Reconstitution of wild type viral DNA in simian cells transfected with early and late SV40 defective genomes.

PubMed

O'Neill, F J; Gao, Y; Xu, X

1993-11-01

The DNAs of polyomaviruses ordinarily exist as a single circular molecule of approximately 5000 base pairs. Variants of SV40, BKV and JCV have been described which contain two complementing defective DNA molecules. These defectives, which form a bipartite genome structure, contain either the viral early region or the late region. The defectives have the unique property of being able to tolerate variable sized reiterations of regulatory and terminus region sequences, and portions of the coding region. They can also exchange coding region sequences with other polyomaviruses. It has been suggested that the bipartite genome structure might be a stage in the evolution of polyomaviruses which can uniquely sustain genome and sequence diversity. However, it is not known if the regulatory and terminus region sequences are highly mutable. Also, it is not known if the bipartite genome structure is reversible and what the conditions might be which would favor restoration of the monomolecular genome structure. We addressed the first question by sequencing the reiterated regulatory and terminus regions of E- and L-SV40 DNAs. This revealed a large number of mutations in the regulatory regions of the defective genomes, including deletions, insertions, rearrangements and base substitutions. We also detected insertions and base substitutions in the T-antigen gene. We addressed the second question by introducing into permissive simian cells, E- and L-SV40 genomes which had been engineered to contain only a single regulatory region. Analysis of viral DNA from transfected cells demonstrated recombined genomes containing a wild type monomolecular DNA structure. However, the complete defectives, containing reiterated regulatory regions, could often compete away the wild type genomes. The recombinant monomolecular genomes were isolated, cloned and found to be infectious. All of the DNA alterations identified in one of the regulatory regions of E-SV40 DNA were present in the recombinant monomolecular genomes. These and other findings indicate that the bipartite genome state can sustain many mutations which wtSV40 cannot directly sustain. However, the mutations can later be introduced into the wild type genomes when the E- and L-SV40 DNAs recombine to generate a new monomolecular genome structure.

Online Schooling: A Cautionary Tale

ERIC Educational Resources Information Center

Saultz, Andrew; Fusarelli, Lance D.

2017-01-01

In this controversy piece, we portray online learning as growing too fast for existing regulatory structures to oversee and generally as having failed to live up to its potential. Operators, particularly for-profit operators, have generally not produced successful schools. We urge reforms of cyber schooling funding mechanisms, data systems, and…

77 FR 55519 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-10

...\\ and Rule 19b-4 thereunder,\\2\\ a proposed rule change to adopt existing NASD Interpretive Material... Policy The proposed rule change would replace several existing provisions in the Front Running Policy...-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving Proposed Rule Change...

Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development1[C][W][OA

PubMed Central

Mounet, Fabien; Moing, Annick; Garcia, Virginie; Petit, Johann; Maucourt, Michael; Deborde, Catherine; Bernillon, Stéphane; Le Gall, Gwénaëlle; Colquhoun, Ian; Defernez, Marianne; Giraudel, Jean-Luc; Rolin, Dominique; Rothan, Christophe; Lemaire-Chamley, Martine

2009-01-01

Variations in early fruit development and composition may have major impacts on the taste and the overall quality of ripe tomato (Solanum lycopersicum) fruit. To get insights into the networks involved in these coordinated processes and to identify key regulatory genes, we explored the transcriptional and metabolic changes in expanding tomato fruit tissues using multivariate analysis and gene-metabolite correlation networks. To this end, we demonstrated and took advantage of the existence of clear structural and compositional differences between expanding mesocarp and locular tissue during fruit development (12–35 d postanthesis). Transcriptome and metabolome analyses were carried out with tomato microarrays and analytical methods including proton nuclear magnetic resonance and liquid chromatography-mass spectrometry, respectively. Pairwise comparisons of metabolite contents and gene expression profiles detected up to 37 direct gene-metabolite correlations involving regulatory genes (e.g. the correlations between glutamine, bZIP, and MYB transcription factors). Correlation network analyses revealed the existence of major hub genes correlated with 10 or more regulatory transcripts and embedded in a large regulatory network. This approach proved to be a valuable strategy for identifying specific subsets of genes implicated in key processes of fruit development and metabolism, which are therefore potential targets for genetic improvement of tomato fruit quality. PMID:19144766

Regulatory and clinical considerations for biosimilar oncology drugs

PubMed Central

Bennett, Charles L; Chen, Brian; Hermanson, Terhi; Wyatt, Michael D; Schulz, Richard M; Georgantopoulos, Peter; Kessler, Samuel; Raisch, Dennis W; Qureshi, Zaina P; Lu, Z Kevin; Love, Bryan L; Noxon, Virginia; Bobolts, Laura; Armitage, Melissa; Bian, John; Ray, Paul; Ablin, Richard J; Hrushesky, William J; Macdougall, Iain C; Sartor, Oliver; Armitage, James O

2015-01-01

Biological oncology products are integral to cancer treatment, but their high costs pose challenges to patients, families, providers, and insurers. The introduction of biosimilar agents—molecules that are similar in structure, function, activity, immunogenicity, and safety to the original biological drugs—provide opportunities both to improve healthcare access and outcomes, and to reduce costs. Several international regulatory pathways have been developed to expedite entry of biosimilars into global marketplaces. The first wave of oncology biosimilar use was in Europe and India in 2007. Oncology biosimilars are now widely marketed in several countries in Europe, and in Australia, Japan, China, Russia, India, and South Korea. Their use is emerging worldwide, with the notable exception of the USA, where several regulatory and cost barriers to biosimilar approval exist. In this Review, we discuss oncology biosimilars and summarise their regulatory frameworks, clinical experiences, and safety concerns. PMID:25456378

75 FR 39307 - Self-Regulatory Organizations; EDGX Exchange, Inc.; Notice of Filing and Immediate Effectiveness...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-08

... rule change reflects a competitive pricing structure designed to incent market participants to direct..., and is similar to existing pricing for this order type on the International Securities Exchange, LLC... that it operates in a highly competitive market in which market participants can readily direct order...

NEGOTIATING STRUCTURAL VULNERABILITY FOLLOWING REGULATORY CHANGES TO A PROVINCIAL METHADONE PROGRAM IN VANCOUVER, CANADA: A QUALITATIVE STUDY

PubMed Central

McNeil, Ryan; Kerr, Thomas; Anderson, Solanna; Maher, Lisa; Keewatin, Chereece; Milloy, MJ; Wood, Evan; Small, Will

2015-01-01

While regulatory frameworks governing methadone maintenance therapy (MMT) require highly regimented treatment programs that shape treatment outcomes, little research has examined the effects of regulatory changes to these programs on those receiving treatment, and located their experiences within the wider context of socialstructural inequities. In British Columbia (BC), Canada, provincial regulations governing MMT have recently been modified, including: replacing the existing methadone formulation with Methadose® (pre-mixed and 10 times more concentrated); prohibiting pharmacy delivery of methadone; and, prohibiting pharmacies incentives for methadone dispensation. We undertook this study to examine the impacts of these changes on a structurally vulnerable population enrolled in MMT in Vancouver, BC. Qualitative interviews were conducted with 34 people enrolled in MMT and recruited from two ongoing observational prospective cohort studies comprised of drug-using individuals in the six-month period in 2014 following these regulatory changes. Interview transcripts were analyzed thematically, and by drawing on the concept of ‘structural vulnerability’. Findings underscore how these regulatory changes disrupted treatment engagement, producing considerable health and social harms. The introduction of Methadose® precipitated increased withdrawal symptoms. The discontinuation of pharmacy delivery services led to interruptions in MMT and codispensed HIV medications due to constraints stemming from their structural vulnerability (e.g., poverty, homelessness). Meanwhile, the loss of pharmacy incentives limited access to material supports utilized by participants to overcome barriers to MMT, while diminishing their capacity to assert some degree of agency in negotiating dispensation arrangements with pharmacies. Collectively, these changes functioned to compromise MMT engagement and increased structural vulnerability to harm, including re-initiation of injection drug use and participation in high-risk incomegenerating strategies. Greater attention to the impacts of social-structural inequities on MMT engagement is needed when modifying MMT programs, especially as other jurisdictions are adopting similar changes. Comprehensive environmental supports should be provided to minimize adverse outcomes during transitional periods. PMID:25875323

Structural basis for ligand-dependent dimerization of phenylalanine hydroxylase regulatory domain

PubMed Central

Patel, Dipali; Kopec, Jolanta; Fitzpatrick, Fiona; McCorvie, Thomas J.; Yue, Wyatt W.

2016-01-01

The multi-domain enzyme phenylalanine hydroxylase (PAH) catalyzes the hydroxylation of dietary I-phenylalanine (Phe) to I-tyrosine. Inherited mutations that result in PAH enzyme deficiency are the genetic cause of the autosomal recessive disorder phenylketonuria. Phe is the substrate for the PAH active site, but also an allosteric ligand that increases enzyme activity. Phe has been proposed to bind, in addition to the catalytic domain, a site at the PAH N-terminal regulatory domain (PAH-RD), to activate the enzyme via an unclear mechanism. Here we report the crystal structure of human PAH-RD bound with Phe at 1.8 Å resolution, revealing a homodimer of ACT folds with Phe bound at the dimer interface. This work delivers the structural evidence to support previous solution studies that a binding site exists in the RD for Phe, and that Phe binding results in dimerization of PAH-RD. Consistent with our structural observation, a disease-associated PAH mutant impaired in Phe binding disrupts the monomer:dimer equilibrium of PAH-RD. Our data therefore support an emerging model of PAH allosteric regulation, whereby Phe binds to PAH-RD and mediates the dimerization of regulatory modules that would bring about conformational changes to activate the enzyme. PMID:27049649

A novel statistical approach for identification of the master regulator transcription factor.

PubMed

Sikdar, Sinjini; Datta, Susmita

2017-02-02

Transcription factors are known to play key roles in carcinogenesis and therefore, are gaining popularity as potential therapeutic targets in drug development. A 'master regulator' transcription factor often appears to control most of the regulatory activities of the other transcription factors and the associated genes. This 'master regulator' transcription factor is at the top of the hierarchy of the transcriptomic regulation. Therefore, it is important to identify and target the master regulator transcription factor for proper understanding of the associated disease process and identifying the best therapeutic option. We present a novel two-step computational approach for identification of master regulator transcription factor in a genome. At the first step of our method we test whether there exists any master regulator transcription factor in the system. We evaluate the concordance of two ranked lists of transcription factors using a statistical measure. In case the concordance measure is statistically significant, we conclude that there is a master regulator. At the second step, our method identifies the master regulator transcription factor, if there exists one. In the simulation scenario, our method performs reasonably well in validating the existence of a master regulator when the number of subjects in each treatment group is reasonably large. In application to two real datasets, our method ensures the existence of master regulators and identifies biologically meaningful master regulators. An R code for implementing our method in a sample test data can be found in http://www.somnathdatta.org/software . We have developed a screening method of identifying the 'master regulator' transcription factor just using only the gene expression data. Understanding the regulatory structure and finding the master regulator help narrowing the search space for identifying biomarkers for complex diseases such as cancer. In addition to identifying the master regulator our method provides an overview of the regulatory structure of the transcription factors which control the global gene expression profiles and consequently the cell functioning.

Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits

PubMed Central

2016-01-01

Ions regulate the assembly and mechanical properties of actin filaments. Recent work using structural bioinformatics and site-specific mutagenesis favors the existence of two discrete and specific divalent cation binding sites on actin filaments, positioned in the long axis between actin subunits. Cation binding at one site drives polymerization, while the other modulates filament stiffness and plays a role in filament severing by the regulatory protein, cofilin. Existing structural methods have not been able to resolve filament-associated cations, and so in this work we turn to molecular dynamics simulations to suggest a candidate binding pocket geometry for each site and to elucidate the mechanism by which occupancy of the “stiffness site” affects filament mechanical properties. Incorporating a magnesium ion in the “polymerization site” does not seem to require any large-scale change to an actin subunit’s conformation. Binding of a magnesium ion in the “stiffness site” adheres the actin DNase-binding loop (D-loop) to its long-axis neighbor, which increases the filament torsional stiffness and bending persistence length. Our analysis shows that bound D-loops occupy a smaller region of accessible conformational space. Cation occupancy buries key conserved residues of the D-loop, restricting accessibility to regulatory proteins and enzymes that target these amino acids. PMID:27146246

75 FR 30890 - Self-Regulatory Organizations; New York Stock Exchange LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-02

... structure which is based on member organizations. The Exchange ceased to be a member-owned organization in... left that member organization to become an independent floor broker without a public business or to become associated with a new member organization without a public business that was comprised of existing...

Consumer Trust in the U.S. Food System: An Examination of the Recreancy Theorem

ERIC Educational Resources Information Center

Sapp, Stephen G.; Arnot, Charlie; Fallon, James; Fleck, Terry; Soorholtz, David; Sutton-Vermeulen, Matt; Wilson, Jannette J. H.

2009-01-01

Because consumer opinions to an increasing extent affect the structure and management of the U.S. food system, it is important for social scientists to accurately model consumer trust in this system so they can better understand and anticipate public responses to existing or proposed food-related regulatory policies and facilitate effective…

Portrait of a molecule.

PubMed

Ball, Philip

2003-01-23

The double helix is idealized for its aesthetic elegant structure, but the reality of DNA's physical existence is quite different. Most DNA in the cell is compressed into a tangled package that somehow still exposes itself to meticulous gene-regulatory control. Philip Ball holds a mirror up to what we truly know about the mysteries of DNA's life inside a cell.

GMO Reignited in Science but Not in Law: A Flawed Framework Fuels France's Stalemate.

PubMed

Robbins, Patricia B

2014-01-01

Following a statement released by a multitude of prominent scientists contesting the idea that there is a consensus on the safety of genetically modified organisms ("GMO"), this article addresses the European Union's ("EU") GMO regulatory framework, which has reluctantly permitted France to maintain an illegal ban on. MON8 10 for over a decade now. It notes that while the statement did nothing more than reignite the debate on GMO, much could and should be done to improve the framework to accommodate for the lack of true scientific understanding about the effects of GMO. This article identifies the specific areas of weakness in the EU GMO regulatory framework and recommends specific alterations. It concludes that although France's MON810 ban is illegal under existing law, the country's fears are neither unfounded nor unsupported and that the EU should work to alter its existing legal structure to parallel today's scientific uncertainty regarding GMO safety.

Computational methods in sequence and structure prediction

NASA Astrophysics Data System (ADS)

Lang, Caiyi

This dissertation is organized into two parts. In the first part, we will discuss three computational methods for cis-regulatory element recognition in three different gene regulatory networks as the following: (a) Using a comprehensive "Phylogenetic Footprinting Comparison" method, we will investigate the promoter sequence structures of three enzymes (PAL, CHS and DFR) that catalyze sequential steps in the pathway from phenylalanine to anthocyanins in plants. Our result shows there exists a putative cis-regulatory element "AC(C/G)TAC(C)" in the upstream of these enzyme genes. We propose this cis-regulatory element to be responsible for the genetic regulation of these three enzymes and this element, might also be the binding site for MYB class transcription factor PAP1. (b) We will investigate the role of the Arabidopsis gene glutamate receptor 1.1 (AtGLR1.1) in C and N metabolism by utilizing the microarray data we obtained from AtGLR1.1 deficient lines (antiAtGLR1.1). We focus our investigation on the putatively co-regulated transcript profile of 876 genes we have collected in antiAtGLR1.1 lines. By (a) scanning the occurrence of several groups of known abscisic acid (ABA) related cisregulatory elements in the upstream regions of 876 Arabidopsis genes; and (b) exhaustive scanning of all possible 6-10 bps motif occurrence in the upstream regions of the same set of genes, we are able to make a quantative estimation on the enrichment level of each of the cis-regulatory element candidates. We finally conclude that one specific cis-regulatory element group, called "ABRE" elements, are statistically highly enriched within the 876-gene group as compared to their occurrence within the genome. (c) We will introduce a new general purpose algorithm, called "fuzzy REDUCE1", which we have developed recently for automated cis-regulatory element identification. In the second part, we will discuss our newly devised protein design framework. With this framework we have developed a software package which is capable of designing novel protein structures at the atomic resolution. This software package allows us to perform protein structure design with a flexible backbone. The backbone flexibility includes loop region relaxation as well as a secondary structure collective mode relaxation scheme. (Abstract shortened by UMI.)

[Convergence of healthcare regulation in the Americas: history, development, and new challenges].

PubMed

Silva, Ana Paula Jucá; Tagliari, Patrícia Oliveira Pereira

2016-05-01

The present article describes the changing relationship among healthcare regulatory authorities in various international settings, with special emphasis on the Americas. As other sectors, healthcare also faces the need to regulate international practices, while at the same time taking into consideration the specific realities of each country. Regulatory convergence - a movement towards technical alignment to enable the adoption of local regulatory mechanisms that take into account internationally recognized standards and principles to promote a single sanitary goal - has emerged as a means to address this challenge. Organizations that already use this tool, such as the International Conference of Drug Regulatory Authorities (ICDRA), Pan American Network for Drug Regulatory Harmonization (PANDRH), International Generic Drug Regulators Programme (IGDRP), and the International Medical Device Regulators Forum (IMDRF), among others, are currently working to gather knowledge, data, and specialists from different countries to build an international technical and scientific standard that can be used for decision-making by local regulators. This would ensure convergence of national regulations despite the need to adapt international standards to local needs, structure, and capacities. The most recent resolutions issued by the World Health Organization recognize the need to bring regulatory systems closer to the reality of national healthcare systems, and underscore the advantages of using existing local guidelines as input for cooperation with regulatory authorities.

75 FR 36756 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of Filing of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-28

... existing paragraph (b)(4) of the Rule, entitled ``Numerical Guidelines Applicable to Volatile Market Opens... existing paragraph (b)(2), which provides flexibility to FINRA to use different Numerical Guidelines or... of paragraph (b)(4) (``Numerical Guidelines Applicable to Volatile Market Opens'') of the existing...

Pharmaceutical Regulatory Framework in Ethiopia: A Critical Evaluation of Its Legal Basis and Implementation.

PubMed

Suleman, Sultan; Woliyi, Abdulkadir; Woldemichael, Kifle; Tushune, Kora; Duchateau, Luc; Degroote, Agnes; Vancauwenberghe, Roy; Bracke, Nathalie; De Spiegeleer, Bart

2016-05-01

Effective and enforceable national regulations describing the manufacture and (re)packaging, export and import, distribution and storage, supply and sale, information and pharmaco-vigilance of medicines are required to consistently ensure optimal patient benefit. Expansion of pharmaceutical industries in many countries with advancement in transport technologies facilitated not only trade of genuine pharmaceutical products but also the circulation of poor quality medicines across the globe. In Ethiopia, even though "The Pharmacists and Druggists Proclamation No 43/1942" was used to regulate both the professions and the facilities where they were practiced, comprehensive regulation of the pharmaceutical market was introduced in 1964 by a regulation called "Pharmacy Regulation No. 288/ 1964". This legislation formed the legal basis for official establishment of drug regulation in the history of Ethiopia, enabling the regulation of the practice of pharmacists, druggists and pharmacy technicians; manufacturing, distribution, and sale of medicines. In June 1999, a new regulation called the "Drug Administration and Control Proclamation No. 176/1999" repealed most parts of the regulation 288/1964. The law established an independent Drug Administration and Control Authority (DACA) with further mandate of setting standards of competence for licensing institutions/facilities. DACA was re-structured as Food, Medicine and Health Care Administration and Control Authority (EFMHACA) of Ethiopia by the "Proclamation No. 661/2009" in 2010 bearing additional responsibilities like regulation of food, health care personnel and settings. The mere existence of this legal framework does not guarantee complete absence of illegal, substandard and falsified products as well as illegal establishments in the pharmaceutical chain. Therefore, the objective of the research is to assess the pharmaceutical regulatory system in Ethiopia and to reveal possible reasons for deficiencies in the pharmaceutical chain. An archival review, an in-depth interview of key informants and an institutions-based cross-sectional survey study were conducted during March to April 2013. The comprehensiveness of the pharmaceutical law to protect public health relative to three selected African countries (South Africa, Tanzania and Uganda) and European Union, and implementation was assessed. The study revealed that Ethiopia does have a written national drug policy upon which the Medicines Regulatory Proclamation 661/2009 is based. According to this proclamation, the Ethiopian The Food, Medicines and Healthcare Administration and Control Authority is mandated to execute the regulatory activities as per the council of ministers regulation 189/2010. The legal framework for pharmaceutical regulation of Ethiopia was founded to fulfill all the medicines regulatory functions potentially enabling to combat illegal, substandard and falsified medicines and illegal establishments. Moreover, all the key informants witnessed that the government is commited and proclamation 661/2009 is comprehensive, but they stressed the compelling need of regulatory tools for effective implementation. From the institution-based cross-sectional study, it was revealed that there exist illegal sources formedicine in the pharmaceutical market. The main reasons for their existence were regulatory factors including weak regulatory enforcement (64.5%), lack of informal market control (60.8%), weak port control (50.0%), and poor cooperation between executive bodies (39.6%); and resource constraint (27.8%), which is an institutional factor. From legislative point of view, the medicines regulatory framework in Ethiopia fulfils all regulatory functions required for effective medicines regulation. However, the existence of the legislation by its own is not a guarantee to prevent the existence of unauthorized/illegal medicine sources since this requires effective implementation of the legislation, which is in fact affected by the governments political commitment, resource and intergovernmental cooperation.

Summary of SMIRT20 Preconference Topical Workshop – Identifying Structural Issues in Advanced Reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

William Richins; Stephen Novascone; Cheryl O'Brien

Summary of SMIRT20 Preconference Topical Workshop – Identifying Structural Issues in Advanced Reactors William Richins1, Stephen Novascone1, and Cheryl O’Brien1 1Idaho National Laboratory, US Dept. of Energy, Idaho Falls, Idaho, USA, e-mail: William.Richins@inl.gov The Idaho National Laboratory (INL, USA) and IASMiRT sponsored an international forum Nov 5-6, 2008 in Porvoo, Finland for nuclear industry, academic, and regulatory representatives to identify structural issues in current and future advanced reactor design, especially for extreme conditions and external threats. The purpose of this Topical Workshop was to articulate research, engineering, and regulatory Code development needs. The topics addressed by the Workshop were selectedmore » to address critical industry needs specific to advanced reactor structures that have long lead times and can be the subject of future SMiRT technical sessions. The topics were; 1) structural/materials needs for extreme conditions and external threats in contemporary (Gen. III) and future (Gen. IV and NGNP) advanced reactors and 2) calibrating simulation software and methods that address topic 1 The workshop discussions and research needs identified are presented. The Workshop successfully produced interactive discussion on the two topics resulting in a list of research and technology needs. It is recommended that IASMiRT communicate the results of the discussion to industry and researchers to encourage new ideas and projects. In addition, opportunities exist to retrieve research reports and information that currently exists, and encourage more international cooperation and collaboration. It is recommended that IASMiRT continue with an off-year workshop series on select topics.« less

30 CFR 761.16 - Submission and processing of requests for valid existing rights determinations.

Code of Federal Regulations, 2011 CFR

2011-07-01

...) Requirements for property rights demonstration. You must provide a property rights demonstration under... matter Regulatory authority Regulatory program 2 (d) Public roads Does not matter Regulatory authority Regulatory program 2 (e) Occupied dwellings Does not matter Regulatory authority Regulatory program 2 (f...

Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework.

PubMed

Maeso, Ignacio; Tena, Juan J

2016-09-01

Cis-regulatory changes are arguably the primary evolutionary source of animal morphological diversity. With the recent explosion of genome-wide comparisons of the cis-regulatory content in different animal species is now possible to infer general principles underlying enhancer evolution. However, these studies have also revealed numerous discrepancies and paradoxes, suggesting that the mechanistic causes and modes of cis-regulatory evolution are still not well understood and are probably much more complex than generally appreciated. Here, we argue that the mutational mechanisms and genomic regions generating new regulatory activities must comply with the constraints imposed by the molecular properties of cis-regulatory elements (CREs) and the organizational features of long-range chromatin interactions. Accordingly, we propose a new integrative evolutionary framework for cis-regulatory evolution based on two major premises for the origin of novel enhancer activity: (i) an accessible chromatin environment and (ii) compatibility with the 3D structure and interactions of pre-existing CREs. Mechanisms and DNA sequences not fulfilling these premises, will be less likely to have a measurable impact on gene expression and as such, will have a minor contribution to the evolution of gene regulation. Finally, we discuss current comparative cis-regulatory data under the light of this new evolutionary model, and propose that the two most prominent mechanisms for the evolution of cis-regulatory changes are the overprinting of ancestral CREs and the exaptation of transposable elements. Copyright © 2015 Elsevier Ltd. All rights reserved.

75 FR 11967 - Self-Regulatory Organizations; NASDAQ OMX PHLX, Inc.; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-12

... Order Entry Port from $250 to $500 and only charge per mnemonic instead of per mnemonic per port; (xii) amend the SQF Port Fee to assess a $500 per month per SQF port in lieu of the existing structure of $250 for the first five ports and $1000 for additional port thereafter and also rename the SQF Port Fee as...

Nuclear regulation: an evaluative study. [Monograph

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, W.C.

This paper gives an overview of nuclear regulation, followed by an account of the legislative rationale and the economic rationale for safety regulation of nuclear technology. It goes on to review the structure and safety programs of the Nuclear Regulatory Commission (NRC) and to show how many of the NRC's problems are unlike those facing other regulatory agencies. In assessing the results of nuclear regulation, it examines whether regulation has produced an acceptable level of safety and the nature of the evidence on acceptability. It concludes that the existing level of safety achievement is not cost-effective, and identifies some sourcesmore » of regulatory failure as a failure to make hard decisions on risk, diffuse responsibility for safety, and economic dissincentives to cost-effective safety. Recommendations for reforming NRC are to separate technical issues from social ones and to correct the incentives for safety. 153 references, 6 figures, 4 tables.« less

It Comes With the Job: Work Organizational, Job Design, and Self-Regulatory Barriers to Improving the Health Status of Train Drivers.

PubMed

Naweed, Anjum; Chapman, Janine; Allan, Matthew; Trigg, Joshua

2017-03-01

This study aimed to examine the impacts of key barriers to improving the occupational health status of Australian train drivers. From May to June, 2015, five semi-structured qualitative focus groups were conducted with 29 train drivers from South Australian, Victorian, and New South Wales-based rail organizations in Australia. Occupational health was impeded by multiple barriers regarding sleep (patterns/fatigue), diet (planning/context), mental health (occupational stress), rostering (low autonomy), sedentary time, low fitness motivation, and family/social life conflicts. Work organizational barriers included communication issues, low organizational support, and existing social norms. Job design barriers included rostering, fatigue, stimulant reliance, and family/social life imbalances. Self-regulatory barriers included dietary and exercise patterns habits and patterns. Occupational health interventions for Australian train drivers must address work organizational, job design, and self-regulatory barriers to healthier lifestyle behaviors.

Challenges for the registration of vaccines in emerging countries: Differences in dossier requirements, application and evaluation processes.

PubMed

Dellepiane, Nora; Pagliusi, Sonia

2018-06-07

The divergence of regulatory requirements and processes in developing and emerging countries contributes to hamper vaccines' registration, and therefore delay access to high-quality, safe and efficacious vaccines for their respective populations. This report focuses on providing insights on the heterogeneity of registration requirements in terms of numbering structure and overall content of dossiers for marketing authorisation applications for vaccines in different areas of the world. While it also illustrates the divergence of regulatory processes in general, as well as the need to avoid redundant reviews, it does not claim to provide a comprehensive view of all processes nor existing facilitating mechanisms, nor is it intended to touch upon the differences in assessments made by different regulatory authorities. This report describes the work analysed by regulatory experts from vaccine manufacturing companies during a meeting held in Geneva in May 2017, in identifying and quantifying differences in the requirements for vaccine registration in three aspects for comparison: the dossier numbering structure and contents, the application forms, and the evaluation procedures, in different countries and regions. The Module 1 of the Common Technical Document (CTD) of 10 countries were compared. Modules 2-5 of the CTDs of two regions and three countries were compared to the CTD of the US FDA. The application forms of eight countries were compared and the registration procedures of 134 importing countries were compared as well. The analysis indicates a high degree of divergence in numbering structure and content requirements. Possible interventions that would lead to significant improvements in registration efficiency include alignment in CTD numbering structure, a standardised model-application form, and better convergence of evaluation procedures. Copyright © 2018.

Team structure and regulatory focus: the impact of regulatory fit on team dynamic.

PubMed

Dimotakis, Nikolaos; Davison, Robert B; Hollenbeck, John R

2012-03-01

We report a within-teams experiment testing the effects of fit between team structure and regulatory task demands on task performance and satisfaction through average team member positive affect and helping behaviors. We used a completely crossed repeated-observations design in which 21 teams enacted 2 tasks with different regulatory focus characteristics (prevention and promotion) in 2 organizational structures (functional and divisional), resulting in 84 observations. Results suggested that salient regulatory demands inherent in the task interacted with structure to determine objective and subjective team-level outcomes, such that functional structures were best suited to (i.e., had best fit with) tasks with a prevention regulatory focus and divisional structures were best suited to tasks with a promotion regulatory focus. This contingency finding integrates regulatory focus and structural contingency theories, and extends them to the team level with implications for models of performance, satisfaction, and team dynamics.

75 FR 79049 - Notice of Issuance of Regulatory Guide

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-17

..., Division of Engineering, Office of Nuclear Regulatory Research, U.S. Nuclear Regulatory Commission... INFORMATION: I. Introduction The U.S. Nuclear Regulatory Commission (NRC) is issuing a revision to an existing... Development Branch, Division of Engineering, Office of Nuclear Regulatory Research. [FR Doc. 2010-31731 Filed...

40 CFR 92.6 - Regulatory structure.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Regulatory structure. 92.6 Section 92... Regulations for Locomotives and Locomotive Engines § 92.6 Regulatory structure. This section provides an overview of the regulatory structure of this part. (a) The regulations of this part 92 are intended to...

40 CFR 94.6 - Regulatory structure.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Regulatory structure. 94.6 Section 94... for Compression-Ignition Marine Engines § 94.6 Regulatory structure. This section provides an overview of the regulatory structure of this part. (a) The regulations of this Part 94 are intended to control...

[Computer simulation of thyroid regulatory mechanisms in health and malignancy].

PubMed

Abduvaliev, A A; Gil'dieva, M S; Khidirov, B N; Saĭdalieva, M; Saatov, T S

2010-07-01

The paper describes a computer model for regulation of the number of thyroid follicular cells in health and malignancy. The authors'computer program for mathematical simulation of the regulatory mechanisms of a thyroid follicular cellular community cannot be now referred to as good commercial products. For commercialization of this product, it is necessary to draw up a direct relation of the introduced corrected values from the actually existing normal values, such as the peripheral blood concentrations of thyroid hormones or the mean values of endocrine tissue mitotic activity. However, the described computer program has been also used in researches by our scientific group in the study of thyroid cancer. The available biological experimental data and theoretical provisions on thyroid structural and functional organization at the cellular level allow one to construct mathematical models for quantitative analysis of the regulation of the size of a cellular community of a thyroid follicle in health and abnormalities, by using the method for simulation of the regulatory mechanisms of living systems and the equations of cellular community regulatory communities.

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach

PubMed Central

Henriques, David; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R.

2015-01-01

Motivation: Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters. Results: In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: julio@iim.csic.es or saezrodriguez@ebi.ac.uk PMID:26002881

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.

PubMed

Henriques, David; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R

2015-09-15

Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters. In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells. Supplementary data are available at Bioinformatics online. julio@iim.csic.es or saezrodriguez@ebi.ac.uk. © The Author 2015. Published by Oxford University Press.

Shaping skeletal growth by modular regulatory elements in the Bmp5 gene.

PubMed

Guenther, Catherine; Pantalena-Filho, Luiz; Kingsley, David M

2008-12-01

Cartilage and bone are formed into a remarkable range of shapes and sizes that underlie many anatomical adaptations to different lifestyles in vertebrates. Although the morphological blueprints for individual cartilage and bony structures must somehow be encoded in the genome, we currently know little about the detailed genomic mechanisms that direct precise growth patterns for particular bones. We have carried out large-scale enhancer surveys to identify the regulatory architecture controlling developmental expression of the mouse Bmp5 gene, which encodes a secreted signaling molecule required for normal morphology of specific skeletal features. Although Bmp5 is expressed in many skeletal precursors, different enhancers control expression in individual bones. Remarkably, we show here that different enhancers also exist for highly restricted spatial subdomains along the surface of individual skeletal structures, including ribs and nasal cartilages. Transgenic, null, and regulatory mutations confirm that these anatomy-specific sequences are sufficient to trigger local changes in skeletal morphology and are required for establishing normal growth rates on separate bone surfaces. Our findings suggest that individual bones are composite structures whose detailed growth patterns are built from many smaller lineage and gene expression domains. Individual enhancers in BMP genes provide a genomic mechanism for controlling precise growth domains in particular cartilages and bones, making it possible to separately regulate skeletal anatomy at highly specific locations in the body.

Insights into Autoregulation of Notch3 from Structural and Functional Studies of Its Negative Regulatory Region.

PubMed

Xu, Xiang; Choi, Sung Hee; Hu, Tiancen; Tiyanont, Kittichoat; Habets, Roger; Groot, Arjan J; Vooijs, Marc; Aster, Jon C; Chopra, Rajiv; Fryer, Christy; Blacklow, Stephen C

2015-07-07

Notch receptors are transmembrane proteins that undergo activating proteolysis in response to ligand stimulation. A negative regulatory region (NRR) maintains receptor quiescence by preventing protease cleavage prior to ligand binding. We report here the X-ray structure of the NRR of autoinhibited human Notch3, and compare it with the Notch1 and Notch2 NRRs. The overall architecture of the autoinhibited conformation, in which three LIN12-Notch repeat (LNR) modules wrap around a heterodimerization domain, is preserved in Notch3, but the autoinhibited conformation of the Notch3 NRR is less stable. The Notch3 NRR uses a highly conserved surface on the third LNR module to form a dimer in the crystal. Similar homotypic interfaces exist in Notch1 and Notch2. Together, these studies reveal distinguishing structural features associated with increased basal activity of Notch3, demonstrate increased ligand-independent signaling for disease-associated mutations that map to the Notch3 NRR, and identify a conserved dimerization interface present in multiple Notch receptors. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Portuguese electric system and the role of the Portuguese regulatory entity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santana, J.

1998-07-01

According to the organization model of the Portuguese Electric System, there is the coexistence of two subsystems with different characteristics: the Public Electric System, which has public service obligations and the Independent Electric System which does not have such obligations, and part of it obeys a market logic. Nowadays, the Public Electric System is the main component of the electric sector, however there are reasons to believe that the Independent System can increase its participation. The 1995 Portuguese legislation established the existence of an independent structure to regulate the electric sector: the Electric Sector Regulatory Entity. In this paper, themore » organization of this entity is described, as well as its objectives and main powers.« less

Knowledge enabled plan of care and documentation prototype.

PubMed

DaDamio, Rebecca; Gugerty, Brian; Kennedy, Rosemary

2006-01-01

There exist significant challenges in integrating the plan of care into documentation and point of care operational processes. A plan of care is often a static artifact that meets regulatory standards with limited influence on supporting goal-directed care delivery processes. Although this prototype is applicable to many clinical disciplines, we will highlight nursing processes in demonstrating a knowledge-driven computerized solution that fully integrates the plan of care within documentation. The knowledge-driven solution reflects evidenced-based practice; is an effective tool for managing problems, orders/interventions, and the patient's progress towards expected outcomes; meets regulatory standards; and drives quality and process improvement. The knowledge infrastructure consists of fully represented terminology, structured clinical expressions utilizing the controlled terminology and clinical knowledge representing evidence-based practice.

76 FR 59066 - Notice of Regulatory Review Plan

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-23

... [No. 2011-N-10] Notice of Regulatory Review Plan AGENCY: Federal Housing Finance Agency. ACTION... of and requesting comments on the FHFA interim regulatory review plan for review of existing... comments on all aspects of the interim regulatory review plan, including legal and policy considerations...

75 FR 43207 - Notice of Issuance of Regulatory Guide

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-23

... INFORMATION: I. Introduction The U.S. Nuclear Regulatory Commission (NRC) is issuing a revision to an existing.... Jervey, Acting Chief, Regulatory Guide Development Branch, Division of Engineering, Office of Nuclear...

The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts.

PubMed

Monteiro, Pedro Tiago; Pais, Pedro; Costa, Catarina; Manna, Sauvagya; Sá-Correia, Isabel; Teixeira, Miguel Cacho

2017-01-04

We present the PATHOgenic YEAst Search for Transcriptional Regulators And Consensus Tracking (PathoYeastract - http://pathoyeastract.org) database, a tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in the pathogenic yeasts Candida albicans and C. glabrata Upon data retrieval from hundreds of publications, followed by curation, the database currently includes 28 000 unique documented regulatory associations between transcription factors (TF) and target genes and 107 DNA binding sites, considering 134 TFs in both species. Following the structure used for the YEASTRACT database, PathoYeastract makes available bioinformatics tools that enable the user to exploit the existing information to predict the TFs involved in the regulation of a gene or genome-wide transcriptional response, while ranking those TFs in order of their relative importance. Each search can be filtered based on the selection of specific environmental conditions, experimental evidence or positive/negative regulatory effect. Promoter analysis tools and interactive visualization tools for the representation of TF regulatory networks are also provided. The PathoYeastract database further provides simple tools for the prediction of gene and genomic regulation based on orthologous regulatory associations described for other yeast species, a comparative genomics setup for the study of cross-species evolution of regulatory networks. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

78 FR 58580 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-24

... proposed rule change, FINRA would no longer require a customer to elect one of the two existing panel...-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving Proposed Rule Change...,\\2\\ a proposed rule change amending the Code of Arbitration Procedure for Customer Disputes...

ORNL Remedial Action Program strategy (FY 1987-FY 1992)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trabalka, J.R.; Myrick, T.E.

1987-12-01

Over 40 years of Oak Ridge National Laboratory (ORNL) operations have produced a diverse legacy of contaminated inactive facilities, research areas, and waste disposal areas that are potential candidates for remedial action. The ORNL Remedial Action Program (RAP) represents a comprehensive effort to meet new regulatory requirements and ensure adequate protection of on-site workers, the public, and the environment by providing appropriate corrective measures at over 130 sites contaminated historically with radioactive, hazardous chemical, or mixed wastes. A structured path of program planning, site characterization, alternatives assessment, technology development, engineering design, continued site maintenance and surveillance, interim corrective action, andmore » eventual site closure or decommissioning is required to meet these objectives. This report documents the development of the Remedial Action Program, through its preliminary characterization, regulatory interface, and strategy development activities. It provides recommendations for a comprehensive, long-term strategy consistent with existing technical, institutional, and regulatory information, along with a six-year plan for achieving its initial objectives. 53 refs., 8 figs., 12 tabs.« less

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach.

PubMed

Steggles, L Jason; Banks, Richard; Shaw, Oliver; Wipat, Anil

2007-02-01

New developments in post-genomic technology now provide researchers with the data necessary to study regulatory processes in a holistic fashion at multiple levels of biological organization. One of the major challenges for the biologist is to integrate and interpret these vast data resources to gain a greater understanding of the structure and function of the molecular processes that mediate adaptive and cell cycle driven changes in gene expression. In order to achieve this biologists require new tools and techniques to allow pathway related data to be modelled and analysed as network structures, providing valuable insights which can then be validated and investigated in the laboratory. We propose a new technique for constructing and analysing qualitative models of genetic regulatory networks based on the Petri net formalism. We take as our starting point the Boolean network approach of treating genes as binary switches and develop a new Petri net model which uses logic minimization to automate the construction of compact qualitative models. Our approach addresses the shortcomings of Boolean networks by providing access to the wide range of existing Petri net analysis techniques and by using non-determinism to cope with incomplete and inconsistent data. The ideas we present are illustrated by a case study in which the genetic regulatory network controlling sporulation in the bacterium Bacillus subtilis is modelled and analysed. The Petri net model construction tool and the data files for the B. subtilis sporulation case study are available at http://bioinf.ncl.ac.uk/gnapn.

Structural investigation of protein kinase C inhibitors

NASA Technical Reports Server (NTRS)

Barak, D.; Shibata, M.; Rein, R.

1991-01-01

The phospholipid and Ca2+ dependent protein kinase (PKC) plays an essential role in a variety of cellular events. Inhibition of PKC was shown to arrest growth in tumor cell cultures making it a target for possible antitumor therapy. Calphostins are potent inhibitors of PKC with high affinity for the enzyme regulatory site. Structural characteristics of calphostins, which confer the inhibitory activity, are investigated by comparing their optimized structures with the existing models for PKC activation. The resulting model of inhibitory activity assumes interaction with two out of the three electrostatic interaction sites postulated for activators. The model shows two sites of hydrophobic interaction and enables the inhibitory activity of gossypol to be accounted for.

Enterprising health: creating the conditions for entrepreneurial behaviour as a strategy for effective and sustainable change in health services.

PubMed

Exton, Rosemary

2010-01-01

This paper seeks to investigate conditions under which entrepreneurs emerge as agents of effective and sustainable change in UK National Health Service Trusts. The research synthesises literature on changing regulatory structures ("post-bureaucracy") and entrepreneurial behaviour to understand how individual identity construction is informed both by context and by individual attributes. Thematic analysis of interview data involving managers from 11 NHS Trusts, including detailed analysis of six transcripts, focuses on regulatory processes, the emergence of entrepreneurial behaviour and outcome variations in workplace innovation and improvement. This study identifies co-existing modes of regulation, which interact with individual behaviour, generating strategies differentiated as entrepreneurial or conformist. Four ideal types are identified: organisational entrepreneurship, resisted or dissonant entrepreneurship, conformity, and symbolic entrepreneurship. Analysis reinforces those literature findings, which suggest that the interaction of regulatory structures and the identity work of individuals influence the emergence of entrepreneurial behaviour and the effectiveness of change. The ability to achieve effective and sustainable outcomes varies considerably even between NHS Trusts faced with comparable challenges in implementing nationally prescribed targets. This variance is explained in terms of the organisation's ability to generate the structures, processes, individual competence and motivation which enable employees at all levels to act entrepreneurially with the ability and legitimacy to achieve strategic goals by working creatively in the spaces between formal organisational structures. The study identifies specific conditions, which stimulate the emergence of entrepreneurs as agents of effective and sustainable change in the NHS, identifying factors that policymakers should consider when implementing change.

Large Scale Comparative Visualisation of Regulatory Networks with TRNDiff

DOE PAGES

Chua, Xin-Yi; Buckingham, Lawrence; Hogan, James M.; ...

2015-06-01

The advent of Next Generation Sequencing (NGS) technologies has seen explosive growth in genomic datasets, and dense coverage of related organisms, supporting study of subtle, strain-specific variations as a determinant of function. Such data collections present fresh and complex challenges for bioinformatics, those of comparing models of complex relationships across hundreds and even thousands of sequences. Transcriptional Regulatory Network (TRN) structures document the influence of regulatory proteins called Transcription Factors (TFs) on associated Target Genes (TGs). TRNs are routinely inferred from model systems or iterative search, and analysis at these scales requires simultaneous displays of multiple networks well beyond thosemore » of existing network visualisation tools [1]. In this paper we describe TRNDiff, an open source system supporting the comparative analysis and visualization of TRNs (and similarly structured data) from many genomes, allowing rapid identification of functional variations within species. The approach is demonstrated through a small scale multiple TRN analysis of the Fur iron-uptake system of Yersinia, suggesting a number of candidate virulence factors; and through a larger study exploiting integration with the RegPrecise database (http://regprecise.lbl.gov; [2]) - a collection of hundreds of manually curated and predicted transcription factor regulons drawn from across the entire spectrum of prokaryotic organisms.« less

Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.

PubMed

Glinsky, Gennadi V

2018-03-01

Transposable elements have made major evolutionary impacts on creation of primate-specific and human-specific genomic regulatory loci and species-specific genomic regulatory networks (GRNs). Molecular and genetic definitions of human-specific changes to GRNs contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of diverse families of human-specific genomic regulatory loci (HSGRL) identified topologically associating domains (TADs) that are significantly enriched for HSGRL and designated rapidly evolving in human TADs. Here, the analysis of HSGRL, hESC-enriched enhancers, super-enhancers (SEs), and specific sub-TAD structures termed super-enhancer domains (SEDs) has been performed. In the hESC genome, 331 of 504 (66%) of SED-harboring TADs contain HSGRL and 68% of SEDs co-localize with HSGRL, suggesting that emergence of HSGRL may have rewired SED-associated GRNs within specific TADs by inserting novel and/or erasing existing non-coding regulatory sequences. Consequently, markedly distinct features of the principal regulatory structures of interphase chromatin evolved in the hESC genome compared to mouse: the SED quantity is 3-fold higher and the median SED size is significantly larger. Concomitantly, the overall TAD quantity is increased by 42% while the median TAD size is significantly decreased (p = 9.11E-37) in the hESC genome. Present analyses illustrate a putative global role for transposable elements and HSGRL in shaping the human-specific features of the interphase chromatin organization and functions, which are facilitated by accelerated creation of novel transcription factor binding sites and new enhancers driven by targeted placement of HSGRL at defined genomic coordinates. A trend toward the convergence of TAD and SED architectures of interphase chromatin in the hESC genome may reflect changes of 3D-folding patterns of linear chromatin fibers designed to enhance both regulatory complexity and functional precision of GRNs by creating predominantly a single gene (or a set of functionally linked genes) per regulatory domain structures. Collectively, present analyses reveal critical evolutionary contributions of transposable elements and distal enhancers to creation of thousands primate- and human-specific elements of a chromatin folding code, which defines the 3D context of interphase chromatin both restricting and facilitating biological functions of GRNs.

Development of an acute oral toxicity dataset to facilitate assessment of existing QSARs and development of new models (WC10)

EPA Science Inventory

Acute oral toxicity data are used to meet both regulatory and non-regulatory needs. Recently, there have been efforts to explore alternative approaches for predicting acute oral toxicity such as QSARs. Evaluating the performance and scope of existing models and investigating the ...

DISTRIBUTED STRUCTURE-SEARCHABLE TOXICITY ...

EPA Pesticide Factsheets

The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, SAR model development, or building of chemical relational databases (CRD). The Distributed Structure-Searchable Toxicity (DSSTox) Public Database Network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: 1) to adopt and encourage the use of a common standard file format (SDF) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; 2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure-toxicity data files, and that will effectively link knowledgeable toxicity data s

α -Actinin TvACTN3 of Trichomonas vaginalis is an RNA-binding protein that could participate in its posttranscriptional iron regulatory mechanism.

PubMed

Calla-Choque, Jaeson Santos; Figueroa-Angulo, Elisa Elvira; Ávila-González, Leticia; Arroyo, Rossana

2014-01-01

Trichomonas vaginalis is a sexually transmitted flagellated protist parasite responsible for trichomoniasis. This parasite is dependent on high levels of iron, favoring its growth and multiplication. Iron also differentially regulates some trichomonad virulence properties by unknown mechanisms. However, there is evidence to support the existence of gene regulatory mechanisms at the transcriptional and posttranscriptional levels that are mediated by iron concentration in T. vaginalis. Thus, the goal of this study was to identify an RNA-binding protein in T. vaginalis that interacts with the tvcp4 RNA stem-loop structure, which may participate in a posttranscriptional iron regulatory mechanism mediated by RNA-protein interactions. We performed RNA electrophoretic mobility shift assay (REMSA) and supershift, UV cross-linking, Northwestern blot, and western blot (WB) assays using cytoplasmic protein extracts from T. vaginalis with the tvcp4 RNA hairpin structure as a probe. We identified a 135-kDa protein isolated by the UV cross-linking assays as α-actinin 3 (TvACTN3) by MALDI-TOF-MS that was confirmed by LS-MS/MS and de novo sequencing. TvACTN3 is a cytoplasmic protein that specifically binds to hairpin RNA structures from trichomonads and humans when the parasites are grown under iron-depleted conditions. Thus, TvACTN3 could participate in the regulation of gene expression by iron in T. vaginalis through a parallel posttranscriptional mechanism similar to that of the IRE/IRP system.

α-Actinin TvACTN3 of Trichomonas vaginalis Is an RNA-Binding Protein That Could Participate in Its Posttranscriptional Iron Regulatory Mechanism

PubMed Central

Calla-Choque, Jaeson Santos; Figueroa-Angulo, Elisa Elvira; Ávila-González, Leticia; Arroyo, Rossana

2014-01-01

Trichomonas vaginalis is a sexually transmitted flagellated protist parasite responsible for trichomoniasis. This parasite is dependent on high levels of iron, favoring its growth and multiplication. Iron also differentially regulates some trichomonad virulence properties by unknown mechanisms. However, there is evidence to support the existence of gene regulatory mechanisms at the transcriptional and posttranscriptional levels that are mediated by iron concentration in T. vaginalis. Thus, the goal of this study was to identify an RNA-binding protein in T. vaginalis that interacts with the tvcp4 RNA stem-loop structure, which may participate in a posttranscriptional iron regulatory mechanism mediated by RNA-protein interactions. We performed RNA electrophoretic mobility shift assay (REMSA) and supershift, UV cross-linking, Northwestern blot, and western blot (WB) assays using cytoplasmic protein extracts from T. vaginalis with the tvcp4 RNA hairpin structure as a probe. We identified a 135-kDa protein isolated by the UV cross-linking assays as α-actinin 3 (TvACTN3) by MALDI-TOF-MS that was confirmed by LS-MS/MS and de novo sequencing. TvACTN3 is a cytoplasmic protein that specifically binds to hairpin RNA structures from trichomonads and humans when the parasites are grown under iron-depleted conditions. Thus, TvACTN3 could participate in the regulation of gene expression by iron in T. vaginalis through a parallel posttranscriptional mechanism similar to that of the IRE/IRP system. PMID:24719864

5 CFR 880.102 - Regulatory structure.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Regulatory structure. 880.102 Section 880.102 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS... Regulatory structure. (a) This part contains the following subparts: (1) Subpart A contains general...

Parallel evolution of chordate cis-regulatory code for development.

PubMed

Doglio, Laura; Goode, Debbie K; Pelleri, Maria C; Pauls, Stefan; Frabetti, Flavia; Shimeld, Sebastian M; Vavouri, Tanya; Elgar, Greg

2013-11-01

Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non-coding elements (ciCNEs) are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of cis-regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations.

5 CFR 847.102 - Regulatory structure.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Regulatory structure. 847.102 Section 847.102 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS... INSTRUMENTALITIES General Provisions § 847.102 Regulatory structure. (a)(1) Subpart A of this part contains...

Medical revalidation as professional regulatory reform: Challenging the power of enforceable trust in the United Kingdom.

PubMed

Spendlove, Zoey

2018-05-01

For more than two decades, international healthcare crises and ensuing political debates have led to increasing professional governance and regulatory policy reform. Governance and policy reforms, commonly representing a shift from embodied trust in professionals to state enforceable trust, have challenged professional power and self-regulatory privileges. However, controversy remains as to whether such policies do actually shift the balance of power and what the resulting effects of policy introduction would be. This paper explores the roll-out and operationalisation of revalidation as medical regulatory reform within a United Kingdom National Health Service hospital from 2012 to 2013, and its impact upon professional power. Revalidation policy was subject to the existing governance and management structures of the organisation, resulting in the formal policy process being shaped at the local level. This paper explores how the disorganised nature of the organisation hindered rather than facilitated robust processes of professional governance and regulation, fostering formalistic rather than genuine professional engagement with the policy process. Formalistic engagement seemingly assisted the medical profession in retaining self-regulatory privileges whilst maintaining professional power over the policy process. The paper concludes by challenging the concept of state enforceable trust and the theorisation that professional groups are effectively regulated and controlled by means of national and organisational objectives, such as revalidation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Distributed structure-searchable toxicity (DSSTox) public database network: a proposal.

PubMed

Richard, Ann M; Williams, ClarLynda R

2002-01-29

The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, Structure-Activity Relationship (SAR) model development, or building of chemical relational databases (CRD). The distributed structure-searchable toxicity (DSSTox) public database network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: (1) to adopt and encourage the use of a common standard file format (structure data file (SDF)) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; (2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure-toxicity data files, and that will effectively link knowledgeable toxicity data sources with potential users of these data from other disciplines (such as chemistry, modeling, and computer science); and (3) to engage public/commercial/academic/industry groups in contributing to and expanding this community-wide, public data sharing and distribution effort. The DSSTox project's overall aims are to effect the closer association of chemical structure information with existing toxicity data, and to promote and facilitate structure-based exploration of these data within a common chemistry-based framework that spans toxicological disciplines.

Analysis of network motifs in cellular regulation: Structural similarities, input-output relations and signal integration.

PubMed

Straube, Ronny

2017-12-01

Much of the complexity of regulatory networks derives from the necessity to integrate multiple signals and to avoid malfunction due to cross-talk or harmful perturbations. Hence, one may expect that the input-output behavior of larger networks is not necessarily more complex than that of smaller network motifs which suggests that both can, under certain conditions, be described by similar equations. In this review, we illustrate this approach by discussing the similarities that exist in the steady state descriptions of a simple bimolecular reaction, covalent modification cycles and bacterial two-component systems. Interestingly, in all three systems fundamental input-output characteristics such as thresholds, ultrasensitivity or concentration robustness are described by structurally similar equations. Depending on the system the meaning of the parameters can differ ranging from protein concentrations and affinity constants to complex parameter combinations which allows for a quantitative understanding of signal integration in these systems. We argue that this approach may also be extended to larger regulatory networks. Copyright © 2017 Elsevier B.V. All rights reserved.

Algebraic properties of automata associated to Petri nets and applications to computation in biological systems.

PubMed

Egri-Nagy, Attila; Nehaniv, Chrystopher L

2008-01-01

Biochemical and genetic regulatory networks are often modeled by Petri nets. We study the algebraic structure of the computations carried out by Petri nets from the viewpoint of algebraic automata theory. Petri nets comprise a formalized graphical modeling language, often used to describe computation occurring within biochemical and genetic regulatory networks, but the semantics may be interpreted in different ways in the realm of automata. Therefore, there are several different ways to turn a Petri net into a state-transition automaton. Here, we systematically investigate different conversion methods and describe cases where they may yield radically different algebraic structures. We focus on the existence of group components of the corresponding transformation semigroups, as these reflect symmetries of the computation occurring within the biological system under study. Results are illustrated by applications to the Petri net modelling of intermediary metabolism. Petri nets with inhibition are shown to be computationally rich, regardless of the particular interpretation method. Along these lines we provide a mathematical argument suggesting a reason for the apparent all-pervasiveness of inhibitory connections in living systems.

77 FR 12898 - Self-Regulatory Organizations; Midwest Securities Trust Company; Order Cancelling Clearing Agency...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-02

... the event any self-regulatory organization is no longer in existence or has ceased to do business in... SECURITIES AND EXCHANGE COMMISSION [Release No. 34-66461; File No. 600-7] Self-Regulatory Organizations; Midwest Securities Trust Company; Order Cancelling Clearing Agency Registration February 24, 2012...

77 FR 12896 - Self-Regulatory Organizations; Midwest Clearing Corporation; Order Cancelling Clearing Agency...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-02

... Act provides that in the event any self- regulatory organization is no longer in existence or has... SECURITIES AND EXCHANGE COMMISSION [Release No. 34-66458; File No. 600-9] Self-Regulatory Organizations; Midwest Clearing Corporation; Order Cancelling Clearing Agency Registration February 24, 2012. I...

78 FR 36278 - Fuel Oil Systems for Emergency Power Supplies

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-17

... this notice (if that document is available in ADAMS) is provided the first time that a document is..., Office of Nuclear Regulatory Research, U.S. Nuclear Regulatory Commission, Washington, DC 20555-0001... issuing a revision to an existing guide in the NRC's ``Regulatory Guide'' series. This series was...

Market Structure, Financial Dependence and Industrial Growth: Evidence from the Banking Industry in Emerging Asian Economies.

PubMed

Khan, Habib Hussain; Ahmad, Rubi Binit; Gee, Chan Sok

2016-01-01

In this study, we examine the role of market structure for growth in financially dependent industries from 10 emerging Asian economies over the period of 1995-2011. Our approach departs from existing studies in that we apply four alternative measures of market structure based on structural and non-structural approaches and compare their outcomes. Results indicate that higher bank concentration may slow down the growth of financially dependent industries. Bank competition on the other hand, allows financially dependent industries to grow faster. These findings are consistent across a number of sensitivity checks such as alternative measures of financial dependence, institutional factors (including property rights, quality of accounting standards and bank ownership), and endogeneity consideration. In sum, our study suggests that financially dependent industries grow more in more competitive/less concentrated banking systems. Therefore, regulatory authorities need to be careful while pursuing a consolidation policy for banking sector in emerging Asian economies.

Development and implementation of clinical trial protocol templates at the National Institute of Allergy and Infectious Diseases.

PubMed

Bridge, Heather; Smolskis, Mary; Bianchine, Peter; Dixon, Dennis O; Kelly, Grace; Herpin, Betsey; Tavel, Jorge

2009-08-01

A clinical research protocol document must reflect both sound scientific rationale as well as local, national and, when applicable, international regulatory and human subject protections requirements. These requirements originate from a variety of sources, undergo frequent revision and are subject to interpretation. Tools to assist clinical investigators in the production of clinical protocols could facilitate navigating these requirements and ultimately increase the efficiency of clinical research. The National Institute of Allergy and Infectious Diseases (NIAID) developed templates for investigators to serve as the foundation for protocol development. These protocol templates are designed as tools to support investigators in developing clinical protocols. NIAID established a series of working groups to determine how to improve its capacity to conduct clinical research more efficiently and effectively. The Protocol Template Working Group was convened to determine what protocol templates currently existed within NIAID and whether standard NIAID protocol templates should be produced. After review and assessment of existing protocol documents and requirements, the group reached consensus about required and optional content, determined the format and identified methods for distribution as well as education of investigators in the use of these templates. The templates were approved by the NIAID Executive Committee in 2006 and posted as part of the NIAID Clinical Research Toolkit [1] website for broad access. These documents require scheduled revisions to stay current with regulatory and policy changes. The structure of any clinical protocol template, whether comprehensive or specific to a particular study phase, setting or design, affects how it is used by investigators. Each structure presents its own set of advantages and disadvantages. While useful, protocol templates are not stand-alone tools for creating an optimal protocol document, but must be complemented by institutional resources and support. Education and guidance of investigators in the appropriate use of templates is necessary to ensure a complete yet concise protocol document. Due to changing regulatory requirements, clinical protocol templates cannot become static, but require frequent revisions.

Team Structure and Regulatory Focus: The Impact of Regulatory Fit on Team Dynamic

ERIC Educational Resources Information Center

Dimotakis, Nikolaos; Davison, Robert B.; Hollenbeck, John R.

2012-01-01

We report a within-teams experiment testing the effects of fit between team structure and regulatory task demands on task performance and satisfaction through average team member positive affect and helping behaviors. We used a completely crossed repeated-observations design in which 21 teams enacted 2 tasks with different regulatory focus…

Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks.

PubMed

Yu, Bowen; Doraiswamy, Harish; Chen, Xi; Miraldi, Emily; Arrieta-Ortiz, Mario Luis; Hafemeister, Christoph; Madar, Aviv; Bonneau, Richard; Silva, Cláudio T

2014-12-01

Elucidation of transcriptional regulatory networks (TRNs) is a fundamental goal in biology, and one of the most important components of TRNs are transcription factors (TFs), proteins that specifically bind to gene promoter and enhancer regions to alter target gene expression patterns. Advances in genomic technologies as well as advances in computational biology have led to multiple large regulatory network models (directed networks) each with a large corpus of supporting data and gene-annotation. There are multiple possible biological motivations for exploring large regulatory network models, including: validating TF-target gene relationships, figuring out co-regulation patterns, and exploring the coordination of cell processes in response to changes in cell state or environment. Here we focus on queries aimed at validating regulatory network models, and on coordinating visualization of primary data and directed weighted gene regulatory networks. The large size of both the network models and the primary data can make such coordinated queries cumbersome with existing tools and, in particular, inhibits the sharing of results between collaborators. In this work, we develop and demonstrate a web-based framework for coordinating visualization and exploration of expression data (RNA-seq, microarray), network models and gene-binding data (ChIP-seq). Using specialized data structures and multiple coordinated views, we design an efficient querying model to support interactive analysis of the data. Finally, we show the effectiveness of our framework through case studies for the mouse immune system (a dataset focused on a subset of key cellular functions) and a model bacteria (a small genome with high data-completeness).

Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213

PubMed Central

2012-01-01

Background Computational methods for structural gene annotation have propelled gene discovery but face certain drawbacks with regards to prokaryotic genome annotation. Identification of transcriptional start sites, demarcating overlapping gene boundaries, and identifying regulatory elements such as small RNA are not accurate using these approaches. In this study, we re-visit the structural annotation of Mannheimia haemolytica PHL213, a bovine respiratory disease pathogen. M. haemolytica is one of the causative agents of bovine respiratory disease that results in about $3 billion annual losses to the cattle industry. We used RNA-Seq and analyzed the data using freely-available computational methods and resources. The aim was to identify previously unannotated regions of the genome using RNA-Seq based expression profile to complement the existing annotation of this pathogen. Results Using the Illumina Genome Analyzer, we generated 9,055,826 reads (average length ~76 bp) and aligned them to the reference genome using Bowtie. The transcribed regions were analyzed using SAMTOOLS and custom Perl scripts in conjunction with BLAST searches and available gene annotation information. The single nucleotide resolution map enabled the identification of 14 novel protein coding regions as well as 44 potential novel sRNA. The basal transcription profile revealed that 2,506 of the 2,837 annotated regions were expressed in vitro, at 95.25% coverage, representing all broad functional gene categories in the genome. The expression profile also helped identify 518 potential operon structures involving 1,086 co-expressed pairs. We also identified 11 proteins with mutated/alternate start codons. Conclusions The application of RNA-Seq based transcriptome profiling to structural gene annotation helped correct existing annotation errors and identify potential novel protein coding regions and sRNA. We used computational tools to predict regulatory elements such as promoters and terminators associated with the novel expressed regions for further characterization of these novel functional elements. Our study complements the existing structural annotation of Mannheimia haemolytica PHL213 based on experimental evidence. Given the role of sRNA in virulence gene regulation and stress response, potential novel sRNA described in this study can form the framework for future studies to determine the role of sRNA, if any, in M. haemolytica pathogenesis. PMID:23046475

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

PubMed Central

Tripathi, Sushil; Vercruysse, Steven; Chawla, Konika; Christie, Karen R.; Blake, Judith A.; Huntley, Rachael P.; Orchard, Sandra; Hermjakob, Henning; Thommesen, Liv; Lægreid, Astrid; Kuiper, Martin

2016-01-01

A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives. Yet the availability of comprehensive knowledge in databases is crucial for exploiting existing background knowledge, both for designing follow-up experiments and for interpreting new experimental data. Structured resources also underpin the computational integration and modeling of regulatory pathways, which further aids our understanding of regulatory dynamics. We argue how cooperation between the scientific community and professional curators can increase the capacity of capturing precise knowledge from literature. We demonstrate this with a project in which we mobilize biological domain experts who curate large amounts of DNA binding transcription factors, and show that they, although new to the field of curation, can make valuable contributions by harvesting reported knowledge from scientific papers. Such community curation can enhance the scientific epistemic process. Database URL: http://www.tfcheckpoint.org PMID:27270715

The Temperature Fuzzy Control System of Barleythe Malt Drying Based on Microcontroller

NASA Astrophysics Data System (ADS)

Gao, Xiaoyang; Bi, Yang; Zhang, Lili; Chen, Jingjing; Yun, Jianmin

The control strategy of temperature and humidity in the beer barley malt drying chamber based on fuzzy logic control was implemented.Expounded in this paper was the selection of parameters for the structure of the regulatory device, as well as the essential design from control rules based on the existing experience. A temperature fuzzy controller was thus constructed using relevantfuzzy logic, and humidity control was achieved by relay, ensured the situation of the humidity to control the temperature. The temperature's fuzzy control and the humidity real-time control were all processed by single chip microcomputer with assembly program. The experimental results showed that the temperature control performance of this fuzzy regulatory system,especially in the ways of working stability and responding speed and so on,was better than normal used PID control. The cost of real-time system was inquite competitive position. It was demonstrated that the system have a promising prospect of extensive application.

Regulation of microtubule nucleation mediated by γ-tubulin complexes.

PubMed

Sulimenko, Vadym; Hájková, Zuzana; Klebanovych, Anastasiya; Dráber, Pavel

2017-05-01

The microtubule cytoskeleton is critically important for spatio-temporal organization of eukaryotic cells. The nucleation of new microtubules is typically restricted to microtubule organizing centers (MTOCs) and requires γ-tubulin that assembles into multisubunit complexes of various sizes. γ-Tubulin ring complexes (TuRCs) are efficient microtubule nucleators and are associated with large number of targeting, activating and modulating proteins. γ-Tubulin-dependent nucleation of microtubules occurs both from canonical MTOCs, such as spindle pole bodies and centrosomes, and additional sites such as Golgi apparatus, nuclear envelope, plasma membrane-associated sites, chromatin and surface of pre-existing microtubules. Despite many advances in structure of γ-tubulin complexes and characterization of γTuRC interacting factors, regulatory mechanisms of microtubule nucleation are not fully understood. Here, we review recent work on the factors and regulatory mechanisms that are involved in centrosomal and non-centrosomal microtubule nucleation.

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes.

PubMed

Parker, Brian J; Moltke, Ida; Roth, Adam; Washietl, Stefan; Wen, Jiayu; Kellis, Manolis; Breaker, Ronald; Pedersen, Jakob Skou

2011-11-01

Regulatory RNA structures are often members of families with multiple paralogous instances across the genome. Family members share functional and structural properties, which allow them to be studied as a whole, facilitating both bioinformatic and experimental characterization. We have developed a comparative method, EvoFam, for genome-wide identification of families of regulatory RNA structures, based on primary sequence and secondary structure similarity. We apply EvoFam to a 41-way genomic vertebrate alignment. Genome-wide, we identify 220 human, high-confidence families outside protein-coding regions comprising 725 individual structures, including 48 families with known structural RNA elements. Known families identified include both noncoding RNAs, e.g., miRNAs and the recently identified MALAT1/MEN β lincRNA family; and cis-regulatory structures, e.g., iron-responsive elements. We also identify tens of new families supported by strong evolutionary evidence and other statistical evidence, such as GO term enrichments. For some of these, detailed analysis has led to the formulation of specific functional hypotheses. Examples include two hypothesized auto-regulatory feedback mechanisms: one involving six long hairpins in the 3'-UTR of MAT2A, a key metabolic gene that produces the primary human methyl donor S-adenosylmethionine; the other involving a tRNA-like structure in the intron of the tRNA maturation gene POP1. We experimentally validate the predicted MAT2A structures. Finally, we identify potential new regulatory networks, including large families of short hairpins enriched in immunity-related genes, e.g., TNF, FOS, and CTLA4, which include known transcript destabilizing elements. Our findings exemplify the diversity of post-transcriptional regulation and provide a resource for further characterization of new regulatory mechanisms and families of noncoding RNAs.

Regulatory Approaches for Adding Capacity to Existing Hydropower Facilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Levine, Aaron L.; Curtis, Taylor L.; Kazerooni, Borna

In 2015, hydroelectric generation accounted for more than 6 percent of total net electricity generation in the United States and 46 percent of electricity generation from all renewables. The United States has considerable hydroelectric potential beyond what is already being developed. Nearly 7 GW of this potential is found by adding capacity to existing hydropower facilities. To optimize the value of hydroelectric generation, the U.S. Department of Energy's Hydropower Vision Study highlights the importance of adding capacity to existing facilities. This report provides strategic approaches and considerations for Federal Energy Regulatory Commission licensed and exempt hydropower facilities seeking to increasemore » generation capacity, which may include increases from efficiency upgrades. The regulatory approaches reviewed for this report include capacity and non-capacity amendments, adding capacity during relicensing, and adding capacity when converting a license to a 10-MW exemption.« less

76 FR 32331 - Preliminary Plan for Retrospective Review of Existing Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-06

... review. In addition, DHS launched an IdeaScale Web page; this social media tool provided an additional... agency's regulatory program more effective or less burdensome in achieving its regulatory objectives. DHS...

77 FR 7980 - Department Regulatory Agenda; Semiannual Summary

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-13

...The Regulatory Agenda is a semiannual summary of all current and projected rulemakings, reviews of existing regulations, and completed actions of the Department. The Agenda provides the public with information about the Department of Transportation's regulatory activity. It is expected that this information will enable the public to be more aware of and allow it to more effectively participate in the Department's regulatory activity. The public is also invited to submit comments on any aspect of this Agenda.

75 FR 79811 - Department Regulatory Agenda; Semiannual Summary

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-20

...The regulatory agenda is a semiannual summary of all current and projected rulemakings, reviews of existing regulations, and completed actions of the Department. The agenda provides the public with information about the Department of Transportation's regulatory activity. It is expected that this information will enable the public to be more aware of and allow it to more effectively participate in the Department's regulatory activity. The public is also invited to submit comments on any aspect of this agenda.

75 FR 21839 - Department Regulatory Agenda; Semiannual Summary

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-26

...The regulatory agenda is a semiannual summary of all current and projected rulemakings, reviews of existing regulations, and completed actions of the Department. The agenda provides the public with information about the Department of Transportation's regulatory activity. It is expected that this information will enable the public to be more aware of and allow it to more effectively participate in the Department's regulatory activity. The public is also invited to submit comments on any aspect of this agenda.

The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios.

PubMed

Kao, Damian; Felix, Daniel; Aboobaker, Aziz

2013-11-16

Planarians can regenerate entire animals from a small fragment of the body. The regenerating fragment is able to create new tissues and remodel existing tissues to form a complete animal. Thus different fragments with very different starting components eventually converge on the same solution. In this study, we performed an extensive RNA-seq time-course on regenerating head and tail fragments to observe the differences and similarities of the transcriptional landscape between head and tail fragments during regeneration. We have consolidated existing transcriptomic data for S. mediterranea to generate a high confidence set of transcripts for use in genome wide expression studies. We performed a RNA-seq time-course on regenerating head and tail fragments from 0 hours to 3 days. We found that the transcriptome profiles of head and tail regeneration were very different at the start of regeneration; however, an unexpected convergence of transcriptional profiles occurred at 48 hours when head and tail fragments are still morphologically distinct. By comparing differentially expressed transcripts at various time-points, we revealed that this divergence/convergence pattern is caused by a shared regulatory program that runs early in heads and later in tails.Additionally, we also performed RNA-seq on smed-prep(RNAi) tail fragments which ultimately fail to regenerate anterior structures. We find the gene regulation program in response to smed-prep(RNAi) to display the opposite regulatory trend compared to the previously mentioned share regulatory program during regeneration. Using annotation data and comparative approaches, we also identified a set of approximately 4,800 triclad specific transcripts that were enriched amongst the genes displaying differential expression during the regeneration time-course. The regeneration transcriptome of head and tail regeneration provides us with a rich resource for investigating the global expression changes that occurs during regeneration. We show that very different regenerative scenarios utilize a shared core regenerative program. Furthermore, our consolidated transcriptome and annotations allowed us to identity triclad specific transcripts that are enriched within this core regulatory program. Our data support the hypothesis that both conserved aspects of animal developmental programs and recent evolutionarily innovations work in concert to control regeneration.

76 FR 69613 - Special Local Regulations and Safety Zones; Recurring Events in Captain of the Port New York Zone

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-09

... regulatory text: Safety zones listed in Table 1 to Sec. 165.160 have been reordered and renumbered to more accurately reflect their geographical locations. In the published NPRM regulatory text, the Rumson, NJ... included in this recurring events regulation. In the regulatory text under Sec. 165.160(a), the existing...

78 FR 58574 - Maintenance, Testing, and Replacement of Vented Lead-Acid Storage Batteries for Nuclear Power Plants

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-24

... time that a document is referenced. Revision 3 of Regulatory Guide 1.129 is available in ADAMS under...-251-7455; email: [email protected] . Both of the Office of Nuclear Regulatory Research, U.S... NRC is issuing a revision to an existing guide in the NRC's ``Regulatory Guide'' series. This series...

The regulatory sciences for stem cell-based medicinal products.

PubMed

Yuan, Bao-Zhu; Wang, Junzhi

2014-06-01

Over the past few years, several new achievements have been made from stem cell studies, many of which have moved up from preclinical stages to early, or from early to middle or late, stages thanks to relatively safe profile and preliminary evidence of effectiveness. Moreover, some stem cell-based products have been approved for marketing by different national regulatory authorities. However, many critical issues associated mainly with incomplete understanding of stem cell biology and the relevant risk factors, and lack of effective regulations still exist and need to be urgently addressed, especially in countries where establishment of appropriate regulatory system just commenced. More relevantly, the stem cell regulatory sciences need to be established or improved to more effectively evaluate quality, safety and efficacy of stem cell products, and for building up the appropriate regulatory framework. In this review, we summarize some new achievements in stem cell studies, especially the preclinical and clinical studies, the existing regulations, and the associated challenges, and we then propose some considerations for improving stem cell regulatory sciences with a goal of promoting the steadfast growth of the well-regulated stem cell therapies abreast of evolvement of stem cell sciences and technologies.

Three-Dimensional RNA Structure of the Major HIV-1 Packaging Signal Region

PubMed Central

Stephenson, James D.; Li, Haitao; Kenyon, Julia C.; Symmons, Martyn; Klenerman, Dave; Lever, Andrew M.L.

2013-01-01

Summary HIV-1 genomic RNA has a noncoding 5′ region containing sequential conserved structural motifs that control many parts of the life cycle. Very limited data exist on their three-dimensional (3D) conformation and, hence, how they work structurally. To assemble a working model, we experimentally reassessed secondary structure elements of a 240-nt region and used single-molecule distances, derived from fluorescence resonance energy transfer, between defined locations in these elements as restraints to drive folding of the secondary structure into a 3D model with an estimated resolution below 10 Å. The folded 3D model satisfying the data is consensual with short nuclear-magnetic-resonance-solved regions and reveals previously unpredicted motifs, offering insight into earlier functional assays. It is a 3D representation of this entire region, with implications for RNA dimerization and protein binding during regulatory steps. The structural information of this highly conserved region of the virus has the potential to reveal promising therapeutic targets. PMID:23685210

Economic regulation of ambulance services in California.

PubMed

Narad, R A

1997-01-01

This study was intended to identify economic regulatory programs used by California counties (including ambulance franchising and rate setting), to inventory their foci and application, and to identify differences around the state. By studying the variety of programs used in one state, this study establishes a framework for evaluation of state and local regulatory programs elsewhere. This study surveyed all California local EMS agencies (LEMSAs); these are California's equivalent of regional EMS organizations. The survey achieved a 100% response rate, and all data involve population parameters obviating the need for inferential statistics. Seventy-three percent of California counties use economic regulations. Large-population counties and those that operate their own LEMSAs are more likely to use economic regulations than are small counties and those that participate in multicounty EMS agencies. Despite a preference for competition in the authorizing statute, most franchises were granted without competition to existing providers. The majority of franchises in the state were granted to public services. Most ambulance rate setting occurs outside of a competitive process. Economic regulations that were intended to provide a structured marketplace are often being used to protect existing providers, particularly public services, from competition. The growing interest by fire departments in entering the market for emergency ambulance service, along with the existing bias toward them in granting of franchises, does not bode well for use of the competitive process. The growth of managed care may change or eliminate the need for economic regulations but, if they are to continue, more state oversight should be considered.

Regulatory Technology Development Plan - Sodium Fast Reactor. Mechanistic Source Term - Trial Calculation. Work Plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grabaskas, David; Bucknor, Matthew; Jerden, James

2016-02-01

The overall objective of the SFR Regulatory Technology Development Plan (RTDP) effort is to identify and address potential impediments to the SFR regulatory licensing process. In FY14, an analysis by Argonne identified the development of an SFR-specific MST methodology as an existing licensing gap with high regulatory importance and a potentially long lead-time to closure. This work was followed by an initial examination of the current state-of-knowledge regarding SFR source term development (ANLART-3), which reported several potential gaps. Among these were the potential inadequacies of current computational tools to properly model and assess the transport and retention of radionuclides duringmore » a metal fuel pool-type SFR core damage incident. The objective of the current work is to determine the adequacy of existing computational tools, and the associated knowledge database, for the calculation of an SFR MST. To accomplish this task, a trial MST calculation will be performed using available computational tools to establish their limitations with regard to relevant radionuclide release/retention/transport phenomena. The application of existing modeling tools will provide a definitive test to assess their suitability for an SFR MST calculation, while also identifying potential gaps in the current knowledge base and providing insight into open issues regarding regulatory criteria/requirements. The findings of this analysis will assist in determining future research and development needs.« less

Unique Regulatory Approach for Licensing the Port Hope Remediation Project in Canada - 13315

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kostova, M.; Howard, D.; Elder, P.

2013-07-01

The Port Hope remediation project is a part of a larger initiative of the Canadian Federal Government the Port Hope Area Initiative (PHAI) which is based upon a community proposal. The Government of Canada, through Natural Resources Canada (NRCan) is investing $1.28 billion over 10 years to clean up historic low-level radioactive waste in the Port Hope Area and to provide long-term safe management of the low-level radioactive wastes in the Port Hope Area. These wastes arose from the activities of a former Federal Crown Corporation (Eldorado Nuclear) and its private sector predecessors. In Canada, historic waste are defined asmore » low-level radioactive waste that was managed in a manner no longer considered acceptable, but for which the original producer cannot reasonably be held responsible or no longer exists and for which the Federal Government has accepted responsibility. In Canada, under the current regulatory framework, the environmental remediation is not considered as a distinct phase of the nuclear cycle. The regulatory approach for dealing with existing sites contaminated with radioactive residues is defined on the basis of risk and application of existing regulations. A unique regulatory approach was taken by the Canadian Nuclear Safety Commission (CNSC) to address the various licensing issues and to set out the requirements for licensing of the Port Hope Project within the current regulatory framework. (authors)« less

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

PubMed

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

2013-09-02

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

The structure of the regulatory domain of the adenylyl cyclase Rv1264 from Mycobacterium tuberculosis with bound oleic acid.

PubMed

Findeisen, Felix; Linder, Jürgen U; Schultz, Anita; Schultz, Joachim E; Brügger, Britta; Wieland, Felix; Sinning, Irmgard; Tews, Ivo

2007-06-22

The universal secondary messenger cAMP is produced by adenylyl cyclases (ACs). Most bacterial and all eukaryotic ACs belong to class III of six divergent classes. A class III characteristic is formation of the catalytic pocket at a dimer interface and the presence of additional regulatory domains. Mycobacterium tuberculosis possesses 15 class III ACs, including Rv1264, which is activated at acidic pH due to pH-dependent structural transitions of the Rv1264 dimer. It has been shown by X-ray crystallography that the N-terminal regulatory and C-terminal catalytic domains of Rv1264 interact in completely different ways in the active and inhibited states. Here, we report an in-depth structural and functional analysis of the regulatory domain of Rv1264. The 1.6 A resolution crystal structure shows the protein in a tight, disk-shaped dimer, formed around a helical bundle, and involving a protein chain crossover. To understand pH regulation, we determined structures at acidic and basic pH values and employed structure-based mutagenesis in the holoenzyme to elucidate regulation using an AC activity assay. It has been shown that regulatory and catalytic domains must be linked in a single protein chain. The new studies demonstrate that the length of the linker segment is decisive for regulation. Several amino acids on the surface of the regulatory domain, when exchanged, altered the pH-dependence of AC activity. However, these residues are not conserved amongst a number of related ACs. The closely related mycobacterial Rv2212, but not Rv1264, is strongly activated by the addition of fatty acids. The structure resolved the presence of a deeply embedded fatty acid, characterised as oleic acid by mass spectrometry, which may serve as a hinge. From these data, we conclude that the regulatory domain is a structural scaffold used for distinct regulatory purposes.

Reassessing policy paradigms: A comparison of the global tobacco and alcohol industries.

PubMed

Hawkins, Benjamin; Holden, Chris; Eckhardt, Jappe; Lee, Kelley

2018-01-01

Tobacco is widely considered to be a uniquely harmful product for human health. Since the mid-1990s, the strategies of transnational tobacco corporations to undermine effective tobacco control policy has been extensively documented through internal industry documents. Consequently, the sale, use and marketing of tobacco products are subject to extensive regulation and formal measures to exclude the industry from policy-making have been adopted in the Framework Convention on Tobacco Control. In contrast to tobacco, alcohol is subject to less stringent forms of regulation, and the alcohol industry continues to play a central role in policy-making in many countries and at the global level. This article examines whether there is a sufficient rationale for such different regulatory approaches, through a comparative analysis of the political economy of the tobacco and alcohol industries including the structure of the industries, and the market and political strategies they pursue. Despite some important differences, the extensive similarities which exist between the tobacco and alcohol industries in terms of market structure and strategy, and political strategy, call into question the rationale for both the relatively weak regulatory approach taken towards alcohol, and the continued participation of alcohol corporations in policy-making processes.

77 FR 65645 - Retrospective Analysis of Existing Rules: Notice of Staff Memorandum

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-30

...] Retrospective Analysis of Existing Rules: Notice of Staff Memorandum SUMMARY: Take notice that the Commission... Analysis of Existing Rules prepared in response to Executive Order 13579, which requested independent regulatory agencies issue plans for periodic retrospective analysis of their existing regulations. [[Page...

Improving medical device regulation: the United States and Europe in perspective.

PubMed

Sorenson, Corinna; Drummond, Michael

2014-03-01

Recent debates and events have brought into question the effectiveness of existing regulatory frameworks for medical devices in the United States and Europe to ensure their performance, safety, and quality. This article provides a comparative analysis of medical device regulation in the two jurisdictions, explores current reforms to improve the existing systems, and discusses additional actions that should be considered to fully meet this aim. Medical device regulation must be improved to safeguard public health and ensure that high-quality and effective technologies reach patients. We explored and analyzed medical device regulatory systems in the United States and Europe in accordance with the available gray and peer-reviewed literature and legislative documents. The two regulatory systems differ in their mandate and orientation, organization, pre- and postmarket evidence requirements, and transparency of process. Despite these differences, both jurisdictions face similar challenges for ensuring that only safe and effective devices reach the market, monitoring real-world use, and exchanging pertinent information on devices with key users such as clinicians and patients. To address these issues, reforms have recently been introduced or debated in the United States and Europe that are principally focused on strengthening regulatory processes, enhancing postmarket regulation through more robust surveillance systems, and improving the traceability and monitoring of devices. Some changes in premarket requirements for devices are being considered. Although the current reforms address some of the outstanding challenges in device regulation, additional steps are needed to improve existing policy. We examine a number of actions to be considered, such as requiring high-quality evidence of benefit for medium- and high-risk devices; moving toward greater centralization and coordination of regulatory approval in Europe; creating links between device identifier systems and existing data collection tools, such as electronic health records; and fostering increased and more effective use of registries to ensure safe postmarket use of new and existing devices. © 2014 Milbank Memorial Fund.

Improving Medical Device Regulation: The United States and Europe in Perspective

PubMed Central

SORENSON, CORINNA; DRUMMOND, MICHAEL

2014-01-01

Context: Recent debates and events have brought into question the effectiveness of existing regulatory frameworks for medical devices in the United States and Europe to ensure their performance, safety, and quality. This article provides a comparative analysis of medical device regulation in the two jurisdictions, explores current reforms to improve the existing systems, and discusses additional actions that should be considered to fully meet this aim. Medical device regulation must be improved to safeguard public health and ensure that high-quality and effective technologies reach patients. Methods: We explored and analyzed medical device regulatory systems in the United States and Europe in accordance with the available gray and peer-reviewed literature and legislative documents. Findings: The two regulatory systems differ in their mandate and orientation, organization, pre-and postmarket evidence requirements, and transparency of process. Despite these differences, both jurisdictions face similar challenges for ensuring that only safe and effective devices reach the market, monitoring real-world use, and exchanging pertinent information on devices with key users such as clinicians and patients. To address these issues, reforms have recently been introduced or debated in the United States and Europe that are principally focused on strengthening regulatory processes, enhancing postmarket regulation through more robust surveillance systems, and improving the traceability and monitoring of devices. Some changes in premarket requirements for devices are being considered. Conclusions: Although the current reforms address some of the outstanding challenges in device regulation, additional steps are needed to improve existing policy. We examine a number of actions to be considered, such as requiring high-quality evidence of benefit for medium-and high-risk devices; moving toward greater centralization and coordination of regulatory approval in Europe; creating links between device identifier systems and existing data collection tools, such as electronic health records; and fostering increased and more effective use of registries to ensure safe postmarket use of new and existing devices. PMID:24597558

75 FR 13 - Alternate Fracture Toughness Requirements for Protection Against Pressurized Thermal Shock Events

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-04

...The Nuclear Regulatory Commission (NRC) is amending its regulations to provide alternate fracture toughness requirements for protection against pressurized thermal shock (PTS) events for pressurized water reactor (PWR) pressure vessels. This final rule provides alternate PTS requirements based on updated analysis methods. This action is desirable because the existing requirements are based on unnecessarily conservative probabilistic fracture mechanics analyses. This action reduces regulatory burden for those PWR licensees who expect to exceed the existing requirements before the expiration of their licenses, while maintaining adequate safety, and may choose to comply with the final rule as an alternative to complying with the existing requirements.

The European Regulatory Environment of RNA-Based Vaccines.

PubMed

Hinz, Thomas; Kallen, Kajo; Britten, Cedrik M; Flamion, Bruno; Granzer, Ulrich; Hoos, Axel; Huber, Christoph; Khleif, Samir; Kreiter, Sebastian; Rammensee, Hans-Georg; Sahin, Ugur; Singh-Jasuja, Harpreet; Türeci, Özlem; Kalinke, Ulrich

2017-01-01

A variety of different mRNA-based drugs are currently in development. This became possible, since major breakthroughs in RNA research during the last decades allowed impressive improvements of translation, stability and delivery of mRNA. This article focuses on antigen-encoding RNA-based vaccines that are either directed against tumors or pathogens. mRNA-encoded vaccines are developed both for preventive or therapeutic purposes. Most mRNA-based vaccines are directly administered to patients. Alternatively, primary autologous cells from cancer patients are modified ex vivo by the use of mRNA and then are adoptively transferred to patients. In the EU no regulatory guidelines presently exist that specifically address mRNA-based vaccines. The existing regulatory framework, however, clearly defines that mRNA-based vaccines in most cases have to be centrally approved. Interestingly, depending on whether RNA-based vaccines are directed against tumors or infectious disease, they are formally considered gene therapy products or not, respectively. Besides an overview on the current clinical use of mRNA vaccines in various therapeutic areas a detailed discussion of the current regulatory situation is provided and regulatory perspectives are discussed.

The 3’-Jα Region of the TCRα Locus Bears Gene Regulatory Activity in Thymic and Peripheral T Cells

PubMed Central

Kučerová-Levisohn, Martina; Knirr, Stefan; Mejia, Rosa I.; Ortiz, Benjamin D.

2015-01-01

Much progress has been made in understanding the important cis-mediated controls on mouse TCRα gene function, including identification of the Eα enhancer and TCRα locus control region (LCR). Nevertheless, previous data have suggested that other cis-regulatory elements may reside in the locus outside of the Eα/LCR. Based on prior findings, we hypothesized the existence of gene regulatory elements in a 3.9-kb region 5’ of the Cα exons. Using DNase hypersensitivity assays and TCRα BAC reporter transgenes in mice, we detected gene regulatory activity within this 3.9-kb region. This region is active in both thymic and peripheral T cells, and selectively affects upstream, but not downstream, gene expression. Together, these data indicate the existence of a novel cis-acting regulatory complex that contributes to TCRα transgene expression in vivo. The active chromatin sites we discovered within this region would remain in the locus after TCRα gene rearrangement, and thus may contribute to endogenous TCRα gene activity, particularly in peripheral T cells, where the Eα element has been found to be inactive. PMID:26177549

76 FR 64403 - Self-Regulatory Organizations; The Fixed Income Clearing Corporation; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-18

... Schedule of Timeframes, and Fee Structure in the GSD Rules. II. Self-Regulatory Organization's Statement of...-Regulatory Organizations; The Fixed Income Clearing Corporation; Notice of Filing and Immediate Effectiveness... Timeframes, and Fee Structure in the GSD Rules October 12, 2011. Pursuant to Section 19(b)(1) of the...

The roles of RIIbeta linker and N-terminal cyclic nucleotide-binding domain in determining the unique structures of Type IIbeta Protein Kinase A. A small angle X-ray and neutron scattering study

DOE PAGES

Blumenthal, Donald K.; Copps, Jeffrey; Smith-Nguyen, Eric V.; ...

2014-08-11

Protein kinase A (PKA) is ubiquitously expressed and is responsible for regulating many important cellular functions in response to changes in intracellular cAMP concentrations. Moreover, the PKA holoenzyme is a tetramer (R 2:C 2), with a regulatory subunit homodimer (R 2) that binds and inhibits two catalytic (C) subunits; binding of cAMP to the regulatory subunit homodimer causes activation of the catalytic subunits. Four different R subunit isoforms exist in mammalian cells, and these confer different structural features, subcellular localization, and biochemical properties upon the PKA holoenzymes they form. The holoenzyme containing RIIβ is structurally unique in that the typemore » IIβ holoenzyme is much more compact than the free RIIβ homodimer. We have used small angle x-ray scattering and small angle neutron scattering to study the solution structure and subunit organization of a holoenzyme containing an RIIβ C-terminal deletion mutant (RIIβ(1–280)), which is missing the C-terminal cAMP-binding domain to better understand the structural organization of the type IIβ holoenzyme and the RIIβ domains that contribute to stabilizing the holoenzyme conformation. These results demonstrate that compaction of the type IIβ holoenzyme does not require the C-terminal cAMP-binding domain but rather involves large structural rearrangements within the linker and N-terminal cyclic nucleotide-binding domain of the RIIβ homodimer. The structural rearrangements are significantly greater than seen previously with RIIα and are likely to be important in mediating short range and long range interdomain and intersubunit interactions that uniquely regulate the activity of the type IIβ isoform of PKA.« less

The roles of the RIIβ linker and N-terminal cyclic nucleotide-binding domain in determining the unique structures of the type IIβ protein kinase A: a small angle x-ray and neutron scattering study.

PubMed

Blumenthal, Donald K; Copps, Jeffrey; Smith-Nguyen, Eric V; Zhang, Ping; Heller, William T; Taylor, Susan S

2014-10-10

Protein kinase A (PKA) is ubiquitously expressed and is responsible for regulating many important cellular functions in response to changes in intracellular cAMP concentrations. The PKA holoenzyme is a tetramer (R2:C2), with a regulatory subunit homodimer (R2) that binds and inhibits two catalytic (C) subunits; binding of cAMP to the regulatory subunit homodimer causes activation of the catalytic subunits. Four different R subunit isoforms exist in mammalian cells, and these confer different structural features, subcellular localization, and biochemical properties upon the PKA holoenzymes they form. The holoenzyme containing RIIβ is structurally unique in that the type IIβ holoenzyme is much more compact than the free RIIβ homodimer. We have used small angle x-ray scattering and small angle neutron scattering to study the solution structure and subunit organization of a holoenzyme containing an RIIβ C-terminal deletion mutant (RIIβ(1-280)), which is missing the C-terminal cAMP-binding domain to better understand the structural organization of the type IIβ holoenzyme and the RIIβ domains that contribute to stabilizing the holoenzyme conformation. Our results demonstrate that compaction of the type IIβ holoenzyme does not require the C-terminal cAMP-binding domain but rather involves large structural rearrangements within the linker and N-terminal cyclic nucleotide-binding domain of the RIIβ homodimer. The structural rearrangements are significantly greater than seen previously with RIIα and are likely to be important in mediating short range and long range interdomain and intersubunit interactions that uniquely regulate the activity of the type IIβ isoform of PKA. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

78 FR 37246 - New Postal Product

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-20

... POSTAL REGULATORY COMMISSION [Docket No. CP2013-67; Order No. 1749] New Postal Product AGENCY: Postal Regulatory Commission. ACTION: Notice SUMMARY: The Commission is noticing a recently filed Postal... the introductory (``Whereas'') paragraphs of the Agreement; revisions to existing articles; and new...

Key findings on legal and regulatory barriers to HIV testing and access to care across Europe.

PubMed

Power, L; Hows, J; Jakobsen, S F

2018-02-01

The aim of this work within OptTEST by HiE has been to demonstrate the role of legal and regulatory barriers in hindering access to HIV testing, treatment and care across Europe and to produce tools to help dismantle them. An online survey to assess country-specific data on legal and regulatory barriers distributed widely across the WHO Europe region. Literature reviews conducted in January-October 2015 in English, in November 2015 in Russian, and updated in April 2017. Semi-structured interviews were conducted with 25 key actors within the HIV field to feed into case studies and tip sheets on how to dismantle legal and regulatory barriers. More than 160 individuals and organisations from 49 countries across the WHO European region provided responses which were analysed and cross checked with other data sources and a searchable database produced (legalbarriers.peoplewithhiveurope.org). The conducted literature reviews yielded 88 papers and reports which identify legal and regulatory barriers to key populations' access to HV testing and care. Based on the interviews with key actors, ranging from PLHIV activists to government officials, on lessons-learned, a series of tip sheets and ten case studies were written-up intended to inform and inspire the HIV community to address and overcome existing barriers (opttest.eu/Tools). While some of the barriers identified may require major changes to wider health systems, or long term legal reform, many are open to a simple change in regulations or custom and practice. We have the tools. Why can't we finish the job? © 2018 British HIV Association.

Market Structure, Financial Dependence and Industrial Growth: Evidence from the Banking Industry in Emerging Asian Economies

PubMed Central

Khan, Habib Hussain; Ahmad, Rubi Binit; Gee, Chan Sok

2016-01-01

In this study, we examine the role of market structure for growth in financially dependent industries from 10 emerging Asian economies over the period of 1995–2011. Our approach departs from existing studies in that we apply four alternative measures of market structure based on structural and non-structural approaches and compare their outcomes. Results indicate that higher bank concentration may slow down the growth of financially dependent industries. Bank competition on the other hand, allows financially dependent industries to grow faster. These findings are consistent across a number of sensitivity checks such as alternative measures of financial dependence, institutional factors (including property rights, quality of accounting standards and bank ownership), and endogeneity consideration. In sum, our study suggests that financially dependent industries grow more in more competitive/less concentrated banking systems. Therefore, regulatory authorities need to be careful while pursuing a consolidation policy for banking sector in emerging Asian economies. PMID:27490847

Identification of N-Terminal Lobe Motifs that Determine the Kinase Activity of the Catalytic Domains and Regulatory Strategies of Src and Csk Protein Tyrosine Kinases†

PubMed Central

Huang, Kezhen; Wang, Yue-Hao; Brown, Alex; Sun, Gongqin

2009-01-01

Csk and Src protein tyrosine kinases are structurally homologous, but use opposite regulatory strategies. The isolated catalytic domain of Csk is intrinsically inactive and is activated by interactions with the regulatory SH3 and SH2 domains, while the isolated catalytic domain of Src is intrinsically active and is suppressed by interactions with the regulatory SH3 and SH2 domains. The structural basis for why one isolated catalytic domain is intrinsically active while the other is inactive is not clear. In this current study, we identify the structural elements in the N-terminal lobe of the catalytic domain that render the Src catalytic domain active. These structural elements include the α-helix C region, a β-turn between the β-4 and β-5 strands, and an Arg residue at the beginning of the catalytic domain. These three motifs interact with each other to activate the Src catalytic domain, but the equivalent motifs in Csk directly interact with the regulatory domains that are important for Csk activation. The Src motifs can be grafted to the Csk catalytic domain to obtain an active Csk catalytic domain. These results, together with available Src and Csk tertiary structures, reveal an important structural switch that determines the kinase activity of a catalytic domain and dictates the regulatory strategy of a kinase. PMID:19244618

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balser, S.; Sankar, S.; Miller, R.

In order to more fully integrate renewable resources, such as wind and solar, into the transmission system, additional capacity must be realized in the short term using the installed transmission capacity that exists today. The U.S. Department of Energy (DOE) and the National Renewable Energy Laboratory Transmission and Grid Integration Group supported this study to assemble the history of regulations and status of transmission technology to expand existing grid capacity. This report compiles data on various transmission technology methods and upgrades for increased capacity utilization of the existing transmission system and transmission corridors. The report discusses the technical merit ofmore » each method and explains how the method could be applied within the current regulatory structure to increase existing transmission conductor and/or corridor capacity. The history and current state of alternatives to new construction is presented for regulators, legislators, and other policy makers wrestling with issues surrounding integration of variable generation. Current regulations are assessed for opportunities to change them to promote grid expansion. To support consideration of these alternatives for expanding grid capacity, the report lists relevant rules, standards, and policy changes.« less

77 FR 71458 - New International Mail Contract

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-30

... POSTAL REGULATORY COMMISSION [Docket No. CP2013-20; Order No. 1553] New International Mail Contract AGENCY: Postal Regulatory Commission. ACTION: Notice. SUMMARY: The Commission is noticing a...\\ Id. at 5-7. \\3\\ Differences include numerous revisions to existing Articles and five new Articles. Id...

78 FR 42566 - New Postal Product

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-16

... POSTAL REGULATORY COMMISSION [Docket No. CP2013-72; Order No. 1775] New Postal Product AGENCY: Postal Regulatory Commission. ACTION: Notice. SUMMARY: The Commission is noticing a recent Postal Service... Agreement; revisions to several existing articles; and new, deleted, and renumbered articles. Id. at 3-7...

33 CFR 1.05-10 - Regulatory process overview.

Code of Federal Regulations, 2011 CFR

2011-07-01

... regulation, alternatives considered, and potential cost and benefits, including possible environmental... or for changes to an existing regulation. The need may arise due to statutory changes, or be based on... Federal Register. These may include regulatory evaluations, environmental analyses, requests for comments...

33 CFR 1.05-10 - Regulatory process overview.

Code of Federal Regulations, 2010 CFR

2010-07-01

... regulation, alternatives considered, and potential cost and benefits, including possible environmental... or for changes to an existing regulation. The need may arise due to statutory changes, or be based on... Federal Register. These may include regulatory evaluations, environmental analyses, requests for comments...

Current limitations and recommendations to improve testing for the environmental assessment of endocrine active substances

EPA Science Inventory

In this paper existing regulatory frameworks and test systems for assessing potential endocrine-active chemicals are described, and associated challenges discussed, along with proposed approaches to address these challenges. Regulatory frameworks vary somewhat across organizatio...

SmARTest regulation? Comparing the regulatory structures for ART in the UK and Australia.

PubMed

Petersen, Kerry; Johnson, Martin H

2007-08-01

Assisted reproductive technologies are regulated in both the UK and Australia, thereby curtailing both reproductive and professional autonomy. Different regulatory models have developed in each jurisdiction, despite the similar legal, scientific and cultural histories of the two jurisdictions. In the UK the regulatory structures are under review, largely in the absence of empirical research on the costs and benefits of regulation. The regulatory structures in each jurisdiction are compared and some key differences identified. The UK regulatory structure governing assisted reproductive technologies is currently simpler, more accountable and more transparent than that in Australia. On the other hand, despite administrative and legislative restrictions (particularly in Victoria), the medical scientists and clinicians in Australia generally have more control than their British counterparts over the technical aspects of their work in the provision of IVF and other treatment services, and to a lesser extent in embryo research. Recent proposals appear to move the UK regulatory structure towards a less accountable and less transparent model, but with no evident increase in reproductive or professional autonomy. It is suggested that this change is not in the interests of patients, doctors and the public, and a different model is outlined for devolution of both authority and accountability to the professions.

Adolescent cocaine exposure simplifies orbitofrontal cortical dendritic arbors

PubMed Central

DePoy, Lauren M.; Perszyk, Riley E.; Zimmermann, Kelsey S.; Koleske, Anthony J.; Gourley, Shannon L.

2014-01-01

Cocaine and amphetamine remodel dendritic spines within discrete cortico-limbic brain structures including the orbitofrontal cortex (oPFC). Whether dendrite structure is similarly affected, and whether pre-existing cellular characteristics influence behavioral vulnerabilities to drugs of abuse, remain unclear. Animal models provide an ideal venue to address these issues because neurobehavioral phenotypes can be defined both before, and following, drug exposure. We exposed mice to cocaine from postnatal days 31–35, corresponding to early adolescence, using a dosing protocol that causes impairments in an instrumental reversal task in adulthood. We then imaged and reconstructed excitatory neurons in deep-layer oPFC. Prior cocaine exposure shortened and simplified arbors, particularly in the basal region. Next, we imaged and reconstructed orbital neurons in a developmental-genetic model of cocaine vulnerability—the p190rhogap+/– mouse. p190RhoGAP is an actin cytoskeleton regulatory protein that stabilizes dendrites and dendritic spines, and p190rhogap+/– mice develop rapid and robust locomotor activation in response to cocaine. Despite this, oPFC dendritic arbors were intact in drug-naïve p190rhogap+/– mice. Together, these findings provide evidence that adolescent cocaine exposure has long-term effects on dendrite structure in the oPFC, and they suggest that cocaine-induced modifications in dendrite structure may contribute to the behavioral effects of cocaine more so than pre-existing structural abnormalities in this cell population. PMID:25452728

[Evaluation of regulatory policies: the prevention of traffic accidents in Spain].

PubMed

Villalbí, Joan R; Pérez, Catherine

2006-03-01

Traffic accident injuries may be reduced with public policies. We review regulatory policies extending beyond the health sector by studying the case of traffic accident injuries. They have been the object of other analyses in Spain by both health professionals and professionals from other sectors, but we have not found a previous thorough review including regulatory aspects. We analyze the evolution of fatal victims of traffic accidents as collected by the Dirección General de Tráfico, stratifying for pedestrians, two-wheel vehicle occupants and occupants of other vehicles, and breaking down accidents between those occurring in roads and in urban settings. Despite the increase in exposure factors between 1970 and 2003, we observe a strong impact of regulatory policies in accident mortality. A favorable impact is seen for regulations and enforcement actions on motorcycle helmets, speed limits and the control of alcohol use, and a lower impact for safety belts, perhaps because its actual effective implementation was not equally sharp. The adoption of comprehensive plans or complex legislation packages seems to have had a positive impact, perhaps attributable to its triggering of more effective enforcement of already existing regulations. Although the existence of legal norms is not enough in itself, as its impact is low without active enforcement, compliance improves over time. In any case, the existence of specific initiatives to influence this field is important to obtain the best results of regulatory policies in public health.

MapReduce Algorithms for Inferring Gene Regulatory Networks from Time-Series Microarray Data Using an Information-Theoretic Approach.

PubMed

Abduallah, Yasser; Turki, Turki; Byron, Kevin; Du, Zongxuan; Cervantes-Cervantes, Miguel; Wang, Jason T L

2017-01-01

Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections are known as gene regulatory networks (GRNs). Elucidating GRNs is crucial to understand the inner workings of the cell and the complexity of gene interactions. To date, numerous algorithms have been developed to infer gene regulatory networks. However, as the number of identified genes increases and the complexity of their interactions is uncovered, networks and their regulatory mechanisms become cumbersome to test. Furthermore, prodding through experimental results requires an enormous amount of computation, resulting in slow data processing. Therefore, new approaches are needed to expeditiously analyze copious amounts of experimental data resulting from cellular GRNs. To meet this need, cloud computing is promising as reported in the literature. Here, we propose new MapReduce algorithms for inferring gene regulatory networks on a Hadoop cluster in a cloud environment. These algorithms employ an information-theoretic approach to infer GRNs using time-series microarray data. Experimental results show that our MapReduce program is much faster than an existing tool while achieving slightly better prediction accuracy than the existing tool.

Modularity and design principles in the sea urchin embryo gene regulatory network

PubMed Central

Peter, Isabelle S.; Davidson, Eric H.

2010-01-01

The gene regulatory network (GRN) established experimentally for the pre-gastrular sea urchin embryo provides causal explanations of the biological functions required for spatial specification of embryonic regulatory states. Here we focus on the structure of the GRN which controls the progressive increase in complexity of territorial regulatory states during embryogenesis; and on the types of modular subcircuits of which the GRN is composed. Each of these subcircuit topologies executes a particular operation of spatial information processing. The GRN architecture reflects the particular mode of embryogenesis represented by sea urchin development. Network structure not only specifies the linkages constituting the genomic regulatory code for development, but also indicates the various regulatory requirements of regional developmental processes. PMID:19932099

Clinical trial regulation in Argentina: overview and analysis of regulatory framework, use of existing tools, and researchers' perspectives to identify potential barriers.

PubMed

White, Lauren; Ortiz, Zulma; Cuervo, Luis G; Reveiz, Ludovic

2011-11-01

To review and analyze the regulatory framework of clinical trial registration, use of existing tools (publicly accessible national/international registration databases), and users' perspectives to identify possible barriers to registration compliance by sponsors and researchers in Argentina. Internationally registered trials recruiting patients in Argentina were found through clincialtrials.gov and the International Clinical Trial Registration Platform (ICTRP) and compared with publically available clinical trials registered through the National Administration of Drugs, Foods, and Medical Devices (ANMAT). A questionnaire addressing hypothesized attitudinal, knowledge-related, idiomatic, technical, economic, and regulatory barriers that could discourage or impede registration of clinical trials was developed, and semi-structured, in-depth interviews were conducted with a purposively selected sample of researchers (investigators, sponsors, and monitors) in Argentina. A response rate of 74.3% (n = 29) was achieved, and 27 interviews were ultimately used for analysis. Results suggested that the high proportion of foreign-sponsored or multinational trials (64.8% of all protocols approved by ANMAT from 1994-2006) may contribute to a communication gap between locally based investigators and foreign-based administrative officials. A lack of knowledge about available international registration tools and limited awareness of the importance of registration were also identified as limiting factors for local investigators and sponsors. To increase compliance and promote clinical trial registration in Argentina, national health authorities, sponsors, and local investigators could take the following steps: implement a grassroots educational campaign to improve clinical trial regulation, support local investigator-sponsor-initiated clinical trials, and/or encourage local and regional scientific journal compliance with standards from the International Committee of Medical Journal Editors (ICMJE) and/or the World Association of Medical Editors (WAME).

76 FR 11395 - Reducing Regulatory Burden; Retrospective Review Under E.O. 13563

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-02

... identify specific current regulations that may be outdated, ineffective, or excessively burdensome. The purpose of this regulatory review is to make the Department's regulations more effective and less... review existing significant regulations to determine if they are outmoded, ineffective, insufficient or...

A Web-Accessible Protein Structure Prediction Pipeline

DTIC Science & Technology

2009-06-01

Abstract Proteins are the molecular basis of nearly all structural, catalytic, sensory, and regulatory functions in living organisms. The biological...sensory, and regulatory functions in living organisms. The structure of a protein is essential in understanding its function at the molecular level...Characterizing sequence-structure and structure-function relationships have been the goals of molecular biology for more than three decades

Safety of plant-made pharmaceuticals: product development and regulatory considerations based on case studies of two autologous human cancer vaccines.

PubMed

Tusé, Daniel

2011-03-01

Guidelines issued by regulatory agencies for the development of plant-made pharmaceutical (PMP) products provide criteria for product manufacturing and characterization, safety determination, containment and mitigation of environmental risks. Features of plant-made products do not always enable an easy fit within the criteria subscribed to by regulators. The unconventional nature of plant-based manufacturing processes and peculiarities of plant biology relative to that of traditional biological production systems have led to special considerations in the regulatory scrutiny of PMP. Presented in this review are case studies of two plant-made autologous (patient-specific) cancer vaccines, the nature of which introduced challenges to conventional and standardized development and preclinical evaluation routes. The rationale presented to FDA by the sponsors of each vaccine to build consensus and obtain variances to existing guidelines is discussed. While development of many plant-made biologics can be accomplished within the existing regulatory framework, the development of specialized products can be defended with rational arguments based on strong science.

Planned residential units: New development trajectories

NASA Astrophysics Data System (ADS)

Fedchenko, Irina

2017-01-01

The paper summarizes the transformation patterns of functional, morphological, social, and administrative structures of planned residential units - district (Russia, Eastern Europe), neighborhood (USA), community (UK, Europe), as the smallest structural and planning elements of the settlements. The study is based on the author's own on-site survey of the existing and new planned residential units, as well as on the analysis of theoretical sources. The multidisciplinary analysis of the theoretical concepts and on-site survey results showed that planned residential units formed in the early twentieth century retain their social and planning importance and identity, evolve and acquire new features and forms. At the same time, according to the current regulatory and legal instruments they remain basic planning elements of urban structure in the early twenty-first century. This paper also includes experimental analysis of the theoretical concepts of planned residential units' transformation, their conceptual planning model and formation principles in the early twenty-first century.

78 FR 15755 - Proposed Revision to Design of Structures, Components, Equipment and Systems; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-12

... NUCLEAR REGULATORY COMMISSION [NRC-2013-0041] Proposed Revision to Design of Structures, Components, Equipment and Systems; Correction AGENCY: Nuclear Regulatory Commission. ACTION: Standard review... for comments of the proposed revision in Chapter 3, ``Design of Structures, Components, Equipment, and...

78 FR 19541 - Proposed Revision to Design of Structures, Components, Equipment and Systems

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-01

... NUCLEAR REGULATORY COMMISSION [NRC-2013-0041] Proposed Revision to Design of Structures, Components, Equipment and Systems AGENCY: Nuclear Regulatory Commission. ACTION: Standard review plan-draft..., ``Design of Structures, Components, Equipment, and Systems;'' and the request for comment on NUREG-0800...

An mRNA-Derived Noncoding RNA Targets and Regulates the Ribosome

PubMed Central

Pircher, Andreas; Bakowska-Zywicka, Kamilla; Schneider, Lukas; Zywicki, Marek; Polacek, Norbert

2014-01-01

Summary The structural and functional repertoire of small non-protein-coding RNAs (ncRNAs) is central for establishing gene regulation networks in cells and organisms. Here, we show that an mRNA-derived 18-nucleotide-long ncRNA is capable of downregulating translation in Saccharomyces cerevisiae by targeting the ribosome. This 18-mer ncRNA binds to polysomes upon salt stress and is crucial for efficient growth under hyperosmotic conditions. Although the 18-mer RNA originates from the TRM10 locus, which encodes a tRNA methyltransferase, genetic analyses revealed the 18-mer RNA nucleotide sequence, rather than the mRNA-encoded enzyme, as the translation regulator. Our data reveal the ribosome as a target for a small regulatory ncRNA and demonstrate the existence of a yet unkown mechanism of translation regulation. Ribosome-targeted small ncRNAs are found in all domains of life and represent a prevalent but so far largely unexplored class of regulatory molecules. PMID:24685157

New insights into the complex regulation of the glycolytic pathway in Lactococcus lactis. I. Construction and diagnosis of a comprehensive dynamic model.

PubMed

Dolatshahi, Sepideh; Fonseca, Luis L; Voit, Eberhard O

2016-01-01

This article and the companion paper use computational systems modeling to decipher the complex coordination of regulatory signals controlling the glycolytic pathway in the dairy bacterium Lactococcus lactis. In this first article, the development of a comprehensive kinetic dynamic model is described. The model is based on in vivo NMR data that consist of concentration trends in key glycolytic metabolites and cofactors. The model structure and parameter values are identified with a customized optimization strategy that uses as its core the method of dynamic flux estimation. For the first time, a dynamic model with a single parameter set fits all available glycolytic time course data under anaerobic operation. The model captures observations that had not been addressed so far and suggests the existence of regulatory effects that had been observed in other species, but not in L. lactis. The companion paper uses this model to analyze details of the dynamic control of glycolysis under aerobic and anaerobic conditions.

Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stingele, Julian; Bellelli, Roberto; Alte, Ferdinand

Covalent DNA-protein crosslinks (DPCs) are toxic DNA lesions that interfere with essential chromatin transactions, such as replication and transcription. Little was known about DPC-specific repair mechanisms until the recent identification of a DPC-processing protease in yeast. The existence of a DPC protease in higher eukaryotes is inferred from data in Xenopus laevis egg extracts, but its identity remains elusive. Here we identify the metalloprotease SPRTN as the DPC protease acting in metazoans. Loss of SPRTN results in failure to repair DPCs and hypersensitivity to DPC-inducing agents. SPRTN accomplishes DPC processing through a unique DNA-induced protease activity, which is controlled bymore » several sophisticated regulatory mechanisms. Cellular, biochemical, and structural studies define a DNA switch triggering its protease activity, a ubiquitin switch controlling SPRTN chromatin accessibility, and regulatory autocatalytic cleavage. Our data also provide a molecular explanation on how SPRTN deficiency causes the premature aging and cancer predisposition disorder Ruijs-Aalfs syndrome.« less

Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN

DOE PAGES

Stingele, Julian; Bellelli, Roberto; Alte, Ferdinand; ...

2016-10-27

Covalent DNA-protein crosslinks (DPCs) are toxic DNA lesions that interfere with essential chromatin transactions, such as replication and transcription. Little was known about DPC-specific repair mechanisms until the recent identification of a DPC-processing protease in yeast. The existence of a DPC protease in higher eukaryotes is inferred from data in Xenopus laevis egg extracts, but its identity remains elusive. Here we identify the metalloprotease SPRTN as the DPC protease acting in metazoans. Loss of SPRTN results in failure to repair DPCs and hypersensitivity to DPC-inducing agents. SPRTN accomplishes DPC processing through a unique DNA-induced protease activity, which is controlled bymore » several sophisticated regulatory mechanisms. Cellular, biochemical, and structural studies define a DNA switch triggering its protease activity, a ubiquitin switch controlling SPRTN chromatin accessibility, and regulatory autocatalytic cleavage. Our data also provide a molecular explanation on how SPRTN deficiency causes the premature aging and cancer predisposition disorder Ruijs-Aalfs syndrome.« less

Self-regulatory fatigue in hematologic malignancies: impact on quality of life, coping, and adherence to medical recommendations.

PubMed

Solberg Nes, Lise; Ehlers, Shawna L; Patten, Christi A; Gastineau, Dennis A

2013-03-01

Hematopoietic stem cell transplantation (HSCT) is an intensive cancer therapy entailing numerous physical, emotional, cognitive, and practical challenges. Patients' ability to adjust and cope with such challenges may depend on their ability to exert control over cognitive, emotional, and behavioral processes, that is, ability to self-regulate. Self-regulatory capacity is a limited resource that can be depleted or fatigued (i.e., "self-regulatory fatigue"), particularly in the context of stressful life events such as cancer diagnosis and treatment. This is one of the first studies to examine self-regulatory fatigue in a cancer population. The current study aimed to (1) extract items for a specific scale of self-regulatory capacity and (2) examine the impact of such capacity on adaptation in patients with hematologic malignancies preparing for HSCT. Factor analysis of four existing scales gauging psychological adjustment and well-being in 314 patients preparing for HSCT (63% male and 89% Caucasian) identified 23 items (α = 0.85) related to self-regulatory control or fatigue. This measure was then examined using existing clinical data obtained from 178 patients (57% male and 91% Caucasian) undergoing treatment for hematologic malignancies in relationship to quality of life, coping, and self-reported adherence to physicians' recommendations. Controlling for pain severity, physical fatigue, and depression, self-regulatory fatigue scores were incrementally associated with decreased quality of life, use of avoidance coping strategies, and decreased adherence to physicians' recommendations. These results emphasize the potential role of self-regulatory capacity in coping with and adjusting to hematologic cancers and future research is warranted.

Opportunities for Energy Development in Water Conduits: A Report Prepared in Response to Section 7 of the Hydropower Regulatory Efficiency Act of 2013

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sale, Michael J.; Bishop, Norman A.; Reiser, Sonya L.

2014-09-01

In Section 7 of the Hydropower Regulatory Efficiency Act (HREA) of 2013 (P.L. 113-23), Congress directed the U.S. Department of Energy (DOE) to prepare an analysis of conduit hydropower opportunities available in the United States and to present case studies that describe the potential energy generation from these types of hydropower projects. Those analyses have been included in a new DOE report to Congress, and this ORNL/TM provides additional technical details supporting that report. Conduit hydropower offers important new ways to enhance renewable energy portfolios in the United States, as well as to increase the energy efficiency of water deliverymore » systems. Conduit hydropower projects are constructed on existing water-conveyance structures, such as irrigation canals or pressurized pipelines that deliver water to municipalities, industry, or agricultural water users. Although water conveyance infrastructures are usually designed for non-power purposes, new renewable energy can often be harvested from them without affecting their original purpose and without the need to construct new dams or diversions. Conduit hydropower differs from more conventional hydropower development in that it is generally not located on natural rivers or waterways and therefore does not involve the types of environmental impacts that are associated with hydropower. The addition of hydropower to existing water conduits can provide valuable new revenue sources from clean, renewable energy. The new energy can be used within the existing water distribution systems to offset other energy demands, or it can be sold into regional transmission systems.« less

Criticality Is an Emergent Property of Genetic Networks that Exhibit Evolvability

PubMed Central

Torres-Sosa, Christian; Huang, Sui; Aldana, Maximino

2012-01-01

Accumulating experimental evidence suggests that the gene regulatory networks of living organisms operate in the critical phase, namely, at the transition between ordered and chaotic dynamics. Such critical dynamics of the network permits the coexistence of robustness and flexibility which are necessary to ensure homeostatic stability (of a given phenotype) while allowing for switching between multiple phenotypes (network states) as occurs in development and in response to environmental change. However, the mechanisms through which genetic networks evolve such critical behavior have remained elusive. Here we present an evolutionary model in which criticality naturally emerges from the need to balance between the two essential components of evolvability: phenotype conservation and phenotype innovation under mutations. We simulated the Darwinian evolution of random Boolean networks that mutate gene regulatory interactions and grow by gene duplication. The mutating networks were subjected to selection for networks that both (i) preserve all the already acquired phenotypes (dynamical attractor states) and (ii) generate new ones. Our results show that this interplay between extending the phenotypic landscape (innovation) while conserving the existing phenotypes (conservation) suffices to cause the evolution of all the networks in a population towards criticality. Furthermore, the networks produced by this evolutionary process exhibit structures with hubs (global regulators) similar to the observed topology of real gene regulatory networks. Thus, dynamical criticality and certain elementary topological properties of gene regulatory networks can emerge as a byproduct of the evolvability of the phenotypic landscape. PMID:22969419

78 FR 37261 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of Filing of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-20

... Change Relating to Amendments to the Discovery Guide Used in Customer Arbitration Proceedings June 13... Discovery Guide (``Guide'') used in customer arbitration proceedings to provide general guidance on electronic discovery (``e-discovery'') issues and product cases and to clarify the existing provision...

77 FR 18872 - Availability of Electric Power Sources

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-28

... the first time that document is referenced. Revision 1 of Regulatory Guide 1.93 is available.... Introduction The NRC is issuing a revision to an existing guide in the NRC's ``Regulatory Guide'' series. This series was developed to describe and make available to the public information such as methods that are...

78 FR 23199 - NASA FAR Supplement Regulatory Review No. 1

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-18

... 2700-AE01 NASA FAR Supplement Regulatory Review No. 1 AGENCY: National Aeronautics and Space Administration. ACTION: Proposed rule. SUMMARY: NASA is updating the NASA FAR Supplement (NFS) with the goal of... existing regulations. The revisions to this rule are part of NASA's retrospective plan under EO 13563...

78 FR 30342 - United States Enrichment Corporation, Paducah Gaseous Diffusion Plant

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-22

... Corporation, Paducah Gaseous Diffusion Plant AGENCY: Nuclear Regulatory Commission. ACTION: Notice of... Compliance (CoC) for the Paducah Gaseous Diffusion Plant (PGDP). The existing CoC (No. GDP-1) authorizes... compliance for PGDP on November 26, 1996, and assumed regulatory oversight for the plant on March 3, 1997...

78 FR 44325 - Unified Agenda of Federal Regulatory and Deregulatory Actions

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-23

... developed under the guidelines of Executive Order 12866 ``Regulatory Planning and Review.'' GSA's purpose in.... GSA also invites interested persons to recommend existing significant regulations for review to... available online at www.reginfo.gov , in a format that offers users a greatly enhanced ability to obtain...

75 FR 16202 - Notice of Issuance of Regulatory Guide

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-31

..., Revision 2, ``An Acceptable Model and Related Statistical Methods for the Analysis of Fuel Densification.... Introduction The U.S. Nuclear Regulatory Commission (NRC) is issuing a revision to an existing guide in the... nuclear power reactors. To meet these objectives, the guide describes statistical methods related to...

76 FR 32133 - FAR Council's Plan for Retrospective Review Under Executive Order 13563-Preliminary Plan

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-03

... (E.O.) 13563, ``Improving Regulation and Regulatory Review.'' The E.O. sets forth principles and... resources and regulatory priorities, under which the agency will periodically review its existing... retrospective analysis. The Council's plan has tentatively identified eight priority initiatives for new or...

The medical dictionary for regulatory activities (MedDRA).

PubMed

Brown, E G; Wood, L; Wood, S

1999-02-01

The International Conference on Harmonisation has agreed upon the structure and content of the Medical Dictionary for Regulatory Activities (MedDRA) version 2.0 which should become available in the early part of 1999. This medical terminology is intended for use in the pre- and postmarketing phases of the medicines regulatory process, covering diagnoses, symptoms and signs, adverse drug reactions and therapeutic indications, the names and qualitative results of investigations, surgical and medical procedures, and medical/social history. It can be used for recording adverse events and medical history in clinical trials, in the analysis and tabulations of data from these trials and in the expedited submission of safety data to government regulatory authorities, as well as in constructing standard product information and documentation for applications for marketing authorisation. After licensing of a medicine, it may be used in pharmacovigilance and is expected to be the preferred terminology for international electronic regulatory communication. MedDRA is a hierarchical terminology with 5 levels and is multiaxial: terms may exist in more than 1 vertical axis, providing specificity of terms for data entry and flexibility in data retrieval. Terms in MedDRA were derived from several sources including the WHO's adverse reaction terminology (WHO-ART), Coding Symbols for a Thesaurus of Adverse Reaction Terms (COSTART), International Classification of Diseases (ICD) 9 and ICD9-CM. It will be maintained, further developed and distributed by a Maintenance Support Services Organisation (MSSO). It is anticipated that using MedDRA will improve the quality of data captured on databases, support effective analysis by providing clinically relevant groupings of terms and facilitate electronic communication of data, although as a new tool, users will need to invest time in gaining expertise in its use.

Researchers', Regulators', and Sponsors' Views on Pediatric Clinical Trials: A Multinational Study.

PubMed

Joseph, Pathma D; Craig, Jonathan C; Tong, Allison; Caldwell, Patrina H Y

2016-10-01

The last decade has seen dramatic changes in the regulatory landscape to support more trials involving children, but child-specific challenges and inequitable conduct across income regions persist. The goal of this study was to describe the attitudes and opinions of stakeholders toward trials in children, to inform additional strategies to promote more high-quality, relevant pediatric trials across the globe. Key informant semi-structured interviews were conducted with stakeholders (researchers, regulators, and sponsors) who were purposively sampled from low- to middle-income countries and high-income countries. The transcripts were thematically analyzed. Thirty-five stakeholders from 10 countries were interviewed. Five major themes were identified: addressing pervasive inequities (paucity of safety and efficacy data, knowledge disparities, volatile environment, double standards, contextual relevance, market-driven forces, industry sponsorship bias and prohibitive costs); contending with infrastructural barriers (resource constraints, dearth of pediatric trial expertise, and logistical complexities); navigating complex ethical and regulatory frameworks ("draconian" oversight, ambiguous requirements, exploitation, excessive paternalism and precariousness of coercion versus volunteerism); respecting uniqueness of children (pediatric research paradigms, child-appropriate approaches, and family-centered empowerment); and driving evidence-based child health (advocacy, opportunities, treatment access, best practices, and research prioritization). Stakeholders acknowledge that changes in the regulatory environment have encouraged more trials in children, but they contend that inequities and political, regulatory, and resource barriers continue to exist. Embedding trials as part of routine clinical care, addressing the unique needs of children, and streamlining regulatory approvals were suggested. Stakeholders recommended increasing international collaboration, establishing centralized trials infrastructure, and aligning research to child health priorities to encourage trials that address global child health care needs. Copyright © 2016 by the American Academy of Pediatrics.

Inferring Gene Regulatory Networks by Singular Value Decomposition and Gravitation Field Algorithm

PubMed Central

Zheng, Ming; Wu, Jia-nan; Huang, Yan-xin; Liu, Gui-xia; Zhou, You; Zhou, Chun-guang

2012-01-01

Reconstruction of gene regulatory networks (GRNs) is of utmost interest and has become a challenge computational problem in system biology. However, every existing inference algorithm from gene expression profiles has its own advantages and disadvantages. In particular, the effectiveness and efficiency of every previous algorithm is not high enough. In this work, we proposed a novel inference algorithm from gene expression data based on differential equation model. In this algorithm, two methods were included for inferring GRNs. Before reconstructing GRNs, singular value decomposition method was used to decompose gene expression data, determine the algorithm solution space, and get all candidate solutions of GRNs. In these generated family of candidate solutions, gravitation field algorithm was modified to infer GRNs, used to optimize the criteria of differential equation model, and search the best network structure result. The proposed algorithm is validated on both the simulated scale-free network and real benchmark gene regulatory network in networks database. Both the Bayesian method and the traditional differential equation model were also used to infer GRNs, and the results were used to compare with the proposed algorithm in our work. And genetic algorithm and simulated annealing were also used to evaluate gravitation field algorithm. The cross-validation results confirmed the effectiveness of our algorithm, which outperforms significantly other previous algorithms. PMID:23226565

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling

PubMed Central

Pardo-Diaz, Carolina; Hanly, Joseph J.; Martin, Simon H.; Mallet, James; Dasmahapatra, Kanchon K.; Salazar, Camilo; Joron, Mathieu; Nadeau, Nicola; McMillan, W. Owen; Jiggins, Chris D.

2016-01-01

An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation. PMID:26771987

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling.

PubMed

Wallbank, Richard W R; Baxter, Simon W; Pardo-Diaz, Carolina; Hanly, Joseph J; Martin, Simon H; Mallet, James; Dasmahapatra, Kanchon K; Salazar, Camilo; Joron, Mathieu; Nadeau, Nicola; McMillan, W Owen; Jiggins, Chris D

2016-01-01

An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation.

Computational architecture of the yeast regulatory network

NASA Astrophysics Data System (ADS)

Maslov, Sergei; Sneppen, Kim

2005-12-01

The topology of regulatory networks contains clues to their overall design principles and evolutionary history. We find that while in- and out-degrees of a given protein in the regulatory network are not correlated with each other, there exists a strong negative correlation between the out-degree of a regulatory protein and in-degrees of its targets. Such correlation positions large regulatory modules on the periphery of the network and makes them rather well separated from each other. We also address the question of relative importance of different classes of proteins quantified by the lethality of null-mutants lacking one of them as well as by the level of their evolutionary conservation. It was found that in the yeast regulatory network highly connected proteins are in fact less important than their low-connected counterparts.

Cogeneration feasibility: Otis Elevator Company and Polychrome Corporation. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1982-05-01

The purpose of this study was to assess the feasibility of cogeneration at Otis Elevator Company and Polychrome Corporation located in Westchester County, New York. Each plant and its associated thermal and electrical load is reviewed. Three basic cycles for the cogeneration are investigated: power only, power generation with waste heat recovery, and combined cycle. Each case was assessed economically, beginning with a screening method to suggest those configurations most likely to be implemented and continuing through an assessment of the regulatory environment for cogeneration and an analysis of rate structures for buy back power, displaced power, and supplementing service.more » It is concluded that: for a plant designed to supply the combined loads of the two corporations, interconnection costs coupled to the coincidence of load result in unfavorable economics; for separate cogeneration plants, owned and operated by each individual corporation, energy consumption patterns and the current regulatory environment, in particular the existing and proposed cogeneration system rate structures, do not permit viable economics for the proposed plants; but if the proposed cycle were owned and operated by a new entity (neither Otis/Polychrome nor the utility), an economic scheme with marginal financial benefits can be developed and may be worthy of further study. (LEW)« less

Implementation of a commercial-grade dedication program - Benefits and lessons learned

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harrington, M.; MacFarlane, I.

1991-01-01

The recent issuance of industry guidelines, the Nuclear Management and Resources Council procurement initiative, and a US Nuclear Regulatory Commission NRC generic letter on commercial-grade item dedication (CGD) has been viewed by many utility managers and executives as only adding to the existing burden of compliance with regulatory requirements. While the incorporation of these documents into existing CGD programs has created additional costs, the resulting enhanced dedication programs have also produced benefits beyond regulatory compliance, and some lessons have been learned. This paper discusses the benefits and the lessons learned during implementation of an enhanced CGD program at New Hampshiremore » Yankee's (NHY's) Seabrook nuclear plant. Based on NHY's experience, it is believed that the benefits described in this paper can be realized by other utilities implementing CGD programs.« less

Outside-in control -Does plant cell wall integrity regulate cell cycle progression?

PubMed

Gigli-Bisceglia, Nora; Hamann, Thorsten

2018-04-13

During recent years it has become accepted that plant cell walls are not inert objects surrounding all plant cells but are instead highly dynamic, plastic structures. They are involved in a large number of cell biological processes and contribute actively to plant growth, development and interaction with environment. Therefore, it is not surprising that cellular processes can control plant cell wall integrity while, simultaneously, cell wall integrity can influence cellular processes. In yeast and animal cells such a bi-directional relationship also exists between the yeast/animal extra-cellular matrices and the cell cycle. In yeast, the cell wall integrity maintenance mechanism and a dedicated plasmamembrane integrity checkpoint are mediating this relationship. Recent research has yielded insights into the mechanism controlling plant cell wall metabolism during cytokinesis. However, knowledge regarding putative regulatory pathways controlling adaptive modifications in plant cell cycle activity in response to changes in the state of the plant cell wall are not yet identified. In this review, we summarize similarities and differences in regulatory mechanisms coordinating extra cellular matrices and cell cycle activity in animal and yeast cells, discuss the available evidence supporting the existence of such a mechanism in plants and suggest that the plant cell wall integrity maintenance mechanism might also control cell cycle activity in plant cells. This article is protected by copyright. All rights reserved.

Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Svintradze, David V.; Virginia Commonwealth University, Richmond, VA 23219-1540; Peterson, Darrell L.

Differences in OxyR regulated expression of oxidative stress genes between Escherichia coli and Porphyromonas gingivalis are explained by very minor differences in structure and amino-acid sequence of the respective oxidized and reduced OxyR regulatory domains. These differences affect OxyR quaternary structures and are predicted from model building of full length OxyR–DNA complexes to confer distinct modes of DNA binding on this transcriptional regulator. OxyR transcriptionally regulates Escherichia coli oxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationally transmitted to the dimer subunit interfaces,more » which alters dimer and tetramer interactions with DNA. In contrast to E. coli OxyR regulatory-domain structures, crystal structures of Porphyromonas gingivalis OxyR regulatory domains show minimal differences in dimer configuration on changes in cysteine disulfide redox status. This locked configuration of the P. gingivalis OxyR regulatory-domain dimer closely resembles the oxidized (activating) form of the E. coli OxyR regulatory-domain dimer. It correlates with the observed constitutive activation of some oxidative stress genes in P. gingivalis and is attributable to a single amino-acid insertion in P. gingivalis OxyR relative to E. coli OxyR. Modelling of full-length P. gingivalis, E. coli and Neisseria meningitidis OxyR–DNA complexes predicts different modes of DNA binding for the reduced and oxidized forms of each.« less

NASA's Agency-Wide Strategy for Environmental Regulatory Risk Analysis and Communication

NASA Technical Reports Server (NTRS)

Duda, Kristen; Scroggins, Sharon

2008-01-01

NASA's mission is to pioneer the future in space exploration, scientific discovery, and aeronautics research. To help enable existing and future programs to pursue this mission, NASA has established the Principal Center for Regulatory Risk Analysis and Communication (RRAC PC) to proactively identify, analyze, and communicate environmental regulatory risks to the NASA community. The RRAC PC is chartered to evaluate the risks posed to NASA Programs and facilities by environmentally related drivers. The RRAC PC focuses on emerging environmental regulations, as well as risks related to operational changes that can trigger existing environmental requirements. Changing regulations have the potential to directly affect program activities. For example, regulatory changes can restrict certain activities or operations by mandating changes in how operations may be done or limiting where or how certain operations can take place. Regulatory changes also can directly affect the ability to use certain materials by mandating a production phase-out or restricting usage applications of certain materials. Such changes can result in NASA undertaking material replacement efforts. Even if a regulation does not directly affect NASA operations, U.S. and international regulations can pose program risks indirectly through requirements levied on manufacturers and vendors of components and materials. For example, manufacturers can change their formulations to comply with new regulatory requirements. Such changes can require time-consuming and costly requalification certification for use in human spaceflight programs. The RRAC PC has implemented several strategies for proactively managing regulatory change to minimize potential adverse impacts to NASA Programs and facilities. This presentation highlights the lessons learned through establishing the RRAC PC, the process by which the RRAC PC monitors and distributes information about emerging regulatory requirements, and the cross-Agency cooperation that is vital to supporting NASA's mission.

NASA's Agency-wide Strategy for Environmental Regulatory Risk Analysis and Communication

NASA Technical Reports Server (NTRS)

Duda, Kristen; Scroggins. Sharon

2008-01-01

NASA's mission is to pioneer the future in space exploration, scientific discovery, and aeronautics research. To help enable existing and future programs to pursue this mission, NASA has established the Principal Center for Regulatory Risk Analysis and Communication (RRAC PC) to proactively identify, analyze, and communicate environmental regulatory risks to the NASA community. The RRAC PC is chartered to evaluate the risks posed to NASA Programs and facilities by environmentally related drivers. The RRAC PC focuses on emerging environmental regulations, as well as risks related to operational changes that can trigger existing environmental requirements. Changing regulations have the potential to directly affect program activities. For example, regulatory changes can restrict certain activities or operations by mandating changes in how operations may be done or limiting where or how certain operations can take place. Regulatory changes also can directly affect the ability to use certain materials by mandating a production phase-out or restricting usage aPi'iications of certain materials. Such changes can result in NASA undertaking material replacement efforts. Even if a regulation does not directly affect NASA operations, U.S. and international regulations can pose program risks indirectly through requirements levied on manufacturers and vendors of components and materials. For example, manufacturers can change their formulations to comply with new regulatory requirements. Such changes can require time-consuming and costly requalification certification for use in human spaceflight programs. The RRAC PC has implemented several strategies for proactively managing regulatory change to minimize potential adverse impacts to NASA Programs and facilities. This presentation highlights the lessons learned through establishing the RRAC PC, the process by which the RRAC PC monitors and distributes information about emerging regulatory requirements, and the cross-Agency cooperation that is vital to supporting NASA's mission.

RCRA, superfund and EPCRA hotline training module. Introduction to: RCRA corrective action updated July 1996

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1996-07-01

The module discusses the regulatory and statutory requirements and authorities governing the Resource Conservation and Recovery Act (RCRA) corrective action process. There are minimal regulatory requirements at present, but the Agency has issued a proposed rule (55 FR 30798; July 27, 1990) that would establish a comprehensive regulatory framework for implementing the corrective action program. This proposed rule and other guidance developed pursuant to statutory authorities are used to structure corrective action requirements in facility permits and orders. This module describes the current statutory and regulatory structure and discusses the future of the proposed rule.

Redesigning the Regulatory Framework for Ambulatory Care Services in New York

PubMed Central

Chokshi, Dave A; Rugge, John; Shah, Nirav R

2014-01-01

Context While hospitals remain important centers of gravity in the health system, services are increasingly being delivered through ambulatory care. This shift to ambulatory care is giving rise to new delivery structures, such as retail clinics and urgent care centers, as well as reinventing existing ambulatory care capacity, as seen with the patient-centered medical home model and the movement toward team-based care. To protect the public's interests, oversight of ambulatory care services must keep pace with these rapid changes. With this purpose, in January 2013 the New York Public Health and Health Planning Council undertook a redesign of the regulatory framework for the state's ambulatory care services. This article describes the principles undergirding the framework as well as the regulatory recommendations themselves. Methods We explored and analyzed the regulation of ambulatory care services in New York in accordance with the available gray and peer-reviewed literature and legislative documents. The deliberations of the Public Health and Health Planning Council informed our review. Findings The vision of high-performing ambulatory care should be rooted in the Triple Aim (better health, higher-quality care, lower costs), with a particular emphasis on continuity of care for patients. There is a pressing need to better define the taxonomy of ambulatory care services. From the state government's perspective, this clarification requires better reporting from new health care entities (eg, retail clinics), connections with regional and state health information technology hubs, and coordination among state agencies. A uniform nomenclature also would improve consumers’ understanding of rights and responsibilities. Finally, the regulatory mechanisms employed—from mandatory reporting to licensure to regional planning to the certificate of need—should remain flexible and match the degree of consensus regarding the appropriate regulatory path. Conclusions Few other states have embarked on a wide-ranging assessment of their regulation of ambulatory care services. By moving toward adopting the regulatory approach described here, New York aims to balance sound oversight with pluralism and innovation in health care delivery. PMID:25492604

Reflections on the implementation of governance structures for early-stage clinical innovation.

PubMed

Cowie, Luke; Sandall, Jane; Ehrich, Kathryn

2013-12-01

This paper seeks to further explore the question of how best to monitor and govern innovative clinical procedures in their earliest phase of development. We examine the potential value of proposed governance frameworks, such as the IDEAL model, and examine the functioning of a novel procedures review committee. The paper draws upon 20 qualitative, semi-structured interviews. Nine interviews were conducted with members of a committee that was established as a means of governing innovative procedures within a large National Health Service Foundation Trust hospital in the UK. Eleven interviews were conducted with health providers involved with the development of a variety of novel clinical procedures. Prominent themes from the data include the potential willingness of clinicians to engage with regulatory frameworks for innovative procedures, existing ways in which clinicians and others attempt to ensure patient's safety and manage uncertainty in the context of novel procedures, views on the potential benefits and drawbacks of engaging with a review committee for novel procedures, and the pragmatic considerations and potential unintended consequences that are entailed in the implementation of regulatory requirements for the monitoring of innovative procedures. The views of committee members and clinical innovators help us to understand the practical issues of implementing governance structures for novel clinical procedures. The data illustrate those factors that must be taken into account if governance is to support innovation rather than act as an inhibiting factor in the development of new clinical procedures. © 2012 John Wiley & Sons Ltd.

47 CFR 1.1910 - Effect of insufficient fee payments, delinquent debts, or debarment.

Code of Federal Regulations, 2010 CFR

2010-10-01

... determine if the applicant has paid the appropriate application fee, appropriate regulatory fees, is... proper application or regulatory fee will be handled pursuant to the rules set forth in 47 CFR part 1... challenge through an administrative appeal or a contested judicial proceeding either to the existence or...

Forest Conservation, Value Conflict, and Interest Formation in a Honduran National Park

ERIC Educational Resources Information Center

Pfeffer, Max J.; Schelhas, John W.; Day, Leyla Ann

2001-01-01

We argue that attempts to superimpose park regulatory regimes on existing land uses in the tropics represent conflicts between alternative cultural models of natural resource management. The results of such conflicts are unique regulatory regimes emerging from distinctive processes that redefine the terms and limits of natural resource use. In…

76 FR 77034 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of Filing...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-09

... Accelerated Approval of Proposed Rule Change To Amend FINRA Rule 4512 (Customer Account Information) December... the Proposed Rule Change FINRA proposes to amend FINRA Rule 4512 (Customer Account Information) to... requires firms to maintain certain information relating to customer accounts, and it is based on existing...

Common Carrier Access to Cable Communications: Regulatory and Economic Issues.

ERIC Educational Resources Information Center

Kestenbaum, Lionel

The implications of cable television (CATV) common carrier access and economic and regulatory issues associated with it are examined in this paper. The first section provides a discussion of the feasibility and legal basis of common carrier access; the next section contrasts common carrier access with existing over-the-air television broadcasting…

CONSIDERATIONS FOR A REGULATORY FRAMEWORK FOR LARGE-SCALE GEOLOGIC SEQUESTRATION OF CARBON DIOXIDE: A NORTH AMERICAN PERSPECTIVE

EPA Science Inventory

Large scale geologic sequestration (GS) of carbon dioxide poses a novel set of challenges for regulators. This paper focuses on the unique needs of large scale GS projects in light of the existing regulatory regimes in the United States and Canada and identifies several differen...

76 FR 9213 - Small Business Jobs Act: 504 Loan Program Debt Refinancing

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-17

... negative impact on the availability of financing for small businesses. SBA finds that good cause exists to... 27, 2012 and would have less impact if delayed until notice and comment rulemaking could be completed... requiring Regulatory Impact Analysis as set forth below. A. Regulatory Objective of the Interim Final Rule...

75 FR 66183 - Self-Regulatory Organizations; BATS Exchange, Inc.; Notice of Filing and Immediate Effectiveness...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-27

... technological changes for one or more of the new routing strategies in place to support the proposed rule change... ``Order Execution,'' to add certain new routing strategies and to modify the description of certain existing Exchange routing strategies. II. Self-Regulatory Organization's Statement of the Purpose of, and...

76 FR 70190 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-10

... concern about dark pools and their potential impact on the fairness and transparency of the national market system.\\12\\ One of these commenters suggested that dark pools be prohibited entirely.\\13\\ FINRA... transparency that currently exists.\\14\\ FINRA stated that all trades executed on an ATS, including a dark pool...

A Transcriptome Map of Actinobacillus pleuropneumoniae at Single-Nucleotide Resolution Using Deep RNA-Seq

PubMed Central

Su, Zhipeng; Zhu, Jiawen; Xu, Zhuofei; Xiao, Ran; Zhou, Rui; Li, Lu; Chen, Huanchun

2016-01-01

Actinobacillus pleuropneumoniae is the pathogen of porcine contagious pleuropneumoniae, a highly contagious respiratory disease of swine. Although the genome of A. pleuropneumoniae was sequenced several years ago, limited information is available on the genome-wide transcriptional analysis to accurately annotate the gene structures and regulatory elements. High-throughput RNA sequencing (RNA-seq) has been applied to study the transcriptional landscape of bacteria, which can efficiently and accurately identify gene expression regions and unknown transcriptional units, especially small non-coding RNAs (sRNAs), UTRs and regulatory regions. The aim of this study is to comprehensively analyze the transcriptome of A. pleuropneumoniae by RNA-seq in order to improve the existing genome annotation and promote our understanding of A. pleuropneumoniae gene structures and RNA-based regulation. In this study, we utilized RNA-seq to construct a single nucleotide resolution transcriptome map of A. pleuropneumoniae. More than 3.8 million high-quality reads (average length ~90 bp) from a cDNA library were generated and aligned to the reference genome. We identified 32 open reading frames encoding novel proteins that were mis-annotated in the previous genome annotations. The start sites for 35 genes based on the current genome annotation were corrected. Furthermore, 51 sRNAs in the A. pleuropneumoniae genome were discovered, of which 40 sRNAs were never reported in previous studies. The transcriptome map also enabled visualization of 5'- and 3'-UTR regions, in which contained 11 sRNAs. In addition, 351 operons covering 1230 genes throughout the whole genome were identified. The RNA-Seq based transcriptome map validated annotated genes and corrected annotations of open reading frames in the genome, and led to the identification of many functional elements (e.g. regions encoding novel proteins, non-coding sRNAs and operon structures). The transcriptional units described in this study provide a foundation for future studies concerning the gene functions and the transcriptional regulatory architectures of this pathogen. PMID:27018591

Controlling Methane Emissions in the Natural Gas Sector. A Review of Federal and State Regulatory Frameworks Governing Production, Gathering, Processing, Transmission, and Distribution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paranhos, Elizabeth; Kozak, Tracy G.; Boyd, William

This report provides an overview of the regulatory frameworks governing natural gas supply chain infrastructure siting, construction, operation, and maintenance. Information was drawn from a number of sources, including published analyses, government reports, in addition to relevant statutes, court decisions and regulatory language, as needed. The scope includes all onshore facilities that contribute to methane emissions from the natural gas sector, focusing on three areas of state and federal regulations: (1) natural gas pipeline infrastructure siting and transportation service (including gathering, transmission, and distribution pipelines), (2) natural gas pipeline safety, and (3) air emissions associated with the natural gas supplymore » chain. In addition, the report identifies the incentives under current regulatory frameworks to invest in measures to reduce leakage, as well as the barriers facing investment in infrastructure improvement to reduce leakage. Policy recommendations regarding how federal or state authorities could regulate methane emissions are not provided; rather, existing frameworks are identified and some of the options for modifying existing regulations or adopting new regulations to reduce methane leakage are discussed.« less

Statistical Considerations Concerning Dissimilar Regulatory Requirements for Dissolution Similarity Assessment. The Example of Immediate-Release Dosage Forms.

PubMed

Jasińska-Stroschein, Magdalena; Kurczewska, Urszula; Orszulak-Michalak, Daria

2017-05-01

When performing in vitro dissolution testing, especially in the area of biowaivers, it is necessary to follow regulatory guidelines to minimize the risk of an unsafe or ineffective product being approved. The present study examines model-independent and model-dependent methods of comparing dissolution profiles based on various compared and contrasted international guidelines. Dissolution profiles for immediate release solid oral dosage forms were generated. The test material comprised tablets containing several substances, with at least 85% of the labeled amount dissolved within 15 min, 20-30 min, or 45 min. Dissolution profile similarity can vary with regard to the following criteria: time point selection (including the last time point), coefficient of variation, and statistical method selection. Variation between regulatory guidance and statistical methods can raise methodological questions and result potentially in a different outcome when reporting dissolution profile testing. The harmonization of existing guidelines would address existing problems concerning the interpretation of regulatory recommendations and research findings. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

75 FR 30453 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-01

... closely the governance structure of the FINRA Board. Section 4.3--Qualifications The proposed rule change would amend Article IV, section 4.3(a) to reflect FINRA's current governance structure by establishing... to Article IV, section 4.3 as follows: Re-structure the Board to remove the President of NASD Dispute...

Unzippers, Resolvers and Sensors: A Structural and Functional Biochemistry Tale of RNA Helicases

PubMed Central

Leitão, Ana Lúcia; Costa, Marina C.; Enguita, Francisco J.

2015-01-01

The centrality of RNA within the biological world is an irrefutable fact that currently attracts increasing attention from the scientific community. The panoply of functional RNAs requires the existence of specific biological caretakers, RNA helicases, devoted to maintain the proper folding of those molecules, resolving unstable structures. However, evolution has taken advantage of the specific position and characteristics of RNA helicases to develop new functions for these proteins, which are at the interface of the basic processes for transference of information from DNA to proteins. RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Structural biology studies during the last decade, founded in X-ray crystallography, have characterized in detail several RNA-helicases. This comprehensive review summarizes the structural knowledge accumulated in the last two decades within this family of proteins, with special emphasis on the structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes. PMID:25622248

Regulation of Toxin Production in Clostridium perfringens

PubMed Central

Ohtani, Kaori; Shimizu, Tohru

2016-01-01

The Gram-positive anaerobic bacterium Clostridium perfringens is widely distributed in nature, especially in soil and the gastrointestinal tracts of humans and animals. C. perfringens causes gas gangrene and food poisoning, and it produces extracellular enzymes and toxins that are thought to act synergistically and contribute to its pathogenesis. A complicated regulatory network of toxin genes has been reported that includes a two-component system for regulatory RNA and cell-cell communication. It is necessary to clarify the global regulatory system of these genes in order to understand and treat the virulence of C. perfringens. We summarize the existing knowledge about the regulatory mechanisms here. PMID:27399773

Boolean network inference from time series data incorporating prior biological knowledge.

PubMed

Haider, Saad; Pal, Ranadip

2012-01-01

Numerous approaches exist for modeling of genetic regulatory networks (GRNs) but the low sampling rates often employed in biological studies prevents the inference of detailed models from experimental data. In this paper, we analyze the issues involved in estimating a model of a GRN from single cell line time series data with limited time points. We present an inference approach for a Boolean Network (BN) model of a GRN from limited transcriptomic or proteomic time series data based on prior biological knowledge of connectivity, constraints on attractor structure and robust design. We applied our inference approach to 6 time point transcriptomic data on Human Mammary Epithelial Cell line (HMEC) after application of Epidermal Growth Factor (EGF) and generated a BN with a plausible biological structure satisfying the data. We further defined and applied a similarity measure to compare synthetic BNs and BNs generated through the proposed approach constructed from transitions of various paths of the synthetic BNs. We have also compared the performance of our algorithm with two existing BN inference algorithms. Through theoretical analysis and simulations, we showed the rarity of arriving at a BN from limited time series data with plausible biological structure using random connectivity and absence of structure in data. The framework when applied to experimental data and data generated from synthetic BNs were able to estimate BNs with high similarity scores. Comparison with existing BN inference algorithms showed the better performance of our proposed algorithm for limited time series data. The proposed framework can also be applied to optimize the connectivity of a GRN from experimental data when the prior biological knowledge on regulators is limited or not unique.

Assessing the health impact of transnational corporations: a case study on McDonald's Australia.

PubMed

Anaf, Julia; Baum, Frances E; Fisher, Matt; Harris, Elizabeth; Friel, Sharon

2017-02-06

The practices of transnational corporations affect population health through production methods, shaping social determinants of health, or influencing the regulatory structures governing their activities. There has been limited research on community exposures to TNC policies and practices. Our pilot research used McDonald's Australia to test methods for assessing the health impacts of one TNC within Australia. We adapted existing Health Impact Assessment methods to assess McDonald's activities. Data identifying potential impacts were sourced through document analysis, including McDonald's corporate literature; media analysis and semi-structured interviews. We commissioned a spatial and socioeconomic analysis of McDonald's restaurants in Australia through Geographic Information System technology. The data was mapped against a corporate health impact assessment framework which included McDonald's Australia's political and business practices; products and marketing; workforce, social, environmental and economic conditions; and consumers' health related behaviours. We identified both positive and detrimental aspects of McDonald's Australian operations across the scope of the CHIA framework. We found that McDonald's outlets were slightly more likely to be located in areas of lower socioeconomic status. McDonald's workplace conditions were found to be more favourable than those in many other countries which reflects compliance with Australian employment regulations. The breadth of findings revealed the need for governments to strengthen regulatory mechanisms that are conducive to health; the opportunity for McDonald's to augment their corporate social responsibility initiatives and bolster reputational endorsement; and civil society actors to inform their advocacy towards health and equity outcomes from TNC operations. Our study indicates that undertaking a corporate health impact assessment is possible, with the different methods revealing sufficient information to realise that strong regulatory frameworks are need to help to avoid or to mediate negative health impacts.

76 FR 2725 - Draft Regulatory Guide: Issuance, Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-14

.... The draft regulatory guide, entitled, ``Inspection of Water-Control Structures Associated with Nuclear... and surveillance program for dams, slopes, canals, and other water-control structures associated with emergency cooling water systems or flood protection of nuclear power plants. II. Further Information The NRC...

Inference of Expanded Lrp-Like Feast/Famine Transcription Factor Targets in a Non-Model Organism Using Protein Structure-Based Prediction

PubMed Central

Ashworth, Justin; Plaisier, Christopher L.; Lo, Fang Yin; Reiss, David J.; Baliga, Nitin S.

2014-01-01

Widespread microbial genome sequencing presents an opportunity to understand the gene regulatory networks of non-model organisms. This requires knowledge of the binding sites for transcription factors whose DNA-binding properties are unknown or difficult to infer. We adapted a protein structure-based method to predict the specificities and putative regulons of homologous transcription factors across diverse species. As a proof-of-concept we predicted the specificities and transcriptional target genes of divergent archaeal feast/famine regulatory proteins, several of which are encoded in the genome of Halobacterium salinarum. This was validated by comparison to experimentally determined specificities for transcription factors in distantly related extremophiles, chromatin immunoprecipitation experiments, and cis-regulatory sequence conservation across eighteen related species of halobacteria. Through this analysis we were able to infer that Halobacterium salinarum employs a divergent local trans-regulatory strategy to regulate genes (carA and carB) involved in arginine and pyrimidine metabolism, whereas Escherichia coli employs an operon. The prediction of gene regulatory binding sites using structure-based methods is useful for the inference of gene regulatory relationships in new species that are otherwise difficult to infer. PMID:25255272

Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction.

PubMed

Ashworth, Justin; Plaisier, Christopher L; Lo, Fang Yin; Reiss, David J; Baliga, Nitin S

2014-01-01

Widespread microbial genome sequencing presents an opportunity to understand the gene regulatory networks of non-model organisms. This requires knowledge of the binding sites for transcription factors whose DNA-binding properties are unknown or difficult to infer. We adapted a protein structure-based method to predict the specificities and putative regulons of homologous transcription factors across diverse species. As a proof-of-concept we predicted the specificities and transcriptional target genes of divergent archaeal feast/famine regulatory proteins, several of which are encoded in the genome of Halobacterium salinarum. This was validated by comparison to experimentally determined specificities for transcription factors in distantly related extremophiles, chromatin immunoprecipitation experiments, and cis-regulatory sequence conservation across eighteen related species of halobacteria. Through this analysis we were able to infer that Halobacterium salinarum employs a divergent local trans-regulatory strategy to regulate genes (carA and carB) involved in arginine and pyrimidine metabolism, whereas Escherichia coli employs an operon. The prediction of gene regulatory binding sites using structure-based methods is useful for the inference of gene regulatory relationships in new species that are otherwise difficult to infer.

THE ROLES OF METAL IONS IN REGULATION BY RIBOSWITCHES

PubMed Central

2012-01-01

Metal ions are required by all organisms in order to execute an array of essential molecular functions. They play a critical role in many catalytic mechanisms and structural properties. Proper homeostasis of ions is critical; levels that are aberrantly low or high are deleterious to cellular physiology. To maintain stable intracellular pools, metal ion-sensing regulatory (metalloregulatory) proteins couple metal ion concentration fluctuations with expression of genes encoding for cation transport or sequestration. However, these transcriptional-based regulatory strategies are not the only mechanisms by which organisms coordinate metal ions with gene expression. Intriguingly, a few classes of signal-responsive RNA elements have also been discovered to function as metalloregulatory agents. This suggests that RNA-based regulatory strategies can be precisely tuned to intracellular metal ion pools, functionally akin to metalloregulatory proteins. In addition to these metal-sensing regulatory RNAs, there is a yet broader role for metal ions in directly assisting the structural integrity of other signal-responsive regulatory RNA elements. In this chapter, we discuss how the intimate physicochemical relationship between metal ions and nucleic acids is important for the structure and function of metal ion- and metabolite-sensing regulatory RNAs. PMID:22010271

Regulatory focus as a mediator of the influence of initiating structure and servant leadership on employee behavior.

PubMed

Neubert, Mitchell J; Kacmar, K Michele; Carlson, Dawn S; Chonko, Lawrence B; Roberts, James A

2008-11-01

In this research, the authors test a model in which the regulatory focus of employees at work mediates the influence of leadership on employee behavior. In a nationally representative sample of 250 workers who responded over 2 time periods, prevention focus mediated the relationship of initiating structure to in-role performance and deviant behavior, whereas promotion focus mediated the relationship of servant leadership to helping and creative behavior. The results indicate that even though initiating structure and servant leadership share some variance in explaining other variables, each leadership style incrementally predicts disparate outcomes after controlling for the other style and dispositional tendencies. A new regulatory focus scale, the Work Regulatory Focus (WRF) Scale, also was developed and initially validated for this study. Implications for the results and the WRF Scale are discussed.

30 CFR 735.14 - Coverage of grants.

Code of Federal Regulations, 2010 CFR

2010-07-01

... other personnel; (4) New or revised organizational structures; (5) Information and communications... approved State regulatory program; (2) Providing supporting and administrative services required by the State regulatory program; (3) Providing equipment required for the regulatory program and its support...

Homo sapiens-Specific Binding Site Variants within Brain Exclusive Enhancers Are Subject to Accelerated Divergence across Human Population.

PubMed

Zehra, Rabail; Abbasi, Amir Ali

2018-03-01

Empirical assessments of human accelerated noncoding DNA frgaments have delineated presence of many cis-regulatory elements. Enhancers make up an important category of such accelerated cis-regulatory elements that efficiently control the spatiotemporal expression of many developmental genes. Establishing plausible reasons for accelerated enhancer sequence divergence in Homo sapiens has been termed significant in various previously published studies. This acceleration by including closely related primates and archaic human data has the potential to open up evolutionary avenues for deducing present-day brain structure. This study relied on empirically confirmed brain exclusive enhancers to avoid any misjudgments about their regulatory status and categorized among them a subset of enhancers with an exceptionally accelerated rate of lineage specific divergence in humans. In this assorted set, 13 distinct transcription factor binding sites were located that possessed unique existence in humans. Three of 13 such sites belonging to transcription factors SOX2, RUNX1/3, and FOS/JUND possessed single nucleotide variants that made them unique to H. sapiens upon comparisons with Neandertal and Denisovan orthologous sequences. These variants modifying the binding sites in modern human lineage were further substantiated as single nucleotide polymorphisms via exploiting 1000 Genomes Project Phase3 data. Long range haplotype based tests laid out evidence of positive selection to be governing in African population on two of the modern human motif modifying alleles with strongest results for SOX2 binding site. In sum, our study acknowledges acceleration in noncoding regulatory landscape of the genome and highlights functional parts within it to have undergone accelerated divergence in present-day human population.

77 FR 69522 - Self-Regulatory Organizations; National Stock Exchange, Inc.; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-19

... participants to: (1) Charge a flat fee per quotation update; (2) charge a separate flat fee per quotation... to: (1) Charge a flat fee per quotation update; (2) charge a separate flat fee per quotation update... fund the NSX's regulatory oversight of Order Delivery participants. Quotation Update Fee for Existing...

78 FR 1624 - Fall 2012 Regulatory Agenda

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-08

...The Environmental Protection Agency (EPA) publishes the semiannual regulatory agenda online (the e-Agenda) at http:// www.reginfo.gov and at www.regulations.gov to update the public about: Regulations and major policies currently under development; reviews of existing regulations and major policies; and rules and major policy makings completed or canceled since the publication of the last agenda.

77 FR 22374 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of Filing of...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-13

... I. Gross, Director, Edward Pekarek, Assistant Director, and Genavieve Shingle, Student Intern... finds good cause, pursuant to Section 19(b)(2) of the Act \\11\\ for approving the proposed rule change... that good cause exists to approve the proposal, as modified by Amendment No. 1, on an accelerated basis...

77 FR 24748 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Granting...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-25

... establish a real-time market data set for disseminated Asset-Backed Security transaction information (``ABS Data Set'') and to amend Rule 7730(d) to establish a historic data set for such information (``Historic ABS Data Set'').\\16\\ The provisions of Rule 7730 that currently apply to the two existing real-time...

77 FR 75453 - Self-Regulatory Organizations; The Depository Trust Company; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-20

... SECURITIES AND EXCHANGE COMMISSION [Release No. 68443; File No. SR-DTC-2012-09] Self-Regulatory Organizations; The Depository Trust Company; Notice of Filing and Immediate Effectiveness of Proposed Rule Change To Make Ministerial Changes to the Existing Reorganization Service Guide December 14, 2012. Pursuant to Section 19(b)(1) of the Securitie...

The Nature of Self-Regulatory Fatigue and "Ego Depletion": Lessons From Physical Fatigue.

PubMed

Evans, Daniel R; Boggero, Ian A; Segerstrom, Suzanne C

2015-07-30

Self-regulation requires overriding a dominant response and leads to temporary self-regulatory fatigue. Existing theories of the nature and causes of self-regulatory fatigue highlight physiological substrates such as glucose, or psychological processes such as motivation, but these explanations are incomplete on their own. Historically, theories of physical fatigue demonstrate a similar pattern of useful but incomplete explanations, as recent views of physical fatigue emphasize the roles of both physiological and psychological factors. In addition to accounting for multiple inputs, these newer views also explain how fatigue can occur even in the presence of sufficient resources. Examining these newer theories of physical fatigue can serve as a foundation on which to build a more comprehensive understanding of self-regulatory fatigue that integrates possible neurobiological underpinnings of physical and self-regulatory fatigue, and suggests the possible function of self-regulatory fatigue. © 2015 by the Society for Personality and Social Psychology, Inc.

The nature of self-regulatory fatigue and “ego depletion”: Lessons from physical fatigue

PubMed Central

Evans, Daniel R.; Boggero, Ian A.; Segerstrom, Suzanne C.

2016-01-01

Self-regulation requires overriding a dominant response, and leads to temporary self-regulatory fatigue. Existing theories of the nature and causes of self-regulatory fatigue highlight physiological substrates such as glucose or psychological processes such as motivation, but these explanations are incomplete on their own. Historically, theories of physical fatigue demonstrate a similar pattern of useful but incomplete explanations, as recent views of physical fatigue emphasize the roles of both physiological and psychological factors. In addition to accounting for multiple inputs, these newer views also explain how fatigue can occur even in the presence of sufficient resources. Examining these newer theories of physical fatigue can serve as a foundation on which to build a more comprehensive understanding of self-regulatory fatigue that integrates possible neurobiological underpinnings of physical and self-regulatory fatigue, and suggests the possible function of self-regulatory fatigue. PMID:26228914

Flight training efforts would benefit from more flexible aviation regulatory structures.

PubMed

Bent, J

1996-10-01

Training and regulatory issues related to modern flight deck systems are reviewed. Philosophical differences in regulatory bodies in the United States and Europe are highlighted. Methods of changing regulations in Europe and the United States are discussed.

Clinical social work practice and technology: personal, practical, regulatory, and ethical considerations for the twenty-first century.

PubMed

Dombo, Eileen A; Kays, Lisa; Weller, Katelyn

2014-10-01

The world that social work exists in is no longer defined by traditional physical settings and boundaries, such as schools, agencies, or even offices. With the advent of the Internet and digital communications, social work now exists in a far more complex reality, with clients and social workers engaging across multiple platforms, and sometimes even unintentionally and without one another's awareness. The implications of this can be ethical, practical, regulatory, and personal. This article explores these areas of concern and suggests strategies professionals can use to navigate these complex issues related to technology and clinical practice.

Divergent regulation of the sarcomere and the cytoskeleton.

PubMed

Schevzov, Galina; Fath, Thomas; Vrhovski, Bernadette; Vlahovich, Nicole; Rajan, Sudarsan; Hook, Jeff; Joya, Josephine E; Lemckert, Frances; Puttur, Franz; Lin, Jim J-C; Hardeman, Edna C; Wieczorek, David F; O'Neill, Geraldine M; Gunning, Peter W

2008-01-04

The existence of a feedback mechanism regulating the precise amounts of muscle structural proteins, such as actin and the actin-associated protein tropomyosin (Tm), in the sarcomeres of striated muscles is well established. However, the regulation of nonmuscle or cytoskeletal actin and Tms in nonmuscle cell structures has not been elucidated. Unlike the thin filaments of striated muscles, the actin cytoskeleton in nonmuscle cells is intrinsically dynamic. Given the differing requirements for the structural integrity of the actin thin filaments of the sarcomere compared with the requirement for dynamicity of the actin cytoskeleton in nonmuscle cells, we postulated that different regulatory mechanisms govern the expression of sarcomeric versus cytoskeletal Tms, as key regulators of the properties of the actin cytoskeleton. Comprehensive analyses of tissues from transgenic and knock-out mouse lines that overexpress the cytoskeletal Tms, Tm3 and Tm5NM1, and a comparison with sarcomeric Tms provide evidence for this. Moreover, we show that overexpression of a cytoskeletal Tm drives the amount of filamentous actin.

Aquatic toxicity of acrylates and methacrylates: quantitative structure-activity relationships based on Kow and LC50

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reinert, K.H.

1987-12-01

Recent EPA scrutiny of acrylate and methacrylate monomers has resulted in restrictive consent orders and Significant New Use Rules under the Toxic Substances Control Act, based on structure-activity relationships using mouse skin painting studies. The concern is centered on human health issues regarding worker and consumer exposure. Environmental issues, such as aquatic toxicity, are still of concern. Understanding the relationships and environmental risks to aquatic organisms may improve the understanding of the potential risks to human health. This study evaluates the quantitative structure-activity relationships from measured log Kow's and log LC50's for Pimephales promelas (fathead minnow) and Carassius auratus (goldfish).more » Scientific support of the current regulations is also addressed. Two monomer classes were designated: acrylates and methacrylates. Spearman rank correlation and linear regression were run. Based on this study, an ecotoxicological difference exists between acrylates and methacrylates. Regulatory activities and scientific study should reflect this difference.« less

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression.

PubMed

Mars, Ruben A T; Nicolas, Pierre; Denham, Emma L; van Dijl, Jan Maarten

2016-12-01

Bacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include trans-acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5' untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as Escherichia coli and Salmonella. Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium Bacillus subtilis. A recent study identified 1,583 putative regulatory RNAs in B. subtilis, whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in B. subtilis, and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation in B. subtilis mostly involves elements at the 5' ends of mRNA molecules. These can include 5' secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in B. subtilis. Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in B. subtilis. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

PubMed Central

Mars, Ruben A. T.; Nicolas, Pierre; Denham, Emma L.

2016-01-01

SUMMARY Bacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include trans-acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5′ untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as Escherichia coli and Salmonella. Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium Bacillus subtilis. A recent study identified 1,583 putative regulatory RNAs in B. subtilis, whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in B. subtilis, and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation in B. subtilis mostly involves elements at the 5′ ends of mRNA molecules. These can include 5′ secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in B. subtilis. Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in B. subtilis. PMID:27784798

Chemical action: what is it, and why does it really matter?

NASA Astrophysics Data System (ADS)

Koolage, W. John; Hall, Ralph

2011-04-01

Nanotechnology, as with many technologies before it, places a strain on existing legislation and poses a challenge to all administrative agencies tasked with regulating technology-based products. It is easy to see how statutory schemes become outdated, as our ability to understand and affect the world progresses. In this article, we address the regulatory problems that nanotechnology posses for the Food and Drug Administration's (FDA) classification structure for "drugs" and "devices." The last major modification to these terms was in 1976, with the enactment of the Medical Device Amendments. There are serious practical differences for a classification as a drug or device in terms of time to market and research. Drugs are classified, primarily, as acting by "chemical action." We lay out some legal, philosophic, and scientific tools that serve to provide a useful, as well as legally and scientifically faithful, distinction between drugs and devices for the purpose of regulatory classification. These issues we raise are worth the consideration of anyone who is interested in the regulation of nano-products or other novel technologies.

Biosimilars: biologics that meet patients' needs and healthcare economics.

PubMed

McCamish, Mark; Yoon, William; McKay, James

2016-09-01

Biologics have revolutionized medical care, yet uniform access to these effective medicines remains difficult due to the increasing costs of healthcare. As patent exclusivity on the early biologics wanes, regulatory and legal systems are adapting to bring competition to the field in the form of biosimilars. Biosimilars are biologics that offer the same clinical benefit in one or more of the same indications as the reference biologic drug and bring competition to the biologics space. Legislation creating a pathway resulting in the first US approvals of biosimilars has been in place since 2010, but the regulatory methodology and science of evaluating the sameness of two biologics has been in use for decades. The demonstration of biosimilarity is based on the "totality of the evidence" concept, in which all structural, functional, nonclinical, and clinical data for a biosimilar product are evaluated to show high similarity to the reference product. Clinical trials for biosimilars, therefore, are designed to confirm similarity, or discover clinically relevant differences between the reference product and the biosimilar, should differences exist. It is hoped that competition from biosimilars will drive biologic innovation and increase patient access to biologics.

Comparing Distributions of Environmental Outcomes for Regulatory Environmental Justice Analysis

PubMed Central

Maguire, Kelly; Sheriff, Glenn

2011-01-01

Economists have long been interested in measuring distributional impacts of policy interventions. As environmental justice (EJ) emerged as an ethical issue in the 1970s, the academic literature has provided statistical analyses of the incidence and causes of various environmental outcomes as they relate to race, income, and other demographic variables. In the context of regulatory impacts, however, there is a lack of consensus regarding what information is relevant for EJ analysis, and how best to present it. This paper helps frame the discussion by suggesting a set of questions fundamental to regulatory EJ analysis, reviewing past approaches to quantifying distributional equity, and discussing the potential for adapting existing tools to the regulatory context. PMID:21655146

Incentive regulation and performance measurement of the Portuguese solid waste management services.

PubMed

Marques, Rui Cunha; Simões, Pedro

2009-03-01

Measuring the performance of solid waste management services usually uncovers very high potential for gains in efficiency and productivity. This circumstance occurs, naturally, due to the fact that these services are outside the market and because they are subjected to various market failures in their organizational framework. The aim of this study was to examine the Portuguese regulatory model and to measure the performance of the Portuguese solid waste management services in order to identify the major reforms carried out and their outcomes. As a first objective, the sunshine regulatory approach adopted in Portugal, in which performance comparison and its public discussion are the main tools, was investigated. The second objective was to compute the efficiency of the Portuguese solid waste management services by means of the non-parametric technique of data envelopment analysis (DEA), evaluating the Portuguese regulatory model and the existing market structure, as well as the influence of the operational environment on efficiency. The benchmarking frontier technique of DEA is particularly useful in the efficiency measurement of public utilities, in which knowledge of the production function is relatively scarce. Several DEA models were used and they all depicted significant inefficiency. The study also proved that efficiency did not depend on ownership (public or private) and that there was no difference in efficiency between the players, irrespective of whether they were regulated or not.

Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations.

PubMed

Wu, Shuang; Liu, Zhi-Ping; Qiu, Xing; Wu, Hulin

2014-01-01

The immune response to viral infection is regulated by an intricate network of many genes and their products. The reverse engineering of gene regulatory networks (GRNs) using mathematical models from time course gene expression data collected after influenza infection is key to our understanding of the mechanisms involved in controlling influenza infection within a host. A five-step pipeline: detection of temporally differentially expressed genes, clustering genes into co-expressed modules, identification of network structure, parameter estimate refinement, and functional enrichment analysis, is developed for reconstructing high-dimensional dynamic GRNs from genome-wide time course gene expression data. Applying the pipeline to the time course gene expression data from influenza-infected mouse lungs, we have identified 20 distinct temporal expression patterns in the differentially expressed genes and constructed a module-based dynamic network using a linear ODE model. Both intra-module and inter-module annotations and regulatory relationships of our inferred network show some interesting findings and are highly consistent with existing knowledge about the immune response in mice after influenza infection. The proposed method is a computationally efficient, data-driven pipeline bridging experimental data, mathematical modeling, and statistical analysis. The application to the influenza infection data elucidates the potentials of our pipeline in providing valuable insights into systematic modeling of complicated biological processes.

A reverse engineering approach to optimize experiments for the construction of biological regulatory networks.

PubMed

Zhang, Xiaomeng; Shao, Bin; Wu, Yangle; Qi, Ouyang

2013-01-01

One of the major objectives in systems biology is to understand the relation between the topological structures and the dynamics of biological regulatory networks. In this context, various mathematical tools have been developed to deduct structures of regulatory networks from microarray expression data. In general, from a single data set, one cannot deduct the whole network structure; additional expression data are usually needed. Thus how to design a microarray expression experiment in order to get the most information is a practical problem in systems biology. Here we propose three methods, namely, maximum distance method, trajectory entropy method, and sampling method, to derive the optimal initial conditions for experiments. The performance of these methods is tested and evaluated in three well-known regulatory networks (budding yeast cell cycle, fission yeast cell cycle, and E. coli. SOS network). Based on the evaluation, we propose an efficient strategy for the design of microarray expression experiments.

76 FR 74831 - Aging Management of Stainless Steel Structures and Components in Treated Borated Water

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-01

... exposed to treated borated water. In response to a request from the Nuclear Energy Institute (NEI), the... NUCLEAR REGULATORY COMMISSION [NRC-2011-0256] Aging Management of Stainless Steel Structures and Components in Treated Borated Water AGENCY: Nuclear Regulatory Commission. ACTION: Draft interim staff...

A Review of International Telecommunications Industry Issues, Structure, and Regulatory Problems.

ERIC Educational Resources Information Center

Cole, Jack E.; And Others

Industry structure studies prior to 1968 are briefly reviewed, and an overview of industrial and technological developments up to the present is provided through synopses of more recent studies. Areas covered include overseas telephone and record carriers; the creation of the Communications Satellite Corporation; the current regulatory and…

76 FR 21932 - Self-Regulatory Organizations; New York Stock Exchange LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-19

... transition to the new fee structure. B. Self-Regulatory Organization's Statement on Burden on Competition The...-Regulatory Organizations; New York Stock Exchange LLC; Notice of Filing and Immediate Effectiveness of.... \\1\\ 15 U.S.C. 78s(b)(1). \\2\\ 17 CFR 240.19b-4. I. Self-Regulatory Organization's Statement of the...

Development and Implementation of Clinical Trial Protocol Templates at the National Institute of Allergy and Infectious Diseases

PubMed Central

Bridge, Heather; Smolskis, Mary; Bianchine, Peter; Dixon, Dennis O.; Kelly, Grace; Herpin, Betsey; Tavel, Jorge

2009-01-01

Background: A clinical research protocol document must reflect both sound scientific rationale as well as local, national and, when applicable, international regulatory and human subject protections requirements. These requirements originate from a variety of sources, undergo frequent revision and are subject to interpretation. Tools to assist clinical investigators in the production of clinical protocols could facilitate navigating these requirements and ultimately increase the efficiency of clinical research. Purpose: The National Institute of Allergy and Infectious Diseases (NIAID) developed templates for investigators to serve as the foundation for protocol development. These protocol templates are designed as tools to support investigators in developing clinical protocols. Methods: NIAID established a series of working groups to determine how to improve its capacity to conduct clinical research more efficiently and effectively. The Protocol Template Working Group was convened to determine what protocol templates currently existed within NIAID and whether standard NIAID protocol templates should be produced. After review and assessment of existing protocol documents and requirements, the group reached consensus about required and optional content, determined the format and identified methods for distribution as well as education of investigators in the use of these templates. Results: The templates were approved by the NIAID Executive Committee in 2006 and posted as part of the NIAID Clinical Research Toolkit[1]website for broad access. These documents require scheduled revisions to stay current with regulatory and policy changes. Limitations: The structure of any clinical protocol template, whether comprehensive or specific to a particular study phase, setting or design, affects how it is used by investigators. Each structure presents its own set of advantages and disadvantages. While useful, protocol templates are not stand-alone tools for creating an optimal protocol document but must be complemented by institutional resources and support. Education and guidance of investigators in the appropriate use of templates is necessary to ensure a complete yet concise protocol document. Due to changing regulatory requirements, clinical protocol templates cannot become static but require frequent revisions. Conclusions: Standard protocol templates that meet applicable regulations can be important tools to assist investigators in the effective conduct of clinical research, but they require dedicated resources and ongoing input from key stakeholders. PMID:19625326

Generic oncology drugs: are they all safe?

PubMed

Yang, Y Tony; Nagai, Sumimasa; Chen, Brian K; Qureshi, Zaina P; Lebby, Akida A; Kessler, Samuel; Georgantopoulos, Peter; Raisch, Dennis W; Sartor, Oliver; Hermanson, Terhi; Kane, Robert C; Hrushesky, William J; Riente, Joshua J; Norris, LeAnn B; Bobolts, Laura R; Armitage, James O; Bennett, Charles L

2016-11-01

Although the availability of generic oncology drugs allows access to contemporary care and reduces costs, there is international variability in the safety of this class of drugs. In this Series paper, we review clinical, policy, safety, and regulatory considerations for generic oncology drugs focusing on the USA, Canada, the European Union (EU), Japan, China, and India. Safety information about generic formulations is reviewed from one agent in each class, for heavy metal drugs (cisplatin), targeted agents (imatinib), and cytotoxic agents (docetaxel). We also review regulatory reports from Japan and the USA, countries with the largest pharmaceutical expenditures. Empirical studies did not identify safety concerns in the USA, Canada, the EU, and Japan, where regulations and enforcement are strong. Although manufacturing problems for generic pharmaceuticals exist in India, where 40% of all generic pharmaceuticals used in the USA are manufactured, increased inspections and communication by the US Food and Drug Administration are occurring, facilitating oversight and enforcement. No safety outbreaks among generic oncology drugs were reported in developed countries. For developing countries, oversight is less intensive, and concerns around drug safety still exist. Regulatory agencies should collaboratively develop procedures to monitor the production, shipment, storage, and post-marketing safety of generic oncology drugs. Regulatory agencies for each country should also aim towards identical definitions of bioequivalence, the cornerstone of regulatory approval. Copyright © 2016 Elsevier Ltd. All rights reserved.

10 CFR 4.550 - Program accessibility: Existing facilities.

Code of Federal Regulations, 2010 CFR

2010-01-01

... ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE FROM THE COMMISSION Enforcement of Nondiscrimination on the Basis of Handicap in Programs or Activities Conducted by the U.S. Nuclear Regulatory Commission § 4.550 Program accessibility: Existing facilities. (a) General. The agency shall operate each program or activity...

The Optical Nation.

ERIC Educational Resources Information Center

Rubin, Philip A.

If the Corporation for Public Broadcasting (CPB) is eventually to serve all citizens with public radio and television, technological and regulatory innovation will be required. Service to rural America and service to specific groups within urban areas cannot be accomplished within the limits of existing technology and existing spectrum allocation…

Investigating Eight- to Nine-Year-Olds' Self-Regulatory Self-Talk in the Context of Their Classroom Tasks

ERIC Educational Resources Information Center

Lee, Scott; McDonough, Andrea; Bird, Jo

2014-01-01

Self-talk has been recognised as an important tool used by children to regulate their thinking and behaviour. Existing studies typically characterise children's self-talk according to broad categories that do not allow for investigation of self-regulatory aspects of children's internalised self-talk. The findings reported in this paper are based…

AP1 Keeps Chromatin Poised for Action | Center for Cancer Research

Cancer.gov

The human genome harbors gene-encoding DNA, the blueprint for building proteins that regulate cellular function. Embedded across the genome, in non-coding regions, are DNA elements to which regulatory factors bind. The interaction of regulatory factors with DNA at these sites modifies gene expression to modulate cell activity. In cells, DNA exists in a complex with proteins

Investment, regulation, and uncertainty: managing new plant breeding techniques.

PubMed

Smyth, Stuart J; McDonald, Jillian; Falck-Zepeda, Jose

2014-01-01

As with any technological innovation, time refines the technology, improving upon the original version of the innovative product. The initial GM crops had single traits for either herbicide tolerance or insect resistance. Current varieties have both of these traits stacked together and in many cases other abiotic and biotic traits have also been stacked. This innovation requires investment. While this is relatively straight forward, certain conditions need to exist such that investments can be facilitated. The principle requirement for investment is that regulatory frameworks render consistent and timely decisions. If the certainty of regulatory outcomes weakens, the potential for changes in investment patterns increases.   This article provides a summary background to the leading plant breeding technologies that are either currently being used to develop new crop varieties or are in the pipeline to be applied to plant breeding within the next few years. Challenges for existing regulatory systems are highlighted. Utilizing an option value approach from investment literature, an assessment of uncertainty regarding the regulatory approval for these varying techniques is undertaken. This research highlights which technology development options have the greatest degree of uncertainty and hence, which ones might be expected to see an investment decline.

A synthetic biology approach to the development of transcriptional regulatory models and custom enhancer design☆,☆☆

PubMed Central

Martinez, Carlos A.; Barr, Kenneth; Kim, Ah-Ram; Reinitz, John

2013-01-01

Synthetic biology offers novel opportunities for elucidating transcriptional regulatory mechanisms and enhancer logic. Complex cis-regulatory sequences—like the ones driving expression of the Drosophila even-skipped gene—have proven difficult to design from existing knowledge, presumably due to the large number of protein-protein interactions needed to drive the correct expression patterns of genes in multicellular organisms. This work discusses two novel computational methods for the custom design of enhancers that employ a sophisticated, empirically validated transcriptional model, optimization algorithms, and synthetic biology. These synthetic elements have both utilitarian and academic value, including improving existing regulatory models as well as evolutionary questions. The first method involves the use of simulated annealing to explore the sequence space for synthetic enhancers whose expression output fit a given search criterion. The second method uses a novel optimization algorithm to find functionally accessible pathways between two enhancer sequences. These paths describe a set of mutations wherein the predicted expression pattern does not significantly vary at any point along the path. Both methods rely on a predictive mathematical framework that maps the enhancer sequence space to functional output. PMID:23732772

Investment, regulation, and uncertainty

PubMed Central

Smyth, Stuart J; McDonald, Jillian; Falck-Zepeda, Jose

2014-01-01

As with any technological innovation, time refines the technology, improving upon the original version of the innovative product. The initial GM crops had single traits for either herbicide tolerance or insect resistance. Current varieties have both of these traits stacked together and in many cases other abiotic and biotic traits have also been stacked. This innovation requires investment. While this is relatively straight forward, certain conditions need to exist such that investments can be facilitated. The principle requirement for investment is that regulatory frameworks render consistent and timely decisions. If the certainty of regulatory outcomes weakens, the potential for changes in investment patterns increases.   This article provides a summary background to the leading plant breeding technologies that are either currently being used to develop new crop varieties or are in the pipeline to be applied to plant breeding within the next few years. Challenges for existing regulatory systems are highlighted. Utilizing an option value approach from investment literature, an assessment of uncertainty regarding the regulatory approval for these varying techniques is undertaken. This research highlights which technology development options have the greatest degree of uncertainty and hence, which ones might be expected to see an investment decline. PMID:24499745

Protecting workers and the environment: An environmental NGO's perspective on nanotechnology

NASA Astrophysics Data System (ADS)

Balbus, John M.; Florini, Karen; Denison, Richard A.; Walsh, Scott A.

2007-01-01

Nanotechnology, the design and manipulation of materials at the atomic scale, may well revolutionize many of the ways our society manufactures products, produces energy, and treats diseases. New materials based on nanotechnology are already reaching the market in a wide variety of consumer products. Some of the observed properties of nanomaterials call into question the adequacy of current methods for determining hazard and exposure and for controlling resulting risks. Given the limitations of existing regulatory tools and policies, we believe two distinct kinds of initiatives are needed: first, a major increase in the federal investment in nanomaterial risk research; second, rapid development and implementation of voluntary standards of care pending development of adequate regulatory safeguards in the longer term. Several voluntary programs are currently at various stages of evolution, though the eventual outputs of each of these are still far from clear. Ultimately, effective regulatory safeguards are necessary to provide a level playing field for industry while adequately protecting human health and the environment. This paper reviews the existing toxicological literature on nanomaterials, outlines and analyzes the current regulatory framework, and provides our recommendations, as an environmental non-profit organization, for safe nanotechnology development.

Pluripotency and lineages in the mammalian blastocyst: an evolutionary view.

PubMed

Cañon, Susana; Fernandez-Tresguerres, Beatriz; Manzanares, Miguel

2011-06-01

Early mammalian development is characterized by a highly specific stage, the blastocyst, by which embryonic and extraembryonic lineages have been determined, but pattern formation has not yet begun. The blastocyst is also of interest because cell precursors of the embryo proper retain for a certain time the capability to generate all the cell types of the adult animal. This embryonic pluripotency is established and maintained by a regulatory network under the control of a small set of transcription factors, comprising Oct4, Sox2 and Nanog. This network is largely conserved in eutherian mammals, but there is scarce information about how it arose in vertebrates. We have analysed the conservation of gene regulatory networks controlling blastocyst lineages and pluripotency in the mouse by comparison with the chick. We found that few of elements of the network are novel to mammals; rather, most of them were present before the separation of the mammalian lineage from other amniotes, but acquired novel expression domains during early mammalian development. Our results strongly support the hypothesis that mammalian blastocyst regulatory networks evolved through rewiring of pre-existing components, involving the co-option and duplication of existing genes and the establishment of new regulatory interactions among them.

FPGA implementation of current-sharing strategy for parallel-connected SEPICs

NASA Astrophysics Data System (ADS)

Ezhilarasi, A.; Ramaswamy, M.

2016-01-01

The attempt echoes to evolve an equal current-sharing algorithm over a number of single-ended primary inductance converters connected in parallel. The methodology involves the development of state-space model to predict the condition for the existence of a stable equilibrium portrait. It acquires the role of a variable structure controller to guide the trajectory, with a view to circumvent the circuit non-linearities and arrive at a stable performance through a preferred operating range. The design elicits an acceptable servo and regulatory characteristics, the desired time response and ensures regulation of the load voltage. The simulation results validated through a field programmable gate array-based prototype serves to illustrate its suitability for present-day applications.

Network Reconstruction From High-Dimensional Ordinary Differential Equations.

PubMed

Chen, Shizhe; Shojaie, Ali; Witten, Daniela M

2017-01-01

We consider the task of learning a dynamical system from high-dimensional time-course data. For instance, we might wish to estimate a gene regulatory network from gene expression data measured at discrete time points. We model the dynamical system nonparametrically as a system of additive ordinary differential equations. Most existing methods for parameter estimation in ordinary differential equations estimate the derivatives from noisy observations. This is known to be challenging and inefficient. We propose a novel approach that does not involve derivative estimation. We show that the proposed method can consistently recover the true network structure even in high dimensions, and we demonstrate empirical improvement over competing approaches. Supplementary materials for this article are available online.

75 FR 27548 - Quality GearBox, LLC; Notice of Competing Preliminary Permit Application Accepted for Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-17

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Project No. 13718-000] Quality GearBox... project would consist of: (1) An existing 8.5-foot- high by 325-foot-long gravity dam; (2) an existing 19-acre impoundment with a storage capacity of 133 acre feet; (3) an existing filtration plant to be...

Are Suicide Attempters Wired Differently?: A Comparison With Nonsuicidal Depressed Individuals Using Plan Analysis.

PubMed

Brüdern, Juliane; Berger, Thomas; Michel, Konrad; Maillart, Anja Gysin; Held, Isabelle Schmutz; Caspar, Franz

2015-07-01

Limited research exists on internal risk processes in suicide attempters and factors that distinguish them from nonsuicidal depressive individuals. In this qualitative study, we investigated Plans, motives, and underlying self-regulatory processes of the two groups and conducted a comparative analysis. We analyzed narrative interviews of 17 suicide attempters and intake interviews of 17 nonsuicidal depressive patients using Plan Analysis. Then, we developed a prototypical Plan structure for both groups. Suicidal behavior serves various Plans found only in suicide attempters. Plans of this group are especially related to social perfectionism and withdrawal to protect their self-esteem. Depressive patients use several interpersonal control and coping strategies, which might help prevent suicidal behavior. The prototypical Plan structure of suicide attempters may be a valuable tool for clinicians to detect critical Plans and motives in their interaction with patients, which are related to suicide risk.

Narcissism is associated with weakened frontostriatal connectivity: a DTI study

PubMed Central

Lynam, Donald R.; Powell, David K.; DeWall, C. Nathan

2016-01-01

Narcissism is characterized by the search for affirmation and admiration from others. Might this motivation to find external sources of acclaim exist to compensate for neurostructural deficits that link the self with reward? Greater structural connectivity between brain areas that process self-relevant stimuli (i.e. the medial prefrontal cortex) and reward (i.e. the ventral striatum) is associated with fundamentally positive self-views. We predicted that narcissism would be associated with less integrity of this frontostriatal pathway. We used diffusion tensor imaging to assess the frontostriatal structural connectivity among 50 healthy undergraduates (32 females, 18 males) who also completed a measure of grandiose narcissism. White matter integrity in the frontostriatal pathway was negatively associated with narcissism. Our findings, while purely correlational, suggest that narcissism arises, in part, from a neural disconnect between the self and reward. The exhibitionism and immodesty of narcissists may then be a regulatory strategy to compensate for this neural deficit. PMID:26048178

A 3D bioprinting exemplar of the consequences of the regulatory requirements on customized processes.

PubMed

Hourd, Paul; Medcalf, Nicholas; Segal, Joel; Williams, David J

2015-01-01

Computer-aided 3D printing approaches to the industrial production of customized 3D functional living constructs for restoration of tissue and organ function face significant regulatory challenges. Using the manufacture of a customized, 3D-bioprinted nasal implant as a well-informed but hypothetical exemplar, we examine how these products might be regulated. Existing EU and USA regulatory frameworks do not account for the differences between 3D printing and conventional manufacturing methods or the ability to create individual customized products using mechanized rather than craft approaches. Already subject to extensive regulatory control, issues related to control of the computer-aided design to manufacture process and the associated software system chain present additional scientific and regulatory challenges for manufacturers of these complex 3D-bioprinted advanced combination products.

The Protein Kingdom Extended: Ordered and Intrinsically Disordered Proteins, Their Folding, Supramolecular Complex Formation, and Aggregation

PubMed Central

Turoverov, Konstantin K.; Kuznetsova, Irina M.; Uversky, Vladimir N.

2010-01-01

The native state of a protein is usually associated with a compact globular conformation possessing a rigid and highly ordered structure. At the turn of the last century certain studies arose which concluded that many proteins cannot, in principle, form a rigid globular structure in an aqueous environment, but they are still able to fulfill their specific functions — i.e., they are native. The existence of the disordered regions allows these proteins to interact with their numerous binding partners. Such interactions are often accompanied by the formation of complexes that possess a more ordered structure than the original components. The functional diversity of these proteins, combined with the variability of signals related to the various intra-and intercellular processes handled by these proteins and their capability to produce multi-variant and multi-directional responses allow them to form a unique regulatory net in a cell. The abundance of disordered proteins inside the cell is precisely controlled at the synthesis and clearance levels as well as via interaction with specific binding partners and posttranslational modifications. Another recently recognized biologically active state of proteins is the functional amyloid. The formation of such functional amyloids is tightly controlled and therefore differs from the uncontrolled formation of pathogenic amyloids which are associated with the pathogenesis of several conformational diseases, the development of which is likely to be determined by the failures of the cellular regulatory systems rather than by the formation of the proteinaceous deposits and/or by the protofibril toxicity. PMID:20097220

10 CFR 4.550 - Program accessibility: Existing facilities.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Program accessibility: Existing facilities. 4.550 Section 4.550 Energy NUCLEAR REGULATORY COMMISSION NONDISCRIMINATION IN FEDERALLY ASSISTED PROGRAMS OR... changes shall be made by August 22, 1989, but in any event as expeditiously as possible. (d) Transition...

10 CFR 4.550 - Program accessibility: Existing facilities.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Program accessibility: Existing facilities. 4.550 Section 4.550 Energy NUCLEAR REGULATORY COMMISSION NONDISCRIMINATION IN FEDERALLY ASSISTED PROGRAMS OR... changes shall be made by August 22, 1989, but in any event as expeditiously as possible. (d) Transition...

Crystal structures of the CBS and DRTGG domains of the regulatory region of Clostridiumperfringens pyrophosphatase complexed with the inhibitor, AMP, and activator, diadenosine tetraphosphate.

PubMed

Tuominen, H; Salminen, A; Oksanen, E; Jämsen, J; Heikkilä, O; Lehtiö, L; Magretova, N N; Goldman, A; Baykov, A A; Lahti, R

2010-05-07

Nucleotide-binding cystathionine beta-synthase (CBS) domains serve as regulatory units in numerous proteins distributed in all kingdoms of life. However, the underlying regulatory mechanisms remain to be established. Recently, we described a subfamily of CBS domain-containing pyrophosphatases (PPases) within family II PPases. Here, we express a novel CBS-PPase from Clostridium perfringens (CPE2055) and show that the enzyme is inhibited by AMP and activated by a novel effector, diadenosine 5',5-P1,P4-tetraphosphate (AP(4)A). The structures of the AMP and AP(4)A complexes of the regulatory region of C. perfringens PPase (cpCBS), comprising a pair of CBS domains interlinked by a DRTGG domain, were determined at 2.3 A resolution using X-ray crystallography. The structures obtained are the first structures of a DRTGG domain as part of a larger protein structure. The AMP complex contains two AMP molecules per cpCBS dimer, each bound to a single monomer, whereas in the activator-bound complex, one AP(4)A molecule bridges two monomers. In the nucleotide-bound structures, activator binding induces significant opening of the CBS domain interface, compared with the inhibitor complex. These results provide structural insight into the mechanism of CBS-PPase regulation by nucleotides. Copyright 2010 Elsevier Ltd. All rights reserved.

Impact of illness and its treatment on workplace costs: regulatory and measurement issues.

PubMed

Greenberg, P E; Birnbaum, H G; Kessler, R C; Morgan, M; Stang, P

2001-01-01

In an attempt to document a broader spectrum of the benefits of their pharmaceutical products, drug companies increasingly seek to include productivity claims in their promotional campaigns. We describe the existing regulatory framework of the Food and Drug Administration (FDA) for considering productivity claims, distinguishing between the traditional "substantial evidence" standard and the "competent and reliable scientific evidence" standard. But the notion of competent and reliable scientific evidence may itself be problematic, even when it is the appropriate regulatory standard, because there exists no consistent measurement approach across diseases, workplaces, jobs, and worker capabilities that is widely accepted in this emerging area of health outcomes research. We examine the various measurement approaches that have been used to quantify the impact of illness and its treatment on workplace productivity, and we describe some of the shortcomings associated with each alternative. This discussion highlights the possible difficulties faced by the FDA in reviewing productivity-based promotional claims. Finally, we suggest possible strategies for furthering this field of investigation.

Gene regulatory network identification from the yeast cell cycle based on a neuro-fuzzy system.

PubMed

Wang, B H; Lim, J W; Lim, J S

2016-08-30

Many studies exist for reconstructing gene regulatory networks (GRNs). In this paper, we propose a method based on an advanced neuro-fuzzy system, for gene regulatory network reconstruction from microarray time-series data. This approach uses a neural network with a weighted fuzzy function to model the relationships between genes. Fuzzy rules, which determine the regulators of genes, are very simplified through this method. Additionally, a regulator selection procedure is proposed, which extracts the exact dynamic relationship between genes, using the information obtained from the weighted fuzzy function. Time-series related features are extracted from the original data to employ the characteristics of temporal data that are useful for accurate GRN reconstruction. The microarray dataset of the yeast cell cycle was used for our study. We measured the mean squared prediction error for the efficiency of the proposed approach and evaluated the accuracy in terms of precision, sensitivity, and F-score. The proposed method outperformed the other existing approaches.

Human Genome Editing in the Clinic: New Challenges in Regulatory Benefit-Risk Assessment.

PubMed

Abou-El-Enein, Mohamed; Cathomen, Toni; Ivics, Zoltán; June, Carl H; Renner, Matthias; Schneider, Christian K; Bauer, Gerhard

2017-10-05

As genome editing rapidly progresses toward the realization of its clinical promise, assessing the suitability of current tools and processes used for its benefit-risk assessment is critical. Although current regulations may initially provide an adequate regulatory framework, improvements are recommended to overcome several existing technology-based safety and efficacy issues. Copyright © 2017 Elsevier Inc. All rights reserved.

Inference of Gene Regulatory Networks Incorporating Multi-Source Biological Knowledge via a State Space Model with L1 Regularization

PubMed Central

Hasegawa, Takanori; Yamaguchi, Rui; Nagasaki, Masao; Miyano, Satoru; Imoto, Seiya

2014-01-01

Comprehensive understanding of gene regulatory networks (GRNs) is a major challenge in the field of systems biology. Currently, there are two main approaches in GRN analysis using time-course observation data, namely an ordinary differential equation (ODE)-based approach and a statistical model-based approach. The ODE-based approach can generate complex dynamics of GRNs according to biologically validated nonlinear models. However, it cannot be applied to ten or more genes to simultaneously estimate system dynamics and regulatory relationships due to the computational difficulties. The statistical model-based approach uses highly abstract models to simply describe biological systems and to infer relationships among several hundreds of genes from the data. However, the high abstraction generates false regulations that are not permitted biologically. Thus, when dealing with several tens of genes of which the relationships are partially known, a method that can infer regulatory relationships based on a model with low abstraction and that can emulate the dynamics of ODE-based models while incorporating prior knowledge is urgently required. To accomplish this, we propose a method for inference of GRNs using a state space representation of a vector auto-regressive (VAR) model with L1 regularization. This method can estimate the dynamic behavior of genes based on linear time-series modeling constructed from an ODE-based model and can infer the regulatory structure among several tens of genes maximizing prediction ability for the observational data. Furthermore, the method is capable of incorporating various types of existing biological knowledge, e.g., drug kinetics and literature-recorded pathways. The effectiveness of the proposed method is shown through a comparison of simulation studies with several previous methods. For an application example, we evaluated mRNA expression profiles over time upon corticosteroid stimulation in rats, thus incorporating corticosteroid kinetics/dynamics, literature-recorded pathways and transcription factor (TF) information. PMID:25162401

Legal and regulatory responses to innovative treatment.

PubMed

Chan, Tracey Evans

2013-01-01

Developments in medical technology, healthcare delivery, and commercial interests in medicine have increased both the potential for conflicts of interest on the part of physicians, and doubts over the sufficiency of patient autonomy as a justification for administering innovative therapy. The legal and regulatory treatment of innovative therapy is therefore an important question, on which there is a current lack of consensus on a number of issues. This paper discusses recent developments in Singapore and uses them as a springboard to flesh out basic regulatory issues that arise from the deployment of innovative treatment: the distinction between innovative treatment and clinical research, the adequacy of the current post hoc scrutiny of innovative therapy under existing legal principles and the need for further specialised regulatory oversight.

75 FR 26832 - Self-Regulatory Organizations; Notice of Filing and Immediate Effectiveness of Proposed Rule...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-12

..., Inc. to Clarify, Eliminate, Revise, or Delete Certain Out-Dated or Obsolete Rules May 6, 2010... its rules by clarifying existing provisions, eliminating superfluous provisions, and revising or... rules in order to clarify existing provisions, eliminate superfluous provisions, delete certain out...

76 FR 63276 - Reducing Regulatory Burden; Retrospective Review Under E.O. 13563

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-12

... retrospective analysis of existing regulations and develop a preliminary plan to review periodically significant... a voluntary basis, an analysis of its existing regulations. On May 18, 2011, the Board's Chairman..., Nat'l Trails System Act & R.R. Rights-of-Way; EP 699, Assessment of Mediation and Arbitration...

76 FR 32330 - Reducing Regulatory Burden; Retrospective Review Under E.O. 13563

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-06

... information from interested parties to assist DoD in reviewing its existing regulations to determine whether... business community to determine how its regulations can increase efficiency, transparency, and provide... for the periodic review of its existing regulations and reporting obligations. DoD's plan is designed...

Regulation of the Synthesis of the Angucyclinone Antibiotic Alpomycin in Streptomyces ambofaciens by the Autoregulator Receptor AlpZ and Its Specific Ligand▿

PubMed Central

Bunet, Robert; Mendes, Marta V.; Rouhier, Nicolas; Pang, Xiuhua; Hotel, Laurence; Leblond, Pierre; Aigle, Bertrand

2008-01-01

Streptomyces ambofaciens produces an orange pigment and the antibiotic alpomycin, both of which are products of a type II polyketide synthase gene cluster identified in each of the terminal inverted repeats of the linear chromosome. Five regulatory genes encoding Streptomyces antibiotic regulatory proteins (alpV, previously shown to be an essential activator gene; alpT; and alpU) and TetR family receptors (alpZ and alpW) were detected in this cluster. Here, we demonstrate that AlpZ, which shows high similarity to γ-butyrolactone receptors, is at the top of a pathway-specific regulatory hierarchy that prevents synthesis of the alp polyketide products. Deletion of the two copies of alpZ resulted in the precocious production of both alpomycin and the orange pigment, suggesting a repressor role for AlpZ. Consistent with this, expression of the five alp-located regulatory genes and of two representative biosynthetic structural genes (alpA and alpR) was induced earlier in the alpZ deletion strain. Furthermore, recombinant AlpZ was shown to bind to specific DNA sequences within the promoter regions of alpZ, alpV, and alpXW, suggesting direct transcriptional control of these genes by AlpZ. Analysis of solvent extracts of S. ambofaciens cultures identified the existence of a factor which induces precocious production of alpomycin and pigment in the wild-type strain and which can disrupt the binding of AlpZ to its DNA targets. This activity is reminiscent of γ-butyrolactone-type molecules. However, the AlpZ-interacting molecule(s) was shown to be resistant to an alkali treatment capable of inactivating γ-butyrolactones, suggesting that the AlpZ ligand(s) does not possess a lactone functional group. PMID:18296523

Regulation of the synthesis of the angucyclinone antibiotic alpomycin in Streptomyces ambofaciens by the autoregulator receptor AlpZ and its specific ligand.

PubMed

Bunet, Robert; Mendes, Marta V; Rouhier, Nicolas; Pang, Xiuhua; Hotel, Laurence; Leblond, Pierre; Aigle, Bertrand

2008-05-01

Streptomyces ambofaciens produces an orange pigment and the antibiotic alpomycin, both of which are products of a type II polyketide synthase gene cluster identified in each of the terminal inverted repeats of the linear chromosome. Five regulatory genes encoding Streptomyces antibiotic regulatory proteins (alpV, previously shown to be an essential activator gene; alpT; and alpU) and TetR family receptors (alpZ and alpW) were detected in this cluster. Here, we demonstrate that AlpZ, which shows high similarity to gamma-butyrolactone receptors, is at the top of a pathway-specific regulatory hierarchy that prevents synthesis of the alp polyketide products. Deletion of the two copies of alpZ resulted in the precocious production of both alpomycin and the orange pigment, suggesting a repressor role for AlpZ. Consistent with this, expression of the five alp-located regulatory genes and of two representative biosynthetic structural genes (alpA and alpR) was induced earlier in the alpZ deletion strain. Furthermore, recombinant AlpZ was shown to bind to specific DNA sequences within the promoter regions of alpZ, alpV, and alpXW, suggesting direct transcriptional control of these genes by AlpZ. Analysis of solvent extracts of S. ambofaciens cultures identified the existence of a factor which induces precocious production of alpomycin and pigment in the wild-type strain and which can disrupt the binding of AlpZ to its DNA targets. This activity is reminiscent of gamma-butyrolactone-type molecules. However, the AlpZ-interacting molecule(s) was shown to be resistant to an alkali treatment capable of inactivating gamma-butyrolactones, suggesting that the AlpZ ligand(s) does not possess a lactone functional group.

E3Net: a system for exploring E3-mediated regulatory networks of cellular functions.

PubMed

Han, Youngwoong; Lee, Hodong; Park, Jong C; Yi, Gwan-Su

2012-04-01

Ubiquitin-protein ligase (E3) is a key enzyme targeting specific substrates in diverse cellular processes for ubiquitination and degradation. The existing findings of substrate specificity of E3 are, however, scattered over a number of resources, making it difficult to study them together with an integrative view. Here we present E3Net, a web-based system that provides a comprehensive collection of available E3-substrate specificities and a systematic framework for the analysis of E3-mediated regulatory networks of diverse cellular functions. Currently, E3Net contains 2201 E3s and 4896 substrates in 427 organisms and 1671 E3-substrate specific relations between 493 E3s and 1277 substrates in 42 organisms, extracted mainly from MEDLINE abstracts and UniProt comments with an automatic text mining method and additional manual inspection and partly from high throughput experiment data and public ubiquitination databases. The significant functions and pathways of the extracted E3-specific substrate groups were identified from a functional enrichment analysis with 12 functional category resources for molecular functions, protein families, protein complexes, pathways, cellular processes, cellular localization, and diseases. E3Net includes interactive analysis and navigation tools that make it possible to build an integrative view of E3-substrate networks and their correlated functions with graphical illustrations and summarized descriptions. As a result, E3Net provides a comprehensive resource of E3s, substrates, and their functional implications summarized from the regulatory network structures of E3-specific substrate groups and their correlated functions. This resource will facilitate further in-depth investigation of ubiquitination-dependent regulatory mechanisms. E3Net is freely available online at http://pnet.kaist.ac.kr/e3net.

Dietary Supplements: Regulatory Challenges and Research Resources.

PubMed

Dwyer, Johanna T; Coates, Paul M; Smith, Michael J

2018-01-04

Many of the scientific and regulatory challenges that exist in research on the safety, quality and efficacy of dietary supplements are common to all countries as the marketplace for them becomes increasingly global. This article summarizes some of the challenges in supplement science and provides a case study of research at the Office of Dietary Supplements at the National Institutes of Health, USA, along with some resources it has developed that are available to all scientists. It includes examples of some of the regulatory challenges faced and some resources for those who wish to learn more about them.

Dietary Supplements: Regulatory Challenges and Research Resources

PubMed Central

Dwyer, Johanna T.; Coates, Paul M.; Smith, Michael J.

2018-01-01

Many of the scientific and regulatory challenges that exist in research on the safety, quality and efficacy of dietary supplements are common to all countries as the marketplace for them becomes increasingly global. This article summarizes some of the challenges in supplement science and provides a case study of research at the Office of Dietary Supplements at the National Institutes of Health, USA, along with some resources it has developed that are available to all scientists. It includes examples of some of the regulatory challenges faced and some resources for those who wish to learn more about them. PMID:29300341

Human Germline CRISPR-Cas Modification: Toward a Regulatory Framework

PubMed Central

Evitt, Niklaus H.; Mascharak, Shamik; Altman, Russ B.

2015-01-01

CRISPR germline editing therapies (CGETs) hold unprecedented potential to eradicate hereditary disorders. However, the prospect of altering the human germline has sparked a debate over the safety, efficacy, and morality of CGETs, triggering a funding moratorium by the NIH. There is an urgent need for practical paths for the evaluation of these capabilities. We propose a model regulatory framework for CGET research, clinical development, and distribution. Our model takes advantage of existing legal and regulatory institutions but adds elevated scrutiny at each stage of CGET development to accommodate the unique technical and ethical challenges posed by germline editing. PMID:26632357

The role of long noncoding RNAs in the epigenetic control of gene expression.

PubMed

Morlando, Mariangela; Ballarino, Monica; Fatica, Alessandro; Bozzoni, Irene

2014-03-01

Recent advances in the methodologies employed to deeply analyse the complexity of transcriptomes have unveiled the existence of a new class of transcripts, long noncoding RNAs (lncRNAs). A significant amount of effort has been dedicated to the study of lncRNAs, and a large body of evidence now exists indicating their relevant role in different regulatory steps of gene expression. Given the role of epigenetics in disease development and progression, this Minireview focuses on lncRNAs involved in epigenetic control and provides an overview of the mechanisms used to guide epigenetic-modifying complexes to adjacent (cis-acting) or independent (trans-acting) genomic loci. Furthermore, it describes the activities of these transcripts in controlling the formation and spreading of heterochromatin domains. Just as other RNA molecules have found therapeutic application, though much remains to be elucidated about the structure and function of these lncRNAs, they too could hold potential as biomarkers, targets, and therapeutic agents. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Regulatory Perspectives on Continuous Pharmaceutical Manufacturing: Moving From Theory to Practice: September 26-27, 2016, International Symposium on the Continuous Manufacturing of Pharmaceuticals.

PubMed

Nasr, Moheb M; Krumme, Markus; Matsuda, Yoshihiro; Trout, Bernhardt L; Badman, Clive; Mascia, Salvatore; Cooney, Charles L; Jensen, Keith D; Florence, Alastair; Johnston, Craig; Konstantinov, Konstantin; Lee, Sau L

2017-11-01

Continuous manufacturing plays a key role in enabling the modernization of pharmaceutical manufacturing. The fate of this emerging technology will rely, in large part, on the regulatory implementation of this novel technology. This paper, which is based on the 2nd International Symposium on the Continuous Manufacturing of Pharmaceuticals, describes not only the advances that have taken place since the first International Symposium on Continuous Manufacturing of Pharmaceuticals in 2014, but the regulatory landscape that exists today. Key regulatory concepts including quality risk management, batch definition, control strategy, process monitoring and control, real-time release testing, data processing and management, and process validation/verification are outlined. Support from regulatory agencies, particularly in the form of the harmonization of regulatory expectations, will be crucial to the successful implementation of continuous manufacturing. Collaborative efforts, among academia, industry, and regulatory agencies, are the optimal solution for ensuring a solid future for this promising manufacturing technology. Copyright © 2017 American Pharmacists Association®. All rights reserved.

Giving Drugs a Second Chance: Overcoming Regulatory and Financial Hurdles in Repurposing Approved Drugs As Cancer Therapeutics

PubMed Central

Hernandez, J. Javier; Pryszlak, Michael; Smith, Lindsay; Yanchus, Connor; Kurji, Naheed; Shahani, Vijay M.; Molinski, Steven V.

2017-01-01

The repositioning or “repurposing” of existing therapies for alternative disease indications is an attractive approach that can save significant investments of time and money during drug development. For cancer indications, the primary goal of repurposed therapies is on efficacy, with less restriction on safety due to the immediate need to treat this patient population. This report provides a high-level overview of how drug developers pursuing repurposed assets have previously navigated funding efforts, regulatory affairs, and intellectual property laws to commercialize these “new” medicines in oncology. This article provides insight into funding programs (e.g., government grants and philanthropic organizations) that academic and corporate initiatives can leverage to repurpose drugs for cancer. In addition, we highlight previous examples where secondary uses of existing, Food and Drug Administration- or European Medicines Agency-approved therapies have been predicted in silico and successfully validated in vitro and/or in vivo (i.e., animal models and human clinical trials) for certain oncology indications. Finally, we describe the strategies that the pharmaceutical industry has previously employed to navigate regulatory considerations and successfully commercialize their drug products. These factors must be carefully considered when repurposing existing drugs for cancer to best benefit patients and drug developers alike. PMID:29184849

Giving Drugs a Second Chance: Overcoming Regulatory and Financial Hurdles in Repurposing Approved Drugs As Cancer Therapeutics.

PubMed

Hernandez, J Javier; Pryszlak, Michael; Smith, Lindsay; Yanchus, Connor; Kurji, Naheed; Shahani, Vijay M; Molinski, Steven V

2017-01-01

The repositioning or "repurposing" of existing therapies for alternative disease indications is an attractive approach that can save significant investments of time and money during drug development. For cancer indications, the primary goal of repurposed therapies is on efficacy, with less restriction on safety due to the immediate need to treat this patient population. This report provides a high-level overview of how drug developers pursuing repurposed assets have previously navigated funding efforts, regulatory affairs, and intellectual property laws to commercialize these "new" medicines in oncology. This article provides insight into funding programs (e.g., government grants and philanthropic organizations) that academic and corporate initiatives can leverage to repurpose drugs for cancer. In addition, we highlight previous examples where secondary uses of existing, Food and Drug Administration- or European Medicines Agency-approved therapies have been predicted in silico and successfully validated in vitro and/or in vivo (i.e., animal models and human clinical trials) for certain oncology indications. Finally, we describe the strategies that the pharmaceutical industry has previously employed to navigate regulatory considerations and successfully commercialize their drug products. These factors must be carefully considered when repurposing existing drugs for cancer to best benefit patients and drug developers alike.

Hemovigilance in Massachusetts and the adoption of statewide hospital blood bank reporting using the National Healthcare Safety Network.

PubMed

Cumming, Melissa; Osinski, Anthony; O'Hearn, Lynne; Waksmonski, Pamela; Herman, Michele; Gordon, Deborah; Griffiths, Elzbieta; Knox, Kim; McHale, Eileen; Quillen, Karen; Rios, Jorge; Pisciotto, Patricia; Uhl, Lynne; DeMaria, Alfred; Andrzejewski, Chester

2017-02-01

A collaboration that grew over time between local hemovigilance stakeholders and the Massachusetts Department of Public Health (MDPH) resulted in the change from a paper-based method of reporting adverse reactions and monthly transfusion activity for regulatory compliance purposes to statewide adoption of electronic reporting via the National Healthcare Safety Network (NHSN). The NHSN is a web-based surveillance system that offers the capacity to capture transfusion-related adverse events, incidents, and monthly transfusion statistics from participating facilities. Massachusetts' hospital blood banks share the data they enter into NHSN with the MDPH to satisfy reporting requirements. Users of the NHSN Hemovigilance Module adhere to specified data entry guidelines, resulting in data that are comparable and standardized. Keys to successful statewide adoption of this reporting method include the fostering of strong partnerships with local hemovigilance champions and experts, engagement of regulatory and epidemiology divisions at the state health department, the leveraging of existing relationships with hospital NHSN administrators, and the existence of a regulatory deadline for implementation. Although limitations exist, successful implementation of statewide use of the NHSN Hemovigilance Module for hospital blood bank reporting is possible. The result is standardized, actionable data at both the hospital and state level that can facilitate interfacility comparisons, benchmarking, and opportunities for practice improvement. © 2016 AABB.

77 FR 42533 - Self-Regulatory Organizations; NYSE Arca, Inc.; Order Granting Approval of Proposed Rule Change...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-19

...-Regulatory Organizations; NYSE Arca, Inc.; Order Granting Approval of Proposed Rule Change Amending Its Rules... Ownership Structure of the Exchange July 13, 2012. I. Introduction On May 14, 2012, NYSE Arca, Inc. (``NYSE... Holdings from the ownership structure of the Exchange (the ``Merger''). The proposed rule changes were...

Telemental Health for Children and Adolescents: An Overview of Legal, Regulatory, and Risk Management Issues.

PubMed

Kramer, Gregory M; Luxton, David D

2016-04-01

The use of technology to provide telemental healthcare continues to increase; however, little has been written about the legal and regulatory issues involved in providing this form of care to children and adolescents. This article reviews existing laws and regulations to summarize the risk management issues relevant to providing telemental healthcare to children and adolescents. There are several legal and regulatory areas in which telemental health clinicians need to have awareness. These areas include: 1) Licensure, 2) malpractice liability, 3) credentialing and privileging, 4) informed consent, 5) security and privacy, and 6) emergency management. Although legal and regulatory challenges remain in providing telemental healthcare to children and adolescents, it is possible to overcome these challenges with knowledge of the issues and appropriate risk management strategies. We provide general knowledge of these key legal and regulatory issues, along with some risk management recommendations.

Life's attractors : understanding developmental systems through reverse engineering and in silico evolution.

PubMed

Jaeger, Johannes; Crombach, Anton

2012-01-01

We propose an approach to evolutionary systems biology which is based on reverse engineering of gene regulatory networks and in silico evolutionary simulations. We infer regulatory parameters for gene networks by fitting computational models to quantitative expression data. This allows us to characterize the regulatory structure and dynamical repertoire of evolving gene regulatory networks with a reasonable amount of experimental and computational effort. We use the resulting network models to identify those regulatory interactions that are conserved, and those that have diverged between different species. Moreover, we use the models obtained by data fitting as starting points for simulations of evolutionary transitions between species. These simulations enable us to investigate whether such transitions are random, or whether they show stereotypical series of regulatory changes which depend on the structure and dynamical repertoire of an evolving network. Finally, we present a case study-the gap gene network in dipterans (flies, midges, and mosquitoes)-to illustrate the practical application of the proposed methodology, and to highlight the kind of biological insights that can be gained by this approach.

Regulatory Fit Improves Fitness for People With Low Exercise Experience.

PubMed

Kay, Sophie A; Grimm, Lisa R

2017-04-01

Considering only 20.8% of American adults meet current physical activity recommendations, it is important to examine the psychological processes that affect exercise motivation and behavior. Drawing from regulatory fit theory, this study examined how manipulating regulatory focus and reward structures would affect exercise performance, with a specific interest in investigating whether exercise experience would moderate regulatory fit effects. We predicted that regulatory fit effects would appear only for participants with low exercise experience. One hundred and sixty-five young adults completed strength training exercise tasks (i.e., sit-ups, squats, plank, and wall-sit) in regulatory match or mismatch conditions. Consistent with predictions, only participants low in experience in regulatory match conditions exercised more compared with those in regulatory mismatch conditions. Although this is the first study manipulating regulatory fit in a controlled setting to examine exercise behavior, findings suggest that generating regulatory fit could positively influence those low in exercise experience.

Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics.

PubMed

Li, Sanshu; Breaker, Ronald R

2017-10-13

With the development of rapid and inexpensive DNA sequencing, the genome sequences of more than 100 fungal species have been made available. This dataset provides an excellent resource for comparative genomics analyses, which can be used to discover genetic elements, including noncoding RNAs (ncRNAs). Bioinformatics tools similar to those used to uncover novel ncRNAs in bacteria, likewise, should be useful for searching fungal genomic sequences, and the relative ease of genetic experiments with some model fungal species could facilitate experimental validation studies. We have adapted a bioinformatics pipeline for discovering bacterial ncRNAs to systematically analyze many fungal genomes. This comparative genomics pipeline integrates information on conserved RNA sequence and structural features with alternative splicing information to reveal fungal RNA motifs that are candidate regulatory domains, or that might have other possible functions. A total of 15 prominent classes of structured ncRNA candidates were identified, including variant HDV self-cleaving ribozyme representatives, atypical snoRNA candidates, and possible structured antisense RNA motifs. Candidate regulatory motifs were also found associated with genes for ribosomal proteins, S-adenosylmethionine decarboxylase (SDC), amidase, and HexA protein involved in Woronin body formation. We experimentally confirm that the variant HDV ribozymes undergo rapid self-cleavage, and we demonstrate that the SDC RNA motif reduces the expression of SAM decarboxylase by translational repression. Furthermore, we provide evidence that several other motifs discovered in this study are likely to be functional ncRNA elements. Systematic screening of fungal genomes using a computational discovery pipeline has revealed the existence of a variety of novel structured ncRNAs. Genome contexts and similarities to known ncRNA motifs provide strong evidence for the biological and biochemical functions of some newly found ncRNA motifs. Although initial examinations of several motifs provide evidence for their likely functions, other motifs will require more in-depth analysis to reveal their functions.

Actual operation and regulatory activities on steam generator replacement in Japan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saeki, Hitoshi

1997-02-01

This paper summarizes the operating reactors in Japan, and the status of the steam generators in these plants. It reviews plans for replacement of existing steam generators, and then goes into more detail on the planning and regulatory steps which must be addressed in the process of accomplishing this maintenance. The paper also reviews the typical steps involved in the process of removal and replacement of steam generators.

Cloning and bioinformatic analysis of lovastatin biosynthesis regulatory gene lovE.

PubMed

Huang, Xin; Li, Hao-ming

2009-08-05

Lovastatin is an effective drug for treatment of hyperlipidemia. This study aimed to clone lovastatin biosynthesis regulatory gene lovE and analyze the structure and function of its encoding protein. According to the lovastatin synthase gene sequence from genebank, primers were designed to amplify and clone the lovastatin biosynthesis regulatory gene lovE from Aspergillus terrus genomic DNA. Bioinformatic analysis of lovE and its encoding animo acid sequence was performed through internet resources and software like DNAMAN. Target fragment lovE, almost 1500 bp in length, was amplified from Aspergillus terrus genomic DNA and the secondary and three-dimensional structures of LovE protein were predicted. In the lovastatin biosynthesis process lovE is a regulatory gene and LovE protein is a GAL4-like transcriptional factor.

Regulating the for-profit private healthcare providers towards universal health coverage: A qualitative study of legal and organizational framework in Mongolia.

PubMed

Tsevelvaanchig, Uranchimeg; Narula, Indermohan S; Gouda, Hebe; Hill, Peter S

2018-01-01

Regulating the behavior of private providers in the context of mixed health systems has become increasingly important and challenging in many developing countries moving towards universal health coverage including Mongolia. This study examines the current regulatory architecture for private healthcare in Mongolia exploring its role for improving accessibility, affordability, and quality of private care and identifies gaps in policy design and implementation. Qualitative research methods were used including documentary review, analysis, and in-depth interviews with 45 representatives of key actors involved in and affected by regulations in Mongolia's mixed health system, along with long-term participant observation. There has been extensive legal documentation developed regulating private healthcare, with specific organizations assigned to conduct health regulations and inspections. However, the regulatory architecture for healthcare in Mongolia is not optimally designed to improve affordability and quality of private care. This is not limited only to private care: important regulatory functions targeted to quality of care do not exist at the national level. The imprecise content and details of regulations in laws inviting increased political interference, governance issues, unclear roles, and responsibilities of different government regulatory bodies have contributed to failures in implementation of existing regulations. Copyright © 2017 John Wiley & Sons, Ltd.

Who owns Australia's water--elements of an effective regulatory model.

PubMed

McKay, J

2003-01-01

This paper identifies and describes a number of global trends in regulatory theory and legal scholarship. It points out the huge level of complexity demanded by globalisation and the unfortunate complication of this is that there is legal indeterminacy. The legal indeterminacy springs from the desire to amend and alter existing models. That has been the thrust of the Council of Australian Governments changes to adapt and add huge amounts of complexity to a flawed system. This paper argues that an effective water regulatory model requires a fundamental re-examination of the concept of water ownership and a capturing by the State of the right to allocate rainfall. This foundation is effective and the way forward to deal with the key issues in this transition phase. The second key element to an effective regulatory model is the concept of performance-based assessment. This requires information and schemes to be set up to work out ways to monitor and evaluate the performance of the utility on selected criteria. For Australia at present there is a dire lack of agreed criteria on these key issues and these have the potential to pull apart the whole process. The key issues are indigenous rights, governance issues, public participation, alteration of pre-existing rights and incorporation of environmental requirements.

A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems.

PubMed

Yin, Weiwei; Garimalla, Swetha; Moreno, Alberto; Galinski, Mary R; Styczynski, Mark P

2015-08-28

There are increasing efforts to bring high-throughput systems biology techniques to bear on complex animal model systems, often with a goal of learning about underlying regulatory network structures (e.g., gene regulatory networks). However, complex animal model systems typically have significant limitations on cohort sizes, number of samples, and the ability to perform follow-up and validation experiments. These constraints are particularly problematic for many current network learning approaches, which require large numbers of samples and may predict many more regulatory relationships than actually exist. Here, we test the idea that by leveraging the accuracy and efficiency of classifiers, we can construct high-quality networks that capture important interactions between variables in datasets with few samples. We start from a previously-developed tree-like Bayesian classifier and generalize its network learning approach to allow for arbitrary depth and complexity of tree-like networks. Using four diverse sample networks, we demonstrate that this approach performs consistently better at low sample sizes than the Sparse Candidate Algorithm, a representative approach for comparison because it is known to generate Bayesian networks with high positive predictive value. We develop and demonstrate a resampling-based approach to enable the identification of a viable root for the learned tree-like network, important for cases where the root of a network is not known a priori. We also develop and demonstrate an integrated resampling-based approach to the reduction of variable space for the learning of the network. Finally, we demonstrate the utility of this approach via the analysis of a transcriptional dataset of a malaria challenge in a non-human primate model system, Macaca mulatta, suggesting the potential to capture indicators of the earliest stages of cellular differentiation during leukopoiesis. We demonstrate that by starting from effective and efficient approaches for creating classifiers, we can identify interesting tree-like network structures with significant ability to capture the relationships in the training data. This approach represents a promising strategy for inferring networks with high positive predictive value under the constraint of small numbers of samples, meeting a need that will only continue to grow as more high-throughput studies are applied to complex model systems.

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks

PubMed Central

Roy, Sushmita; Lagree, Stephen; Hou, Zhonggang; Thomson, James A.; Stewart, Ron; Gasch, Audrey P.

2013-01-01

Regulatory networks that control gene expression are important in diverse biological contexts including stress response and development. Each gene's regulatory program is determined by module-level regulation (e.g. co-regulation via the same signaling system), as well as gene-specific determinants that can fine-tune expression. We present a novel approach, Modular regulatory network learning with per gene information (MERLIN), that infers regulatory programs for individual genes while probabilistically constraining these programs to reveal module-level organization of regulatory networks. Using edge-, regulator- and module-based comparisons of simulated networks of known ground truth, we find MERLIN reconstructs regulatory programs of individual genes as well or better than existing approaches of network reconstruction, while additionally identifying modular organization of the regulatory networks. We use MERLIN to dissect global transcriptional behavior in two biological contexts: yeast stress response and human embryonic stem cell differentiation. Regulatory modules inferred by MERLIN capture co-regulatory relationships between signaling proteins and downstream transcription factors thereby revealing the upstream signaling systems controlling transcriptional responses. The inferred networks are enriched for regulators with genetic or physical interactions, supporting the inference, and identify modules of functionally related genes bound by the same transcriptional regulators. Our method combines the strengths of per-gene and per-module methods to reveal new insights into transcriptional regulation in stress and development. PMID:24146602

75 FR 36739 - Self-Regulatory Organizations; Chicago Board Options Exchange, Incorporated; Notice of Filing of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-28

....'' Second, the Exchange proposes replacing existing paragraph (c)(4) of Rule 52.4, entitled ``Numerical... eliminate the ability of the Exchange to deviate from the Numerical Guidelines contained in paragraph (c)(1... existing paragraph (c)(2), which provides flexibility to the Exchange to use different Numerical Guidelines...

78 FR 28666 - Self-Regulatory Organizations; Chicago Board Options Exchange, Incorporated; Notice of Filing of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-15

... enable the TPH to meet its existing obligations to customers. In addition, such procedures must address the TPH's existing relationships with other broker-dealers and third parties. The business continuity... business continuity plan if such TPH has public customers. If the TPH does not have public customers, the...

76 FR 2160 - Self-Regulatory Organizations; Chicago Board Options Exchange, Incorporated; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-12

... Exchange's rules also expressly set forth reciprocity provisions.\\6\\ In other words, the Exchange is... exchanges that employ a similar program under their rules. Reciprocity provisions also exist for the $2.50... reciprocity provision, the Exchange's existing strike setting programs demonstrate the intent [[Page 2161

76 FR 4244 - Regulation and Enforcement; Renewable Energy Alternate Uses of Existing Facilities on the Outer...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-25

... DEPARTMENT OF THE INTERIOR Bureau of Ocean Energy Management 30 CFR Part 285 [Docket ID: BOEM-2010-0045] RIN 1010-AD71 Regulation and Enforcement; Renewable Energy Alternate Uses of Existing Facilities...: BOEMRE is withdrawing the direct final rule to amend BOEMRE's renewable energy regulatory provisions that...

Regulatory Focus as a Mediator of the Influence of Initiating Structure and Servant Leadership on Employee Behavior

ERIC Educational Resources Information Center

Neubert, Mitchell J.; Kacmar, K. Michele; Carlson, Dawn S.; Chonko, Lawrence B.; Roberts, James A.

2008-01-01

In this research, the authors test a model in which the regulatory focus of employees at work mediates the influence of leadership on employee behavior. In a nationally representative sample of 250 workers who responded over 2 time periods, prevention focus mediated the relationship of initiating structure to in-role performance and deviant…

The Regulatory Structure Supporting Basic Education in Indonesia: Analysis Covering 1989 to Present. Working Paper.

ERIC Educational Resources Information Center

Cohen, Joseph

This report examines the legal and regulatory structure of basic education in Indonesia beginning in 1989, when Education Law Number 2 was enacted (from which all current regulations, policies, and procedures can be traced). In 1999, two key laws (Number 22 and Number 25) were passed that required the decentralization of many government functions.…

Understanding regulatory networks requires more than computing a multitude of graph statistics. Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O.C. Martin et al.

NASA Astrophysics Data System (ADS)

Tkačik, Gašper

2016-07-01

The article by O. Martin and colleagues provides a much needed systematic review of a body of work that relates the topological structure of genetic regulatory networks to evolutionary selection for function. This connection is very important. Using the current wealth of genomic data, statistical features of regulatory networks (e.g., degree distributions, motif composition, etc.) can be quantified rather easily; it is, however, often unclear how to interpret the results. On a graph theoretic level the statistical significance of the results can be evaluated by comparing observed graphs to ;randomized; ones (bravely ignoring the issue of how precisely to randomize!) and comparing the frequency of appearance of a particular network structure relative to a randomized null expectation. While this is a convenient operational test for statistical significance, its biological meaning is questionable. In contrast, an in-silico genotype-to-phenotype model makes explicit the assumptions about the network function, and thus clearly defines the expected network structures that can be compared to the case of no selection for function and, ultimately, to data.

Integrative analysis of Arabidopsis thaliana transcriptomics reveals intuitive splicing mechanism for circular RNA.

PubMed

Sun, Xiaoyong; Wang, Lin; Ding, Jiechao; Wang, Yanru; Wang, Jiansheng; Zhang, Xiaoyang; Che, Yulei; Liu, Ziwei; Zhang, Xinran; Ye, Jiazhen; Wang, Jie; Sablok, Gaurav; Deng, Zhiping; Zhao, Hongwei

2016-10-01

A new regulatory class of small endogenous RNAs called circular RNAs (circRNAs) has been described as miRNA sponges in animals. Using 16 Arabidopsis thaliana RNA-Seq data sets, we identified 803 circRNAs in RNase R-/non-RNase R-treated samples. The results revealed the following features: Canonical and noncanonical splicing can generate circRNAs; chloroplasts are a hotspot for circRNA generation; furthermore, limited complementary sequences exist not only in introns, but also in the sequences flanking splice sites. The latter finding suggests that multiple combinations between complementary sequences may facilitate the formation of the circular structure. Our results contribute to a better understanding of this novel class of plant circRNAs. © 2016 Federation of European Biochemical Societies.

Enhancing antimicrobial stewardship by strengthening the veterinary drug regulatory framework

PubMed Central

Mehrotra, M; Li, X-Z; Ireland, MJ

2017-01-01

Antimicrobial resistance is a major and growing public health threat. Recently, Health Canada introduced multiple regulatory changes to strengthen the oversight of antimicrobial drugs for veterinary use. These changes aim specifically at increasing control over importation of veterinary drugs and active pharmaceutical ingredients, mandatory reporting of antimicrobial sales data from manufacturers, importers and compounders and facilitating access to low risk veterinary health products. Additional policy changes under existing authorities are also being made to enhance veterinary supervision of antimicrobial use and to remove production claims for food animals from labels of medically important antimicrobial drugs. These important interlinked initiatives are aimed towards enhancing antimicrobial stewardship in Canada to preserve the effectiveness of existing antimicrobials and to protect the health of Canadians. PMID:29770050

Clinical trials bureaucracy: unintended consequences of well-intentioned policy.

PubMed

Califf, Robert M

2006-01-01

As randomized controlled trials have become the 'gold standard' for medical research, a complex regulatory structure for the conduct of clinical trials has emerged. However, this structure has not been adequately assessed to ensure that regulations governing human subjects research actually produce the desired effects. Our purpose is to identify some of the major shortcomings in the current regulatory system of human clinical trials oversight, and to propose some potential solutions to these problems. We discuss the evolution of the current US regulatory environment and its application in the context of several widely-used drug therapies. Despite numerous randomized controlled trials, performed within a structure of extensive documentation and data collection, serious shortcomings in a number of pharmaceutical therapies were not detected until after the drugs were approved and widely adopted by clinicians. The current system of regulatory bureaucracy in clinical trials has led to an extremely expensive research paradigm that, in spite of complex systems of oversight and exhaustive data collection, cannot be shown to adequately ensure the integrity of the research process and the protection of human research subjects. Some parts of the system, including Research Ethics Review Boards, may not be well-suited to carrying out their core mission of overseeing research conduct, and other aspects of clinical trials regulatory structure, such as monitoring/auditing review and adverse event reporting, may constitute a waste of money and resources. Misdirected data collection and adverse events reporting divert valuable resources and hamper development of large, simple clinical trials powered to definitively answer important research questions. Careful scrutiny of the utility of current or proposed regulatory schemes is required to ensure the integrity of human subjects research and to enhance the effectiveness of research dollars.

A two-way street: regulatory interplay between RNA polymerase and nascent RNA structure

PubMed Central

Zhang, Jinwei; Landick, Robert

2016-01-01

The vectorial (5′-to-3′ at varying velocity) synthesis of RNA by cellular RNA polymerases 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 RNA polymerase and nascent RNA structure. We categorize and attempt to rationalize the extensive linkage between the transcriptional machinery and its product, and provide a framework for future studies. PMID:26822487

76 FR 33389 - Self-Regulatory Organizations; NYSE Amex LLC; Notice of Filing and Immediate Effectiveness of...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-08

... situated member organizations will be subject to the same fee structure and access to the Exchange's market...-Regulatory Organizations; NYSE Amex LLC; Notice of Filing and Immediate Effectiveness of Proposed Rule Change..., and III below, which Items have been prepared by the self-regulatory organization. The Commission is...

76 FR 66078 - Notice of Industry Workshop on Technical and Regulatory Challenges in Deep and Ultra-Deep Outer...

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2011-10-25

...-0087] Notice of Industry Workshop on Technical and Regulatory Challenges in Deep and Ultra-Deep Outer... and gas exploration and production in deep and ultra-deep OCS waters. Through this workshop, BSEE will... structured venue for consultation among offshore deepwater oil and gas industry and regulatory experts in...

Regulatory networks and connected components of the neutral space. A look at functional islands

NASA Astrophysics Data System (ADS)

Boldhaus, G.; Klemm, K.

2010-09-01

The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory systems is neutrality - typically a large number of alternative network structures give rise to the necessary dynamics. Here we study the discretized regulatory dynamics of the yeast cell cycle [Li et al., PNAS, 2004] and the set of networks capable of reproducing it, which we call functional. Among these, the empirical yeast wildtype network is close to optimal with respect to sparse wiring. Under point mutations, which establish or delete single interactions, the neutral space of functional networks is fragmented into ≈ 4.7 × 108 components. One of the smaller ones contains the wildtype network. On average, functional networks reachable from the wildtype by mutations are sparser, have higher noise resilience and fewer fixed point attractors as compared with networks outside of this wildtype component.

Overview of cancer vaccines

PubMed Central

Kudrin, Alex

2012-01-01

Cancer immunotherapy has seen a tremendous number of failures and only few recent regulatory successes. This is a review dedicated to determine major regulatory and developmental issues around cancer immunotherapeutics. A three pillar approach should be used in setting a development path: discovery platforms and sufficient pool of validated tumor antigens, product development strategy enabling to bring the product closer to the patient and clinical development strategy accounting for competitive landscape, treatment paradigm, technical and commercial risks. Regulatory framework existing around cancer vaccines in the EU, US, Japan and some developing countries is outlined. In addition, the review covers some specific issues on the design and conduct of clinical trials with cancer vaccines. PMID:22894970

Deep conservation of cis-regulatory elements in metazoans

PubMed Central

Maeso, Ignacio; Irimia, Manuel; Tena, Juan J.; Casares, Fernando; Gómez-Skarmeta, José Luis

2013-01-01

Despite the vast morphological variation observed across phyla, animals share multiple basic developmental processes orchestrated by a common ancestral gene toolkit. These genes interact with each other building complex gene regulatory networks (GRNs), which are encoded in the genome by cis-regulatory elements (CREs) that serve as computational units of the network. Although GRN subcircuits involved in ancient developmental processes are expected to be at least partially conserved, identification of CREs that are conserved across phyla has remained elusive. Here, we review recent studies that revealed such deeply conserved CREs do exist, discuss the difficulties associated with their identification and describe new approaches that will facilitate this search. PMID:24218633

Antimicrobials in animal agriculture: parables and policy.

PubMed

Scott, H M; Midgley, G; Loneragan, G H

2015-04-01

In addition to the scientific, economic, regulatory and other policy factors that impact on antimicrobial decision-making in different jurisdictions around the world, there exist ethical, social and cultural bases for the contemporary use of these products in animal agriculture. Thus, the use of the word 'parable' to describe the contemporary moral stories that help to guide ethical antimicrobial use practices and broader policy decisions in animal agriculture is appropriate. Several of these stories reflect difficult decisions that arise from conflicting moral imperatives (i.e. both towards animal welfare and towards human health). Understanding the factors that combine to define the past and present paradigms of antimicrobial usage is crucial to mapping a path forward. There exist barriers, as well as opportunities, for advancing scenarios for reducing antimicrobial usage under a variety of voluntary, regulatory and legal policy frameworks. Any new approaches will ideally be structured to extend the use of present-day antimicrobials into the future, to provide novel alternatives for regulating any newly introduced antimicrobial products so as to maximize their useful life span and to ensure the optimal use of these products in animal agriculture to protect not only the health of animals and the interests of animal health/agriculture stakeholders, but also the human health and the interests of the public at large. A full range of policy approaches, which span the realm from strictly enforced regulations and laws to voluntary guidelines and compliance, should be explored with respect to their risks and benefits in a variety of worldwide settings and in full consideration of a range of stakeholder values. © 2015 Blackwell Verlag GmbH.

[Structures and processes in outpatient neurorehabilitation].

PubMed

Pöppl, Dominik; Deck, R; Kringler, W; Reuther, P

2014-06-01

Quality of structures, processes and outcome are commonly accepted as dimensions of quality management and quality assurance. Data of structures and processes are not published to date for German outpatient neurorehabilitation. Rehabilitative care and service providers are legally bound to apply concepts of quality management and quality assurance. The service providers pass recommendations, which have to be implemented by outpatient neurorehabilitation centres. Data analysis of existing structures and processes in outpatient neurorehabilitation centres are embedded as a part of a long-term multicentres outcome study. 22 outpatient neurorehabilitation centres participated in an online survey with 227 items using the google tool "Docs" between September and December 2011. Following issues were asked: general information about the centres (e. g. date of establishment, number of therapy places, kind of patients, responsible organization), utility supply contracts with service providers, local cooperation and networking, staff and equipment and appliances, treatment concepts, processes of therapy (e. g. individual and group therapy, frequency, concentration, planning), team processes, goals and team development, quality management and documentation. In the meantime outpatient centres of neurorehabilitation are well-established as care providers and commonly accepted by service providers. However a comprehensive availability does not exist. The results show comparable structures of the centres, what is mostly determined by the service provider audited regulatory framework. Different concepts result in different processes. There are a lot of hints with respect to different concepts in form and content to implement the legally obligated mandate. In general their work with context -factors is still a frequently unused potential. It can be countered by the therapeutic inclusion of the social and environmental living conditions of the patients. © Georg Thieme Verlag KG Stuttgart · New York.

An additional substrate binding site in a bacterial phenylalanine hydroxylase

PubMed Central

Ronau, Judith A.; Paul, Lake N.; Fuchs, Julian E.; Corn, Isaac R.; Wagner, Kyle T.; Liedl, Klaus R.; Abu-Omar, Mahdi M.; Das, Chittaranjan

2014-01-01

Phenylalanine hydroxylase (PAH) is a non-heme iron enzyme that catalyzes phenylalanine oxidation to tyrosine, a reaction that must be kept under tight regulatory control. Mammalian PAH features a regulatory domain where binding of the substrate leads to allosteric activation of the enzyme. However, existence of PAH regulation in evolutionarily distant organisms, such as certain bacteria in which it occurs, has so far been underappreciated. In an attempt to crystallographically characterize substrate binding by PAH from Chromobacterium violaceum (cPAH), a single-domain monomeric enzyme, electron density for phenylalanine was observed at a distal site, 15.7Å from the active site. Isothermal titration calorimetry (ITC) experiments revealed a dissociation constant of 24 ± 1.1 µM for phenylalanine. Under the same conditions, no detectable binding was observed in ITC for alanine, tyrosine, or isoleucine, indicating the distal site may be selective for phenylalanine. Point mutations of residues in the distal site that contact phenylalanine (F258A, Y155A, T254A) lead to impaired binding, consistent with the presence of distal site binding in solution. Kinetic analysis reveals that the distal site mutants suffer a discernible loss in their catalytic activity. However, x-ray structures of Y155A and F258A, two of the mutants showing more noticeable defect in their activity, show no discernible change in their active site structure, suggesting that the effect of distal binding may transpire through protein dynamics in solution. PMID:23860686

Patient safety issues in office-based surgery and anaesthesia in Switzerland: a qualitative study.

PubMed

McLennan, Stuart; Schwappach, David; Harder, Yves; Staender, Sven; Elger, Bernice

2017-08-01

To identify the spectrum of patient safety issues in office-based surgery and anaesthesia in Switzerland. Purposive sample of 23 experts in surgery and anaesthesia and quality and regulation in Switzerland. Data were collected via individual qualitative interviews using a researcher-developed semi-structured interview guide between March 2016 and September 2016. Interviews were transcribed and analysed using conventional content analysis. Issues were categorised under the headings "structure", "process", and "outcome". Experts identified two key overarching patient safety and regulatory issues in relation to office-based surgery and anaesthesia in Switzerland. First, experts repeatedly raised the current lack of data and transparency of the setting. It is unknown how many surgeons are operating in offices, how many and what types of operations are being done, and what the outcomes are. Secondly, experts also noted the limited oversight and regulation of the setting. While some standards exists, most experts felt that more minimal safety standards are needed regarding the requirements that must be met to do office-based surgery and what can and cannot be done in the office-based setting are needed, but they advocated a self-regulatory approach. There is a lack of empirical data regarding the quantity and quality office-based surgery and anaesthesia in Switzerland. Further research is needed to address these research gaps and inform health policy in relation to patient safety in office-based surgery and anaesthesia in Switzerland. Copyright © 2017. Published by Elsevier GmbH.

Establishing a Quality Control System for Stem Cell-Based Medicinal Products in China

PubMed Central

2015-01-01

Stem cell-based medicinal products (SCMPs) are emerging as novel therapeutic products. The success of its development depends on the existence of an effective quality control system, which is constituted by quality control technologies, standards, reference materials, guidelines, and the associated management system in accordance with regulatory requirements along product lifespan. However, a worldwide, effective quality control system specific for SCMPs is still far from established partially due to the limited understanding of stem cell sciences and lack of quality control technologies for accurately assessing the safety and biological effectiveness of SCMPs before clinical use. Even though, based on the existing regulations and current stem cell sciences and technologies, initial actions toward the goal of establishing such a system have been taken as exemplified by recent development of new “interim guidelines” for governing quality control along development of SCMPs and new development of the associated quality control technologies in China. In this review, we first briefly introduced the major institutions involved in the regulation of cell substrates and therapeutic cell products in China and the existing regulatory documents and technical guidelines used as critical references for developing the new interim guidelines. With focus only on nonhematopoietic stem cells, we then discussed the principal quality attributes of SCMPs as well as our thinking of proper testing approaches to be established with relevant evaluation technologies to ensure all quality requirements of SCMPs along different manufacturing processes and development stages. At the end, some regulatory and technical challenges were also discussed with the conclusion that combined efforts should be taken to promote stem cell regulatory sciences to establish the effective quality control system for SCMPs. PMID:25471126

Legacies of Lead in Charm City’s Soil: Lessons from the Baltimore Ecosystem Study

PubMed Central

Schwarz, Kirsten; Pouyat, Richard V.; Yesilonis, Ian

2016-01-01

Understanding the spatial distribution of soil lead has been a focus of the Baltimore Ecosystem Study since its inception in 1997. Through multiple research projects that span spatial scales and use different methodologies, three overarching patterns have been identified: (1) soil lead concentrations often exceed state and federal regulatory limits; (2) the variability of soil lead concentrations is high; and (3) despite multiple sources and the highly heterogeneous and patchy nature of soil lead, discernable patterns do exist. Specifically, housing age, the distance to built structures, and the distance to a major roadway are strong predictors of soil lead concentrations. Understanding what drives the spatial distribution of soil lead can inform the transition of underutilized urban space into gardens and other desirable land uses while protecting human health. A framework for management is proposed that considers three factors: (1) the level of contamination; (2) the desired land use; and (3) the community’s preference in implementing the desired land use. The goal of the framework is to promote dialogue and resultant policy changes that support consistent and clear regulatory guidelines for soil lead, without which urban communities will continue to be subject to the potential for lead exposure. PMID:26861371

A new metal binding domain involved in cadmium, cobalt and zinc transport

DOE PAGES

Smith, Aaron T.; Barupala, Dulmini; Stemmler, Timothy L.; ...

2015-07-20

The P 1B-ATPases, which couple cation transport across membranes to ATP hydrolysis, are central to metal homeostasis in all organisms. An important feature of P 1B-ATPases is the presence of soluble metal binding domains (MBDs) that regulate transport activity. Only one type of MBD has been characterized extensively, but bioinformatics analyses indicate that a diversity of MBDs may exist in nature. In this paper, we report the biochemical, structural and functional characterization of a new MBD from the Cupriavidus metallidurans P 1B-4-ATPase CzcP (CzcP MBD). The CzcP MBD binds two Cd 2+, Co 2+ or Zn 2+ ions in distinctmore » and unique sites and adopts an unexpected fold consisting of two fused ferredoxin-like domains. Both in vitro and in vivo activity assays using full-length CzcP, truncated CzcP and several variants indicate a regulatory role for the MBD and distinct functions for the two metal binding sites. Finally, taken together, these findings elucidate a previously unknown MBD and suggest new regulatory mechanisms for metal transport by P 1B-ATPases.« less

Skin peptide tyrosine-tyrosine, a member of the pancreatic polypeptide family: isolation, structure, synthesis, and endocrine activity.

PubMed

Mor, A; Chartrel, N; Vaudry, H; Nicolas, P

1994-10-25

Pancreatic polypeptide, peptide tyrosine-tyrosine (PYY), and neuropeptide tyrosine (NPY), three members of a family of structurally related peptides, are mainly expressed in the endocrine pancreas, in endocrine cells of the gut, and in the brain, respectively. In the present study, we have isolated a peptide of the pancreatic polypeptide family from the skin of the South American arboreal frog Phyllomedusa bicolor. The primary structure of the peptide was established as Tyr-Pro-Pro-Lys-Pro-Glu-Ser-Pro-Gly-Glu10-Asp-Ala-Ser-Pro-Glu-Glu- Met-Asn- Lys-Tyr20-Leu-Thr-Ala-Leu-Arg-His-Tyr-Ile-Asn-Leu30-Val-Thr- Arg-Gln-Arg-Tyr-NH2 . This unusual peptide, named skin peptide tyrosine-tyrosine (SPYY), exhibits 94% similarity with PYY from the frog Rana ridibunda. A synthetic replicate of SPYY inhibits melanotropin release from perifused frog neurointermediate lobes in very much the same way as NPY. These results demonstrate the occurrence of a PYY-like peptide in frog skin. Our data also suggest the existence of a pituitary-skin regulatory loop in amphibians.

Skin peptide tyrosine-tyrosine, a member of the pancreatic polypeptide family: isolation, structure, synthesis, and endocrine activity.

PubMed Central

Mor, A; Chartrel, N; Vaudry, H; Nicolas, P

1994-01-01

Pancreatic polypeptide, peptide tyrosine-tyrosine (PYY), and neuropeptide tyrosine (NPY), three members of a family of structurally related peptides, are mainly expressed in the endocrine pancreas, in endocrine cells of the gut, and in the brain, respectively. In the present study, we have isolated a peptide of the pancreatic polypeptide family from the skin of the South American arboreal frog Phyllomedusa bicolor. The primary structure of the peptide was established as Tyr-Pro-Pro-Lys-Pro-Glu-Ser-Pro-Gly-Glu10-Asp-Ala-Ser-Pro-Glu-Glu- Met-Asn- Lys-Tyr20-Leu-Thr-Ala-Leu-Arg-His-Tyr-Ile-Asn-Leu30-Val-Thr- Arg-Gln-Arg-Tyr-NH2 . This unusual peptide, named skin peptide tyrosine-tyrosine (SPYY), exhibits 94% similarity with PYY from the frog Rana ridibunda. A synthetic replicate of SPYY inhibits melanotropin release from perifused frog neurointermediate lobes in very much the same way as NPY. These results demonstrate the occurrence of a PYY-like peptide in frog skin. Our data also suggest the existence of a pituitary-skin regulatory loop in amphibians. PMID:7937944

Conformational Ensembles of Calmodulin Revealed by Nonperturbing Site-Specific Vibrational Probe Groups.

PubMed

Kelly, Kristen L; Dalton, Shannon R; Wai, Rebecca B; Ramchandani, Kanika; Xu, Rosalind J; Linse, Sara; Londergan, Casey H

2018-03-22

Seven native residues on the regulatory protein calmodulin, including three key methionine residues, were replaced (one by one) by the vibrational probe amino acid cyanylated cysteine, which has a unique CN stretching vibration that reports on its local environment. Almost no perturbation was caused by this probe at any of the seven sites, as reported by CD spectra of calcium-bound and apo calmodulin and binding thermodynamics for the formation of a complex between calmodulin and a canonical target peptide from skeletal muscle myosin light chain kinase measured by isothermal titration. The surprising lack of perturbation suggests that this probe group could be applied directly in many protein-protein binding interfaces. The infrared absorption bands for the probe groups reported many dramatic changes in the probes' local environments as CaM went from apo- to calcium-saturated to target peptide-bound conditions, including large frequency shifts and a variety of line shapes from narrow (interpreted as a rigid and invariant local environment) to symmetric to broad and asymmetric (likely from multiple coexisting and dynamically exchanging structures). The fast intrinsic time scale of infrared spectroscopy means that the line shapes report directly on site-specific details of calmodulin's variable structural distribution. Though quantitative interpretation of the probe line shapes depends on a direct connection between simulated ensembles and experimental data that does not yet exist, formation of such a connection to data such as that reported here would provide a new way to evaluate conformational ensembles from data that directly contains the structural distribution. The calmodulin probe sites developed here will also be useful in evaluating the binding mode of calmodulin with many uncharacterized regulatory targets.

Structure of the 26S proteasome with ATP-γS bound provides insights into the mechanism of nucleotide-dependent substrate translocation

PubMed Central

Śledź, Paweł; Unverdorben, Pia; Beck, Florian; Pfeifer, Günter; Schweitzer, Andreas; Förster, Friedrich; Baumeister, Wolfgang

2013-01-01

The 26S proteasome is a 2.5-MDa, ATP-dependent multisubunit proteolytic complex that processively destroys proteins carrying a degradation signal. The proteasomal ATPase heterohexamer is a key module of the 19S regulatory particle; it unfolds substrates and translocates them into the 20S core particle where degradation takes place. We used cryoelectron microscopy single-particle analysis to obtain insights into the structural changes of 26S proteasome upon the binding and hydrolysis of ATP. The ATPase ring adopts at least two distinct helical staircase conformations dependent on the nucleotide state. The transition from the conformation observed in the presence of ATP to the predominant conformation in the presence of ATP-γS induces a sliding motion of the ATPase ring over the 20S core particle ring leading to an alignment of the translocation channels of the ATPase and the core particle gate, a conformational state likely to facilitate substrate translocation. Two types of intersubunit modules formed by the large ATPase domain of one ATPase subunit and the small ATPase domain of its neighbor exist. They resemble the contacts observed in the crystal structures of ClpX and proteasome-activating nucleotidase, respectively. The ClpX-like contacts are positioned consecutively and give rise to helical shape in the hexamer, whereas the proteasome-activating nucleotidase-like contact is required to close the ring. Conformational switching between these forms allows adopting different helical conformations in different nucleotide states. We postulate that ATP hydrolysis by the regulatory particle ATPase (Rpt) 5 subunit initiates a cascade of conformational changes, leading to pulling of the substrate, which is primarily executed by Rpt1, Rpt2, and Rpt6. PMID:23589842

Structural analysis of a 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with an N-terminal chorismate mutase-like regulatory domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Light, Samuel H.; Halavaty, Andrei S.; Minasov, George

2012-06-27

3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS) catalyzes the first step in the biosynthesis of a number of aromatic metabolites. Likely because this reaction is situated at a pivotal biosynthetic gateway, several DAHPS classes distinguished by distinct mechanisms of allosteric regulation have independently evolved. One class of DAHPSs contains a regulatory domain with sequence homology to chorismate mutase - an enzyme further downstream of DAHPS that catalyzes the first committed step in tyrosine/phenylalanine biosynthesis - and is inhibited by chorismate mutase substrate (chorismate) and product (prephenate). Described in this work, structures of the Listeria monocytogenes chorismate/prephenate regulated DAHPS in complex with Mn{sup 2+}more » and Mn{sup 2+} + phosphoenolpyruvate reveal an unusual quaternary architecture: DAHPS domains assemble as a tetramer, from either side of which chorismate mutase-like (CML) regulatory domains asymmetrically emerge to form a pair of dimers. This domain organization suggests that chorismate/prephenate binding promotes a stable interaction between the discrete regulatory and catalytic domains and supports a mechanism of allosteric inhibition similar to tyrosine/phenylalanine control of a related DAHPS class. We argue that the structural similarity of chorismate mutase enzyme and CML regulatory domain provides a unique opportunity for the design of a multitarget antibacterial.« less

Resolving the problem of compliance with the ever increasing and changing regulations

NASA Astrophysics Data System (ADS)

Leigh, Harley

1992-01-01

The most common problem identified at several U.S. Department of Energy (DOE) sites is regulatory compliance. Simply, the project viability depends on identifying regulatory requirements at the beginning of a specific project to avoid possible delays and cost overruns. The Radioisotope Power Systems Facility (RPSF) is using the Regulatory Compliance System (RCS) to deal with the problem that well over 1000 regulatory documents had to be reviewed for possible compliance requirements applicable to the facility. This overwhelming number of possible documents is not atypical of all DOE facilities thus far reviewed using the RCS system. The RCS was developed to provide control and tracking of all the regulatory and institutional requirements on a given project. WASTREN, Inc., developed the RCS through various DOE contracts and continues to enhance and update the system for existing and new contracts. The RCS provides the information to allow the technical expert to assimilate and manage accurate resource information, compile the necessary checklists, and document that the project or facility fulfills all of the appropriate regulatory requirements. The RCS provides on-line information, including status throughout the project life, thereby allowing more intelligent and proactive decision making. Also, consistency and traceability are provided for regulatory compliance documentation.

Application of USNRC NUREG/CR-6661 and draft DG-1108 to evolutionary and advanced reactor designs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang 'Apollo', Chen

2006-07-01

For the seismic design of evolutionary and advanced nuclear reactor power plants, there are definite financial advantages in the application of USNRC NUREG/CR-6661 and draft Regulatory Guide DG-1108. NUREG/CR-6661, 'Benchmark Program for the Evaluation of Methods to Analyze Non-Classically Damped Coupled Systems', was by Brookhaven National Laboratory (BNL) for the USNRC, and Draft Regulatory Guide DG-1108 is the proposed revision to the current Regulatory Guide (RG) 1.92, Revision 1, 'Combining Modal Responses and Spatial Components in Seismic Response Analysis'. The draft Regulatory Guide DG-1108 is available at http://members.cox.net/apolloconsulting, which also provides a link to the USNRC ADAMS site to searchmore » for NUREG/CR-6661 in text file or image file. The draft Regulatory Guide DG-1108 removes unnecessary conservatism in the modal combinations for closely spaced modes in seismic response spectrum analysis. Its application will be very helpful in coupled seismic analysis for structures and heavy equipment to reduce seismic responses and in piping system seismic design. In the NUREG/CR-6661 benchmark program, which investigated coupled seismic analysis of structures and equipment or piping systems with different damping values, three of the four participants applied the complex mode solution method to handle different damping values for structures, equipment, and piping systems. The fourth participant applied the classical normal mode method with equivalent weighted damping values to handle differences in structural, equipment, and piping system damping values. Coupled analysis will reduce the equipment responses when equipment, or piping system and structure are in or close to resonance. However, this reduction in responses occurs only if the realistic DG-1108 modal response combination method is applied, because closely spaced modes will be produced when structure and equipment or piping systems are in or close to resonance. Otherwise, the conservatism in the current Regulatory Guide 1.92, Revision 1, will overshadow the advantage of coupled analysis. All four participants applied the realistic modal combination method of DG-1108. Consequently, more realistic and reduced responses were obtained. (authors)« less

Chemical Manufacturing Sector (NAICS 325)

EPA Pesticide Factsheets

find EPA regulatory information for the chemical manufacturing sector, including NESHAPs, the SNAP program for ozone depleting substances,effluent guidelines, and new and existing chemicals testing requirements under TSCA.

Mapping cis-Regulatory Domains in the Human Genome UsingMulti-Species Conservation of Synteny

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahituv, Nadav; Prabhakar, Shyam; Poulin, Francis

2005-06-13

Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle is the large genomic space surrounding targeted genes in which such elements could potentially reside. In order to delineate gene regulatory boundaries we used whole-genome human-mouse-chicken (HMC) and human-mouse-frog (HMF) multiple alignments to compile conserved blocks of synteny (CBS), under the hypothesis that these blocks have been kept intact throughout evolution at least in part by the requirement of regulatory elements to stay linked to the genes that they regulate. A totalmore » of 2,116 and 1,942 CBS>200 kb were assembled for HMC and HMF respectively, encompassing 1.53 and 0.86 Gb of human sequence. To support the existence of complex long-range regulatory domains within these CBS we analyzed the prevalence and distribution of chromosomal aberrations leading to position effects (disruption of a genes regulatory environment), observing a clear bias not only for mapping onto CBS but also for longer CBS size. Our results provide a genome wide data set characterizing the regulatory domains of genes and the conserved regulatory elements within them.« less

Modeling disordered protein interactions from biophysical principles

PubMed Central

Christoffer, Charles; Terashi, Genki

2017-01-01

Disordered protein-protein interactions (PPIs), those involving a folded protein and an intrinsically disordered protein (IDP), are prevalent in the cell, including important signaling and regulatory pathways. IDPs do not adopt a single dominant structure in isolation but often become ordered upon binding. To aid understanding of the molecular mechanisms of disordered PPIs, it is crucial to obtain the tertiary structure of the PPIs. However, experimental methods have difficulty in solving disordered PPIs and existing protein-protein and protein-peptide docking methods are not able to model them. Here we present a novel computational method, IDP-LZerD, which models the conformation of a disordered PPI by considering the biophysical binding mechanism of an IDP to a structured protein, whereby a local segment of the IDP initiates the interaction and subsequently the remaining IDP regions explore and coalesce around the initial binding site. On a dataset of 22 disordered PPIs with IDPs up to 69 amino acids, successful predictions were made for 21 bound and 18 unbound receptors. The successful modeling provides additional support for biophysical principles. Moreover, the new technique significantly expands the capability of protein structure modeling and provides crucial insights into the molecular mechanisms of disordered PPIs. PMID:28394890

Personal responsibility or shared responsibility: What is the appropriate role of the law in obesity prevention?

PubMed

Brooks, Benjamin

2015-09-01

Sensitive to allegations of "nanny state" paternalism, Australian governments support the doctrine that combating obesity is a matter of personal responsibility. Policy-makers endorse the "holistic" approach to obesity prevention, with a view to managing both sides of the nutritional energy equation. This paradigm allows the food and drinks industry to deflect its contributory responsibility for the epidemic and to avoid more stringent regulatory intervention beyond existing self-regulatory and corporate social responsibility regimes. This article argues that the industry must bear shared responsibility for the extent of the obesity crisis, although it cannot bear sole responsibility It defends the public interest case for more invasive, government-led regulation, reframing the crisis as one of public not individual burdens. Mindful of the political risk associated with unfocused calls for regulatory intervention, it articulates a set of regulatory principles to ensure that the interests of consumers and industry are properly acknowledged prior to further regulatory intervention. Finally, the article clarifies the subject, object and content of possible regulatory initiatives, offering an evaluation of their efficacy, practicality and fairness.

All-atom four-body knowledge-based statistical potential to distinguish native tertiary RNA structures from nonnative folds.

PubMed

Masso, Majid

2018-09-14

Scientific breakthroughs in recent decades have uncovered the capability of RNA molecules to fulfill a wide array of structural, functional, and regulatory roles in living cells, leading to a concomitantly significant increase in both the number and diversity of experimentally determined RNA three-dimensional (3D) structures. Atomic coordinates from a representative training set of solved RNA structures, displaying low sequence and structure similarity, facilitate derivation of knowledge-based energy functions. Here we develop an all-atom four-body statistical potential and evaluate its capacity to distinguish native RNA 3D structures from nonnative folds based on calculated free energy scores. Atomic four-body nearest-neighbors are objectively identified by their occurrence as tetrahedral vertices in the Delaunay tessellations of RNA structures, and rates of atomic quadruplet interactions expected by chance are obtained from a multinomial reference distribution. Our four-body energy function, referred to as RAMP (ribonucleic acids multibody potential), is subsequently derived by applying the inverted Boltzmann principle to the frequency data, yielding an energy score for each type of atomic quadruplet interaction. Several well-known benchmark datasets reveal that RAMP is comparable with, and often outperforms, existing knowledge- and physics-based energy functions. To the best of our knowledge, this is the first study detailing an RNA tertiary structure-based multibody statistical potential and its comparative evaluation. Copyright © 2018 Elsevier Ltd. All rights reserved.

75 FR 36762 - Self-Regulatory Organizations; EDGA Exchange, Inc.; Notice of Filing of Proposed Rule Change, as...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-28

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Juvenile skeletogenesis in anciently diverged sea urchin clades.

PubMed

Gao, Feng; Thompson, Jeffrey R; Petsios, Elizabeth; Erkenbrack, Eric; Moats, Rex A; Bottjer, David J; Davidson, Eric H

2015-04-01

Mechanistic understanding of evolutionary divergence in animal body plans devolves from analysis of those developmental processes that, in forms descendant from a common ancestor, are responsible for their morphological differences. The last common ancestor of the two extant subclasses of sea urchins, i.e., euechinoids and cidaroids, existed well before the Permian/Triassic extinction (252 mya). Subsequent evolutionary divergence of these clades offers in principle a rare opportunity to solve the developmental regulatory events underlying a defined evolutionary divergence process. Thus (i) there is an excellent and fairly dense (if yet incompletely analyzed) fossil record; (ii) cladistically confined features of the skeletal structures of modern euechinoid and cidaroid sea urchins are preserved in fossils of ancestral forms; (iii) euechinoids and cidaroids are among current laboratory model systems in molecular developmental biology (here Strongylocentrotus purpuratus [Sp] and Eucidaris tribuloides [Et]); (iv) skeletogenic specification in sea urchins is uncommonly well understood at the causal level of interactions of regulatory genes with one another, and with known skeletogenic effector genes, providing a ready arsenal of available molecular tools. Here we focus on differences in test and perignathic girdle skeletal morphology that distinguish all modern euechinoid from all modern cidaroid sea urchins. We demonstrate distinct canonical test and girdle morphologies in juveniles of both species by use of SEM and X-ray microtomography. Among the sharply distinct morphological features of these clades are the internal skeletal structures of the perignathic girdle to which attach homologous muscles utilized for retraction and protraction of Aristotles׳ lantern and its teeth. We demonstrate that these structures develop de novo between one and four weeks after metamorphosis. In order to study the underlying developmental processes, a method of section whole mount in situ hybridization was adapted. This method displays current gene expression in the developing test and perignathic girdle skeletal elements of both Sp and Et juveniles. Active, specific expression of the sm37 biomineralization gene in these muscle attachment structures accompanies morphogenetic development of these clade-specific features in juveniles of both species. Skeletogenesis at these clade-specific muscle attachment structures displays molecular earmarks of the well understood embryonic skeletogenic GRN: thus the upstream regulatory gene alx1 and the gene encoding the vegfR signaling receptor are both expressed at the sites where they are formed. This work opens the way to analysis of the alternative spatial specification processes that were installed at the evolutionary divergence of the two extant subclasses of sea urchins. Copyright © 2015 Elsevier Inc. All rights reserved.

Legal and regulatory aspects of prescribing and marketing emergency contraception in Nigeria.

PubMed

Adekunle, A O; Babarinsa, I A; Akinyemi, Z; Okediran, A Y

2001-01-01

Emergency contraception remains so little used or understood and the lack of its awareness can be traced to a myriad of factors including legal and regulatory obstacles. The aim of this study was to determine the legal and regulatory aspects of dispensing or marketing a contraceptive method for reasons (especially emergency purposes) other than stated by the manufacturers. The existing drugs' and devices' regulatory systems in Nigeria, especially those governing family planning methods, were reviewed. A questionnaire was administered to 363 health workers, comprising of physicians, pharmacists, nurses and midwives, to determine the implications of dispensing some currently available oral contraceptives (OCs) for emergency purposes despite the fact that there is no explicit description of emergency use in the labelling of such drugs. In addition, in-depth interviews were conducted with regulatory bodies. It was observed that, with the exception of Postinor, the drug manufacturers' leaflets did not indicate that they could be used for emergency contraceptive purposes. Although 64.5% of the healthcare providers were aware that OCs and intrauterine contraceptive devices (IUCDs) can be used for emergency purposes, 42.1% actually prescribed or recommended them. Many health workers (62.3%) were unaware of any legal implication with regards to prescribing unregistered drugs in Nigeria. The existing guidelines stipulate that a manufacturer or marketer should 're-register' a product if a new indication or use not contained in the initial application was found later. To satisfy legal requirements, it does appear that the currently available OCs and IUCDs in Nigeria must be labelled and registered for emergency contraceptive purposes.

A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure.

PubMed

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.

Reverse engineering highlights potential principles of large gene regulatory network design and learning.

PubMed

Carré, Clément; Mas, André; Krouk, Gabriel

2017-01-01

Inferring transcriptional gene regulatory networks from transcriptomic datasets is a key challenge of systems biology, with potential impacts ranging from medicine to agronomy. There are several techniques used presently to experimentally assay transcription factors to target relationships, defining important information about real gene regulatory networks connections. These techniques include classical ChIP-seq, yeast one-hybrid, or more recently, DAP-seq or target technologies. These techniques are usually used to validate algorithm predictions. Here, we developed a reverse engineering approach based on mathematical and computer simulation to evaluate the impact that this prior knowledge on gene regulatory networks may have on training machine learning algorithms. First, we developed a gene regulatory networks-simulating engine called FRANK (Fast Randomizing Algorithm for Network Knowledge) that is able to simulate large gene regulatory networks (containing 10 4 genes) with characteristics of gene regulatory networks observed in vivo. FRANK also generates stable or oscillatory gene expression directly produced by the simulated gene regulatory networks. The development of FRANK leads to important general conclusions concerning the design of large and stable gene regulatory networks harboring scale free properties (built ex nihilo). In combination with supervised (accepting prior knowledge) support vector machine algorithm we (i) address biologically oriented questions concerning our capacity to accurately reconstruct gene regulatory networks and in particular we demonstrate that prior-knowledge structure is crucial for accurate learning, and (ii) draw conclusions to inform experimental design to performed learning able to solve gene regulatory networks in the future. By demonstrating that our predictions concerning the influence of the prior-knowledge structure on support vector machine learning capacity holds true on real data ( Escherichia coli K14 network reconstruction using network and transcriptomic data), we show that the formalism used to build FRANK can to some extent be a reasonable model for gene regulatory networks in real cells.

Genome-wide colonization of gene regulatory elements by G4 DNA motifs

PubMed Central

Du, Zhuo; Zhao, Yiqiang; Li, Ning

2009-01-01

G-quadruplex (or G4 DNA), a stable four-stranded structure found in guanine-rich regions, is implicated in the transcriptional regulation of genes involved in growth and development. Previous studies on the role of G4 DNA in gene regulation mostly focused on genomic regions proximal to transcription start sites (TSSs). To gain a more comprehensive understanding of the regulatory role of G4 DNA, we examined the landscape of potential G4 DNA (PG4Ms) motifs in the human genome and found that G4 motifs, not restricted to those found in the TSS-proximal regions, are bias toward gene-associated regions. Significantly, analyses of G4 motifs in seven types of well-known gene regulatory elements revealed a constitutive enrichment pattern and the clusters of G4 motifs tend to be colocalized with regulatory elements. Considering our analysis from a genome evolutionary perspective, we found evidence that the occurrence and accumulation of certain progenitors and canonical G4 DNA motifs within regulatory regions were progressively favored by natural selection. Our results suggest that G4 DNA motifs are ‘colonized’ in regulatory regions, supporting a likely genome-wide role of G4 DNA in gene regulation. We hypothesize that G4 DNA is a regulatory apparatus situated in regulatory elements, acting as a molecular switch that can modulate the role of the host functional regions, by transition in DNA structure. PMID:19759215

Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters

NASA Astrophysics Data System (ADS)

Nott, Timothy J.; Craggs, Timothy D.; Baldwin, Andrew J.

2016-06-01

Membraneless organelles are cellular compartments made from drops of liquid protein inside a cell. These compartments assemble via the phase separation of disordered regions of proteins in response to changes in the cellular environment and the cell cycle. Here we demonstrate that the solvent environment within the interior of these cellular bodies behaves more like an organic solvent than like water. One of the most-stable biological structures known, the DNA double helix, can be melted once inside the liquid droplet, and simultaneously structures formed from regulatory single-stranded nucleic acids are stabilized. Moreover, proteins are shown to have a wide range of absorption or exclusion from these bodies, and can act as importers for otherwise-excluded nucleic acids, which suggests the existence of a protein-mediated trafficking system. A common strategy in organic chemistry is to utilize different solvents to influence the behaviour of molecules and reactions. These results reveal that cells have also evolved this capability by exploiting the interiors of membraneless organelles.

Experimental and theoretical study of microalgal competition in laboratory and natural ecosystems

NASA Astrophysics Data System (ADS)

Pisman, T. I.; Somova, L. A.

An important aspect of studying mixed cultures of microalgae is the artificial ecosystems containing algal culture as a regeneration link and a source of vegetable substances. The peculiarities of studying the stability of microalgae mixed cultures in the laboratory and natural environment have been considered in the work. The role of factors most essentially affecting the species structure of phytoplankton community (temperature factor, light intensity, pH environments, elements of mineral nutrition, algal metabolites, predation and fluctuation of environmental conditions) has been displayed. As a result of experimental and theoretical modelling of the microalgae Chlorella vulgaris and Scenedesmus quadricauda competition under limitation on nitrogen, the impossibility of their co-existence has been revealed. Under these conditions Chl. vulgaris turned out to be less competitive than Sc. quadricauda. The influence of the ratio of biogenic elements concentration in the environment, which should be recognized as an independent regulatory factor limiting growth of populations in the community and, thus affecting its structure, has been analyzed.

Heterogeneous but “Standard” Coding Systems for Adverse Events: Issues in Achieving Interoperability between Apples and Oranges

PubMed Central

Richesson, Rachel L.; Fung, Kin Wah; Krischer, Jeffrey P.

2008-01-01

Monitoring adverse events (AEs) is an important part of clinical research and a crucial target for data standards. The representation of adverse events themselves requires the use of controlled vocabularies with thousands of needed clinical concepts. Several data standards for adverse events currently exist, each with a strong user base. The structure and features of these current adverse event data standards (including terminologies and classifications) are different, so comparisons and evaluations are not straightforward, nor are strategies for their harmonization. Three different data standards - the Medical Dictionary for Regulatory Activities (MedDRA) and the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) terminologies, and Common Terminology Criteria for Adverse Events (CTCAE) classification - are explored as candidate representations for AEs. This paper describes the structural features of each coding system, their content and relationship to the Unified Medical Language System (UMLS), and unsettled issues for future interoperability of these standards. PMID:18406213

Narcissism is associated with weakened frontostriatal connectivity: a DTI study.

PubMed

Chester, David S; Lynam, Donald R; Powell, David K; DeWall, C Nathan

2016-07-01

Narcissism is characterized by the search for affirmation and admiration from others. Might this motivation to find external sources of acclaim exist to compensate for neurostructural deficits that link the self with reward? Greater structural connectivity between brain areas that process self-relevant stimuli (i.e. the medial prefrontal cortex) and reward (i.e. the ventral striatum) is associated with fundamentally positive self-views. We predicted that narcissism would be associated with less integrity of this frontostriatal pathway. We used diffusion tensor imaging to assess the frontostriatal structural connectivity among 50 healthy undergraduates (32 females, 18 males) who also completed a measure of grandiose narcissism. White matter integrity in the frontostriatal pathway was negatively associated with narcissism. Our findings, while purely correlational, suggest that narcissism arises, in part, from a neural disconnect between the self and reward. The exhibitionism and immodesty of narcissists may then be a regulatory strategy to compensate for this neural deficit. © The Author (2015). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Pausing kinetics dominates strand-displacement polymerization by reverse transcriptase

PubMed Central

Malik, Omri; Khamis, Hadeel; Rudnizky, Sergei; Marx, Ailie

2017-01-01

Abstract Reverse transcriptase (RT) catalyzes the conversion of the viral RNA into an integration-competent double-stranded DNA, with a variety of enzymatic activities that include the ability to displace a non-template strand concomitantly with polymerization. Here, using high-resolution optical tweezers to follow the activity of the murine leukemia Virus RT, we show that strand-displacement polymerization is frequently interrupted. Abundant pauses are modulated by the strength of the DNA duplex ∼8 bp ahead, indicating the existence of uncharacterized RT/DNA interactions, and correspond to backtracking of the enzyme, whose recovery is also modulated by the duplex strength. Dissociation and reinitiation events, which induce long periods of inactivity and are likely the rate-limiting step in the synthesis of the genome in vivo, are modulated by the template structure and the viral nucleocapsid protein. Our results emphasize the potential regulatory role of conserved structural motifs, and may provide useful information for the development of potent and specific inhibitors. PMID:28973474

Effects of different regulatory methods on improvement of greenhouse saline soils, tomato quality, and yield.

PubMed

Maomao, Hou; Xiaohou, Shao; Yaming, Zhai

2014-01-01

To identify effective regulatory methods scheduling with the compromise between the soil desalination and the improvement of tomato quality and yield, a 3-year field experiment was conducted to evaluate and compare the effect of straw mulching and soil structure conditioner and water-retaining agent on greenhouse saline soils, tomato quality, and yield. A higher salt removing rate of 80.72% in plough layer with straw mulching was obtained based on the observation of salt mass fraction in 0 ~ 20 cm soil layer before and after the experiment. Salts were also found to move gradually to the deeper soil layer with time. Straw mulching enhanced the content of soil organic matter significantly and was conductive to reserve soil available N, P, and K, while available P and K in soils of plough layer with soil structure conditioner decreased obviously; thus a greater usage of P fertilizer and K fertilizer was needed when applying soil structure conditioner. Considering the evaluation indexes including tomato quality, yield, and desalination effects of different regulatory methods, straw mulching was recommended as the main regulatory method to improve greenhouse saline soils in south China. Soil structure conditioner was the suboptimal method, which could be applied in concert with straw mulching.

[Mechanisms of endogenous drug resistance acquisition by spontaneous chromosomal gene mutation].

PubMed

Fukuda, H; Hiramatsu, K

1997-05-01

Endogenous resistance in bacteria is caused by a change or loss of function and generally genetically recessive. However, this type of resistance acquisition are now prevalent in clinical setting. Chromosomal genes that afford endogenous resistance are the genes correlated with the target of the drug, the drug inactivating enzymes, and permeability of the molecules including the antibacterial agents. Endogenous alteration of the drug target are mediated by the spontaneous mutation of their structural gene. This mutation provides much lower affinity of the drugs for the target. Gene expression of the inactivating enzymes, such as class C beta-lactamase, is generally regulated by regulatory genes. Spontaneous mutations in the regulatory genes cause constitutive enzyme production and provides the resistant to the agent which is usually stable for such enzymes. Spontaneous mutation in the structural gene gives the enzyme extra-spectrum substrate specificity, like ESBL (Extra-Spectrum-beta-Lactamase). Expression of structural genes encoding the permeability systems are also regulated by some regulatory genes. The spontaneous mutation of the regulatory genes reduce an amount of porin protein. This mutation causes much lower influx of the drug in the cell. Spontaneous mutation in promoter region of the structural gene of efflux protein was observed. This mutation raised the gene transcription and overproduced efflux protein. This protein progresses the drug efflux from the cell.

Regulatory experience in applying a radiological environmental protection framework for existing and planned nuclear facilities.

PubMed

Mihok, S; Thompson, P

2012-01-01

Frameworks and methods for the radiological protection of non-human biota have been evolving rapidly at the International Commission on Radiological Protection and through various European initiatives. The International Atomic Energy Agency has incorporated a requirement for environmental protection in the latest revision of its Basic Safety Standards. In Canada, the Canadian Nuclear Safety Commission has been legally obligated to prevent unreasonable risk to the environment since 2000. Licensees have therefore been meeting generic legal requirements to demonstrate adequate control of releases of radioactive substances for the protection of both people and biota for many years. In the USA, in addition to the generic requirements of the Environmental Protection Agency and the Nuclear Regulatory Commission, Department of Energy facilities have also had to comply with specific dose limits after a standard assessment methodology was finalised in 2002. Canadian regulators developed a similar framework for biota dose assessment through a regulatory assessment under the Canadian Environmental Protection Act in the late 1990s. Since then, this framework has been applied extensively to satisfy legal requirements under the Canadian Environmental Assessment Act and the Nuclear Safety and Control Act. After approximately a decade of experience in applying these methods, it is clear that simple methods are fit for purpose, and can be used for making regulatory decisions for existing and planned nuclear facilities. Copyright © 2012. Published by Elsevier Ltd.

Patient Experience Data in US Food and Drug Administration (FDA) Regulatory Decision Making:: A Policy Process Perspective.

PubMed

Kuehn, Carrie M

2018-01-01

The influence of patient advocates on FDA regulatory decision making has increased. Despite enhanced engagement with FDA, there remain challenges to achieving the regulatory goals of patients within FDA's regulatory framework. Gaps exist between patient advocates' knowledge of the agency's processes and FDA's need for rigorous, clinically meaningful patient experience data. This study examined the policy process in which patient experience data are collected by patient advocates and provided to FDA for regulatory decision making. Semistructured, narrative interviews were conducted with 14 professionals working in patient advocacy or at FDA. The purpose was to examine, in depth, participants' perceptions and experiences regarding this new regulatory process. Interviews were coded and examined for themes. The use of patient experience data by FDA is an evolving regulatory process. Participants identified a number of barriers and contributors to regulatory success. Well-organized and sophisticated patient advocacy groups with access to scientific and policy expertise are more likely to find success meeting FDA's patient experience data requirements. A conceptual model of this regulatory process was developed. Use of patient experience data by FDA has the potential to positively influence the regulation of medical products in the United States. Success within this new regulatory process will depend on clear guidance from FDA regarding the collection, analysis, and use of patient experience data. Patient advocacy groups must enhance internal capacity and expertise while engaging in substantive collaborations with FDA and other stakeholders in order to meaningfully contribute to the regulatory review of new therapeutics.

Electron cryo-microscopy structure of Ebola nucleoprotein reveals a mechanism for nucleocapsid-like assembly

PubMed Central

Su, Zhaoming; Wu, Chao; Shi, Liuqing; Luthra, Priya; Pintilie, Grigore D.; Johnson, Britney; Porter, Justin R.; Ge, Peng; Chen, Muyuan; Liu, Gai; Frederick, Thomas E.; Binning, Jennifer M.; Bowman, Gregory R.; Zhou, Z. Hong; Basler, Christopher F.; Gross, Michael L.; Leung, Daisy W.

2018-01-01

Summary Ebola virus nucleoprotein (eNP) assembles into higher-ordered structures that form the viral nucleocapsid (NC) and serve as the scaffold for viral RNA synthesis. However, molecular insights into the NC assembly process are lacking. Using a hybrid approach, we characterized the NC-like assembly of eNP, identified novel regulatory elements, and described how these elements impact function. We generated a three-dimensional structure of the eNP NC-like assembly at 5.8 Å using electron cryo-microscopy and identified a new regulatory role for eNP helices α22–α23. Biochemical, biophysical, and mutational analysis revealed inter-eNP contacts within α22–α23 are critical for viral NC-assembly and regulate viral RNA synthesis. These observations suggest that the N-terminus and α22–α23 of eNP function as context dependent regulatory modules (CDRMs). Our current study provides a framework for a structural mechanism for NC-like assembly and a new therapeutic target. PMID:29474922

Lessons on RNA Silencing Mechanisms in Plants from Eukaryotic Argonaute Structures[W

PubMed Central

Poulsen, Christian; Vaucheret, Hervé; Brodersen, Peter

2013-01-01

RNA silencing refers to a collection of gene regulatory mechanisms that use small RNAs for sequence specific repression. These mechanisms rely on ARGONAUTE (AGO) proteins that directly bind small RNAs and thereby constitute the central component of the RNA-induced silencing complex (RISC). AGO protein function has been probed extensively by mutational analyses, particularly in plants where large allelic series of several AGO proteins have been isolated. Structures of entire human and yeast AGO proteins have only very recently been obtained, and they allow more precise analyses of functional consequences of mutations obtained by forward genetics. To a large extent, these analyses support current models of regions of particular functional importance of AGO proteins. Interestingly, they also identify previously unrecognized parts of AGO proteins with profound structural and functional importance and provide the first hints at structural elements that have important functions specific to individual AGO family members. A particularly important outcome of the analysis concerns the evidence for existence of Gly-Trp (GW) repeat interactors of AGO proteins acting in the plant microRNA pathway. The parallel analysis of AGO structures and plant AGO mutations also suggests that such interactions with GW proteins may be a determinant of whether an endonucleolytically competent RISC is formed. PMID:23303917

Revisiting the mechanism of coagulation factor XIII activation and regulation from a structure/functional perspective

PubMed Central

Gupta, Sneha; Biswas, Arijit; Akhter, Mohammad Suhail; Krettler, Christoph; Reinhart, Christoph; Dodt, Johannes; Reuter, Andreas; Philippou, Helen; Ivaskevicius, Vytautas; Oldenburg, Johannes

2016-01-01

The activation and regulation of coagulation Factor XIII (FXIII) protein has been the subject of active research for the past three decades. Although discrete evidence exists on various aspects of FXIII activation and regulation a combinatorial structure/functional view in this regard is lacking. In this study, we present results of a structure/function study of the functional chain of events for FXIII. Our study shows how subtle chronological submolecular changes within calcium binding sites can bring about the detailed transformation of the zymogenic FXIII to its activated form especially in the context of FXIIIA and FXIIIB subunit interactions. We demonstrate what aspects of FXIII are important for the stabilization (first calcium binding site) of its zymogenic form and the possible modes of deactivation (thrombin mediated secondary cleavage) of the activated form. Our study for the first time provides a structural outlook of the FXIIIA2B2 heterotetramer assembly, its association and dissociation. The FXIIIB subunits regulatory role in the overall process has also been elaborated upon. In summary, this study provides detailed structural insight into the mechanisms of FXIII activation and regulation that can be used as a template for the development of future highly specific therapeutic inhibitors targeting FXIII in pathological conditions like thrombosis. PMID:27453290

Lessons on RNA silencing mechanisms in plants from eukaryotic argonaute structures.

PubMed

Poulsen, Christian; Vaucheret, Hervé; Brodersen, Peter

2013-01-01

RNA silencing refers to a collection of gene regulatory mechanisms that use small RNAs for sequence specific repression. These mechanisms rely on ARGONAUTE (AGO) proteins that directly bind small RNAs and thereby constitute the central component of the RNA-induced silencing complex (RISC). AGO protein function has been probed extensively by mutational analyses, particularly in plants where large allelic series of several AGO proteins have been isolated. Structures of entire human and yeast AGO proteins have only very recently been obtained, and they allow more precise analyses of functional consequences of mutations obtained by forward genetics. To a large extent, these analyses support current models of regions of particular functional importance of AGO proteins. Interestingly, they also identify previously unrecognized parts of AGO proteins with profound structural and functional importance and provide the first hints at structural elements that have important functions specific to individual AGO family members. A particularly important outcome of the analysis concerns the evidence for existence of Gly-Trp (GW) repeat interactors of AGO proteins acting in the plant microRNA pathway. The parallel analysis of AGO structures and plant AGO mutations also suggests that such interactions with GW proteins may be a determinant of whether an endonucleolytically competent RISC is formed.

The commercial development of space: is an international regulatory framework needed?

PubMed

Contant, Corinne M; Logsdon, John M

2004-04-01

The commercial space sector to date has failed to develop comprehensive regulations--"rules of the road"--for its international activities. Within the next 5 years, conflicts with respect to international trade in satellite sales and launch services could emerge, highlighting the need for such a regulatory framework. If the commercial space sector is to continue to develop, it is important to begin discussions now, before these conflicts become significant, on the elements of an appropriate international regulatory framework. The existing framework for space activities was developed when government, not commercial, space activities were dominant, or was adapted from regulations in other sectors such as terrestrial telecommunications. c2003 Elsevier Ltd. All rights reserved.

U.S. Nuclear Regulatory Commission natural analogue research program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kovach, L.A.; Ott, W.R.

1995-09-01

This article describes the natural analogue research program of the U.S. Nuclear Regulatory Commission (US NRC). It contains information on the regulatory context and organizational structure of the high-level radioactive waste research program plan. It also includes information on the conditions and processes constraining selection of natural analogues, describes initiatives of the US NRC, and describes the role of analogues in the licensing process.

Immunoresponses to Neisseria meningitidis epitopes: suppression of secondary response to phosphorylcholine is carrier specific.

PubMed Central

Faro, J; Seoane, R; Eiras, A; Lareo, I; Couceiro, J; Regueiro, B J

1986-01-01

Results of our previous work have shown that Neisseria meningitidis serogroup B M986 can induce a phosphorylcholine (PC)-specific plaque-forming cell immunoresponse in mice. Also, a single injection of a relatively low dose of meningococci in NBF1 female mice induced a priming time-dependent suppression on subsequent meningococcus challenge. This suppression was not due to switching to another class of immunoglobulin nor to the presence of a capsule on N. meningitidis. In this study we show that suppression induced by meningococcus is carrier specific. Furthermore, we offer evidence suggesting that the structure(s) on meningococcus that trigger this suppression is heat labile and different from the antigenic structure(s) recognized by the suppressed B cells. In addition, we found that there is a gradual increase in antibody secretion rates of N. meningitidis-induced anti-PC plaque-forming cells that correlates with N. meningitidis priming time. Rather unexpected was the fact that pretreatment of mice with PC-keyhole limpet hemocyanin (thymus-dependent antigen) had a great influence on the subsequent PC-specific immunoresponses induced by N. meningitidis and PC-coupled heat-inactivated meningococcus [PC-(NMB)HI], as shown by (i) a striking decrease in T15 idiotype expression, (ii) concomitant direct anti-PC plaque-forming cells reduction, (iii) switching to immunoglobulin G (N. meningitidis-induced immunoresponse) or immunoglobulin G plus immunoglobulin A [PC-(NMB)HI-induced immunoresponse], and (iv) a significant increase in heterogeneity of plaque-forming cell secretion rates. The possibility that N. meningitidis, PC-(NMB)HI, and PC-KLH stimulate B lymphocytes pertaining to three different subpopulations embedded in distinct regulatory circuits is discussed, with emphasis on the interrelationships between T-dependent and T-independent lymphocyte compartments. We focus on the possibility of the existence of high-level regulatory circuits in which lymphocyte subpopulations or sets of lymphocyte subpopulations with different requirements of activation are connected. PMID:2416688

Crystal structures of RIalpha subunit of cyclic adenosine 5'-monophosphate (cAMP)-dependent protein kinase complexed with (Rp)-adenosine 3',5'-cyclic monophosphothioate and (Sp)-adenosine 3',5'-cyclic monophosphothioate, the phosphothioate analogues of cAMP.

PubMed

Wu, Jian; Jones, John M; Nguyen-Huu, Xuong; Ten Eyck, Lynn F; Taylor, Susan S

2004-06-01

Cyclic adenosine 5'-monophosphate (cAMP) is an ancient signaling molecule, and in vertebrates, a primary target for cAMP is cAMP-dependent protein kinase (PKA). (R(p))-adenosine 3',5'-cyclic monophosphothioate ((R(p))-cAMPS) and its analogues are the only known competitive inhibitors and antagonists for cAMP activation of PKA, while (S(p))-adenosine 3',5'-cyclic monophosphothioate ((S(p))-cAMPS) functions as an agonist. The crystal structures of a Delta(1-91) deletion mutant of the RIalpha regulatory subunit of PKA bound to (R(p))-cAMPS and (S(p))-cAMPS were determined at 2.4 and 2.3 A resolution, respectively. While the structures are similar to each other and to the crystal structure of RIalpha bound to cAMP, differences in the dynamical properties of the protein when (R(p))-cAMPS is bound are apparent. The structures highlight the critical importance of the exocyclic oxygen's interaction with the invariant arginine in the phosphate binding cassette (PBC) and the importance of this interaction for the dynamical properties of the interactions that radiate out from the PBC. The conformations of the phosphate binding cassettes containing two invariant arginine residues (Arg209 on domain A, and Arg333 on domain B) are somewhat different due to the sulfur interacting with this arginine. Furthermore, the B-site ligand together with the entire domain B show significant differences in their overall dynamic properties in the crystal structure of Delta(1-91) RIalpha complexed with (R(p))-cAMPS phosphothioate analogue ((R(p))-RIalpha) compared to the cAMP- and (S(p))-cAMPS-bound type I and II regulatory subunits, based on the temperature factors. In all structures, two structural solvent molecules exist within the A-site ligand binding pocket; both mediate water-bridged interactions between the ligand and the protein. No structured waters are in the B-site pocket. Owing to the higher resolution data, the N-terminal segment (109-117) of the RIalpha subunit can also be traced. This strand forms an intermolecular antiparallel beta-sheet with the same strand in an adjacent molecule and implies that the RIalpha subunit can form a weak homodimer even in the absence of its dimerization domain.

Sociocognitive self-regulatory mechanisms governing transgressive behavior.

PubMed

Bandura, A; Caprara, G V; Barbaranelli, C; Pastorelli, C; Regalia, C

2001-01-01

This longitudinal research examined a structural model of the self-regulatory mechanisms governing transgressive conduct. Perceived academic and self-regulatory efficacy concurrently and longitudinally deterred transgressiveness both directly and by fostering prosocialness and adherence to moral self-sanctions for harmful conduct. The impact of perceived social self-efficacy was mediated through prosocialness. Moral disengagement and prosocialness affected transgressiveness through the mediating influence of irascible affectivity and hostile rumination. Ruminative affectivity, in turn, both concurrently and longitudinally affected transgressiveness. Moral disengagement also contributed independently to variance in transgressiveness over time. This pattern of relations was obtained after controlling for prior transgressiveness. The structural model was replicated across gender and provided a better fit to the data than did several alternative models.

Trichomes: different regulatory networks lead to convergent structures.

PubMed

Serna, Laura; Martin, Cathie

2006-06-01

Sometimes, proteins, biological structures or even organisms have similar functions and appearances but have evolved through widely divergent pathways. There is experimental evidence to suggest that different developmental pathways have converged to produce similar outgrowths of the aerial plant epidermis, referred to as trichomes. The emerging picture suggests that trichomes in Arabidopsis thaliana and, perhaps, in cotton develop through a transcriptional regulatory network that differs from those regulating trichome formation in Antirrhinum and Solanaceous species. Several lines of evidence suggest that the duplication of a gene controlling anthocyanin production and subsequent divergence might be the major force driving trichome formation in Arabidopsis, whereas the multicellular trichomes of Antirrhinum and Solanaceous species appear to have a different regulatory origin.

Computational modeling of RNA 3D structures, with the aid of experimental restraints

PubMed Central

Magnus, Marcin; Matelska, Dorota; Łach, Grzegorz; Chojnowski, Grzegorz; Boniecki, Michal J; Purta, Elzbieta; Dawson, Wayne; Dunin-Horkawicz, Stanislaw; Bujnicki, Janusz M

2014-01-01

In addition to mRNAs whose primary function is transmission of genetic information from DNA to proteins, numerous other classes of RNA molecules exist, which are involved in a variety of functions, such as catalyzing biochemical reactions or performing regulatory roles. In analogy to proteins, the function of RNAs depends on their structure and dynamics, which are largely determined by the ribonucleotide sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that simulate either the physical process of RNA structure formation (“Greek science” approach) or utilize information derived from known structures of other RNA molecules (“Babylonian science” approach). All computational methods suffer from various limitations that make them generally unreliable for structure prediction of long RNA sequences. However, in many cases, the limitations of computational and experimental methods can be overcome by combining these two complementary approaches with each other. In this work, we review computational approaches for RNA structure prediction, with emphasis on implementations (particular programs) that can utilize restraints derived from experimental analyses. We also list experimental approaches, whose results can be relatively easily used by computational methods. Finally, we describe case studies where computational and experimental analyses were successfully combined to determine RNA structures that would remain out of reach for each of these approaches applied separately. PMID:24785264

Function does not follow form in gene regulatory circuits.

PubMed

Payne, Joshua L; Wagner, Andreas

2015-08-20

Gene regulatory circuits are to the cell what arithmetic logic units are to the chip: fundamental components of information processing that map an input onto an output. Gene regulatory circuits come in many different forms, distinct structural configurations that determine who regulates whom. Studies that have focused on the gene expression patterns (functions) of circuits with a given structure (form) have examined just a few structures or gene expression patterns. Here, we use a computational model to exhaustively characterize the gene expression patterns of nearly 17 million three-gene circuits in order to systematically explore the relationship between circuit form and function. Three main conclusions emerge. First, function does not follow form. A circuit of any one structure can have between twelve and nearly thirty thousand distinct gene expression patterns. Second, and conversely, form does not follow function. Most gene expression patterns can be realized by more than one circuit structure. And third, multifunctionality severely constrains circuit form. The number of circuit structures able to drive multiple gene expression patterns decreases rapidly with the number of these patterns. These results indicate that it is generally not possible to infer circuit function from circuit form, or vice versa.

A global regulatory science agenda for vaccines.

PubMed

Elmgren, Lindsay; Li, Xuguang; Wilson, Carolyn; Ball, Robert; Wang, Junzhi; Cichutek, Klaus; Pfleiderer, Michael; Kato, Atsushi; Cavaleri, Marco; Southern, James; Jivapaisarnpong, Teeranart; Minor, Philip; Griffiths, Elwyn; Sohn, Yeowon; Wood, David

2013-04-18

The Decade of Vaccines Collaboration and development of the Global Vaccine Action Plan provides a catalyst and unique opportunity for regulators worldwide to develop and propose a global regulatory science agenda for vaccines. Regulatory oversight is critical to allow access to vaccines that are safe, effective, and of assured quality. Methods used by regulators need to constantly evolve so that scientific and technological advances are applied to address challenges such as new products and technologies, and also to provide an increased understanding of benefits and risks of existing products. Regulatory science builds on high-quality basic research, and encompasses at least two broad categories. First, there is laboratory-based regulatory science. Illustrative examples include development of correlates of immunity; or correlates of safety; or of improved product characterization and potency assays. Included in such science would be tools to standardize assays used for regulatory purposes. Second, there is science to develop regulatory processes. Illustrative examples include adaptive clinical trial designs; or tools to analyze the benefit-risk decision-making process of regulators; or novel pharmacovigilance methodologies. Included in such science would be initiatives to standardize regulatory processes (e.g., definitions of terms for adverse events [AEs] following immunization). The aim of a global regulatory science agenda is to transform current national efforts, mainly by well-resourced regulatory agencies, into a coordinated action plan to support global immunization goals. This article provides examples of how regulatory science has, in the past, contributed to improved access to vaccines, and identifies gaps that could be addressed through a global regulatory science agenda. The article also identifies challenges to implementing a regulatory science agenda and proposes strategies and actions to fill these gaps. A global regulatory science agenda will enable regulators, academics, and other stakeholders to converge around transformative actions for innovation in the regulatory process to support global immunization goals. Copyright © 2012 Elsevier Ltd. All rights reserved.

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The influence of government actions on innovative activities in the development of environmental technologies to control sulfur dioxide emissions from stationary sources

NASA Astrophysics Data System (ADS)

Taylor, Margaret R.

2001-12-01

A better understanding of the influence of government actions on innovation is needed to inform future policy endeavors in areas ranging from industrial competitiveness to environmentally sustainable growth. Environmental control technology is a rich area for the study of this influence, since government has stronger incentives to promote innovation in these technologies than does the private sector. This dissertation investigated the case of sulfur dioxide (SO2) control technologies for electric power plants. In studying innovation in these technologies, it was very important to understand the details of these technologies as well as their long organizational history. These technologies have been affected by government actions ranging from government-sponsored research and technology transfer mechanisms to national regulatory events. The dissertation integrated insights from several complementary and repeatable innovation evaluation methods; this approach supported a fuller understanding of innovation while it structured the research results for potential future comparative analysis. Innovative activities were investigated through: patent activity analysis; technical content analysis and researcher co-authorship network analysis in a conference held for over twenty years; learning curve analysis for eighty-eight U.S. power plants; and a dozen expert interviews from a variety of innovative actors. Innovative outcomes were investigated through: analysis of observed improvements in newly installed technologies over time; evaluation of historic cost studies on standardized systems; and expert interviews. Several policy-relevant findings resulted from this dissertation. (1) The existence of national government regulation stimulated inventive activity more than government research support alone. (2) The existence and the anticipation of government regulation appeared to spur inventive activity, while regulatory stringency appeared to drive inventive activity and the communication process underlying knowledge transfer and diffusion. (3) The regulatory-forced adoption of SO2 control technologies led to a learning curve effect in which operating experience with the equipment resulted in significant cost improvements. This learning curve effect is comparable with findings in many other industries and is likely to be useful in predictions of the costs of future environmental technologies. (4) Performance improvements and cost reductions occurred in a quantifiable fashion as the technology became more widely adopted.

Governance of nanotechnology and nanomaterials: principles, regulation, and renegotiating the social contract.

PubMed

Kimbrell, George A

2009-01-01

Good governance for nanotechnology and nanomaterials is predicated on principles of general good governance. This paper discusses on what lessons we can learn from the oversight of past emerging technologies in formulating these principles. Nanotechnology provides us a valuable opportunity to apply these lessons and a duty to avoid repeating past mistakes. To do that will require mandatory regulation, grounded in precaution, that takes into account the uniqueness of nanomaterials. Moreover, this policy dialogue is not taking place in a vacuum. In applying the lessons of the past, nanotechnology provides a window to renegotiate our public's social contract on chemicals, health, the environment, and risks. Emerging technologies illuminate structural weaknesses, providing a crucial chance to ameliorate lingering regulatory inadequacies and provide much needed updates of existing laws.

77 FR 3514 - Protection Against Turbine Missiles

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-24

... NUCLEAR REGULATORY COMMISSION [NRC-2009-0481] Protection Against Turbine Missiles AGENCY: Nuclear... (NRC or Commission) is issuing a revision to Regulatory Guide 1.115, ``Protection Against Turbine... structures, systems, and components against missiles resulting from turbine failure by the appropriate...

Enhancing gene regulatory network inference through data integration with markov random fields

DOE PAGES

Banf, Michael; Rhee, Seung Y.

2017-02-01

Here, a gene regulatory network links transcription factors to their target genes and represents a map of transcriptional regulation. Much progress has been made in deciphering gene regulatory networks computationally. However, gene regulatory network inference for most eukaryotic organisms remain challenging. To improve the accuracy of gene regulatory network inference and facilitate candidate selection for experimentation, we developed an algorithm called GRACE (Gene Regulatory network inference ACcuracy Enhancement). GRACE exploits biological a priori and heterogeneous data integration to generate high- confidence network predictions for eukaryotic organisms using Markov Random Fields in a semi-supervised fashion. GRACE uses a novel optimization schememore » to integrate regulatory evidence and biological relevance. It is particularly suited for model learning with sparse regulatory gold standard data. We show GRACE’s potential to produce high confidence regulatory networks compared to state of the art approaches using Drosophila melanogaster and Arabidopsis thaliana data. In an A. thaliana developmental gene regulatory network, GRACE recovers cell cycle related regulatory mechanisms and further hypothesizes several novel regulatory links, including a putative control mechanism of vascular structure formation due to modifications in cell proliferation.« less

Enhancing gene regulatory network inference through data integration with markov random fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Banf, Michael; Rhee, Seung Y.

Here, a gene regulatory network links transcription factors to their target genes and represents a map of transcriptional regulation. Much progress has been made in deciphering gene regulatory networks computationally. However, gene regulatory network inference for most eukaryotic organisms remain challenging. To improve the accuracy of gene regulatory network inference and facilitate candidate selection for experimentation, we developed an algorithm called GRACE (Gene Regulatory network inference ACcuracy Enhancement). GRACE exploits biological a priori and heterogeneous data integration to generate high- confidence network predictions for eukaryotic organisms using Markov Random Fields in a semi-supervised fashion. GRACE uses a novel optimization schememore » to integrate regulatory evidence and biological relevance. It is particularly suited for model learning with sparse regulatory gold standard data. We show GRACE’s potential to produce high confidence regulatory networks compared to state of the art approaches using Drosophila melanogaster and Arabidopsis thaliana data. In an A. thaliana developmental gene regulatory network, GRACE recovers cell cycle related regulatory mechanisms and further hypothesizes several novel regulatory links, including a putative control mechanism of vascular structure formation due to modifications in cell proliferation.« less

A Self-Regulatory Model of Behavioral Disinhibition in Late Adolescence: Integrating Personality Traits, Externalizing Psychopathology, and Cognitive Capacity

PubMed Central

Bogg, Tim; Finn, Peter R.

2011-01-01

Two samples with heterogeneous prevalence of externalizing psychopathology were used to investigate the structure of self-regulatory models of behavioral disinhibition and cognitive capacity. Consistent with expectations, structural equation modeling in the first sample (N = 541) showed a hierarchical model with three lower-order factors of impulsive sensation-seeking, anti-sociality/unconventionality, and lifetime externalizing problem counts, with a behavioral disinhibition superfactor best accounted for the pattern of covariation among six disinhibited personality trait indicators and four externalizing problem indicators. The structure was replicated in a second sample (N = 463) and showed that the behavioral disinhibition superfactor, and not the lower-order impulsive sensation-seeking, anti-sociality/unconventionality, and externalizing problem factors, was associated with lower IQ, reduced short-term memory capacity, and reduced working memory capacity. The results provide a systemic and meaningful integration of major self-regulatory influences during a developmentally important stage of life. PMID:20433626

Transposable elements and G-quadruplexes.

PubMed

Kejnovsky, Eduard; Tokan, Viktor; Lexa, Matej

2015-09-01

A significant part of eukaryotic genomes is formed by transposable elements (TEs) containing not only genes but also regulatory sequences. Some of the regulatory sequences located within TEs can form secondary structures like hairpins or three-stranded (triplex DNA) and four-stranded (quadruplex DNA) conformations. This review focuses on recent evidence showing that G-quadruplex-forming sequences in particular are often present in specific parts of TEs in plants and humans. We discuss the potential role of these structures in the TE life cycle as well as the impact of G-quadruplexes on replication, transcription, translation, chromatin status, and recombination. The aim of this review is to emphasize that TEs may serve as vehicles for the genomic spread of G-quadruplexes. These non-canonical DNA structures and their conformational switches may constitute another regulatory system that, together with small and long non-coding RNA molecules and proteins, contribute to the complex cellular network resulting in the large diversity of eukaryotes.

Automatic Design of Digital Synthetic Gene Circuits

PubMed Central

Marchisio, Mario A.; Stelling, Jörg

2011-01-01

De novo computational design of synthetic gene circuits that achieve well-defined target functions is a hard task. Existing, brute-force approaches run optimization algorithms on the structure and on the kinetic parameter values of the network. However, more direct rational methods for automatic circuit design are lacking. Focusing on digital synthetic gene circuits, we developed a methodology and a corresponding tool for in silico automatic design. For a given truth table that specifies a circuit's input–output relations, our algorithm generates and ranks several possible circuit schemes without the need for any optimization. Logic behavior is reproduced by the action of regulatory factors and chemicals on the promoters and on the ribosome binding sites of biological Boolean gates. Simulations of circuits with up to four inputs show a faithful and unequivocal truth table representation, even under parametric perturbations and stochastic noise. A comparison with already implemented circuits, in addition, reveals the potential for simpler designs with the same function. Therefore, we expect the method to help both in devising new circuits and in simplifying existing solutions. PMID:21399700

LINKING NUTRIENTS TO ALTERATIONS IN AQUATIC LIFE ...

EPA Pesticide Factsheets

This report estimates the natural background and ambient concentrations of primary producer abundance indicators in California wadeable streams, identifies thresholds of adverse effects of nutrient-stimulated primary producer abundance on benthic macroinvertebrate and algal community structure in CA wadeable streams, and evaluates existing nutrient-algal response models for CA wadeable streams (Tetra Tech 2006), with recommendations for improvements. This information will be included in an assessment of the science forming the basis of recommendations for stream nutrient criteria for the state of California. The objectives of the project are three-fold: 1. Estimate the natural background and ambient concentrations of nutrients and candidate indicators of primary producer abundance in California wadeable streams; 2. Explore relationships and identify thresholds of adverse effects of nutrient concentrations and primary producer abundance on indicators of aquatic life use in California wadeable streams; and 3. Evaluate the Benthic Biomass Spreadsheet Tool (BBST) for California wadeable streams using existing data sets, and recommend avenues for refinement. The intended outcome of this study is NOT final regulatory endpoints for nutrient and response indicators for California wadeable streams.

Development of Regulatory Documents for Creation (Upgrade) of Physical Protection Systems under the Russian/American MPC&A Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Izmaylov, Alexandr V.; Babkin, Vladimir; Kurov, Valeriy

2009-10-07

The development of new or the upgrade of existing physical protection systems (PPS) for nuclear facilities involves a multi-step and multidimensional process. The process consists of conceptual design, design, and commissioning stages. The activities associated with each of these stages are governed by Russian government and agency regulations. To ensure a uniform approach to development or upgrading of PPS at Russian nuclear facilities, the development of a range of regulatory and methodological documents is necessary. Some issues of PPS development are covered by the regulatory documents developed by Rosatom, as well as other Russian agencies with nuclear facilities under theirmore » control. This regulatory development has been accomplished as part of the U.S.-Russian MPC&A cooperation or independently by the Russian Federation. While regulatory coverage is extensive, there are a number of issues such as vulnerability analysis, effectiveness assessment, upgrading PPS, and protection of information systems for PPS that require additional regulations be developed. This paper reports on the status of regulatory coverage for PPS development or upgrade, and outlines a new approach to regulatory document development. It describes the evolutionary process of regulatory development through experience gained in the design, development and implementation of PPS as well as experience gained through the cooperative efforts of Russian and U.S. experts involved the development of MPC&A regulations.« less

Fifty years of the European medicines regulatory network: reflections for strengthening intra-regional cooperation in the Region of the Americas.

PubMed

Allchurch, Martin Harvey; Barbano, Dirceu Brás Aparecido; Pinheiro, Marie-Hélène; Lazdin-Helds, Janis

2016-05-01

This report considers how the experience of the European regulatory system might be applied to help strengthen the regulatory systems for medicines in the Region of the Americas. The work of the European Medicines Agencies (EMA) is carried out through its scientific committees, composed of members from European Economic Area countries. A robust legal framework allows EMA to coordinate resources from Member States' competent authorities, including, for example, assisting candidate countries as they prepare to join the European Union (EU). Capacity-building programs help countries adjust their regulatory systems ahead of full participation in the European medicines regulatory network. These programs facilitate adoption of common technical requirements, identify areas where action might be needed to ensure the smooth transposition of EU pharmaceutical law into national legislation, and prepare candidate countries for participation in EMA committees and the European regulatory network. The methodology of these programs could be of potential interest to the Pan American Health Organization (PAHO), the Regional Office of the World Health Organization for the Americas. Given resolutions adopted by the World Health Assembly and the PAHO Directing Council, there is a strong indication that the countries of the Region of the Americas wish to assemble a system that uses the existing regulatory capacity of some countries to strengthen local regulatory capacities in others.

Directed evolution of a synthetic phylogeny of programmable Trp repressors.

PubMed

Ellefson, Jared W; Ledbetter, Michael P; Ellington, Andrew D

2018-04-01

As synthetic regulatory programs expand in sophistication, an ever increasing number of biological components with predictable phenotypes is required. Regulators are often 'part mined' from a diverse, but uncharacterized, array of genomic sequences, often leading to idiosyncratic behavior. Here, we generate an entire synthetic phylogeny from the canonical allosteric transcription factor TrpR. Iterative rounds of positive and negative compartmentalized partnered replication (CPR) led to the exponential amplification of variants that responded with high affinity and specificity to halogenated tryptophan analogs and novel operator sites. Fourteen repressor variants were evolved with unique regulatory profiles across five operators and three ligands. The logic of individual repressors can be modularly programmed by creating heterodimeric fusions, resulting in single proteins that display logic functions, such as 'NAND'. Despite the evolutionarily limited regulatory role of TrpR, vast functional spaces exist around this highly conserved protein scaffold and can be harnessed to create synthetic regulatory programs.

Prediction of regulatory gene pairs using dynamic time warping and gene ontology.

PubMed

Yang, Andy C; Hsu, Hui-Huang; Lu, Ming-Da; Tseng, Vincent S; Shih, Timothy K

2014-01-01

Selecting informative genes is the most important task for data analysis on microarray gene expression data. In this work, we aim at identifying regulatory gene pairs from microarray gene expression data. However, microarray data often contain multiple missing expression values. Missing value imputation is thus needed before further processing for regulatory gene pairs becomes possible. We develop a novel approach to first impute missing values in microarray time series data by combining k-Nearest Neighbour (KNN), Dynamic Time Warping (DTW) and Gene Ontology (GO). After missing values are imputed, we then perform gene regulation prediction based on our proposed DTW-GO distance measurement of gene pairs. Experimental results show that our approach is more accurate when compared with existing missing value imputation methods on real microarray data sets. Furthermore, our approach can also discover more regulatory gene pairs that are known in the literature than other methods.

Regulatory T cells: present facts and future hopes.

PubMed

Becker, Christian; Stoll, Sabine; Bopp, Tobias; Schmitt, Edgar; Jonuleit, Helmut

2006-09-01

Naturally occurring CD4(+)CD25(+)Foxp3(+) regulatory T cells and several subsets of induced suppressor T cells are key players of the immune tolerance network and control the induction and effector phase of our immunological defense system. These T cell populations actively control the properties of other immune cells by suppressing their functional activity to prevent autoimmunity and transplant rejection but also influence the immune response to allergens as well as against tumor cells and pathogens. Even though we are far from completely understanding the molecular and cellular mechanisms that manage the different regulatory T cell populations, increasing evidence exists about their functional importance. The knowledge on their induction and activation opens the possibility for their selective manipulation in vivo as an attractive approach for an immunotherapy of unwanted immune responses. This review summarizes this knowledge and discusses the potential of regulatory T cells for novel immunointervention strategies in the future.

Expert Views on Regulatory Preparedness for Managing the Risks of Nanotechnologies

PubMed Central

Beaudrie, Christian E. H.; Satterfield, Terre; Kandlikar, Milind; Harthorn, Barbara H.

2013-01-01

The potential and promise of nanotechnologies depends in large part on the ability for regulatory systems to assess and manage their benefits and risks. However, considerable uncertainty persists regarding the health and environmental implications of nanomaterials, hence the capacity for existing regulations to meet this challenge has been widely questioned. Here we draw from a survey (N=254) of US-based nano-scientists and engineers, environmental health and safety scientists, and regulatory scientists and decision-makers, to ask whether nano experts regard regulatory agencies as prepared for managing nanomaterial risks. We find that all three expert groups view regulatory agencies as unprepared. The effect is strongest for regulators themselves, and less so for scientists conducting basic, applied, or health and safety work on nanomaterials. Those who see nanotechnology risks as novel, uncertain, and difficult to assess are particularly likely to see agencies as unprepared. Trust in regulatory agencies, views of stakeholder responsibility regarding the management of risks, and socio-political values were also found to be small but significant drivers of perceived agency preparedness. These results underscore the need for new tools and methods to enable the assessment of nanomaterial risks, and to renew confidence in regulatory agencies’ ability to oversee their growing use and application in society. PMID:24244662

Resolving the problem of compliance with the ever increasing and changing regulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leigh, H.

1991-06-01

The most common problem identified at several US Department of Energy (DOE) sites is regulatory compliance. Simply, the project viability depends on identifying regulatory requirements at the beginning of a specific project to avoid possible delays and cost overruns. The Radioisotope Power Systems Facility (RFSP) is using the Regulatory Compliance System (RCS) to deal with the problem that well over 1000 regulatory documents had to be reviewed for possible compliance requirements applicable to the facility. This overwhelming number of possible documents is not atypical of all DOE facilities thus far reviewed using the RCS system. The RCS was developed tomore » provide a control and tracking of all the regulatory and institutional requirements on a given project. WASTREN, Inc., developed the RCS through various DOE contracts and continues to enhance and update the system for existing and new contracts. The RCS provides the information to allow the technical expert to assimilate and manage accurate resource information, compile the checklists, and document that the project or facility fulfills all of the appropriate regulatory requirements. The RCS provides on-line information, including status throughput the project life, thereby allowing more intelligent and proactive decision making. Also, consistency and traceability are provided for regulatory compliance documentation. 1 ref., 1 fig.« less

GeneNetFinder2: Improved Inference of Dynamic Gene Regulatory Relations with Multiple Regulators.

PubMed

Han, Kyungsook; Lee, Jeonghoon

2016-01-01

A gene involved in complex regulatory interactions may have multiple regulators since gene expression in such interactions is often controlled by more than one gene. Another thing that makes gene regulatory interactions complicated is that regulatory interactions are not static, but change over time during the cell cycle. Most research so far has focused on identifying gene regulatory relations between individual genes in a particular stage of the cell cycle. In this study we developed a method for identifying dynamic gene regulations of several types from the time-series gene expression data. The method can find gene regulations with multiple regulators that work in combination or individually as well as those with single regulators. The method has been implemented as the second version of GeneNetFinder (hereafter called GeneNetFinder2) and tested on several gene expression datasets. Experimental results with gene expression data revealed the existence of genes that are not regulated by individual genes but rather by a combination of several genes. Such gene regulatory relations cannot be found by conventional methods. Our method finds such regulatory relations as well as those with multiple, independent regulators or single regulators, and represents gene regulatory relations as a dynamic network in which different gene regulatory relations are shown in different stages of the cell cycle. GeneNetFinder2 is available at http://bclab.inha.ac.kr/GeneNetFinder and will be useful for modeling dynamic gene regulations with multiple regulators.

Secondary structural entropy in RNA switch (Riboswitch) identification.

PubMed

Manzourolajdad, Amirhossein; Arnold, Jonathan

2015-04-28

RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA. Riboswitch-mediated mechanisms are ubiquitous across bacterial genomes. A typical class of riboswitch has its own unique structural and biological complexity, making de novo riboswitch identification a formidable task. Traditionally, riboswitches have been identified through comparative genomics based on sequence and structural homology. The limitations of structural-homology-based approaches, coupled with the assumption that there is a great diversity of undiscovered riboswitches, suggests the need for alternative methods for riboswitch identification, possibly based on features intrinsic to their structure. As of yet, no such reliable method has been proposed. We used structural entropy of riboswitch sequences as a measure of their secondary structural dynamics. Entropy values of a diverse set of riboswitches were compared to that of their mutants, their dinucleotide shuffles, and their reverse complement sequences under different stochastic context-free grammar folding models. Significance of our results was evaluated by comparison to other approaches, such as the base-pairing entropy and energy landscapes dynamics. Classifiers based on structural entropy optimized via sequence and structural features were devised as riboswitch identifiers and tested on Bacillus subtilis, Escherichia coli, and Synechococcus elongatus as an exploration of structural entropy based approaches. The unusually long untranslated region of the cotH in Bacillus subtilis, as well as upstream regions of certain genes, such as the sucC genes were associated with significant structural entropy values in genome-wide examinations. Various tests show that there is in fact a relationship between higher structural entropy and the potential for the RNA sequence to have alternative structures, within the limitations of our methodology. This relationship, though modest, is consistent across various tests. Understanding the behavior of structural entropy as a fairly new feature for RNA conformational dynamics, however, may require extensive exploratory investigation both across RNA sequences and folding models.

The locus of evolution: evo devo and the genetics of adaptation.

PubMed

Hoekstra, Hopi E; Coyne, Jerry A

2007-05-01

An important tenet of evolutionary developmental biology ("evo devo") is that adaptive mutations affecting morphology are more likely to occur in the cis-regulatory regions than in the protein-coding regions of genes. This argument rests on two claims: (1) the modular nature of cis-regulatory elements largely frees them from deleterious pleiotropic effects, and (2) a growing body of empirical evidence appears to support the predominant role of gene regulatory change in adaptation, especially morphological adaptation. Here we discuss and critique these assertions. We first show that there is no theoretical or empirical basis for the evo devo contention that adaptations involving morphology evolve by genetic mechanisms different from those involving physiology and other traits. In addition, some forms of protein evolution can avoid the negative consequences of pleiotropy, most notably via gene duplication. In light of evo devo claims, we then examine the substantial data on the genetic basis of adaptation from both genome-wide surveys and single-locus studies. Genomic studies lend little support to the cis-regulatory theory: many of these have detected adaptation in protein-coding regions, including transcription factors, whereas few have examined regulatory regions. Turning to single-locus studies, we note that the most widely cited examples of adaptive cis-regulatory mutations focus on trait loss rather than gain, and none have yet pinpointed an evolved regulatory site. In contrast, there are many studies that have both identified structural mutations and functionally verified their contribution to adaptation and speciation. Neither the theoretical arguments nor the data from nature, then, support the claim for a predominance of cis-regulatory mutations in evolution. Although this claim may be true, it is at best premature. Adaptation and speciation probably proceed through a combination of cis-regulatory and structural mutations, with a substantial contribution of the latter.

Current regulatory issues in cell and tissue therapy.

PubMed

Burger, S R

2003-01-01

Cell-based therapies have grown dramatically in power and scope in recent years. Once limited to blood and BM transplantation, these therapies now encompass tissue repair and regeneration, metabolic support, gene replacement, and immune effector functions, with established and investigational clinical applications in disorders affecting nearly every tissue and organ system. The complexity and novel applications of human cells, tissues, and cellular and tissue-based products (HCT/Ps), however, present potential risks for adverse events. The US Food and Drug Administration, responding to these concerns, has established a tiered, risk-based regulatory structure, in which more rigorous controls and safeguards are required for products thought to pose increased risk. The proposed good tissue practices (GTP) rule and existing good manufacturing practices (GMP) requirements form the principal elements of this regulatory framework. The proposed GTPs are intended to prevent HCT/P contamination with infectious disease agents, and to ensure that these cells and tissues maintain their integrity and function. GMPs focus on production of safe, pure, and potent products, and entail a higher level of process control and product characterization. All HCT/Ps will be required to comply with GTPs. HCT/Ps considered to present greater risks of adverse events, however, will be subject to both GTPs and GMPs, and must obtain premarket approval using the Investigational New Drug (IND) mechanism established for biologics. Although these requirements will present significant challenges for clinician- investigators and laboratories producing HCT/Ps, the regulations fundamentally support good clinical care by increasing safety and control, and enable good science by improving the quality and reliability of data.

Development of More Cost-Effective Methods for Long-Term Monitoring of Soil Vapor Intrusion to Indoor Air Using Quantitative Passive Diffusive-Adsorptive Sampling Techniques

DTIC Science & Technology

2015-05-01

challenging component of assessing human health risks associated with contaminated soil and groundwater since the late 1990s, during which time...and analysis. 1.3 REGULATORY DRIVERS Regulatory guidance for assessment and management of risks associated with VI has been issued by at least 27...requirements to assess potential human health risks , and this possibility exists where VOCs are present in the subsurface near occupied buildings

No Sunset and Extended Policies Cases (released in AEO2010)

EIA Publications

2010-01-01

The Annual Energy Outlook 2010 Reference case is best described as a current laws and regulations case, because it generally assumes that existing laws and fully promulgated regulations will remain unchanged throughout the projection period, unless the legislation establishing them specifically calls for them to end or change. The Reference case often serves as a starting point for the analysis of proposed legislative or regulatory changes, a task that would be difficult if the Reference case included projected legislative or regulatory changes.

Dietary Exposure Potential Model

EPA Science Inventory

Existing food consumption and contaminant residue databases, typically products of nutrition and regulatory monitoring, contain useful information to characterize dietary intake of environmental chemicals. A PC-based model with resident database system, termed the Die...

Lead and Copper Rule Revisions White Paper

EPA Pesticide Factsheets

The Lead and Copper Rule (LCR) Revisions White Paper provides examples of regulatory options to improve the existing rule. The paper highlights key challenges, opportunities, and analytical issues presented by these options.

77 FR 28518 - Reducing Regulatory Burden

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-15

... maintaining a consistent culture of retrospective review and analysis. DOE will continually engage in review... existing requirements. (10) Are there regulations that are working well that can be expanded or used as a...

Evolutionary toxicology: Meta-analysis of evolutionary events in response to chemical stressors.

PubMed

M Oziolor, Elias; De Schamphelaere, Karel; Matson, Cole W

2016-12-01

The regulatory decision-making process regarding chemical safety is most often informed by evidence based on ecotoxicity tests that consider growth, reproduction and survival as end-points, which can be quantitatively linked to short-term population outcomes. Changes in these end-points resulting from chemical exposure can cause alterations in micro-evolutionary forces (mutation, drift, selection and gene flow) that control the genetic composition of populations. With multi-generation exposures, anthropogenic contamination can lead to a population with an altered genetic composition, which may respond differently to future stressors. These evolutionary changes are rarely discussed in regulatory or risk assessment frameworks, but the growing body of literature that documents their existence suggests that these important population-level impacts should be considered. In this meta-analysis we have compared existing contamination levels of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) that have been documented to be associated with evolutionary changes in resident aquatic organisms to regulatory benchmarks for these contaminants. The original intent of this project was to perform a meta-analysis on evolutionary events associated with PCB and PAH contamination. However, this effort was hindered by a lack of consistency in congener selection for "total" PCB or PAH measurements. We expanded this manuscript to include a discussion of methods used to determine PCB and PAH total contamination in addition to comparing regulatory guidelines and contamination that has caused evolutionary effects. Micro-evolutionary responses often lead populations onto unique and unpredictable trajectories. Therefore, to better understand the risk of population-wide alterations occurring, we need to improve comparisons of chemical contamination between affected locations. In this manuscript we offer several possibilities to unify chemical comparisons for PCBs and PAHs that would improve comparability among evolutionary toxicology investigations, and with regulatory guidelines. In addition, we identify studies documenting evolutionary change in the presence of PCB and PAH contamination levels below applicable regulatory benchmarks.

Small RNA-mediated regulation in bacteria: A growing palette of diverse mechanisms.

PubMed

Dutta, Tanmay; Srivastava, Shubhangi

2018-05-20

Small RNAs (sRNAs) in bacteria have evolved with diverse mechanisms to balance their target gene expression in response to changes in the environment. Accumulating studies on bacterial regulatory processes firmly established that sRNAs modulate their target gene expression generally at the posttranscriptional level. Identification of large number of sRNAs by advanced technologies, like deep sequencing, tilling microarray, indicates the existence of a plethora of distinctive sRNA-mediated regulatory mechanisms in bacteria. Types of the novel mechanisms are increasing with the discovery of new sRNAs. Complementary base pairing between sRNAs and target RNAs assisted by RNA chaperones like Hfq and ProQ, in many occasions, to regulate the cognate gene expression is prevalent in sRNA mechanisms. sRNAs, in most studied cases, can directly base pair with target mRNA to remodel its expression. Base pairing can happen either in the untranslated regions or in the coding regions of mRNA to activate/repress its translation. sRNAs also act as target mimic to titrate away different regulatory RNAs from its target. Other mechanism includes the sequestration of regulatory proteins, especially transcription factors, by sRNAs. Numerous sRNAs, following analogous mechanism, are widespread in bacteria, and thus, has drawn immense attention for the development of RNA-based technologies. Nevertheless, typical sRNA mechanisms are also discovered to be confined in some bacteria. Analysis of the sRNA mechanisms unravels their existence in both the single step processes and the complex regulatory networks with a global effect on cell physiology. This review deals with the diverse array of mechanisms, which sRNAs follow to maintain bacterial lifestyle. Copyright © 2018 Elsevier B.V. All rights reserved.

Facing regulatory challenges of on-line hemodiafiltration.

PubMed

Kümmerle, Wolfgang

2011-01-01

On-line hemodiafiltration (on-line HDF) is the result of a vision that triggered multifarious changes in very different areas. Driven by the idea to offer better medical treatment for renal patients, technological innovations were developed and established that also constituted new challenges in the field of regulatory affairs. The existing regulations predominantly addressed the quality and safety of those products needed to perform dialysis treatment which were supplied by industrial manufacturers. However, the complexity of treatment system required for the provision of on-line fluids demanded a holistic approach encompassing all components involved. Hence, focus was placed not only on single products, but much more on their interfacing, and the clinical infrastructure, in particular, had to undergo substantial changes. The overall understanding of the interaction between such factors, quite different in their nature, was crucial to overcome the arising regulatory obstacles. This essay describes the evolution of the on-line HDF procedure from the regulatory point of view. A simplified diagram demonstrates the path taken from the former regulatory understanding to the realization of necessary changes. That achievement was only possible through 'management of preview' and consequent promotion of technical and medical innovations as well as regulatory re-evaluations. Copyright © 2011 S. Karger AG, Basel.

Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information

PubMed Central

2013-01-01

Background In recent years, various types of cellular networks have penetrated biology and are nowadays used omnipresently for studying eukaryote and prokaryote organisms. Still, the relation and the biological overlap among phenomenological and inferential gene networks, e.g., between the protein interaction network and the gene regulatory network inferred from large-scale transcriptomic data, is largely unexplored. Results We provide in this study an in-depth analysis of the structural, functional and chromosomal relationship between a protein-protein network, a transcriptional regulatory network and an inferred gene regulatory network, for S. cerevisiae and E. coli. Further, we study global and local aspects of these networks and their biological information overlap by comparing, e.g., the functional co-occurrence of Gene Ontology terms by exploiting the available interaction structure among the genes. Conclusions Although the individual networks represent different levels of cellular interactions with global structural and functional dissimilarities, we observe crucial functions of their network interfaces for the assembly of protein complexes, proteolysis, transcription, translation, metabolic and regulatory interactions. Overall, our results shed light on the integrability of these networks and their interfacing biological processes. PMID:23663484

A map of human microRNA variation uncovers unexpectedly high levels of variability

PubMed Central

2012-01-01

Background MicroRNAs (miRNAs) are key components of the gene regulatory network in many species. During the past few years, these regulatory elements have been shown to be involved in an increasing number and range of diseases. Consequently, the compilation of a comprehensive map of natural variability in a healthy population seems an obvious requirement for future research on miRNA-related pathologies. Methods Data on 14 populations from the 1000 Genomes Project were analyzed, along with new data extracted from 60 exomes of healthy individuals from a population from southern Spain, sequenced in the context of the Medical Genome Project, to derive an accurate map of miRNA variability. Results Despite the common belief that miRNAs are highly conserved elements, analysis of the sequences of the 1,152 individuals indicated that the observed level of variability is double what was expected. A total of 527 variants were found. Among these, 45 variants affected the recognition region of the corresponding miRNA and were found in 43 different miRNAs, 26 of which are known to be involved in 57 diseases. Different parts of the mature structure of the miRNA were affected to different degrees by variants, which suggests the existence of a selective pressure related to the relative functional impact of the change. Moreover, 41 variants showed a significant deviation from the Hardy-Weinberg equilibrium, which supports the existence of a selective process against some alleles. The average number of variants per individual in miRNAs was 28. Conclusions Despite an expectation that miRNAs would be highly conserved genomic elements, our study reports a level of variability comparable to that observed for coding genes. PMID:22906193

Mathematical modeling of the process of determining the standards for process losses in the transfer of thermal energy of the coolant

NASA Astrophysics Data System (ADS)

Akhmetova, I. G.; Chichirova, N. D.

2017-11-01

Currently the actual problem is a precise definition of the normative and actual heat loss. Existing methods - experimental, on metering devices, on the basis of mathematical modeling methods are not without drawbacks. Heat losses establishing during the heat carrier transport has an impact on the tariff structure of heat supply organizations. This quantity determination also promotes proper choice of main and auxiliary equipment power, temperature chart of heat supply networks, as well as the heating system structure choice with the decentralization. Calculation of actual heat loss and their comparison with standard values justifies the performance of works on improvement of the heat networks with the replacement of piping or its insulation. To determine the cause of discrepancies between normative and actual heat losses thermal tests on the magnitude of the actual heat losses in the 124 sections of heat networks in Kazan. As were carried out the result mathematical model of the regulatory definition of heat losses is developed and tested. This model differ from differs the existing according the piping insulation type. The application of this factor will bring the value of calculative normative losses heat energy to their actual value. It is of great importance for enterprises operating distribution networks and because of the conditions of their configuration and extensions do not have the technical ability to produce thermal testing.

Avian Antimicrobial Host Defense Peptides: From Biology to Therapeutic Applications

PubMed Central

Zhang, Guolong; Sunkara, Lakshmi T.

2014-01-01

Host defense peptides (HDPs) are an important first line of defense with antimicrobial and immunomoduatory properties. Because they act on the microbial membranes or host immune cells, HDPs pose a low risk of triggering microbial resistance and therefore, are being actively investigated as a novel class of antimicrobials and vaccine adjuvants. Cathelicidins and β-defensins are two major families of HDPs in avian species. More than a dozen HDPs exist in birds, with the genes in each HDP family clustered in a single chromosomal segment, apparently as a result of gene duplication and diversification. In contrast to their mammalian counterparts that adopt various spatial conformations, mature avian cathelicidins are mostly α-helical. Avian β-defensins, on the other hand, adopt triple-stranded β-sheet structures similar to their mammalian relatives. Besides classical β-defensins, a group of avian-specific β-defensin-related peptides, namely ovodefensins, exist with a different six-cysteine motif. Like their mammalian counterparts, avian cathelicidins and defensins are derived from either myeloid or epithelial origin expressed in a majority of tissues with broad-spectrum antibacterial and immune regulatory activities. Structure-function relationship studies with several avian HDPs have led to identification of the peptide analogs with potential for use as antimicrobials and vaccine adjuvants. Dietary modulation of endogenous HDP synthesis has also emerged as a promising alternative approach to disease control and prevention in chickens. PMID:24583933

76 FR 8940 - Regulatory Review of Existing DOT Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-16

... and determine whether they are crafted effectively to solve current problems. As part of this review... the perceived problem, though such comments are welcome. Lastly, we also want to stress that this...

Conventional Reduced Risk Pesticide Program

EPA Pesticide Factsheets

Find out about the Conventional Reduced Risk Pesticide Program, which expedites the review and regulatory decision-making process of conventional pesticides that pose less risk to human health and the environment than existing conventional alternatives.

Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation

PubMed Central

Xu, Jiajia; Bräutigam, Andrea; Weber, Andreas P. M.; Zhu, Xin-Guang

2016-01-01

Identification of potential cis-regulatory motifs controlling the development of C4 photosynthesis is a major focus of current research. In this study, we used time-series RNA-seq data collected from etiolated maize and rice leaf tissues sampled during a de-etiolation process to systematically characterize the expression patterns of C4-related genes and to further identify potential cis elements in five different genomic regions (i.e. promoter, 5′UTR, 3′UTR, intron, and coding sequence) of C4 orthologous genes. The results demonstrate that although most of the C4 genes show similar expression patterns, a number of them, including chloroplast dicarboxylate transporter 1, aspartate aminotransferase, and triose phosphate transporter, show shifted expression patterns compared with their C3 counterparts. A number of conserved short DNA motifs between maize C4 genes and their rice orthologous genes were identified not only in the promoter, 5′UTR, 3′UTR, and coding sequences, but also in the introns of core C4 genes. We also identified cis-regulatory motifs that exist in maize C4 genes and also in genes showing similar expression patterns as maize C4 genes but that do not exist in rice C3 orthologs, suggesting a possible recruitment of pre-existing cis-elements from genes unrelated to C4 photosynthesis into C4 photosynthesis genes during C4 evolution. PMID:27436282

Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila

DOE PAGES

Stoiber, Marcus H.; Olson, Sara; May, Gemma E.; ...

2015-08-20

In eukaryotic cells, RNAs exist as ribonucleoprotein particles (RNPs). Despite the importance of these complexes in many biological processes, including splicing, polyadenylation, stability, transportation, localization, and translation, their compositions are largely unknown. We affinity-purified 20 distinct RNA-binding proteins (RBPs) from cultured Drosophila melanogaster cells under native conditions and identified both the RNA and protein compositions of these RNP complexes. We identified “high occupancy target” (HOT) RNAs that interact with the majority of the RBPs we surveyed. HOT RNAs encode components of the nonsense-mediated decay and splicing machinery, as well as RNA-binding and translation initiation proteins. The RNP complexes contain proteinsmore » and mRNAs involved in RNA binding and post-transcriptional regulation. Genes with the capacity to produce hundreds of mRNA isoforms, ultracomplex genes, interact extensively with heterogeneous nuclear ribonuclear proteins (hnRNPs). Our data are consistent with a model in which subsets of RNPs include mRNA and protein products from the same gene, indicating the widespread existence of auto-regulatory RNPs. Lastly, from the simultaneous acquisition and integrative analysis of protein and RNA constituents of RNPs, we identify extensive cross-regulatory and hierarchical interactions in post-transcriptional control.« less

Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoiber, Marcus H.; Olson, Sara; May, Gemma E.

In eukaryotic cells, RNAs exist as ribonucleoprotein particles (RNPs). Despite the importance of these complexes in many biological processes, including splicing, polyadenylation, stability, transportation, localization, and translation, their compositions are largely unknown. We affinity-purified 20 distinct RNA-binding proteins (RBPs) from cultured Drosophila melanogaster cells under native conditions and identified both the RNA and protein compositions of these RNP complexes. We identified “high occupancy target” (HOT) RNAs that interact with the majority of the RBPs we surveyed. HOT RNAs encode components of the nonsense-mediated decay and splicing machinery, as well as RNA-binding and translation initiation proteins. The RNP complexes contain proteinsmore » and mRNAs involved in RNA binding and post-transcriptional regulation. Genes with the capacity to produce hundreds of mRNA isoforms, ultracomplex genes, interact extensively with heterogeneous nuclear ribonuclear proteins (hnRNPs). Our data are consistent with a model in which subsets of RNPs include mRNA and protein products from the same gene, indicating the widespread existence of auto-regulatory RNPs. Lastly, from the simultaneous acquisition and integrative analysis of protein and RNA constituents of RNPs, we identify extensive cross-regulatory and hierarchical interactions in post-transcriptional control.« less

Redesigning the regulatory framework for ambulatory care services in New York.

PubMed

Chokshi, Dave A; Rugge, John; Shah, Nirav R

2014-12-01

Policy Points: The landscape of ambulatory care services in the United States is rapidly changing on account of payment reform, primary care transformation, and the rise of convenient care options such as retail clinics. New York State has undertaken a redesign of regulatory policy for ambulatory care rooted in the Triple Aim (better health, higher-quality care, lower costs)-with a particular emphasis on continuity of care for patients. Key tenets of the regulatory approach include defining and tracking the taxonomy of ambulatory care services as well as ensuring that convenient care options do not erode continuity of care for patients. While hospitals remain important centers of gravity in the health system, services are increasingly being delivered through ambulatory care. This shift to ambulatory care is giving rise to new delivery structures, such as retail clinics and urgent care centers, as well as reinventing existing ambulatory care capacity, as seen with the patient-centered medical home model and the movement toward team-based care. To protect the public's interests, oversight of ambulatory care services must keep pace with these rapid changes. With this purpose, in January 2013 the New York Public Health and Health Planning Council undertook a redesign of the regulatory framework for the state's ambulatory care services. This article describes the principles undergirding the framework as well as the regulatory recommendations themselves. We explored and analyzed the regulation of ambulatory care services in New York in accordance with the available gray and peer-reviewed literature and legislative documents. The deliberations of the Public Health and Health Planning Council informed our review. The vision of high-performing ambulatory care should be rooted in the Triple Aim (better health, higher-quality care, lower costs), with a particular emphasis on continuity of care for patients. There is a pressing need to better define the taxonomy of ambulatory care services. From the state government's perspective, this clarification requires better reporting from new health care entities (eg, retail clinics), connections with regional and state health information technology hubs, and coordination among state agencies. A uniform nomenclature also would improve consumers' understanding of rights and responsibilities. Finally, the regulatory mechanisms employed-from mandatory reporting to licensure to regional planning to the certificate of need-should remain flexible and match the degree of consensus regarding the appropriate regulatory path. Few other states have embarked on a wide-ranging assessment of their regulation of ambulatory care services. By moving toward adopting the regulatory approach described here, New York aims to balance sound oversight with pluralism and innovation in health care delivery. © 2014 Milbank Memorial Fund.

78 FR 70380 - Self-Regulatory Organizations; NYSE MKT LLC; Notice of Filing and Immediate Effectiveness of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-25

... Revising Rule 61(a)(iii)--Equities To Harmonize the Existing Rule Text With the Recent Amendment to the CTA... the existing rule text with the recent amendment to the CTA Plan (and concordant change to the Nasdaq... text of the proposed rule change is available on the Exchange's Web site at www.nyse.com , at the...

Primate-specific evolution of an LDLR enhancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Qian-Fei; Prabhakar, Shyam; Wang, Qianben

2005-12-01

Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. In this study we identified an anthropoid primate-specific sequence element that contributed to the regulatory evolution of the low-density lipoprotein receptor. Using a combination of close and distant species genomic sequence comparisons coupled with in vivo and in vitro studies, we found that a functional cholesterol-sensing sequence motif arose and was fixed within a pre-existing enhancer in the common ancestor of anthropoid primates. Our study demonstrates one molecular mechanism by which ancestral mammalian regulatory elementsmore » can evolve to perform new functions in the primate lineage leading to human.« less

A Sparse Reconstruction Approach for Identifying Gene Regulatory Networks Using Steady-State Experiment Data

PubMed Central

Zhang, Wanhong; Zhou, Tong

2015-01-01

Motivation Identifying gene regulatory networks (GRNs) which consist of a large number of interacting units has become a problem of paramount importance in systems biology. Situations exist extensively in which causal interacting relationships among these units are required to be reconstructed from measured expression data and other a priori information. Though numerous classical methods have been developed to unravel the interactions of GRNs, these methods either have higher computing complexities or have lower estimation accuracies. Note that great similarities exist between identification of genes that directly regulate a specific gene and a sparse vector reconstruction, which often relates to the determination of the number, location and magnitude of nonzero entries of an unknown vector by solving an underdetermined system of linear equations y = Φx. Based on these similarities, we propose a novel framework of sparse reconstruction to identify the structure of a GRN, so as to increase accuracy of causal regulation estimations, as well as to reduce their computational complexity. Results In this paper, a sparse reconstruction framework is proposed on basis of steady-state experiment data to identify GRN structure. Different from traditional methods, this approach is adopted which is well suitable for a large-scale underdetermined problem in inferring a sparse vector. We investigate how to combine the noisy steady-state experiment data and a sparse reconstruction algorithm to identify causal relationships. Efficiency of this method is tested by an artificial linear network, a mitogen-activated protein kinase (MAPK) pathway network and the in silico networks of the DREAM challenges. The performance of the suggested approach is compared with two state-of-the-art algorithms, the widely adopted total least-squares (TLS) method and those available results on the DREAM project. Actual results show that, with a lower computational cost, the proposed method can significantly enhance estimation accuracy and greatly reduce false positive and negative errors. Furthermore, numerical calculations demonstrate that the proposed algorithm may have faster convergence speed and smaller fluctuation than other methods when either estimate error or estimate bias is considered. PMID:26207991

Differential T cell response against BK virus regulatory and structural antigens: A viral dynamics modelling approach.

PubMed

Blazquez-Navarro, Arturo; Schachtner, Thomas; Stervbo, Ulrik; Sefrin, Anett; Stein, Maik; Westhoff, Timm H; Reinke, Petra; Klipp, Edda; Babel, Nina; Neumann, Avidan U; Or-Guil, Michal

2018-05-01

BK virus (BKV) associated nephropathy affects 1-10% of kidney transplant recipients, leading to graft failure in about 50% of cases. Immune responses against different BKV antigens have been shown to have a prognostic value for disease development. Data currently suggest that the structural antigens and regulatory antigens of BKV might each trigger a different mode of action of the immune response. To study the influence of different modes of action of the cellular immune response on BKV clearance dynamics, we have analysed the kinetics of BKV plasma load and anti-BKV T cell response (Elispot) in six patients with BKV associated nephropathy using ODE modelling. The results show that only a small number of hypotheses on the mode of action are compatible with the empirical data. The hypothesis with the highest empirical support is that structural antigens trigger blocking of virus production from infected cells, whereas regulatory antigens trigger an acceleration of death of infected cells. These differential modes of action could be important for our understanding of BKV resolution, as according to the hypothesis, only regulatory antigens would trigger a fast and continuous clearance of the viral load. Other hypotheses showed a lower degree of empirical support, but could potentially explain the clearing mechanisms of individual patients. Our results highlight the heterogeneity of the dynamics, including the delay between immune response against structural versus regulatory antigens, and its relevance for BKV clearance. Our modelling approach is the first that studies the process of BKV clearance by bringing together viral and immune kinetics and can provide a framework for personalised hypotheses generation on the interrelations between cellular immunity and viral dynamics.

New Era of Studying RNA Secondary Structure and Its Influence on Gene Regulation in Plants.

PubMed

Yang, Xiaofei; Yang, Minglei; Deng, Hongjing; Ding, Yiliang

2018-01-01

The dynamic structure of RNA plays a central role in post-transcriptional regulation of gene expression such as RNA maturation, degradation, and translation. With the rise of next-generation sequencing, the study of RNA structure has been transformed from in vitro low-throughput RNA structure probing methods to in vivo high-throughput RNA structure profiling. The development of these methods enables incremental studies on the function of RNA structure to be performed, revealing new insights of novel regulatory mechanisms of RNA structure in plants. Genome-wide scale RNA structure profiling allows us to investigate general RNA structural features over 10s of 1000s of mRNAs and to compare RNA structuromes between plant species. Here, we provide a comprehensive and up-to-date overview of: (i) RNA structure probing methods; (ii) the biological functions of RNA structure; (iii) genome-wide RNA structural features corresponding to their regulatory mechanisms; and (iv) RNA structurome evolution in plants.

Molecular structure of EmbR, a response element of Ser/Thr kinase signaling in Mycobacterium tuberculosis

PubMed Central

Alderwick, Luke J.; Molle, Virginie; Kremer, Laurent; Cozzone, Alain J.; Dafforn, Timothy R.; Besra, Gurdyal S.; Fütterer, Klaus

2006-01-01

Ser/Thr phosphorylation has emerged as a critical regulatory mechanism in a number of bacteria, including Mycobacterium tuberculosis. This problematic pathogen encodes 11 eukaryotic-like Ser/Thr kinases, yet few substrates or signaling targets have been characterized. Here, we report the structure of EmbR (2.0 Å), a putative transcriptional regulator of key arabinosyltransferases (EmbC, -A, and -B), and an endogenous substrate of the Ser/Thr-kinase PknH. EmbR presents a unique domain architecture: the N-terminal winged-helix DNA-binding domain forms an extensive interface with the all-helical central bacterial transcriptional activation domain and is positioned adjacent to the regulatory C-terminal forkhead-associated (FHA) domain, which mediates binding to a Thr-phosphorylated site in PknH. The structure in complex with a phospho-peptide (1.9 Å) reveals a conserved mode of phospho-threonine recognition by the FHA domain and evidence for specific recognition of the cognate kinase. The present structures suggest hypotheses as to how EmbR might propagate the phospho-relay signal from its cognate kinase, while serving as a template for the structurally uncharacterized Streptomyces antibiotic regulatory protein family of transcription factors. PMID:16477027

Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role.

PubMed

Kleftogiannis, Dimitrios; Korfiati, Aigli; Theofilatos, Konstantinos; Likothanassis, Spiros; Tsakalidis, Athanasios; Mavroudi, Seferina

2013-06-01

Traditional biology was forced to restate some of its principles when the microRNA (miRNA) genes and their regulatory role were firstly discovered. Typically, miRNAs are small non-coding RNA molecules which have the ability to bind to the 3'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. Existing experimental techniques for their identification and the prediction of the target genes share some important limitations such as low coverage, time consuming experiments and high cost reagents. Hence, many computational methods have been proposed for these tasks to overcome these limitations. Recently, many researchers emphasized on the development of computational approaches to predict the participation of miRNA genes in regulatory networks and to analyze their transcription mechanisms. All these approaches have certain advantages and disadvantages which are going to be described in the present survey. Our work is differentiated from existing review papers by updating the methodologies list and emphasizing on the computational issues that arise from the miRNA data analysis. Furthermore, in the present survey, the various miRNA data analysis steps are treated as an integrated procedure whose aims and scope is to uncover the regulatory role and mechanisms of the miRNA genes. This integrated view of the miRNA data analysis steps may be extremely useful for all researchers even if they work on just a single step. Copyright © 2013 Elsevier Inc. All rights reserved.

CAAT Altex workshop paper entitled "Towards Good Read ...

EPA Pesticide Factsheets

Grouping of substances and utilizing read-across within those groups represents an important data gap filling technique for chemical safety assessments. Categories/analogue groups are typically developed based on structural similarity, and increasingly often, also on mechanistic similarity. While read-across can play a key role in complying with legislations such as the European REACH legislation, the lack of consensus regarding the extent and type of evidence necessary to support it often hampers it’s successful application and acceptance by regulatory authorities. Despite a potentially broad user community, expertise is still concentrated across a handful of organizations and individuals. In order to facilitate the effective use of read-across, this document aims to summarize the state-of-the-art, summarise insights learned from reviewing ECHA published decisions as far as the relative successes/pitfalls surrounding read-across under the REACH and compile the relevant activities and guidance documents. Special emphasis is given to the available existing tools and approaches, the consideration and expression of uncertainty, the use of biological support data and the potential impact of the ECHA Read-Across Assessment Framework (RAAF) which was published in 2015. This is a paper that summarises different activities and research needs for read-across for regulatory purposes that has been compiled as a result of a CAAT initiative led by Thomas Hartung.

[Interaction of free fatty acids with mitochondria during uncoupling of oxidative phosphorylation].

PubMed

Samartsev, V N; Rybakova, S R; Dubinin, M V

2013-01-01

The activity of free saturated fatty acids (caprylic, capric, lauric, myristic, palmitic and stearic) as inducers and regulators of uncoupling of oxidative phosphorylation with participation of ADP/ATP antiporter, aspartate/glutamate antiporter and cyclosporin A-sensitive structure was investigated in experiments on rat liver mitochondria. It is established that at equal uncoupling activity of fatty acids the regulatory effect is minimal for caprylic acid and raised with increasing the hydrophobicity of fatty acids reaching the maximum value for stearic acid. There exists the linear dependence of the regulatory effect value of fatty acids on fatty acids content in the hydrophobic region of the inner membrane. The model that describes the interaction of fatty acids with the hydrophobic region of the mitochondrial inner membrane preserving functional activity of organelles is developed. It is established that if molecules of various fatty acids being in the hydrophobic region of the membrane are equally effective as uncoupling regulators, their specific uncoupling activity is different. Caprylic acid, a short-chain fatty acid, possesses the highest uncoupling activity. As the acyl chain length increases, the specific uncoupling activity of fatty acids reduces exponentially. Under these conditions components of the uncoupling activity sensitive to glutamate and carboxyatractylate and glutamate and insensitive to these reagents (but sensitive to cyclosporin A) change approximately equally.

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs

PubMed Central

Kenny, N J; Chan, K W; Nong, W; Qu, Z; Maeso, I; Yip, H Y; Chan, T F; Kwan, H S; Holland, P W H; Chu, K H; Hui, J H L

2016-01-01

Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs—Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa. PMID:26419336

Inhibition of homologous phosphorolytic ribonucleases by citrate may represent an evolutionarily conserved communicative link between RNA degradation and central metabolism

PubMed Central

Stone, Carlanne M.; Butt, Louise E.; Bufton, Joshua C.; Lourenco, Daniel C.; Gowers, Darren M.; Pickford, Andrew R.; Cox, Paul A.

2017-01-01

Abstract Ribonucleases play essential roles in all aspects of RNA metabolism, including the coordination of post-transcriptional gene regulation that allows organisms to respond to internal changes and environmental stimuli. However, as inherently destructive enzymes, their activity must be carefully controlled. Recent research exemplifies the repertoire of regulatory strategies employed by ribonucleases. The activity of the phosphorolytic exoribonuclease, polynucleotide phosphorylase (PNPase), has previously been shown to be modulated by the Krebs cycle metabolite citrate in Escherichia coli. Here, we provide evidence for the existence of citrate-mediated inhibition of ribonucleases in all three domains of life. In silico molecular docking studies predict that citrate will bind not only to bacterial PNPases from E. coli and Streptomyces antibioticus, but also PNPase from human mitochondria and the structurally and functionally related archaeal exosome complex from Sulfolobus solfataricus. Critically, we show experimentally that citrate also inhibits the exoribonuclease activity of bacterial, eukaryotic and archaeal PNPase homologues in vitro. Furthermore, bioinformatics data, showing key citrate-binding motifs conserved across a broad range of PNPase homologues, suggests that this regulatory mechanism may be widespread. Overall, our data highlight a communicative link between ribonuclease activity and central metabolism that may have been conserved through the course of evolution. PMID:28334892

Infection control in design and construction work.

PubMed

Collinge, William H

2015-01-01

To clarify how infection control requirements are represented, communicated, and understood in work interactions through the medical facility construction project life cycle. To assist project participants with effective infection control management by highlighting the nature of such requirements and presenting recommendations to aid practice. A 4-year study regarding client requirement representation and use on National Health Service construction projects in the United Kingdom provided empirical evidence of infection control requirement communication and understanding through design and construction work interactions. An analysis of construction project resources (e.g., infection control regulations and room data sheets) was combined with semi-structured interviews with hospital client employees and design and construction professionals to provide valuable insights into the management of infection control issues. Infection control requirements are representationally indistinct but also omnipresent through all phases of the construction project life cycle: Failure to recognize their nature, relevance, and significance can result in delays, stoppages, and redesign work. Construction project resources (e.g., regulatory guidance and room data sheets) can mask or obscure the meaning of infection control issues. A preemptive identification of issues combined with knowledge sharing activities among project stakeholders can enable infection control requirements to be properly understood and addressed. Such initiatives should also reference existing infection control regulatory guidance and advice. © The Author(s) 2015.

Optimized mixed Markov models for motif identification

PubMed Central

Huang, Weichun; Umbach, David M; Ohler, Uwe; Li, Leping

2006-01-01

Background Identifying functional elements, such as transcriptional factor binding sites, is a fundamental step in reconstructing gene regulatory networks and remains a challenging issue, largely due to limited availability of training samples. Results We introduce a novel and flexible model, the Optimized Mixture Markov model (OMiMa), and related methods to allow adjustment of model complexity for different motifs. In comparison with other leading methods, OMiMa can incorporate more than the NNSplice's pairwise dependencies; OMiMa avoids model over-fitting better than the Permuted Variable Length Markov Model (PVLMM); and OMiMa requires smaller training samples than the Maximum Entropy Model (MEM). Testing on both simulated and actual data (regulatory cis-elements and splice sites), we found OMiMa's performance superior to the other leading methods in terms of prediction accuracy, required size of training data or computational time. Our OMiMa system, to our knowledge, is the only motif finding tool that incorporates automatic selection of the best model. OMiMa is freely available at [1]. Conclusion Our optimized mixture of Markov models represents an alternative to the existing methods for modeling dependent structures within a biological motif. Our model is conceptually simple and effective, and can improve prediction accuracy and/or computational speed over other leading methods. PMID:16749929

Structure of the protein phosphatase 2A holoenzyme.

PubMed

Xu, Yanhui; Xing, Yongna; Chen, Yu; Chao, Yang; Lin, Zheng; Fan, Eugene; Yu, Jong W; Strack, Stefan; Jeffrey, Philip D; Shi, Yigong

2006-12-15

Protein Phosphatase 2A (PP2A) plays an essential role in many aspects of cellular physiology. The PP2A holoenzyme consists of a heterodimeric core enzyme, which comprises a scaffolding subunit and a catalytic subunit, and a variable regulatory subunit. Here we report the crystal structure of the heterotrimeric PP2A holoenzyme involving the regulatory subunit B'/B56/PR61. Surprisingly, the B'/PR61 subunit has a HEAT-like (huntingtin-elongation-A subunit-TOR-like) repeat structure, similar to that of the scaffolding subunit. The regulatory B'/B56/PR61 subunit simultaneously interacts with the catalytic subunit as well as the conserved ridge of the scaffolding subunit. The carboxyterminus of the catalytic subunit recognizes a surface groove at the interface between the B'/B56/PR61 subunit and the scaffolding subunit. Compared to the scaffolding subunit in the PP2A core enzyme, formation of the holoenzyme forces the scaffolding subunit to undergo pronounced conformational rearrangements. This structure reveals significant ramifications for understanding the function and regulation of PP2A.

40 CFR 194.54 - Scope of compliance assessments.

Code of Federal Regulations, 2010 CFR

2010-07-01

... processes and events that may occur over the regulatory time frame; (2) Identifies the processes, events, or... effects on the disposal system of: (1) Existing boreholes in the vicinity of the disposal system, with...

Regulatory aviation medicine : its philosophies and limitations.

DOT National Transportation Integrated Search

1982-09-01

The application of aviation medicine is relatively standardized throughout the world, both in civil and military operations. Substantial differences exist, however, in the way different countries, or even different agencies in the same country, deter...

The logic of the floral transition: Reverse-engineering the switch controlling the identity of lateral organs.

PubMed

Dinh, Jean-Louis; Farcot, Etienne; Hodgman, Charlie

2017-09-01

Much laboratory work has been carried out to determine the gene regulatory network (GRN) that results in plant cells becoming flowers instead of leaves. However, this also involves the spatial distribution of different cell types, and poses the question of whether alternative networks could produce the same set of observed results. This issue has been addressed here through a survey of the published intercellular distribution of expressed regulatory genes and techniques both developed and applied to Boolean network models. This has uncovered a large number of models which are compatible with the currently available data. An exhaustive exploration had some success but proved to be unfeasible due to the massive number of alternative models, so genetic programming algorithms have also been employed. This approach allows exploration on the basis of both data-fitting criteria and parsimony of the regulatory processes, ruling out biologically unrealistic mechanisms. One of the conclusions is that, despite the multiplicity of acceptable models, an overall structure dominates, with differences mostly in alternative fine-grained regulatory interactions. The overall structure confirms the known interactions, including some that were not present in the training set, showing that current data are sufficient to determine the overall structure of the GRN. The model stresses the importance of relative spatial location, through explicit references to this aspect. This approach also provides a quantitative indication of how likely some regulatory interactions might be, and can be applied to the study of other developmental transitions.

From road to lab to math: the co-evolution of technological, regulatory, and organizational innovations for automotive crash testing.

PubMed

Leonardi, Paul M

2010-04-01

Today, in the midst of economic crisis, senior executives at US automakers and influential industry analysts frequently reflect on the progression that safety testing has taken from the crude trials done on the road, to controlled laboratory experiments, and to today's complex math-based simulation models. They use stories of this seemingly linear and natural sequence to justify further investment in simulation technologies. The analysis presented in this paper shows that change in the structures of automakers' organizations co-evolved with regulations specifying who was at fault in vehicle impacts, how vehicles should be built to withstand the force of an impact, and how testing should be done to assure that vehicles met those requirements. Changes in the regulatory environment were bolstered by new theories about crash test dynamics and changing technologies with which to test those theories. Thus, as new technological and regulatory innovations co-evolved with innovations in organizational structuring, ideas about how to best conduct crash tests shifted and catalyzed new cycles of technological, regulatory, and organizational innovation. However, this co-evolutionary story tells us that the move from road to lab to math was not natural or linear as today's managerial rhetoric would have us believe. Rather, the logic of math-based simulation was the result of technological, regulatory and organizational changes that created an industry-wide ideology that supported the move toward math while making it appear natural within the shifting structure of the industry.

Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space.

PubMed

Ahnert, S E; Fink, T M A

2016-07-01

Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have found that the structure of a motif does not strongly determine its function, if this is defined in terms of the gene expression patterns the motif can produce. Here, we offer a different, higher-level definition of the 'function' of a motif, in terms of two fundamental properties of its dynamical state space as a Boolean network. One is the basin entropy, which is a complexity measure of the dynamics of Boolean networks. The other is the diversity of cyclic attractor lengths that a given motif can produce. Using these two measures, we examine all 104 topologically distinct three-node motifs and show that the structural properties of a motif, such as the presence of feedback loops and feed-forward loops, predict fundamental characteristics of its dynamical state space, which in turn determine aspects of its functional versatility. We also show that these higher-level properties have a direct bearing on real regulatory networks, as both basin entropy and cycle length diversity show a close correspondence with the prevalence, in neural and genetic regulatory networks, of the 13 connected motifs without self-interactions that have been studied extensively in the literature. © 2016 The Authors.

75 FR 62436 - Notice of Issuance of Regulatory Guide

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-08

... Power Plants,'' includes in its scope safety- related structures, systems, and components (SSCs) that... monitor the effectiveness of maintenance for protective coatings within its scope (as discrete systems or... and Management System (ADAMS) under Accession No. ML102230359. Electronic copies of Regulatory Guide 1...

Prediction of physical protein protein interactions

NASA Astrophysics Data System (ADS)

Szilágyi, András; Grimm, Vera; Arakaki, Adrián K.; Skolnick, Jeffrey

2005-06-01

Many essential cellular processes such as signal transduction, transport, cellular motion and most regulatory mechanisms are mediated by protein-protein interactions. In recent years, new experimental techniques have been developed to discover the protein-protein interaction networks of several organisms. However, the accuracy and coverage of these techniques have proven to be limited, and computational approaches remain essential both to assist in the design and validation of experimental studies and for the prediction of interaction partners and detailed structures of protein complexes. Here, we provide a critical overview of existing structure-independent and structure-based computational methods. Although these techniques have significantly advanced in the past few years, we find that most of them are still in their infancy. We also provide an overview of experimental techniques for the detection of protein-protein interactions. Although the developments are promising, false positive and false negative results are common, and reliable detection is possible only by taking a consensus of different experimental approaches. The shortcomings of experimental techniques affect both the further development and the fair evaluation of computational prediction methods. For an adequate comparative evaluation of prediction and high-throughput experimental methods, an appropriately large benchmark set of biophysically characterized protein complexes would be needed, but is sorely lacking.

Crystal Structures of RMI1 and RMI2, Two OB-Fold Regulatory Subunits of the BLM Complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Feng; Yang, Yuting; Singh, Thiyam Ramsing

Mutations in BLM, a RecQ-like helicase, are linked to the autosomal recessive cancer-prone disorder Bloom's syndrome. BLM associates with topoisomerase (Topo) III{alpha}, RMI1, and RMI2 to form the BLM complex that is essential for genome stability. The RMI1-RMI2 heterodimer stimulates the dissolution of double Holliday junction into non-crossover recombinants mediated by BLM-Topo III{alpha} and is essential for stabilizing the BLM complex. However, the molecular basis of these functions of RMI1 and RMI2 remains unclear. Here we report the crystal structures of multiple domains of RMI1-RMI2, providing direct confirmation of the existence of three oligonucleotide/oligosaccharide binding (OB)-folds in RMI1-RMI2. Our structuralmore » and biochemical analyses revealed an unexpected insertion motif in RMI1N-OB, which is important for stimulating the dHJ dissolution. We also revealed the structural basis of the interaction between RMI1C-OB and RMI2-OB and demonstrated the functional importance of the RMI1-RMI2 interaction in genome stability maintenance.« less

G Quadruplex in Plants: A Ubiquitous Regulatory Element and Its Biological Relevance.

PubMed

Yadav, Vikas; Hemansi; Kim, Nayun; Tuteja, Narendra; Yadav, Puja

2017-01-01

G quadruplexes (G4) are higher-order DNA and RNA secondary structures formed by G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential G4 quadruplex sequences have been identified in G-rich eukaryotic non-telomeric and telomeric genomic regions. Upon function, G4 formation is known to involve in chromatin remodeling, gene regulation and has been associated with genomic instability, genetic diseases and cancer progression. The natural role and biological validation of G4 structures is starting to be explored, and is of particular interest for the therapeutic interventions for human diseases. However, the existence and physiological role of G4 DNA and G4 RNA in plants species have not been much investigated yet and therefore, is of great interest for the development of improved crop varieties for sustainable agriculture. In this context, several recent studies suggests that these highly diverse G4 structures in plants can be employed to regulate expression of genes involved in several pathophysiological conditions including stress response to biotic and abiotic stresses as well as DNA damage. In the current review, we summarize the recent findings regarding the emerging functional significance of G4 structures in plants and discuss their potential value in the development of improved crop varieties.

Structural Insights into Functional Overlapping and Differentiation among Myosin V Motors*

PubMed Central

Nascimento, Andrey F. Z.; Trindade, Daniel M.; Tonoli, Celisa C. C.; de Giuseppe, Priscila O.; Assis, Leandro H. P.; Honorato, Rodrigo V.; de Oliveira, Paulo S. L.; Mahajan, Pravin; Burgess-Brown, Nicola A.; von Delft, Frank; Larson, Roy E.; Murakami, Mario T.

2013-01-01

Myosin V (MyoV) motors have been implicated in the intracellular transport of diverse cargoes including vesicles, organelles, RNA-protein complexes, and regulatory proteins. Here, we have solved the cargo-binding domain (CBD) structures of the three human MyoV paralogs (Va, Vb, and Vc), revealing subtle structural changes that drive functional differentiation and a novel redox mechanism controlling the CBD dimerization process, which is unique for the MyoVc subclass. Moreover, the cargo- and motor-binding sites were structurally assigned, indicating the conservation of residues involved in the recognition of adaptors for peroxisome transport and providing high resolution insights into motor domain inhibition by CBD. These results contribute to understanding the structural requirements for cargo transport, autoinhibition, and regulatory mechanisms in myosin V motors. PMID:24097982

Regionalization as an approach to regulatory systems strengthening: a case study in CARICOM member states.

PubMed

Preston, Charles; Chahal, Harinder S; Porrás, Analia; Cargill, Lucette; Hinds, Maryam; Olowokure, Babatunde; Cummings, Rudolph; Hospedales, James

2016-05-01

Improving basic capacities for regulation of medicines and health technologies through regulatory systems strengthening is particularly challenging in resource-constrained settings. "Regionalization"-an approach in which countries with common histories, cultural values, languages, and economic conditions work together to establish more efficient systems-may be one answer. This report describes the Caribbean Regulatory System (CRS), a regionalization initiative being implemented in the mostly small countries of the Caribbean Community and Common Market (CARICOM). This initiative is an innovative effort to strengthen regulatory systems in the Caribbean, where capacity is limited compared to other subregions of the Americas. The initiative's concept and design includes a number of features and steps intended to enhance sustainability in resource-constrained contexts. The latter include 1) leveraging existing platforms for centralized cooperation, governance, and infrastructure; 2) strengthening regulatory capacities with the largest potential public health impact; 3) incorporating policies that promote reliance on reference authorities; 4) changing the system to encourage industry to market their products in CARICOM (e.g., using a centralized portal of entry to reduce regulatory burdens); and 5) building human resource capacity. If implemented properly, the CRS will be self-sustaining through user fees. The experience and lessons learned thus far in implementing this initiative, described in this report, can serve as a case study for the development of similar regulatory strengthening initiatives in resource-constrained environments.

Thermodynamic study of the native and phosphorylated regulatory domain of the CFTR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marasini, Carlotta, E-mail: marasini@ge.ibf.cnr.it; Galeno, Lauretta; Moran, Oscar

2012-07-06

Highlights: Black-Right-Pointing-Pointer CFTR mutations produce cystic fibrosis. Black-Right-Pointing-Pointer Chloride transport depends on the regulatory domain phosphorylation. Black-Right-Pointing-Pointer Regulatory domain is intrinsically disordered. Black-Right-Pointing-Pointer Secondary structure and protein stability change upon phosphorylation. -- Abstract: The regulatory domain (RD) of the cystic fibrosis transmembrane conductance regulator (CFTR), the defective protein in cystic fibrosis, is the region of the channel that regulates the CFTR activity with multiple phosphorylation sites. This domain is an intrinsically disordered protein, characterized by lack of stable or unique tertiary structure. The disordered character of a protein is directly correlated with its function. The flexibility of RD may bemore » important for its regulatory role: the continuous conformational change may be necessary for the progressive phosphorylation, and thus activation, of the channel. However, the lack of a defined and stable structure results in a considerable limitation when trying to in build a unique molecular model for the RD. Moreover, several evidences indicate significant structural differences between the native, non-phosphorylated state, and the multiple phosphorylated state of the protein. The aim of our work is to provide data to describe the conformations and the thermodynamic properties in these two functional states of RD. We have done the circular dichroism (CD) spectra in samples with a different degree of phosphorylation, from the non-phosphorylated state to a bona fide completely phosphorylated state. Analysis of CD spectra showed that the random coil and {beta}-sheets secondary structure decreased with the polypeptide phosphorylation, at expenses of an increase of {alpha}-helix. This observation lead to interpret phosphorylation as a mechanism favoring a more structured state. We also studied the thermal denaturation curves of the protein in the two conditions, monitoring the changes of the mean residue ellipticity measured at 222 nm as a function of temperature, between 20 and 95 Degree-Sign C. The thermodynamic analysis of the denaturation curves shows that phosphorylation of the protein induces a state of lower stability of R domain, characterized by a lower transition temperature, and by a smaller Gibbs free energy difference between the native and the unfolded states.« less

76 FR 52961 - Agency Information Collection Activities: Form N-300; Revision of an Existing Information...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-24

... documentary requirements for those seeking to work in certain occupations or professions, or to obtain various... 18, 2011. Liana Miranda-Valido, Management and Program Analyst, Regulatory Products Division, Office...

[Neurobiología y psicoanálisis].

PubMed

Rosler, J Roberto

2002-01-01

There would be a conceptual bridge between Psychoanalysis and the Neurosciences that would allow the translation of psychoanalytic concepts into neural mechanisms and vice-versa. Different Freudian postulates, such as that different types of anxiety would emerge from various cerebral interactions, the motivational regulatory functions of the impulse, the conscious emotion as the perception of something basically unconscious, the mechanism of repression in the traumatic memory, the existence of a system associated with the unconscious affective processes and regulated by the principle of pleasure - displeasure, the emotional representation as a basis of the more primitive cerebral structures, and the Oedipo complex, among others, are finding their biological ratification in different laboratory studies. This conceptual bridge would not only be a "Psychoanalysis-Neurobiological mechanisms" translator, but would also, through the integrated conceptualization of the psychoanalytical neurobiological aspects of emotion, generate relevant therapeutic models.

FEATURES, EVENTS, AND PROCESSES: SYSTEM-LEVEL AND CRITICALITY

DOE Office of Scientific and Technical Information (OSTI.GOV)

D.L. McGregor

The primary purpose of this Analysis/Model Report (AMR) is to identify and document the screening analyses for the features, events, and processes (FEPs) that do not easily fit into the existing Process Model Report (PMR) structure. These FEPs include the 3 1 FEPs designated as System-Level Primary FEPs and the 22 FEPs designated as Criticality Primary FEPs. A list of these FEPs is provided in Section 1.1. This AMR (AN-WIS-MD-000019) documents the Screening Decision and Regulatory Basis, Screening Argument, and Total System Performance Assessment (TSPA) Disposition for each of the subject Primary FEPs. This AMR provides screening information and decisionsmore » for the TSPA-SR report and provides the same information for incorporation into a project-specific FEPs database. This AMR may also assist reviewers during the licensing-review process.« less

Rules of Engagement: The Type VI Secretion System in Vibrio cholerae.

PubMed

Joshi, Avatar; Kostiuk, Benjamin; Rogers, Andrew; Teschler, Jennifer; Pukatzki, Stefan; Yildiz, Fitnat H

2017-04-01

Microbial species often exist in complex communities where they must avoid predation and compete for favorable niches. The type VI secretion system (T6SS) is a contact-dependent bacterial weapon that allows for direct killing of competitors through the translocation of proteinaceous toxins. Vibrio cholerae is a Gram-negative pathogen that can use its T6SS during antagonistic interactions with neighboring prokaryotic and eukaryotic competitors. The T6SS not only promotes V. cholerae's survival during its aquatic and host life cycles, but also influences its evolution by facilitating horizontal gene transfer. This review details the recent insights regarding the structure and function of the T6SS as well as the diverse signals and regulatory pathways that control its activation in V. cholerae. Copyright © 2016 Elsevier Ltd. All rights reserved.

From Coexpression to Coregulation: An Approach to Inferring Transcriptional Regulation Among Gene Classes from Large-Scale Expression Data

NASA Technical Reports Server (NTRS)

Mjolsness, Eric; Castano, Rebecca; Mann, Tobias; Wold, Barbara

2000-01-01

We provide preliminary evidence that existing algorithms for inferring small-scale gene regulation networks from gene expression data can be adapted to large-scale gene expression data coming from hybridization microarrays. The essential steps are (I) clustering many genes by their expression time-course data into a minimal set of clusters of co-expressed genes, (2) theoretically modeling the various conditions under which the time-courses are measured using a continuous-time analog recurrent neural network for the cluster mean time-courses, (3) fitting such a regulatory model to the cluster mean time courses by simulated annealing with weight decay, and (4) analysing several such fits for commonalities in the circuit parameter sets including the connection matrices. This procedure can be used to assess the adequacy of existing and future gene expression time-course data sets for determining transcriptional regulatory relationships such as coregulation.

The impact of biotechnology on agricultural worker safety and health.

PubMed

Shutske, J M; Jenkins, S M

2002-08-01

Biotechnology applications such as the use and production of genetically modified organisms (GMOs) have been widely promoted, adopted, and employed by agricultural producers throughout the world. Yet, little research exists that examines the implications of agricultural biotechnology on the health and safety of workers involved in agricultural production and processing. Regulatory frameworks do exist to examine key issues related to food safety and environmental protection in GMO applications. However, based on the lack of research and regulatory oversight, it would appear that the potential impact on the safety and health of workers is of limited interest. This article examines some of the known worker health and safety implications related to the use and production of GMOs using the host, agent, and environment framework. The characteristics of employers, workers, inputs, production practices, and socio-economic environments in which future agricultural workers perform various tasks is likely to change based on the research summarized here.

Self Organized Criticality as a new paradigm of sleep regulation

NASA Astrophysics Data System (ADS)

Ivanov, Plamen Ch.; Bartsch, Ronny P.

2012-02-01

Humans and animals often exhibit brief awakenings from sleep (arousals), which are traditionally viewed as random disruptions of sleep caused by external stimuli or pathologic perturbations. However, our recent findings show that arousals exhibit complex temporal organization and scale-invariant behavior, characterized by a power-law probability distribution for their durations, while sleep stage durations exhibit exponential behavior. The co-existence of both scale-invariant and exponential processes generated by a single regulatory mechanism has not been observed in physiological systems until now. Such co-existence resembles the dynamical features of non-equilibrium systems exhibiting self-organized criticality (SOC). Our empirical analysis and modeling approaches based on modern concepts from statistical physics indicate that arousals are an integral part of sleep regulation and may be necessary to maintain and regulate healthy sleep by releasing accumulated excitations in the regulatory neuronal networks, following a SOC-type temporal organization.

Hazardous waste management system--Environmental Protection Agency. Notice of regulatory reform actions; request for comments.

PubMed

1982-12-13

In response to Executive Order 12291 and the President's Task Force on Regulatory Relief, the Environmental Protection Agency is reviewing and reassessing the hazardous waste regulations developed under the Resource Conservation and Recovery Act (RCRA). A variety of activities are underway that will simplify procedures and reduce paperwork, modify existing regulations to make them more workable and cost effective, and control new wastes and new processes. The purpose of this notice is to inform the public of these activities and invite comments on the general approaches being taken.

"Must-know" legal issues for healthcare CFOS.

PubMed

Peregrine, Michael W; Schwartz, James R

2002-03-01

Healthcare financial managers are finding that regulatory agencies' customary focus on Medicare and tax-exemption concerns is shifting to other issues directly related to financial management. Regulatory agencies, such as the Securities and Exchange Commission, are scrutinizing not-for-profit and charitable trust law matters. Because of this renewed attention to existing regulations, healthcare financial managers need to increase their diligence in ensuring their organizations' compliance with those laws governing areas for which they traditionally have been accountable, including auditor relationships, restricted gifts, consulting arrangements, investment management, and financial reporting.

The current status of NORM/TENORM industries and establishment of regulatory framework in Korea.

PubMed

Chang, Byung-Uck; Kim, Yongjae; Oh, Jang-Jin

2011-07-01

During the last several years, a nationwide survey on naturally occurring radioactive material (NORM)/technologically enhanced naturally occurring radioactive materials (TENORM) industries has been conducted. Because of the rapid economic growth in Korea, the huge amount of raw materials, including NORM have been consumed in various industrial areas, and some representative TENORM industries exist in Korea. Recently, the Korean government decided to establish a regulatory framework for natural radiation, including NORM/TENORM and is making efforts to introduce relevant publically consent regulations on the basis of international safety standards.

Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development.

PubMed

Rebeiz, Mark; Patel, Nipam H; Hinman, Veronica F

2015-01-01

The molecular and genetic basis for the evolution of anatomical diversity is a major question that has inspired evolutionary and developmental biologists for decades. Because morphology takes form during development, a true comprehension of how anatomical structures evolve requires an understanding of the evolutionary events that alter developmental genetic programs. Vast gene regulatory networks (GRNs) that connect transcription factors to their target regulatory sequences control gene expression in time and space and therefore determine the tissue-specific genetic programs that shape morphological structures. In recent years, many new examples have greatly advanced our understanding of the genetic alterations that modify GRNs to generate newly evolved morphologies. Here, we review several aspects of GRN evolution, including their deep preservation, their mechanisms of alteration, and how they originate to generate novel developmental programs.

Architecture of the 99 bp DNA-six-protein regulatory complex of the lambda att site.

PubMed

Sun, Xingmin; Mierke, Dale F; Biswas, Tapan; Lee, Sang Yeol; Landy, Arthur; Radman-Livaja, Marta

2006-11-17

The highly directional and tightly regulated recombination reaction used to site-specifically excise the bacteriophage lambda chromosome out of its E. coli host chromosome requires the binding of six sequence-specific proteins to a 99 bp segment of the phage att site. To gain structural insights into this recombination pathway, we measured 27 FRET distances between eight points on the 99 bp regulatory DNA bound with all six proteins. Triangulation of these distances using a metric matrix distance-geometry algorithm provided coordinates for these eight points. The resulting path for the protein-bound regulatory DNA, which fits well with the genetics, biochemistry, and X-ray crystal structures describing the individual proteins and their interactions with DNA, provides a new structural perspective into the molecular mechanism and regulation of the recombination reaction and illustrates a design by which different families of higher-order complexes can be assembled from different numbers and combinations of the same few proteins.

Neural model of gene regulatory network: a survey on supportive meta-heuristics.

PubMed

Biswas, Surama; Acharyya, Sriyankar

2016-06-01

Gene regulatory network (GRN) is produced as a result of regulatory interactions between different genes through their coded proteins in cellular context. Having immense importance in disease detection and drug finding, GRN has been modelled through various mathematical and computational schemes and reported in survey articles. Neural and neuro-fuzzy models have been the focus of attraction in bioinformatics. Predominant use of meta-heuristic algorithms in training neural models has proved its excellence. Considering these facts, this paper is organized to survey neural modelling schemes of GRN and the efficacy of meta-heuristic algorithms towards parameter learning (i.e. weighting connections) within the model. This survey paper renders two different structure-related approaches to infer GRN which are global structure approach and substructure approach. It also describes two neural modelling schemes, such as artificial neural network/recurrent neural network based modelling and neuro-fuzzy modelling. The meta-heuristic algorithms applied so far to learn the structure and parameters of neutrally modelled GRN have been reviewed here.

Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization.

PubMed

Donderis, Jorge; Bowring, Janine; Maiques, Elisa; Ciges-Tomas, J Rafael; Alite, Christian; Mehmedov, Iltyar; Tormo-Mas, María Angeles; Penadés, José R; Marina, Alberto

2017-09-01

The dUTPase (Dut) enzymes, encoded by almost all free-living organisms and some viruses, prevent the misincorporation of uracil into DNA. We previously proposed that trimeric Duts are regulatory proteins involved in different cellular processes; including the phage-mediated transfer of the Staphylococcus aureus pathogenicity island SaPIbov1. Recently, it has been shown that the structurally unrelated dimeric Dut encoded by phage ϕNM1 is similarly able to mobilize SaPIbov1, suggesting dimeric Duts could also be regulatory proteins. How this is accomplished remains unsolved. Here, using in vivo, biochemical and structural approaches, we provide insights into the signaling mechanism used by the dimeric Duts to induce the SaPIbov1 cycle. As reported for the trimeric Duts, dimeric Duts contain an extremely variable region, here named domain VI, which is involved in the regulatory capacity of these enzymes. Remarkably, our results also show that the dimeric Dut signaling mechanism is modulated by dUTP, as with the trimeric Duts. Overall, our results demonstrate that although unrelated both in sequence and structure, dimeric and trimeric Duts control SaPI transfer by analogous mechanisms, representing a fascinating example of convergent evolution. This conserved mode of action highlights the biological significance of Duts as regulatory molecules.

Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization

PubMed Central

Ciges-Tomas, J. Rafael; Mehmedov, Iltyar; Tormo-Mas, María Angeles; Penadés, José R.

2017-01-01

The dUTPase (Dut) enzymes, encoded by almost all free-living organisms and some viruses, prevent the misincorporation of uracil into DNA. We previously proposed that trimeric Duts are regulatory proteins involved in different cellular processes; including the phage-mediated transfer of the Staphylococcus aureus pathogenicity island SaPIbov1. Recently, it has been shown that the structurally unrelated dimeric Dut encoded by phage ϕNM1 is similarly able to mobilize SaPIbov1, suggesting dimeric Duts could also be regulatory proteins. How this is accomplished remains unsolved. Here, using in vivo, biochemical and structural approaches, we provide insights into the signaling mechanism used by the dimeric Duts to induce the SaPIbov1 cycle. As reported for the trimeric Duts, dimeric Duts contain an extremely variable region, here named domain VI, which is involved in the regulatory capacity of these enzymes. Remarkably, our results also show that the dimeric Dut signaling mechanism is modulated by dUTP, as with the trimeric Duts. Overall, our results demonstrate that although unrelated both in sequence and structure, dimeric and trimeric Duts control SaPI transfer by analogous mechanisms, representing a fascinating example of convergent evolution. This conserved mode of action highlights the biological significance of Duts as regulatory molecules. PMID:28892519

Differential identity of Filopodia and Tunneling Nanotubes revealed by the opposite functions of actin regulatory complexes.

PubMed

Delage, Elise; Cervantes, Diégo Cordero; Pénard, Esthel; Schmitt, Christine; Syan, Sylvie; Disanza, Andrea; Scita, Giorgio; Zurzolo, Chiara

2016-12-23

Tunneling Nanotubes (TNTs) are actin enriched filopodia-like protrusions that play a pivotal role in long-range intercellular communication. Different pathogens use TNT-like structures as "freeways" to propagate across cells. TNTs are also implicated in cancer and neurodegenerative diseases, making them promising therapeutic targets. Understanding the mechanism of their formation, and their relation with filopodia is of fundamental importance to uncover their physiological function, particularly since filopodia, differently from TNTs, are not able to mediate transfer of cargo between distant cells. Here we studied different regulatory complexes of actin, which play a role in the formation of both these structures. We demonstrate that the filopodia-promoting CDC42/IRSp53/VASP network negatively regulates TNT formation and impairs TNT-mediated intercellular vesicle transfer. Conversely, elevation of Eps8, an actin regulatory protein that inhibits the extension of filopodia in neurons, increases TNT formation. Notably, Eps8-mediated TNT induction requires Eps8 bundling but not its capping activity. Thus, despite their structural similarities, filopodia and TNTs form through distinct molecular mechanisms. Our results further suggest that a switch in the molecular composition in common actin regulatory complexes is critical in driving the formation of either type of membrane protrusion.

The Chinese health care regulatory institutions in an era of transition.

PubMed

Fang, Jing

2008-02-01

The purpose of this paper is to contribute to a better understanding of Chinese health care regulation in an era of transition. It describes the major health care regulatory institutions operating currently in China and analyzes the underlying factors. The paper argues that in the transition from a planned to a market economy, the Chinese government has been employing a hybrid approach where both old and new institutions have a role in the management of emerging markets, including the health care market. This approach is consistent with the incremental reform strategy adopted by the Party-state. Although a health care regulatory framework has gradually taken shape, the framework is incomplete, with a particular lack of emphasis on professional self-regulation. In addition, its effectiveness is limited despite the existence of many regulatory institutions. In poor rural areas, the effectiveness of the regulatory framework is further undermined or distorted by the extremely difficult financial position that local governments find themselves in. The interpretations of the principle of 'rule of law' by policy makers and officials at different levels and the widespread informal network of relations between known individuals (Guanxi) play an important role in the operation of the regulatory framework. The findings of this paper reveal the complex nature of regulating health care in transitional China.

Regulation of stem cell-based therapies in Canada: current issues and concerns.

PubMed

von Tigerstrom, Barbara; Nguyen, Thu Minh; Knoppers, Bartha Maria

2012-09-01

Stem cell therapies offer enormous potential for the treatment of a wide range of diseases and conditions. Despite the excitement over such advances, regulators are faced with the challenge of determining criteria to ensure stem cells and their products are safe and effective for human use. However, stem cell-based products and therapies present unique regulatory challenges because standard drug development models do not wholly apply given the complexity and diversity of these products and therapies. As a result, regulatory requirements are often unclear and ambiguous creating unnecessary barriers for research. In order to better understand the barriers that might affect Canadian stem cell researchers, we sought feedback from stakeholders regarding areas of uncertainty or concern about existing regulatory oversight of cell therapies. A selection of Canadian researchers and clinicians working in the area of stem cell research were interviewed to assess certain key questions: 1) whether current regulatory requirements are easily accessible and well understood; 2) whether regulatory requirements create important challenges or barriers; and 3) whether there is a need for further guidance on the issue. The results of this survey are summarized and compared to issues and concerns experienced in other countries, as reported in the literature, to identify challenges which may be on the horizon and to provide possible solutions for regulatory reform.

The R2R3-MYB–Like Regulatory Factor EOBI, Acting Downstream of EOBII, Regulates Scent Production by Activating ODO1 and Structural Scent-Related Genes in Petunia[C][W

PubMed Central

Spitzer-Rimon, Ben; Farhi, Moran; Albo, Boaz; Cna’ani, Alon; Ben Zvi, Michal Moyal; Masci, Tania; Edelbaum, Orit; Yu, Yixun; Shklarman, Elena; Ovadis, Marianna; Vainstein, Alexander

2012-01-01

Flower scent is a highly dynamic trait, under developmental, spatial, and diurnal regulation. The mechanism governing scent production is only beginning to be unraveled. In petunia (Petunia hybrida), EMISSION OF BENZENOIDS II (EOBII) controls transcription of both the shikimate pathway-regulating MYB factor ODORANT1 (ODO1) and phenylpropanoid scent-related structural genes. A promoter-activation screen identified an R2R3-MYB–like regulatory factor of phenylpropanoid volatile biosynthesis acting downstream of EOBII, designated EOBI. EOBI silencing led to downregulation of ODO1 and numerous structural scent-related genes from both the shikimate and phenylpropanoid pathways. The ability of EOBI to directly activate ODO1, as revealed by electrophoretic mobility shift assay and yeast one-hybrid analysis, place EOBI upstream of ODO1 in regulating substrate availability for volatile biosynthesis. Interestingly, ODO1-silenced transgenic petunia flowers accumulated higher EOBI transcript levels than controls, suggesting a complex feedback loop between these regulatory factors. The accumulation pattern of EOBI transcript relative to EOBII and ODO1, and the effect of up/downregulation of EOBII on transcript levels of EOBI and ODO1, further support these factors' hierarchical relationships. The dependence of scent production on EOBI expression and its direct interaction with both regulatory and structural genes provide evidence for EOBI’s wide-ranging involvement in the production of floral volatiles. PMID:23275577

The R2R3-MYB-like regulatory factor EOBI, acting downstream of EOBII, regulates scent production by activating ODO1 and structural scent-related genes in petunia.

PubMed

Spitzer-Rimon, Ben; Farhi, Moran; Albo, Boaz; Cna'ani, Alon; Ben Zvi, Michal Moyal; Masci, Tania; Edelbaum, Orit; Yu, Yixun; Shklarman, Elena; Ovadis, Marianna; Vainstein, Alexander

2012-12-01

Flower scent is a highly dynamic trait, under developmental, spatial, and diurnal regulation. The mechanism governing scent production is only beginning to be unraveled. In petunia (Petunia hybrida), EMISSION OF BENZENOIDS II (EOBII) controls transcription of both the shikimate pathway-regulating MYB factor ODORANT1 (ODO1) and phenylpropanoid scent-related structural genes. A promoter-activation screen identified an R2R3-MYB-like regulatory factor of phenylpropanoid volatile biosynthesis acting downstream of EOBII, designated EOBI. EOBI silencing led to downregulation of ODO1 and numerous structural scent-related genes from both the shikimate and phenylpropanoid pathways. The ability of EOBI to directly activate ODO1, as revealed by electrophoretic mobility shift assay and yeast one-hybrid analysis, place EOBI upstream of ODO1 in regulating substrate availability for volatile biosynthesis. Interestingly, ODO1-silenced transgenic petunia flowers accumulated higher EOBI transcript levels than controls, suggesting a complex feedback loop between these regulatory factors. The accumulation pattern of EOBI transcript relative to EOBII and ODO1, and the effect of up/downregulation of EOBII on transcript levels of EOBI and ODO1, further support these factors' hierarchical relationships. The dependence of scent production on EOBI expression and its direct interaction with both regulatory and structural genes provide evidence for EOBI's wide-ranging involvement in the production of floral volatiles.

Effects of musicality and motivational orientation on auditory category learning: a test of a regulatory-fit hypothesis.

PubMed

McAuley, J Devin; Henry, Molly J; Wedd, Alan; Pleskac, Timothy J; Cesario, Joseph

2012-02-01

Two experiments investigated the effects of musicality and motivational orientation on auditory category learning. In both experiments, participants learned to classify tone stimuli that varied in frequency and duration according to an initially unknown disjunctive rule; feedback involved gaining points for correct responses (a gains reward structure) or losing points for incorrect responses (a losses reward structure). For Experiment 1, participants were told at the start that musicians typically outperform nonmusicians on the task, and then they were asked to identify themselves as either a "musician" or a "nonmusician." For Experiment 2, participants were given either a promotion focus prime (a performance-based opportunity to gain entry into a raffle) or a prevention focus prime (a performance-based criterion that needed to be maintained to avoid losing an entry into a raffle) at the start of the experiment. Consistent with a regulatory-fit hypothesis, self-identified musicians and promotion-primed participants given a gains reward structure made more correct tone classifications and were more likely to discover the optimal disjunctive rule than were musicians and promotion-primed participants experiencing losses. Reward structure (gains vs. losses) had inconsistent effects on the performance of nonmusicians, and a weaker regulatory-fit effect was found for the prevention focus prime. Overall, the findings from this study demonstrate a regulatory-fit effect in the domain of auditory category learning and show that motivational orientation may contribute to musician performance advantages in auditory perception.

Structure of soybean serine acetyltransferase and formation of the cysteine regulatory complex as a molecular chaperone

USDA-ARS?s Scientific Manuscript database

Serine acetyltransferase (SAT) catalyzes the limiting reaction in plant and microbial biosynthesis of cysteine. In addition to its enzymatic function, SAT forms a macromolecular complex with O-acetylserine sulfhydrylase (OASS). Formation of the cysteine regulatory complex (CRC) is a critical biochem...

Electric Industry Restructuring in Ohio: Residential and Low Income Customer Impacts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eisenberg, J

2001-03-26

Throughout the country the long standing administratively based regulatory structure for determining the cost and service parameters for electric utilities is changing. More and more market elements are coming into the structure. There is a push by many players to eliminate much of the current regulation. For the production side of electricity at least, these players argue that a market approach will do a better n job of pricing power and making it available to customers. However, the electricity industry currently has a large base of investment in power production equipment, some of which may have difficulty competing in amore » market-based system. What to do about this potentially uneconomic existing investment is an important question receiving a great deal of attention at the policy discussion level. Some argue that if the investment in existing facilities is uneconomic in a new market based system, that is too bad for the owners of the above-market cost facilities, and customers should bear no responsibility to help make those owners whole. Others argue that the owners of above-market cost facilities invested in those facilities in good faith and should not be made to bear the cost of a changing underlying industry structure. The arguments on both sides are long and involved, and this paper is not the place to explore them. However, it is clear that the result of the debate is uncertain, and both approaches must be explored. The purpose of this report is to analyze the current electric utility cost structure in Ohio, estimate the expected changes in that structure and cost levels under various restructuring proposals, and determine the likely impact on low income and other residential customers. The report analyzes the likely cost impacts of a variety of approaches to the above-market cost facility problem. The range of potential outcomes is very wide.« less

Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation.

PubMed

Xu, Jiajia; Bräutigam, Andrea; Weber, Andreas P M; Zhu, Xin-Guang

2016-09-01

Identification of potential cis-regulatory motifs controlling the development of C4 photosynthesis is a major focus of current research. In this study, we used time-series RNA-seq data collected from etiolated maize and rice leaf tissues sampled during a de-etiolation process to systematically characterize the expression patterns of C4-related genes and to further identify potential cis elements in five different genomic regions (i.e. promoter, 5'UTR, 3'UTR, intron, and coding sequence) of C4 orthologous genes. The results demonstrate that although most of the C4 genes show similar expression patterns, a number of them, including chloroplast dicarboxylate transporter 1, aspartate aminotransferase, and triose phosphate transporter, show shifted expression patterns compared with their C3 counterparts. A number of conserved short DNA motifs between maize C4 genes and their rice orthologous genes were identified not only in the promoter, 5'UTR, 3'UTR, and coding sequences, but also in the introns of core C4 genes. We also identified cis-regulatory motifs that exist in maize C4 genes and also in genes showing similar expression patterns as maize C4 genes but that do not exist in rice C3 orthologs, suggesting a possible recruitment of pre-existing cis-elements from genes unrelated to C4 photosynthesis into C4 photosynthesis genes during C4 evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Smart Markets for Transferable Pumping Rights

NASA Astrophysics Data System (ADS)

Brozovic, N.; Young, R.

2016-12-01

While no national policy on groundwater use exists in the United States, local groundwater management is emerging across the country in response to concerns and conflicts over declining well yields, land subsidence, and the depletion of hydrologically connected surface waters. Management strategies include well drilling moratoria, pumping restrictions, and restrictions on the expansion of irrigated land. To provide flexibility to groundwater users, local regulatory authorities increasingly have begun to allow the transfer of groundwater rights as a cost-effective management tool. Markets can be a versatile risk management tool, helping communities to cope with scarcity, to meet goals for sustainability, and to grow resilient local economies. For example, active groundwater rights transfers exist in the High Plains region of the United States. Yet, several barriers to trade exist: high search costs for interested parties, complicated requirements for regulatory compliance, and reluctance to share sensitive financial information. Additionally, groundwater pumping leads to several kinds of spatial and intertemporal externalities such as stream depletion. Indeed, groundwater management schemes that reallocate water between alternate pumping locations are often explicitly designed to change the distribution and magnitude of pumping externalities. Reallocation may be designed to minimize unwanted impacts on third parties or to encourage trades that reduce the magnitude of externalities. We discuss how smart markets can deal with complex biophysical constraints while also encouraging active trading, therefore ensuring local goals for aquifer sustainability while growing local economies. Smart markets address these issues by providing a centralized hub for trading, automating the process of regulatory compliance by only matching buyers and sellers eligible to trade as specified in the regulations, and maintaining anonymous, confidential bidding.

75 FR 62893 - Draft Regulatory Guide: Issuance, Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-13

... for using portland cement grout to protect prestressing steel from corrosion. The prestressing tendon system of a prestressed concrete containment structure is a principal strength element of the structure... of the structure depends on the functional reliability of the structure's principal strength elements...

Better by design: business preferences for environmental regulatory reform.

PubMed

Taylor, Christopher M; Pollard, Simon J T; Rocks, Sophie A; Angus, Andrew J

2015-04-15

We present the preferences for environmental regulatory reform expressed by 30 UK businesses and industry bodies from 5 sectors. While five strongly preferred voluntary regulation, seven expressed doubts about its effectiveness, and 18 expressed no general preference between instrument types. Voluntary approaches were valued for flexibility and lower burdens, but direct regulation offered stability and a level playing field. Respondents sought regulatory frameworks that: are coherent; balance clarity, prescription and flexibility; are enabled by positive regulatory relationships; administratively efficient; targeted according to risk magnitude and character; evidence-based and that deliver long-term market stability for regulatees. Anticipated differences in performance between types of instrument can be undermined by poor implementation. Results underline the need for policy makers and regulators to tailor an effective mix of instruments for a given sector, and to overcome analytical, institutional and political barriers to greater coherence, to better coordinate existing instruments and tackle new environmental challenges as they emerge. Copyright © 2015 Elsevier B.V. All rights reserved.

Private governance, public purpose? Assessing transparency and accountability in self-regulation of food advertising to children.

PubMed

Reeve, Belinda

2013-06-01

Reducing non-core food advertising to children is an important priority in strategies to address childhood obesity. Public health researchers argue for government intervention on the basis that food industry self-regulation is ineffective; however, the industry contends that the existing voluntary scheme adequately addresses community concerns. This paper examines the operation of two self-regulatory initiatives governing food advertising to children in Australia, in order to determine whether these regulatory processes foster transparent and accountable self-regulation. The paper concludes that while both codes appear to establish transparency and accountability mechanisms, they do not provide for meaningful stakeholder participation in the self-regulatory scheme. Accordingly, food industry self-regulation is unlikely to reflect public health concerns or to be perceived as a legitimate form of governance by external stakeholders. If industry regulation is to remain a feasible alternative to statutory regulation, there is a strong argument for strengthening government oversight and implementing a co-regulatory scheme.

Passing messages between biological networks to refine predicted interactions.

PubMed

Glass, Kimberly; Huttenhower, Curtis; Quackenbush, John; Yuan, Guo-Cheng

2013-01-01

Regulatory network reconstruction is a fundamental problem in computational biology. There are significant limitations to such reconstruction using individual datasets, and increasingly people attempt to construct networks using multiple, independent datasets obtained from complementary sources, but methods for this integration are lacking. We developed PANDA (Passing Attributes between Networks for Data Assimilation), a message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to reconstruct genome-wide, condition-specific regulatory networks in yeast as a model. The resulting networks were not only more accurate than those produced using individual data sets and other existing methods, but they also captured information regarding specific biological mechanisms and pathways that were missed using other methodologies. PANDA is scalable to higher eukaryotes, applicable to specific tissue or cell type data and conceptually generalizable to include a variety of regulatory, interaction, expression, and other genome-scale data. An implementation of the PANDA algorithm is available at www.sourceforge.net/projects/panda-net.

Mutual Regulation of NOD2 and RIG-I in Zebrafish Provides Insights into the Coordination between Innate Antibacterial and Antiviral Signaling Pathways.

PubMed

Nie, Li; Xu, Xiao-Xiao; Xiang, Li-Xin; Shao, Jian-Zhong; Chen, Jiong

2017-05-27

Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) and retinoic acid-inducible gene I (RIG-I) are two important cytosolic pattern recognition receptors (PRRs) in the recognition of pathogen-associated molecular patterns (PAMPs), initiating innate antibacterial and antiviral signaling pathways. However, the relationship between these PRRs, especially in teleost fish models, is rarely reported. In this article, we describe the mutual regulation of zebrafish NOD2 ( Dr NOD2) and RIG-I ( Dr RIG-I) in innate immune responses. Luciferase assays were conducted to determine the activation of NF-κB and interferon signaling. Morpholino-mediated knockdown and mRNA-mediated rescue were performed to further confirm the regulatory roles between Dr NOD2 and Dr RIG-I. Results showed that Dr NOD2 and Dr RIG-I shared conserved structural hallmarks with their mammalian counterparts, and activated Dr RIG-I signaling can induce Dr NOD2 production. Surprisingly, Dr NOD2-initiated signaling can also induce Dr RIG-I expression, indicating that a mutual regulatory mechanism may exist between them. Studies conducted using HEK293T cells and zebrafish embryos showed that Dr RIG-I could negatively regulate Dr NOD2-activated NF-κB signaling, and Dr NOD2 could inhibit Dr RIG-I-induced IFN signaling. Moreover, knocking down Dr RIG-I expression by morpholino could enhance Dr NOD2-initiated NF-κB activation, and vice versa, which could be rescued by their corresponding mRNAs. Results revealed a mutual feedback regulatory mechanism underlying NOD2 and RIG-I signaling pathways in teleosts. This mechanism reflects the coordination between cytosolic antibacterial and antiviral PRRs in the complex network of innate immunity.

Manufacturing models permitting roll out/scale out of clinically led autologous cell therapies: regulatory and scientific challenges for comparability.

PubMed

Hourd, Paul; Ginty, Patrick; Chandra, Amit; Williams, David J

2014-08-01

Manufacturing of more-than-minimally manipulated autologous cell therapies presents a number of unique challenges driven by complex supply logistics and the need to scale out production to multiple manufacturing sites or near the patient within hospital settings. The existing regulatory structure in Europe and the United States imposes a requirement to establish and maintain comparability between sites. Under a single market authorization, this is likely to become an unsurmountable burden beyond two or three sites. Unless alternative manufacturing approaches can be found to bridge the regulatory challenge of comparability, realizing a sustainable and investable business model for affordable autologous cell therapy supply is likely to be extremely demanding. Without a proactive approach by the regulators to close this "translational gap," these products may not progress down the development pipeline, threatening patient accessibility to an increasing number of clinician-led autologous cellular therapies that are already demonstrating patient benefits. We propose three prospective manufacturing models for the scale out/roll out of more-than-minimally manipulated clinically led autologous cell therapy products and test their prospects for addressing the challenge of product comparability with a selected expert reference panel of US and UK thought leaders. This paper presents the perspectives and insights of the panel and identifies where operational, technological and scientific improvements should be prioritized. The main purpose of this report is to solicit feedback and seek input from key stakeholders active in the field of autologous cell therapy in establishing a consensus-based manufacturing approach that may permit the roll out of clinically led autologous cell therapies. Copyright © 2014 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

African swine fever: background, present time and prospects

USDA-ARS?s Scientific Manuscript database

The purpose of this monograph is to summarize the existing international and national experience of monitoring, diagnostics, forecasting, and implementing measures of management and control of ASF. This publication contains national and international regulatory documents, reference materials and the...

78 FR 69167 - Self-Regulatory Organizations; ICE Clear Credit LLC; Order Approving Proposed Rule Change To...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-18

..., the Bolivian Republic of Venezuela, the Argentine Republic, the Republic of Turkey and the Russian... transactions, and ICC's proposal, in combination with its existing rules, policies, and procedures for clearing...

75 FR 48381 - Final Regulatory Guide: Issuance, Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-10

..., (2) demonstrating containment structural integrity related to combustible gas control, and (3... pertain to the containment structural capacity above design-basis pressures, to combustible gas control...

Dehydration responsive element binding transcription factors and their applications for the engineering of stress tolerance.

PubMed

Agarwal, Pradeep K; Gupta, Kapil; Lopato, Sergiy; Agarwal, Parinita

2017-04-01

Dehydration responsive element binding (DREB) factors or CRT element binding factors (CBFs) are members of the AP2/ERF family, which comprises a large number of stress-responsive regulatory genes. This review traverses almost two decades of research, from the discovery of DREB/CBF factors to their optimization for application in plant biotechnology. In this review, we describe (i) the discovery, classification, structure, and evolution of DREB genes and proteins; (ii) induction of DREB genes by abiotic stresses and involvement of their products in stress responses; (iii) protein structure and DNA binding selectivity of different groups of DREB proteins; (iv) post-transcriptional and post-translational mechanisms of DREB transcription factor (TF) regulation; and (v) physical and/or functional interaction of DREB TFs with other proteins during plant stress responses. We also discuss existing issues in applications of DREB TFs for engineering of enhanced stress tolerance and improved performance under stress of transgenic crop plants. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Structure-guided mutational analysis reveals the functional requirements for product specificity of DOT1 enzymes.

PubMed

Dindar, Gülcin; Anger, Andreas M; Mehlhorn, Christine; Hake, Sandra B; Janzen, Christian J

2014-11-12

DOT1 enzymes are conserved methyltransferases that catalyse the methylation of lysine 79 on histone H3 (H3K79). Most eukaryotes contain one DOT1 enzyme, whereas African trypanosomes have two homologues, DOT1A and DOT1B, with different enzymatic activities. DOT1A mediates mono- and dimethylation of H3K76, the homologue of H3K79 in other organisms, whereas DOT1B additionally catalyses H3K76 trimethylation. However, it is unclear how these different enzymatic activities are achieved. Here we employ a trypanosomal nucleosome reconstitution system and structure-guided homology modelling to identify critical residues within and outside the catalytic centre that modulate product specificity. Exchange of these residues transfers the product specificity from one enzyme to the other, and reveals the existence of distinct regulatory domains adjacent to the catalytic centre. Our study provides the first evidence that a few crucial residues in DOT1 enzymes are sufficient to catalyse methyl-state-specific reactions. These results might also have far-reaching consequences for the functional understanding of homologous enzymes in higher eukaryotes.

Structural decoding of netrin-4 reveals a regulatory function towards mature basement membranes

PubMed Central

Reuten, Raphael; Patel, Trushar R.; McDougall, Matthew; Rama, Nicolas; Nikodemus, Denise; Gibert, Benjamin; Delcros, Jean-Guy; Prein, Carina; Meier, Markus; Metzger, Stéphanie; Zhou, Zhigang; Kaltenberg, Jennifer; McKee, Karen K.; Bald, Tobias; Tüting, Thomas; Zigrino, Paola; Djonov, Valentin; Bloch, Wilhelm; Clausen-Schaumann, Hauke; Poschl, Ernst; Yurchenco, Peter D.; Ehrbar, Martin; Mehlen, Patrick; Stetefeld, Jörg; Koch, Manuel

2016-01-01

Netrins, a family of laminin-related molecules, have been proposed to act as guidance cues either during nervous system development or the establishment of the vascular system. This was clearly demonstrated for netrin-1 via its interaction with the receptors DCC and UNC5s. However, mainly based on shared homologies with netrin-1, netrin-4 was also proposed to play a role in neuronal outgrowth and developmental/pathological angiogenesis via interactions with netrin-1 receptors. Here, we present the high-resolution structure of netrin-4, which shows unique features in comparison with netrin-1, and show that it does not bind directly to any of the known netrin-1 receptors. We show that netrin-4 disrupts laminin networks and basement membranes (BMs) through high-affinity binding to the laminin γ1 chain. We hypothesize that this laminin-related function is essential for the previously described effects on axon growth promotion and angiogenesis. Our study unveils netrin-4 as a non-enzymatic extracellular matrix protein actively disrupting pre-existing BMs. PMID:27901020

Use of physiologically relevant biopharmaceutics tools within the pharmaceutical industry and in regulatory sciences: Where are we now and what are the gaps?

PubMed

Flanagan, Talia; Van Peer, Achiel; Lindahl, Anders

2016-08-25

Regulatory interactions are an important part of the drug development and licensing process. A survey on the use of biopharmaceutical tools for regulatory purposes has been carried out within the industry community of the EU project OrBiTo within Innovative Medicines Initiative (IMI). The aim was to capture current practice and experience in using in vitro and in silico biopharmaceutics tools at various stages of development, what barriers exist or are perceived, and to understand the current gaps in regulatory biopharmaceutics. The survey indicated that biorelevant dissolution testing and physiologically based modelling and simulation are widely applied throughout development to address a number of biopharmaceutics issues. However, data from these in vitro and in silico predictive biopharmaceutics tools are submitted to regulatory authorities far less often than they are used for internal risk assessment and decision making. This may prevent regulators from becoming familiar with these tools and how they are applied in industry, and limits the opportunities for biopharmaceutics scientists working in industry to understand the acceptability of these tools in the regulatory environment. It is anticipated that the advanced biopharmaceutics tools and understanding delivered in the next years by OrBiTo and other initiatives in the area of predictive tools will also be of value in the regulatory setting, and provide a basis for more informed and confident biopharmaceutics risk assessment and regulatory decision making. To enable the regulatory potential of predictive biopharmaceutics tools to be realized, further scientific dialogue is needed between industry, regulators and scientists in academia, and more examples need to be published to demonstrate the applicability of these tools. Copyright © 2016 Elsevier B.V. All rights reserved.

Pharmaceuticals in the environment: scientific evidence of risks and its regulation

PubMed Central

Küster, Anette; Adler, Nicole

2014-01-01

During the past two decades scientists, regulatory agencies and the European Commission have acknowledged pharmaceuticals to be an emerging environmental problem. In parallel, a regulatory framework for environmental risk assessment (ERA) of pharmaceutical products has been developed. Since the regulatory guidelines came into force the German Federal Agency (UBA) has been evaluating ERAs for human and veterinary pharmaceutical products before they are marketed. The results show that approximately 10% of pharmaceutical products are of note regarding their potential environmental risk. For human medicinal products, hormones, antibiotics, analgesics, antidepressants and antineoplastics indicated an environmental risk. For veterinary products, hormones, antibiotics and parasiticides were most often discussed as being environmentally relevant. These results are in good correlation with the results within the open scientific literature of prioritization approaches for pharmaceuticals in the environment. UBA results revealed that prospective approaches, such as ERA of pharmaceuticals, play an important role in minimizing problems caused by pharmaceuticals in the environment. However, the regulatory ERA framework could be improved by (i) inclusion of the environment in the risk–benefit analysis for human pharmaceuticals, (ii) improvement of risk management options, (iii) generation of data on existing pharmaceuticals, and (iv) improving the availability of ERA data. In addition, more general and integrative steps of regulation, legislation and research have been developed and are presented in this article. In order to minimize the quantity of pharmaceuticals in the environment these should aim to (i) improve the existing legislation for pharmaceuticals, (ii) prioritize pharmaceuticals in the environment and (iii) improve the availability and collection of pharmaceutical data. PMID:25405974

Regulatory categories of probiotics across the globe: a review representing existing and recommended categorization.

PubMed

Arora, M; Baldi, A

2015-02-01

Probiotics are friendly live microorganisms (in most cases, bacteria) that are similar to beneficial micro-organisms found in the human gut, whenever consumed, have potential to confer benefit to the health of consumers by maintaining, or improving their intestinal microbial flora and are available to consumers mainly in the form of dietary supplements and foods. All-time high interest in the field of probiotics is due to emerging probiotic industry. Probiotics are available in foods and dietary supplements, even as pharmaceutical formulations (capsules, tablets and powders) and in some other forms as well, but their claims of health benefits may challenge the traditional border between food and medicine. A number of probiotic products have been already introduced into the international market as food supplements, dietary supplements, natural health products, functional foods and many more other categories; as a result, the position of regulatory system for probiotics within existing categories become vague and quite unclear. Common terminology for probiotic products has become a necessity to achieve adequate regulatory control for discussion of probiotic-related issues among government, producers and consumers. The lack of a consistent terminology across the globe leads to legal uncertainty and confusion instead of being a direct obstacle for development of a mature market. This article will explain differences in regulatory categorizations across the globe; discuss the terms like food and drugs with a close relationship to probiotics, the problems associated with unsatisfactorily approached categorization as well as suggestive consolidations for the new categorization which will demarcate probiotics into categories explaining their nutritive claims, health claims or both.

Drug Lag and Key Regulatory Barriers in the Emerging Markets

PubMed Central

Wileman, Harriet; Mishra, Arun

2010-01-01

There have been numerous investigations targeted at identifying whether a drug lag exists in the mature markets of the US, EU and Japan. This work focuses on the emerging markets because of the potential they hold for the future of the pharmaceutical industry as a consequence of rapid economic and political development. The aims of this work are to ascertain whether a drug lag exists in the emerging markets and how it has changed over time from the 1960s to the 2000s. It will also highlight key regulatory barriers which may contribute to drug lag. The date of the marketing authorisation (MA) approval by the US Food and Drug Administration (FDA) was used as a reference point. A comparison against the company database regarding emerging market specific approval enabled the difference in time and thus the drug lag for that particular market to be calculated. This work concludes that the overall relative drug lag in the emerging markets has decreased over time and that there are seven key regulatory barriers which need to be targeted in order to make further improvements; ‘Western Approval’, local clinical development (LCD), Certificate of Pharmaceutical Product (CPP), Good Manufacturing Practice (GMP), pricing approval, document authentication and harmonisation. PMID:21829782

G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch.

PubMed

Kaplan, Oktay I; Berber, Burak; Hekim, Nezih; Doluca, Osman

2016-11-02

Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

AKAP18:PKA-RIIα structure reveals crucial anchor points for recognition of regulatory subunits of PKA

PubMed Central

Götz, Frank; Roske, Yvette; Schulz, Maike Svenja; Autenrieth, Karolin; Bertinetti, Daniela; Faelber, Katja; Zühlke, Kerstin; Kreuchwig, Annika; Kennedy, Eileen J.; Krause, Gerd; Daumke, Oliver; Herberg, Friedrich W.; Heinemann, Udo; Klussmann, Enno

2016-01-01

A-kinase anchoring proteins (AKAPs) interact with the dimerization/docking (D/D) domains of regulatory subunits of the ubiquitous protein kinase A (PKA). AKAPs tether PKA to defined cellular compartments establishing distinct pools to increase the specificity of PKA signalling. Here, we elucidated the structure of an extended PKA-binding domain of AKAP18β bound to the D/D domain of the regulatory RIIα subunits of PKA. We identified three hydrophilic anchor points in AKAP18β outside the core PKA-binding domain, which mediate contacts with the D/D domain. Such anchor points are conserved within AKAPs that bind regulatory RII subunits of PKA. We derived a different set of anchor points in AKAPs binding regulatory RI subunits of PKA. In vitro and cell-based experiments confirm the relevance of these sites for the interaction of RII subunits with AKAP18 and of RI subunits with the RI-specific smAKAP. Thus we report a novel mechanism governing interactions of AKAPs with PKA. The sequence specificity of each AKAP around the anchor points and the requirement of these points for the tight binding of PKA allow the development of selective inhibitors to unequivocally ascribe cellular functions to the AKAP18-PKA and other AKAP-PKA interactions. PMID:27102985

Partial cooperative unfolding in proteins as observed by hydrogen exchange mass spectrometry

PubMed Central

Engen, John R.; Wales, Thomas E.; Chen, Shugui; Marzluff, Elaine M.; Hassell, Kerry M.; Weis, David D.; Smithgall, Thomas E.

2013-01-01

Many proteins do not exist in a single rigid conformation. Protein motions, or dynamics, exist and in many cases are important for protein function. The analysis of protein dynamics relies on biophysical techniques that can distinguish simultaneously existing populations of molecules and their rates of interconversion. Hydrogen exchange (HX) detected by mass spectrometry (MS) is contributing to our understanding of protein motions by revealing unfolding and dynamics on a wide timescale, ranging from seconds to hours to days. In this review we discuss HX MS-based analyses of protein dynamics, using our studies of multi-domain kinases as examples. Using HX MS, we have successfully probed protein dynamics and unfolding in the isolated SH3, SH2 and kinase domains of the c-Src and Abl kinase families, as well as the role of inter- and intra-molecular interactions in the global control of kinase function. Coupled with high-resolution structural information, HX MS has proved to be a powerful and versatile tool for the analysis of the conformational dynamics in these kinase systems, and has provided fresh insight regarding the regulatory control of these important signaling proteins. HX MS studies of dynamics are applicable not only to the proteins we illustrate here, but to a very wide range of proteins and protein systems, and should play a role in both classification of and greater understanding of the prevalence of protein motion. PMID:23682200

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants.

PubMed

Jin, Jinpu; Tian, Feng; Yang, De-Chang; Meng, Yu-Qi; Kong, Lei; Luo, Jingchu; Gao, Ge

2017-01-04

With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements. In addition, we upgraded previous TF prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. Finally, we set up a novel companion portal PlantRegMap (http://plantregmap.cbi.pku.edu.cn) for users to access the regulation resource and analysis tools conveniently. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Regulating the path from legacy recognition, through recovery to release from regulatory control.

PubMed

Sneve, Malgorzata Karpow; Smith, Graham

2015-04-01

Past development of processes and technologies using radioactive material led to construction of many facilities worldwide. Some of these facilities were built and operated before the regulatory infrastructure was in place to ensure adequate control of radioactive material during operation and decommissioning. In other cases, controls were in place but did not meet modern standards, leading to what is now considered to have been inadequate control. Accidents and other events have occurred resulting in loss of control of radioactive material and unplanned releases to the environment. The legacy from these circumstances is that many countries have areas or facilities at which abnormal radiation conditions exist at levels that give rise to concerns about environmental and human health of potential interest to regulatory authorities. Regulation of these legacy situations is complex. This paper examines the regulatory challenges associated with such legacy management and brings forward suggestions for finding the path from: legacy recognition; implementation, as necessary, of urgent mitigation measures; development of a longer-term management strategy, through to release from regulatory control. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Adaptive Benefits of Storage Strategy and Dual AMPK/TOR Signaling in Metabolic Stress Response

PubMed Central

Pfeuty, Benjamin; Thommen, Quentin

2016-01-01

Cellular metabolism must ensure that supply of nutrient meets the biosynthetic and bioenergetic needs. Cells have therefore developed sophisticated signaling and regulatory pathways in order to cope with dynamic fluctuations of both resource and demand and to regulate accordingly diverse anabolic and catabolic processes. Intriguingly, these pathways are organized around a relatively small number of regulatory hubs, such as the highly conserved AMPK and TOR kinase families in eukaryotic cells. Here, the global metabolic adaptations upon dynamic environment are investigated using a prototypical model of regulated metabolism. In this model, the optimal enzyme profiles as well as the underlying regulatory architecture are identified by combining perturbation and evolutionary methods. The results reveal the existence of distinct classes of adaptive strategies, which differ in the management of storage reserve depending on the intensity of the stress and in the regulation of ATP-producing reaction depending on the nature of the stress. The regulatory architecture that optimally implements these adaptive features is characterized by a crosstalk between two specialized signaling pathways, which bears close similarities with the sensing and regulatory properties of AMPK and TOR pathways. PMID:27505075

Paving the road to personalized medicine: recommendations on regulatory, intellectual property and reimbursement challenges

PubMed Central

Knowles, Lori; Luth, Westerly; Bubela, Tania

2017-01-01

Abstract Personalized medicine (PM) aims to harness a wave of ‘omics’ discoveries to facilitate research and discovery of targeted diagnostics and therapies and increase the efficiency of healthcare systems by predicting and treating individual predispositions to diseases or conditions. Despite significant investment, limited progress has been made bringing PM to market. We describe the major perceived regulatory, intellectual property, and reimbursement challenges to the development, translation, adoption, and implementation of PM products into clinical care. We conducted a scoping review to identify (i) primary challenges for the development and implementation of PM identified in the academic literature; (ii) solutions proposed in the academic literature to address these challenges; and (iii) gaps that exist in that literature. We identified regulatory barriers to PM development and recommendations in 344 academic papers. Regulatory uncertainty was a cross-cutting theme that appeared in conjunction with other themes including: reimbursement; clinical trial regulation; regulation of co-development; unclear evidentiary requirements; insufficient incentives for research and development; incompatible information systems; and different regulation of different diagnostics. To fully realize the benefits of PM for healthcare systems and patients, regulatory, intellectual property, and reimbursement challenges need to be addressed in lock step with scientific advances. PMID:29868182

Groundwater contamination from waste management sites: The interaction between risk-based engineering design and regulatory policy: 1. Methodology

NASA Astrophysics Data System (ADS)

Massmann, Joel; Freeze, R. Allan

1987-02-01

This paper puts in place a risk-cost-benefit analysis for waste management facilities that explicitly recognizes the adversarial relationship that exists in a regulated market economy between the owner/operator of a waste management facility and the government regulatory agency under whose terms the facility must be licensed. The risk-cost-benefit analysis is set up from the perspective of the owner/operator. It can be used directly by the owner/operator to assess alternative design strategies. It can also be used by the regulatory agency to assess alternative regulatory policy, but only in an indirect manner, by examining the response of an owner/operator to the stimuli of various policies. The objective function is couched in terms of a discounted stream of benefits, costs, and risks over an engineering time horizon. Benefits are in the form of revenues for services provided; costs are those of construction and operation of the facility. Risk is defined as the cost associated with the probability of failure, with failure defined as the occurrence of a groundwater contamination event that violates the licensing requirements established for the facility. Failure requires a breach of the containment structure and contaminant migration through the hydrogeological environment to a compliance surface. The probability of failure can be estimated on the basis of reliability theory for the breach of containment and with a Monte-Carlo finite-element simulation for the advective contaminant transport. In the hydrogeological environment the hydraulic conductivity values are defined stochastically. The probability of failure is reduced by the presence of a monitoring network operated by the owner/operator and located between the source and the regulatory compliance surface. The level of reduction in the probability of failure depends on the probability of detection of the monitoring network, which can be calculated from the stochastic contaminant transport simulations. While the framework is quite general, the development in this paper is specifically suited for a landfill in which the primary design feature is one or more synthetic liners in parallel. Contamination is brought about by the release of a single, inorganic nonradioactive species into a saturated, high-permeability, advective, steady state horizontal flow system which can be analyzed with a two-dimensional analysis. It is possible to carry out sensitivity analyses for a wide variety of influences on this system, including landfill size, liner design, hydrogeological parameters, amount of exploration, extent of monitoring network, nature of remedial schemes, economic factors, and regulatory policy.

Depressive symptoms, post-traumatic stress symptoms and suicide risk among graduate students: The mediating influence of emotional regulatory self-efficacy.

PubMed

Zeng, Baoer; Zhao, Jiubo; Zou, Laiquan; Yang, Xueling; Zhang, Xiaoyuan; Wang, Wanjun; Zhao, Jingbo; Chen, Jie

2018-06-01

The current study was to examine the relationship among depressive symptoms, post-traumatic stress symptoms, emotion regulatory self-efficacy and suicide risk. A cross-sectional survey was conducted among 3257 graduate students from a medical college of China. Lifetime prevalence of suicidal ideation, plan and attempt were 25.7%, 1.6%, 1.1%, respectively, with one-year suicidal ideation showing at 6.3%. Structural equation modeling was employed to examine the relative contribution of depressive symptoms, post-traumatic stress symptoms and emotion regulatory self-efficacy on suicide risk. Structural equation model had a highly satisfactory fit [χ 2  = 7.782, df = 4, p = 0.096; RMSEA = 0.021; CFI = 0.992; GFI = 0.997]. Post-traumatic stress symptoms had a direct effect and an indirect effect on suicide risk via emotion regulatory self-efficacy. Depressive symptoms also had a direct effect and an indirect effect on suicide risk via emotion regulatory self-efficacy. The depressive and post-traumatic stress symptoms increased the risk of suicide risk, but the variable of emotion regulatory self-efficacy would be served as a buffering factor, decreasing the risk of suicide. The interaction term of depressive symptoms and post-traumatic stress symptoms had a direct effect on suicide risk. A significant interactive effect of depressive and post-traumatic stress symptoms on suicide risk was found. Copyright © 2018 Elsevier B.V. All rights reserved.

Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence

PubMed Central

Iskow, Rebecca C.; Austermann, Christian; Scharer, Christopher D.; Raj, Towfique; Boss, Jeremy M.; Sunyaev, Shamil; Price, Alkes; Stranger, Barbara; Simon, Viviana; Lee, Charles

2013-01-01

Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10−15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003) and positive Tajima's D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human–Neandertal divergence and is evolving under balancing selection, especially among European populations. PMID:23593015

Self-Regulatory Behaviors and Approaches to Learning of Arts Students: A Comparison between Professional Training and English Learning

ERIC Educational Resources Information Center

Tseng, Min-chen; Chen, Chia-cheng

2017-01-01

This study investigated the self-regulatory behaviors of arts students, namely memory strategy, goal-setting, self-evaluation, seeking assistance, environmental structuring, learning responsibility, and planning and organizing. We also explored approaches to learning, including deep approach (DA) and surface approach (SA), in a comparison between…

78 FR 970 - Self-Regulatory Organizations; Fixed Income Clearing Corporation; Notice of Filing and Immediate...

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Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory NolR

USDA-ARS?s Scientific Manuscript database

The symbiosis between rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. As part of the transcriptional machinery for nodulation and symbiosis across a range of Rhizobium, NolR serves as a global regulatory...

Biomechanical cell regulatory networks as complex adaptive systems in relation to cancer.

PubMed

Feller, Liviu; Khammissa, Razia Abdool Gafaar; Lemmer, Johan

2017-01-01

Physiological structure and function of cells are maintained by ongoing complex dynamic adaptive processes in the intracellular molecular pathways controlling the overall profile of gene expression, and by genes in cellular gene regulatory circuits. Cytogenetic mutations and non-genetic factors such as chronic inflammation or repetitive trauma, intrinsic mechanical stresses within extracellular matrix may induce redirection of gene regulatory circuits with abnormal reactivation of embryonic developmental programmes which can now drive cell transformation and cancer initiation, and later cancer progression and metastasis. Some of the non-genetic factors that may also favour cancerization are dysregulation in epithelial-mesenchymal interactions, in cell-to-cell communication, in extracellular matrix turnover, in extracellular matrix-to-cell interactions and in mechanotransduction pathways. Persistent increase in extracellular matrix stiffness, for whatever reason, has been shown to play an important role in cell transformation, and later in cancer cell invasion. In this article we review certain cell regulatory networks driving carcinogenesis, focussing on the role of mechanical stresses modulating structure and function of cells and their extracellular matrices.

Disciplining Qualitative Research

ERIC Educational Resources Information Center

Denzin, Norman K.; Lincoln, Yvonna S.; Giardina, Michael D.

2006-01-01

Qualitative research exists in a time of global uncertainty. Around the world, governments are attempting to regulate scientific inquiry by defining what counts as "good" science. These regulatory activities raise fundamental, philosophical epistemological, political and pedagogical issues for scholarship and freedom of speech in the…

Setting the stage to advance the adverse outcome pathway (AOP) framework through horizon scanning

EPA Science Inventory

Recognizing the international interest surrounding the adverse outcome pathway framework, which captures existing information describing causal linkages between a molecular initiating event through levels of biological organization to an adverse outcome of regulatory significance...

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Hierarchical coordinate systems for understanding complexity and its evolution, with applications to genetic regulatory networks.

PubMed

Egri-Nagy, Attila; Nehaniv, Chrystopher L

2008-01-01

Beyond complexity measures, sometimes it is worthwhile in addition to investigate how complexity changes structurally, especially in artificial systems where we have complete knowledge about the evolutionary process. Hierarchical decomposition is a useful way of assessing structural complexity changes of organisms modeled as automata, and we show how recently developed computational tools can be used for this purpose, by computing holonomy decompositions and holonomy complexity. To gain insight into the evolution of complexity, we investigate the smoothness of the landscape structure of complexity under minimal transitions. As a proof of concept, we illustrate how the hierarchical complexity analysis reveals symmetries and irreversible structure in biological networks by applying the methods to the lac operon mechanism in the genetic regulatory network of Escherichia coli.

Organizing Environmental Flow Frameworks to Meet Hydropower Mitigation Needs

NASA Astrophysics Data System (ADS)

McManamay, Ryan A.; Brewer, Shannon K.; Jager, Henriette I.; Troia, Matthew J.

2016-09-01

The global recognition of the importance of natural flow regimes to sustain the ecological integrity of river systems has led to increased societal pressure on the hydropower industry to change plant operations to improve downstream aquatic ecosystems. However, a complete reinstatement of natural flow regimes is often unrealistic when balancing water needs for ecosystems, energy production, and other human uses. Thus, stakeholders must identify a prioritized subset of flow prescriptions that meet ecological objectives in light of realistic constraints. Yet, isolating aspects of flow regimes to restore downstream of hydropower facilities is among the greatest challenges of environmental flow science due, in part, to the sheer volume of available environmental flow tools in conjunction with complex negotiation-based regulatory procedures. Herein, we propose an organizational framework that structures information and existing flow paradigms into a staged process that assists stakeholders in implementing environmental flows for hydropower facilities. The framework identifies areas where regulations fall short of the needed scientific process, and provide suggestions for stakeholders to ameliorate those situations through advanced preparation. We highlight the strengths of existing flow paradigms in their application to hydropower settings and suggest when and where tools are most applicable. Our suggested framework increases the effectiveness and efficiency of the e-flow implementation process by rapidly establishing a knowledge base and decreasing uncertainty so more time can be devoted to filling knowledge gaps. Lastly, the framework provides the structure for a coordinated research agenda to further the science of environmental flows related to hydropower environments.

Organizing environmental flow frameworks to meet hydropower mitigation needs

USGS Publications Warehouse

McManamay, Ryan A.; Brewer, Shannon K.; Jager, Henriette; Troia, Matthew J.

2016-01-01

The global recognition of the importance of natural flow regimes to sustain the ecological integrity of river systems has led to increased societal pressure on the hydropower industry to change plant operations to improve downstream aquatic ecosystems. However, a complete reinstatement of natural flow regimes is often unrealistic when balancing water needs for ecosystems, energy production, and other human uses. Thus, stakeholders must identify a prioritized subset of flow prescriptions that meet ecological objectives in light of realistic constraints. Yet, isolating aspects of flow regimes to restore downstream of hydropower facilities is among the greatest challenges of environmental flow science due, in part, to the sheer volume of available environmental flow tools in conjunction with complex negotiation-based regulatory procedures. Herein, we propose an organizational framework that structures information and existing flow paradigms into a staged process that assists stakeholders in implementing environmental flows for hydropower facilities. The framework identifies areas where regulations fall short of the needed scientific process, and provide suggestions for stakeholders to ameliorate those situations through advanced preparation. We highlight the strengths of existing flow paradigms in their application to hydropower settings and suggest when and where tools are most applicable. Our suggested framework increases the effectiveness and efficiency of the e-flow implementation process by rapidly establishing a knowledge base and decreasing uncertainty so more time can be devoted to filling knowledge gaps. Lastly, the framework provides the structure for a coordinated research agenda to further the science of environmental flows related to hydropower environments.

Organizing Environmental Flow Frameworks to Meet Hydropower Mitigation Needs.

PubMed

McManamay, Ryan A; Brewer, Shannon K; Jager, Henriette I; Troia, Matthew J

2016-09-01

The global recognition of the importance of natural flow regimes to sustain the ecological integrity of river systems has led to increased societal pressure on the hydropower industry to change plant operations to improve downstream aquatic ecosystems. However, a complete reinstatement of natural flow regimes is often unrealistic when balancing water needs for ecosystems, energy production, and other human uses. Thus, stakeholders must identify a prioritized subset of flow prescriptions that meet ecological objectives in light of realistic constraints. Yet, isolating aspects of flow regimes to restore downstream of hydropower facilities is among the greatest challenges of environmental flow science due, in part, to the sheer volume of available environmental flow tools in conjunction with complex negotiation-based regulatory procedures. Herein, we propose an organizational framework that structures information and existing flow paradigms into a staged process that assists stakeholders in implementing environmental flows for hydropower facilities. The framework identifies areas where regulations fall short of the needed scientific process, and provide suggestions for stakeholders to ameliorate those situations through advanced preparation. We highlight the strengths of existing flow paradigms in their application to hydropower settings and suggest when and where tools are most applicable. Our suggested framework increases the effectiveness and efficiency of the e-flow implementation process by rapidly establishing a knowledge base and decreasing uncertainty so more time can be devoted to filling knowledge gaps. Lastly, the framework provides the structure for a coordinated research agenda to further the science of environmental flows related to hydropower environments.

Cytoprotective Polyphenols Against Chronological Skin Aging and Cutaneous Photodamage.

PubMed

Davinelli, Sergio; Bertoglio, Juan Carlos; Polimeni, Ascanio; Scapagnini, Giovanni

2018-01-01

Skin aging is a complex biological process influenced by a combination of intrinsic and extrinsic factors, leading to cumulative alterations of skin structure, function and appearance. Polyphenols, which are secondary plant metabolites, represent one of the largest classes of compounds used in dermatology and nutricosmetics to combat skin aging. The main objective is to provide an overview of the existing literature linking skin aging and the ability of polyphenols as regulatory elements able to maintain skin homeostasis. In this review, we discuss recent progress in understanding the molecular bases of skin aging, with specific emphasis on some well known and extensively studied polyphenols which have significant anti-aging influences and photoprotective effects. Although no relevant clinical data exist and standard delivery systems have not been established, promising results have been obtained in many in vitro and animal models. A wide variety of polyphenols may minimize mechanisms underlying the functional manifestations of photoaging and chronological skin aging. Polyphenols exert their influence mostly through their antioxidant and anti-inflammatory effects, thereby abrogating collagen degradation and/or increasing procollagen synthesis. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

A novel swarm intelligence algorithm for finding DNA motifs.

PubMed

Lei, Chengwei; Ruan, Jianhua

2009-01-01

Discovering DNA motifs from co-expressed or co-regulated genes is an important step towards deciphering complex gene regulatory networks and understanding gene functions. Despite significant improvement in the last decade, it still remains one of the most challenging problems in computational molecular biology. In this work, we propose a novel motif finding algorithm that finds consensus patterns using a population-based stochastic optimisation technique called Particle Swarm Optimisation (PSO), which has been shown to be effective in optimising difficult multidimensional problems in continuous domains. We propose to use a word dissimilarity graph to remap the neighborhood structure of the solution space of DNA motifs, and propose a modification of the naive PSO algorithm to accommodate discrete variables. In order to improve efficiency, we also propose several strategies for escaping from local optima and for automatically determining the termination criteria. Experimental results on simulated challenge problems show that our method is both more efficient and more accurate than several existing algorithms. Applications to several sets of real promoter sequences also show that our approach is able to detect known transcription factor binding sites, and outperforms two of the most popular existing algorithms.

Fibroblast heterogeneity: implications for human disease.

PubMed

Lynch, Magnus D; Watt, Fiona M

2018-01-02

Fibroblasts synthesize the extracellular matrix of connective tissue and play an essential role in maintaining the structural integrity of most tissues. Researchers have long suspected that fibroblasts exhibit functional specialization according to their organ of origin, body site, and spatial location. In recent years, a number of approaches have revealed the existence of fibroblast subtypes in mice. Here, we discuss fibroblast heterogeneity with a focus on the mammalian dermis, which has proven an accessible and tractable system for the dissection of these relationships. We begin by considering differences in fibroblast identity according to anatomical site of origin. Subsequently, we discuss new results relating to the existence of multiple fibroblast subtypes within the mouse dermis. We consider the developmental origin of fibroblasts and how this influences heterogeneity and lineage restriction. We discuss the mechanisms by which fibroblast heterogeneity arises, including intrinsic specification by transcriptional regulatory networks and epigenetic factors in combination with extrinsic effects of the spatial context within tissue. Finally, we discuss how fibroblast heterogeneity may provide insights into pathological states including wound healing, fibrotic diseases, and aging. Our evolving understanding suggests that ex vivo expansion or in vivo inhibition of specific fibroblast subtypes may have important therapeutic applications.

Modus operandi and affect in Sweden: the Swedish version of the Regulatory Mode Questionnaire

PubMed Central

Nima, Ali Al; Mihailovic, Marko

2017-01-01

Background The Regulatory Mode Questionnaire (RMQ) is the most used and internationally well-known instrument for the measurement of individual differences in the two self-regulatory modes: locomotion (i.e., the aspect of self-regulation that is concerned with movement from state to state) and assessment (i.e., the comparative aspect of self-regulation). The aim of the present study was to verify the independence of the two regulatory modes, as postulated by the Regulatory Mode Theory (Kruglanski et al., 2000), and the psychometric properties of the RMQ in the Swedish context. Furthermore, we investigated the relationship between regulatory modes (locomotion and assessment) and affective well-being (i.e., positive affect and negative affect). Method A total of 655 university and high school students in the West of Sweden (males = 408 females = 242, and five participants who didn’t report their gender; agemean = 21.93 ± 6.51) responded to the RMQ and the Positive Affect Negative Affect Schedule. We conducted two confirmatory factor analyses using structural equation modeling (SEM). A third SEM was conducted to test the relationship between locomotion and assessment to positive affect and negative affect. Results The first analyses confirmed the unidimensional factor structure of locomotion and assessment and both scales showed good reliability. The assessment scale, however, was modified by dropping item 10 (“I don’t spend much time thinking about ways others could improve themselves”.) because it showed low loading (.07, p = .115). Furthermore, the effect of locomotion on positive affect was stronger than the effect of assessment on positive affect (Z = −15.16, p < .001), while the effect of assessment on negative affect was stronger than the effect of locomotion on negative affect (Z = 10.73, p < .001). Conclusion The factor structure of the Swedish version of the RMQ is, as Regulatory Mode Theory suggests, unidimensional and it showed good reliability. The scales discriminated between the two affective well-being dimensions. We suggest that the Swedish version of the RMQ, with only minor modifications, is a useful instrument to tap individual differences in locomotion and assessment. Hence, the present study contributes to the validation of the RMQ in the Swedish culture and adds support to the theoretical framework of self-regulatory mode. PMID:29181282

rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks.

PubMed

Guo, Liyuan; Wang, Jing

2018-01-04

Here, we present the updated rSNPBase 3.0 database (http://rsnp3.psych.ac.cn), which provides human SNP-related regulatory elements, element-gene pairs and SNP-based regulatory networks. This database is the updated version of the SNP regulatory annotation database rSNPBase and rVarBase. In comparison to the last two versions, there are both structural and data adjustments in rSNPBase 3.0: (i) The most significant new feature is the expansion of analysis scope from SNP-related regulatory elements to include regulatory element-target gene pairs (E-G pairs), therefore it can provide SNP-based gene regulatory networks. (ii) Web function was modified according to data content and a new network search module is provided in the rSNPBase 3.0 in addition to the previous regulatory SNP (rSNP) search module. The two search modules support data query for detailed information (related-elements, element-gene pairs, and other extended annotations) on specific SNPs and SNP-related graphic networks constructed by interacting transcription factors (TFs), miRNAs and genes. (3) The type of regulatory elements was modified and enriched. To our best knowledge, the updated rSNPBase 3.0 is the first data tool supports SNP functional analysis from a regulatory network prospective, it will provide both a comprehensive understanding and concrete guidance for SNP-related regulatory studies. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks

PubMed Central

2018-01-01

Abstract Here, we present the updated rSNPBase 3.0 database (http://rsnp3.psych.ac.cn), which provides human SNP-related regulatory elements, element-gene pairs and SNP-based regulatory networks. This database is the updated version of the SNP regulatory annotation database rSNPBase and rVarBase. In comparison to the last two versions, there are both structural and data adjustments in rSNPBase 3.0: (i) The most significant new feature is the expansion of analysis scope from SNP-related regulatory elements to include regulatory element–target gene pairs (E–G pairs), therefore it can provide SNP-based gene regulatory networks. (ii) Web function was modified according to data content and a new network search module is provided in the rSNPBase 3.0 in addition to the previous regulatory SNP (rSNP) search module. The two search modules support data query for detailed information (related-elements, element-gene pairs, and other extended annotations) on specific SNPs and SNP-related graphic networks constructed by interacting transcription factors (TFs), miRNAs and genes. (3) The type of regulatory elements was modified and enriched. To our best knowledge, the updated rSNPBase 3.0 is the first data tool supports SNP functional analysis from a regulatory network prospective, it will provide both a comprehensive understanding and concrete guidance for SNP-related regulatory studies. PMID:29140525

An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.

PubMed

Liu, Bingqiang; Zhang, Hanyuan; Zhou, Chuan; Li, Guojun; Fennell, Anne; Wang, Guanghui; Kang, Yu; Liu, Qi; Ma, Qin

2016-08-09

Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif prediction. Here we present an integrative phylogenetic footprinting framework for accurate motif predictions in prokaryotic genomes (MP(3)). The framework includes a new orthologous data preparation procedure, an additional promoter scoring and pruning method and an integration of six existing motif finding algorithms as basic motif search engines. Specifically, we collected orthologous genes from available prokaryotic genomes and built the orthologous regulatory regions based on sequence similarity of promoter regions. This procedure made full use of the large-scale genomic data and taxonomy information and filtered out the promoters with limited contribution to produce a high quality orthologous promoter set. The promoter scoring and pruning is implemented through motif voting by a set of complementary predicting tools that mine as many motif candidates as possible and simultaneously eliminate the effect of random noise. We have applied the framework to Escherichia coli k12 genome and evaluated the prediction performance through comparison with seven existing programs. This evaluation was systematically carried out at the nucleotide and binding site level, and the results showed that MP(3) consistently outperformed other popular motif finding tools. We have integrated MP(3) into our motif identification and analysis server DMINDA, allowing users to efficiently identify and analyze motifs in 2,072 completely sequenced prokaryotic genomes. The performance evaluation indicated that MP(3) is effective for predicting regulatory motifs in prokaryotic genomes. Its application may enhance progress in elucidating transcription regulation mechanism, thus provide benefit to the genomic research community and prokaryotic genome researchers in particular.

Leveraging existing information for use in a National Nuclear Forensics Library (NNFL)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davydov, Jerry; Dion, Heather; LaMont, Stephen

A National Nuclear Forensics Library (NNFL) assists a State to assess whether nuclear material encountered out of regulatory control is of domestic or international origin. And by leveraging nuclear material registries, nuclear enterprise records, and safeguards accountancy information, as well as existing domestic technical capability and subject-matter domain expertise, states can better assess the effort required for setting up an NNFL. For states who are largely recipients of nuclear and radiological materials and have no internal production capabilities may create an NNFL that relies on existing information rather than carry out advanced analyses on domestic materials.

Leveraging existing information for use in a National Nuclear Forensics Library (NNFL)

DOE PAGES

Davydov, Jerry; Dion, Heather; LaMont, Stephen; ...

2015-12-16

A National Nuclear Forensics Library (NNFL) assists a State to assess whether nuclear material encountered out of regulatory control is of domestic or international origin. And by leveraging nuclear material registries, nuclear enterprise records, and safeguards accountancy information, as well as existing domestic technical capability and subject-matter domain expertise, states can better assess the effort required for setting up an NNFL. For states who are largely recipients of nuclear and radiological materials and have no internal production capabilities may create an NNFL that relies on existing information rather than carry out advanced analyses on domestic materials.

Efficient Reverse-Engineering of a Developmental Gene Regulatory Network

PubMed Central

Cicin-Sain, Damjan; Ashyraliyev, Maksat; Jaeger, Johannes

2012-01-01

Understanding the complex regulatory networks underlying development and evolution of multi-cellular organisms is a major problem in biology. Computational models can be used as tools to extract the regulatory structure and dynamics of such networks from gene expression data. This approach is called reverse engineering. It has been successfully applied to many gene networks in various biological systems. However, to reconstitute the structure and non-linear dynamics of a developmental gene network in its spatial context remains a considerable challenge. Here, we address this challenge using a case study: the gap gene network involved in segment determination during early development of Drosophila melanogaster. A major problem for reverse-engineering pattern-forming networks is the significant amount of time and effort required to acquire and quantify spatial gene expression data. We have developed a simplified data processing pipeline that considerably increases the throughput of the method, but results in data of reduced accuracy compared to those previously used for gap gene network inference. We demonstrate that we can infer the correct network structure using our reduced data set, and investigate minimal data requirements for successful reverse engineering. Our results show that timing and position of expression domain boundaries are the crucial features for determining regulatory network structure from data, while it is less important to precisely measure expression levels. Based on this, we define minimal data requirements for gap gene network inference. Our results demonstrate the feasibility of reverse-engineering with much reduced experimental effort. This enables more widespread use of the method in different developmental contexts and organisms. Such systematic application of data-driven models to real-world networks has enormous potential. Only the quantitative investigation of a large number of developmental gene regulatory networks will allow us to discover whether there are rules or regularities governing development and evolution of complex multi-cellular organisms. PMID:22807664

Compliance Groundwater Monitoring of Nonpoint Sources - Emerging Approaches

NASA Astrophysics Data System (ADS)

Harter, T.

2008-12-01

Groundwater monitoring networks are typically designed for regulatory compliance of discharges from industrial sites. There, the quality of first encountered (shallow-most) groundwater is of key importance. Network design criteria have been developed for purposes of determining whether an actual or potential, permitted or incidental waste discharge has had or will have a degrading effect on groundwater quality. The fundamental underlying paradigm is that such discharge (if it occurs) will form a distinct contamination plume. Networks that guide (post-contamination) mitigation efforts are designed to capture the shape and dynamics of existing, finite-scale plumes. In general, these networks extend over areas less than one to ten hectare. In recent years, regulatory programs such as the EU Nitrate Directive and the U.S. Clean Water Act have forced regulatory agencies to also control groundwater contamination from non-incidental, recharging, non-point sources, particularly agricultural sources (fertilizer, pesticides, animal waste application, biosolids application). Sources and contamination from these sources can stretch over several tens, hundreds, or even thousands of square kilometers with no distinct plumes. A key question in implementing monitoring programs at the local, regional, and national level is, whether groundwater monitoring can be effectively used as a landowner compliance tool, as is currently done at point-source sites. We compare the efficiency of such traditional site-specific compliance networks in nonpoint source regulation with various designs of regional nonpoint source monitoring networks that could be used for compliance monitoring. We discuss advantages and disadvantages of the site vs. regional monitoring approaches with respect to effectively protecting groundwater resources impacted by nonpoint sources: Site-networks provide a tool to enforce compliance by an individual landowner. But the nonpoint source character of the contamination and its typically large spatial extend requires extensive networks at an individual site to accurately and fairly monitor individual compliance. In contrast, regional networks seemingly fail to hold individual landowners accountable. But regional networks can effectively monitor large-scale impacts and water quality trends; and thus inform regulatory programs that enforce management practices tied to nonpoint source pollution. Regional monitoring networks for compliance purposes can face significant challenges in the implementation due to a regulatory and legal landscape that is exclusively structured to address point sources and individual liability, and due to the non-intensive nature of a regional monitoring program (lack of control of hot spots; lack of accountability of individual landowners).

An assessment of the supply, programmatic use, and regulatory issues of single low-dose primaquine as a Plasmodium falciparum gametocytocide for sub-Saharan Africa.

PubMed

Chen, Ingrid; Poirot, Eugenie; Newman, Mark; Kandula, Deepika; Shah, Renee; Hwang, Jimee; Cohen, Justin M; Gosling, Roly; Rooney, Luke

2015-05-15

Global ambitions to eliminate malaria are intensifying, underscoring a critical need for transmission blocking tools. In 2012, the WHO recommended the use of 0.25 mg/kg of single low-dose (SLD) primaquine to stop Plasmodium falciparum transmission. To ensure the availability of SLD primaquine to countries in need of this tool, more information on the supply, programmatic, and regulatory barriers to the rollout of SLD primaquine is required. Challenges to the rollout of SLD primaquine in sub-Saharan Africa were established through semi-structured qualitative interviews with three primaquine manufacturers, 43 key informants from Ethiopia, Senegal, Swaziland, Zambia, and Tanzania, and 16 malaria research experts. Sanofi and Remedica are the only two sources of SRA-approved primaquine suitable for procurement by international donors. Neither manufacturer produces primaquine tablet strengths suitable for the transmission blocking indication. In-country key informants revealed that the WHO weight-based recommendation to use SLD primaquine is challenging to implement in actual field settings. Malaria programmes expressed safety concerns of SLD primaquine use in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency, as well as potential interactions between primaquine and co-morbidities, and drug-drug interactions with HIV and/or tuberculosis treatments. Regulatory processes are a major barrier to the rollout of SLD primaquine, requiring multiple steps at both the country and global level. Despite these barriers, demand for SLD primaquine is growing, and malaria researchers are interested in primaquine deployment through mass screen and treat and/or mass drug administration campaigns. Demand for primaquine as a transmission blocking agent is growing rapidly yet multiple barriers to SLD primaquine use exist. Research is needed to define the therapeutic dose range, which will guide dosing regimens in the field, inform the development of new, lower strength primaquine tablets and/or formulation(s), and allay programmatic safety concerns in individuals with G6PD deficiency. Potential interactions between primaquine and co-morbidities and treatments should be explored. To minimize regulatory delays, countries need to prepare for product registration at an early stage, WHO prequalification for suitable primaquine tablet strengths and/or new formulations should be sought, and in the meanwhile only Stringent Regulatory Authority (SRA)-approved primaquine should be used.

40 CFR 165.87 - Design and capacity requirements for existing structures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... existing containment structure: (1) The containment structure must be constructed of steel, reinforced... existing structures. 165.87 Section 165.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Structures § 165.87 Design and capacity requirements for existing structures. (a) For all existing...

40 CFR 165.87 - Design and capacity requirements for existing structures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... existing containment structure: (1) The containment structure must be constructed of steel, reinforced... existing structures. 165.87 Section 165.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Structures § 165.87 Design and capacity requirements for existing structures. (a) For all existing...

40 CFR 165.87 - Design and capacity requirements for existing structures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... existing containment structure: (1) The containment structure must be constructed of steel, reinforced... existing structures. 165.87 Section 165.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Structures § 165.87 Design and capacity requirements for existing structures. (a) For all existing...

40 CFR 165.87 - Design and capacity requirements for existing structures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... existing containment structure: (1) The containment structure must be constructed of steel, reinforced... existing structures. 165.87 Section 165.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Structures § 165.87 Design and capacity requirements for existing structures. (a) For all existing...

The impact of transposable elements on mammalian development

PubMed Central

Garcia-Perez, Jose L.; Widmann, Thomas J.; Adams, Ian R.

2018-01-01

Summary Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that significantly impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues. Importantly, the ongoing domestication and evolution of TEs appears to provide a rich source of regulatory elements, functional modules and genetic variation that fuels the evolution of mammalian developmental processes. Here, we review the functional impact that TEs exert on mammalian developmental processes and how the somatic activity of TEs can influence gene regulatory networks. PMID:27875251

AP1 Keeps Chromatin Poised for Action | Center for Cancer Research

Cancer.gov

The human genome harbors gene-encoding DNA, the blueprint for building proteins that regulate cellular function. Embedded across the genome, in non-coding regions, are DNA elements to which regulatory factors bind. The interaction of regulatory factors with DNA at these sites modifies gene expression to modulate cell activity. In cells, DNA exists in a complex with proteins called chromatin that compacts the DNA in the nucleus, strongly restricting access to DNA sequences. As a result, regulatory factors only interact with a small subset of their potential binding elements in a given cell to regulate genes. How factors recognize and select sites in chromatin across the genome is not well understood -- but several discoveries in CCR’s Laboratory of Receptor Biology and Gene Expression (LRBGE) have shed light on the mechanisms that direct factors to DNA.

[Marketing approval and market surveillance of medical devices in Germany: Where does policy integration take place?].

PubMed

Lang, Achim

2014-01-01

Since 2011 new regulatory measures regarding medical devices have been set up with the aim to eliminate obstacles to innovations and to find more coordinated ways to marketing authorisation and market surveillance. This essay investigates whether these new and existing coordination mechanisms build up to a Joined-up Government approach. The analysis shows that the regulatory process should be adjusted along several dimensions. First, many organisations lack awareness regarding their stakeholders and focus solely on their immediate organisational activities. Second, the regulatory process (marketing authorisation and market surveillance) is too fragmented for an effective communication to take place. Finally, the underlying strategy process is an ad-hoc approach lacking continuity and continued involvement of, in particular, the responsible federal ministries. Copyright © 2013. Published by Elsevier GmbH.

Information theory in systems biology. Part I: Gene regulatory and metabolic networks.

PubMed

Mousavian, Zaynab; Kavousi, Kaveh; Masoudi-Nejad, Ali

2016-03-01

"A Mathematical Theory of Communication", was published in 1948 by Claude Shannon to establish a framework that is now known as information theory. In recent decades, information theory has gained much attention in the area of systems biology. The aim of this paper is to provide a systematic review of those contributions that have applied information theory in inferring or understanding of biological systems. Based on the type of system components and the interactions between them, we classify the biological systems into 4 main classes: gene regulatory, metabolic, protein-protein interaction and signaling networks. In the first part of this review, we attempt to introduce most of the existing studies on two types of biological networks, including gene regulatory and metabolic networks, which are founded on the concepts of information theory. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cross-β Polymerization of Low Complexity Sequence Domains.

PubMed

Kato, Masato; McKnight, Steven L

2017-03-01

Most transcription factors and RNA regulatory proteins encoded by eukaryotic genomes ranging from yeast to humans contain polypeptide domains variously described as intrinsically disordered, prion-like, or of low complexity (LC). These LC domains exist in an unfolded state when DNA and RNA regulatory proteins are studied in biochemical isolation from cells. Upon incubation in the purified state, many of these LC domains polymerize into homogeneous, labile amyloid-like fibers. Here, we consider several lines of evidence that may favor biologic utility for LC domain polymers. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Plant evolution at the interface of paleontology and developmental biology: An organism-centered paradigm.

PubMed

Rothwell, Gar W; Wyatt, Sarah E; Tomescu, Alexandru M F

2014-06-01

Paleontology yields essential evidence for inferring not only the pattern of evolution, but also the genetic basis of evolution within an ontogenetic framework. Plant fossils provide evidence for the pattern of plant evolution in the form of transformational series of structure through time. Developmentally diagnostic structural features that serve as "fingerprints" of regulatory genetic pathways also are preserved by plant fossils, and here we provide examples of how those fingerprints can be used to infer the mechanisms by which plant form and development have evolved. When coupled with an understanding of variations and systematic distributions of specific regulatory genetic pathways, this approach provides an avenue for testing evolutionary hypotheses at the organismal level that is analogous to employing bioinformatics to explore genetics at the genomic level. The positions where specific genes, gene families, and developmental regulatory mechanisms first appear in phylogenies are correlated with the positions where fossils with the corresponding structures occur on the tree, thereby yielding testable hypotheses that extend our understanding of the role of developmental changes in the evolution of the body plans of vascular plant sporophytes. As a result, we now have new and powerful methodologies for characterizing major evolutionary changes in morphology, anatomy, and physiology that have resulted from combinations of genetic regulatory changes and that have produced the synapomorphies by which we recognize major clades of plants. © 2014 Botanical Society of America, Inc.

77 FR 27815 - Aging Management of Stainless Steel Structures and Components in Treated Borated Water

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-11

... NUCLEAR REGULATORY COMMISSION [NRC-2011-0256] Aging Management of Stainless Steel Structures and... Guidance (LR-ISG), LR-ISG-2011-01, ``Aging Management of Stainless Steel Structures and Components in...) Report for the aging management of stainless steel structures and components exposed to treated borated...

76 FR 69292 - Aging Management of Stainless Steel Structures and Components in Treated Borated Water

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-08

... NUCLEAR REGULATORY COMMISSION [NRC-2011-0256] Aging Management of Stainless Steel Structures and... Stainless Steel Structures and Components in Treated Borated Water.'' This LR-ISG revises the guidance in...) and Generic Aging Lessons Learned (GALL) Report for the aging management of stainless steel structures...

77 FR 74883 - Aging Management of Stainless Steel Structures and Components in Treated Borated Water; Revision 1

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-18

... NUCLEAR REGULATORY COMMISSION [NRC-2011-0256] Aging Management of Stainless Steel Structures and..., ``Aging Management of Stainless Steel Structures and Components in Treated Borated Water,'' which was... Staff Guidance LR-ISG-2011-01, ``Aging Management of Stainless Steel Structures and Components in...

Signal Correlations in Ecological Niches Can Shape the Organization and Evolution of Bacterial Gene Regulatory Networks

PubMed Central

Dufour, Yann S.; Donohue, Timothy J.

2015-01-01

Transcriptional regulation plays a significant role in the biological response of bacteria to changing environmental conditions. Therefore, mapping transcriptional regulatory networks is an important step not only in understanding how bacteria sense and interpret their environment but also to identify the functions involved in biological responses to specific conditions. Recent experimental and computational developments have facilitated the characterization of regulatory networks on a genome-wide scale in model organisms. In addition, the multiplication of complete genome sequences has encouraged comparative analyses to detect conserved regulatory elements and infer regulatory networks in other less well-studied organisms. However, transcription regulation appears to evolve rapidly, thus, creating challenges for the transfer of knowledge to nonmodel organisms. Nevertheless, the mechanisms and constraints driving the evolution of regulatory networks have been the subjects of numerous analyses, and several models have been proposed. Overall, the contributions of mutations, recombination, and horizontal gene transfer are complex. Finally, the rapid evolution of regulatory networks plays a significant role in the remarkable capacity of bacteria to adapt to new or changing environments. Conversely, the characteristics of environmental niches determine the selective pressures and can shape the structure of regulatory network accordingly. PMID:23046950

A retrospective analysis of in vivo eye irritation, skin irritation and skin sensitisation studies with agrochemical formulations: Setting the scene for development of alternative strategies.

PubMed

Corvaro, M; Gehen, S; Andrews, K; Chatfield, R; Macleod, F; Mehta, J

2017-10-01

Analysis of the prevalence of health effects in large scale databases is key in defining testing strategies within the context of Integrated Approaches on Testing and Assessment (IATA), and is relevant to drive policy changes in existing regulatory toxicology frameworks towards non-animal approaches. A retrospective analysis of existing results from in vivo skin irritation, eye irritation, and skin sensitisation studies on a database of 223 agrochemical formulations is herein published. For skin or eye effects, high prevalence of mild to non-irritant formulations (i.e. per GHS, CLP or EPA classification) would generally suggest a bottom-up approach. Severity of erythema or corneal opacity, for skinor eye effects respectively, were the key drivers for classification, consistent with existing literature. The reciprocal predictivity of skin versus eye irritation and the good negative predictivity of the GHS additivity calculation approach (>85%) provided valuable non-testing evidence for irritation endpoints. For dermal sensitisation, concordance on data from three different methods confirmed the high false negative rate for the Buehler method in this product class. These results have been reviewed together with existing literature on the use of in vitro alternatives for agrochemical formulations, to propose improvements to current regulatory strategies and to identify further research needs. Copyright © 2017 Elsevier Inc. All rights reserved.

Using Inequality Measures to Incorporate Environmental Justice into Regulatory Analyses

PubMed Central

Harper, Sam; Ruder, Eric; Roman, Henry A.; Geggel, Amelia; Nweke, Onyemaechi; Payne-Sturges, Devon; Levy, Jonathan I.

2013-01-01

Formally evaluating how specific policy measures influence environmental justice is challenging, especially in the context of regulatory analyses in which quantitative comparisons are the norm. However, there is a large literature on developing and applying quantitative measures of health inequality in other settings, and these measures may be applicable to environmental regulatory analyses. In this paper, we provide information to assist policy decision makers in determining the viability of using measures of health inequality in the context of environmental regulatory analyses. We conclude that quantification of the distribution of inequalities in health outcomes across social groups of concern, considering both within-group and between-group comparisons, would be consistent with both the structure of regulatory analysis and the core definition of environmental justice. Appropriate application of inequality indicators requires thorough characterization of the baseline distribution of exposures and risks, leveraging data generally available within regulatory analyses. Multiple inequality indicators may be applicable to regulatory analyses, and the choice among indicators should be based on explicit value judgments regarding the dimensions of environmental justice of greatest interest. PMID:23999551

The control of branching morphogenesis

PubMed Central

Iber, Dagmar; Menshykau, Denis

2013-01-01

Many organs of higher organisms are heavily branched structures and arise by an apparently similar process of branching morphogenesis. Yet the regulatory components and local interactions that have been identified differ greatly in these organs. It is an open question whether the regulatory processes work according to a common principle and how far physical and geometrical constraints determine the branching process. Here, we review the known regulatory factors and physical constraints in lung, kidney, pancreas, prostate, mammary gland and salivary gland branching morphogenesis, and describe the models that have been formulated to analyse their impacts. PMID:24004663

State Regulatory Authority (SRA) Coordination of Safety, Security, and Safeguards of Nuclear Facilities: A Framework for Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mladineo, Stephen V.; Frazar, Sarah L.; Kurzrok, Andrew J.

This paper will explore the development of a framework for conducting an assessment of safety-security-safeguards integration within a State. The goal is to examine State regulatory structures to identify conflicts and gaps that hinder management of the three disciplines at nuclear facilities. Such an analysis could be performed by a State Regulatory Authority (SRA) to provide a self-assessment or as part of technical cooperation with either a newcomer State, or to a State with a fully developed SRA.

Analysis of Regulatory Guidance for Health Monitoring

NASA Technical Reports Server (NTRS)

Munns, Thomas E.; Beard, Richard E.; Culp, Aubrey M.; Murphy, Dennis A.; Kent, Renee M.; Cooper, Eric G. (Technical Monitor)

2000-01-01

The purpose of this study was to assess the connection between current FAA regulations and the incorporation of Health Management (HM) systems into commercial aircraft. To address the overall objectives ARINC: (1) investigated FAA regulatory guidance, (2) investigated airline maintenance practices, (3) systematically identified regulations and practices that would be affected or could act as barriers to the introduction of HM technology, and (4) assessed regulatory and operational tradeoffs that should be considered for implementation. The assessment procedure was validated on a postulated structural HM capability for the B757 horizontal stabilizer.

JCell--a Java-based framework for inferring regulatory networks from time series data.

PubMed

Spieth, C; Supper, J; Streichert, F; Speer, N; Zell, A

2006-08-15

JCell is a Java-based application for reconstructing gene regulatory networks from experimental data. The framework provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems. Owing to the modular structure, researchers can easily implement new methods. JCell is a pure Java application with additional scripting capabilities and thus widely usable, e.g. on parallel or cluster computers. The software is freely available for download at http://www-ra.informatik.uni-tuebingen.de/software/JCell.

Gene context conservation of a higher order than operons.

PubMed

Lathe, W C; Snel, B; Bork, P

2000-10-01

Operons, co-transcribed and co-regulated contiguous sets of genes, are poorly conserved over short periods of evolutionary time. The gene order, gene content and regulatory mechanisms of operons can be very different, even in closely related species. Here, we present several lines of evidence which suggest that, although an operon and its individual genes and regulatory structures are rearranged when comparing the genomes of different species, this rearrangement is a conservative process. Genomic rearrangements invariably maintain individual genes in very specific functional and regulatory contexts. We call this conserved context an uber-operon.

Construction of regulatory networks using expression time-series data of a genotyped population.

PubMed

Yeung, Ka Yee; Dombek, Kenneth M; Lo, Kenneth; Mittler, John E; Zhu, Jun; Schadt, Eric E; Bumgarner, Roger E; Raftery, Adrian E

2011-11-29

The inference of regulatory and biochemical networks from large-scale genomics data is a basic problem in molecular biology. The goal is to generate testable hypotheses of gene-to-gene influences and subsequently to design bench experiments to confirm these network predictions. Coexpression of genes in large-scale gene-expression data implies coregulation and potential gene-gene interactions, but provide little information about the direction of influences. Here, we use both time-series data and genetics data to infer directionality of edges in regulatory networks: time-series data contain information about the chronological order of regulatory events and genetics data allow us to map DNA variations to variations at the RNA level. We generate microarray data measuring time-dependent gene-expression levels in 95 genotyped yeast segregants subjected to a drug perturbation. We develop a Bayesian model averaging regression algorithm that incorporates external information from diverse data types to infer regulatory networks from the time-series and genetics data. Our algorithm is capable of generating feedback loops. We show that our inferred network recovers existing and novel regulatory relationships. Following network construction, we generate independent microarray data on selected deletion mutants to prospectively test network predictions. We demonstrate the potential of our network to discover de novo transcription-factor binding sites. Applying our construction method to previously published data demonstrates that our method is competitive with leading network construction algorithms in the literature.

FoxP3 Expression in Macrophages, Cancer, and B Cells-Is It Real?

PubMed

Vadasz, Zahava; Toubi, Elias

2017-06-01

During the last decade, B regulatory cells are appreciated to have a central role in preventing autoimmunity and maintaining self-tolerance. They are characterized by expressing different phenotypic markers and the production of either IL-10 or TGF-β or both. The recent recognition of Fas ligand expressing B regulatory cells as "killer" cells established their role in maintaining viral persistence by preventing effective antiviral immune responses. The forkhead lineage-transcription factor (FoxP3) was considered for many years to be a highly specific intracellular regulatory marker of CD4+CD25+ T regulatory cells. The possibility of FoxP3 being expressed in B regulatory cells was suggested in many studies. Though controversial, FoxP3 expression was also reported in macrophages and cancer cells. Aiming to avoid artifact staining, many researchers required the usage of FoxP3 messenger RNA (mRNA) and PCR in order to prove a true expression of FoxP3 in these different cells. In addition, most studies' report on that FoxP3 expression in all abovementioned cells is related to their status of activation since naïve (non-activated cells) were found poorly FoxP3 expressing. In this review, we present the existing data on FoxP3 expression in non-T-regulatory cells, but we suggest that further studies are needed to better establish this concept.

75 FR 13620 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-22

... other things, that if NASDAQ Regulation staff has reason to believe that a disqualification exists... person waives the following (in summary): (a) The right to a hearing and any right of appeal to challenge... 13622

Developing and applying adverse outcome pathways: What you need to know

EPA Science Inventory

Adverse outcome pathways (AOPs) are a conceptual framework for organizing existing information concerning the predictive linkages between the initiation or early progression of a biological perturbation in an organism and the adverse outcome(s) of regulatory relevance (e.g., impa...

Final Regulatory Impact Analysis (RIA) for the NO2 National Ambient Air Quality Standards (NAAQS)

EPA Pesticide Factsheets

This RIA provides illustrative estimates, as of January 2010, of the incremental costs and monetized human health benefits of attaining the revised NO2 NAAQS within the the existing community-wide monitoring network of 409 monitors.

FIELD QUALITY CONTROL STRATEGIES ASSESSING SOLIDIFICATION/STABILIZATION

EPA Science Inventory

Existing regulatory mobility reduction (leaching) tests are not amenable to real time quality control because of the time required to perform sample extraction and chemical analysis. This is of conccern because the leaching test is the most important parameter used to relate trea...