzyme. Copyright © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  1. Circular RNA (circRNA) was an important bridge in the switch from the RNA world to the DNA world.

    Science.gov (United States)

    Soslau, Gerald

    2018-06-14

    The concept that life on Earth began as an RNA world has been built upon extensive experimentation demonstrating that many of the building blocks required for living cells could be synthesized in the laboratory under conditions approximating our primordial world. Many of the building blocks for life have also been found in meteorites indicating that meteors may have been a source for these molecules, or more likely, that they represent the chemical library present in most/all bodies in the universe after the big bang. Perhaps the most important support for the concept comes from the fact that some RNA species possess catalytic activity, ribozymes, and that RNA could be reverse transcribe to DNA. The thrust of numerous papers on this topic has been to explore how the available molecules on Earth, at its birth, gave rise to life as we know it today. This paper focuses more on a reverse view of the topic. The "how" molecular building blocks were synthesized is not addressed nor how the "first" RNA molecules were synthesized. We can clearly speculate on the variable environmental conditions and chemistry available on Earth billions of years ago. However, we can never truly replicate the changing conditions or know the chemical composition of Earth at the beginning of time. We can, however, confirm that over millions, perhaps billions of years the basic building blocks for life accumulated sufficiently to initiate evolution to an RNA world followed by our RNA/DNA world. Here we are attempting to take the information from our current knowledge of biology and by inference and extrapolation work backward to hypothesize biological events in the march forward from RNA to DNA. It is proposed that the primordial replicating RNA cell, the ribocyte, evolved from liposomes encompassing required reactants and products for "life" and that ribonucleopeptide complexes formed membrane pores to support bidirectional ion and molecular transport to maintain biological functions and

  2. Privileged scaffolds or promiscuous binders: a glance of pyrrolo[2,1-f][1,2,4]triazines and related bridgehead nitrogen heterocycles in medicinal chemistry.

    Science.gov (United States)

    Song, Yu'ning; Zhan, Peng; Zhang, Qingzhu; Liu, Xinyong

    2013-01-01

    Pyrrolo[2,1-f][1,2,4]triazine template, a unique bridgehead nitrogen heterocycle, certainly deserves the title of "privileged scaffold" in the drug discovery field because of the versatility and potential to yield derivatives with a wide range of biological activities, such as anti-anaplastic lymphoma kinase (ALK), Janus kinase 2 (JAK2), VEGFR-2, EGFR and/or HER2, Met kinase, p38α mitogen-activated protein (MAP) kinase and insulin-like growth factor receptor (IGF-1R) kinase activities, etc. These different biological properties of pyrrolo[2,1-f][1,2,4]triazine derivatives have motivated new studies in searching for novel derivatives with improved activity and also other applications in pharmaceutical field. However, no systematic review is available in the literature on the pyrrolo[2,1- f][1,2,4]triazine derivatives concerning the design of potent drug-like compounds. Owing to the importance of this heterocyclic system, the present paper is an attempt to the pharmacological activities, structural modifications and the structure-activity relationship (SAR) reported for bridgehead nitrogen heterocycles in the current literature, making an effort to highlight the importance and therapeutic potentials of the pyrrolo[2,1-f][1,2,4]triazine scaffold and its bridgehead nitrogen bioisosters as heterocyclic privileged medicinal scaffolds.

  3. Race, space, place: notes on the racialisation and spatialisation of commercial sex work in Dubai, UAE.

    Science.gov (United States)

    Mahdavi, Pardis

    2010-11-01

    This paper focuses on the perceived racialisation and resultant spatialisation of commercial sex in Dubai. In recent years, the sex industry in Dubai has grown to include women from the Middle East, Eastern Europe, East Asia and Africa. With the increase in sex workers of different nationalities has come a form of localised racism that is embedded in structures and desires seen within specific locations. The physical spatialisation of sex work hinges on perceived race and produces distinct income generating potential for women engaged in the sex industry in Dubai. The social and physical topography of Dubai is important in marginalising or privileging these various groups of sex workers, which correlates race, space and place with rights and assistance. I begin with a description of the multidirectional flows of causality between race, space, place and demand. I then discuss how these various groups are inversely spatialised within the discourse on assistance, protection and rights. The findings presented here are based on ethnographic research conducted with transnational migrants in the UAE in 2004, 2008 and 2009.

  4. 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.

  5. RNA2DMut: a web tool for the design and analysis of RNA structure mutations.

    Science.gov (United States)

    Moss, Walter N

    2018-03-01

    With the widespread application of high-throughput sequencing, novel RNA sequences are being discovered at an astonishing rate. The analysis of function, however, lags behind. In both the cis - and trans -regulatory functions of RNA, secondary structure (2D base-pairing) plays essential regulatory roles. In order to test RNA function, it is essential to be able to design and analyze mutations that can affect structure. This was the motivation for the creation of the RNA2DMut web tool. With RNA2DMut, users can enter in RNA sequences to analyze, constrain mutations to specific residues, or limit changes to purines/pyrimidines. The sequence is analyzed at each base to determine the effect of every possible point mutation on 2D structure. The metrics used in RNA2DMut rely on the calculation of the Boltzmann structure ensemble and do not require a robust 2D model of RNA structure for designing mutations. This tool can facilitate a wide array of uses involving RNA: for example, in designing and evaluating mutants for biological assays, interrogating RNA-protein interactions, identifying key regions to alter in SELEX experiments, and improving RNA folding and crystallization properties for structural biology. Additional tools are available to help users introduce other mutations (e.g., indels and substitutions) and evaluate their effects on RNA structure. Example calculations are shown for five RNAs that require 2D structure for their function: the MALAT1 mascRNA, an influenza virus splicing regulatory motif, the EBER2 viral noncoding RNA, the Xist lncRNA repA region, and human Y RNA 5. RNA2DMut can be accessed at https://rna2dmut.bb.iastate.edu/. © 2018 Moss; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  6. Cognitive load privileges memory-based over data-driven processing, not group-level over person-level processing.

    Science.gov (United States)

    Skorich, Daniel P; Mavor, Kenneth I

    2013-09-01

    In the current paper, we argue that categorization and individuation, as traditionally discussed and as experimentally operationalized, are defined in terms of two confounded underlying dimensions: a person/group dimension and a memory-based/data-driven dimension. In a series of three experiments, we unconfound these dimensions and impose a cognitive load. Across the three experiments, two with laboratory-created targets and one with participants' friends as the target, we demonstrate that cognitive load privileges memory-based over data-driven processing, not group- over person-level processing. We discuss the results in terms of their implications for conceptualizations of the categorization/individuation distinction, for the equivalence of person and group processes, for the ultimate 'purpose' and meaningfulness of group-based perception and, fundamentally, for the process of categorization, broadly defined. © 2012 The British Psychological Society.

  7. Introduction to the Navigation Team: Johnson Space Center EG6 Internship

    Science.gov (United States)

    Gualdoni, Matthew

    2017-01-01

    The EG6 navigation team at NASA Johnson Space Center, like any team of engineers, interacts with the engineering process from beginning to end; from exploring solutions to a problem, to prototyping and studying the implementations, all the way to polishing and verifying a final flight-ready design. This summer, I was privileged enough to gain exposure to each of these processes, while also getting to truly experience working within a team of engineers. My summer can be broken up into three projects: i) Initial study and prototyping: investigating a manual navigation method that can be utilized onboard Orion in the event of catastrophic failure of navigation systems; ii) Finalizing and verifying code: altering a software routine to improve its robustness and reliability, as well as designing unit tests to verify its performance; and iii) Development of testing equipment: assisting in developing and integrating of a high-fidelity testbed to verify the performance of software and hardware.

  8. 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.

  9. Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy

    Directory of Open Access Journals (Sweden)

    Liu Lin

    2009-12-01

    Full Text Available Abstract Background microRNAs (miRNAs regulate target gene expression by controlling their mRNAs post-transcriptionally. Increasing evidence demonstrates that miRNAs play important roles in various biological processes. However, the functions and precise regulatory mechanisms of most miRNAs remain elusive. Current research suggests that miRNA regulatory modules are complicated, including up-, down-, and mix-regulation for different physiological conditions. Previous computational approaches for discovering miRNA-mRNA interactions focus only on down-regulatory modules. In this work, we present a method to capture complex miRNA-mRNA interactions including all regulatory types between miRNAs and mRNAs. Results We present a method to capture complex miRNA-mRNA interactions using Bayesian network structure learning with splitting-averaging strategy. It is designed to explore all possible miRNA-mRNA interactions by integrating miRNA-targeting information, expression profiles of miRNAs and mRNAs, and sample categories. We also present an analysis of data sets for epithelial and mesenchymal transition (EMT. Our results show that the proposed method identified all possible types of miRNA-mRNA interactions from the data. Many interactions are of tremendous biological significance. Some discoveries have been validated by previous research, for example, the miR-200 family negatively regulates ZEB1 and ZEB2 for EMT. Some are consistent with the literature, such as LOX has wide interactions with the miR-200 family members for EMT. Furthermore, many novel interactions are statistically significant and worthy of validation in the near future. Conclusions This paper presents a new method to explore the complex miRNA-mRNA interactions for different physiological conditions using Bayesian network structure learning with splitting-averaging strategy. The method makes use of heterogeneous data including miRNA-targeting information, expression profiles of miRNAs and

  10. Nucleocapsid-Independent Specific Viral RNA Packaging via Viral Envelope Protein and Viral RNA Signal

    OpenAIRE

    Narayanan, Krishna; Chen, Chun-Jen; Maeda, Junko; Makino, Shinji

    2003-01-01

    For any of the enveloped RNA viruses studied to date, recognition of a specific RNA packaging signal by the virus's nucleocapsid (N) protein is the first step described in the process of viral RNA packaging. In the murine coronavirus a selective interaction between the viral transmembrane envelope protein M and the viral ribonucleoprotein complex, composed of N protein and viral RNA containing a short cis-acting RNA element, the packaging signal, determines the selective RNA packaging into vi...

  11. Mapping protein-RNA interactions by RCAP, RNA-cross-linking and peptide fingerprinting.

    Science.gov (United States)

    Vaughan, Robert C; Kao, C Cheng

    2015-01-01

    RNA nanotechnology often feature protein RNA complexes. The interaction between proteins and large RNAs are difficult to study using traditional structure-based methods like NMR or X-ray crystallography. RCAP, an approach that uses reversible-cross-linking affinity purification method coupled with mass spectrometry, has been developed to map regions within proteins that contact RNA. This chapter details how RCAP is applied to map protein-RNA contacts within virions.

  12. Purification and crystallization of Bacillus subtilis NrnA, a novel enzyme involved in nanoRNA degradation

    Energy Technology Data Exchange (ETDEWEB)

    Nelersa, Claudiu M.; Schmier, Brad J.; Malhotra, Arun (Miami-MED)

    2012-05-08

    The final step in RNA degradation is the hydrolysis of RNA fragments five nucleotides or less in length (nanoRNA) to mononucleotides. In Escherichia coli this step is carried out by oligoribonuclease (Orn), a DEDD-family exoribonuclease that is conserved throughout eukaryotes. However, many bacteria lack Orn homologs, and an unrelated DHH-family phosphoesterase, NrnA, has recently been identified as one of the enzymes responsible for nanoRNA degradation in Bacillus subtilis. To understand its mechanism of action, B. subtilis NrnA was purified and crystallized at room temperature using the hanging-drop vapor-diffusion method with PEG 4000, PEG 3350 or PEG MME 2000 as precipitant. The crystals belonged to the primitive monoclinic space group P2{sub 1}, with unit-cell parameters a = 50.62, b = 121.3, c = 123.4 {angstrom}, {alpha} = 90, {beta} = 91.31, {gamma} = 90{sup o}.

  13. RNA İNTERFERANS (RNAİ)

    OpenAIRE

    GÜNDOĞDU, Ramazan; ÇELİK, Venhar

    2009-01-01

    RNA interferans, uygun çift zincirli RNA’nın hücreye girdiği zaman, endojenik komplementer mRNA dizisinin parçalanmasına yol açan, transkripsiyon sonrası gen susturma mekanizmasıdır. RNA interferans, Dicer adı verilen bir RNase III enzimi tarafından çift zincirli RNA’nın küçük engelleyici RNA’lara (siRNA) kesilmesi ile başlamaktadır. Bu siRNA’lar daha sonra, bir multiprotein-RNA nükleaz kompleksi olan, RNA- indükleyici baskılama kompleksine (RISC) bağlanır. RISC, siRNA’ları komplementer mRNA’...

  14. 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.

  15. Human Milk MicroRNA and Total RNA Differ Depending on Milk Fractionation.

    Science.gov (United States)

    Alsaweed, Mohammed; Hepworth, Anna R; Lefèvre, Christophe; Hartmann, Peter E; Geddes, Donna T; Hassiotou, Foteini

    2015-10-01

    MicroRNA have been recently discovered in human milk signifying potentially important functions for both the lactating breast and the infant. Whilst human milk microRNA have started to be explored, little data exist on the evaluation of sample processing, and analysis to ensure that a full spectrum of microRNA can be obtained. Human milk comprises three main fractions: cells, skim milk, and lipids. Typically, the skim milk fraction has been measured in isolation despite evidence that the lipid fraction may contain more microRNA. This study aimed to standardize isolation of microRNA and total RNA from all three fractions of human milk to determine the most appropriate sampling and analysis procedure for future studies. Three different methods from eight commercially available kits were tested for their efficacy in extracting total RNA and microRNA from the lipid, skim, and cell fractions of human milk. Each fraction yielded different concentrations of RNA and microRNA, with the highest quantities found in the cell and lipid fractions, and the lowest in skim milk. The column-based phenol-free method was the most efficient extraction method for all three milk fractions. Two microRNAs were expressed and validated in the three milk fractions by qPCR using the three recommended extraction kits for each fraction. High expression levels were identified in the skim and lipid milk factions for these microRNAs. These results suggest that careful consideration of both the human milk sample preparation and extraction protocols should be made prior to embarking upon research in this area. © 2015 The Authors. Journal of Cellular Biochemistry Published by Wiley Periodicals, Inc.

  16. Affinity maturation of a portable Fab–RNA module for chaperone-assisted RNA crystallography

    Science.gov (United States)

    Koirala, Deepak; Shelke, Sandip A; Dupont, Marcel; Ruiz, Stormy; DasGupta, Saurja; Bailey, Lucas J; Benner, Steven A; Piccirilli, Joseph A

    2018-01-01

    Abstract Antibody fragments such as Fabs possess properties that can enhance protein and RNA crystallization and therefore can facilitate macromolecular structure determination. In particular, Fab BL3–6 binds to an AAACA RNA pentaloop closed by a GC pair with ∼100 nM affinity. The Fab and hairpin have served as a portable module for RNA crystallization. The potential for general application make it desirable to adjust the properties of this crystallization module in a manner that facilitates its use for RNA structure determination, such as ease of purification, surface entropy or binding affinity. In this work, we used both in vitro RNA selection and phage display selection to alter the epitope and paratope sides of the binding interface, respectively, for improved binding affinity. We identified a 5′-GNGACCC-3′ consensus motif in the RNA and S97N mutation in complimentarity determining region L3 of the Fab that independently impart about an order of magnitude improvement in affinity, resulting from new hydrogen bonding interactions. Using a model RNA, these modifications facilitated crystallization under a wider range of conditions and improved diffraction. The improved features of the Fab–RNA module may facilitate its use as an affinity tag for RNA purification and imaging and as a chaperone for RNA crystallography. PMID:29309709

  17. 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.

  18. 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.

  19. Recoding aminoacyl-tRNA synthetases for synthetic biology by rational protein-RNA engineering.

    Science.gov (United States)

    Hadd, Andrew; Perona, John J

    2014-12-19

    We have taken a rational approach to redesigning the amino acid binding and aminoacyl-tRNA pairing specificities of bacterial glutaminyl-tRNA synthetase. The four-stage engineering incorporates generalizable design principles and improves the pairing efficiency of noncognate glutamate with tRNA(Gln) by over 10(5)-fold compared to the wild-type enzyme. Better optimized designs of the protein-RNA complex include substantial reengineering of the globular core region of the tRNA, demonstrating a role for specific tRNA nucleotides in specifying the identity of the genetically encoded amino acid. Principles emerging from this engineering effort open new prospects for combining rational and genetic selection approaches to design novel aminoacyl-tRNA synthetases that ligate noncanonical amino acids onto tRNAs. This will facilitate reconstruction of the cellular translation apparatus for applications in synthetic biology.

  20. 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.

  1. Shapes of interacting RNA complexes

    DEFF Research Database (Denmark)

    Fu, Benjamin Mingming; Reidys, Christian

    2014-01-01

    Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops.This shape-projection preserves the topological core of the RNA complex and for fixed topological...... genus there are only finitely many such shapes. Our main result is a new bijection that relates the shapes of RNA complexes with shapes of RNA structures. This allows to compute the shape polynomial of RNA complexes via the shape polynomial of RNA structures. We furthermore present a linear time uniform...... sampling algorithm for shapes of RNA complexes of fixed topological genus....

  2. Methods for RNA Analysis

    DEFF Research Database (Denmark)

    Olivarius, Signe

    of the transcriptome, 5’ end capture of RNA is combined with next-generation sequencing for high-throughput quantitative assessment of transcription start sites by two different methods. The methods presented here allow for functional investigation of coding as well as noncoding RNA and contribute to future...... RNAs rely on interactions with proteins, the establishment of protein-binding profiles is essential for the characterization of RNAs. Aiming to facilitate RNA analysis, this thesis introduces proteomics- as well as transcriptomics-based methods for the functional characterization of RNA. First, RNA...

  3. Capturing microRNA targets using an RNA-induced silencing complex (RISC)-trap approach.

    Science.gov (United States)

    Cambronne, Xiaolu A; Shen, Rongkun; Auer, Paul L; Goodman, Richard H

    2012-12-11

    Identifying targets is critical for understanding the biological effects of microRNA (miRNA) expression. The challenge lies in characterizing the cohort of targets for a specific miRNA, especially when targets are being actively down-regulated in miRNA- RNA-induced silencing complex (RISC)-messengerRNA (mRNA) complexes. We have developed a robust and versatile strategy called RISCtrap to stabilize and purify targets from this transient interaction. Its utility was demonstrated by determining specific high-confidence target datasets for miR-124, miR-132, and miR-181 that contained known and previously unknown transcripts. Two previously unknown miR-132 targets identified with RISCtrap, adaptor protein CT10 regulator of kinase 1 (CRK1) and tight junction-associated protein 1 (TJAP1), were shown to be endogenously regulated by miR-132 in adult mouse forebrain. The datasets, moreover, differed in the number of targets and in the types and frequency of microRNA recognition element (MRE) motifs, thus revealing a previously underappreciated level of specificity in the target sets regulated by individual miRNAs.

  4. Mycobacterium smegmatis HelY Is an RNA-Activated ATPase/dATPase and 3'-to-5' Helicase That Unwinds 3'-Tailed RNA Duplexes and RNA:DNA Hybrids.

    Science.gov (United States)

    Uson, Maria Loressa; Ordonez, Heather; Shuman, Stewart

    2015-10-01

    Mycobacteria have a large and distinctive ensemble of DNA helicases that function in DNA replication, repair, and recombination. Little is known about the roster of RNA helicases in mycobacteria or their roles in RNA transactions. The 912-amino-acid Mycobacterium smegmatis HelY (MSMEG_3885) protein is a bacterial homolog of the Mtr4 and Ski2 helicases that regulate RNA 3' processing and turnover by the eukaryal exosome. Here we characterize HelY as an RNA-stimulated ATPase/dATPase and an ATP/dATP-dependent 3'-to-5' helicase. HelY requires a 3' single-strand RNA tail (a loading RNA strand) to displace the complementary strand of a tailed RNA:RNA or RNA:DNA duplex. The findings that HelY ATPase is unresponsive to a DNA polynucleotide cofactor and that HelY is unable to unwind a 3'-tailed duplex in which the loading strand is DNA distinguish HelY from other mycobacterial nucleoside triphosphatases/helicases characterized previously. The biochemical properties of HelY, which resemble those of Mtr4/Ski2, hint at a role for HelY in mycobacterial RNA catabolism. RNA helicases play crucial roles in transcription, RNA processing, and translation by virtue of their ability to alter RNA secondary structure or remodel RNA-protein interactions. In eukarya, the RNA helicases Mtr4 and Ski2 regulate RNA 3' resection by the exosome. Mycobacterium smegmatis HelY, a bacterial homolog of Mtr4/Ski2, is characterized here as a unidirectional helicase, powered by RNA-dependent ATP/dATP hydrolysis, that tracks 3' to 5' along a loading RNA strand to displace the complementary strand of a tailed RNA:RNA or RNA:DNA duplex. The biochemical properties of HelY suggest a role in bacterial RNA transactions. HelY homologs are present in pathogenic mycobacteria (e.g., M. tuberculosis and M. leprae) and are widely prevalent in Actinobacteria and Cyanobacteria but occur sporadically elsewhere in the bacterial domain. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  5. RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerases.

    Science.gov (United States)

    Hunter, Lydia J R; Brockington, Samuel F; Murphy, Alex M; Pate, Adrienne E; Gruden, Kristina; MacFarlane, Stuart A; Palukaitis, Peter; Carr, John P

    2016-03-16

    Cellular RNA-dependent RNA polymerases (RDRs) catalyze synthesis of double-stranded RNAs that can serve to initiate or amplify RNA silencing. Arabidopsis thaliana has six RDR genes; RDRs 1, 2 and 6 have roles in anti-viral RNA silencing. RDR6 is constitutively expressed but RDR1 expression is elevated following plant treatment with defensive phytohormones. RDR1 also contributes to basal virus resistance. RDR1 has been studied in several species including A. thaliana, tobacco (Nicotiana tabacum), N. benthamiana, N. attenuata and tomato (Solanum lycopersicum) but not to our knowledge in potato (S. tuberosum). StRDR1 was identified and shown to be salicylic acid-responsive. StRDR1 transcript accumulation decreased in transgenic potato plants constitutively expressing a hairpin construct and these plants were challenged with three viruses: potato virus Y, potato virus X, and tobacco mosaic virus. Suppression of StRDR1 gene expression did not increase the susceptibility of potato to these viruses. Phylogenetic analysis of RDR genes present in potato and in a range of other plant species identified a new RDR gene family, not present in potato and found only in Rosids (but apparently lost in the Rosid A. thaliana) for which we propose the name RDR7.

  6. mRNA decay proteins are targeted to poly(A+ RNA and dsRNA-containing cytoplasmic foci that resemble P-bodies in Entamoeba histolytica.

    Directory of Open Access Journals (Sweden)

    Itzel López-Rosas

    Full Text Available In higher eukaryotes, mRNA degradation and RNA-based gene silencing occur in cytoplasmic foci referred to as processing bodies (P-bodies. In protozoan parasites, the presence of P-bodies and their putative role in mRNA decay have yet to be comprehensively addressed. Identification of P-bodies might provide information on how mRNA degradation machineries evolved in lower eukaryotes. Here, we used immunofluorescence and confocal microscopy assays to investigate the cellular localization of mRNA degradation proteins in the human intestinal parasite Entamoeba histolytica and found evidence of the existence of P-bodies. Two mRNA decay factors, namely the EhXRN2 exoribonuclease and the EhDCP2 decapping enzyme, were localized in cytoplasmic foci in a pattern resembling P-body organization. Given that amoebic foci appear to be smaller and less rounded than those described in higher eukaryotes, we have named them "P-body-like structures". These foci contain additional mRNA degradation factors, including the EhCAF1 deadenylase and the EhAGO2-2 protein involved in RNA interference. Biochemical analysis revealed that EhCAF1 co-immunoprecipitated with EhXRN2 but not with EhDCP2 or EhAGO2-2, thus linking deadenylation to 5'-to-3' mRNA decay. The number of EhCAF1-containing foci significantly decreased after inhibition of transcription and translation with actinomycin D and cycloheximide, respectively. Furthermore, results of RNA-FISH assays showed that (i EhCAF1 colocalized with poly(A(+ RNA and (ii during silencing of the Ehpc4 gene by RNA interference, EhAGO2-2 colocalized with small interfering RNAs in cytoplasmic foci. Our observation of decapping, deadenylation and RNA interference proteins within P-body-like foci suggests that these structures have been conserved after originating in the early evolution of eukaryotic lineages. To the best of our knowledge, this is the first study to report on the localization of mRNA decay proteins within P

  7. A Viral RNA Structural Element Alters Host Recognition of Nonself RNA

    Energy Technology Data Exchange (ETDEWEB)

    Hyde, J. L.; Gardner, C. L.; Kimura, T.; White, J. P.; Liu, G.; Trobaugh, D. W.; Huang, C.; Tonelli, M.; Paessler, S.; Takeda, K.; Klimstra, W. B.; Amarasinghe, G. K.; Diamond, M. S.

    2014-01-30

    Although interferon (IFN) signaling induces genes that limit viral infection, many pathogenic viruses overcome this host response. As an example, 2'-O methylation of the 5' cap of viral RNA subverts mammalian antiviral responses by evading restriction of Ifit1, an IFN-stimulated gene that regulates protein synthesis. However, alphaviruses replicate efficiently in cells expressing Ifit1 even though their genomic RNA has a 5' cap lacking 2'-O methylation. We show that pathogenic alphaviruses use secondary structural motifs within the 5' untranslated region (UTR) of their RNA to alter Ifit1 binding and function. Mutations within the 5'-UTR affecting RNA structural elements enabled restriction by or antagonism of Ifit1 in vitro and in vivo. These results identify an evasion mechanism by which viruses use RNA structural motifs to avoid immune restriction.

  8. The interplay between polymerase organization and nucleosome occupancy along DNA : How dynamic roadblocks on the DNA induce the formation of RNA polymerase pelotons

    NARCIS (Netherlands)

    van den Berg, A.A.

    2017-01-01

    During transcription RNA polymerase (RNAP) moves along a DNA molecule to copy the information on the DNA to an RNA molecule. Many textbook pictures show an RNAP sliding along empty DNA, but in reality it is crowded on the DNA and RNAP competes for space with many proteins such as other RNAP’s and

  9. Analysis of hepatitis C virus RNA dimerization and core–RNA interactions

    Science.gov (United States)

    Ivanyi-Nagy, Roland; Kanevsky, Igor; Gabus, Caroline; Lavergne, Jean-Pierre; Ficheux, Damien; Penin, François; Fossé, Philippe; Darlix, Jean-Luc

    2006-01-01

    The core protein of hepatitis C virus (HCV) has been shown previously to act as a potent nucleic acid chaperone in vitro, promoting the dimerization of the 3′-untranslated region (3′-UTR) of the HCV genomic RNA, a process probably mediated by a small, highly conserved palindromic RNA motif, named DLS (dimer linkage sequence) [G. Cristofari, R. Ivanyi-Nagy, C. Gabus, S. Boulant, J. P. Lavergne, F. Penin and J. L. Darlix (2004) Nucleic Acids Res., 32, 2623–2631]. To investigate in depth HCV RNA dimerization, we generated a series of point mutations in the DLS region. We find that both the plus-strand 3′-UTR and the complementary minus-strand RNA can dimerize in the presence of core protein, while mutations in the DLS (among them a single point mutation that abolished RNA replication in a HCV subgenomic replicon system) completely abrogate dimerization. Structural probing of plus- and minus-strand RNAs, in their monomeric and dimeric forms, indicate that the DLS is the major if not the sole determinant of UTR RNA dimerization. Furthermore, the N-terminal basic amino acid clusters of core protein were found to be sufficient to induce dimerization, suggesting that they retain full RNA chaperone activity. These findings may have important consequences for understanding the HCV replicative cycle and the genetic variability of the virus. PMID:16707664

  10. Analysis of hepatitis C virus RNA dimerization and core-RNA interactions.

    Science.gov (United States)

    Ivanyi-Nagy, Roland; Kanevsky, Igor; Gabus, Caroline; Lavergne, Jean-Pierre; Ficheux, Damien; Penin, François; Fossé, Philippe; Darlix, Jean-Luc

    2006-01-01

    The core protein of hepatitis C virus (HCV) has been shown previously to act as a potent nucleic acid chaperone in vitro, promoting the dimerization of the 3'-untranslated region (3'-UTR) of the HCV genomic RNA, a process probably mediated by a small, highly conserved palindromic RNA motif, named DLS (dimer linkage sequence) [G. Cristofari, R. Ivanyi-Nagy, C. Gabus, S. Boulant, J. P. Lavergne, F. Penin and J. L. Darlix (2004) Nucleic Acids Res., 32, 2623-2631]. To investigate in depth HCV RNA dimerization, we generated a series of point mutations in the DLS region. We find that both the plus-strand 3'-UTR and the complementary minus-strand RNA can dimerize in the presence of core protein, while mutations in the DLS (among them a single point mutation that abolished RNA replication in a HCV subgenomic replicon system) completely abrogate dimerization. Structural probing of plus- and minus-strand RNAs, in their monomeric and dimeric forms, indicate that the DLS is the major if not the sole determinant of UTR RNA dimerization. Furthermore, the N-terminal basic amino acid clusters of core protein were found to be sufficient to induce dimerization, suggesting that they retain full RNA chaperone activity. These findings may have important consequences for understanding the HCV replicative cycle and the genetic variability of the virus.

  11. 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

  12. ARMOUR - A Rice miRNA: mRNA Interaction Resource.

    Science.gov (United States)

    Sanan-Mishra, Neeti; Tripathi, Anita; Goswami, Kavita; Shukla, Rohit N; Vasudevan, Madavan; Goswami, Hitesh

    2018-01-01

    ARMOUR was developed as A Rice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of miRNA:mRNA interactome in regulation of functional cellular machinery is supported by the sequence information of the mature and hairpin structures. ARMOUR provides flexibility to users in querying the database using multiple ways like known gene identifiers, gene ontology identifiers, KEGG identifiers and also allows on the fly fold change analysis and sequence search query with inbuilt BLAST algorithm. ARMOUR database provides a cohesive platform for novel and mature miRNAs and their expression in different experimental conditions and allows searching for their interacting mRNA targets, GO annotation and their involvement in various biological pathways. The ARMOUR database includes a provision for adding more experimental data from users, with an aim to develop it as a platform for sharing and comparing experimental data contributed by research groups working on rice.

  13. Flock House virus subgenomic RNA3 is replicated and its replication correlates with transactivation of RNA2

    International Nuclear Information System (INIS)

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

    2003-01-01

    The nodavirus Flock House virus has a bipartite genome composed of RNAs 1 and 2, which encode the catalytic component of the RNA-dependent RNA polymerase (RdRp) and the capsid protein precursor, respectively. In addition to catalyzing replication of the viral genome, the RdRp also transcribes from RNA1 a subgenomic RNA3, which is both required for and suppressed by RNA2 replication. Here, we show that in the absence of RNA1 replication, FHV RdRp replicated positive-sense RNA3 transcripts fully and copied negative-sense RNA3 transcripts into positive strands. The two nonstructural proteins encoded by RNA3 were dispensable for replication, but sequences in the 3'-terminal 58 nucleotides were required. RNA3 variants that failed to replicate also failed to transactivate RNA2. These results imply that RNA3 is naturally produced both by transcription from RNA1 and by subsequent RNA1-independent replication and that RNA3 replication may be necessary for transactivation of RNA2

  14. The use of 125iodine-labeled RNA for detection of the RNA binding to ribosomes

    International Nuclear Information System (INIS)

    Mori, Tomohiko; Fukuda, Mitsuru

    1975-01-01

    The in vitro labeling of RNA with radioactive iodine is the efficient method to obtain the RNA with high specific activity. The present paper reports on the application of this technique to the production of iodine-labeled RNA for use in the experiment of binding RNA to ribosomes. Tobacco mosaic virus (TMV) RNA was used as natural mRNA, and E. coli S-30 preparation was used as a source of ribosomes. The TMV-RNA was prepared by bentonite-phenol extraction from TMV, and the method used for the iodation of RNA was based on the procedure described by Getz et al. The iodine-labeled RNA was incubated in a cell-free protein synthesizing system (S-30) prepared from E. coli K-12. After the incubation, the reaction mixture was layered onto sucrose gradient, centrifuged, and fractionated into 18 fractions. Optical density at 260 nm was measured, and radioactivity was counted, for each fraction. The binding of mRNA to ribosomes occurred even at 0 deg C, and the occurrence of the nonspecific binding was also shown. Consequently, the specific binding, i.e. the formation of the initiation complex being involved in amino acid incorporation, may be estimated by subtracting the radioactivity associated with monosomes in the presence of both rRNA and ATA from that in the presence of rRNA only. It was shown that the iodine-labeled RNA can be used for the studies of binding RNA to ribosomes. (Kako, I.)

  15. CD11c(hi) Dendritic Cells Regulate Ly-6C(hi) Monocyte Differentiation to Preserve Immune-privileged CNS in Lethal Neuroinflammation.

    Science.gov (United States)

    Kim, Jin Hyoung; Choi, Jin Young; Kim, Seong Bum; Uyangaa, Erdenebelig; Patil, Ajit Mahadev; Han, Young Woo; Park, Sang-Youel; Lee, John Hwa; Kim, Koanhoi; Eo, Seong Kug

    2015-12-02

    Although the roles of dendritic cells (DCs) in adaptive defense have been defined well, the contribution of DCs to T cell-independent innate defense and subsequent neuroimmunopathology in immune-privileged CNS upon infection with neurotropic viruses has not been completely defined. Notably, DC roles in regulating innate CD11b(+)Ly-6C(hi) monocyte functions during neuroinflammation have not yet been addressed. Using selective ablation of CD11c(hi)PDCA-1(int/lo) DCs without alteration in CD11c(int)PDCA-1(hi) plasmacytoid DC number, we found that CD11c(hi) DCs are essential to control neuroinflammation caused by infection with neurotropic Japanese encephalitis virus, through early and increased infiltration of CD11b(+)Ly-6C(hi) monocytes and higher expression of CC chemokines. More interestingly, selective CD11c(hi) DC ablation provided altered differentiation and function of infiltrated CD11b(+)Ly-6C(hi) monocytes in the CNS through Flt3-L and GM-CSF, which was closely associated with severely enhanced neuroinflammation. Furthermore, CD11b(+)Ly-6C(hi) monocytes generated in CD11c(hi) DC-ablated environment had a deleterious rather than protective role during neuroinflammation, and were more quickly recruited into inflamed CNS, depending on CCR2, thereby exacerbating neuroinflammation via enhanced supply of virus from the periphery. Therefore, our data demonstrate that CD11c(hi) DCs provide a critical and unexpected role to preserve the immune-privileged CNS in lethal neuroinflammation via regulating the differentiation, function, and trafficking of CD11b(+)Ly-6C(hi) monocytes.

  16. Conformational Selection and Induced Fit for RNA Polymerase and RNA/DNA Hybrid Backtracked Recognition

    Directory of Open Access Journals (Sweden)

    Haifeng eChen

    2015-11-01

    Full Text Available RNA polymerase catalyzes transcription with a high fidelity. If DNA/RNA mismatch or DNA damage occurs downstream, a backtracked RNA polymerase can proofread this situation. However, the backtracked mechanism is still poorly understood. Here we have performed multiple explicit-solvent molecular dynamics (MD simulations on bound and apo DNA/RNA hybrid to study backtracked recognition. MD simulations at room temperature suggest that specific electrostatic interactions play key roles in the backtracked recognition between the polymerase and DNA/RNA hybrid. Kinetics analysis at high temperature shows that bound and apo DNA/RNA hybrid unfold via a two-state process. Both kinetics and free energy landscape analyses indicate that bound DNA/RNA hybrid folds in the order of DNA/RNA contracting, the tertiary folding and polymerase binding. The predicted Φ-values suggest that C7, G9, dC12, dC15 and dT16 are key bases for the backtracked recognition of DNA/RNA hybrid. The average RMSD values between the bound structures and the corresponding apo ones and Kolmogorov-Smirnov (KS P test analyses indicate that the recognition between DNA/RNA hybrid and polymerase might follow an induced fit mechanism for DNA/RNA hybrid and conformation selection for polymerase. Furthermore, this method could be used to relative studies of specific recognition between nucleic acid and protein.

  17. Cooperation of an RNA Packaging Signal and a Viral Envelope Protein in Coronavirus RNA Packaging

    OpenAIRE

    Narayanan, Krishna; Makino, Shinji

    2001-01-01

    Murine coronavirus mouse hepatitis virus (MHV) produces a genome-length mRNA, mRNA 1, and six or seven species of subgenomic mRNAs in infected cells. Among these mRNAs, only mRNA 1 is efficiently packaged into MHV particles. MHV N protein binds to all MHV mRNAs, whereas envelope M protein interacts only with mRNA 1. This M protein-mRNA 1 interaction most probably determines the selective packaging of mRNA 1 into MHV particles. A short cis-acting MHV RNA packaging signal is necessary and suffi...

  18. Intrinsic noise of microRNA-regulated genes and the ceRNA hypothesis.

    Directory of Open Access Journals (Sweden)

    Javad Noorbakhsh

    Full Text Available MicroRNAs are small noncoding RNAs that regulate genes post-transciptionally by binding and degrading target eukaryotic mRNAs. We use a quantitative model to study gene regulation by inhibitory microRNAs and compare it to gene regulation by prokaryotic small non-coding RNAs (sRNAs. Our model uses a combination of analytic techniques as well as computational simulations to calculate the mean-expression and noise profiles of genes regulated by both microRNAs and sRNAs. We find that despite very different molecular machinery and modes of action (catalytic vs stoichiometric, the mean expression levels and noise profiles of microRNA-regulated genes are almost identical to genes regulated by prokaryotic sRNAs. This behavior is extremely robust and persists across a wide range of biologically relevant parameters. We extend our model to study crosstalk between multiple mRNAs that are regulated by a single microRNA and show that noise is a sensitive measure of microRNA-mediated interaction between mRNAs. We conclude by discussing possible experimental strategies for uncovering the microRNA-mRNA interactions and testing the competing endogenous RNA (ceRNA hypothesis.

  19. Free energy minimization to predict RNA secondary structures and computational RNA design.

    Science.gov (United States)

    Churkin, Alexander; Weinbrand, Lina; Barash, Danny

    2015-01-01

    Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

  20. 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.

  1. Species-independent MicroRNA Gene Discovery

    KAUST Repository

    Kamanu, Timothy K.

    2012-12-01

    MicroRNA (miRNA) are a class of small endogenous non-coding RNA that are mainly negative transcriptional and post-transcriptional regulators in both plants and animals. Recent studies have shown that miRNA are involved in different types of cancer and other incurable diseases such as autism and Alzheimer’s. Functional miRNAs are excised from hairpin-like sequences that are known as miRNA genes. There are about 21,000 known miRNA genes, most of which have been determined using experimental methods. miRNA genes are classified into different groups (miRNA families). This study reports about 19,000 unknown miRNA genes in nine species whereby approximately 15,300 predictions were computationally validated to contain at least one experimentally verified functional miRNA product. The predictions are based on a novel computational strategy which relies on miRNA family groupings and exploits the physics and geometry of miRNA genes to unveil the hidden palindromic signals and symmetries in miRNA gene sequences. Unlike conventional computational miRNA gene discovery methods, the algorithm developed here is species-independent: it allows prediction at higher accuracy and resolution from arbitrary RNA/DNA sequences in any species and thus enables examination of repeat-prone genomic regions which are thought to be non-informative or ’junk’ sequences. The information non-redundancy of uni-directional RNA sequences compared to information redundancy of bi-directional DNA is demonstrated, a fact that is overlooked by most pattern discovery algorithms. A novel method for computing upstream and downstream miRNA gene boundaries based on mathematical/statistical functions is suggested, as well as cutoffs for annotation of miRNA genes in different miRNA families. Another tool is proposed to allow hypotheses generation and visualization of data matrices, intra- and inter-species chromosomal distribution of miRNA genes or miRNA families. Our results indicate that: miRNA and miRNA

  2. 2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.

    Science.gov (United States)

    Choi, Junhong; Indrisiunaite, Gabriele; DeMirci, Hasan; Ieong, Ka-Weng; Wang, Jinfan; Petrov, Alexey; Prabhakar, Arjun; Rechavi, Gideon; Dominissini, Dan; He, Chuan; Ehrenberg, Måns; Puglisi, Joseph D

    2018-03-01

    Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2'-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2'-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon-anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading. Our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.

  3. Orotidine-Containing RNA: Implications for the Hierarchical Selection (Systems Chemistry Emergence) of RNA.

    Science.gov (United States)

    Kim, Eun-Kyong; Martin, Vincent; Krishnamurthy, Ramanarayanan

    2017-09-12

    The prebiotic synthesis of canonical nucleobases from HCN is a cornerstone for the RNA world hypothesis. However, their role in the primordial pathways to RNA is still debated. The very same process starting from HCN also gives rise to orotic acid, which (via orotidine) plays a crucial role in extant biology in the de novo synthesis of uridine and cytidine, the informational base-pairs in RNA. However, orotidine itself is absent in RNA. Given the prebiotic and biological relevance of orotic acid vis-à-vis uracil, we investigated orotidine-containing RNA oligonucleotides and show that they have severely compromised base-pairing properties. While not unexpected, these results suggest that the emergence of extant RNA cannot just be a consequence of the plausible prebiotic formation of its chemical constituents/building blocks. In combination with other investigations on alternative prebiotic nucleobases, sugars, and linkers, these findings imply that the selection of the components of extant RNA occurred at a higher hierarchical level of an oligomer/polymer based on its functional properties-pointing to a systems chemistry emergence of RNA from a library of precursors. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. 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.

  5. miRNA-mediated 'tug-of-war' model reveals ceRNA propensity of genes in cancers.

    Science.gov (United States)

    Swain, Arpit Chandan; Mallick, Bibekanand

    2018-06-01

    Competing endogenous RNA (ceRNA) are transcripts that cross-regulate each other at the post-transcriptional level by competing for shared microRNA response elements (MREs). These have been implicated in various biological processes impacting cell-fate decisions and diseases including cancer. There are several studies that predict possible ceRNA pairs by adopting various machine-learning and mathematical approaches; however, there is no method that enables us to gauge as well as compare the propensity of the ceRNA of a gene and precisely envisages which among a pair exerts a stronger pull on the shared miRNA pool. In this study, we developed a method that uses the 'tug of war of genes' concept to predict and quantify ceRNA potential of a gene for the shared miRNA pool in cancers based on a score represented by SoCeR (score of competing endogenous RNA). The method was executed on the RNA-Seq transcriptional profiles of genes and miRNA available at TCGA along with CLIP-supported miRNA-target sites to predict ceRNA in 32 cancer types which were validated with already reported cases. The proposed method can be used to determine the sequestering capability of the gene of interest as well as in ranking the probable ceRNA candidates of a gene. Finally, we developed standalone applications (SoCeR tool) to aid researchers in easier implementation of the method in analysing different data sets or diseases. © 2018 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.

  6. 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

  7. Modelling the structure of a ceRNA-theoretical, bipartite microRNA-mRNA interaction network regulating intestinal epithelial cellular pathways using R programming.

    Science.gov (United States)

    Robinson, J M; Henderson, W A

    2018-01-12

    We report a method using functional-molecular databases and network modelling to identify hypothetical mRNA-miRNA interaction networks regulating intestinal epithelial barrier function. The model forms a data-analysis component of our cell culture experiments, which produce RNA expression data from Nanostring Technologies nCounter ® system. The epithelial tight-junction (TJ) and actin cytoskeleton interact as molecular components of the intestinal epithelial barrier. Upstream regulation of TJ-cytoskeleton interaction is effected by the Rac/Rock/Rho signaling pathway and other associated pathways which may be activated or suppressed by extracellular signaling from growth factors, hormones, and immune receptors. Pathway activations affect epithelial homeostasis, contributing to degradation of the epithelial barrier associated with osmotic dysregulation, inflammation, and tumor development. The complexity underlying miRNA-mRNA interaction networks represents a roadblock for prediction and validation of competing-endogenous RNA network function. We developed a network model to identify hypothetical co-regulatory motifs in a miRNA-mRNA interaction network related to epithelial function. A mRNA-miRNA interaction list was generated using KEGG and miRWalk2.0 databases. R-code was developed to quantify and visualize inherent network structures. We identified a sub-network with a high number of shared, targeting miRNAs, of genes associated with cellular proliferation and cancer, including c-MYC and Cyclin D.

  8. Mutations that alter a conserved element upstream of the potato virus X triple block and coat protein genes affect subgenomic RNA accumulation.

    Science.gov (United States)

    Kim, K H; Hemenway, C

    1997-05-26

    The putative subgenomic RNA (sgRNA) promoter regions upstream of the potato virus X (PVX) triple block and coat protein (CP) genes contain sequences common to other potexviruses. The importance of these sequences to PVX sgRNA accumulation was determined by inoculation of Nicotiana tabacum NT1 cell suspension protoplasts with transcripts derived from wild-type and modified PVX cDNA clones. Analyses of RNA accumulation by S1 nuclease digestion and primer extension indicated that a conserved octanucleotide sequence element and the spacing between this element and the start-site for sgRNA synthesis are critical for accumulation of the two major sgRNA species. The impact of mutations on CP sgRNA levels was also reflected in the accumulation of CP. In contrast, genomic minus- and plus-strand RNA accumulation were not significantly affected by mutations in these regions. Studies involving inoculation of tobacco plants with the modified transcripts suggested that the conserved octanucleotide element functions in sgRNA accumulation and some other aspect of the infection process.

  9. Enzymatic activities of the GB virus-B RNA-dependent RNA polymerase

    International Nuclear Information System (INIS)

    Ranjith-Kumar, C.T.; Santos, Jan Lee; Gutshall, Lester L.; Johnston, Victor K.; Juili, L.-G.; Kim, M.-J.; Porter, David J.; Maley, Derrick; Greenwood, Cathy; Earnshaw, David L.; Baker, Audrey; Gu Baohua; Silverman, Carol; Sarisky, Robert T.; Kao Cheng

    2003-01-01

    The GB virus-B (GBV-B) nonstructural protein 5B (NS5B) encodes an RNA-dependent RNA polymerase (RdRp) with greater than 50% sequence similarity to the hepatitis C virus (HCV) NS5B. Recombinant GBV-B NS5B was reported to possess RdRp activity (W. Zhong et al., 2000, J. Viral Hepat. 7, 335-342). In this study, the GBV-B RdRp was examined more thoroughly for different RNA synthesis activities, including primer-extension, de novo initiation, template switch, terminal nucleotide addition, and template specificity. The results can be compared with previous characterizations of the HCV RdRp. The two RdRps share similarities in terms of metal ion and template preference, the abilities to add nontemplated nucleotides, perform both de novo initiation and extension from a primer, and switch templates. However, several differences in RNA synthesis between the GBV-B and HCV RdRps were observed, including (i) optimal temperatures for activity, (ii) ranges of Mn 2+ concentration tolerated for activity, and (iii) cation requirements for de novo RNA synthesis and terminal transferase activity. To assess whether the recombinant GBV-B RdRp may represent a relevant surrogate system for testing HCV antiviral agents, two compounds demonstrated to be active at nanomolar concentrations against HCV NS5B were tested on the GBV RdRp. A chain terminating nucleotide analog could prevent RNA synthesis, while a nonnucleoside HCV inhibitor was unable to affect RNA synthesis by the GBV RdRp

  10. A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure.

    Science.gov (United States)

    Zhang, Jinwei; Landick, Robert

    2016-04-01

    The vectorial (5'-to-3' at varying velocity) synthesis of RNA by cellular RNA polymerases (RNAPs) creates a rugged kinetic landscape, demarcated by frequent, sometimes long-lived, pauses. In addition to myriad gene-regulatory roles, these pauses temporally and spatially program the co-transcriptional, hierarchical folding of biologically active RNAs. Conversely, these RNA structures, which form inside or near the RNA exit channel, interact with the polymerase and adjacent protein factors to influence RNA synthesis by modulating pausing, termination, antitermination, and slippage. Here, we review the evolutionary origin, mechanistic underpinnings, and regulatory consequences of this interplay between RNAP and nascent RNA structure. We categorize and rationalize the extensive linkage between the transcriptional machinery and its product, and provide a framework for future studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. RNA-DNA Differences Are Generated in Human Cells within Seconds after RNA Exits Polymerase II

    Directory of Open Access Journals (Sweden)

    Isabel X. Wang

    2014-03-01

    Full Text Available RNA sequences are expected to be identical to their corresponding DNA sequences. Here, we found all 12 types of RNA-DNA sequence differences (RDDs in nascent RNA. Our results show that RDDs begin to occur in RNA chains ∼55 nt from the RNA polymerase II (Pol II active site. These RDDs occur so soon after transcription that they are incompatible with known deaminase-mediated RNA-editing mechanisms. Moreover, the 55 nt delay in appearance indicates that they do not arise during RNA synthesis by Pol II or as a direct consequence of modified base incorporation. Preliminary data suggest that RDD and R-loop formations may be coupled. These findings identify sequence substitution as an early step in cotranscriptional RNA processing.

  12. Fluorescent whole-mount RNA in situ hybridization (F-WISH) in plant germ cells and the fertilized ovule.

    Science.gov (United States)

    Bleckmann, Andrea; Dresselhaus, Thomas

    2016-04-01

    First evidence on gene function and regulation is provided by the cellular expression pattern in complex tissues. However, to understand the activity of a specific gene, it is essential to analyze the regulatory network, which controls the spatio-temporal translation pattern during the entire life span of the transcribed mRNA. To explore mechanisms which control mRNA abundance and localization in space and time, it is necessary to visualize mRNAs quantitatively with a subcellular resolution, without sectioning the tissues. We have adapted and optimized a protocol for colorimetric whole-mount RNA in situ hybridization (WISH) using egg cell-specific digoxigenin (DIG) labeled probes (Hejátko et al., 2006) [1] on ovules and early seeds of Arabidopsis. Furthermore, we established a fluorescent whole-mount RNA in situ hybridization (F-WISH) protocol, which allows mRNA visualization on a subcellular level. The polar localized mRNA of SBT4.13, encoding a subtilase, was identified using this protocol. Both methods are described and discussed in detail. Additionally a (F)-WISH flow-chart is provided along with a troubleshooting table. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Deletions in cox2 mRNA result in loss of splicing and RNA editing and gain of novel RNA editing sites.

    Directory of Open Access Journals (Sweden)

    Stefanie Grüttner

    Full Text Available As previously demonstrated, the maize cox2 RNA is fully edited in cauliflower mitochondria. Use of constructs with a deleted cox2 intron, however, led to a loss of RNA editing at almost all editing sites, with only a few sites still partially edited. Likewise, one deletion in exon 1 and three in exon 2 abolish RNA editing at all cox2 sites analyzed. Furthermore, intron splicing is abolished using these deletions. Mutation of a cytosine residue, which is normally edited and localized directly adjacent to the intron, to thymidine did not result in restoration of splicing, indicating that the loss of splicing was not due to loss of RNA editing. One deletion in exon 2 did not lead to loss of splicing. Instead, most editing sites were found to be edited, only three were not edited. Unexpectedly, we observed additional RNA editing events at new sites. Thus it appears that deletions in the cox2 RNA sequence can have a strong effect on RNA processing, leading to loss of splicing, loss of editing at all sites, or even to a gain of new editing sites. As these effects are not limited to the vicinity of the respective deletions, but appear to be widespread or even affect all editing sites, they may not be explained by the loss of PPR binding sites. Instead, it appears that several parts of the cox2 transcript are required for proper RNA processing. This indicates the roles of the RNA sequence and structural elements in the recognition of the editing sites.

  14. siRNA and innate immunity.

    Science.gov (United States)

    Robbins, Marjorie; Judge, Adam; MacLachlan, Ian

    2009-06-01

    Canonical small interfering RNA (siRNA) duplexes are potent activators of the mammalian innate immune system. The induction of innate immunity by siRNA is dependent on siRNA structure and sequence, method of delivery, and cell type. Synthetic siRNA in delivery vehicles that facilitate cellular uptake can induce high levels of inflammatory cytokines and interferons after systemic administration in mammals and in primary human blood cell cultures. This activation is predominantly mediated by immune cells, normally via a Toll-like receptor (TLR) pathway. The siRNA sequence dependency of these pathways varies with the type and location of the TLR involved. Alternatively nonimmune cell activation may also occur, typically resulting from siRNA interaction with cytoplasmic RNA sensors such as RIG1. As immune activation by siRNA-based drugs represents an undesirable side effect due to the considerable toxicities associated with excessive cytokine release in humans, understanding and abrogating this activity will be a critical component in the development of safe and effective therapeutics. This review describes the intracellular mechanisms of innate immune activation by siRNA, the design of appropriate sequences and chemical modification approaches, and suitable experimental methods for studying their effects, with a view toward reducing siRNA-mediated off-target effects.

  15. 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.

  16. 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.

  17. TGF-β Suppression of HBV RNA through AID-Dependent Recruitment of an RNA Exosome Complex

    Science.gov (United States)

    Kitamura, Kouichi; Wang, Zhe; Chowdhury, Sajeda; Monjurul, Ahasan Md; Wakae, Kousho; Koura, Miki; Shimadu, Miyuki; Kinoshita, Kazuo; Muramatsu, Masamichi

    2015-01-01

    Transforming growth factor (TGF)-β inhibits hepatitis B virus (HBV) replication although the intracellular effectors involved are not determined. Here, we report that reduction of HBV transcripts by TGF-β is dependent on AID expression, which significantly decreases both HBV transcripts and viral DNA, resulting in inhibition of viral replication. Immunoprecipitation reveals that AID physically associates with viral P protein that binds to specific virus RNA sequence called epsilon. AID also binds to an RNA degradation complex (RNA exosome proteins), indicating that AID, RNA exosome, and P protein form an RNP complex. Suppression of HBV transcripts by TGF-β was abrogated by depletion of either AID or RNA exosome components, suggesting that AID and the RNA exosome involve in TGF-β mediated suppression of HBV RNA. Moreover, AID-mediated HBV reduction does not occur when P protein is disrupted or when viral transcription is inhibited. These results suggest that induced expression of AID by TGF-β causes recruitment of the RNA exosome to viral RNP complex and the RNA exosome degrades HBV RNA in a transcription-coupled manner. PMID:25836330

  18. Creating spaces for Eziko Sipheka Sisophula theoretical framework ...

    African Journals Online (AJOL)

    Within the academy, science and theories have historically been constructed in ways that maintain and privilege the centrality, superiority, legitimacy and universality of western thinking as 'regimes of truth'. The theoretical value of indigenous theories and science has often been denied because theorizing has been ...

  19. 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.

  20. Practice-centred evaluation and the privileging of care in health information technology evaluation.

    Science.gov (United States)

    Darking, Mary; Anson, Rachel; Bravo, Ferdinand; Davis, Julie; Flowers, Steve; Gillingham, Emma; Goldberg, Lawrence; Helliwell, Paul; Henwood, Flis; Hudson, Claire; Latimer, Simon; Lowes, Paul; Stirling, Ian

    2014-06-05

    Our contribution, drawn from our experience of the case study provided, is a protocol for practice-centred, participative evaluation of technology in the clinical setting that privileges care. In this context 'practice-centred' evaluation acts as a scalable, coordinating framework for evaluation that recognises health information technology supported care as an achievement that is contingent and ongoing. We argue that if complex programmes of technology-enabled service innovation are understood in terms of their contribution to patient care and supported by participative, capability-building evaluation methodologies, conditions are created for practitioners and patients to realise the potential of technologies and make substantive contributions to the evidence base underpinning health innovation programmes. Electronic Patient Records (EPRs) and telemedicine are positioned by policymakers as health information technologies that are integral to achieving improved clinical outcomes and efficiency savings. However, evaluating the extent to which these aims are met poses distinct evaluation challenges, particularly where clinical and cost outcomes form the sole focus of evaluation design. We propose that a practice-centred approach to evaluation - in which those whose day-to-day care practice is altered (or not) by the introduction of new technologies are placed at the centre of evaluation efforts - can complement and in some instances offer advantages over, outcome-centric evaluation models. We carried out a regional programme of innovation in renal services where a participative approach was taken to the introduction of new technologies, including: a regional EPR system and a system to support video clinics. An 'action learning' approach was taken to procurement, pre-implementation planning, implementation, ongoing development and evaluation. Participants included clinicians, technology specialists, patients and external academic researchers. Whilst undergoing these

  1. Shielding the messenger (RNA): microRNA-based anticancer therapies

    Science.gov (United States)

    Sotillo, Elena; Thomas-Tikhonenko, Andrei

    2011-01-01

    It has been a decade since scientists realized that microRNAs (miRNAs) are not an oddity invented by worms to regulate gene expression at post-transcriptional levels. Rather, many of these 21–22-nucleotide-short RNAs exist in invertebrates and vertebrates alike and some of them are in fact highly conserved. miRNAs are now recognized as an important class of non-coding small RNAs that inhibit gene expression by targeting mRNA stability and translation. In the last ten years, our knowledge of the miRNAs world was expanding at vertiginous speed, propelled by the development of computational engines for miRNA identification and target prediction, biochemical tools and techniques to modulate miRNA activity, and last but not least, the emergence of miRNA-centric animal models. One important conclusion that has emerged from this effort is that many microRNAs and their cognate targets are strongly implicated in cancer, either as oncogenes or tumor and metastasis suppressors. In this review we will discuss the diverse role that miRNAs play in cancer initiation and progression and also the tools with which miRNA expression could be corrected in vivo. While the idea of targeting microRNAs towards therapeutic ends is getting considerable traction, basic, translational, and clinical research done in the next few years will tell whether this promise is well-founded. PMID:21514318

  2. Transfer RNA and human disease

    Directory of Open Access Journals (Sweden)

    Jamie A Abbott

    2014-06-01

    Full Text Available Pathological mutations in tRNA genes and tRNA processing enzymes are numerous and result in very complicated clinical phenotypes. Mitochondrial tRNA (mt-tRNA genes are hotspots for pathological mutations and over 200 mt-tRNA mutations have been linked to various disease states. Often these mutations prevent tRNA aminoacylation. Disrupting this primary function affects protein synthesis and the expression, folding, and function of oxidative phosphorylation enzymes. Mitochondrial tRNA mutations manifest in a wide panoply of diseases related to cellular energetics, including COX deficiency (cytochrome C oxidase, mitochondrial myopathy, MERRF (Myoclonic Epilepsy with Ragged Red Fibers, and MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes. Diseases caused by mt-tRNA mutations can also affect very specific tissue types, as in the case of neurosensory non-syndromic hearing loss and pigmentary retinopathy, diabetes mellitus, and hypertrophic cardiomyopathy. Importantly, mitochondrial heteroplasmy plays a role in disease severity and age of onset as well. Not surprisingly, mutations in enzymes that modify cytoplasmic and mitochondrial tRNAs are also linked to a diverse range of clinical phenotypes. In addition to compromised aminoacylation of the tRNAs, mutated modifying enzymes can also impact tRNA expression and abundance, tRNA modifications, tRNA folding, and even tRNA maturation (e.g., splicing. Some of these pathological mutations in tRNAs and processing enzymes are likely to affect non-canonical tRNA functions, and contribute to the diseases without significantly impacting on translation. This chapter will review recent literature on the relation of mitochondrial and cytoplasmic tRNA, and enzymes that process tRNAs, to human disease. We explore the mechanisms involved in the clinical presentation of these various diseases with an emphasis on neurological disease.

  3. Transfer RNA and human disease.

    Science.gov (United States)

    Abbott, Jamie A; Francklyn, Christopher S; Robey-Bond, Susan M

    2014-01-01

    Pathological mutations in tRNA genes and tRNA processing enzymes are numerous and result in very complicated clinical phenotypes. Mitochondrial tRNA (mt-tRNA) genes are "hotspots" for pathological mutations and over 200 mt-tRNA mutations have been linked to various disease states. Often these mutations prevent tRNA aminoacylation. Disrupting this primary function affects protein synthesis and the expression, folding, and function of oxidative phosphorylation enzymes. Mitochondrial tRNA mutations manifest in a wide panoply of diseases related to cellular energetics, including COX deficiency (cytochrome C oxidase), mitochondrial myopathy, MERRF (Myoclonic Epilepsy with Ragged Red Fibers), and MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). Diseases caused by mt-tRNA mutations can also affect very specific tissue types, as in the case of neurosensory non-syndromic hearing loss and pigmentary retinopathy, diabetes mellitus, and hypertrophic cardiomyopathy. Importantly, mitochondrial heteroplasmy plays a role in disease severity and age of onset as well. Not surprisingly, mutations in enzymes that modify cytoplasmic and mitochondrial tRNAs are also linked to a diverse range of clinical phenotypes. In addition to compromised aminoacylation of the tRNAs, mutated modifying enzymes can also impact tRNA expression and abundance, tRNA modifications, tRNA folding, and even tRNA maturation (e.g., splicing). Some of these pathological mutations in tRNAs and processing enzymes are likely to affect non-canonical tRNA functions, and contribute to the diseases without significantly impacting on translation. This chapter will review recent literature on the relation of mitochondrial and cytoplasmic tRNA, and enzymes that process tRNAs, to human disease. We explore the mechanisms involved in the clinical presentation of these various diseases with an emphasis on neurological disease.

  4. Integrated mRNA and microRNA transcriptome sequencing characterizes sequence variants and mRNA–microRNA regulatory network in nasopharyngeal carcinoma model systems

    Directory of Open Access Journals (Sweden)

    Carol Ying-Ying Szeto

    2014-01-01

    Full Text Available Nasopharyngeal carcinoma (NPC is a prevalent malignancy in Southeast Asia among the Chinese population. Aberrant regulation of transcripts has been implicated in many types of cancers including NPC. Herein, we characterized mRNA and miRNA transcriptomes by RNA sequencing (RNASeq of NPC model systems. Matched total mRNA and small RNA of undifferentiated Epstein–Barr virus (EBV-positive NPC xenograft X666 and its derived cell line C666, well-differentiated NPC cell line HK1, and the immortalized nasopharyngeal epithelial cell line NP460 were sequenced by Solexa technology. We found 2812 genes and 149 miRNAs (human and EBV to be differentially expressed in NP460, HK1, C666 and X666 with RNASeq; 533 miRNA–mRNA target pairs were inversely regulated in the three NPC cell lines compared to NP460. Integrated mRNA/miRNA expression profiling and pathway analysis show extracellular matrix organization, Beta-1 integrin cell surface interactions, and the PI3K/AKT, EGFR, ErbB, and Wnt pathways were potentially deregulated in NPC. Real-time quantitative PCR was performed on selected mRNA/miRNAs in order to validate their expression. Transcript sequence variants such as short insertions and deletions (INDEL, single nucleotide variant (SNV, and isomiRs were characterized in the NPC model systems. A novel TP53 transcript variant was identified in NP460, HK1, and C666. Detection of three previously reported novel EBV-encoded BART miRNAs and their isomiRs were also observed. Meta-analysis of a model system to a clinical system aids the choice of different cell lines in NPC studies. This comprehensive characterization of mRNA and miRNA transcriptomes in NPC cell lines and the xenograft provides insights on miRNA regulation of mRNA and valuable resources on transcript variation and regulation in NPC, which are potentially useful for mechanistic and preclinical studies.

  5. Semiautomated improvement of RNA alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth; Lind-Thomsen, Allan; Knudsen, Bjarne

    2007-01-01

    connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database...... and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster......: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture...

  6. A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool

    Science.gov (United States)

    Bloom-Ackermann, Zohar; Navon, Sivan; Gingold, Hila; Towers, Ruth; Pilpel, Yitzhak; Dahan, Orna

    2014-01-01

    Deciphering the architecture of the tRNA pool is a prime challenge in translation research, as tRNAs govern the efficiency and accuracy of the process. Towards this challenge, we created a systematic tRNA deletion library in Saccharomyces cerevisiae, aimed at dissecting the specific contribution of each tRNA gene to the tRNA pool and to the cell's fitness. By harnessing this resource, we observed that the majority of tRNA deletions show no appreciable phenotype in rich medium, yet under more challenging conditions, additional phenotypes were observed. Robustness to tRNA gene deletion was often facilitated through extensive backup compensation within and between tRNA families. Interestingly, we found that within tRNA families, genes carrying identical anti-codons can contribute differently to the cellular fitness, suggesting the importance of the genomic surrounding to tRNA expression. Characterization of the transcriptome response to deletions of tRNA genes exposed two disparate patterns: in single-copy families, deletions elicited a stress response; in deletions of genes from multi-copy families, expression of the translation machinery increased. Our results uncover the complex architecture of the tRNA pool and pave the way towards complete understanding of their role in cell physiology. PMID:24453985

  7. Small Molecule Modifiers of the microRNA and RNA Interference Pathway

    OpenAIRE

    Deiters, Alexander

    2009-01-01

    Recently, the RNA interference (RNAi) pathway has become the target of small molecule inhibitors and activators. RNAi has been well established as a research tool in the sequence-specific silencing of genes in eukaryotic cells and organisms by using exogenous, small, double-stranded RNA molecules of approximately 20 nucleotides. Moreover, a recently discovered post-transcriptional gene regulatory mechanism employs microRNAs (miRNAs), a class of endogenously expressed small RNA molecules, whic...

  8. A framework for multiple kernel support vector regression and its applications to siRNA efficacy prediction.

    Science.gov (United States)

    Qiu, Shibin; Lane, Terran

    2009-01-01

    The cell defense mechanism of RNA interference has applications in gene function analysis and promising potentials in human disease therapy. To effectively silence a target gene, it is desirable to select appropriate initiator siRNA molecules having satisfactory silencing capabilities. Computational prediction for silencing efficacy of siRNAs can assist this screening process before using them in biological experiments. String kernel functions, which operate directly on the string objects representing siRNAs and target mRNAs, have been applied to support vector regression for the prediction and improved accuracy over numerical kernels in multidimensional vector spaces constructed from descriptors of siRNA design rules. To fully utilize information provided by string and numerical data, we propose to unify the two in a kernel feature space by devising a multiple kernel regression framework where a linear combination of the kernels is used. We formulate the multiple kernel learning into a quadratically constrained quadratic programming (QCQP) problem, which although yields global optimal solution, is computationally demanding and requires a commercial solver package. We further propose three heuristics based on the principle of kernel-target alignment and predictive accuracy. Empirical results demonstrate that multiple kernel regression can improve accuracy, decrease model complexity by reducing the number of support vectors, and speed up computational performance dramatically. In addition, multiple kernel regression evaluates the importance of constituent kernels, which for the siRNA efficacy prediction problem, compares the relative significance of the design rules. Finally, we give insights into the multiple kernel regression mechanism and point out possible extensions.

  9. Analysis of intermolecular RNA-RNA recombination by rubella virus

    International Nuclear Information System (INIS)

    Adams, Sandra D.; Tzeng, W.-P.; Chen, M.-H.; Frey, Teryl K.

    2003-01-01

    To investigate whether rubella virus (RUB) undergoes intermolecular RNA-RNA recombination, cells were cotransfected with pairs of in vitro transcripts from genomic cDNA plasmid vectors engineered to contain nonoverlapping deletions: the replicative transcript maintained the 5'-proximal nonstructural (NS) ORF (which contained the replicase, making it RNA replication competent), had a deletion in the 3'-proximal structural protein (SP) ORF, and maintained the 3' end of the genome, including the putative 3' cis-acting elements (CSE), while the nonreplicative transcript consisted of the 3' half of the genome including the SP-ORF and 3' CSE. Cotransfection yielded plaque-forming virus that synthesized the standard genomic and subgenomic RNAs and thus was generated by RNA-RNA recombination. Using transcripts tagged with a 3'-terminal deletion, it was found that recombinants contained the 3' end derived from the replicative strand, indicating a cis-preference for initiation of negative-strand synthesis. In cotransfections in which the replicative transcript lacked the 3' CSE, recombination occurred, albeit at lower efficiency, indicating that initiation in trans from the NS-ORF can occur. The 3' CSE was sufficient as a nonreplicative transcript, showing that it can serve as a promoter for negative-strand RNA synthesis. While deletion mutagenesis showed that the presence of the junction untranslated region (J-UTR) between the ORFs appeared to be necessary on both transcripts for recombination in this region of the genome, analysis with transcripts tagged with restriction sites showed that the J-UTR was not a hot spot for recombination compared to neighboring regions in both ORFs. Sequence analysis of recombinants revealed that both precise (homologous) and imprecise recombination (aberrant, homologous resulting in duplications) occurred; however, imprecise recombination only involved the J-UTR or the 3' end of the NS-ORF and the J-UTR (maintaining the NS-ORF), indicating

  10. 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.

  11. 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.

  12. miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy.

    Directory of Open Access Journals (Sweden)

    Alexander S Baras

    Full Text Available Small RNA RNA-seq for microRNAs (miRNAs is a rapidly developing field where opportunities still exist to create better bioinformatics tools to process these large datasets and generate new, useful analyses. We built miRge to be a fast, smart small RNA-seq solution to process samples in a highly multiplexed fashion. miRge employs a Bayesian alignment approach, whereby reads are sequentially aligned against customized mature miRNA, hairpin miRNA, noncoding RNA and mRNA sequence libraries. miRNAs are summarized at the level of raw reads in addition to reads per million (RPM. Reads for all other RNA species (tRNA, rRNA, snoRNA, mRNA are provided, which is useful for identifying potential contaminants and optimizing small RNA purification strategies. miRge was designed to optimally identify miRNA isomiRs and employs an entropy based statistical measurement to identify differential production of isomiRs. This allowed us to identify decreasing entropy in isomiRs as stem cells mature into retinal pigment epithelial cells. Conversely, we show that pancreatic tumor miRNAs have similar entropy to matched normal pancreatic tissues. In a head-to-head comparison with other miRNA analysis tools (miRExpress 2.0, sRNAbench, omiRAs, miRDeep2, Chimira, UEA small RNA Workbench, miRge was faster (4 to 32-fold and was among the top-two methods in maximally aligning miRNAs reads per sample. Moreover, miRge has no inherent limits to its multiplexing. miRge was capable of simultaneously analyzing 100 small RNA-Seq samples in 52 minutes, providing an integrated analysis of miRNA expression across all samples. As miRge was designed for analysis of single as well as multiple samples, miRge is an ideal tool for high and low-throughput users. miRge is freely available at http://atlas.pathology.jhu.edu/baras/miRge.html.

  13. Deep sequencing of cardiac microRNA-mRNA interactomes in clinical and experimental cardiomyopathy.

    Science.gov (United States)

    Matkovich, Scot J; Dorn, Gerald W

    2015-01-01

    MicroRNAs are a family of short (~21 nucleotide) noncoding RNAs that serve key roles in cellular growth and differentiation and the response of the heart to stress stimuli. As the sequence-specific recognition element of RNA-induced silencing complexes (RISCs), microRNAs bind mRNAs and prevent their translation via mechanisms that may include transcript degradation and/or prevention of ribosome binding. Short microRNA sequences and the ability of microRNAs to bind to mRNA sites having only partial/imperfect sequence complementarity complicate purely computational analyses of microRNA-mRNA interactomes. Furthermore, computational microRNA target prediction programs typically ignore biological context, and therefore the principal determinants of microRNA-mRNA binding: the presence and quantity of each. To address these deficiencies we describe an empirical method, developed via studies of stressed and failing hearts, to determine disease-induced changes in microRNAs, mRNAs, and the mRNAs targeted to the RISC, without cross-linking mRNAs to RISC proteins. Deep sequencing methods are used to determine RNA abundances, delivering unbiased, quantitative RNA data limited only by their annotation in the genome of interest. We describe the laboratory bench steps required to perform these experiments, experimental design strategies to achieve an appropriate number of sequencing reads per biological replicate, and computer-based processing tools and procedures to convert large raw sequencing data files into gene expression measures useful for differential expression analyses.

  14. The replisome uses mRNA as a primer after colliding with RNA polymerase.

    Science.gov (United States)

    Pomerantz, Richard T; O'Donnell, Mike

    2008-12-11

    Replication forks are impeded by DNA damage and protein-nucleic acid complexes such as transcribing RNA polymerase. For example, head-on collision of the replisome with RNA polymerase results in replication fork arrest. However, co-directional collision of the replisome with RNA polymerase has little or no effect on fork progression. Here we examine co-directional collisions between a replisome and RNA polymerase in vitro. We show that the Escherichia coli replisome uses the RNA transcript as a primer to continue leading-strand synthesis after the collision with RNA polymerase that is displaced from the DNA. This action results in a discontinuity in the leading strand, yet the replisome remains intact and bound to DNA during the entire process. These findings underscore the notable plasticity by which the replisome operates to circumvent obstacles in its path and may explain why the leading strand is synthesized discontinuously in vivo.

  15. RNA interference analyses suggest a transcript-specific regulatory role for mitochondrial RNA-binding proteins MRP1 and MRP2 in RNA editing and other RNA processing in Trypanosoma brucei

    NARCIS (Netherlands)

    Vondrusková, Eva; van den Burg, Janny; Zíková, Alena; Ernst, Nancy Lewis; Stuart, Kenneth; Benne, Rob; Lukes, Julius

    2005-01-01

    Mitochondrial RNA-binding proteins MRP1 and MRP2 occur in a heteromeric complex that appears to play a role in U-insertion/deletion editing in trypanosomes. Reduction in the levels of MRP1 (gBP21) and/or MRP2 (gBP25) mRNA by RNA interference in procyclic Trypanosoma brucei resulted in severe growth

  16. Assembling RNA Nanoparticles.

    Science.gov (United States)

    Xiao, Shou-Jun

    2017-01-01

    RNA nanoparticles are designed and self-assembled according to noncanonical interactions of naturally conserved RNA motifs and/or canonical Watson-Crick base-pairing interactions, which have potential applications in gene therapy and nanomedicine. These artificially engineered nanoparticles are mainly synthesized from in vitro transcribed RNAs, purified by denaturing and native polyacrylamide gel electrophoresis (PAGE), and characterized with native PAGE, AFM, and TEM technologies. The protocols of in vitro transcription, denaturing and native PAGE, and RNA nanoparticle self-assembly are described in detail.

  17. In vitro transcription of Sonchus yellow net virus RNA by a virus-associated RNA-dependent RNA polymerase

    NARCIS (Netherlands)

    Flore, P.H.

    1986-01-01

    The aim of the investigation presented in this thesis was to elucidate the nature of the RNA- dependent RNA polymerase, thought to be associated with Sonchus yellow net virus (SYNV), a rhabdovirus infecting plants. This research was initiated to shed light on the

  18. Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Xiaofei [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036 (China); Deng, Ping; Cui, Hongguang [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); Wang, Aiming, E-mail: aiming.wang@agr.gc.ca [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada)

    2015-11-15

    Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

  19. Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

    International Nuclear Information System (INIS)

    Cheng, Xiaofei; Deng, Ping; Cui, Hongguang; Wang, Aiming

    2015-01-01

    Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

  20. RNA polymerase II mediated transcription from the polymerase III promoters in short hairpin RNA expression vector

    International Nuclear Information System (INIS)

    Rumi, Mohammad; Ishihara, Shunji; Aziz, Monowar; Kazumori, Hideaki; Ishimura, Norihisa; Yuki, Takafumi; Kadota, Chikara; Kadowaki, Yasunori; Kinoshita, Yoshikazu

    2006-01-01

    RNA polymerase III promoters of human ribonuclease P RNA component H1, human U6, and mouse U6 small nuclear RNA genes are commonly used in short hairpin RNA (shRNA) expression vectors due their precise initiation and termination sites. During transient transfection of shRNA vectors, we observed that H1 or U6 promoters also express longer transcripts enough to express several reporter genes including firefly luciferase, green fluorescent protein EGFP, and red fluorescent protein JRed. Expression of such longer transcripts was augmented by upstream RNA polymerase II enhancers and completely inhibited by downstream polyA signal sequences. Moreover, the transcription of firefly luciferase from human H1 promoter was sensitive to RNA polymerase II inhibitor α-amanitin. Our findings suggest that commonly used polymerase III promoters in shRNA vectors are also prone to RNA polymerase II mediated transcription, which may have negative impacts on their targeted use