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Sample records for regulatory targets comparisons

  1. A comparison of regulatory impacts to real target impacts

    SciTech Connect

    Ammerman, D.J.

    1998-05-01

    The purpose of this paper is to discuss the relative severity of regulatory impacts onto an essentially rigid target to impacts at higher velocities onto real targets. For impacts onto the essentially rigid target all of the kinetic energy of the package is absorbed by deformation of the package. For impacts onto real targets the kinetic energy is absorbed by deformation of the target as well as by deformation of the package. The amount of kinetic energy absorbed by the target does not increase the severity of the impact.

  2. Targeting regulatory T cells.

    PubMed

    Ménétrier-Caux, Christine; Curiel, Tyler; Faget, Julien; Manuel, Manuarii; Caux, Christophe; Zou, Weiping

    2012-03-01

    Cancers express tumor-associated antigens that should elicit immune response to antagonize the tumor growth, but spontaneous immune rejection of established cancer is rare, suggesting an immunosuppressive environment hindering host antitumor immunity. Among the specific and active tumor-mediated mechanisms, CD4(+)CD25(high) T regulatory cells (Treg) are important mediators of active immune evasion in cancer. In this review, we will discuss Treg subpopulations and the mechanisms of their suppressive functions. Treg depletion improves endogenous antitumor immunity and the efficacy of active immunotherapy in animal models for cancer, suggesting that inhibiting Treg function could also improve the limited successes of human cancer immunotherapy. We will also discuss specific strategies for devising effective cancer immunotherapy targeting Treg.

  3. Target activation by regulatory RNAs in bacteria

    PubMed Central

    Papenfort, Kai; Vanderpool, Carin K.

    2015-01-01

    Bacterial small regulatory RNAs (sRNAs) are commonly known to repress gene expression by base pairing to target mRNAs. In many cases, sRNAs base pair with and sequester mRNA ribosome-binding sites, resulting in translational repression and accelerated transcript decay. In contrast, a growing number of examples of translational activation and mRNA stabilization by sRNAs have now been documented. A given sRNA often employs a conserved region to interact with and regulate both repressed and activated targets. However, the mechanisms underlying activation differ substantially from repression. Base pairing resulting in target activation can involve sRNA interactions with the 5′ untranslated region (UTR), the coding sequence or the 3′ UTR of the target mRNAs. Frequently, the activities of protein factors such as cellular ribonucleases and the RNA chaperone Hfq are required for activation. Bacterial sRNAs, including those that function as activators, frequently control stress response pathways or virulence-associated functions required for immediate responses to changing environments. This review aims to summarize recent advances in knowledge regarding target mRNA activation by bacterial sRNAs, highlighting the molecular mechanisms and biological relevance of regulation. PMID:25934124

  4. Neutron and x-ray scattering studies of the interactions between Ca{sup 2+}-binding proteins and their regulatory targets: Comparisons of troponin C and calmodulin

    SciTech Connect

    Trewhella, J.; Olah, G.A.

    1993-11-01

    The regulatory proteins calmodulin and troponin C share a strikingly unusual overall structure. Their crystal structures show each protein consists of two structurally homologous globular domains connected by an extended, solvent exposed alpha-helix of = 8 turns. Calmodulin regulates a variety of enzymes that show remarkable functional and structural diversity. This diversity extends to the amino acid sequences of the calmodulin-binding domains in the target enzymes. In contrast with calodulin, troponin C appears to have a single very specialized function. It is an integral part of the troponin complex, and Ca{sup 2+} binding to troponin c results in the release of the inhibitory function of troponin I, which eventually leads to actin-binding to myosin and the triggering of muscle contraction. Small-angle scattering has been particularly useful for studying the dumbbell shaped proteins because the technique is very sensitive to changes in the relative dispositions of the two globular domains. Small-angle scattering, using x-rays or neutrons, gives information on the overall shapes of proteins in solution. Small-angle scattering studies of calmodulin and its complexes with calmodulin-binding domains from various target enzymes have played an important role in helping us understand the functional role of its unusual solvent exposed helix. Likewise, small-angle scattering has been used to study troponin C with various peptides, to shed light on the similarities and differences between calmodulin and troponin C.

  5. What's the Regulatory Value of a Target Product Profile?

    PubMed

    Breder, Christopher D; Du, Wenny; Tyndall, Adria

    2017-07-01

    Target product profiles (TPPs) are used as a regulatory tool for dialog on clinical development or manufacturing plans. Drugs and biologics approved by the FDA that mention TPPs are associated with more efficient regulatory review times, perhaps as a result of increased planning or because the TPP promotes well-organized regulatory dialog. Published by Elsevier Ltd.

  6. Safeguards inventory and process monitoring regulatory comparison

    SciTech Connect

    Cavaluzzi, Jack M.; Gibbs, Philip W.

    2013-06-27

    Detecting the theft or diversion of the relatively small amount of fissile material needed to make a nuclear weapon given the normal operating capacity of many of today’s running nuclear production facilities is a difficult task. As throughput increases, the ability of the Material Control and Accountability (MC&A) Program to detect the material loss decreases because the statistical measurement uncertainty also increases. The challenge faced is the ability of current accounting, measurement, and material control programs to detect small yet significant losses under some regulatory approaches can decrease to the point where it is extremely low if not practically non-existent at normal operating capacities. Adding concern to this topic is that there are variations among regulatory bodies as far as what is considered a Significant Quantity (SQ). Some research suggests that thresholds should be lower than those found in any current regulation which if adopted would make meeting detection goals even more difficult. This paper reviews and compares the current regulatory requirements for the MA elements related to physical inventory, uncertainty of the Inventory Difference (ID), and Process Monitoring (PM) in the United States Department of Energy (DOE) and Nuclear Regulatory Commission (NRC), Rosatom of the Russian Federation and the Chinese Atomic Energy Agency (CAEA) of China. The comparison looks at how the regulatory requirements for the implementation of various MA elements perform across a range of operating capacities in example facilities.

  7. Engineering nucleases for gene targeting: safety and regulatory considerations.

    PubMed

    Pauwels, Katia; Podevin, Nancy; Breyer, Didier; Carroll, Dana; Herman, Philippe

    2014-01-25

    Nuclease-based gene targeting (NBGT) represents a significant breakthrough in targeted genome editing since it is applicable from single-celled protozoa to human, including several species of economic importance. Along with the fast progress in NBGT and the increasing availability of customized nucleases, more data are available about off-target effects associated with the use of this approach. We discuss how NBGT may offer a new perspective for genetic modification, we address some aspects crucial for a safety improvement of the corresponding techniques and we also briefly relate the use of NBGT applications and products to the regulatory oversight.

  8. Cell cycle regulatory E3 ubiquitin ligases as anticancer targets.

    PubMed

    Pray, Todd R; Parlati, Francesco; Huang, Jianing; Wong, Brian R; Payan, Donald G; Bennett, Mark K; Issakani, Sarkiz Daniel; Molineaux, Susan; Demo, Susan D

    2002-12-01

    Disregulation of the cell cycle and proliferation play key roles in cellular transformation and tumorigenesis. Such processes are intimately tied to the concentration, localization and activity of enzymes, adapters, receptors, and structural proteins in cells. Ubiquitination of these cellular regulatory proteins, governed by specific enzymes in the ubiquitin (Ub) conjugation cascade, has profound effects on their various functions, most commonly through proteasome targeting and degradation. This review will focus on a variety of E3 Ub ligases as potential oncology drug targets, with particular emphasis on the role of these molecules in the regulation of stability, localization, and activity of key proteins such as tumor suppressors and oncoproteins. E3 ubiquitin ligases that have established roles in cell cycle and apoptosis, such as the anaphase-promoting complex (APC), the Skp-1-Cul1-F-box class, and the murine double minute 2 (MDM2) protein, in addition to more recently discovered E3 ubiquitin ligases which may be similarly important in tumorigenesis, (e.g. Smurf family, CHFR, and Efp), will be discussed. We will present evidence to support E3 ligases as good biological targets in the development of anticancer therapeutics and address challenges in drug discovery for these targets.

  9. The iron-regulatory hormone hepcidin: a possible therapeutic target?

    PubMed

    Rochette, Luc; Gudjoncik, Aurélie; Guenancia, Charles; Zeller, Marianne; Cottin, Yves; Vergely, Catherine

    2015-02-01

    The maintenance of stable extracellular and intracellular iron concentrations requires the coordinated regulation of iron transport into plasma. Iron is a fundamental cofactor for several enzymes involved in oxidation-reduction reactions. The redox ability of iron can lead to the production of oxygen free radicals, which can damage various cellular components. Therefore, the appropriate regulation of systemic iron homeostasis is decisive in vital processes. Hepcidin has emerged as the central regulatory molecule of systemic iron homeostasis. It is synthesized in hepatocytes and in other cells and released into the circulation. It inhibits the release of iron from enterocytes of the duodenum and from macrophages by binding to the iron exporter protein, ferroportin (FPN). FPN is a transmembrane protein responsible for iron export from cells into the plasma. Hepcidin is internalized with FPN and both are degraded in lysosomes. The hepcidin-FPN axis is the principal regulator of extracellular iron homeostasis in health and disease. Its manipulation via agonists and antagonists is an attractive and novel therapeutic strategy. Hepcidin agonists include compounds that mimic the activity of hepcidin and agents that increase the production of hepcidin by targeting hepcidin-regulatory molecules. The inhibition of hepcidin could be a potentially attractive therapeutic strategy in patients suffering from anaemia or chronic inflammation. In this review, we will summarize the role of hepcidin in iron homeostasis and its contribution to the pathophysiology of inflammation and iron disorders. We will examine emerging new strategies that modulate hepcidin metabolism.

  10. Microinterventions Targeting Regulatory Focus and Regulatory Fit Selectively Reduce Dysphoric and Anxious Mood

    PubMed Central

    Strauman, Timothy J.; Socolar, Yvonne; Kwapil, Lori; Cornwell, James F. M.; Franks, Becca; Sehnert, Steen; Higgins, E. Tory

    2015-01-01

    Depression and generalized anxiety, separately and as comorbid states, continue to represent a significant public health challenge. Current cognitive-behavioral treatments are clearly beneficial but there remains a need for continued development of complementary interventions. This manuscript presents two proof-of-concept studies, in analog samples, of “microinterventions” derived from regulatory focus and regulatory fit theories and targeting dysphoric and anxious symptoms. In Study 1, participants with varying levels of dysphoric and/or anxious mood were exposed to a brief intervention either to increase or to reduce engagement in personal goal pursuit, under the hypothesis that dysphoria indicates under-engagement of the promotion system whereas anxiety indicates over-engagement of the prevention system. In Study 2, participants with varying levels of dysphoric and/or anxious mood received brief training in counterfactual thinking, under the hypothesis that inducing individuals in a state of promotion failure to generate subtractive counterfactuals for past failures (a non-fit) will lessen their dejection/depression-related symptoms, whereas inducing individuals in a state of prevention failure to generate additive counterfactuals for past failures (a non-fit) will lessen their agitation/anxiety-related symptoms. In both studies, we observed discriminant patterns of reduction in distress consistent with the hypothesized links between dysfunctional states of the two motivational systems and dysphoric versus anxious symptoms. PMID:26163353

  11. Targeting Immune Regulatory Networks to Counteract Immune Suppression in Cancer.

    PubMed

    Camisaschi, Chiara; Vallacchi, Viviana; Vergani, Elisabetta; Tazzari, Marcella; Ferro, Simona; Tuccitto, Alessandra; Kuchuk, Olga; Shahaj, Eriomina; Sulsenti, Roberta; Castelli, Chiara; Rodolfo, Monica; Rivoltini, Licia; Huber, Veronica

    2016-11-04

    The onset of cancer is unavoidably accompanied by suppression of antitumor immunity. This occurs through mechanisms ranging from the progressive accumulation of regulatory immune cells associated with chronic immune stimulation and inflammation, to the expression of immunosuppressive molecules. Some of them are being successfully exploited as therapeutic targets, with impressive clinical results achieved in patients, as in the case of immune checkpoint inhibitors. To limit immune attack, tumor cells exploit specific pathways to render the tumor microenvironment hostile for antitumor effector cells. Local acidification might, in fact, anergize activated T cells and facilitate the accumulation of immune suppressive cells. Moreover, the release of extracellular vesicles by tumor cells can condition distant immune sites contributing to the onset of systemic immune suppression. Understanding which mechanisms may be prevalent in specific cancers or disease stages, and identifying possible strategies to counterbalance would majorly contribute to improving clinical efficacy of cancer immunotherapy. Here, we intend to highlight these mechanisms, how they could be targeted and the tools that might be available in the near future to achieve this goal.

  12. Targeting Immune Regulatory Networks to Counteract Immune Suppression in Cancer

    PubMed Central

    Camisaschi, Chiara; Vallacchi, Viviana; Vergani, Elisabetta; Tazzari, Marcella; Ferro, Simona; Tuccitto, Alessandra; Kuchuk, Olga; Shahaj, Eriomina; Sulsenti, Roberta; Castelli, Chiara; Rodolfo, Monica; Rivoltini, Licia; Huber, Veronica

    2016-01-01

    The onset of cancer is unavoidably accompanied by suppression of antitumor immunity. This occurs through mechanisms ranging from the progressive accumulation of regulatory immune cells associated with chronic immune stimulation and inflammation, to the expression of immunosuppressive molecules. Some of them are being successfully exploited as therapeutic targets, with impressive clinical results achieved in patients, as in the case of immune checkpoint inhibitors. To limit immune attack, tumor cells exploit specific pathways to render the tumor microenvironment hostile for antitumor effector cells. Local acidification might, in fact, anergize activated T cells and facilitate the accumulation of immune suppressive cells. Moreover, the release of extracellular vesicles by tumor cells can condition distant immune sites contributing to the onset of systemic immune suppression. Understanding which mechanisms may be prevalent in specific cancers or disease stages, and identifying possible strategies to counterbalance would majorly contribute to improving clinical efficacy of cancer immunotherapy. Here, we intend to highlight these mechanisms, how they could be targeted and the tools that might be available in the near future to achieve this goal. PMID:27827921

  13. Targeting the Regulatory Machinery of BIM for Cancer Therapy

    PubMed Central

    Harada, Hisashi; Grant, Steven

    2013-01-01

    BIM represents a BH3-only proapoptotic member of the BCL-2 family of apoptotic regulatory proteins. Recent evidence suggests that in addition to its involvement in normal homeostasis, BIM plays a critical role in tumor cell biology, including the regulation of tumorigenesis through activities as a tumor suppressor, tumor metastasis, and tumor cell survival. Consequently, BIM has become the focus of intense interest as a potential target for cancer chemotherapy. The control of BIM expression is complex, and involves multiple factors, including epigenetic events (i.e., promoter acetylation or methylation, miRNA), transcription factors, posttranscriptional regulation, and posttranslational modifications, most notably phosphorylation. Significantly, the expression of BIM by tumor cells has been shown to play an important role in determining the response of transformed cells to not only conventional cytotoxic agents, but also to a broad array of targeted agents that interrupt cell signaling and survival pathways. Furthermore, modifications in BIM expression may be exploited to improve the therapeutic activity and potentially the selectivity of such agents. It is likely that evolving insights into the factors that regulate BIM expression will ultimately lead to novel BIM-based therapeutic strategies in the future. PMID:22856430

  14. Arenavirus nucleoprotein targets interferon regulatory factor-activating kinase IKKε.

    PubMed

    Pythoud, Christelle; Rodrigo, W W Shanaka I; Pasqual, Giulia; Rothenberger, Sylvia; Martínez-Sobrido, Luis; de la Torre, Juan Carlos; Kunz, Stefan

    2012-08-01

    Arenaviruses perturb innate antiviral defense by blocking induction of type I interferon (IFN) production. Accordingly, the arenavirus nucleoprotein (NP) was shown to block activation and nuclear translocation of interferon regulatory factor 3 (IRF3) in response to virus infection. Here, we sought to identify cellular factors involved in innate antiviral signaling targeted by arenavirus NP. Consistent with previous studies, infection with the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) prevented phosphorylation of IRF3 in response to infection with Sendai virus, a strong inducer of the retinoic acid-inducible gene I (RIG-I)/mitochondrial antiviral signaling (MAVS) pathway of innate antiviral signaling. Using a combination of coimmunoprecipitation and confocal microscopy, we found that LCMV NP associates with the IκB kinase (IKK)-related kinase IKKε but that, rather unexpectedly, LCMV NP did not bind to the closely related TANK-binding kinase 1 (TBK-1). The NP-IKKε interaction was highly conserved among arenaviruses from different clades. In LCMV-infected cells, IKKε colocalized with NP but not with MAVS located on the outer membrane of mitochondria. LCMV NP bound the kinase domain (KD) of IKKε (IKBKE) and blocked its autocatalytic activity and its ability to phosphorylate IRF3, without undergoing phosphorylation. Together, our data identify IKKε as a novel target of arenavirus NP. Engagement of NP seems to sequester IKKε in an inactive complex. Considering the important functions of IKKε in innate antiviral immunity and other cellular processes, the NP-IKKε interaction likely plays a crucial role in arenavirus-host interaction.

  15. Comparison of evolutionary algorithms in gene regulatory network model inference

    PubMed Central

    2010-01-01

    Background The evolution of high throughput technologies that measure gene expression levels has created a data base for inferring GRNs (a process also known as reverse engineering of GRNs). However, the nature of these data has made this process very difficult. At the moment, several methods of discovering qualitative causal relationships between genes with high accuracy from microarray data exist, but large scale quantitative analysis on real biological datasets cannot be performed, to date, as existing approaches are not suitable for real microarray data which are noisy and insufficient. Results This paper performs an analysis of several existing evolutionary algorithms for quantitative gene regulatory network modelling. The aim is to present the techniques used and offer a comprehensive comparison of approaches, under a common framework. Algorithms are applied to both synthetic and real gene expression data from DNA microarrays, and ability to reproduce biological behaviour, scalability and robustness to noise are assessed and compared. Conclusions Presented is a comparison framework for assessment of evolutionary algorithms, used to infer gene regulatory networks. Promising methods are identified and a platform for development of appropriate model formalisms is established. PMID:20105328

  16. Comparison of evolutionary algorithms in gene regulatory network model inference.

    PubMed

    Sîrbu, Alina; Ruskin, Heather J; Crane, Martin

    2010-01-27

    The evolution of high throughput technologies that measure gene expression levels has created a data base for inferring GRNs (a process also known as reverse engineering of GRNs). However, the nature of these data has made this process very difficult. At the moment, several methods of discovering qualitative causal relationships between genes with high accuracy from microarray data exist, but large scale quantitative analysis on real biological datasets cannot be performed, to date, as existing approaches are not suitable for real microarray data which are noisy and insufficient. This paper performs an analysis of several existing evolutionary algorithms for quantitative gene regulatory network modelling. The aim is to present the techniques used and offer a comprehensive comparison of approaches, under a common framework. Algorithms are applied to both synthetic and real gene expression data from DNA microarrays, and ability to reproduce biological behaviour, scalability and robustness to noise are assessed and compared. Presented is a comparison framework for assessment of evolutionary algorithms, used to infer gene regulatory networks. Promising methods are identified and a platform for development of appropriate model formalisms is established.

  17. Regulatory Elements in Vectors for Efficient Generation of Cell Lines Producing Target Proteins

    PubMed Central

    Maksimenko, O.; Gasanov, N. B.; Georgiev, P.

    2015-01-01

    To date, there has been an increasing number of drugs produced in mammalian cell cultures. In order to enhance the expression level and stability of target recombinant proteins in cell cultures, various regulatory elements with poorly studied mechanisms of action are used. In this review, we summarize and discuss the potential mechanisms of action of such regulatory elements. PMID:26483956

  18. Transcriptional Targeting in the Airway Using Novel Gene Regulatory Elements

    PubMed Central

    Burnight, Erin R.; Wang, Guoshun; McCray, Paul B.

    2012-01-01

    The delivery of cystic fibrosis transmembrane conductance regulator (CFTR) to airway epithelia is a goal of many gene therapy strategies to treat cystic fibrosis. Because the native regulatory elements of the CFTR are not well characterized, the development of vectors with heterologous promoters of varying strengths and specificity would aid in our selection of optimal reagents for the appropriate expression of the vector-delivered CFTR gene. Here we contrasted the performance of several novel gene-regulatory elements. Based on airway expression analysis, we selected putative regulatory elements from BPIFA1 and WDR65 to investigate. In addition, we selected a human CFTR promoter region (∼ 2 kb upstream of the human CFTR transcription start site) to study. Using feline immunodeficiency virus vectors containing the candidate elements driving firefly luciferase, we transduced murine nasal epithelia in vivo. Luciferase expression persisted for 30 weeks, which was the duration of the experiment. Furthermore, when the nasal epithelium was ablated using the detergent polidocanol, the mice showed a transient loss of luciferase expression that returned 2 weeks after administration, suggesting that our vectors transduced a progenitor cell population. Importantly, the hWDR65 element drove sufficient CFTR expression to correct the anion transport defect in CFTR-null epithelia. These results will guide the development of optimal vectors for sufficient, sustained CFTR expression in airway epithelia. PMID:22447971

  19. Regulatory T cells as therapeutic targets in rheumatoid arthritis

    PubMed Central

    Esensten, Jonathan H.; Wofsy, David; Bluestone, Jeffrey A.

    2011-01-01

    Regulatory T cells (TREG) are a subset of CD4+ T cells with a critical role in the prevention of autoimmunity. Whether defects in TREG contribute to the pathogenesis of rheumatoid arthritis (RA) is unclear. However, a variety of approved and experimental drugs for RA may work, in part, by promoting the function or increasing numbers of TREG. Furthermore, animal studies demonstrate that direct injection of TREG ameliorates a wide range of experimental models of inflammatory and autoimmune diseases. Thus, cell-based therapy with TREG has the potential to produce durable disease remission in patients with RA. PMID:19798031

  20. Integrative FourD omics approach profiles the target network of the carbon storage regulatory system.

    PubMed

    Sowa, Steven W; Gelderman, Grant; Leistra, Abigail N; Buvanendiran, Aishwarya; Lipp, Sarah; Pitaktong, Areen; Vakulskas, Christopher A; Romeo, Tony; Baldea, Michael; Contreras, Lydia M

    2017-01-26

    Multi-target regulators represent a largely untapped area for metabolic engineering and anti-bacterial development. These regulators are complex to characterize because they often act at multiple levels, affecting proteins, transcripts and metabolites. Therefore, single omics experiments cannot profile their underlying targets and mechanisms. In this work, we used an Integrative FourD omics approach (INFO) that consists of collecting and analyzing systems data throughout multiple time points, using multiple genetic backgrounds, and multiple omics approaches (transcriptomics, proteomics and high throughput sequencing crosslinking immunoprecipitation) to evaluate simultaneous changes in gene expression after imposing an environmental stress that accentuates the regulatory features of a network. Using this approach, we profiled the targets and potential regulatory mechanisms of a global regulatory system, the well-studied carbon storage regulatory (Csr) system of Escherichia coli, which is widespread among bacteria. Using 126 sets of proteomics and transcriptomics data, we identified 136 potential direct CsrA targets, including 50 novel ones, categorized their behaviors into distinct regulatory patterns, and performed in vivo fluorescence-based follow up experiments. The results of this work validate 17 novel mRNAs as authentic direct CsrA targets and demonstrate a generalizable strategy to integrate multiple lines of omics data to identify a core pool of regulator targets.

  1. Integrative FourD omics approach profiles the target network of the carbon storage regulatory system

    PubMed Central

    Sowa, Steven W.; Gelderman, Grant; Leistra, Abigail N.; Buvanendiran, Aishwarya; Lipp, Sarah; Pitaktong, Areen; Vakulskas, Christopher A.; Romeo, Tony; Baldea, Michael

    2017-01-01

    Abstract Multi-target regulators represent a largely untapped area for metabolic engineering and anti-bacterial development. These regulators are complex to characterize because they often act at multiple levels, affecting proteins, transcripts and metabolites. Therefore, single omics experiments cannot profile their underlying targets and mechanisms. In this work, we used an Integrative FourD omics approach (INFO) that consists of collecting and analyzing systems data throughout multiple time points, using multiple genetic backgrounds, and multiple omics approaches (transcriptomics, proteomics and high throughput sequencing crosslinking immunoprecipitation) to evaluate simultaneous changes in gene expression after imposing an environmental stress that accentuates the regulatory features of a network. Using this approach, we profiled the targets and potential regulatory mechanisms of a global regulatory system, the well-studied carbon storage regulatory (Csr) system of Escherichia coli, which is widespread among bacteria. Using 126 sets of proteomics and transcriptomics data, we identified 136 potential direct CsrA targets, including 50 novel ones, categorized their behaviors into distinct regulatory patterns, and performed in vivo fluorescence-based follow up experiments. The results of this work validate 17 novel mRNAs as authentic direct CsrA targets and demonstrate a generalizable strategy to integrate multiple lines of omics data to identify a core pool of regulator targets. PMID:28126921

  2. Oct4 Targets Regulatory Nodes to Modulate Stem Cell Function

    PubMed Central

    Campbell, Pearl A.; Perez-Iratxeta, Carolina; Andrade-Navarro, Miguel A.; Rudnicki, Michael A.

    2007-01-01

    Stem cells are characterized by two defining features, the ability to self-renew and to differentiate into highly specialized cell types. The POU homeodomain transcription factor Oct4 (Pou5f1) is an essential mediator of the embryonic stem cell state and has been implicated in lineage specific differentiation, adult stem cell identity, and cancer. Recent description of the regulatory networks which maintain ‘ES’ have highlighted a dual role for Oct4 in the transcriptional activation of genes required to maintain self-renewal and pluripotency while concomitantly repressing genes which facilitate lineage specific differentiation. However, the molecular mechanism by which Oct4 mediates differential activation or repression at these loci to either maintain stem cell identity or facilitate the emergence of alternate transcriptional programs required for the realization of lineage remains to be elucidated. To further investigate Oct4 function, we employed gene expression profiling together with a robust statistical analysis to identify genes highly correlated to Oct4. Gene Ontology analysis to categorize overrepresented genes has led to the identification of themes which may prove essential to stem cell identity, including chromatin structure, nuclear architecture, cell cycle control, DNA repair, and apoptosis. Our experiments have identified previously unappreciated roles for Oct4 for firstly, regulating chromatin structure in a state consistent with self-renewal and pluripotency, and secondly, facilitating the expression of genes that keeps the cell poised to respond to cues that lead to differentiation. Together, these data define the mechanism by which Oct4 orchestrates cellular regulatory pathways to enforce the stem cell state and provides important insight into stem cell function and cancer. PMID:17579724

  3. Evolution of regulatory targets for drinking water quality.

    PubMed

    Sinclair, Martha; O'Toole, Joanne; Gibney, Katherine; Leder, Karin

    2015-06-01

    The last century has been marked by major advances in the understanding of microbial disease risks from water supplies and significant changes in expectations of drinking water safety. The focus of drinking water quality regulation has moved progressively from simple prevention of detectable waterborne outbreaks towards adoption of health-based targets that aim to reduce infection and disease to a level well below detection limits at the community level. This review outlines the changes in understanding of community disease and waterborne risks that prompted development of these targets, and also describes their underlying assumptions and current context. Issues regarding the appropriateness of selected target values, and how continuing changes in knowledge and practice may influence their evolution, are also discussed.

  4. i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules.

    PubMed

    Herrmann, Carl; Van de Sande, Bram; Potier, Delphine; Aerts, Stein

    2012-08-01

    The field of regulatory genomics today is characterized by the generation of high-throughput data sets that capture genome-wide transcription factor (TF) binding, histone modifications, or DNAseI hypersensitive regions across many cell types and conditions. In this context, a critical question is how to make optimal use of these publicly available datasets when studying transcriptional regulation. Here, we address this question in Drosophila melanogaster for which a large number of high-throughput regulatory datasets are available. We developed i-cisTarget (where the 'i' stands for integrative), for the first time enabling the discovery of different types of enriched 'regulatory features' in a set of co-regulated sequences in one analysis, being either TF motifs or 'in vivo' chromatin features, or combinations thereof. We have validated our approach on 15 co-expressed gene sets, 21 ChIP data sets, 628 curated gene sets and multiple individual case studies, and show that meaningful regulatory features can be confidently discovered; that bona fide enhancers can be identified, both by in vivo events and by TF motifs; and that combinations of in vivo events and TF motifs further increase the performance of enhancer prediction.

  5. MicroRNAs: Processing, Maturation, Target Recognition and Regulatory Functions

    PubMed Central

    Shukla, Girish C.; Singh, Jagjit; Barik, Sailen

    2012-01-01

    The remarkable discovery of small noncoding microRNAs (miRNAs) and their role in posttranscriptional gene regulation have revealed another fine-tuning step in the expression of genetic information. A large number of cellular pathways, which act in organismal development and are important in health and disease, appear to be modulated by miRNAs. At the molecular level, miRNAs restrain the production of proteins by affecting the stability of their target mRNA and/or by down-regulating their translation. This review attempts to offer a snapshot of aspects of miRNA coding, processing, target recognition and function in animals. Our goal here is to provide the readers with a thought-provoking and mechanistic introduction to the miRNA world rather than with a detailed encyclopedia. PMID:22468167

  6. Regulatory Review of Novel Therapeutics — Comparison of Three Regulatory Agencies

    PubMed Central

    Downing, Nicholas S.; Aminawung, Jenerius A.; Shah, Nilay D.; Braunstein, Joel B.; Krumholz, Harlan M.; Ross, Joseph S.

    2012-01-01

    BACKGROUND The upcoming reauthorization of the Prescription Drug User Fee Act focuses on improving the review process for new drug applications at the Food and Drug Administration (FDA). METHODS Using publicly available information from the FDA, the European Medicines Agency (EMA), and Health Canada, we compared the time for completion of the first review and the total review time for all applications involving novel therapeutic agents approved by the three regulatory agencies from 2001 through 2010 and determined the geographic area in which each novel therapeutic agent was first approved for use. RESULTS There were 510 applications for novel therapeutic agents approved from 2001 through 2010 — 225 by the FDA, 186 by the EMA, and 99 by Health Canada; among the applications, there were 289 unique agents. The median length of time for completion of the first review was 303 days (interquartile range, 185 to 372) for applications approved by the FDA, 366 days (interquartile range, 310 to 445) for those approved by the EMA, and 352 days (interquartile range, 255 to 420) for those approved by Health Canada (P<0.001 for the comparison across the three agencies). The median total review time was also shorter at the FDA than at the EMA or Health Canada (P = 0.002). Among the 289 unique novel therapeutic agents, 190 were approved in both the United States and Europe (either by the EMA or through the mutual recognition process), of which 121 (63.7%) were first approved in the United States; similarly, 154 were approved in both the United States and Canada, of which 132 (85.7%) were first approved in the United States. CONCLUSIONS For novel therapeutic agents approved between 2001 and 2010, the FDA reviewed applications involving novel therapeutics more quickly, on average, than did the EMA or Health Canada, and the vast majority of these new therapeutic agents were first approved for use in the United States. (Funded by the Pew Charitable Trusts.) PMID:22591257

  7. The exploration of network motifs as potential drug targets from post-translational regulatory networks.

    PubMed

    Zhang, Xiao-Dong; Song, Jiangning; Bork, Peer; Zhao, Xing-Ming

    2016-02-08

    Phosphorylation and proteolysis are among the most common post-translational modifications (PTMs), and play critical roles in various biological processes. More recent discoveries imply that the crosstalks between these two PTMs are involved in many diseases. In this work, we construct a post-translational regulatory network (PTRN) consists of phosphorylation and proteolysis processes, which enables us to investigate the regulatory interplays between these two PTMs. With the PTRN, we identify some functional network motifs that are significantly enriched with drug targets, some of which are further found to contain multiple proteins targeted by combinatorial drugs. These findings imply that the network motifs may be used to predict targets when designing new drugs. Inspired by this, we propose a novel computational approach called NetTar for predicting drug targets using the identified network motifs. Benchmarking results on real data indicate that our approach can be used for accurate prediction of novel proteins targeted by known drugs.

  8. MicroRNAs targeting TGFβ signalling underlie the regulatory T cell defect in multiple sclerosis.

    PubMed

    Severin, Mary E; Lee, Priscilla W; Liu, Yue; Selhorst, Amanda J; Gormley, Matthew G; Pei, Wei; Yang, Yuhong; Guerau-de-Arellano, Mireia; Racke, Michael K; Lovett-Racke, Amy E

    2016-06-01

    Transforming growth factor beta (TGFβ) signalling is critical for regulatory T cell development and function, and regulatory T cell dysregulation is a common observation in autoimmune diseases, including multiple sclerosis. In a comprehensive miRNA profiling study of patients with multiple sclerosis naïve CD4 T cells, 19 differentially expressed miRNAs predicted to target the TGFβ signalling pathway were identified, leading to the hypothesis that miRNAs may be responsible for the regulatory T cell defect observed in patients with multiple sclerosis. Patients with multiple sclerosis had reduced levels of TGFβ signalling components in their naïve CD4 T cells. The differentially expressed miRNAs negatively regulated the TGFβ pathway, resulting in a reduced capacity of naïve CD4 T cells to differentiate into regulatory T cells. Interestingly, the limited number of regulatory T cells, that did develop when these TGFβ-targeting miRNAs were overexpressed, were capable of suppressing effector T cells. As it has previously been demonstrated that compromising TGFβ signalling results in a reduced regulatory T cell repertoire insufficient to control autoimmunity, and patients with multiple sclerosis have a reduced regulatory T cell repertoire, these data indicate that the elevated expression of multiple TGFβ-targeting miRNAs in naïve CD4 T cells of patients with multiple sclerosis impairs TGFβ signalling, and dampens regulatory T cell development, thereby enhancing susceptibility to developing multiple sclerosis. © The Author (2016). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. Structure-based prediction of DNA target sites by regulatory proteins.

    PubMed

    Kono, H; Sarai, A

    1999-04-01

    Regulatory proteins play a critical role in controlling complex spatial and temporal patterns of gene expression in higher organism, by recognizing multiple DNA sequences and regulating multiple target genes. Increasing amounts of structural data on the protein-DNA complex provides clues for the mechanism of target recognition by regulatory proteins. The analyses of the propensities of base-amino acid interactions observed in those structural data show that there is no one-to-one correspondence in the interaction, but clear preferences exist. On the other hand, the analysis of spatial distribution of amino acids around bases shows that even those amino acids with strong base preference such as Arg with G are distributed in a wide space around bases. Thus, amino acids with many different geometries can form a similar type of interaction with bases. The redundancy and structural flexibility in the interaction suggest that there are no simple rules in the sequence recognition, and its prediction is not straightforward. However, the spatial distributions of amino acids around bases indicate a possibility that the structural data can be used to derive empirical interaction potentials between amino acids and bases. Such information extracted from structural databases has been successfully used to predict amino acid sequences that fold into particular protein structures. We surmised that the structures of protein-DNA complexes could be used to predict DNA target sites for regulatory proteins, because determining DNA sequences that bind to a particular protein structure should be similar to finding amino acid sequences that fold into a particular structure. Here we demonstrate that the structural data can be used to predict DNA target sequences for regulatory proteins. Pairwise potentials that determine the interaction between bases and amino acids were empirically derived from the structural data. These potentials were then used to examine the compatibility between DNA

  10. CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis.

    PubMed

    Kutmon, Martina; Kelder, Thomas; Mandaviya, Pooja; Evelo, Chris T A; Coort, Susan L

    2013-01-01

    The high complexity and dynamic nature of the regulation of gene expression, protein synthesis, and protein activity pose a challenge to fully understand the cellular machinery. By deciphering the role of important players, including transcription factors, microRNAs, or small molecules, a better understanding of key regulatory processes can be obtained. Various databases contain information on the interactions of regulators with their targets for different organisms, data recently being extended with the results of the ENCODE (Encyclopedia of DNA Elements) project. A systems biology approach integrating our understanding on different regulators is essential in interpreting the regulation of molecular biological processes. We developed CyTargetLinker (http://projects.bigcat.unimaas.nl/cytargetlinker), a Cytoscape app, for integrating regulatory interactions in network analysis. Recently we released CyTargetLinker as one of the first apps for Cytoscape 3. It provides a user-friendly and flexible interface to extend biological networks with regulatory interactions, such as microRNA-target, transcription factor-target and/or drug-target. Importantly, CyTargetLinker employs identifier mapping to combine various interaction data resources that use different types of identifiers. Three case studies demonstrate the strength and broad applicability of CyTargetLinker, (i) extending a mouse molecular interaction network, containing genes linked to diabetes mellitus, with validated and predicted microRNAs, (ii) enriching a molecular interaction network, containing DNA repair genes, with ENCODE transcription factor and (iii) building a regulatory meta-network in which a biological process is extended with information on transcription factor, microRNA and drug regulation. CyTargetLinker provides a simple and extensible framework for biologists and bioinformaticians to integrate different regulatory interactions into their network analysis approaches. Visualization options enable

  11. Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plants

    PubMed Central

    2012-01-01

    Background MicroRNAs (miRNAs) play an essential role in gene regulation in plants. At the same time, the expression of miRNA genes is also tightly controlled. Recently, a novel mechanism called “target mimicry” was discovered, providing another layer for modulating miRNA activities. However, except for the artificial target mimics manipulated for functional studies on certain miRNA genes, only one example, IPS1 (Induced by Phosphate Starvation 1)—miR399 was experimentally confirmed in planta. To date, few analyses for comprehensive identification of natural target mimics have been performed in plants. Thus, limited evidences are available to provide detailed information for interrogating the questionable issue whether target mimicry was widespread in planta, and implicated in certain biological processes. Results In this study, genome-wide computational prediction of endogenous miRNA mimics was performed in Arabidopsis and rice, and dozens of target mimics were identified. In contrast to a recent report, the densities of target mimic sites were found to be much higher within the untranslated regions (UTRs) when compared to those within the coding sequences (CDSs) in both plants. Some novel sequence characteristics were observed for the miRNAs that were potentially regulated by the target mimics. GO (Gene Ontology) term enrichment analysis revealed some functional insights into the predicted mimics. After degradome sequencing data-based identification of miRNA targets, the regulatory networks constituted by target mimics, miRNAs and their downstream targets were constructed, and some intriguing subnetworks were further exploited. Conclusions These results together suggest that target mimicry may be widely implicated in regulating miRNA activities in planta, and we hope this study could expand the current understanding of miRNA-involved regulatory networks. PMID:22613869

  12. Predicting miRNA Targets by Integrating Gene Regulatory Knowledge with Expression Profiles

    PubMed Central

    Zhang, Weijia; Le, Thuc Duy; Liu, Lin; Zhou, Zhi-Hua; Li, Jiuyong

    2016-01-01

    Motivation microRNAs (miRNAs) play crucial roles in post-transcriptional gene regulation of both plants and mammals, and dysfunctions of miRNAs are often associated with tumorigenesis and development through the effects on their target messenger RNAs (mRNAs). Identifying miRNA functions is critical for understanding cancer mechanisms and determining the efficacy of drugs. Computational methods analyzing high-throughput data offer great assistance in understanding the diverse and complex relationships between miRNAs and mRNAs. However, most of the existing methods do not fully utilise the available knowledge in biology to reduce the uncertainty in the modeling process. Therefore it is desirable to develop a method that can seamlessly integrate existing biological knowledge and high-throughput data into the process of discovering miRNA regulation mechanisms. Results In this article we present an integrative framework, CIDER (Causal miRNA target Discovery with Expression profile and Regulatory knowledge), to predict miRNA targets. CIDER is able to utilise a variety of gene regulation knowledge, including transcriptional and post-transcriptional knowledge, and to exploit gene expression data for the discovery of miRNA-mRNA regulatory relationships. The benefits of our framework is demonstrated by both simulation study and the analysis of the epithelial-to-mesenchymal transition (EMT) and the breast cancer (BRCA) datasets. Our results reveal that even a limited amount of either Transcription Factor (TF)-miRNA or miRNA-mRNA regulatory knowledge improves the performance of miRNA target prediction, and the combination of the two types of knowledge enhances the improvement further. Another useful property of the framework is that its performance increases monotonically with the increase of regulatory knowledge. PMID:27064982

  13. Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome

    PubMed Central

    Andrews, Erik; Wang, Yue; Xia, Tian; Cheng, Wenqing; Cheng, Chao

    2017-01-01

    Gene expression regulators, such as transcription factors (TFs) and microRNAs (miRNAs), have varying regulatory targets based on the tissue and physiological state (context) within which they are expressed. While the emergence of regulator-characterizing experiments has inferred the target genes of many regulators across many contexts, methods for transferring regulator target genes across contexts are lacking. Further, regulator target gene lists frequently are not curated or have permissive inclusion criteria, impairing their use. Here, we present a method called iterative Contextual Transcriptional Activity Inference of Regulators (icTAIR) to resolve these issues. icTAIR takes a regulator’s previously-identified target gene list and combines it with gene expression data from a context, quantifying that regulator’s activity for that context. It then calculates the correlation between each listed target gene’s expression and the quantitative score of regulatory activity, removes the uncorrelated genes from the list, and iterates the process until it derives a stable list of refined target genes. To validate and demonstrate icTAIR’s power, we use it to refine the MSigDB c3 database of TF, miRNA and unclassified motif target gene lists for breast cancer. We then use its output for survival analysis with clinicopathological multivariable adjustment in 7 independent breast cancer datasets covering 3,430 patients. We uncover many novel prognostic regulators that were obscured prior to refinement, in particular NFY, and offer a detailed look at the composition and relationships among the breast cancer prognostic regulome. We anticipate icTAIR will be of general use in contextually refining regulator target genes for discoveries across many contexts. The icTAIR algorithm can be downloaded from https://github.com/icTAIR. PMID:28103241

  14. Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets

    PubMed Central

    2012-01-01

    Background Altered networks of gene regulation underlie many complex conditions, including cancer. Inferring gene regulatory networks from high-throughput microarray expression data is a fundamental but challenging task in computational systems biology and its translation to genomic medicine. Although diverse computational and statistical approaches have been brought to bear on the gene regulatory network inference problem, their relative strengths and disadvantages remain poorly understood, largely because comparative analyses usually consider only small subsets of methods, use only synthetic data, and/or fail to adopt a common measure of inference quality. Methods We report a comprehensive comparative evaluation of nine state-of-the art gene regulatory network inference methods encompassing the main algorithmic approaches (mutual information, correlation, partial correlation, random forests, support vector machines) using 38 simulated datasets and empirical serous papillary ovarian adenocarcinoma expression-microarray data. We then apply the best-performing method to infer normal and cancer networks. We assess the druggability of the proteins encoded by our predicted target genes using the CancerResource and PharmGKB webtools and databases. Results We observe large differences in the accuracy with which these methods predict the underlying gene regulatory network depending on features of the data, network size, topology, experiment type, and parameter settings. Applying the best-performing method (the supervised method SIRENE) to the serous papillary ovarian adenocarcinoma dataset, we infer and rank regulatory interactions, some previously reported and others novel. For selected novel interactions we propose testable mechanistic models linking gene regulation to cancer. Using network analysis and visualization, we uncover cross-regulation of angiogenesis-specific genes through three key transcription factors in normal and cancer conditions. Druggabilty analysis

  15. Task Characteristics and Target Choice in Social Comparison.

    ERIC Educational Resources Information Center

    Gorenflo, Daniel W.

    Festinger's (1954) theory of social comparison holds that in the absence of objective standards, people use the attitudes or judgments of similar others to determine the correctness of their own positions. More recent studies have suggested, however, that people often prefer dissimilar comparison targets. A study was undertaken to examine the…

  16. A comparison of immunotoxic effects of nanomedicinal products with regulatory immunotoxicity testing requirements

    PubMed Central

    Giannakou, Christina; Park, Margriet VDZ; de Jong, Wim H; van Loveren, Henk; Vandebriel, Rob J; Geertsma, Robert E

    2016-01-01

    Nanomaterials (NMs) are attractive for biomedical and pharmaceutical applications because of their unique physicochemical and biological properties. A major application area of NMs is drug delivery. Many nanomedicinal products (NMPs) currently on the market or in clinical trials are most often based on liposomal products or polymer conjugates. NMPs can be designed to target specific tissues, eg, tumors. In virtually all cases, NMPs will eventually reach the immune system. It has been shown that most NMs end up in organs of the mononuclear phagocytic system, notably liver and spleen. Adverse immune effects, including allergy, hypersensitivity, and immunosuppression, have been reported after NMP administration. Interactions of NMPs with the immune system may therefore constitute important side effects. Currently, no regulatory documents are specifically dedicated to evaluate the immunotoxicity of NMs or NMPs. Their immunotoxicity assessment is performed based on existing guidelines for conventional substances or medicinal products. Due to the unique properties of NMPs when compared with conventional medicinal products, it is uncertain whether the currently prescribed set of tests provides sufficient information for an adequate evaluation of potential immunotoxicity of NMPs. The aim of this study was therefore, to compare the current regulatory immunotoxicity testing requirements with the accumulating knowledge on immunotoxic effects of NMPs in order to identify potential gaps in the safety assessment. This comparison showed that immunotoxic effects, such as complement activation-related pseudoallergy, myelosuppression, inflammasome activation, and hypersensitivity, are not readily detected by using current testing guidelines. Immunotoxicity of NMPs would be more accurately evaluated by an expanded testing strategy that is equipped to stratify applicable testing for the various types of NMPs. PMID:27382281

  17. A comparison of immunotoxic effects of nanomedicinal products with regulatory immunotoxicity testing requirements.

    PubMed

    Giannakou, Christina; Park, Margriet Vdz; de Jong, Wim H; van Loveren, Henk; Vandebriel, Rob J; Geertsma, Robert E

    2016-01-01

    Nanomaterials (NMs) are attractive for biomedical and pharmaceutical applications because of their unique physicochemical and biological properties. A major application area of NMs is drug delivery. Many nanomedicinal products (NMPs) currently on the market or in clinical trials are most often based on liposomal products or polymer conjugates. NMPs can be designed to target specific tissues, eg, tumors. In virtually all cases, NMPs will eventually reach the immune system. It has been shown that most NMs end up in organs of the mononuclear phagocytic system, notably liver and spleen. Adverse immune effects, including allergy, hypersensitivity, and immunosuppression, have been reported after NMP administration. Interactions of NMPs with the immune system may therefore constitute important side effects. Currently, no regulatory documents are specifically dedicated to evaluate the immunotoxicity of NMs or NMPs. Their immunotoxicity assessment is performed based on existing guidelines for conventional substances or medicinal products. Due to the unique properties of NMPs when compared with conventional medicinal products, it is uncertain whether the currently prescribed set of tests provides sufficient information for an adequate evaluation of potential immunotoxicity of NMPs. The aim of this study was therefore, to compare the current regulatory immunotoxicity testing requirements with the accumulating knowledge on immunotoxic effects of NMPs in order to identify potential gaps in the safety assessment. This comparison showed that immunotoxic effects, such as complement activation-related pseudoallergy, myelosuppression, inflammasome activation, and hypersensitivity, are not readily detected by using current testing guidelines. Immunotoxicity of NMPs would be more accurately evaluated by an expanded testing strategy that is equipped to stratify applicable testing for the various types of NMPs.

  18. Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms

    PubMed Central

    Allen, Mary Ann; Andrysik, Zdenek; Dengler, Veronica L; Mellert, Hestia S; Guarnieri, Anna; Freeman, Justin A; Sullivan, Kelly D; Galbraith, Matthew D; Luo, Xin; Kraus, W Lee; Dowell, Robin D; Espinosa, Joaquin M

    2014-01-01

    The p53 transcription factor is a potent suppressor of tumor growth. We report here an analysis of its direct transcriptional program using Global Run-On sequencing (GRO-seq). Shortly after MDM2 inhibition by Nutlin-3, low levels of p53 rapidly activate ∼200 genes, most of them not previously established as direct targets. This immediate response involves all canonical p53 effector pathways, including apoptosis. Comparative global analysis of RNA synthesis vs steady state levels revealed that microarray profiling fails to identify low abundance transcripts directly activated by p53. Interestingly, p53 represses a subset of its activation targets before MDM2 inhibition. GRO-seq uncovered a plethora of gene-specific regulatory features affecting key survival and apoptotic genes within the p53 network. p53 regulates hundreds of enhancer-derived RNAs. Strikingly, direct p53 targets harbor pre-activated enhancers highly transcribed in p53 null cells. Altogether, these results enable the study of many uncharacterized p53 target genes and unexpected regulatory mechanisms. DOI: http://dx.doi.org/10.7554/eLife.02200.001 PMID:24867637

  19. MEDI1873, a potent, stabilized hexameric agonist of human GITR with regulatory T-cell targeting potential

    PubMed Central

    Tigue, Natalie J.; Bamber, Lisa; Andrews, John; Ireland, Samantha; Hair, James; Carter, Edward; Sridharan, Sudharsan; Jovanović, Jelena; Rees, D. Gareth; Springall, Jeremy S.; Li, Yi-Ming; Chodorge, Matthieu; Perez-Martinez, David; Higazi, Daniel R.; Oberst, Michael; Kennedy, Maureen; Black, Chelsea M.; Yan, Li; Schwickart, Martin; Maguire, Shaun; Young, Lesley L.; Vaughan, Tristan; Wilkinson, Robert W.; Stewart, Ross

    2017-01-01

    ABSTRACT Glucocorticoid-induced tumor necrosis factor receptor-related protein (GITR) is part of a system of signals involved in controlling T-cell activation. Targeting and agonizing GITR in mice promotes antitumor immunity by enhancing the function of effector T cells and inhibiting regulatory T cells. Here, we describe MEDI1873, a novel hexameric human GITR agonist comprising an IgG1 Fc domain, a coronin 1A trimerization domain and the human GITRL extracellular domain (ECD). MEDI1873 was optimized through systematic testing of different trimerization domains, aglycosylation of the GITRL ECD and comparison of different Fc isotypes. MEDI1873 exhibits oligomeric heterogeneity and superiority to an anti-GITR antibody with respect to evoking robust GITR agonism, T-cell activation and clustering of Fc gamma receptors. Further, it recapitulates, in vitro, several aspects of GITR targeting described in mice, including modulation of regulatory T-cell suppression and the ability to increase the CD8+:CD4+ T-cell ratio via antibody-dependent T-cell cytotoxicity. To support translation into a therapeutic setting, we demonstrate that MEDI1873 is a potent T-cell agonist in vivo in non-human primates, inducing marked enhancement of humoral and T-cell proliferative responses against protein antigen, and demonstrate the presence of GITR- and FoxP3-expressing infiltrating lymphocytes in a range of human tumors. Overall our data provide compelling evidence that MEDI1873 is a novel, potent GITR agonist with the ability to modulate T-cell responses, and suggest that previously described GITR biology in mice may translate to the human setting, reinforcing the potential of targeting the GITR pathway as a therapeutic approach to cancer. PMID:28405505

  20. Dietary non-nutritive factors in targeting of regulatory molecules in colorectal cancer: an update.

    PubMed

    Pandurangan, Ashok Kumar; Esa, Norhaizan Mohd

    2013-01-01

    Colorectal cancer (CRC), a complex multi-step process involving progressive disruption of homeostatic mechanisms controlling intestinal epithelial proliferation/inflammation, differentiation, and programmed cell death, is the third most common malignant neoplasm worldwide. A number of promising targets such as inducible nitric acid (iNOS), cyclooxygenase (COX)-2, NF-E2-related factor 2 (Nrf2), Wnt/β-catenin, Notch and apoptotic signaling have been identified by researchers as useful targets to prevent or therapeutically inhibit colon cancer development. In this review article, we aimed to explore the current targets available to eliminate colon cancer with an update of dietary and non-nutritional compounds that could be of potential use for interaction with regulatory molecules to prevent CRC.

  1. Electronic cigarettes: A comparison of national regulatory approaches.

    PubMed

    Rose, Adam; Filion, Kristian B; Eisenberg, Mark J; Franck, Caroline

    2015-10-03

    E-cigarettes have been readily available to global markets since 2004. However, regulations have lagged behind popular use and availability. As policies emerging from national health agencies have an important role to play in shaping consumer health, we examined the existing and upcoming national regulations surrounding e-cigarette availability and use in a convenience sample of English- and French-speaking countries, including Canada, the United States, the United Kingdom, France, Australia and New Zealand. There is substantial international variation in regulatory policies and the extent to which these are enforced. Of the countries considered in this review, the US has regulations that remain the most permissive, whereas those in Canada and New Zealand are the most conservative. However, regulations in Canada, Australia and New Zealand are easily bypassed through Internet imports and lenient enforcement. European health agencies are paving the way for Member States to take appropriate steps to regulate e-cigarettes according to their own jurisdictions. Currently, national regulations of e-cigarettes appear to be ill-defined in terms of shaping the future of e-cigarette availability and use. National regulations should be strengthened to reflect the public health implications of e-cigarettes and to emphasize their difference from consumer products.

  2. Cysteine 893 is a target of regulatory thiol modifications of GluA1 AMPA receptors

    PubMed Central

    von Ossowski, Lotta; Li, Li-Li; Möykkynen, Tommi; Coleman, Sarah K.; Courtney, Michael J.

    2017-01-01

    Recent studies indicate that glutamatergic signaling involves, and is regulated by, thiol modifying and redox-active compounds. In this study, we examined the role of a reactive cysteine residue, Cys-893, in the cytosolic C-terminal tail of GluA1 AMPA receptor as a potential regulatory target. Elimination of the thiol function by substitution of serine for Cys-893 led to increased steady-state expression level and strongly reduced interaction with SAP97, a major cytosolic interaction partner of GluA1 C-terminus. Moreover, we found that of the three cysteine residues in GluA1 C-terminal tail, Cys-893 is the predominant target for S-nitrosylation induced by exogenous nitric oxide donors in cultured cells and lysates. Co-precipitation experiments provided evidence for native association of SAP97 with neuronal nitric oxide synthase (nNOS) and for the potential coupling of Ca2+-permeable GluA1 receptors with nNOS via SAP97. Our results show that Cys-893 can serve as a molecular target for regulatory thiol modifications of GluA1 receptors, including the effects of nitric oxide. PMID:28152104

  3. Predictive long-range allele-specific mapping of regulatory variants and target transcripts.

    PubMed

    Lee, Kibaick; Lee, Seulkee; Bang, Hyoeun; Choi, Jung Kyoon

    2017-01-01

    Genome-wide association studies (GWASs) have identified a large number of noncoding associations, calling for systematic mapping to causal regulatory variants and their distal target genes. A widely used method, quantitative trait loci (QTL) mapping for chromatin or expression traits, suffers from sample-to-sample experimental variation and trans-acting or environmental effects. Instead, alleles at heterozygous loci can be compared within a sample, thereby controlling for those confounding factors. Here we introduce a method for chromatin structure-based allele-specific pairing of regulatory variants and target transcripts. With phased genotypes, much of allele-specific expression could be explained by paired allelic cis-regulation across a long range. This approach showed approximately two times greater sensitivity than QTL mapping. There are cases in which allele imbalance cannot be tested because heterozygotes are not available among reference samples. Therefore, we employed a machine learning method to predict missing positive cases based on various features shared by observed allele-specific pairs. We showed that only 10 reference samples are sufficient to achieve high prediction accuracy with a low sampling variation. In conclusion, our method enables highly sensitive fine mapping and target identification for trait-associated variants based on a small number of reference samples.

  4. PreImplantation factor (PIF*) regulates systemic immunity and targets protective regulatory and cytoskeleton proteins.

    PubMed

    Barnea, Eytan R; Hayrabedyan, Soren; Todorova, Krassimira; Almogi-Hazan, Osnat; Or, Reuven; Guingab, Joy; McElhinney, James; Fernandez, Nelson; Barder, Timothy

    2016-07-01

    Secreted by viable embryos, PIF is expressed by the placenta and found in maternal circulation. It promotes implantation and trophoblast invasion, achieving systemic immune homeostasis. Synthetic PIF successfully transposes endogenous PIF features to non-pregnant immune and transplant models. PIF affects innate and activated PBMC cytokines and genes expression. We report that PIF targets similar proteins in CD14+, CD4+ and CD8+ cells instigating integrated immune regulation. PIF-affinity chromatography followed by mass-spectrometry, pathway and heatmap analysis reveals that SET-apoptosis inhibitor, vimentin, myosin-9 and calmodulin are pivotal for immune regulation. PIF acts on macrophages down-stream of LPS (lipopolysaccharide-bacterial antigen) CD14/TLR4/MD2 complex, targeting myosin-9, thymosin-α1 and 14-3-3eta. PIF mainly targets platelet aggregation in CD4+, and skeletal proteins in CD8+ cells. Pathway analysis demonstrates that PIF targets and regulates SET, tubulin, actin-b, and S100 genes expression. PIF targets systemic immunity and has a short circulating half-life. Collectively, PIF targets identified; protective, immune regulatory and cytoskeleton proteins reveal mechanisms involved in the observed efficacy against immune disorders. Copyright © 2016 Elsevier GmbH. All rights reserved.

  5. Graphlet Based Metrics for the Comparison of Gene Regulatory Networks

    PubMed Central

    Martin, Alberto J. M.; Dominguez, Calixto; Contreras-Riquelme, Sebastián; Holmes, David S.; Perez-Acle, Tomas

    2016-01-01

    Understanding the control of gene expression remains one of the main challenges in the post-genomic era. Accordingly, a plethora of methods exists to identify variations in gene expression levels. These variations underlay almost all relevant biological phenomena, including disease and adaptation to environmental conditions. However, computational tools to identify how regulation changes are scarce. Regulation of gene expression is usually depicted in the form of a gene regulatory network (GRN). Structural changes in a GRN over time and conditions represent variations in the regulation of gene expression. Like other biological networks, GRNs are composed of basic building blocks called graphlets. As a consequence, two new metrics based on graphlets are proposed in this work: REConstruction Rate (REC) and REC Graphlet Degree (RGD). REC determines the rate of graphlet similarity between different states of a network and RGD identifies the subset of nodes with the highest topological variation. In other words, RGD discerns how th GRN was rewired. REC and RGD were used to compare the local structure of nodes in condition-specific GRNs obtained from gene expression data of Escherichia coli, forming biofilms and cultured in suspension. According to our results, most of the network local structure remains unaltered in the two compared conditions. Nevertheless, changes reported by RGD necessarily imply that a different cohort of regulators (i.e. transcription factors (TFs)) appear on the scene, shedding light on how the regulation of gene expression occurs when E. coli transits from suspension to biofilm. Consequently, we propose that both metrics REC and RGD should be adopted as a quantitative approach to conduct differential analyses of GRNs. A tool that implements both metrics is available as an on-line web server (http://dlab.cl/loto). PMID:27695050

  6. Graphlet Based Metrics for the Comparison of Gene Regulatory Networks.

    PubMed

    Martin, Alberto J M; Dominguez, Calixto; Contreras-Riquelme, Sebastián; Holmes, David S; Perez-Acle, Tomas

    2016-01-01

    Understanding the control of gene expression remains one of the main challenges in the post-genomic era. Accordingly, a plethora of methods exists to identify variations in gene expression levels. These variations underlay almost all relevant biological phenomena, including disease and adaptation to environmental conditions. However, computational tools to identify how regulation changes are scarce. Regulation of gene expression is usually depicted in the form of a gene regulatory network (GRN). Structural changes in a GRN over time and conditions represent variations in the regulation of gene expression. Like other biological networks, GRNs are composed of basic building blocks called graphlets. As a consequence, two new metrics based on graphlets are proposed in this work: REConstruction Rate (REC) and REC Graphlet Degree (RGD). REC determines the rate of graphlet similarity between different states of a network and RGD identifies the subset of nodes with the highest topological variation. In other words, RGD discerns how th GRN was rewired. REC and RGD were used to compare the local structure of nodes in condition-specific GRNs obtained from gene expression data of Escherichia coli, forming biofilms and cultured in suspension. According to our results, most of the network local structure remains unaltered in the two compared conditions. Nevertheless, changes reported by RGD necessarily imply that a different cohort of regulators (i.e. transcription factors (TFs)) appear on the scene, shedding light on how the regulation of gene expression occurs when E. coli transits from suspension to biofilm. Consequently, we propose that both metrics REC and RGD should be adopted as a quantitative approach to conduct differential analyses of GRNs. A tool that implements both metrics is available as an on-line web server (http://dlab.cl/loto).

  7. Discovering transcription factor regulatory targets using gene expression and binding data.

    PubMed

    Maienschein-Cline, Mark; Zhou, Jie; White, Kevin P; Sciammas, Roger; Dinner, Aaron R

    2012-01-15

    Identifying the target genes regulated by transcription factors (TFs) is the most basic step in understanding gene regulation. Recent advances in high-throughput sequencing technology, together with chromatin immunoprecipitation (ChIP), enable mapping TF binding sites genome wide, but it is not possible to infer function from binding alone. This is especially true in mammalian systems, where regulation often occurs through long-range enhancers in gene-rich neighborhoods, rather than proximal promoters, preventing straightforward assignment of a binding site to a target gene. We present EMBER (Expectation Maximization of Binding and Expression pRofiles), a method that integrates high-throughput binding data (e.g. ChIP-chip or ChIP-seq) with gene expression data (e.g. DNA microarray) via an unsupervised machine learning algorithm for inferring the gene targets of sets of TF binding sites. Genes selected are those that match overrepresented expression patterns, which can be used to provide information about multiple TF regulatory modes. We apply the method to genome-wide human breast cancer data and demonstrate that EMBER confirms a role for the TFs estrogen receptor alpha, retinoic acid receptors alpha and gamma in breast cancer development, whereas the conventional approach of assigning regulatory targets based on proximity does not. Additionally, we compare several predicted target genes from EMBER to interactions inferred previously, examine combinatorial effects of TFs on gene regulation and illustrate the ability of EMBER to discover multiple modes of regulation. All code used for this work is available at http://dinner-group.uchicago.edu/downloads.html.

  8. Close Sequence Comparisons are Sufficient to Identify Humancis-Regulatory Elements

    SciTech Connect

    Prabhakar, Shyam; Poulin, Francis; Shoukry, Malak; Afzal, Veena; Rubin, Edward M.; Couronne, Olivier; Pennacchio, Len A.

    2005-12-01

    Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of evolutionarily close and distant sequence comparisons, due to the lack of a universal metric for sequence conservation, and also the paucity of empirically defined benchmark sets of cis-regulatory elements. To address this problem, we developed a general-purpose algorithm (Gumby) that detects slowly-evolving regions in primate, mammalian and more distant comparisons without requiring adjustment of parameters, and ranks conserved elements by P-value using Karlin-Altschul statistics. We benchmarked Gumby predictions against previously identified cis-regulatory elements at diverse genomic loci, and also tested numerous extremely conserved human-rodent sequences for transcriptional enhancer activity using reporter-gene assays in transgenic mice. Human regulatory elements were identified with acceptable sensitivity and specificity by comparison with 1-5 other eutherian mammals or 6 other simian primates. More distant comparisons (marsupial, avian, amphibian and fish) failed to identify many of the empirically defined functional noncoding elements. We derived an intuitive relationship between ancient and recent noncoding sequence conservation from whole genome comparative analysis, which explains some of these findings. Lastly, we determined that, in addition to strength of conservation, genomic location and/or density of surrounding conserved elements must also be considered in selecting candidate enhancers for testing at embryonic time points.

  9. Detection of Weakly Conserved Ancestral Mammalian RegulatorySequences by Primate Comparisons

    SciTech Connect

    Wang, Qian-fei; Prabhakar, Shyam; Chanan, Sumita; Cheng,Jan-Fang; Rubin, Edward M.; Boffelli, Dario

    2006-06-01

    Genomic comparisons between human and distant, non-primatemammals are commonly used to identify cis-regulatory elements based onconstrained sequence evolution. However, these methods fail to detectcryptic functional elements, which are too weakly conserved among mammalsto distinguish from nonfunctional DNA. To address this problem, weexplored the potential of deep intra-primate sequence comparisons. Wesequenced the orthologs of 558 kb of human genomic sequence, coveringmultiple loci involved in cholesterol homeostasis, in 6 nonhumanprimates. Our analysis identified 6 noncoding DNA elements displayingsignificant conservation among primates, but undetectable in more distantcomparisons. In vitro and in vivo tests revealed that at least three ofthese 6 elements have regulatory function. Notably, the mouse orthologsof these three functional human sequences had regulatory activity despitetheir lack of significant sequence conservation, indicating that they arecryptic ancestral cis-regulatory elements. These regulatory elementscould still be detected in a smaller set of three primate speciesincluding human, rhesus and marmoset. Since the human and rhesus genomesequences are already available, and the marmoset genome is activelybeing sequenced, the primate-specific conservation analysis describedhere can be applied in the near future on a whole-genome scale, tocomplement the annotation provided by more distant speciescomparisons.

  10. Generating political priority for regulatory interventions targeting obesity prevention: an Australian case study.

    PubMed

    Baker, Phillip; Gill, Timothy; Friel, Sharon; Carey, Gemma; Kay, Adrian

    2017-03-01

    rationales to defer political priority. Overcoming these challenges may be important to future collective action efforts attempting to generate and sustain political priority for regulatory interventions targeting obesity.

  11. Targeting a Regulatory Element in Human Thymidylate Synthase mRNA

    PubMed Central

    Brunn, Nicholas D.; Sega, Emily Garcia; Kao, Melody B.

    2013-01-01

    Thymidylate synthase (TS) is a key enzyme in the biosynthesis of thymidine. TS inhibitors, which are used in cancer chemotherapy, suffer from resistance development in tumors through upregulation of TS expression. Autoregulatory translation control has been implicated with TS overexpression. TS binding at its own mRNA, which leads to sequestration of the start codon, is abolished when the enzyme forms an inhibitor complex, thereby relieving translation suppression. We have used the protein binding site from the TS mRNA in the context of a bicistronic expression system to validate targeting the regulatory motif with stabilizing ligands that prevent ribosomal initiation. Stabilization of the RNA by mutations, which were studied as surrogates of ligand binding, suppresses translation of the TS protein. Compounds that stabilize the TS binding RNA motif and thereby inhibit ribosomal initiation might be used in combination with existing TS enzyme-targeting drugs to overcome resistance development during chemotherapy. PMID:23143777

  12. Cardiac-targeted delivery of regulatory RNA molecules and genes for the treatment of heart failure

    PubMed Central

    Poller, Wolfgang; Hajjar, Roger; Schultheiss, Heinz-Peter; Fechner, Henry

    2010-01-01

    Ribonucleic acid (RNA) in its many facets of structure and function is becoming more fully understood, and, therefore, it is possible to design and use RNAs as valuable tools in molecular biology and medicine. Understanding of the role of RNAs within the cell has changed dramatically during the past few years. Therapeutic strategies based on non-coding regulatory RNAs include RNA interference (RNAi) for the silencing of specific genes, and microRNA (miRNA) modulations to alter complex gene expression patterns. Recent progress has allowed the targeting of therapeutic RNAi to the heart for the treatment of heart failure, and we discuss current strategies in this field. Owing to the peculiar biochemical properties of small RNA molecules, the actual therapeutic translation of findings in vitro or in cell cultures is more demanding than with small molecule drugs or proteins. The critical requirement for animal studies after pre-testing of RNAi tools in vitro likewise applies for miRNA modulations, which also have complex consequences for the recipient that are dependent on stability and distribution of the RNA tools. Problems in the field that are not yet fully solved are the prediction of targets and specificity of the RNA tools as well as their tissue-specific and regulatable expression. We discuss analogies and differences between regulatory RNA therapy and classical gene therapy, since recent breakthroughs in vector technology are of importance for both. Recent years have witnessed parallel progress in the fields of gene-based and regulatory RNA-based therapies that are likely to significantly expand the cardiovascular therapeutic repertoire within the next decade. PMID:20176815

  13. USP1 deubiquitinase: cellular functions, regulatory mechanisms and emerging potential as target in cancer therapy

    PubMed Central

    2013-01-01

    Reversible protein ubiquitination is emerging as a key process for maintaining cell homeostasis, and the enzymes that participate in this process, in particular E3 ubiquitin ligases and deubiquitinases (DUBs), are increasingly being regarded as candidates for drug discovery. Human DUBs are a group of approximately 100 proteins, whose cellular functions and regulatory mechanisms remain, with some exceptions, poorly characterized. One of the best-characterized human DUBs is ubiquitin-specific protease 1 (USP1), which plays an important role in the cellular response to DNA damage. USP1 levels, localization and activity are modulated through several mechanisms, including protein-protein interactions, autocleavage/degradation and phosphorylation, ensuring that USP1 function is carried out in a properly regulated spatio-temporal manner. Importantly, USP1 expression is deregulated in certain types of human cancer, suggesting that USP1 could represent a valid target in cancer therapy. This view has gained recent support with the finding that USP1 inhibition may contribute to revert cisplatin resistance in an in vitro model of non-small cell lung cancer (NSCLC). Here, we describe the current knowledge on the cellular functions and regulatory mechanisms of USP1. We also summarize USP1 alterations found in cancer, combining data from the literature and public databases with our own data. Finally, we discuss the emerging potential of USP1 as a target, integrating published data with our novel findings on the effects of the USP1 inhibitor pimozide in combination with cisplatin in NSCLC cells. PMID:23937906

  14. Identification of Novel Targets of the Human Cell Cycle Regulatory Protein Cdc34

    DTIC Science & Technology

    1999-07-01

    hRad21 is differentially expressed in a number of breast cancer derived cell lines in comparison to the normal breast epithelial cells (see below...hCdc34 interactors including ICERIIy, ATF5, Clone #28C (Fission yeast Rad21 homolog), and #42-2 (Leukemia cell differentiation factor) in these breast...of Cdc34 and its targets it is evident that Cdc34 and some of its targets (e.g. ATF5 and hRad2 1) are differentially expressed in the breast cancer

  15. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes

    PubMed Central

    Yao, Lijing; Berman, Benjamin P.; Farnham, Peggy J.

    2015-01-01

    Abstract Enhancers are short regulatory sequences bound by sequence-specific transcription factors and play a major role in the spatiotemporal specificity of gene expression patterns in development and disease. While it is now possible to identify enhancer regions genomewide in both cultured cells and primary tissues using epigenomic approaches, it has been more challenging to develop methods to understand the function of individual enhancers because enhancers are located far from the gene(s) that they regulate. However, it is essential to identify target genes of enhancers not only so that we can understand the role of enhancers in disease but also because this information will assist in the development of future therapeutic options. After reviewing models of enhancer function, we discuss recent methods for identifying target genes of enhancers. First, we describe chromatin structure-based approaches for directly mapping interactions between enhancers and promoters. Second, we describe the use of correlation-based approaches to link enhancer state with the activity of nearby promoters and/or gene expression. Third, we describe how to test the function of specific enhancers experimentally by perturbing enhancer–target relationships using high-throughput reporter assays and genome editing. Finally, we conclude by discussing as yet unanswered questions concerning how enhancers function, how target genes can be identified, and how to distinguish direct from indirect changes in gene expression mediated by individual enhancers. PMID:26446758

  16. Novel anti-HIV therapeutics targeting chemokine receptors and actin regulatory pathways.

    PubMed

    Spear, Mark; Guo, Jia; Wu, Yuntao

    2013-11-01

    The human immunodeficiency virus-1 (HIV-1) infects helper CD4(+) T cells, and causes CD4(+) T-cell depletion and immunodeficiency. In the past 30 years, significant progress has been made in antiretroviral therapy, and the disease has become manageable. Nevertheless, an effective vaccine is still nowhere in sight, and a cure or a functional cure awaits discovery. Among possible curative therapies, traditional antiretroviral therapy, mostly targeting viral proteins, has been proven ineffective. It is possible that targeting HIV-dependent host cofactors may offer alternatives, both for preventing HIV transmission and for forestalling disease progression. Recently, the actin cytoskeleton and its regulators in blood CD4(+) T cells have emerged as major host cofactors that could be targeted. The novel concept that the cortical actin is a barrier to viral entry and early post-entry migration has led to the nascent model of virus-host interaction at the cortical actin layer. Deciphering the cellular regulatory pathways has manifested exciting prospects for future therapeutics. In this review, we describe the study of HIV interactions with actin cytoskeleton. We also examine potential pharmacological targets that emerge from this interaction. In addition, we briefly discuss several actin pathway-based anti-HIV drugs that are currently in development or testing.

  17. Novel anti-HIV therapeutics targeting chemokine receptors and actin regulatory pathways

    PubMed Central

    Spear, Mark; Guo, Jia; Wu, Yuntao

    2013-01-01

    Summary The human immunodeficiency virus-1 (HIV-1) infects helper CD4+ T cells, and causes CD4+ T-cell depletion and immunodeficiency. In the past 30 years, significant progress has been made in antiretroviral therapy, and the disease has become manageable. Nevertheless, an effective vaccine is still nowhere in sight, and a cure or a functional cure awaits discovery. Among possible curative therapies, traditional antiretroviral therapy, mostly targeting viral proteins, has been proven ineffective. It is possible that targeting HIV-dependent host cofactors may offer alternatives, both for preventing HIV transmission and for forestalling disease progression. Recently, the actin cytoskeleton and its regulators in blood CD4+ T cells have emerged as major host cofactors that could be targeted. The novel concept that the cortical actin is a barrier to viral entry and early post-entry migration has led to the nascent model of virus-host interaction at the cortical actin layer. Deciphering the cellular regulatory pathways has manifested exciting prospects for future therapeutics. In this review, we describe the study of HIV interactions with actin cytoskeleton. We also examine potential pharmacological targets that emerge from this interaction. In addition, we briefly discuss several actin pathway-based anti-HIV drugs that are currently in development or testing. PMID:24117829

  18. Establishment of apoptotic regulatory network for genetic markers of colorectal cancer and optimal selection of traditional Chinese medicine target.

    PubMed

    Tian, Tongde; Chen, Chuanliang; Yang, Feng; Tang, Jingwen; Pei, Junwen; Shi, Bian; Zhang, Ning; Zhang, Jianhua

    2017-03-01

    The paper aimed to screen out genetic markers applicable to early diagnosis for colorectal cancer and establish apoptotic regulatory network model for colorectal cancer, and to analyze the current situation of traditional Chinese medicine (TCM) target, thereby providing theoretical evidence for early diagnosis and targeted therapy of colorectal cancer. Taking databases including CNKI, VIP, Wanfang data, Pub Med, and MEDLINE as main sources of literature retrieval, literatures associated with genetic markers that are applied to early diagnosis of colorectal cancer were searched and performed comprehensive and quantitative analysis by Meta analysis, hence screening genetic markers used in early diagnosis of colorectal cancer. KEGG analysis was employed to establish apoptotic regulatory network model based on screened genetic markers, and optimization was conducted on TCM targets. Through Meta analysis, seven genetic markers were screened out, including WWOX, K-ras, COX-2, P53, APC, DCC and PTEN, among which DCC has the highest diagnostic efficiency. Apoptotic regulatory network was built by KEGG analysis. Currently, it was reported that TCM has regulatory function on gene locus in apoptotic regulatory network. The apoptotic regulatory model of colorectal cancer established in this study provides theoretical evidence for early diagnosis and TCM targeted therapy of colorectal cancer in clinic.

  19. Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors.

    PubMed

    Ishihama, Akira; Shimada, Tomohiro; Yamazaki, Yukiko

    2016-03-18

    Bacterial genomes are transcribed by DNA-dependent RNA polymerase (RNAP), which achieves gene selectivity through interaction with sigma factors that recognize promoters, and transcription factors (TFs) that control the activity and specificity of RNAP holoenzyme. To understand the molecular mechanisms of transcriptional regulation, the identification of regulatory targets is needed for all these factors. We then performed genomic SELEX screenings of targets under the control of each sigma factor and each TF. Here we describe the assembly of 156 SELEX patterns of a total of 116 TFs performed in the presence and absence of effector ligands. The results reveal several novel concepts: (i) each TF regulates more targets than hitherto recognized; (ii) each promoter is regulated by more TFs than hitherto recognized; and (iii) the binding sites of some TFs are located within operons and even inside open reading frames. The binding sites of a set of global regulators, including cAMP receptor protein, LeuO and Lrp, overlap with those of the silencer H-NS, suggesting that certain global regulators play an anti-silencing role. To facilitate sharing of these accumulated SELEX datasets with the research community, we compiled a database, 'Transcription Profile of Escherichia coli' (www.shigen.nig.ac.jp/ecoli/tec/). © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets.

    PubMed

    Hazelett, Dennis J; Lakeland, Daniel L; Weiss, Joseph B

    2009-07-01

    A new method was developed for identifying novel transcription factor regulatory targets based on calculating Local Affinity Density. Techniques from the signal-processing field were used, in particular the Hann digital filter, to calculate the relative binding affinity of different regions based on previously published in vitro binding data. To illustrate this approach, the complete genomes of Drosophila melanogaster and D.pseudoobscura were analyzed for binding sites of the homeodomain proteinc Tinman, an essential heart development gene in both Drosophila and Mouse. The significant binding regions were identified relative to genomic background and assigned to putative target genes. Valid candidates common to both species of Drosophila were selected as a test of conservation. The new method was more sensitive than cluster searches for conserved binding motifs with respect to positive identification of known Tinman targets. Our Local Affinity Density method also identified a significantly greater proportion of Tinman-coexpressed genes than equivalent, optimized cluster searching. In addition, this new method predicted a significantly greater than expected number of genes with previously published RNAi phenotypes in the heart. Algorithms were implemented in Python, LISP, R and maxima, using MySQL to access locally mirrored sequence data from Ensembl (D.melanogaster release 4.3) and flybase (D.pseudoobscura). All code is licensed under GPL and freely available at http://www.ohsu.edu/cellbio/dev_biol_prog/affinitydensity/.

  1. Coupling of tandem Smad ubiquitination regulatory factor (Smurf) WW domains modulates target specificity.

    PubMed

    Chong, P Andrew; Lin, Hong; Wrana, Jeffrey L; Forman-Kay, Julie D

    2010-10-26

    Smad ubiquitination regulatory factor 2 (Smurf2) is an E3 ubiquitin ligase that participates in degradation of TGF-β receptors and other targets. Smurf2 WW domains recognize PPXY (PY) motifs on ubiquitin ligase target proteins or on adapters, such as Smad7, that bind to E3 target proteins. We previously demonstrated that the isolated WW3 domain of Smurf2, but not the WW2 domain, can directly bind to a Smad7 PY motif. We show here that the WW2 augments this interaction by binding to the WW3 and making auxiliary contacts with the PY motif and a novel E/D-S/T-P motif, which is N-terminal to all Smad PY motifs. The WW2 likely enhances the selectivity of Smurf2 for the Smad proteins. NMR titrations confirm that Smad1 and Smad2 are bound by Smurf2 with the same coupled WW domain arrangement used to bind Smad7. The analogous WW domains in the short isoform of Smurf1 recognize the Smad7 PY peptide using the same coupled mechanism. However, a longer Smurf1 isoform, which has an additional 26 residues in the inter-WW domain linker, is only partially able to use the coupled WW domain binding mechanism. The longer linker results in a decrease in affinity for the Smad7 peptide. Interdomain coupling of WW domains enhances selectivity and enables the tuning of interactions by isoform switching.

  2. Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors

    PubMed Central

    Ishihama, Akira; Shimada, Tomohiro; Yamazaki, Yukiko

    2016-01-01

    Bacterial genomes are transcribed by DNA-dependent RNA polymerase (RNAP), which achieves gene selectivity through interaction with sigma factors that recognize promoters, and transcription factors (TFs) that control the activity and specificity of RNAP holoenzyme. To understand the molecular mechanisms of transcriptional regulation, the identification of regulatory targets is needed for all these factors. We then performed genomic SELEX screenings of targets under the control of each sigma factor and each TF. Here we describe the assembly of 156 SELEX patterns of a total of 116 TFs performed in the presence and absence of effector ligands. The results reveal several novel concepts: (i) each TF regulates more targets than hitherto recognized; (ii) each promoter is regulated by more TFs than hitherto recognized; and (iii) the binding sites of some TFs are located within operons and even inside open reading frames. The binding sites of a set of global regulators, including cAMP receptor protein, LeuO and Lrp, overlap with those of the silencer H-NS, suggesting that certain global regulators play an anti-silencing role. To facilitate sharing of these accumulated SELEX datasets with the research community, we compiled a database, ‘Transcription Profile of Escherichia coli’ (www.shigen.nig.ac.jp/ecoli/tec/). PMID:26843427

  3. Rotavirus NSP1 mediates degradation of interferon regulatory factors through targeting of the dimerization domain.

    PubMed

    Arnold, Michelle M; Barro, Mario; Patton, John T

    2013-09-01

    Rotavirus nonstructural protein NSP1 can inhibit expression of interferon (IFN) and IFN-stimulated gene products by inducing proteasome-mediated degradation of IFN-regulatory factors (IRFs), including IRF3, IRF5, and IRF7. All IRF proteins share an N-terminal DNA-binding domain (DBD), and IRF3, IRF5, and IRF7 contain a similar C-proximal IRF association domain (IAD) that mediates IRF dimerization. An autoinhibitory domain (ID) at the extreme C terminus interacts with the IAD, burying residues necessary for IRF dimerization. Phosphorylation of serine/threonine residues in the ID induces charge repulsions that unmask the IAD, enabling IRF dimerization and subsequent nuclear translocation. To define the region of IRF proteins targeted for degradation by NSP1, we generated IRF3 and IRF7 truncation mutants and transiently expressed each with simian SA11-4F NSP1. These assays indicated that the IAD represented a necessary and sufficient target for degradation. Because NSP1 did not mediate degradation of truncated forms of the IAD, NSP1 likely requires a structurally intact IAD for recognition and targeting of IRF proteins. IRF9, which contains an IAD-like region that directs interactions with signal inducer and activator of transcription (STAT) proteins, was also targeted for degradation by NSP1, while IRF1, which lacks an IAD, was not. Analysis of mutant forms of IRF3 unable to undergo dimerization or that were constitutively dimeric showed that both were targeted for degradation by NSP1. These results indicate that SA11-4F NSP1 can induce degradation of inactive and activated forms of IAD-containing IRF proteins (IRF3 to IRF9), allowing a multipronged attack on IFN-based pathways that promote antiviral innate and adaptive immune responses.

  4. Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network.

    PubMed

    Richard, Arianne C; Peters, James E; Lee, James C; Vahedi, Golnaz; Schäffer, Alejandro A; Siegel, Richard M; Lyons, Paul A; Smith, Kenneth G C

    2016-07-19

    Tumour necrosis factor (TNF) superfamily cytokines and their receptors regulate diverse immune system functions through a common set of signalling pathways. Genetic variants in and expression of individual TNF superfamily cytokines, receptors and signalling proteins have been associated with autoimmune and inflammatory diseases, but their interconnected biology has been largely unexplored. We took a hypothesis-driven approach using available genome-wide datasets to identify genetic variants regulating gene expression in the TNF superfamily cytokine signalling network and the association of these variants with autoimmune and autoinflammatory disease. Using paired gene expression and genetic data, we identified genetic variants associated with gene expression, expression quantitative trait loci (eQTLs), in four peripheral blood cell subsets. We then examined whether eQTLs were dependent on gene expression level or the presence of active enhancer chromatin marks. Using these eQTLs as genetic markers of the TNF superfamily signalling network, we performed targeted gene set association analysis in eight autoimmune and autoinflammatory disease genome-wide association studies. Comparison of TNF superfamily network gene expression and regulatory variants across four leucocyte subsets revealed patterns that differed between cell types. eQTLs for genes in this network were not dependent on absolute gene expression levels and were not enriched for chromatin marks of active enhancers. By examining autoimmune disease risk variants among our eQTLs, we found that risk alleles can be associated with either increased or decreased expression of co-stimulatory TNF superfamily cytokines, receptors or downstream signalling molecules. Gene set disease association analysis revealed that eQTLs for genes in the TNF superfamily pathway were associated with six of the eight autoimmune and autoinflammatory diseases examined, demonstrating associations beyond single genome-wide significant

  5. Breaking immune tolerance by targeting Foxp3+ regulatory T cells mitigates Alzheimer's disease pathology

    PubMed Central

    Baruch, Kuti; Rosenzweig, Neta; Kertser, Alexander; Deczkowska, Aleksandra; Sharif, Alaa Mohammad; Spinrad, Amit; Tsitsou-Kampeli, Afroditi; Sarel, Ayelet; Cahalon, Liora; Schwartz, Michal

    2015-01-01

    Alzheimer's disease (AD) is a neurodegenerative disorder in which chronic neuroinflammation contributes to disease escalation. Nevertheless, while immunosuppressive drugs have repeatedly failed in treating this disease, recruitment of myeloid cells to the CNS was shown to play a reparative role in animal models. Here we show, using the 5XFAD AD mouse model, that transient depletion of Foxp3+ regulatory T cells (Tregs), or pharmacological inhibition of their activity, is followed by amyloid-β plaque clearance, mitigation of the neuroinflammatory response and reversal of cognitive decline. We further show that transient Treg depletion affects the brain's choroid plexus, a selective gateway for immune cell trafficking to the CNS, and is associated with subsequent recruitment of immunoregulatory cells, including monocyte-derived macrophages and Tregs, to cerebral sites of plaque pathology. Our findings suggest targeting Treg-mediated systemic immunosuppression for treating AD. PMID:26284939

  6. Regulatory T Cells in the Tumor Microenvironment and Cancer Progression: Role and Therapeutic Targeting

    PubMed Central

    Chaudhary, Belal; Elkord, Eyad

    2016-01-01

    Recent years have seen significant efforts in understanding and modulating the immune response in cancer. In this context, immunosuppressive cells, including regulatory T cells (Tregs) and myeloid-derived suppressor cells (MDSCs), have come under intense investigation for their proposed roles in suppressing tumor-specific immune responses and establishing an immunosuppressive tumor microenvironment, thus enabling tumor immune evasion. Additionally, recent evidence indicates that Tregs comprise diverse and heterogeneous subsets; phenotypically and functionally distinct subsets of tumor-infiltrating Tregs could contribute differently to cancer prognosis and clinical outcomes. Understanding Treg biology in the setting of cancer, and specifically the tumor microenvironment, is important for designing effective cancer therapies. In this review, we critically examine the role of Tregs in the tumor microenvironment and in cancer progression focusing on human studies. We also discuss the impact of current therapeutic modalities on Treg biology and the therapeutic opportunities for targeting Tregs to enhance anti-tumor immune responses and clinical benefits. PMID:27509527

  7. Identification of a novel miRNA-target gene regulatory network in osteosarcoma by integrating transcriptome analysis

    PubMed Central

    He, Chunlei; Gao, Hui; Fan, Xiaona; Wang, Maoyuan; Liu, Wuyang; Huang, Weiming; Yang, Yadong

    2015-01-01

    Osteosarcoma remains a leading cause of cancer death in children and young adolescents. Although the introduction of multiagent chemotherapy, survival rates have not improved in two decades. Therefore, it is urgently needed to know the details regarding molecular etiology to driving therapeutic inroads for this disease. In this study we performed an integrated analysis of miRNA and mRNA expression data to explore the dysregulation of miRNA and miRNA-target gene regulatory network underlying OS. 59 differentially expressed miRNAs were identified, with 28 up-regulated and 31 down-regulated miRNAs by integrating OS miRNA expression data sets available. Using miRWalk databases prediction, we performed an anticorrelated analysis of miRNA and genes expression identified by a integrated analysis of gene expression data to identify 109 differently expressed miRNA target genes. A novel miRNA-target gene regulatory network was constructed with the miRNA-target gene pairs. miR-19b-3p, miR-20a-5p, miR-124-3p and their common target CCND2, the nodal points of regulatory network, may play important roles in OS. Bioinformatics analysis of biological functions and pathways demonstrated that target genes of miRNAs are highly correlated with carcinogenesis. Our findings may help to understand the molecular mechanisms of OS and identify targets of effective targeted therapies for OS. PMID:26339404

  8. HAND2 Target Gene Regulatory Networks Control Atrioventricular Canal and Cardiac Valve Development.

    PubMed

    Laurent, Frédéric; Girdziusaite, Ausra; Gamart, Julie; Barozzi, Iros; Osterwalder, Marco; Akiyama, Jennifer A; Lincoln, Joy; Lopez-Rios, Javier; Visel, Axel; Zuniga, Aimée; Zeller, Rolf

    2017-05-23

    The HAND2 transcriptional regulator controls cardiac development, and we uncover additional essential functions in the endothelial to mesenchymal transition (EMT) underlying cardiac cushion development in the atrioventricular canal (AVC). In Hand2-deficient mouse embryos, the EMT underlying AVC cardiac cushion formation is disrupted, and we combined ChIP-seq of embryonic hearts with transcriptome analysis of wild-type and mutants AVCs to identify the functionally relevant HAND2 target genes. The HAND2 target gene regulatory network (GRN) includes most genes with known functions in EMT processes and AVC cardiac cushion formation. One of these is Snai1, an EMT master regulator whose expression is lost from Hand2-deficient AVCs. Re-expression of Snai1 in mutant AVC explants partially restores this EMT and mesenchymal cell migration. Furthermore, the HAND2-interacting enhancers in the Snai1 genomic landscape are active in embryonic hearts and other Snai1-expressing tissues. These results show that HAND2 directly regulates the molecular cascades initiating AVC cardiac valve development. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  9. Axin2 as regulatory and therapeutic target in newborn brain injury and remyelination

    PubMed Central

    Fancy, Stephen P.J.; Harrington, Emily P.; Yuen, Tracy J.; Silbereis, John C.; Zhao, Chao; Baranzini, Sergio E.; Bruce, Charlotte C.; Otero, Jose J.; Huang, Eric J.; Nusse, Roel; Franklin, Robin J.M.; Rowitch, David H.

    2011-01-01

    Permanent damage to white matter tracts, comprising axons and myelinating oligodendrocytes, is an important component of newborn brain injuries that cause cerebral palsy and cognitive disabilities as well as multiple sclerosis (MS) in adults. However, regulatory factors relevant in human developmental myelin disorders and in myelin regeneration are unclear. Here, we report expression of AXIN2 in immature oligodendrocyte progenitor cells (OLP) within white matter lesions of human newborns with neonatal hypoxic-ischemic and gliotic brain damage, as well as active MS lesions in adults. Axin2 is a target of Wnt transcriptional activation that feeds back negatively on the pathway, promoting β-catenin degradation. We show Axin2 function is essential for normal kinetics of remyelination. Small molecule inhibitor XAV939, which targets enzymatic activity of Tankyrase, acts to stabilize Axin2 levels in OLP from brain and spinal cord and accelerates their differentiation and myelination after hypoxic and demyelinating injury. Together, these findings indicate that Axin2 is an essential regulator of remyelination and that it might serve as a pharmacological checkpoint in this process. PMID:21706018

  10. HAND2 Target Gene Regulatory Networks Control Atrioventricular Canal and Cardiac Valve Development

    DOE PAGES

    Laurent, Frédéric; Girdziusaite, Ausra; Gamart, Julie; ...

    2017-05-23

    The HAND2 transcriptional regulator controls cardiac development, and we uncover additional essential functions in the endothelial to mesenchymal transition (EMT) underlying cardiac cushion development in the atrioventricular canal (AVC). In Hand2-deficient mouse embryos, the EMT underlying AVC cardiac cushion formation is disrupted, and we combined ChIP-seq of embryonic hearts with transcriptome analysis of wild-type and mutants AVCs to identify the functionally relevant HAND2 target genes. The HAND2 target gene regulatory network (GRN) includes most genes with known functions in EMT processes and AVC cardiac cushion formation. One of these is Snai1, an EMT master regulator whose expression is lost frommore » Hand2-deficient AVCs. Re-expression of Snai1 in mutant AVC explants partially restores this EMT and mesenchymal cell migration. Furthermore, the HAND2-interacting enhancers in the Snai1 genomic landscape are active in embryonic hearts and other Snai1-expressing tissues. These results show that HAND2 directly regulates the molecular cascades initiating AVC cardiac valve development.« less

  11. Mitochondrial targeting of bilirubin regulatory enzymes: An adaptive response to oxidative stress

    SciTech Connect

    Muhsain, Siti Nur Fadzilah; Lang, Matti A.; Abu-Bakar, A'edah

    2015-01-01

    The intracellular level of bilirubin (BR), an endogenous antioxidant that is cytotoxic at high concentrations, is tightly controlled within the optimal therapeutic range. We have recently described a concerted intracellular BR regulation by two microsomal enzymes: heme oxygenase 1 (HMOX1), essential for BR production and cytochrome P450 2A5 (CYP2A5), a BR oxidase. Herein, we describe targeting of these enzymes to hepatic mitochondria during oxidative stress. The kinetics of microsomal and mitochondrial BR oxidation were compared. Treatment of DBA/2J mice with 200 mg pyrazole/kg/day for 3 days increased hepatic intracellular protein carbonyl content and induced nucleo-translocation of Nrf2. HMOX1 and CYP2A5 proteins and activities were elevated in microsomes and mitoplasts but not the UGT1A1, a catalyst of BR glucuronidation. A CYP2A5 antibody inhibited 75% of microsomal BR oxidation. The inhibition was absent in control mitoplasts but elevated to 50% after treatment. An adrenodoxin reductase antibody did not inhibit microsomal BR oxidation but inhibited 50% of mitochondrial BR oxidation. Ascorbic acid inhibited 5% and 22% of the reaction in control and treated microsomes, respectively. In control mitoplasts the inhibition was 100%, which was reduced to 50% after treatment. Bilirubin affinity to mitochondrial and microsomal CYP2A5 enzyme is equally high. Lastly, the treatment neither released cytochrome c into cytoplasm nor dissipated membrane potential, indicating the absence of mitochondrial membrane damage. Collectively, the observations suggest that BR regulatory enzymes are recruited to mitochondria during oxidative stress and BR oxidation by mitochondrial CYP2A5 is supported by mitochondrial mono-oxygenase system. The induced recruitment potentially confers membrane protection. - Highlights: • Pyrazole induces oxidative stress in the mouse liver. • Pyrazole-induced oxidative stress induces mitochondrial targeting of key bilirubin regulatory enzymes, HMOX1

  12. Comparison of bioequivalence study regulatory requirements for human and veterinary drugs.

    PubMed

    Grabowski, Tomasz; Marczak, Monika; Jaroszewski, Jerzy Jan; Whitmire, Monica

    2012-11-01

    Guidelines published by the European Union Regulatory Authority, regarding the planning of bioequivalence studies, are the primary source of knowledge about the study design optimization. The goal of this paper is to compare the key elements (27 points) of bioequivalence study optimization based on a comparison of the two European Medicines Agency guidelines relating to medicines used for humans (HB) and to veterinary drugs (AB). In case of the latter, one can get the impression that the issues of species differences in relation to the physiology and anatomy have been completely ignored. Many details that the AB guideline omits are included in the new HB guideline and were present in many other guidelines from the last 20 years. Most have not been adopted by the AB document, even though they are the product of many years of work of many teams and specialists from various agencies in the regulatory affairs field.

  13. GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation.

    PubMed

    Han, Kook; Tjaden, Brian; Lory, Stephen

    2016-12-22

    The first step in the post-transcriptional regulatory function of most bacterial small non-coding RNAs (sRNAs) is base pairing with partially complementary sequences of targeted transcripts. We present a simple method for identifying sRNA targets in vivo and defining processing sites of the regulated transcripts. The technique, referred to as global small non-coding RNA target identification by ligation and sequencing (GRIL-seq), is based on preferential ligation of sRNAs to the ends of base-paired targets in bacteria co-expressing T4 RNA ligase, followed by sequencing to identify the chimaeras. In addition to the RNA chaperone Hfq, the GRIL-seq method depends on the activity of the pyrophosphorylase RppH. Using PrrF1, an iron-regulated sRNA in Pseudomonas aeruginosa, we demonstrated that direct regulatory targets of this sRNA can readily be identified. Therefore, GRIL-seq represents a powerful tool not only for identifying direct targets of sRNAs in a variety of environments, but also for uncovering novel roles for sRNAs and their targets in complex regulatory networks.

  14. Pdgfrb is a direct regulatory target of TGFβ signaling in atrioventricular cushion mesenchymal cells.

    PubMed

    Peng, Yin; Yan, Shun; Chen, Dongquan; Cui, Xiangqin; Jiao, Kai

    2017-01-01

    Cushion formation is the initial step for the development of valvuloseptal structures in mammalian hearts. TGFβ signaling plays critical roles in multiple steps of cushion morphogenesis. We used a newly developed conditional immortal atrioventricular cushion mesenchymal cell line, tsA58-AVM, to identify the TGFβ regulatory target genes through microarray analysis. Expression of ~1350 genes was significantly altered by TGFβ1 treatment. Subsequent bioinformatic analysis of TGFβ activated genes revealed that PDGF-BB signaling is the top hit as the potential upstream regulator. Among the 37 target molecules, 10 genes known to be involved in valve development and hemostasis were selected for quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis. Our results confirmed that they are all upregulated by TGFβ1 stimulation in tsA58-AVM cells and in primary atrioventricular cushion cells. We focused on examining regulation of Pdgfrb by TGFβ1, which encodes a tyrosine kinase receptor for PDGF-BB. We found that the ~150bp Pdgfrb promoter can respond to TGFβ stimulation and that this response relies on the two SP1 binding sites within the promoter. Co-immunoprecipitation analysis confirmed SP1 interacts with SMAD2 in a TGFβ-dependent fashion. Furthermore, SMAD2 is associated with the Pdgfrb promoter and this association is diminished by knocking down expression of Sp1. Our data therefore collectively suggest that upon TGFβ stimulation, SP1 recruits SMAD2 to the promoter of Pdgfrb to up-regulate its expression and thus Pdgfrb is a direct downstream target of the TGFβ/SMAD2 signaling.

  15. In silico identified CCR4 antagonists target regulatory T cells and exert adjuvant activity in vaccination

    PubMed Central

    Bayry, Jagadeesh; Tchilian, Elma Z.; Davies, Matthew N.; Forbes, Emily K.; Draper, Simon J.; Kaveri, Srini V.; Hill, Adrian V. S.; Kazatchkine, Michel D.; Beverley, Peter C. L.; Flower, Darren R.; Tough, David F.

    2008-01-01

    Adjuvants are substances that enhance immune responses and thus improve the efficacy of vaccination. Few adjuvants are available for use in humans, and the one that is most commonly used (alum) often induces suboptimal immunity for protection against many pathogens. There is thus an obvious need to develop new and improved adjuvants. We have therefore taken an approach to adjuvant discovery that uses in silico modeling and structure-based drug-design. As proof-of-principle we chose to target the interaction of the chemokines CCL22 and CCL17 with their receptor CCR4. CCR4 was posited as an adjuvant target based on its expression on CD4+CD25+ regulatory T cells (Tregs), which negatively regulate immune responses induced by dendritic cells (DC), whereas CCL17 and CCL22 are chemotactic agents produced by DC, which are crucial in promoting contact between DC and CCR4+ T cells. Molecules identified by virtual screening and molecular docking as CCR4 antagonists were able to block CCL22- and CCL17-mediated recruitment of human Tregs and Th2 cells. Furthermore, CCR4 antagonists enhanced DC-mediated human CD4+ T cell proliferation in an in vitro immune response model and amplified cellular and humoral immune responses in vivo in experimental models when injected in combination with either Modified Vaccinia Ankara expressing Ag85A from Mycobacterium tuberculosis (MVA85A) or recombinant hepatitis B virus surface antigen (rHBsAg) vaccines. The significant adjuvant activity observed provides good evidence supporting our hypothesis that CCR4 is a viable target for rational adjuvant design. PMID:18621704

  16. Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions

    PubMed Central

    Goñi, Josep Ramon; Vaquerizas, Juan Manuel; Dopazo, Joaquin; Orozco, Modesto

    2006-01-01

    Background DNA duplex sequences that can be targets for triplex formation are highly over-represented in the human genome, especially in regulatory regions. Results Here we studied using bioinformatics tools several properties of triplex target sequences in an attempt to determine those that make these sequences so special in the genome. Conclusion Our results strongly suggest that the unique physical properties of these sequences make them particularly suitable as "separators" between protein-recognition sites in the promoter region. PMID:16566817

  17. The genetic regulatory network centered on Pto-Wuschela and its targets involved in wood formation revealed by association studies

    PubMed Central

    Yang, Xiaohui; Wei, Zunzheng; Du, Qingzhang; Chen, Jinhui; Wang, Qingshi; Quan, Mingyang; Song, Yuepeng; Xie, Jianbo; Zhang, Deqiang

    2015-01-01

    Transcription factors (TFs) regulate gene expression and can strongly affect phenotypes. However, few studies have examined TF variants and TF interactions with their targets in plants. Here, we used genetic association in 435 unrelated individuals of Populus tomentosa to explore the variants in Pto-Wuschela and its targets to decipher the genetic regulatory network of Pto-Wuschela. Our bioinformatics and co-expression analysis identified 53 genes with the motif TCACGTGA as putative targets of Pto-Wuschela. Single-marker association analysis showed that Pto-Wuschela was associated with wood properties, which is in agreement with the observation that it has higher expression in stem vascular tissues in Populus. Also, SNPs in the 53 targets were associated with growth or wood properties under additive or dominance effects, suggesting these genes and Pto-Wuschela may act in the same genetic pathways that affect variation in these quantitative traits. Epistasis analysis indicated that 75.5% of these genes directly or indirectly interacted Pto-Wuschela, revealing the coordinated genetic regulatory network formed by Pto-Wuschela and its targets. Thus, our study provides an alternative method for dissection of the interactions between a TF and its targets, which will strength our understanding of the regulatory roles of TFs in complex traits in plants. PMID:26549216

  18. Burglar Target Selection: A Cross-national Comparison.

    PubMed

    Townsley, Michael; Birks, Daniel; Bernasco, Wim; Ruiter, Stijn; Johnson, Shane D; White, Gentry; Baum, Scott

    2015-02-01

    This study builds on research undertaken by Bernasco and Nieuwbeerta and explores the generalizability of a theoretically derived offender target selection model in three cross-national study regions. Taking a discrete spatial choice approach, we estimate the impact of both environment- and offender-level factors on residential burglary placement in the Netherlands, the United Kingdom, and Australia. Combining cleared burglary data from all study regions in a single statistical model, we make statistical comparisons between environments. In all three study regions, the likelihood an offender selects an area for burglary is positively influenced by proximity to their home, the proportion of easily accessible targets, and the total number of targets available. Furthermore, in two of the three study regions, juvenile offenders under the legal driving age are significantly more influenced by target proximity than adult offenders. Post hoc tests indicate the magnitudes of these impacts vary significantly between study regions. While burglary target selection strategies are consistent with opportunity-based explanations of offending, the impact of environmental context is significant. As such, the approach undertaken in combining observations from multiple study regions may aid criminology scholars in assessing the generalizability of observed findings across multiple environments.

  19. Sphaeropsidin A shows promising activity against drug-resistant cancer cells by targeting regulatory volume increase

    PubMed Central

    Mathieu, Véronique; Chantôme, Aurélie; Lefranc, Florence; Cimmino, Alessio; Miklos, Walter; Paulitschke, Verena; Mohr, Thomas; Maddau, Lucia; Kornienko, Alexander; Berger, Walter; Vandier, Christophe; Evidente, Antonio; Delpire, Eric; Kiss, Robert

    2016-01-01

    Despite the recent advances in the treatment of tumors with intrinsic chemotherapy resistance, such as melanoma and renal cancers, their prognosis remains poor and new chemical agents with promising activity against these cancers are urgently needed. Sphaeropsidin A, a fungal metabolite whose anticancer potential had previously received little attention, was isolated from Diplodia cupressi and found to display specific anticancer activity in vitro against melanoma and kidney cancer subpanels in the National Cancer Institute (NCI) 60-cell line screen. The NCI data revealed a mean LC50 of ca. 10 μM and a cellular sensitivity profile that did not match that of any other agent in the 765,000 compound database. Subsequent mechanistic studies in melanoma and other multidrug-resistant in vitro cancer models showed that sphaeropsidin A can overcome apoptosis as well as multidrug resistance by inducing a marked and rapid cellular shrinkage related to the loss of intracellular Cl− and the decreased HCO3− concentration in the culture supernatant. These changes in ion homeostasis and the absence of effects on the plasma membrane potential were attributed to the sphaeropsidin A-induced impairment of regulatory volume increase (RVI). Preliminary results also indicate that depending on the type of cancer, the sphaeropsidin A effects on RVI could be related to Na–K–2Cl electroneutral cotransporter or Cl−/HCO3− anion exchanger(s) targeting. This study underscores the modulation of ion-transporter activity as a promising therapeutic strategy to combat drug-resistant cancers and identifies the fungal metabolite, sphaeropsidin A, as a lead to develop anticancer agents targeting RVI in cancer cells. PMID:25868554

  20. Definition of target antigens for naturally occurring CD4(+) CD25(+) regulatory T cells.

    PubMed

    Nishikawa, Hiroyoshi; Kato, Takuma; Tawara, Isao; Saito, Kanako; Ikeda, Hiroaki; Kuribayashi, Kagemasa; Allen, Paul M; Schreiber, Robert D; Sakaguchi, Shimon; Old, Lloyd J; Shiku, Hiroshi

    2005-03-07

    The antigenic targets recognized by naturally occurring CD4(+) CD25(+) regulatory T cells (T reg cells) have been elusive. We have serologically defined a series of broadly expressed self-antigens derived from chemically induced mouse sarcomas by serological identification of antigens by recombinant expression cloning (SEREX). CD4(+) CD25(+) T cells from mice immunized with SEREX-defined self-antigens had strong suppressive activity on peptide-specific proliferation of CD4(+) CD25(-) T cells and CD8(+) T cells. The suppressive effect was observed without in vitro T cell stimulation. Foxp3 expression in these CD4(+) CD25(+) T cells from immunized mice was 5-10 times greater than CD4(+) CD25(+) T cells derived from naive mice. The suppressive effect required cellular contact and was blocked by anti-glucocorticoid-induced tumor necrosis factor receptor family-related gene antibody. In vitro suppressive activity essentially disappeared 8 wk after the last immunization. However, it was regained by in vitro restimulation with cognate self-antigen protein but not with control protein. We propose that SEREX-defined self-antigens such as those used in this study represent self-antigens that elicit naturally occurring CD4(+) CD25(+) T reg cells.

  1. miRNA-Target Gene Regulatory Networks: A Bayesian Integrative Approach to Biomarker Selection with Application to Kidney Cancer

    PubMed Central

    Chekouo, Thierry; Stingo, Francesco C.; Doecke, James D.; Do, Kim-Anh

    2015-01-01

    Summary The availability of cross-platform, large-scale genomic data has enabled the investigation of complex biological relationships for many cancers. Identification of reliable cancer-related biomarkers requires the characterization of multiple interactions across complex genetic networks. MicroRNAs are small non-coding RNAs that regulate gene expression; however, the direct relationship between a microRNA and its target gene is difficult to measure. We propose a novel Bayesian model to identify microRNAs and their target genes that are associated with survival time by incorporating the microRNA regulatory network through prior distributions. We assume that biomarkers involved in regulatory networks are likely associated with survival time. We employ non-local prior distributions and a stochastic search method for the selection of biomarkers associated with the survival outcome. We use KEGG pathway information to incorporate correlated gene effects within regulatory networks. Using simulation studies, we assess the performance of our method, and apply it to experimental data of kidney renal cell carcinoma (KIRC) obtained from The Cancer Genome Atlas. Our novel method validates previously identified cancer biomarkers and identifies biomarkers specific to KIRC progression that were not previously discovered. Using the KIRC data, we confirm that biomarkers involved in regulatory networks are more likely to be associated with survival time, showing connections in one regulatory network for five out of six such genes we identified. PMID:25639276

  2. An ecological momentary assessment of comparison target as a moderator of the effects of appearance-focused social comparisons.

    PubMed

    Leahey, Tricia M; Crowther, Janis H

    2008-09-01

    This research examined whether comparison target moderates the effects of naturally occurring appearance-focused social comparisons on women's affect, appearance esteem, and dieting thoughts. During daily activities, body-satisfied (BS) women and body-dissatisfied (BD) women recorded their comparison targets and reactions to comparison information. For BS women, upward comparisons with peers were associated with more positive affect (PA) and appearance esteem and less guilt than upward comparisons with media images and downward comparisons with peers were associated with less PA than downward comparisons with media images. For BD women, upward comparisons with peers were associated with more appearance esteem and diet thoughts than upward comparisons with media images and downward comparisons with peers were associated with less PA, appearance esteem, and diet thoughts and more guilt than downward comparisons with media images.

  3. Mapping Association between Long-Range Cis-Regulatory Regions and Their Target Genes Using Comparative Genomics

    NASA Astrophysics Data System (ADS)

    Mongin, Emmanuel; Dewar, Ken; Blanchette, Mathieu

    In chordates, long-range cis-regulatory regions are involved in the control of transcription initiation (either as repressors or enhancers). They can be located as far as 1 Mb from the transcription start site of the target gene and can regulate more than one gene. Therefore, proper characterization of functional interactions between long-range cis-regulatory regions and their target genes remains problematic. We present a novel method to predict such interactions based on the analysis of rearrangements between the human and 16 other vertebrate genomes. Our method is based on the assumption that genome rearrangements that would disrupt the functional interaction between a cis-regulatory region and its target gene are likely to be deleterious. Therefore, conservation of synteny through evolution would be an indication of a functional interaction. We use our algorithm to classify a set of 1,406,084 putative associations from the human genome. This genome-wide map of interactions has many potential applications, including the selection of candidate regions prior to in vivo experimental characterization, a better characterization of regulatory regions involved in position effect diseases, and an improved understanding of the mechanisms and importance of long-range regulation.

  4. Improving food environments and tackling obesity: A realist systematic review of the policy success of regulatory interventions targeting population nutrition

    PubMed Central

    Sisnowski, Jana; Merlin, Tracy

    2017-01-01

    Background This systematic review (PROSPERO: CRD42015025276) employs a realist approach to investigate the effect of “real-world” policies targeting different aspects of the food environment that shape individual and collective nutrition. Objectives We were interested in assessing intermediate outcomes along the assumed causal pathway to “policy success”, in addition to the final outcome of changed consumption patterns. Data sources We performed a search of 16 databases through October 2015, with no initial restriction by language. Study eligibility criteria We included all publications that reported the effect of statutory provisions aimed at reducing the consumption of energy-dense foods and beverages in the general population. We allowed all methodological approaches that contained some measure of comparison, including studies of implementation progress. Study appraisal and synthesis methods We reviewed included studies using the appraisal tools for pre-post and observational studies developed by the National Heart, Lung, and Blood Institute. Given the considerable heterogeneity in interventions assessed, study designs employed, and outcome measures reported, we opted for a narrative synthesis of results. Results and implications Results drawn from 36 peer-reviewed articles and grey literature reports demonstrated that isolated regulatory interventions can improve intermediate outcomes, but fail to affect consumption at clinically significant levels. The included literature covered six different types of interventions, with 19 studies reporting on calorie posting on chain restaurant menus. The large majority of the identified interventions were conducted in the US. Early results from recent taxation measures were published after the review cut-off date but these suggested more favorable effects on consumption levels. Nevertheless, the evidence assessed in this review suggests that current policies are generally falling short of anticipated health impacts

  5. Do pharmacological approaches that prevent opioid tolerance target different elements in the same regulatory machinery?

    PubMed

    Garzón, Javier; Rodríguez-Muñoz, María; Sánchez-Blázquez, Pilar

    2008-06-01

    In the nervous system, the interaction of opioids like heroin and morphine with the G protein-coupled Mu-opioid receptor (MOR) provokes the development of tolerance to these opioids, as well as physical dependence. Tolerance implies that higher doses of these drugs must be consumed in order to obtain an equivalent sensation, a situation that contributes notably to the social problems surrounding recreational opioid abuse. The mechanisms that promote opioid tolerance involve a series of adaptive changes in the MOR and in the post-receptor signalling elements. Pharmacological studies have consistently identified a number of signalling proteins relevant to morphine-induced tolerance, including the delta-opioid receptor (DOR), protein kinase C (PKC), protein kinase A (PKA), calcium/calmodulin-dependent kinase II (CaMKII), nitric oxide synthase (NOS), N-methyl-D-aspartate acid glutamate receptors (NMDAR), and regulators of G-signalling (RGS) proteins. Thus, it is feasible that these treatments which diminish morphine tolerance target distinct elements within the same regulatory machinery. In this scheme, the signals originated at the agonist-activated MORs would be recognised by elements such as the NMDARs, which in turn exert a negative feedback on MOR-evoked signalling. This process involves DOR regulation of MORs, MOR-induced activation of NMDARs (probably via the regulation of Src, recruiting PKC and Galpha subunits) and the NMDAR-mediated activation of CaMKII. The active CaMKII promotes the sequestering of morphine-activated Gbetagamma dimers by phosducin-like proteins (PhLP) and of Galpha subunits by RGS proteins and tolerance to opioids like morphine develops. Future efforts to study these phenomena should focus on fitting additional pieces into this puzzle in order to fully define the mechanism underlying the desensitization of MORs in neural cells.

  6. Mitochondrial targeting of bilirubin regulatory enzymes: An adaptive response to oxidative stress.

    PubMed

    Muhsain, Siti Nur Fadzilah; Lang, Matti A; Abu-Bakar, A'edah

    2015-01-01

    The intracellular level of bilirubin (BR), an endogenous antioxidant that is cytotoxic at high concentrations, is tightly controlled within the optimal therapeutic range. We have recently described a concerted intracellular BR regulation by two microsomal enzymes: heme oxygenase 1 (HMOX1), essential for BR production and cytochrome P450 2A5 (CYP2A5), a BR oxidase. Herein, we describe targeting of these enzymes to hepatic mitochondria during oxidative stress. The kinetics of microsomal and mitochondrial BR oxidation were compared. Treatment of DBA/2J mice with 200mgpyrazole/kg/day for 3days increased hepatic intracellular protein carbonyl content and induced nucleo-translocation of Nrf2. HMOX1 and CYP2A5 proteins and activities were elevated in microsomes and mitoplasts but not the UGT1A1, a catalyst of BR glucuronidation. A CYP2A5 antibody inhibited 75% of microsomal BR oxidation. The inhibition was absent in control mitoplasts but elevated to 50% after treatment. An adrenodoxin reductase antibody did not inhibit microsomal BR oxidation but inhibited 50% of mitochondrial BR oxidation. Ascorbic acid inhibited 5% and 22% of the reaction in control and treated microsomes, respectively. In control mitoplasts the inhibition was 100%, which was reduced to 50% after treatment. Bilirubin affinity to mitochondrial and microsomal CYP2A5 enzyme is equally high. Lastly, the treatment neither released cytochrome c into cytoplasm nor dissipated membrane potential, indicating the absence of mitochondrial membrane damage. Collectively, the observations suggest that BR regulatory enzymes are recruited to mitochondria during oxidative stress and BR oxidation by mitochondrial CYP2A5 is supported by mitochondrial mono-oxygenase system. The induced recruitment potentially confers membrane protection. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

  7. [Micro RNA-451 promoting osteogenesis of mesenchymal stem cells by targeting regulatory calcium binding protein 39].

    PubMed

    Kang, Xia; Kang, Fei; Yang, Bo; Guo, Hongfeng; Quan, Yi; Dong, Shiwu

    2013-09-01

    To investigate the role of micro RNA-451 (miRNA-451) in promoting the osteogenesis of mesenchymal stem cells (MSCs) by targeting regulatory calcium binding protein 39 (CAB39). pMIR-report and pRL-TK vectors were selected to identify the relationship between miRNA-451 and CAB39 by using dual-luciferase reporter assay. pre-miRNA-451 (group A), anti-miRNA-451 (group C), pre-miRNA negative control (group B), and anti-miRNA negative control (group D) were transfected into the C3H10T1/2 cells, respectively. Then, the cells were collected after osteogenic induction for 7 and 14 days. At 7 and 14 days, the real-time fluorescent quantitative PCR and Western blot assays were performed to detect the related osteogenetic biomarkers [Runx2 and alkaline phosphatase (ALP) mRNA] and expressions of CAB39 protein. At 14 days, the extracellular calcium deposition during the osteogenesis of MSCs was tested by Alizarin red staining method. CAB39 was the target gene of miRNA-451. At 7 and 14 days after osteogenic induction, the mRNA expressions of Runx2 and ALP in group A were significantly higher than those in group B (P < 0.05), and the expressions in group C was significantly lower than those in group D (P < 0.05). Furthermore, at 14 days after osteogenic induction, the protein expression of CAB39 in group A (0.55 +/- 0.05) was significantly lower than that in group B (1.00 +/- 0.07), and the protein expression in group C (1.21 +/- 0.05) was significantly higher than that in group D (1.00 +/- 0.04), all showing significant difference (P < 0.05). Finally, at 14 days after osteogenic induction, the extracellular calcium deposition in group A was obviously more than that in group B, and group C was downregulated when compared with group D. miRNA-451 can promote the osteogenesis process of MSCs by downregulating the CAB39.

  8. Genome context as a predictive tool for identifying regulatory targets of the TetR family transcriptional regulators.

    PubMed

    Ahn, Sang Kyun; Cuthbertson, Leslie; Nodwell, Justin R

    2012-01-01

    TetR family transcriptional regulators (TFRs) are found in most bacteria and archea. Most of the family members that have been investigated to date are repressors of their target genes, and the majority of these, like the well-characterized protein TetR, regulate genes that encode transmembrane efflux pumps. In many cases repression by TFR proteins is reversed through the direct binding of a small-molecule ligand. The number of TFRs in the public database has grown rapidly as a result of genome sequencing and there are now thousands of family members; however virtually nothing is known about the biology and biochemistry they regulate. Generally applicable methods for predicting their regulatory targets would assist efforts to characterize the family. Here, we investigate chromosomal context of 372 TFRs from three Streptomyces species. We find that the majority (250 TFRs) are transcribed divergently from one neighboring gene, as is the case for TetR and its target tetA. We explore predicted target gene product identity and intergenic separation to see which either correlates with a direct regulatory relationship. While intergenic separation is a critical factor in regulatory prediction the identity of the putative target gene product is not. Our data suggest that those TFRs that are <200 bp from their divergently oriented neighbors are most likely to regulate them. These target genes include membrane proteins (26% of which 22% are probable membrane-associated pumps), enzymes (60%), other proteins such as transcriptional regulators (1%), and proteins having no predictive sequence motifs (13%). In addition to establishing a solid foundation for identifying targets for TFRs of unknown function, our analysis demonstrates a much greater diversity of TFR-regulated biochemical functions.

  9. Eradication of large tumors in mice by a tritherapy targeting the innate, adaptive, and regulatory components of the immune system.

    PubMed

    Berraondo, Pedro; Nouzé, Clémence; Préville, Xavier; Ladant, Daniel; Leclerc, Claude

    2007-09-15

    Targeting the human papillomavirus (HPV) E7 antigen to dendritic cells with the adenylate cyclase (CyaA) of Bordetella pertussis as a vaccine vector led to potent therapeutic immune responses against TC-1 tumors in a murine model of cervical carcinoma induced by HPV. However, as the time between tumor graft and vaccination increased, the antitumor efficacy of the CyaA-E7 vaccine gradually decreased. The vaccine had no effect if the tumor diameter was >8 mm. Analyses of regulatory cells recruited during TC-1 tumor growth revealed a high number of splenic MDSCs and a large percentage of regulatory T cells, particularly in the tumor. Administration of a tritherapy including CpG complexed with a cationic lipid, low-dose cyclophosphamide, and the CyaA-E7 vaccine completely overcame tumor-associated immunosuppression and eradicated large, established tumors in almost all treated animals. This strong antitumor response was followed by a large expansion of regulatory T cells in tumor, spleen, and tumor-draining lymph nodes and of splenic neutrophils. These findings indicate that immunotherapeutic strategies that simultaneously target innate, adaptive, and regulatory components of the immune system are effective in the eradication of large tumors.

  10. Regulatory Genes Controlling Anthocyanin Pigmentation Are Functionally Conserved among Plant Species and Have Distinct Sets of Target Genes.

    PubMed Central

    Quattrocchio, F; Wing, JF; Leppen, H; Mol, J; Koes, RE

    1993-01-01

    In this study, we demonstrate that in petunia at least four regulatory genes (anthocyanin-1 [an1], an2, an4, and an11) control transcription of a subset of structural genes from the anthocyanin pathway by using a combination of RNA gel blot analysis, transcription run-on assays, and transient expression assays. an2- and an11- mutants could be transiently complemented by the maize regulatory genes Leaf color (Lc) or Colorless-1 (C1), respectively, whereas an1- mutants only by Lc and C1 together. In addition, the combination of Lc and C1 induces pigment accumulation in young leaves. This indicates that Lc and C1 are both necessary and sufficient to produce pigmentation in leaf cells. Regulatory pigmentation genes in maize and petunia control different sets of structural genes. The maize Lc and C1 genes expressed in petunia differentially activate the promoters of the chalcone synthase genes chsA and chsJ in the same way that the homologous petunia genes do. This suggests that the regulatory proteins in both species are functionally similar and that the choice of target genes is determined by their promoter sequences. We present an evolutionary model that explains the differences in regulation of pigmentation pathways of maize, petunia, and snapdragon. PMID:12271045

  11. Self-regulatory Behaviors and Approaches to Learning of Arts Students: A Comparison Between Professional Training and English Learning.

    PubMed

    Tseng, Min-Chen; Chen, Chia-Cheng

    2016-11-17

    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 students' professional training and English learning. The participants consisted of 344 arts majors. The Academic Self-Regulation Questionnaire and the Revised Learning Process Questionnaire were adopted to examine students' self-regulatory behaviors and their approaches to learning. The results show that a positive and significant correlation was found in students' self-regulatory behaviors between professional training and English learning. The results indicated that increases in using self-regulatory behaviors in professional training were associated with increases in applying self-regulatory behaviors in learning English. Seeking assistance, self-evaluation, and planning and organizing were significant predictors for learning English. In addition, arts students used the deep approach more often than the surface approach in both their professional training and English learning. A positive correlation was found in DA, whereas a negative correlation was shown in SA between students' self-regulatory behaviors and their approaches to learning. Students with high self-regulation adopted a deep approach, and they applied the surface approach less in professional training and English learning. In addition, a SEM model confirmed that DA had a positive influence; however, SA had a negative influence on self-regulatory behaviors.

  12. 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…

  13. Regulatory microRNA networks: complex patterns of target pathways for disease-related and housekeeping microRNAs.

    PubMed

    Zafari, Sachli; Backes, Christina; Leidinger, Petra; Meese, Eckart; Keller, Andreas

    2015-06-01

    Blood-based microRNA (miRNA) signatures as biomarkers have been reported for various pathologies, including cancer, neurological disorders, cardiovascular diseases, and also infections. The regulatory mechanism behind respective miRNA patterns is only partially understood. Moreover, "preserved" miRNAs, i.e., miRNAs that are not dysregulated in any disease, and their biological impact have been explored to a very limited extent. We set out to systematically determine their role in regulatory networks by defining groups of highly-dysregulated miRNAs that contribute to a disease signature as opposed to preserved housekeeping miRNAs. We further determined preferential targets and pathways of both dysregulated and preserved miRNAs by computing multi-layer networks, which were compared between housekeeping and dysregulated miRNAs. Of 848 miRNAs examined across 1049 blood samples, 8 potential housekeepers showed very limited expression variations, while 20 miRNAs showed highly-dysregulated expression throughout the investigated blood samples. Our approach provides important insights into miRNAs and their role in regulatory networks. The methodology can be applied to systematically investigate the differences in target genes and pathways of arbitrary miRNA sets.

  14. Overcoming the hurdles of tumor immunity by targeting regulatory pathways in innate and adaptive immune cells.

    PubMed

    Zwirner, Norberto W; Croci, Diego O; Domaica, Carolina I; Rabinovich, Gabriel A

    2010-01-01

    The improved understanding of the biochemical nature of tumor antigens and the identification of cellular and molecular mechanisms leading to activation of innate and adaptive immune cells have been of paramount importance in the progress of tumor immunology. Studies on the intricate network of interactions between tumor and immune cells have revealed novel regulatory signals, including cell surface inhibitory receptors and costimulatory molecules, intracellular regulatory pathways, immunosuppressive cytokines and proapoptotic mediators, which may operate in concert to orchestrate tumor-immune escape. This emerging portfolio of inhibitory checkpoints can influence the physiology of innate immune cells including dendritic cells, macrophages and natural killer (NK) cells, as well as different subsets of T cells to fine tune their effector function. The synergistic combination of strategies aimed at overcoming regulatory signals and/or stimulating effector pathways, may offer therapeutic advantage as adjuvants of conventional anticancer therapies. Based on this premise, we will discuss here how the control of the effector functions of innate and adaptive immune cells and the manipulation of regulatory pathways, either alone or in combination, could be exploited for therapeutic purposes in cancer patients.

  15. Gene Regulatory Mechanisms Underlying the Spatial and Temporal Regulation of Target-Dependent Gene Expression in Drosophila Neurons.

    PubMed

    Berndt, Anthony J E; Tang, Jonathan C Y; Ridyard, Marc S; Lian, Tianshun; Keatings, Kathleen; Allan, Douglas W

    2015-12-01

    Neuronal differentiation often requires target-derived signals from the cells they innervate. These signals typically activate neural subtype-specific genes, but the gene regulatory mechanisms remain largely unknown. Highly restricted expression of the FMRFa neuropeptide in Drosophila Tv4 neurons requires target-derived BMP signaling and a transcription factor code that includes Apterous. Using integrase transgenesis of enhancer reporters, we functionally dissected the Tv4-enhancer of FMRFa within its native cellular context. We identified two essential but discrete cis-elements, a BMP-response element (BMP-RE) that binds BMP-activated pMad, and a homeodomain-response element (HD-RE) that binds Apterous. These cis-elements have low activity and must be combined for Tv4-enhancer activity. Such combinatorial activity is often a mechanism for restricting expression to the intersection of cis-element spatiotemporal activities. However, concatemers of the HD-RE and BMP-RE cis-elements were found to independently generate the same spatiotemporal expression as the Tv4-enhancer. Thus, the Tv4-enhancer atypically combines two low-activity cis-elements that confer the same output from distinct inputs. The activation of target-dependent genes is assumed to 'wait' for target contact. We tested this directly, and unexpectedly found that premature BMP activity could not induce early FMRFa expression; also, we show that the BMP-insensitive HD-RE cis-element is activated at the time of target contact. This led us to uncover a role for the nuclear receptor, seven up (svp), as a repressor of FMRFa induction prior to target contact. Svp is normally downregulated immediately prior to target contact, and we found that maintaining Svp expression prevents cis-element activation, whereas reducing svp gene dosage prematurely activates cis-element activity. We conclude that the target-dependent FMRFa gene is repressed prior to target contact, and that target-derived BMP signaling directly

  16. Gene Regulatory Mechanisms Underlying the Spatial and Temporal Regulation of Target-Dependent Gene Expression in Drosophila Neurons

    PubMed Central

    Ridyard, Marc S.; Lian, Tianshun; Keatings, Kathleen; Allan, Douglas W.

    2015-01-01

    Neuronal differentiation often requires target-derived signals from the cells they innervate. These signals typically activate neural subtype-specific genes, but the gene regulatory mechanisms remain largely unknown. Highly restricted expression of the FMRFa neuropeptide in Drosophila Tv4 neurons requires target-derived BMP signaling and a transcription factor code that includes Apterous. Using integrase transgenesis of enhancer reporters, we functionally dissected the Tv4-enhancer of FMRFa within its native cellular context. We identified two essential but discrete cis-elements, a BMP-response element (BMP-RE) that binds BMP-activated pMad, and a homeodomain-response element (HD-RE) that binds Apterous. These cis-elements have low activity and must be combined for Tv4-enhancer activity. Such combinatorial activity is often a mechanism for restricting expression to the intersection of cis-element spatiotemporal activities. However, concatemers of the HD-RE and BMP-RE cis-elements were found to independently generate the same spatiotemporal expression as the Tv4-enhancer. Thus, the Tv4-enhancer atypically combines two low-activity cis-elements that confer the same output from distinct inputs. The activation of target-dependent genes is assumed to 'wait' for target contact. We tested this directly, and unexpectedly found that premature BMP activity could not induce early FMRFa expression; also, we show that the BMP-insensitive HD-RE cis-element is activated at the time of target contact. This led us to uncover a role for the nuclear receptor, seven up (svp), as a repressor of FMRFa induction prior to target contact. Svp is normally downregulated immediately prior to target contact, and we found that maintaining Svp expression prevents cis-element activation, whereas reducing svp gene dosage prematurely activates cis-element activity. We conclude that the target-dependent FMRFa gene is repressed prior to target contact, and that target-derived BMP signaling directly

  17. The Effects of Sequence Variation on Genome-wide NRF2 Binding—New Target Genes and Regulatory SNPs

    PubMed Central

    Kuosmanen, Suvi M.; Viitala, Sari; Laitinen, Tuomo; Peräkylä, Mikael; Pölönen, Petri; Kansanen, Emilia; Leinonen, Hanna; Raju, Suresh; Wienecke-Baldacchino, Anke; Närvänen, Ale; Poso, Antti; Heinäniemi, Merja; Heikkinen, Sami; Levonen, Anna-Liisa

    2016-01-01

    Transcription factor binding specificity is crucial for proper target gene regulation. Motif discovery algorithms identify the main features of the binding patterns, but the accuracy on the lower affinity sites is often poor. Nuclear factor E2-related factor 2 (NRF2) is a ubiquitous redox-activated transcription factor having a key protective role against endogenous and exogenous oxidant and electrophile stress. Herein, we decipher the effects of sequence variation on the DNA binding sequence of NRF2, in order to identify both genome-wide binding sites for NRF2 and disease-associated regulatory SNPs (rSNPs) with drastic effects on NRF2 binding. Interactions between NRF2 and DNA were studied using molecular modelling, and NRF2 chromatin immunoprecipitation-sequence datasets together with protein binding microarray measurements were utilized to study binding sequence variation in detail. The binding model thus generated was used to identify genome-wide binding sites for NRF2, and genomic binding sites with rSNPs that have strong effects on NRF2 binding and reside on active regulatory elements in human cells. As a proof of concept, miR-126–3p and -5p were identified as NRF2 target microRNAs, and a rSNP (rs113067944) residing on NRF2 target gene (Ferritin, light polypeptide, FTL) promoter was experimentally verified to decrease NRF2 binding and result in decreased transcriptional activity. PMID:26826707

  18. Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.

    PubMed

    Lu, Yulan; Zhou, Yuanpeng; Tian, Weidong

    2013-12-01

    Defining the target genes of distal regulatory elements (DREs), such as enhancer, repressors and insulators, is a challenging task. The recently developed Hi-C technology is designed to capture chromosome conformation structure by high-throughput sequencing, and can be potentially used to determine the target genes of DREs. However, Hi-C data are noisy, making it difficult to directly use Hi-C data to identify DRE-target gene relationships. In this study, we show that DREs-gene pairs that are confirmed by Hi-C data are strongly phylogenetic correlated, and have thus developed a method that combines Hi-C read counts with phylogenetic correlation to predict long-range DRE-target gene relationships. Analysis of predicted DRE-target gene pairs shows that genes regulated by large number of DREs tend to have essential functions, and genes regulated by the same DREs tend to be functionally related and co-expressed. In addition, we show with a couple of examples that the predicted target genes of DREs can help explain the causal roles of disease-associated single-nucleotide polymorphisms located in the DREs. As such, these predictions will be of importance not only for our understanding of the function of DREs but also for elucidating the causal roles of disease-associated noncoding single-nucleotide polymorphisms.

  19. Prospects on Strategies for Therapeutically Targeting Oncogenic Regulatory Factors by Small-Molecule Agents

    PubMed Central

    Chou, Chih-Chien; Salunke, Santosh B.; Kulp, Samuel K.; Chen, Ching-Shih

    2014-01-01

    Although the Human Genome Project has raised much hope for the identification of druggable genetic targets for cancer and other diseases, this genetic target-based approach has not improved productivity in drug discovery over the traditional approach. Analyses of known human target proteins of currently marketed drugs reveal that these drugs target only a limited number of proteins as compared to the whole proteome. In contrast to genome-based targets, mechanistic targets are derived from empirical research, at cellular or molecular levels, in disease models and/or in patients, thereby enabling the exploration of a greater number of druggable targets beyond the genome and epigenome. The paradigm shift has made a tremendous headway in developing new therapeutic agents targeting different clinically relevant mechanisms/pathways in cancer cells. In this Prospects article, we provide an overview of potential drug targets related to the following four emerging areas: (1) tumor metabolism (the Warburg effect), (2) dysregulated protein turnover (E3 ubiquitin ligases), (3) protein–protein interactions, and (4) unique DNA high-order structures and protein–DNA interactions. Nonetheless, considering the genetic and phenotypic heterogeneities that characterize cancer cells, the development of drug resistance in cancer cells by adapting signaling circuitry to take advantage of redundant pathways or feedback/crosstalk systems is possible. This “phenotypic adaptation” underlies the rationale of using therapeutic combinations of these targeted agents with cytotoxic drugs. PMID:24166934

  20. Downstream Regulatory Element Antagonist Modulator (DREAM), a target for anti-thrombotic agents.

    PubMed

    Cho, Jaehyung

    2017-03-01

    Circulating platelets participate in the process of numerous diseases including thrombosis, inflammation, and cancer. Thus, it is of great importance to understand the underlying mechanisms mediating platelet activation under disease conditions. Emerging evidence indicates that despite the lack of a nucleus, platelets possess molecules that are involved in gene transcription in nucleated cells. This review will summarize downstream regulatory element antagonist modulator (DREAM), a transcriptional repressor, and highlight recent findings suggesting its novel non-transcriptional role in hemostasis and thrombosis.

  1. The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome.

    PubMed

    Jenjaroenpun, Piroon; Chew, Chee Siang; Yong, Tai Pang; Choowongkomon, Kiattawee; Thammasorn, Wimada; Kuznetsov, Vladimir A

    2015-01-01

    A triplex target DNA site (TTS), a stretch of DNA that is composed of polypurines, is able to form a triple-helix (triplex) structure with triplex-forming oligonucleotides (TFOs) and is able to influence the site-specific modulation of gene expression and/or the modification of genomic DNA. The co-localization of a genomic TTS with gene regulatory signals and functional genome structures suggests that TFOs could potentially be exploited in antigene strategies for the therapy of cancers and other genetic diseases. Here, we present the TTS Mapping and Integration (TTSMI; http://ttsmi.bii.a-star.edu.sg) database, which provides a catalog of unique TTS locations in the human genome and tools for analyzing the co-localization of TTSs with genomic regulatory sequences and signals that were identified using next-generation sequencing techniques and/or predicted by computational models. TTSMI was designed as a user-friendly tool that facilitates (i) fast searching/filtering of TTSs using several search terms and criteria associated with sequence stability and specificity, (ii) interactive filtering of TTSs that co-localize with gene regulatory signals and non-B DNA structures, (iii) exploration of dynamic combinations of the biological signals of specific TTSs and (iv) visualization of a TTS simultaneously with diverse annotation tracks via the UCSC genome browser.

  2. The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome

    PubMed Central

    Jenjaroenpun, Piroon; Chew, Chee Siang; Yong, Tai Pang; Choowongkomon, Kiattawee; Thammasorn, Wimada; Kuznetsov, Vladimir A.

    2015-01-01

    A triplex target DNA site (TTS), a stretch of DNA that is composed of polypurines, is able to form a triple-helix (triplex) structure with triplex-forming oligonucleotides (TFOs) and is able to influence the site-specific modulation of gene expression and/or the modification of genomic DNA. The co-localization of a genomic TTS with gene regulatory signals and functional genome structures suggests that TFOs could potentially be exploited in antigene strategies for the therapy of cancers and other genetic diseases. Here, we present the TTS Mapping and Integration (TTSMI; http://ttsmi.bii.a-star.edu.sg) database, which provides a catalog of unique TTS locations in the human genome and tools for analyzing the co-localization of TTSs with genomic regulatory sequences and signals that were identified using next-generation sequencing techniques and/or predicted by computational models. TTSMI was designed as a user-friendly tool that facilitates (i) fast searching/filtering of TTSs using several search terms and criteria associated with sequence stability and specificity, (ii) interactive filtering of TTSs that co-localize with gene regulatory signals and non-B DNA structures, (iii) exploration of dynamic combinations of the biological signals of specific TTSs and (iv) visualization of a TTS simultaneously with diverse annotation tracks via the UCSC genome browser. PMID:25324314

  3. EPA/NMED/LANL 1998 water quality results: Statistical analysis and comparison to regulatory standards

    SciTech Connect

    B. Gallaher; T. Mercier; P. Black; K. Mullen

    2000-02-01

    Four governmental agencies conducted a round of groundwater, surface water, and spring water sampling at the Los Alamos National Laboratory during 1998. Samples were split among the four parties and sent to independent analytical laboratories. Results from three of the agencies were available for this study. Comparisons of analytical results that were paired by location and date were made between the various analytical laboratories. The results for over 50 split samples analyzed for inorganic chemicals, metals, and radionuclides were compared. Statistical analyses included non-parametric (sign test and signed-ranks test) and parametric (paired t-test and linear regression) methods. The data pairs were tested for statistically significant differences, defined by an observed significance level, or p-value, less than 0.05. The main conclusion is that the laboratories' performances are similar across most of the analytes that were measured. In some 95% of the laboratory measurements there was agreement on whether contaminant levels exceeded regulatory limits. The most significant differences in performance were noted for the radioactive suite, particularly for gross alpha particle activity and Sr-90.

  4. Assessment of benefits and risks in development of targeted therapies for cancer--The view of regulatory authorities.

    PubMed

    Pignatti, Francesco; Jonsson, Bertil; Blumenthal, Gideon; Justice, Robert

    2015-05-01

    Drug licensing and approval decisions involve the balancing of benefits against the risks (harms) in the presence of uncertainty. Typically, the benefits are estimated from primary efficacy endpoints from confirmatory (phase III) clinical trials although exceptions where promising early data from single-arm studies have led to accelerated approvals are not uncommon, particularly for cancer drugs. The challenge for regulators is to balance early evidence of efficacy that might support approval versus the need to establish clinical benefit based on conclusive evidence. Targeted agents offer the promise that knowledge about the mechanism of the disease will help identify patients with tumors likely to respond, resulting in higher efficacy and less toxicity, and earlier regulatory decisions based on convincing evidence of clinical benefit. In this paper, we describe methods and examples of benefit-risk assessment of targeted drugs, recent initiatives from EMA and FDA on improving communication about benefits and risks, and discuss future steps.

  5. Comparison of Erosion Rates Estimated by Sediment Budget Techniques and Suspended Sediment Monitoring and Regulatory Implications

    NASA Astrophysics Data System (ADS)

    O'Connor, M.; Eads, R.

    2007-12-01

    Watersheds in the northern California Coast Range have been designated as "impaired" with respect to water quality because of excessive sediment loads and/or high water temperature. Sediment budget techniques have typically been used by regulatory authorities to estimate current erosion rates and to develop targets for future desired erosion rates. This study examines erosion rates estimated by various methods for portions of the Gualala River watershed, designated as having water quality impaired by sediment under provisions of the Clean Water Act Section 303(d), located in northwest Sonoma County (~90 miles north of San Francisco). The watershed is underlain by Jurassic age sedimentary and meta-sedimentary rocks of the Franciscan formation. The San Andreas Fault passes through the western edge of watershed, and other active faults are present. A substantial portion of the watershed is mantled by rock slides and earth flows, many of which are considered dormant. The Coast Range is geologically young, and rapid rates of uplift are believed to have contributed to high erosion rates. This study compares quantitative erosion rate estimates developed at different spatial and temporal scales. It is motivated by a proposed vineyard development project in the watershed, and the need to document conditions in the project area, assess project environmental impacts and meet regulatory requirements pertaining to water quality. Erosion rate estimates were previously developed using sediment budget techniques for relatively large drainage areas (~100 to 1,000 km2) by the North Coast Regional Water Quality Control Board and US EPA and by the California Geological Survey. In this study, similar sediment budget techniques were used for smaller watersheds (~3 to 8 km2), and were supplemented by a suspended sediment monitoring program utilizing Turbidity Threshold Sampling techniques (as described in a companion study in this session). The duration of the monitoring program to date

  6. DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems.

    PubMed

    Rajeev, Lara; Luning, Eric G; Mukhopadhyay, Aindrila

    2014-07-21

    In vivo methods such as ChIP-chip are well-established techniques used to determine global gene targets for transcription factors. However, they are of limited use in exploring bacterial two component regulatory systems with uncharacterized activation conditions. Such systems regulate transcription only when activated in the presence of unique signals. Since these signals are often unknown, the in vitro microarray based method described in this video article can be used to determine gene targets and binding sites for response regulators. This DNA-affinity-purified-chip method may be used for any purified regulator in any organism with a sequenced genome. The protocol involves allowing the purified tagged protein to bind to sheared genomic DNA and then affinity purifying the protein-bound DNA, followed by fluorescent labeling of the DNA and hybridization to a custom tiling array. Preceding steps that may be used to optimize the assay for specific regulators are also described. The peaks generated by the array data analysis are used to predict binding site motifs, which are then experimentally validated. The motif predictions can be further used to determine gene targets of orthologous response regulators in closely related species. We demonstrate the applicability of this method by determining the gene targets and binding site motifs and thus predicting the function for a sigma54-dependent response regulator DVU3023 in the environmental bacterium Desulfovibrio vulgaris Hildenborough.

  7. Comparison of ISO 9000 and recent software life cycle standards to nuclear regulatory review guidance

    SciTech Connect

    Preckshot, G.G.; Scott, J.A.

    1998-01-20

    Lawrence Livermore National Laboratory is assisting the Nuclear Regulatory Commission with the assessment of certain quality and software life cycle standards to determine whether additional guidance for the U.S. nuclear regulatory context should be derived from the standards. This report describes the nature of the standards and compares the guidance of the standards to that of the recently updated Standard Review Plan.

  8. Computational Prediction of Intronic microRNA Targets using Host Gene Expression Reveals Novel Regulatory Mechanisms

    PubMed Central

    Radfar, M. Hossein; Wong, Willy; Morris, Quaid

    2011-01-01

    Approximately half of known human miRNAs are located in the introns of protein coding genes. Some of these intronic miRNAs are only expressed when their host gene is and, as such, their steady state expression levels are highly correlated with those of the host gene's mRNA. Recently host gene expression levels have been used to predict the targets of intronic miRNAs by identifying other mRNAs that they have consistent negative correlation with. This is a potentially powerful approach because it allows a large number of expression profiling studies to be used but needs refinement because mRNAs can be targeted by multiple miRNAs and not all intronic miRNAs are co-expressed with their host genes. Here we introduce InMiR, a new computational method that uses a linear-Gaussian model to predict the targets of intronic miRNAs based on the expression profiles of their host genes across a large number of datasets. Our method recovers nearly twice as many true positives at the same fixed false positive rate as a comparable method that only considers correlations. Through an analysis of 140 Affymetrix datasets from Gene Expression Omnibus, we build a network of 19,926 interactions among 57 intronic miRNAs and 3,864 targets. InMiR can also predict which host genes have expression profiles that are good surrogates for those of their intronic miRNAs. Host genes that InMiR predicts are bad surrogates contain significantly more miRNA target sites in their 3′ UTRs and are significantly more likely to have predicted Pol II and Pol III promoters in their introns. We provide a dataset of 1,935 predicted mRNA targets for 22 intronic miRNAs. These prediction are supported both by sequence features and expression. By combining our results with previous reports, we distinguish three classes of intronic miRNAs: Those that are tightly regulated with their host gene; those that are likely to be expressed from the same promoter but whose host gene is highly regulated by miRNAs; and those

  9. Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

    SciTech Connect

    Wang, Yeming; Opperman, Laura; Wickens, Marvin; Tanaka Hall, Traci M.

    2011-11-02

    Caenorhabditis elegans fem-3 binding factor (FBF) is a founding member of the PUMILIO/FBF (PUF) family of mRNA regulatory proteins. It regulates multiple mRNAs critical for stem cell maintenance and germline development. Here, we report crystal structures of FBF in complex with 6 different 9-nt RNA sequences, including elements from 4 natural mRNAs. These structures reveal that FBF binds to conserved bases at positions 1-3 and 7-8. The key specificity determinant of FBF vs. other PUF proteins lies in positions 4-6. In FBF/RNA complexes, these bases stack directly with one another and turn away from the RNA-binding surface. A short region of FBF is sufficient to impart its unique specificity and lies directly opposite the flipped bases. We suggest that this region imposes a flattened curvature on the protein; hence, the requirement for the additional nucleotide. The principles of FBF/RNA recognition suggest a general mechanism by which PUF proteins recognize distinct families of RNAs yet exploit very nearly identical atomic contacts in doing so.

  10. The Hippo pathway as a target of the Drosophila DRE/DREF transcriptional regulatory pathway.

    PubMed

    Vo, Nicole; Horii, Takeshi; Yanai, Hiroshi; Yoshida, Hideki; Yamaguchi, Masamitsu

    2014-11-26

    The DRE/DREF transcriptional regulatory system has been demonstrated to activate a wide variety of genes with various functions. In Drosophila, the Hippo pathway is known to suppress cell proliferation by inducing apoptosis and cell cycle arrest through inactivation of Yorkie, a transcription co-activator. In the present study, we found that half dose reduction of the hippo (hpo) gene induces ectopic DNA synthesis in eye discs that is suppressed by overexpression of DREF. Half reduction of the hpo gene dose reduced apoptosis in DREF-overexpressing flies. Consistent with these observations, overexpression of DREF increased the levels of hpo and phosphorylated Yorkie in eye discs. Interestingly, the diap1-lacZ reporter was seen to be significantly decreased by overexpression of DREF. Luciferase reporter assays in cultured S2 cells revealed that one of two DREs identified in the hpo gene promoter region was responsible for promoter activity in S2 cells. Furthermore, endogenous hpo mRNA was reduced in DREF knockdown S2 cells, and chromatin immnunoprecipitation assays with anti-DREF antibodies proved that DREF binds specifically to the hpo gene promoter region containing DREs in vivo. Together, these results indicate that the DRE/DREF pathway is required for transcriptional activation of the hpo gene to positively control Hippo pathways.

  11. The Hippo pathway as a target of the Drosophila DRE/DREF transcriptional regulatory pathway

    PubMed Central

    Vo, Nicole; Horii, Takeshi; Yanai, Hiroshi; Yoshida, Hideki; Yamaguchi, Masamitsu

    2014-01-01

    The DRE/DREF transcriptional regulatory system has been demonstrated to activate a wide variety of genes with various functions. In Drosophila, the Hippo pathway is known to suppress cell proliferation by inducing apoptosis and cell cycle arrest through inactivation of Yorkie, a transcription co-activator. In the present study, we found that half dose reduction of the hippo (hpo) gene induces ectopic DNA synthesis in eye discs that is suppressed by overexpression of DREF. Half reduction of the hpo gene dose reduced apoptosis in DREF-overexpressing flies. Consistent with these observations, overexpression of DREF increased the levels of hpo and phosphorylated Yorkie in eye discs. Interestingly, the diap1-lacZ reporter was seen to be significantly decreased by overexpression of DREF. Luciferase reporter assays in cultured S2 cells revealed that one of two DREs identified in the hpo gene promoter region was responsible for promoter activity in S2 cells. Furthermore, endogenous hpo mRNA was reduced in DREF knockdown S2 cells, and chromatin immnunoprecipitation assays with anti-DREF antibodies proved that DREF binds specifically to the hpo gene promoter region containing DREs in vivo. Together, these results indicate that the DRE/DREF pathway is required for transcriptional activation of the hpo gene to positively control Hippo pathways. PMID:25424907

  12. TARGETING REGULATORY T CELLS IN THE TREATMENT OF TYPE 1 DIABETES MELLITUS

    PubMed Central

    Cabrera, Susanne M.; Rigby, Mark R.; Mirmira, Raghavendra G.

    2013-01-01

    Type 1 diabetes mellitus (T1DM) is a T cell-mediated autoimmune disease resulting in islet β cell destruction, hypoinsulinemia, and severely altered glucose homeostasis. T1DM has classically been attributed to the pathogenic actions of auto-reactive effector T cells (Teffs) on the β cell. Recent literature now suggests that a failure of a second T cell subtype, known as regulatory T cells (Tregs), plays a critical role in the development of T1DM. During immune homeostasis, Tregs counterbalance the actions of autoreactive Teff cells, thereby participating in peripheral tolerance. An imbalance in the activity between Teff and Tregs may be crucial in the breakdown of peripheral tolerance, leading to the development of T1DM. In this review, we summarize our current understanding of Treg function in health and in T1DM, and examine the effect of experimental therapies for T1DM on Treg cell number and function in both mice and humans. PMID:22709273

  13. Comparison of image processing algorithms for tracking illuminated targets

    NASA Astrophysics Data System (ADS)

    Bukley, Jerry W.; Cramblitt, Robert M.

    1999-07-01

    Pointing the line-of-sight of an acquisition, tracking and pointing (ATP) system at a target requires designation of a reference line of sight (LOS) based principally on the target image. For many system, this will also include registration of a specific fiducial on the target for precision pointing. It is difficult to select a track reference because of algorithm sensitivity to modeling of the image. The selection of a track reference ins further complicated by image variations associated with changes in the viewing geometry and target characteristics. This paper compares several image-processing algorithms for the precision pointing of a near-space ATP platform that is viewing missile targets. The platform has state-of-the-art alignment, stabilization and tracking functions. The algorithms are tested in a full imaging and control system simulation that models an illuminating laser beam, target reflectance, optical effects, the sensor, a high order control system and pointing dynamics. The target models are based on flight dynamics, orientation, measured drawings and surface reflectivity. The simulation results are compared by calculating bias, drift and jitter characteristics of the error incurred when attempting to point the optical line-of- sight at the target. Several algorithms have been identified that provide a pointing reference capable of sustaining sub- microradian error. This paper describes the calculation of the fiducials for the algorithms and compares their relative merits.

  14. Scavenger receptor A gene regulatory elements target gene expression to macrophages and to foam cells of atherosclerotic lesions.

    PubMed Central

    Horvai, A; Palinski, W; Wu, H; Moulton, K S; Kalla, K; Glass, C K

    1995-01-01

    Transcription of the macrophage scavenger receptor A gene is markedly upregulated during monocyte to macrophage differentiation. In these studies, we demonstrate that 291 bp of the proximal scavenger receptor promoter, in concert with a 400-bp upstream enhancer element, is sufficient to direct macrophage-specific expression of a human growth hormone reporter in transgenic mice. These regulatory elements, which contain binding sites for PU.1, AP-1, and cooperating ets-domain transcription factors, are also sufficient to mediate regulation of transgene expression during the in vitro differentiation of bone marrow progenitor cells in response to macrophage colony-stimulating factor. Mutation of the PU.1 binding site within the scavenger receptor promoter severely impairs transgene expression, consistent with a crucial role of PU.1 in regulating the expression of the scavenger receptor gene. The ability of the scavenger receptor promoter and enhancer to target gene expression to macrophages in vivo, including foam cells of atherosclerotic lesions, suggests that these regulatory elements will be of general utility in the study of macrophage differentiation and function by permitting specific modifications of macrophage gene expression. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:7777517

  15. The nude mutant gene Foxn1 is a HOXC13 regulatory target during hair follicle and nail differentiation.

    PubMed

    Potter, Christopher S; Pruett, Nathanael D; Kern, Michael J; Baybo, Mary Ann; Godwin, Alan R; Potter, Kathleen A; Peterson, Ron L; Sundberg, John P; Awgulewitsch, Alexander

    2011-04-01

    Among the Hox genes, homeobox C13 (Hoxc13) has been shown to be essential for proper hair shaft differentiation, as Hoxc13 gene-targeted (Hoxc13(tm1Mrc)) mice completely lack external hair. Because of the remarkable overt phenotypic parallels to the Foxn1(nu) (nude) mutant mice, we sought to determine whether Hoxc13 and forkhead box N1 (Foxn1) might act in a common pathway of hair follicle (HF) differentiation. We show that the alopecia exhibited by both the Hoxc13(tm1Mrc) and Foxn1(nu) mice is because of strikingly similar defects in hair shaft differentiation and that both mutants suffer from a severe nail dystrophy. These phenotypic similarities are consistent with the extensive overlap between Hoxc13 and Foxn1 expression patterns in the HF and the nail matrix. Furthermore, DNA microarray analysis of skin from Hoxc13(tm1Mrc) mice identified Foxn1 as significantly downregulated along with numerous hair keratin genes. This Foxn1 downregulation apparently reflects the loss of direct transcriptional control by HOXC13 as indicated by our results obtained through co-transfection and chromatin immunoprecipitation (ChIP) assays. As presented in the discussion, these data support a regulatory model of keratinocyte differentiation in which HOXC13-dependent activation of Foxn1 is part of a regulatory cascade controlling the expression of terminal differentiation markers.

  16. Prostate cancer progression and metastasis: potential regulatory pathways for therapeutic targeting

    PubMed Central

    Nandana, Srinivas; Chung, Leland WK

    2014-01-01

    Skeletal metastasis in advanced prostate cancer (PCa) patients remains a significant cause of morbidity and mortality. Research utilizing animal models during the past decade has reached a consensus that PCa progression and distant metastasis can be tackled at the molecular level. Although there are a good number of models that have shown to facilitate the study of PCa initiation and progression at the primary site, models that mimic the distant dissemination of cancer cells, particularly bone metastasis, are scarce. Despite this limitation, the field has gleaned valuable knowledge on the underlying molecular mechanisms and pathways of PCa progression, including local invasion and distant metastasis, and has moved forward in developing the concepts of current therapeutic modalities. The purpose of this review is to put together recent work on pathways that are currently being targeted for therapy, as well as other prospective novel therapeutic targets to be developed in the future against metastatic and potentially lethal PCa in patients. PMID:25374910

  17. Functional evolution of the p53 regulatory network through its target response elements

    PubMed Central

    Jegga, Anil G.; Inga, Alberto; Menendez, Daniel; Aronow, Bruce J.; Resnick, Michael A.

    2008-01-01

    Transcriptional network evolution is central to the development of complex biological systems. Networks can evolve through variation of master regulators and/or by changes in regulation of genes within networks. To gain insight into meaningful evolutionary differences in large networks, it is essential to address the functional consequences of sequence differences in response elements (REs) targeted by transcription factors. Using a combination of custom bioinformatics and multispecies alignment of promoter regions, we investigated the functional evolution of REs in terms of responsiveness to the sequence-specific transcription factor p53, a tumor suppressor and master regulator of stress responses. We identified REs orthologous to known p53 targets in human and rodent cells or alternatively REs related to the established p53 consensus. The orthologous REs were assigned p53 transactivation capabilities based on rules determined from model systems, and a functional heat map was developed to visually summarize conservation of sequence and relative level of responsiveness to p53 for 47 REs in 14 species. Individual REs exhibited marked differences in transactivation potentials and widespread evolutionary turnover. Functional differences were often not predicted from consensus sequence evaluations. Of the established human p53 REs analyzed, 91% had sequence conservation in at least one nonprimate species compared with 67.5% for functional conservation. Surprisingly, there was almost no conservation of functional REs for genes involved in DNA metabolism or repair between humans and rodents, suggesting important differences in p53 stress responses and cancer development. PMID:18187580

  18. Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs.

    PubMed

    Deigan, Katherine E; Ferré-D'Amaré, Adrian R

    2011-12-20

    Riboswitches are messenger RNA (mRNA) domains that regulate gene function in response to the intracellular concentration of a variety of metabolites and second messengers. They control essential genes in many pathogenic bacteria, thus representing an inviting new class of biomolecular target for the development of antibiotics and chemical-biological tools. In this Account, we briefly review the discovery of riboswitches in the first years of the 21st century and their ensuing characterization over the past decade. We then discuss the progress achieved so far in using riboswitches as a focus for drug discovery, considering both the value of past serendipity and the particular challenges that confront current researchers. Five mechanisms of gene regulation have been determined for riboswitches. Most bacterial riboswitches modulate either transcription termination or translation initiation in response to ligand binding. All known examples of eukaryotic riboswitches, and some bacterial riboswitches, control gene expression by alternative splicing. The glmS riboswitch, which is widespread in Gram-positive bacteria, is a catalytic RNA activated by ligand binding: its self-cleavage destabilizes the mRNA of which it is part. Finally, one example of a trans-acting riboswitch is known. Three-dimensional structures have been determined for representatives of 13 structurally distinct riboswitch classes, providing atomic-level insight into their mechanisms of ligand recognition. While cellular and viral RNAs have attracted widespread interest as potential drug targets, riboswitches show special promise due to the diversity of small-molecule recognition strategies that are on display in their ligand-binding pockets. Moreover, riboswitches have evolved to recognize small-molecule ligands, which is unique among known structured RNA domains. Structural and biochemical advances in the study of riboswitches provide an impetus for the development of methods for the discovery of novel

  19. Construction and analysis of regulatory genetic networks in cervical cancer based on involved microRNAs, target genes, transcription factors and host genes

    PubMed Central

    WANG, NING; XU, ZHIWEN; WANG, KUNHAO; ZHU, MINGHUI; LI, YANG

    2014-01-01

    Over recent years, genes and microRNA (miRNA/miR) have been considered as key biological factors in human carcinogenesis. During cancer development, genes may act as multiple identities, including target genes of miRNA, transcription factors and host genes. The present study concentrated on the regulatory networks consisting of the biological factors involved in cervical cancer in order to investigate their features and affect on this specific pathology. Numerous raw data was collected and organized into purposeful structures, and adaptive procedures were defined for application to the prepared data. The networks were therefore built with the factors as basic components according to their interacting associations. The networks were constructed at three levels of interdependency, including a differentially-expressed network, a related network and a global network. Comparisons and analyses were made at a systematic level rather than from an isolated gene or miRNA. Critical hubs were extracted in the core networks and notable features were discussed, including self-adaption feedback regulation. The present study expounds the pathogenesis from a novel point of view and is proposed to provide inspiration for further investigation and therapy. PMID:24944708

  20. Evaluation of global sequence comparison and one-to-one FASTA local alignment in regulatory allergenicity assessment of transgenic proteins in food crops.

    PubMed

    Song, Ping; Herman, Rod A; Kumpatla, Siva

    2014-09-01

    To address the high false positive rate using >35% identity over 80 amino acids in the regulatory assessment of transgenic proteins for potential allergenicity and the change of E-value with database size, the Needleman-Wunsch global sequence alignment and a one-to-one (1:1) local FASTA search (one protein in the target database at a time) using FASTA were evaluated by comparing proteins randomly selected from Arabidopsis, rice, corn, and soybean with known allergens in a peer-reviewed allergen database (http://www.allergenonline.org/). Compared with the approach of searching >35%/80aa+, the false positive rate measured by specificity rate for identification of true allergens was reduced by a 1:1 global sequence alignment with a cut-off threshold of ≧30% identity and a 1:1 FASTA local alignment with a cut-off E-value of ≦1.0E-09 while maintaining the same sensitivity. Hence, a 1:1 sequence comparison, especially using the FASTA local alignment tool with a biological relevant E-value of 1.0E-09 as a threshold, is recommended for the regulatory assessment of sequence identities between transgenic proteins in food crops and known allergens.

  1. Low light comparison of target visibility with night vision goggles

    NASA Astrophysics Data System (ADS)

    Craig, Gregory; Brulotte, Michel; Carignan, Stephan; Macuda, Todd; Jennings, Sion

    2008-04-01

    Different night vision goggle image intensification technologies were tested to compare goggle performance in low light conditions. A total of four different night vision goggles were tested in a laboratory dark room. The laboratory tests consisted of viewing Landolt acuity stimuli of different contrast levels with each set of goggles and without the goggles in full light conditions (baseline performance). The results from the laboratory testing indicated that there were significant differences in acuity between the NVGs, particularly for low contrast targets. These data suggest that NVG standards developed using high contrast targets, even in low light conditions may not provide the full story of how the NVG will perform in flight.

  2. Senescence-associated microRNAs target cell cycle regulatory genes in normal human lung fibroblasts.

    PubMed

    Markopoulos, Georgios S; Roupakia, Eugenia; Tokamani, Maria; Vartholomatos, George; Tzavaras, Theodore; Hatziapostolou, Maria; Fackelmayer, Frank O; Sandaltzopoulos, Raphael; Polytarchou, Christos; Kolettas, Evangelos

    2017-10-01

    Senescence recapitulates the ageing process at the cell level. A senescent cell stops dividing and exits the cell cycle. MicroRNAs (miRNAs) acting as master regulators of transcription, have been implicated in senescence. In the current study we investigated and compared the expression of miRNAs in young versus senescent human fibroblasts (HDFs), and analysed the role of mRNAs expressed in replicative senescent HFL-1 HDFs. Cell cycle analysis confirmed that HDFs accumulated in G1/S cell cycle phase. Nanostring analysis of isolated miRNAs from young and senescent HFL-1 showed that a distinct set of 15 miRNAs were significantly up-regulated in senescent cells including hsa-let-7d-5p, hsa-let-7e-5p, hsa-miR-23a-3p, hsa-miR-34a-5p, hsa-miR-122-5p, hsa-miR-125a-3p, hsa-miR-125a-5p, hsa-miR-125b-5p, hsa-miR-181a-5p, hsa-miR-221-3p, hsa-miR-222-3p, hsa-miR-503-5p, hsa-miR-574-3p, hsa-miR-574-5p and hsa-miR-4454. Importantly, pathway analysis of miRNA target genes down-regulated during replicative senescence in a public RNA-seq data set revealed a significant high number of genes regulating cell cycle progression, both G1/S and G2/M cell cycle phase transitions and telomere maintenance. The reduced expression of selected miRNA targets, upon replicative and oxidative-stress induced senescence, such as the cell cycle effectors E2F1, CcnE, Cdc6, CcnB1 and Cdc25C was verified at the protein and/or RNA levels. Induction of G1/S cell cycle phase arrest and down-regulation of cell cycle effectors correlated with the up-regulation of miR-221 upon both replicative and oxidative stress-induced senescence. Transient expression of miR-221/222 in HDFs promoted the accumulation of HDFs in G1/S cell cycle phase. We propose that miRNAs up-regulated during replicative senescence may act in concert to induce cell cycle phase arrest and telomere erosion, establishing a senescent phenotype. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Phosphatase PRL-3 is a direct regulatory target of TGFbeta in colon cancer metastasis.

    PubMed

    Jiang, Yanjun; Liu, Xiao-Qiong; Rajput, Ashwani; Geng, Liying; Ongchin, Melanie; Zeng, Qi; Taylor, Gregory S; Wang, Jing

    2011-01-01

    Metastasis causes most deaths from cancer yet mechanistic understanding and therapeutic options remain limited. Overexpression of the phosphatase PRL-3 (phosphatase of regenerating liver) is associated with metastasis of colon cancer. Here, we show that PRL-3 is a direct target of signaling by TGFβ, which is broadly implicated in progression and metastasis. We found that suppression of PRL-3 expression by TGFβ was mediated by Smad-dependent inhibition of PRL-3 transcription at the level of promoter activity. PRL-3 activation stimulated PI3K/AKT signaling that caused resistance to stress-induced apoptosis. PRL-3 overexpression promoted metastatic colonization in an orthotopic mouse model of colon cancer, whereas PRL-3 knockdown reduced metastatic potential. Altered metastatic phenotypes were not derivative of primary tumor development or local invasion but could be attributed to PRL-3-mediated cell survival. Our findings suggest that inhibiting PRL-3 expression might be an important mechanism through which TGFβ suppresses metastasis in colon cancer. In addition, our findings suggest that loss of TGFβ signaling, which occurs commonly during colon cancer progression, is sufficient to activate a PRL-3-mediated cell survival pathway that can selectively promote metastasis. Therefore, a major implication of our findings is that PRL-3 antagonists may offer significant value for antimetastatic therapy in patients with colon cancer.

  4. Online aggressor/targets, aggressors, and targets: a comparison of associated youth characteristics.

    PubMed

    Ybarra, Michele L; Mitchell, Kimberly J

    2004-10-01

    While most youth report positive experiences and activities online, little is known about experiences of Internet victimization and associated correlates of youth, specifically in regards to Internet harassment. The Youth Internet Safety Survey is a cross-sectional, nationally representative telephone survey of young regular Internet users in the United States. Interviews were conducted between the fall of 1999 and the spring of 2000 and examined characteristics of Internet harassment, unwanted exposure to sexual material, and sexual solicitation that had occurred on the Internet in the previous year. One thousand, five hundred and one regular Internet users between the ages of 10 and 17 years were interviewed, along with one parent or guardian. To assess the characteristics surrounding Internet harassment, four groups of youth were compared: 1) targets of aggression (having been threatened or embarrassed by someone; or feeling worried or threatened by someone's actions); 2) online aggressors (making rude or nasty comments; or harassing or embarrassing someone with whom the youth was mad at); 3) aggressor/targets (youth who report both being an aggressor as well as a target of Internet harassment); and 4) non-harassment involved youth (being neither a target nor an aggressor online). Of the 19% of young regular Internet users involved in online aggression, 3% were aggressor/targets, 4% reported being targets only, and 12% reported being online aggressors only. Youth aggressor/targets reported characteristics similar to conventional bully/victim youth, including many commonalities with aggressor-only youth, and significant psychosocial challenge. Youth aggressor/targets are intense users of the Internet who view themselves as capable web users. Beyond this, however, these youth report significant psychosocial challenge, including depressive symptomatology, problem behavior, and targeting of traditional bullying. Implications for intervention are discussed.

  5. Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study

    PubMed Central

    2011-01-01

    Background Inferring regulatory interactions between genes from transcriptomics time-resolved data, yielding reverse engineered gene regulatory networks, is of paramount importance to systems biology and bioinformatics studies. Accurate methods to address this problem can ultimately provide a deeper insight into the complexity, behavior, and functions of the underlying biological systems. However, the large number of interacting genes coupled with short and often noisy time-resolved read-outs of the system renders the reverse engineering a challenging task. Therefore, the development and assessment of methods which are computationally efficient, robust against noise, applicable to short time series data, and preferably capable of reconstructing the directionality of the regulatory interactions remains a pressing research problem with valuable applications. Results Here we perform the largest systematic analysis of a set of similarity measures and scoring schemes within the scope of the relevance network approach which are commonly used for gene regulatory network reconstruction from time series data. In addition, we define and analyze several novel measures and schemes which are particularly suitable for short transcriptomics time series. We also compare the considered 21 measures and 6 scoring schemes according to their ability to correctly reconstruct such networks from short time series data by calculating summary statistics based on the corresponding specificity and sensitivity. Our results demonstrate that rank and symbol based measures have the highest performance in inferring regulatory interactions. In addition, the proposed scoring scheme by asymmetric weighting has shown to be valuable in reducing the number of false positive interactions. On the other hand, Granger causality as well as information-theoretic measures, frequently used in inference of regulatory networks, show low performance on the short time series analyzed in this study. Conclusions Our

  6. N-Methyl-D-aspartate Receptor Subunits Are Non-myosin Targets of Myosin Regulatory Light Chain*

    PubMed Central

    Bajaj, Gaurav; Zhang, Yong; Schimerlik, Michael I.; Hau, Andrew M.; Yang, Jing; Filtz, Theresa M.; Kioussi, Chrissa; Ishmael, Jane E.

    2009-01-01

    Excitatory synapses contain multiple members of the myosin superfamily of molecular motors for which functions have not been assigned. In this study we characterized the molecular determinants of myosin regulatory light chain (RLC) binding to two major subunits of the N-methyl-d-aspartate receptor (NR). Myosin RLC bound to NR subunits in a manner that could be distinguished from the interaction of RLC with the neck region of non-muscle myosin II-B (NMII-B) heavy chain; NR-RLC interactions did not require the addition of magnesium, were maintained in the absence of the fourth EF-hand domain of the light chain, and were sensitive to RLC phosphorylation. Equilibrium fluorescence spectroscopy experiments indicate that the affinity of myosin RLC for NR1 is high (30 nm) in the context of the isolated light chain. Binding was not favored in the context of a recombinant NMII-B subfragment one, indicating that if the RLC is already bound to NMII-B it is unlikely to form a bridge between two binding partners. We report that sequence similarity in the “GXXXR” portion of the incomplete IQ2 motif found in NMII heavy chain isoforms likely contributes to recognition of NR2A as a non-myosin target of the RLC. Using site-directed mutagenesis to disrupt NR2A-RLC binding in intact cells, we find that RLC interactions facilitate trafficking of NR1/NR2A receptors to the cell membrane. We suggest that myosin RLC can adopt target-dependent conformations and that a role for this light chain in protein trafficking may be independent of the myosin II complex. PMID:18945678

  7. Transcription Factor Binding Probabilities in Orthologous Promoters: An Alignment-Free Approach to the Inference of Functional Regulatory Targets

    NASA Astrophysics Data System (ADS)

    Liu, Xiao; Clarke, Neil D.

    Using a physically principled method of scoring genomic sequences for the potential to be bound by transcription factors, we have developed an algorithm for assessing the conservation of predicted binding occupancy that does not rely on sequence alignment of promoters. The method, which we call ortholog-weighting, assesses the degree to which the predicted binding occupancy of a transcription factor in a reference gene is also predicted in the promoters of orthologous genes. The analysis was performed separately for over 100 different transcription factors in S. cerevisiae. Statistical significance was evaluated by simulation using permuted versions of the position weight matrices. Ortholog-weighting produced about twice as many significantly high scoring genes as were obtained from the S. cerevisiae genome alone. Gene Ontology analysis found a similar two-fold enrichment of genes. Both analyses suggest that ortholog-weighting improves the prediction of true regulatory targets. Interestingly, the method has only a marginal effect on the prediction of binding by chromatin immunoprecipitation (ChIP) assays. We suggest several possibilities for reconciling this result with the improved enrichment that we observe for functionally related promoters and for promoters that are under positive selection.

  8. Targeted mutagenesis of intergenic regions in the Neisseria gonorrhoeae gonococcal genetic island reveals multiple regulatory mechanisms controlling type IV secretion.

    PubMed

    Ramsey, Meghan E; Bender, Tobias; Klimowicz, Amy K; Hackett, Kathleen T; Yamamoto, Ami; Jolicoeur, Adrienne; Callaghan, Melanie M; Wassarman, Karen M; van der Does, Chris; Dillard, Joseph P

    2015-09-01

    Gonococci secrete chromosomal DNA into the extracellular environment using a type IV secretion system (T4SS). The secreted DNA acts in natural transformation and initiates biofilm development. Although the DNA and its effects are detectable, structural components of the T4SS are present at very low levels, suggestive of uncharacterized regulatory control. We sought to better characterize the expression and regulation of T4SS genes and found that the four operons containing T4SS genes are transcribed at very different levels. Increasing transcription of two of the operons through targeted promoter mutagenesis did not increase DNA secretion. The stability and steady-state levels of two T4SS structural proteins were affected by a homolog of tail-specific protease. An RNA switch was also identified that regulates translation of a third T4SS operon. The switch mechanism relies on two putative stem-loop structures contained within the 5' untranslated region of the transcript, one of which occludes the ribosome binding site and start codon. Mutational analysis of these stem loops supports a model in which induction of an alternative structure relieves repression. Taken together, these results identify multiple layers of regulation, including transcriptional, translational and post-translational mechanisms controlling T4SS gene expression and DNA secretion. © 2015 John Wiley & Sons Ltd.

  9. Regulatory (FOXP3+) T cells as target for immune therapy of cervical intraepithelial neoplasia and cervical cancer.

    PubMed

    Loddenkemper, Christoph; Hoffmann, Corinna; Stanke, Jonas; Nagorsen, Dirk; Baron, Udo; Olek, Sven; Huehn, Jochen; Ritz, Joerg-Peter; Stein, Harald; Kaufmann, Andreas M; Schneider, Achim; Cichon, Günter

    2009-06-01

    Regulatory (FOXP3+) T cells (Tregs) comprise a subpopulation of CD4+ T cells that suppress autoreactive immune cells, thereby protecting organs and tissues from autoimmunity. Tregs have also been detected in human malignancies and their depletion or inactivation substantially improves cellular antitumor immunity in preclinical studies. Novel therapeutic strategies for cervical cancer and precancerous cervical intraepithelial neoplasia (CIN) focus on immune-modulatory and cancer vaccination approaches. In this context, the frequency of Tregs in cervical cancer and precancerous CIN could influence therapeutic strategies. We determined the frequency of infiltrating CD4+ and CD8+ T cells as well as FOXP3+ Tregs in high-grade CIN lesions (CIN III) and cervical carcinoma compared to colon carcinoma, skin melanoma, and bronchial carcinoma. We show that human papilloma virus-derived lesions have a significantly higher number of infiltrating lymphocytes and FOXP3+ Tregs compared to three other common tumor entities. In addition we explored the therapeutic effect of agonistic anti-glucocorticoid-induced tumor necrosis factor receptor family-related protein antibodies that, by single systemic application, inactivate Tregs and induce strong intratumoral invasion of CD8+ T cells and complete tumor eradication in 70% of treated animals. The large number of Tregs in human papilloma virus-derived lesions suggests a pivotal role of Tregs for counteracting the host immune response. We therefore regard CIN and cervical cancer as prime targets for new immune-based non-invasive therapies.

  10. Microcytic anemia, erythropoietic protoporphyria, and neurodegeneration in mice with targeted deletion of iron-regulatory protein 2

    PubMed Central

    Cooperman, Sharon S.; Meyron-Holtz, Esther G.; Olivierre-Wilson, Hayden; Ghosh, Manik C.; McConnell, Joseph P.; Rouault, Tracey A.

    2005-01-01

    Iron-regulatory proteins (IRPs) 1 and 2 posttranscriptionally regulate expression of transferrin receptor (TfR), ferritin, and other iron metabolism proteins. Mice with targeted deletion of IRP2 overexpress ferritin and express abnormally low TfR levels in multiple tissues. Despite this misregulation, there are no apparent pathologic consequences in tissues such as the liver and kidney. However, in the central nervous system, evidence of abnormal iron metabolism in IRP2-/- mice precedes the development of adult-onset progressive neurodegeneration, characterized by widespread axonal degeneration and neuronal loss. Here, we report that ablation of IRP2 results in iron-limited erythropoiesis. TfR expression in erythroid precursors of IRP2-/- mice is reduced, and bone marrow iron stores are absent, even though transferrin saturation levels are normal. Marked overexpression of 5-aminolevulinic acid synthase 2 (Alas2) results from loss of IRP-dependent translational repression, and markedly increased levels of free protoporphyrin IX and zinc protoporphyrin are generated in IRP2-/- erythroid cells. IRP2-/- mice represent a new paradigm of genetic microcytic anemia. We postulate that IRP2 mutations or deletions may be a cause of refractory microcytic anemia and bone marrow iron depletion in patients with normal transferrin saturations, elevated serum ferritins, elevated red cell protoporphyrin IX levels, and adult-onset neurodegeneration. PMID:15831703

  11. One target, different effects: a comparison of distinct therapeutic antibodies against the same targets

    PubMed Central

    2011-01-01

    To date, more than 30 antibodies have been approved worldwide for therapeutic use. While the monoclonal antibody market is rapidly growing, the clinical use of therapeutic antibodies is mostly limited to treatment of cancers and immunological disorders. Moreover, antibodies against only five targets (TNF-α, HER2, CD20, EGFR, and VEGF) account for more than 80 percent of the worldwide market of therapeutic antibodies. The shortage of novel, clinically proven targets has resulted in the development of many distinct therapeutic antibodies against a small number of proven targets, based on the premise that different antibody molecules against the same target antigen have distinct biological and clinical effects from one another. For example, four antibodies against TNF-α have been approved by the FDA -- infliximab, adalimumab, golimumab, and certolizumab pegol -- with many more in clinical and preclinical development. The situation is similar for HER2, CD20, EGFR, and VEGF, each having one or more approved antibodies and many more under development. This review discusses the different binding characteristics, mechanisms of action, and biological and clinical activities of multiple monoclonal antibodies against TNF-α, HER-2, CD20, and EGFR and provides insights into the development of therapeutic antibodies. PMID:21811090

  12. Regulatory tasks of national medical associations - international comparison and the Israeli case

    PubMed Central

    2013-01-01

    Background In many countries, NMAs, along with other stakeholders, play a part in the regulation of physicians. The purpose of this paper is to compare and explain the level of involvement of NMAs in physician regulation in several developed countries, with a specific emphasis on Israel. Methods The authors conducted a review of the literature on physician regulation, focusing on licensing and registration, postgraduate training and physician disciplinary measures. Detailed country specific information was also obtained via the websites of relevant NMAs and regulatory bodies and correspondence with select NMAs. Five test cases were examined in detail: Germany, Israel, the Netherlands, the United Kingdom and the United States. The Israeli case will be discussed at greater length. Results Medical licensing usually lies in the hands of the government (on the national or state level). Specialist training, on the other hand, is often self-regulated and entrusted in the hands of the profession, frequently under the direct responsibility of the NMA, as in Israel, the Netherlands and Germany. In all the countries presented, other than Germany, the NMA is not involved in instituting disciplinary procedures in cases of alleged physician misconduct. Discussion The extent to which NMAs fulfill regulatory functions varies greatly from country to country. The relationship between government and the profession in the area of regulation often parallels the dominant mode of governance in the health care system as a whole. Specifically, the level of involvement of the Israeli Medical Association in medical regulation is a result of political, historical and ideological arrangements shaped vis-à-vis the government over the years. Conclusions In Continental Europe, co-operation between the NMA and the government is more common than in the USA and the UK. The Israeli regulatory model emerged in a European-like fashion, closer to the Netherlands than to Germany. The Israeli case, as

  13. [Regulatory requirements regarding cell-based medicinal products for human and veterinary use - a comparison].

    PubMed

    Kuhlmann-Gottke, Johanna; Duchow, Karin

    2015-11-01

    At present, there is no separate regulatory framework for cell-based medicinal products (CBMP) for veterinary use at the European or German level. Current European and national regulations exclusively apply to the corresponding medicinal products for human use. An increasing number of requests for the regulatory classification of CBMP for veterinary use, such as allogeneic stem cell preparations and dendritic cell-based autologous tumour vaccines, and a rise in scientific advice for companies developing these products, illustrate the need for adequate legislation. Currently, advice is given and decisions are made on a case-by-case basis regarding the regulatory classification and authorisation requirements.Since some of the CBMP - in particular in the area of stem-cell products - are developed in parallel for human and veterinary use, there is an urgent need to create specific legal definitions, regulations, and guidelines for these complex innovative products in the veterinary sector as well. Otherwise, there is a risk that that the current legal grey area regarding veterinary medicinal products will impede therapeutic innovations in the long run. A harmonised EU-wide approach is desirable. Currently the European legislation on veterinary medicinal products is under revision. In this context, veterinary therapeutics based on allogeneic cells and tissues will be defined and regulated. Certainly, the legal framework does not have to be as comprehensive as for human CBMP; a leaner solution is conceivable, similar to the special provisions for advanced-therapy medicinal products laid down in the German Medicines Act.

  14. Health insurance expansions for working families: a comparison of targeting strategies.

    PubMed

    Ferry, Danielle H; Garrett, Bowen; Glled, Sherry; Greenman, Emily K; Nichols, Len M

    2002-01-01

    We compare three eligibility criteria for targeting health insurance expansions in working families: poverty, hourly wages, and employment in a small firm. Making pairwise comparisons among these, we find that targeting by poverty is the most effective and efficient. A poverty-based method is also the most effective way to target those lacking access to employer-sponsored insurance and those with low take-up of such coverage. When we examine the effectiveness of targeting by family type, we find that marital status and number of workers in the family make little difference once we control for the presence of children and for poverty level.

  15. Comparison Evaluation of the PFP FSAR and NRC Regulatory Guide 3.39 with DOE-STD-3009-94

    SciTech Connect

    OSCARSON, E.E.

    2000-07-28

    One of the Plutonium Finishing Plant's (PFP) current Authorization Basis (AB) documents is the Final Safety Analysis Report (FSAR). This FSAR (HNF-SD-CP-SAR-02 1) was prepared to the format and content guidance specified in U.S. Nuclear Regulatory Commission (NRC) Regulatory Guide 3.39, Standard Format and Content of License Applications for Plutonium Processing and Fuel Fabrication Plants (RG 3.39). In April 1992, the US Department of Energy (DOE) issued DOE Order 5480.23 which established the FSAR requirements for DOE nonreactor nuclear facilities. In 1994, DOE issued DOE-STD-3009-94, Preparation Guide for US. Department of Energy Nonreactor Nuclear Facility Safety Analysis Reports, which is a format and content guide addressing the preparation of FSARs in accordance with DOE Order 5480.23. During the initial preparation and issuance of the PFP FSAR the format and content guidance contained in NRC Regulatory Guide 3.39 was utilized, since it was the most applicable guidance at the time for the preparation of Safety Analysis Reports for plutonium processing plants. With the adoption of DOE Order 5480.23 and DOE-STD-3009-94, DOE required the preparation of SARs to meet the format and content of those DOE documents. The PFP was granted an exemption to continue with RG 3.39 format for future FSAR revisions. PFP modifications and additions have required PFP FSAR modifications that have typically been prepared to the same NRC Regulatory Guide 3.39 format and content, to provide consistency with the PFP FSAR. This document provides a table comparison between the 3009 and RG 3.39 formats to validate the extent of PFP FSAR compliance with the intent of DOE Order 5480.23 and DOE-STD-3009-94. This evaluation was initially performed on Revisions 1 and 1A of the PFP FSAR. With the preparation of a Revision 2 draft to the FSAR, sections with significant changes were reevaluated for compliance and the tables were updated, as appropriate. The tables resulting from this

  16. Cross-comparison of cancer drug approvals at three international regulatory agencies

    PubMed Central

    Samuel, N.; Verma, S.

    2016-01-01

    Background The primary objective of the present study was to examine the drug approval process and the time to approval (tta) for cancer drugs by 3 major international regulatory bodies—Health Canada, the U.S. Food and Drug Administration (fda), and the European Medicines Agency (ema)—and to explore differences in the drug approval processes that might contribute to any disparities. Methods The publicly available Health Canada Drug Product Database was surveyed for all marketed antineoplastic agents approved between 1 January 2005 and 1 June 2013. For the resulting set of cancer drugs, public records of sponsor submission and approval dates by Health Canada, the fda, and the ema were obtained. Results Overall, the tta for the 37 antineoplastic agents that met the study criteria was significantly less for the fda than for the ema (X̄ = 6.7 months, p < 0.001) or for Health Canada (X̄ = 6.4 months, p < 0.001). The tta was not significantly different for Health Canada and the ema (X̄ = 0.65 months, p = 0.89). An analysis of the review processes demonstrated that the primary reason for the identified discrepancies in tta was the disparate use of accelerated approval mechanisms. Summary In the present study, we systematically compared cancer drug approvals at 3 international regulatory bodies. The differences in tta reflect several important considerations in the regulatory framework of cancer drug approvals. Those findings warrant an enhanced dialogue between clinicians and government agencies to understand opportunities and challenges in the current approval processes and to work toward balancing drug safety with timely access. PMID:27803605

  17. A model comparison study of the flowering time regulatory network in Arabidopsis

    PubMed Central

    2014-01-01

    Background Several dynamic models of a gene regulatory network of the light-induced floral transition process in Arabidopsis have been developed to capture the behavior of gene transcription and infer predictions based on experimental observations. It has been proven that the models can make accurate and novel predictions, which generate testable hypotheses. Two major issues were addressed in this study. First, construction of dynamic models for gene regulatory networks requires the use of mathematic modeling that comprises equations of a large number of parameters. Second, the binding mechanism of the transcription factor with DNA is another factor that requires detailed modeling. The first issue was tackled by adopting an optimization algorithm, and the second was addressed by comparing the performance of three alternative modeling approaches, namely the S-system, the Michaelis-Menten model and the Mass-action model. The efficiencies of parameter estimation and modeling performance were calculated based on least square error (O(p)), mean relative error (MRE) and Akaike Information Criterion (AIC). Results We compared three models to describe gene regulation of the flowering transition process in Arabidopsis. The Mass-action model is the simplest and has the least parameters. It is therefore less computation-intensive with the smallest AIC value. The disadvantage, however, is that it assumes the system is simply a second order reaction which is not the case in our study. The Michaelis-Menten model also assumes the system is homogeneous and ignores the intracellular protein transport process. The S-system model has the best performance and it does describe the diffusion effects. A disadvantage of the S-system is that it involves the most parameters. The largest AIC value also implies an over-fitting may occur in parameter estimation. Conclusions Three dynamic models were adopted to describe the dynamics of the gene regulatory network of the flowering transition

  18. Targeted disruption of the mouse gene encoding steroidogenic acute regulatory protein provides insights into congenital lipoid adrenal hyperplasia.

    PubMed

    Caron, K M; Soo, S C; Wetsel, W C; Stocco, D M; Clark, B J; Parker, K L

    1997-10-14

    An essential component of regulated steroidogenesis is the translocation of cholesterol from the cytoplasm to the inner mitochondrial membrane where the cholesterol side-chain cleavage enzyme carries out the first committed step in steroidogenesis. Recent studies showed that a 30-kDa mitochondrial phosphoprotein, designated steroidogenic acute regulatory protein (StAR), is essential for this translocation. To allow us to explore the roles of StAR in a system amenable to experimental manipulation and to develop an animal model for the human disorder lipoid congenital adrenal hyperplasia (lipoid CAH), we used targeted gene disruption to produce StAR knockout mice. These StAR knockout mice were indistinguishable initially from wild-type littermates, except that males and females had female external genitalia. After birth, they failed to grow normally and died from adrenocortical insufficiency. Hormone assays confirmed severe defects in adrenal steroids-with loss of negative feedback regulation at hypothalamic-pituitary levels-whereas hormones constituting the gonadal axis did not differ significantly from levels in wild-type littermates. Histologically, the adrenal cortex of StAR knockout mice contained florid lipid deposits, with lesser deposits in the steroidogenic compartment of the testis and none in the ovary. The sex-specific differences in gonadal involvement support a two-stage model of the pathogenesis of StAR deficiency, with trophic hormone stimulation inducing progressive accumulation of lipids within the steroidogenic cells and ultimately causing their death. These StAR knockout mice provide a useful model system in which to determine the mechanisms of StAR's essential roles in adrenocortical and gonadal steroidogenesis.

  19. Targeting CD38 Suppresses Induction and Function of T Regulatory Cells to Mitigate Immunosuppression in Multiple Myeloma.

    PubMed

    Feng, Xiaoyan; Zhang, Li; Acharya, Chirag; An, Gang; Wen, Kenneth; Qiu, Lugui; Munshi, Nikhil C; Tai, Yu-Tzu; Anderson, Kenneth C

    2017-08-01

    Purpose: We study CD38 levels in immunosuppressive CD4(+)CD25(high)Foxp3(+) regulatory T cells (Treg) and further define immunomodulating effects of a therapeutic CD38 mAb isatuximab/SAR650984 in multiple myeloma.Experimental Design: We evaluated percentages of CD38-expressing subsets in Tregs from normal donors and multiple myeloma patients. Peripheral blood mononuclear cells (PBMC) were then treated with isatuximab with or without lenalidomide or pomalidomide to identify their impact on the percentage and immunosuppressive activity of Tregs on CD4(+)CD25(-) T cells (Tcons). We investigated the mechanism of increased Tregs in multiple myeloma patients in ex vivo cocultures of multiple myeloma cells with PBMCs or Tcons.Results: CD38 expression is higher on Tregs than Tcons from multiple myeloma patients versus normal donors. CD38 levels and the percentages of CD38(high) Tregs are increased by lenalidomide and pomalidomide. Isatuximab preferentially decreases Treg and increases Tcon frequencies, which is enhanced by pomalidomide/lenalidomide. Isatuximab reduces Foxp3 and IL10 in Tregs and restores proliferation and function of Tcons. It augments multiple myeloma cell lysis by CD8(+) T and natural killer cells. Coculture of multiple myeloma cells with Tcons significantly induces Tregs (iTregs), which express even higher CD38, CD25, and FoxP3 than natural Tregs. This is associated with elevated circulating CD38(+) Tregs in multiple myeloma patients versus normal donors. Conversely, isatuximab decreases multiple myeloma cell- and bone marrow stromal cell-induced iTreg by inhibiting both cell-cell contact and TGFβ/IL10. Finally, CD38 levels correlate with differential inhibition by isatuximab of Tregs from multiple myeloma versus normal donors.Conclusions: Targeting CD38 by isatuximab can preferentially block immunosuppressive Tregs and thereby restore immune effector function against multiple myeloma. Clin Cancer Res; 23(15); 4290-300. ©2017 AACR. ©2017 American

  20. Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast.

    PubMed

    Staschke, Kirk A; Dey, Souvik; Zaborske, John M; Palam, Lakshmi Reddy; McClintick, Jeanette N; Pan, Tao; Edenberg, Howard J; Wek, Ronald C

    2010-05-28

    Two important nutrient-sensing and regulatory pathways, the general amino acid control (GAAC) and the target of rapamycin (TOR), participate in the control of yeast growth and metabolism during changes in nutrient availability. Amino acid starvation activates the GAAC through Gcn2p phosphorylation of translation factor eIF2 and preferential translation of GCN4, a transcription activator. TOR senses nitrogen availability and regulates transcription factors such as Gln3p. We used microarray analyses to address the integration of the GAAC and TOR pathways in directing the yeast transcriptome during amino acid starvation and rapamycin treatment. We found that GAAC is a major effector of the TOR pathway, with Gcn4p and Gln3p each inducing a similar number of genes during rapamycin treatment. Although Gcn4p activates a common core of 57 genes, the GAAC directs significant variations in the transcriptome during different stresses. In addition to inducing amino acid biosynthetic genes, Gcn4p in conjunction with Gln3p activates genes required for the assimilation of secondary nitrogen sources such as gamma-aminobutyric acid (GABA). Gcn2p activation upon shifting to secondary nitrogen sources is suggested to occur by means of a dual mechanism. First, Gcn2p is induced by the release of TOR repression through a mechanism involving Sit4p protein phosphatase. Second, this eIF2 kinase is activated by select uncharged tRNAs, which were shown to accumulate during the shift to the GABA medium. This study highlights the mechanisms by which the GAAC and TOR pathways are integrated to recognize changing nitrogen availability and direct the transcriptome for optimal growth adaptation.

  1. The EBV Latent Antigen 3C Inhibits Apoptosis through Targeted Regulation of Interferon Regulatory Factors 4 and 8

    PubMed Central

    Banerjee, Shuvomoy; Lu, Jie; Cai, Qiliang; Saha, Abhik; Jha, Hem Chandra; Dzeng, Richard Kuo; Robertson, Erle S.

    2013-01-01

    Epstein-Barr virus (EBV) is linked to a broad spectrum of B-cell malignancies. EBV nuclear antigen 3C (EBNA3C) is an encoded latent antigen required for growth transformation of primary human B-lymphocytes. Interferon regulatory factor 4 (IRF4) and 8 (IRF8) are transcription factors of the IRF family that regulate diverse functions in B cell development. IRF4 is an oncoprotein with anti-apoptotic properties and IRF8 functions as a regulator of apoptosis and tumor suppressor in many hematopoietic malignancies. We now demonstrate that EBNA3C can contribute to B-cell transformation by modulating the molecular interplay between cellular IRF4 and IRF8. We show that EBNA3C physically interacts with IRF4 and IRF8 with its N-terminal domain in vitro and forms a molecular complex in cells. We identified the Spi-1/B motif of IRF4 as critical for EBNA3C interaction. We also demonstrated that EBNA3C can stabilize IRF4, which leads to downregulation of IRF8 by enhancing its proteasome-mediated degradation. Further, si-RNA mediated knock-down of endogenous IRF4 results in a substantial reduction in proliferation of EBV-transformed lymphoblastoid cell lines (LCLs), as well as augmentation of DNA damage-induced apoptosis. IRF4 knockdown also showed reduced expression of its targeted downstream signalling proteins which include CDK6, Cyclin B1 and c-Myc all critical for cell proliferation. These studies provide novel insights into the contribution of EBNA3C to EBV-mediated B-cell transformation through regulation of IRF4 and IRF8 and add another molecular link to the mechanisms by which EBV dysregulates cellular activities, increasing the potential for therapeutic intervention against EBV-associated cancers. PMID:23658517

  2. Replication Study: The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors

    PubMed Central

    Horrigan, Stephen K

    2017-01-01

    In 2015, as part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Chroscinski et al., 2015) that described how we intended to replicate selected experiments from the paper “The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors “(Willingham et al., 2012). Here we report the results of those experiments. We found that treatment of immune competent mice bearing orthotopic breast tumors with anti-mouse CD47 antibodies resulted in short-term anemia compared to controls, consistent with the previously described function of CD47 in normal phagocytosis of aging red blood cells and results reported in the original study (Table S4; Willingham et al., 2012). The weight of tumors after 30 days administration of anti-CD47 antibodies or IgG isotype control were not found to be statistically different, whereas the original study reported inhibition of tumor growth with anti-CD47 treatment (Figure 6A,B; Willingham et al., 2012). However, our efforts to replicate this experiment were confounded because spontaneous regression of tumors occurred in several of the mice. Additionally, the excised tumors were scored for inflammatory cell infiltrates. We found IgG and anti-CD47 treated tumors resulted in minimal to moderate lymphocytic infiltrate, while the original study observed sparse lymphocytic infiltrate in IgG-treated tumors and increased inflammatory cell infiltrates in anti-CD47 treated tumors (Figure 6C; Willingham et al., 2012). Furthermore, we observed neutrophilic infiltration was slightly increased in anti-CD47 treated tumors compared to IgG control. Finally, we report a meta-analysis of the result. DOI: http://dx.doi.org/10.7554/eLife.18173.001 PMID:28100392

  3. Comparison of residents' pesticide exposure with predictions obtained using the UK regulatory exposure assessment approach.

    PubMed

    Galea, Karen S; MacCalman, Laura; Jones, Kate; Cocker, John; Teedon, Paul; Cherrie, John W; van Tongeren, Martie

    2015-11-01

    The UK regulatory methods currently used for estimating residents' potential pesticide exposure were assessed to determine whether they provide sufficiently conservative estimates. A non-random sample of 149 residents living within 100 m of fields where pesticides were sprayed provided first morning void urine samples one and/or two days after spraying. Using farmers' spray information, regulatory exposure assessment (REA) models were applied to estimate potential pesticide intake among residents, with a toxicokinetic (TK) model used to estimate urinary biomarker concentrations in the mornings of the two days following the spray. These were compared with actual measured urinary biomarker concentrations obtained following the spray applications. The study focused on five pesticides (cypermethrin, penconazole, captan, chlorpyrifos and chlormequat). All measured cypermethrin urinary biomarker levels were lower than the REA-predicted concentrations. Over 98% and 97% of the measured urinary biomarker concentrations for penconazole and captan respectively were lower than the REA-predicted exposures. Although a number of the chlorpyrifos and chlormequat spray-related urinary biomarker concentrations were greater than the predictions, investigation of the background urinary biomarker concentrations suggests these were not significantly different from the levels expected had no pesticide spraying occurred. The majority of measured concentrations being well below the REA-predicted concentrations indicate that, in these cases, the REA is sufficiently conservative.

  4. Identification of bolting-related microRNAs and their targets reveals complex miRNA-mediated flowering-time regulatory networks in radish (Raphanus sativus L.).

    PubMed

    Nie, Shanshan; Xu, Liang; Wang, Yan; Huang, Danqiong; Muleke, Everlyne M; Sun, Xiaochuan; Wang, Ronghua; Xie, Yang; Gong, Yiqin; Liu, Liwang

    2015-09-15

    MicroRNAs (miRNAs) play vital regulatory roles in plant growth and development. The phase transition from vegetative growth to flowering is crucial in the life cycle of plants. To date, miRNA-mediated flowering regulatory networks remain largely unexplored in radish. In this study, two small RNA libraries from radish leaves at vegetative and reproductive stages were constructed and sequenced by Solexa sequencing. A total of 94 known miRNAs representing 21 conserved and 13 non-conserved miRNA families, and 44 potential novel miRNAs, were identified from the two libraries. In addition, 42 known and 17 novel miRNAs were significantly differentially expressed and identified as bolting-related miRNAs. RT-qPCR analysis revealed that some miRNAs exhibited tissue- or developmental stage-specific expression patterns. Moreover, 154 target transcripts were identified for 50 bolting-related miRNAs, which were predominately involved in plant development, signal transduction and transcriptional regulation. Based on the characterization of bolting-related miRNAs and their target genes, a putative schematic model of miRNA-mediated bolting and flowering regulatory network was proposed. These results could provide insights into bolting and flowering regulatory networks in radish, and facilitate dissecting the molecular mechanisms underlying bolting and flowering time regulation in vegetable crops.

  5. Identification of bolting-related microRNAs and their targets reveals complex miRNA-mediated flowering-time regulatory networks in radish (Raphanus sativus L.)

    PubMed Central

    Nie, Shanshan; Xu, Liang; Wang, Yan; Huang, Danqiong; Muleke, Everlyne M.; Sun, Xiaochuan; Wang, Ronghua; Xie, Yang; Gong, Yiqin; Liu, Liwang

    2015-01-01

    MicroRNAs (miRNAs) play vital regulatory roles in plant growth and development. The phase transition from vegetative growth to flowering is crucial in the life cycle of plants. To date, miRNA-mediated flowering regulatory networks remain largely unexplored in radish. In this study, two small RNA libraries from radish leaves at vegetative and reproductive stages were constructed and sequenced by Solexa sequencing. A total of 94 known miRNAs representing 21 conserved and 13 non-conserved miRNA families, and 44 potential novel miRNAs, were identified from the two libraries. In addition, 42 known and 17 novel miRNAs were significantly differentially expressed and identified as bolting-related miRNAs. RT-qPCR analysis revealed that some miRNAs exhibited tissue- or developmental stage-specific expression patterns. Moreover, 154 target transcripts were identified for 50 bolting-related miRNAs, which were predominately involved in plant development, signal transduction and transcriptional regulation. Based on the characterization of bolting-related miRNAs and their target genes, a putative schematic model of miRNA-mediated bolting and flowering regulatory network was proposed. These results could provide insights into bolting and flowering regulatory networks in radish, and facilitate dissecting the molecular mechanisms underlying bolting and flowering time regulation in vegetable crops. PMID:26369897

  6. A comparison of directed search target detection versus in-scene target detection in Worldview-2 datasets

    NASA Astrophysics Data System (ADS)

    Grossman, S.

    2015-05-01

    Since the events of September 11, 2001, the intelligence focus has moved from large order-of-battle targets to small targets of opportunity. Additionally, the business community has discovered the use of remotely sensed data to anticipate demand and derive data on their competition. This requires the finer spectral and spatial fidelity now available to recognize those targets. This work hypothesizes that directed searches using calibrated data perform at least as well as inscene manually intensive target detection searches. It uses calibrated Worldview-2 multispectral images with NEF generated signatures and standard detection algorithms to compare bespoke directed search capabilities against ENVI™ in-scene search capabilities. Multiple execution runs are performed at increasing thresholds to generate detection rates. These rates are plotted and statistically analyzed. While individual head-to-head comparison results vary, 88% of the directed searches performed at least as well as in-scene searches with 50% clearly outperforming in-scene methods. The results strongly support the premise that directed searches perform at least as well as comparable in-scene searches.

  7. Forest water quality protection: A comparison of regulatory and voluntary programs

    SciTech Connect

    Hawks, L.J. ); Cubbage, F.W. ); Haney, H.L. Jr.; Shaffer, R.M. ); Newman, D.H. )

    1993-05-01

    Based on the legislative manadates, states have taken a number of approaches to implement forest water quality protection. This study compares in detail Maryland's primarily regulatory approach to forestry pollution control with the voluntary approach used in Virginia. The investigators found no direct evidence to suggest that either state's approach is better at obtaining best management practice (BMP) compliance, both seemingly reasonably effective. Ease of administration by government agencies and ease of compliance for private landowners and loggers gives a significant edge to Virginia. Maryland's per unit costs are higher, but the harvest was one fifth of Virginia and the approach a much broader one. These and other comparative factors, briefly listed, should be considered when choosing appropriate government policies for forest resource and water quality protection. 15 refs., 4 tabs.

  8. PBT assessment using the revised annex XIII of REACH: a comparison with other regulatory frameworks.

    PubMed

    Moermond, Caroline T A; Janssen, Martien P M; de Knecht, Joop A; Montforts, Mark H M M; Peijnenburg, Willie J G M; Zweers, Patrick G P C; Sijm, Dick T H M

    2012-04-01

    There is no uniform Persistent, Bioaccumulative, Toxic (PBT) or very Persistent, very Bioaccumulative (vPvB) assessment of chemicals in Europe, as the various regulatory frameworks use only limited or dissimilar PBT assessments, or none at all. The European REACH Regulation requires a PBT/vPvB assessment for all chemical substances that are produced within or imported into the EU in amounts exceeding 10 tonnes per year, using the criteria as described in REACH Annex XIII. However, not all substances on the EU market need to be screened according to these criteria under REACH. For a number of substances, such as those imported or produced in lower volumes, there is no REACH requirement, and for human and veterinary medicinal products, biocides, plant protection products, and food and feed additives, other EU legislation is in force to regulate their marketing and use. Compounds may also be screened for PBT properties within international agreements, such as the Oslo Paris Convention (OSPAR), the IMO Ballast Water Management Convention, the UNECE POP Protocol, and the UNEP Stockholm Convention on Persistent Organic Pollutants (POPs), which all have their own set of PBT or POP criteria. This study compares the PBT/vPvB assessment under REACH with PBT or POP assessments performed within other regulatory frameworks. Attention is paid to the process of PBT/vPvB/POP identification and which legislative steps can be taken if the PBT/vPvB/POP status is assigned. In addition to the different PBT or POP criteria of the various frameworks, descriptions of these criteria and approaches for application of weight of evidence also vary. Some EU frameworks still refer to the criteria in the former Technical Guidance Documents (TGD) of 2003, which preceded REACH. Although differences between the old TGD criteria and those in the REACH Annex XIII are small, this does cause dissimilarities among the frameworks. The risk management follow-up of a PBT or vPvB identification, which may

  9. Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network

    PubMed Central

    Chassaing, Nicolas; Davis, Erica E.; McKnight, Kelly L.; Niederriter, Adrienne R.; Causse, Alexandre; David, Véronique; Desmaison, Annaïck; Lamarre, Sophie; Vincent-Delorme, Catherine; Pasquier, Laurent; Coubes, Christine; Lacombe, Didier; Rossi, Massimiliano; Dufier, Jean-Louis; Dollfus, Helene; Kaplan, Josseline; Katsanis, Nicholas; Etchevers, Heather C.; Faguer, Stanislas; Calvas, Patrick

    2016-01-01

    Ocular developmental anomalies (ODA) such as anophthalmia/microphthalmia (AM) or anterior segment dysgenesis (ASD) have an estimated combined prevalence of 3.7 in 10,000 births. Mutations in SOX2 are the most frequent contributors to severe ODA, yet account for a minority of the genetic drivers. To identify novel ODA loci, we conducted targeted high-throughput sequencing of 407 candidate genes in an initial cohort of 22 sporadic ODA patients. Patched 1 (PTCH1), an inhibitor of sonic hedgehog (SHH) signaling, harbored an enrichment of rare heterozygous variants in comparison to either controls, or to the other candidate genes (four missense and one frameshift); targeted resequencing of PTCH1 in a second cohort of 48 ODA patients identified two additional rare nonsynonymous changes. Using multiple transient models and a CRISPR/Cas9-generated mutant, we show physiologically relevant phenotypes altering SHH signaling and eye development upon abrogation of ptch1 in zebrafish for which in vivo complementation assays using these models showed that all six patient missense mutations affect SHH signaling. Finally, through transcriptomic and ChIP analyses, we show that SOX2 binds to an intronic domain of the PTCH1 locus to regulate PTCH1 expression, findings that were validated both in vitro and in vivo. Together, these results demonstrate that PTCH1 mutations contribute to as much as 10% of ODA, identify the SHH signaling pathway as a novel effector of SOX2 activity during human ocular development, and indicate that ODA is likely the result of overactive SHH signaling in humans harboring mutations in either PTCH1 or SOX2. PMID:26893459

  10. Identifying targets of multiple co-regulating transcription factors from expression time-series by Bayesian model comparison

    PubMed Central

    2012-01-01

    Background Complete transcriptional regulatory network inference is a huge challenge because of the complexity of the network and sparsity of available data. One approach to make it more manageable is to focus on the inference of context-specific networks involving a few interacting transcription factors (TFs) and all of their target genes. Results We present a computational framework for Bayesian statistical inference of target genes of multiple interacting TFs from high-throughput gene expression time-series data. We use ordinary differential equation models that describe transcription of target genes taking into account combinatorial regulation. The method consists of a training and a prediction phase. During the training phase we infer the unobserved TF protein concentrations on a subnetwork of approximately known regulatory structure. During the prediction phase we apply Bayesian model selection on a genome-wide scale and score all alternative regulatory structures for each target gene. We use our methodology to identify targets of five TFs regulating Drosophila melanogaster mesoderm development. We find that confident predicted links between TFs and targets are significantly enriched for supporting ChIP-chip binding events and annotated TF-gene interations. Our method statistically significantly outperforms existing alternatives. Conclusions Our results show that it is possible to infer regulatory links between multiple interacting TFs and their target genes even from a single relatively short time series and in presence of unmodelled confounders and unreliable prior knowledge on training network connectivity. Introducing data from several different experimental perturbations significantly increases the accuracy. PMID:22647244

  11. Human Regulatory Protein Ki-1/57 Is a Target of SUMOylation and Affects PML Nuclear Body Formation.

    PubMed

    Saito, Ângela; Souza, Edmarcia E; Costa, Fernanda C; Meirelles, Gabriela V; Gonçalves, Kaliandra A; Santos, Marcos T; Bressan, Gustavo C; McComb, Mark E; Costello, Catherine E; Whelan, Stephen A; Kobarg, Jörg

    2017-09-01

    Ki-1/57 is a nuclear and cytoplasmic regulatory protein first identified in malignant cells from Hodgkin's lymphoma. It is involved in gene expression regulation on both transcriptional and mRNA metabolism levels. Ki-1/57 belongs to the family of intrinsically unstructured proteins and undergoes phosphorylation by PKC and methylation by PRMT1. Previous characterization of its protein interaction profile by yeast two-hybrid screening showed that Ki-1/57 interacts with proteins of the SUMOylation machinery, the SUMO E2 conjugating enzyme UBC9 and the SUMO E3 ligase PIAS3, which suggested that Ki-1/57 could be involved with this process. Here we identified seven potential SUMO target sites (lysine residues) on Ki-1/57 sequence and observed that Ki-1/57 is modified by SUMO proteins in vitro and in vivo. We showed that SUMOylation of Ki-1/57 occurred on lysines 213, 276, and 336. In transfected cells expressing FLAG-Ki-1/57 wild-type, its paralog FLAG-CGI-55 wild-type, or their non-SUMOylated triple mutants, the number of PML-nuclear bodies (PML-NBs) is reduced compared with the control cells not expressing the constructs. More interestingly, after treating cells with arsenic trioxide (As2O3), the number of PML-NBs is no longer reduced when the non-SUMOylated triple mutant Ki-1/57 is expressed, suggesting that the SUMOylation of Ki-1/57 has a role in the control of As2O3-induced PML-NB formation. A proteome-wide analysis of Ki-1/57 partners in the presence of either SUMO-1 or SUMO-2 suggests that the involvement of Ki-1/57 with the regulation of gene expression is independent of the presence of either SUMO-1 or SUMO-2; however, the presence of SUMO-1 strongly influences the interaction of Ki-1/57 with proteins associated with cellular metabolism, maintenance, and cell cycle.

  12. Characterization of regulatory mechanism of Poncirus trifoliata microRNAs on their target genes with an integrated strategy of newly developed PPM-RACE and RLM-RACE.

    PubMed

    Shangguan, Lingfei; Song, Changnian; Han, Jian; Leng, Xiangpeng; Kibet, Korir Nicholas; Mu, Qian; Kayesh, Emrul; Fang, Jinggui

    2014-02-01

    MicroRNAs (miRNAs) play an important role in post-transcriptional gene regulation that involved various biological and metabolic processes. Many extensive studies have been done in model plant species, to discover miRNAs' regulating expression of their target genes and analyze their functions. But, the function of Poncirus trifoliata miRNAs has not been properly investigated. In this study, we employed the RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-RACE) and the newly developed method called poly (A) polymerase-mediated 3' rapid amplification of cDNA ends (PPM-RACE), which mapped the cleavage site of target mRNAs and detected expression patterns of cleaved fragments that could in turn indicate the regulatory functions of the miRNAs on their target genes. Furthermore, the spatiotemporal expression levels of target genes were analyzed by qRT-PCR, with exhibiting different expression trends from their corresponding miRNAs, thus indicating the cleavage mode of miRNAs on their target genes. The expression patterns of miRNAs, their target mRNAs and cleaved target mRNAs in different organs of juvenile and adult trifoliate orange were studied. The results showed that the expression of miRNAs and their target mRNAs was in a trade-off trend. When the miRNA expression was high, its corresponding target mRNA expression was low, while the cleaved target mRNA expression was high; when the miRNA expression was low, its target mRNA expression was high, while the expression of cleaved target mRNAs follows that of the miRNA. The validation of the cleavage site of target mRNAs and the detection of expression patterns of cleaved fragments can further broaden the knowledge of small RNA-mediated regulation in P. trifoliate.

  13. Comparison of circulating and intratumoral regulatory T cells in patients with renal cell carcinoma.

    PubMed

    Asma, Gati; Amal, Gorrab; Raja, Marrakchi; Amine, Derouiche; Mohammed, Chebil; Amel, Ben Ammar Elgaaied

    2015-05-01

    The clear evidence that tumor-infiltrating lymphocytes (TIL) exists in the tumor microenvironment raises the question why renal cell carcinoma (RCC) progresses. Numerous studies support the implication of CD4(+)CD25(high) regulatory T (Treg) cells in RCC development. We aimed in this study to characterize the phenotype and function of circulating and intratumoral Treg cells of RCC patient in order to evaluate their implication in the inhibition of the local antitumor immune response. Our results demonstrate that the proportion of Treg in TIL was, in average, similar to that found in circulating CD4(+) T cells of patients or healthy donors. However, intratumoral Treg exhibit a marked different phenotype when compared with the autologous circulating Treg. A higher CD25 mean level, HLA-DR, Fas, and GITR, and a lower CD45RA expression were observed in intratumoral Treg, suggesting therefore that these cells are effector in the tumor microenvironment. Additionally, intratumoral Treg showed a higher inhibitory function on autologous CD4(+)CD25(-) T cells when compared with circulating Treg that may be explained by an overexpression of FoxP3 transcription factor. These findings suggest that intratumoral Treg could be major actors in the impairment of local antitumor immune response for RCC patients.

  14. Quantitative Comparison of Tumor Delivery for Multiple Targeted Nanoparticles Simultaneously by Multiplex ICP-MS

    PubMed Central

    Elias, Andrew; Crayton, Samuel H.; Warden-Rothman, Robert; Tsourkas, Andrew

    2014-01-01

    Given the rapidly expanding library of disease biomarkers and targeting agents, the number of unique targeted nanoparticles is growing exponentially. The high variability and expense of animal testing often makes it unfeasible to examine this large number of nanoparticles in vivo. This often leads to the investigation of a single formulation that performed best in vitro. However, nanoparticle performance in vivo depends on many variables, many of which cannot be adequately assessed with cell-based assays. To address this issue, we developed a lanthanide-doped nanoparticle method that allows quantitative comparison of multiple targeted nanoparticles simultaneously. Specifically, superparamagnetic iron oxide (SPIO) nanoparticles with different targeting ligands were created, each with a unique lanthanide dopant. Following the simultaneous injection of the various SPIO compositions into tumor-bearing mice, inductively coupled plasma mass spectroscopy was used to quantitatively and orthogonally assess the concentration of each SPIO composition in serial blood and resected tumor samples. PMID:25068300

  15. Quantitative Comparison of Tumor Delivery for Multiple Targeted Nanoparticles Simultaneously by Multiplex ICP-MS

    NASA Astrophysics Data System (ADS)

    Elias, Andrew; Crayton, Samuel H.; Warden-Rothman, Robert; Tsourkas, Andrew

    2014-07-01

    Given the rapidly expanding library of disease biomarkers and targeting agents, the number of unique targeted nanoparticles is growing exponentially. The high variability and expense of animal testing often makes it unfeasible to examine this large number of nanoparticles in vivo. This often leads to the investigation of a single formulation that performed best in vitro. However, nanoparticle performance in vivo depends on many variables, many of which cannot be adequately assessed with cell-based assays. To address this issue, we developed a lanthanide-doped nanoparticle method that allows quantitative comparison of multiple targeted nanoparticles simultaneously. Specifically, superparamagnetic iron oxide (SPIO) nanoparticles with different targeting ligands were created, each with a unique lanthanide dopant. Following the simultaneous injection of the various SPIO compositions into tumor-bearing mice, inductively coupled plasma mass spectroscopy was used to quantitatively and orthogonally assess the concentration of each SPIO composition in serial blood and resected tumor samples.

  16. Comparison of simulated pesticide concentrations in surface drinking water with monitoring data: explanations for observed differences and proposals for a new regulatory modeling approach.

    PubMed

    Winchell, Michael F; Snyder, Nathan J

    2014-01-15

    A primary component to human health risk assessments required by the U.S. Environmental Protection Agency in the registration of pesticides is an estimation of concentrations in surface drinking water predicted by environmental models. The assumptions used in the current regulatory modeling approach are designed to be "conservative", resulting in higher predicted pesticide concentrations than would actually occur in the environment. This paper compiles previously reported modeling and monitoring comparisons and shows that current regulatory modeling methods result in predictions that universally exceed observed concentrations from the upper end of their distributions. In 50% of the modeling/monitoring comparisons, model predictions were more than 229 times greater than the observations, while, in 25% of the comparisons, model predictions were more than 4500 times greater than the observations. The causes for these overpredictions are identified, followed by suggestions for alternative modeling approaches that would result in predictions of pesticide concentrations closer to those observed.

  17. LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks

    PubMed Central

    Contreras-Riquelme, Sebastián; Dominguez, Calixto; Perez-Acle, Tomas

    2017-01-01

    One of the main challenges of the post-genomic era is the understanding of how gene expression is controlled. Changes in gene expression lay behind diverse biological phenomena such as development, disease and the adaptation to different environmental conditions. Despite the availability of well-established methods to identify these changes, tools to discern how gene regulation is orchestrated are still required. The regulation of gene expression is usually depicted as a Gene Regulatory Network (GRN) where changes in the network structure (i.e., network topology) represent adjustments of gene regulation. Like other networks, GRNs are composed of basic building blocks; small induced subgraphs called graphlets. Here we present LoTo, a novel method that using Graphlet Based Metrics (GBMs) identifies topological variations between different states of a GRN. Under our approach, different states of a GRN are analyzed to determine the types of graphlet formed by all triplets of nodes in the network. Subsequently, graphlets occurring in a state of the network are compared to those formed by the same three nodes in another version of the network. Once the comparisons are performed, LoTo applies metrics from binary classification problems calculated on the existence and absence of graphlets to assess the topological similarity between both network states. Experiments performed on randomized networks demonstrate that GBMs are more sensitive to topological variation than the same metrics calculated on single edges. Additional comparisons with other common metrics demonstrate that our GBMs are capable to identify nodes whose local topology changes between different states of the network. Notably, due to the explicit use of graphlets, LoTo captures topological variations that are disregarded by other approaches. LoTo is freely available as an online web server at http://dlab.cl/loto. PMID:28265516

  18. LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks.

    PubMed

    Martin, Alberto J; Contreras-Riquelme, Sebastián; Dominguez, Calixto; Perez-Acle, Tomas

    2017-01-01

    One of the main challenges of the post-genomic era is the understanding of how gene expression is controlled. Changes in gene expression lay behind diverse biological phenomena such as development, disease and the adaptation to different environmental conditions. Despite the availability of well-established methods to identify these changes, tools to discern how gene regulation is orchestrated are still required. The regulation of gene expression is usually depicted as a Gene Regulatory Network (GRN) where changes in the network structure (i.e., network topology) represent adjustments of gene regulation. Like other networks, GRNs are composed of basic building blocks; small induced subgraphs called graphlets. Here we present LoTo, a novel method that using Graphlet Based Metrics (GBMs) identifies topological variations between different states of a GRN. Under our approach, different states of a GRN are analyzed to determine the types of graphlet formed by all triplets of nodes in the network. Subsequently, graphlets occurring in a state of the network are compared to those formed by the same three nodes in another version of the network. Once the comparisons are performed, LoTo applies metrics from binary classification problems calculated on the existence and absence of graphlets to assess the topological similarity between both network states. Experiments performed on randomized networks demonstrate that GBMs are more sensitive to topological variation than the same metrics calculated on single edges. Additional comparisons with other common metrics demonstrate that our GBMs are capable to identify nodes whose local topology changes between different states of the network. Notably, due to the explicit use of graphlets, LoTo captures topological variations that are disregarded by other approaches. LoTo is freely available as an online web server at http://dlab.cl/loto.

  19. Assessment of the Regulatory Methods for the Comparison of Highly Variable Dissolution Profiles.

    PubMed

    Mangas-Sanjuan, Victor; Colon-Useche, Sarin; Gonzalez-Alvarez, Isabel; Bermejo, Marival; Garcia-Arieta, Alfredo

    2016-11-01

    The objective is to compare the performance of dissolution-profile comparison methods when f 2 is inadequate due to high variability. The 90% confidence region of the Mahalanobis distance and the 90% bootstrap confidence interval (CI) of the f 2 similarity factor (f 2-bootstrap) were explored. A modification of the Mahalanobis distance (new D-Mahalanobis) in which those points >85% were not taken into account for calculation was also used. A population kinetic approach in NONMEM was used to simulate dissolution profiles with the first-order or Weibull kinetic models. The scenarios were designed to have clearly similar, clearly non-similar or borderline situations. Four different conditions of variability were established: high (CV = 20%) and low variability (CV = 5%) for inter-tablet (IIV) and inter-batch variability (IBV) associated to the dissolution parameters (k d or MDT) using an exponential model. Forty-four (44) scenarios were simulated, considering different combinations of IIV, IBV and typical dissolution parameters. The dissolution profiles simulated using a first-order model modified the profile slope. The Weibull model allows profiles with different shapes and asymptotes and crossing each other. The results show that the f 2-bootstrap is the most adequate method in cases of high variability. The method based on the 90% confidence region of the Mahalanobis distance (D-Mahalanobis) is not able to detect large differences that can be detected simply with f 2 (i.e. low specificity and positive predictive value due to false positives). The new D-Mahalanobis exhibits superior sensitivity to detect differences (i.e. specificity as a diagnostic test), but it is not as good as the f 2-bootstrap method.

  20. Comparison of Stack Measurement Data from R&D Facilities to Regulatory Criteria. A Case Study from PNNL

    SciTech Connect

    Ballinger, Marcel Y.; Duchsherer, Cheryl J.; Woodruff, Rodger K.; Larson, Timothy V.

    2013-10-30

    Chemical emissions from research and development (R&D) activities are difficult to estimate because of the large number of chemicals used and the potential for continual changes in processes. In this case study, stack measurements taken from R&D facilities at Pacific Northwest National Laboratory (PNNL) were examined, including extreme worst-case emissions estimates and alternate analyses using a Monte Carlo method that takes into account the full distribution of sampling results. The results from these analyses were then compared to emissions estimated from chemical inventories. Results showed that downwind ambient air concentrations calculated from the stack measurement data were below acceptable source impact levels (ASILs) for almost all compounds, even under extreme worst-case analyses. However, for compounds with averaging periods of a year, the unrealistic but simplifying extreme worst-case analysis often resulted in exceedances of lower level regulatory criteria used to determine modeling requirements or to define trivial releases. Compounds with 24-hour averaging periods were nearly all several orders of magnitude below all, including the trivial release, criteria. The alternate analysis supplied a more realistic basis of comparison and an ability to explore effects under different operational modes.

  1. Identification of Submergence-Responsive MicroRNAs and Their Targets Reveals Complex MiRNA-Mediated Regulatory Networks in Lotus (Nelumbo nucifera Gaertn)

    PubMed Central

    Jin, Qijiang; Xu, Yingchun; Mattson, Neil; Li, Xin; Wang, Bei; Zhang, Xiao; Jiang, Hongwei; Liu, Xiaojing; Wang, Yanjie; Yao, Dongrui

    2017-01-01

    MicroRNAs (miRNAs) are endogenous non-coding RNAs with important regulatory functions in plant development and stress responses. However, their population abundance in lotus (Nelumbo nucifera Gaertn) has so far been poorly described, particularly in response to stresses. In this work, submergence-related miRNAs and their target genes were systematically identified, compared, and validated at the transcriptome-wide level using high-throughput sequencing data of small RNA, Mrna, and the degradome. A total of 128 known and 20 novel miRNAs were differentially expressed upon submergence. We identified 629 target transcripts for these submergence-responsive miRNAs. Based on the miRNA expression profiles and GO and KEGG annotation of miRNA target genes, we suggest possible molecular responses and physiological changes of lotus in response to submergence. Several metabolic, physiological and morphological adaptations-related miRNAs, i.e., NNU_far-miR159, NNU_gma-miR393h, and NNU_aly-miR319c-3p, were found to play important regulatory roles in lotus response to submergence. This work will contribute to a better understanding of miRNA-regulated adaption responses of lotus to submergence stress. PMID:28149304

  2. Establishing a Framework for the Ad/Abaxial Regulatory Network of Arabidopsis: Ascertaining Targets of Class III HOMEODOMAIN LEUCINE ZIPPER and KANADI Regulation[W

    PubMed Central

    Reinhart, Brenda J.; Liu, Tie; Newell, Nicole R.; Magnani, Enrico; Huang, Tengbo; Kerstetter, Randall; Michaels, Scott; Barton, M. Kathryn

    2013-01-01

    The broadly conserved Class III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) and KANADI transcription factors have opposing and transformational effects on polarity and growth in all tissues and stages of the plant's life. To obtain a comprehensive understanding of how these factors work, we have identified transcripts that change in response to induced HD-ZIPIII or KANADI function. Additional criteria used to identify high-confidence targets among this set were presence of an adjacent HD-ZIPIII binding site, expression enriched within a subdomain of the shoot apical meristem, mutant phenotype showing defect in polar leaf and/or meristem development, physical interaction between target gene product and HD-ZIPIII protein, opposite regulation by HD-ZIPIII and KANADI, and evolutionary conservation of the regulator–target relationship. We find that HD-ZIPIII and KANADI regulate tissue-specific transcription factors involved in subsidiary developmental decisions, nearly all major hormone pathways, and new actors (such as INDETERMINATE DOMAIN4) in the ad/abaxial regulatory network. Multiple feedback loops regulating HD-ZIPIII and KANADI are identified, as are mechanisms through which HD-ZIPIII and KANADI oppose each other. This work lays the foundation needed to understand the components, structure, and workings of the ad/abaxial regulatory network directing basic plant growth and development. PMID:24076978

  3. Establishing a framework for the Ad/abaxial regulatory network of Arabidopsis: ascertaining targets of class III homeodomain leucine zipper and KANADI regulation.

    PubMed

    Reinhart, Brenda J; Liu, Tie; Newell, Nicole R; Magnani, Enrico; Huang, Tengbo; Kerstetter, Randall; Michaels, Scott; Barton, M Kathryn

    2013-09-01

    The broadly conserved Class III homeodomain leucine zipper (HD-ZIPIII) and KANADI transcription factors have opposing and transformational effects on polarity and growth in all tissues and stages of the plant's life. To obtain a comprehensive understanding of how these factors work, we have identified transcripts that change in response to induced HD-ZIPIII or KANADI function. Additional criteria used to identify high-confidence targets among this set were presence of an adjacent HD-ZIPIII binding site, expression enriched within a subdomain of the shoot apical meristem, mutant phenotype showing defect in polar leaf and/or meristem development, physical interaction between target gene product and HD-ZIPIII protein, opposite regulation by HD-ZIPIII and KANADI, and evolutionary conservation of the regulator-target relationship. We find that HD-ZIPIII and KANADI regulate tissue-specific transcription factors involved in subsidiary developmental decisions, nearly all major hormone pathways, and new actors (such as indeterminate domain4) in the ad/abaxial regulatory network. Multiple feedback loops regulating HD-ZIPIII and KANADI are identified, as are mechanisms through which HD-ZIPIII and KANADI oppose each other. This work lays the foundation needed to understand the components, structure, and workings of the ad/abaxial regulatory network directing basic plant growth and development.

  4. In-Depth Proteome Analysis of Arabidopsis Leaf Peroxisomes Combined with in Vivo Subcellular Targeting Verification Indicates Novel Metabolic and Regulatory Functions of Peroxisomes1[W][OA

    PubMed Central

    Reumann, Sigrun; Quan, Sheng; Aung, Kyaw; Yang, Pingfang; Manandhar-Shrestha, Kalpana; Holbrook, Danielle; Linka, Nicole; Switzenberg, Robert; Wilkerson, Curtis G.; Weber, Andreas P.M.; Olsen, Laura J.; Hu, Jianping

    2009-01-01

    Peroxisomes are metabolically diverse organelles with essential roles in plant development. The major protein constituents of plant peroxisomes are well characterized, whereas only a few low-abundance and regulatory proteins have been reported to date. We performed an in-depth proteome analysis of Arabidopsis (Arabidopsis thaliana) leaf peroxisomes using one-dimensional gel electrophoresis followed by liquid chromatography and tandem mass spectrometry. We detected 65 established plant peroxisomal proteins, 30 proteins whose association with Arabidopsis peroxisomes had been previously demonstrated only by proteomic data, and 55 putative novel proteins of peroxisomes. We subsequently tested the subcellular targeting of yellow fluorescent protein fusions for selected proteins and confirmed the peroxisomal localization for 12 proteins containing predicted peroxisome targeting signals type 1 or 2 (PTS1/2), three proteins carrying PTS-related peptides, and four proteins that lack conventional targeting signals. We thereby established the tripeptides SLM> and SKV> (where > indicates the stop codon) as new PTS1s and the nonapeptide RVx5HF as a putative new PTS2. The 19 peroxisomal proteins conclusively identified from this study potentially carry out novel metabolic and regulatory functions of peroxisomes. Thus, this study represents an important step toward defining the complete plant peroxisomal proteome. PMID:19329564

  5. A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein fur.

    PubMed

    Yu, Chunxiao; Lopez, Carlos A; Hu, Han; Xia, Yu; Freedman, David S; Reddington, Alexander P; Daaboul, George G; Unlü, M Selim; Genco, Caroline Attardo

    2014-01-01

    The Ferric uptake regulatory protein (Fur) is a transcriptional regulatory protein that functions to control gene transcription in response to iron in a number of pathogenic bacteria. In this study, we applied a label-free, quantitative and high-throughput analysis method, Interferometric Reflectance Imaging Sensor (IRIS), to rapidly characterize Fur-DNA interactions in vitro with predicted Fur binding sequences in the genome of Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhea. IRIS can easily be applied to examine multiple protein-protein, protein-nucleotide and nucleotide-nucleotide complexes simultaneously and demonstrated here that seventy percent of the predicted Fur boxes in promoter regions of iron-induced genes bound to Fur in vitro with a range of affinities as observed using this microarray screening technology. Combining binding data with mRNA expression levels in a gonococcal fur mutant strain allowed us to identify five new gonococcal genes under Fur-mediated direct regulation.

  6. Development of a software for quantitative evaluation radiotherapy target and organ-at-risk segmentation comparison.

    PubMed

    Kalpathy-Cramer, Jayashree; Awan, Musaddiq; Bedrick, Steven; Rasch, Coen R N; Rosenthal, David I; Fuller, Clifton D

    2014-02-01

    Modern radiotherapy requires accurate region of interest (ROI) inputs for plan optimization and delivery. Target delineation, however, remains operator-dependent and potentially serves as a major source of treatment delivery error. In order to optimize this critical, yet observer-driven process, a flexible web-based platform for individual and cooperative target delineation analysis and instruction was developed in order to meet the following unmet needs: (1) an open-source/open-access platform for automated/semiautomated quantitative interobserver and intraobserver ROI analysis and comparison, (2) a real-time interface for radiation oncology trainee online self-education in ROI definition, and (3) a source for pilot data to develop and validate quality metrics for institutional and cooperative group quality assurance efforts. The resultant software, Target Contour Testing/Instructional Computer Software (TaCTICS), developed using Ruby on Rails, has since been implemented and proven flexible, feasible, and useful in several distinct analytical and research applications.

  7. i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly.

    PubMed

    Imrichová, Hana; Hulselmans, Gert; Atak, Zeynep Kalender; Potier, Delphine; Aerts, Stein

    2015-07-01

    i-cisTarget is a web tool to predict regulators of a set of genomic regions, such as ChIP-seq peaks or co-regulated/similar enhancers. i-cisTarget can also be used to identify upstream regulators and their target enhancers starting from a set of co-expressed genes. Whereas the original version of i-cisTarget was focused on Drosophila data, the 2015 update also provides support for human and mouse data. i-cisTarget detects transcription factor motifs (position weight matrices) and experimental data tracks (e.g. from ENCODE, Roadmap Epigenomics) that are enriched in the input set of regions. As experimental data tracks we include transcription factor ChIP-seq data, histone modification ChIP-seq data and open chromatin data. The underlying processing method is based on a ranking-and-recovery procedure, allowing accurate determination of enrichment across heterogeneous datasets, while also discriminating direct from indirect target regions through a 'leading edge' analysis. We illustrate i-cisTarget on various Ewing sarcoma datasets to identify EWS-FLI1 targets starting from ChIP-seq, differential ATAC-seq, differential H3K27ac and differential gene expression data. Use of i-cisTarget is free and open to all, and there is no login requirement. Address: http://gbiomed.kuleuven.be/apps/lcb/i-cisTarget. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Targeted resequencing of regulatory regions at schizophrenia risk loci: Role of rare functional variants at chromatin repressive states.

    PubMed

    González-Peñas, Javier; Amigo, Jorge; Santomé, Luis; Sobrino, Beatriz; Brenlla, Julio; Agra, Santiago; Paz, Eduardo; Páramo, Mario; Carracedo, Ángel; Arrojo, Manuel; Costas, Javier

    2016-07-01

    There is mounting evidence that regulatory variation plays an important role in genetic risk for schizophrenia. Here, we specifically search for regulatory variants at risk by sequencing promoter regions of twenty-three genes implied in schizophrenia by copy number variant or genome-wide association studies. After strict quality control, a total of 55,206bp per sample were analyzed in 526 schizophrenia cases and 516 controls from Galicia, NW Spain, using the Applied Biosystems SOLiD System. Variants were filtered based on frequency from public databases, chromatin states from the RoadMap Epigenomics Consortium at tissues relevant for schizophrenia, such as fetal brain, mid-frontal lobe, and angular gyrus, and prediction of functionality from RegulomeDB. The proportion of rare variants at polycomb repressive chromatin state at relevant tissues was higher in cases than in controls. The proportion of rare variants with predicted regulatory role was significantly higher in cases than in controls (P=0.0028, OR=1.93, 95% C.I.=1.23-3.04). Combination of information from both sources led to the identification of an excess of carriers of rare variants with predicted regulatory role located at polycomb repressive chromatin state at relevant tissues in cases versus controls (P=0.0016, OR=19.34, 95% C.I.=2.45-2495.26). The variants are located at two genes affected by the 17q12 copy number variant, LHX1 and HNF1B. These data strongly suggest that a specific epigenetic mechanism, chromatin remodeling by histone modification during early development, may be impaired in a subset of schizophrenia patients, in agreement with previous data. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Regulatory T Cells, a Potent Immunoregulatory Target for CAM Researchers: Modulating Allergic and Infectious Disease Pathology (II)

    PubMed Central

    Vojdani, Aristo; Erde, Jonathan

    2006-01-01

    Regulatory T (Treg) cells maintain dominant control of immune responses to foreign materials and microbes. Appropriate Treg cell suppression of immune responses is essential for the maintenance of efficacious defensive responses and the limitation of collateral tissue damage due to excess inflammation. Allergy and infection are well studied and frequent afflictions in which Treg cells play an essential role. As such, they provide excellent models to communicate the significance and relevance of Treg cells to complementary and alternative medicine (CAM). PMID:16786050

  10. Target selection and comparison of mission design for space debris removal by DLR's advanced study group

    NASA Astrophysics Data System (ADS)

    van der Pas, Niels; Lousada, Joao; Terhes, Claudia; Bernabeu, Marc; Bauer, Waldemar

    2014-09-01

    Space debris is a growing problem. Models show that the Kessler syndrome, the exponential growth of debris due to collisions, has become unavoidable unless an active debris removal program is initiated. The debris population in LEO with inclination between 60° and 95° is considered as the most critical zone. In order to stabilize the debris population in orbit, especially in LEO, 5 to 10 objects will need to be removed every year. The unique circumstances of such a mission could require that several objects are removed with a single launch. This will require a mission to rendezvous with a multitude of objects orbiting on different altitudes, inclinations and planes. Removal models have assumed that the top priority targets will be removed first. However this will lead to a suboptimal mission design and increase the ΔV-budget. Since there is a multitude of targets to choose from, the targets can be selected for an optimal mission design. In order to select a group of targets for a removal mission the orbital parameters and political constraints should also be taken into account. Within this paper a number of the target selection criteria are presented. The possible mission targets and their order of retrieval is dependent on the mission architecture. A comparison between several global mission architectures is given. Under consideration are 3 global missions of which a number of parameters are varied. The first mission launches multiple separate deorbit kits. The second launches a mother craft with deorbit kits. The third launches an orbital tug which pulls the debris in a lower orbit, after which a deorbit kit performs the final deorbit burn. A RoM mass and cost comparison is presented. The research described in this paper has been conducted as part of an active debris removal study by the Advanced Study Group (ASG). The ASG is an interdisciplinary student group working at the DLR, analyzing existing technologies and developing new ideas into preliminary

  11. A systems biology approach identified different regulatory networks targeted by KSHV miR-K12-11 in B cells and endothelial cells.

    PubMed

    Yang, Yajie; Boss, Isaac W; McIntyre, Lauren M; Renne, Rolf

    2014-08-08

    Kaposi's sarcoma associated herpes virus (KSHV) is associated with tumors of endothelial and lymphoid origin. During latent infection, KSHV expresses miR-K12-11, an ortholog of the human tumor gene hsa-miR-155. Both gene products are microRNAs (miRNAs), which are important post-transcriptional regulators that contribute to tissue specific gene expression. Advances in target identification technologies and molecular interaction databases have allowed a systems biology approach to unravel the gene regulatory networks (GRNs) triggered by miR-K12-11 in endothelial and lymphoid cells. Understanding the tissue specific function of miR-K12-11 will help to elucidate underlying mechanisms of KSHV pathogenesis. Ectopic expression of miR-K12-11 differentially affected gene expression in BJAB cells of lymphoid origin and TIVE cells of endothelial origin. Direct miRNA targeting accounted for a small fraction of the observed transcriptome changes: only 29 genes were identified as putative direct targets of miR-K12-11 in both cell types. However, a number of commonly affected biological pathways, such as carbohydrate metabolism and interferon response related signaling, were revealed by gene ontology analysis. Integration of transcriptome profiling, bioinformatic algorithms, and databases of protein-protein interactome from the ENCODE project identified different nodes of GRNs utilized by miR-K12-11 in a tissue-specific fashion. These effector genes, including cancer associated transcription factors and signaling proteins, amplified the regulatory potential of a single miRNA, from a small set of putative direct targets to a larger set of genes. This is the first comparative analysis of miRNA-K12-11's effects in endothelial and B cells, from tissues infected with KSHV in vivo. MiR-K12-11 was able to broadly modulate gene expression in both cell types. Using a systems biology approach, we inferred that miR-K12-11 establishes its GRN by both repressing master TFs and influencing

  12. A comparison of machine learning techniques for detection of drug target articles.

    PubMed

    Danger, Roxana; Segura-Bedmar, Isabel; Martínez, Paloma; Rosso, Paolo

    2010-12-01

    Important progress in treating diseases has been possible thanks to the identification of drug targets. Drug targets are the molecular structures whose abnormal activity, associated to a disease, can be modified by drugs, improving the health of patients. Pharmaceutical industry needs to give priority to their identification and validation in order to reduce the long and costly drug development times. In the last two decades, our knowledge about drugs, their mechanisms of action and drug targets has rapidly increased. Nevertheless, most of this knowledge is hidden in millions of medical articles and textbooks. Extracting knowledge from this large amount of unstructured information is a laborious job, even for human experts. Drug target articles identification, a crucial first step toward the automatic extraction of information from texts, constitutes the aim of this paper. A comparison of several machine learning techniques has been performed in order to obtain a satisfactory classifier for detecting drug target articles using semantic information from biomedical resources such as the Unified Medical Language System. The best result has been achieved by a Fuzzy Lattice Reasoning classifier, which reaches 98% of ROC area measure.

  13. Cross-talk between freezing response and signaling for regulatory transcriptions of MIR475b and its targets by miR475b promoter in Populus suaveolens

    PubMed Central

    Niu, Jun; Wang, Jia; Hu, Huiwen; Chen, Yinlei; An, Jiyong; Cai, Jian; Sun, Runze; Sheng, Zhongting; Liu, Xieping; Lin, Shanzhi

    2016-01-01

    MicroRNAs (miRNAs) are small, non-coding RNAs that play important roles in post-transcriptional regulation of their target genes, yet the transcriptional regulation of plant miRNAs by promoter is poorly understood. Here, we firstly clone pri-miR475b cDNA and its native promoter from P. suaveolens, and characterize Psu-MIR475b as class-II gene transcribed by RNA polymerase II. By 5′ deletion analysis of Psu-miR475b promoter in a series of promoter-GUS chimeric vectors, we functionally identify three positive regulatory regions and multiple cis-acting elements responsible for Psu-miR475b promoter activity in response to freezing stress and exogenous hormone treatment. Moreover, the Psu-miR475b promoter activity displays a tissue-specific manner, negatively regulated by freezing stress and positively by MeJA, SA or GA treatment. Importantly, we comparatively analyze the time-course transcriptional profiles of Psu-miR475b and its targets in Psu-miR475b over-expression transgenic plants controlled by Psu-miR475b-specific promoter or CaMV 35S constitutive promoter, and explore the regulatory mechanism of Psu-miR475b promoter controlling transcriptional expressions of Psu-MIR475b and its targets in response to freezing stress and exogenous hormone treatment. Our results reveal that Psu-miR475b promoter-mediated transcriptions of Psu-MIR475b and its targets in response to freezing stress may be involved in a cross-talk between freezing response and stress signaling process. PMID:26853706

  14. Cross-talk between freezing response and signaling for regulatory transcriptions of MIR475b and its targets by miR475b promoter in Populus suaveolens.

    PubMed

    Niu, Jun; Wang, Jia; Hu, Huiwen; Chen, Yinlei; An, Jiyong; Cai, Jian; Sun, Runze; Sheng, Zhongting; Liu, Xieping; Lin, Shanzhi

    2016-02-08

    MicroRNAs (miRNAs) are small, non-coding RNAs that play important roles in post-transcriptional regulation of their target genes, yet the transcriptional regulation of plant miRNAs by promoter is poorly understood. Here, we firstly clone pri-miR475b cDNA and its native promoter from P. suaveolens, and characterize Psu-MIR475b as class-II gene transcribed by RNA polymerase II. By 5' deletion analysis of Psu-miR475b promoter in a series of promoter-GUS chimeric vectors, we functionally identify three positive regulatory regions and multiple cis-acting elements responsible for Psu-miR475b promoter activity in response to freezing stress and exogenous hormone treatment. Moreover, the Psu-miR475b promoter activity displays a tissue-specific manner, negatively regulated by freezing stress and positively by MeJA, SA or GA treatment. Importantly, we comparatively analyze the time-course transcriptional profiles of Psu-miR475b and its targets in Psu-miR475b over-expression transgenic plants controlled by Psu-miR475b-specific promoter or CaMV 35S constitutive promoter, and explore the regulatory mechanism of Psu-miR475b promoter controlling transcriptional expressions of Psu-MIR475b and its targets in response to freezing stress and exogenous hormone treatment. Our results reveal that Psu-miR475b promoter-mediated transcriptions of Psu-MIR475b and its targets in response to freezing stress may be involved in a cross-talk between freezing response and stress signaling process.

  15. MicroRNA regulatory pathway analysis identifies miR-142-5p as a negative regulator of TGF-β pathway via targeting SMAD3

    PubMed Central

    Huang, Wei; Liu, Hui; Zhang, Hong-Mei; Li, Qiubai; Chen, Zhichao; Guo, An-Yuan

    2016-01-01

    MicroRNAs (miRNAs) are non-coding RNAs with functions of posttranscriptional regulation. The abnormally expressed miRNAs have been shown to be crucial contributors and may serve as biomarkers in many diseases. However, determining the biological function of miRNAs is an ongoing challenge. By combining miRNA targets prediction, miRNA and mRNA expression profiles in TCGA cancers, and pathway data, we performed a miRNA-pathway regulation inference by Fisher's exact test for enrichment analysis. Then we constructed a database to show the cancer related miRNA-pathway regulatory network (http://bioinfo.life.hust.edu.cn/miR_path). As one of the miRNAs targeting many cancer related pathways, miR-142-5p potentially regulates the maximum number of genes in TGF-β signaling pathway. We experimentally confirmed that miR-142-5p directly targeted and suppressed SMAD3, a key component in TGF-β signaling. Ectopic overexpression of miR-142-5p significantly promoted tumor cell proliferation and inhibited apoptosis, while silencing of miR-142-5p inhibited the tumor cell proliferation and promoted apoptosis in vitro. These findings indicate that miR-142-5p plays as a negative regulator in TGF-β pathway by targeting SMAD3 and suppresses TGF-β-induced growth inhibition in cancer cells. Our study proved the feasibility of miRNA regulatory pathway analysis and shed light on combining bioinformatics with experiments in the research of complex diseases. PMID:27683030

  16. Randomized comparison of universal and targeted HIV screening in the emergency department.

    PubMed

    Lyons, Michael S; Lindsell, Christopher J; Ruffner, Andrew H; Wayne, D Beth; Hart, Kimberly W; Sperling, Matthew I; Trott, Alexander T; Fichtenbaum, Carl J

    2013-11-01

    Universal HIV screening is recommended but challenging to implement. Selectively targeting those at risk is thought to miss cases, but previous studies are limited by narrow risk criteria, incomplete implementation, and absence of direct comparisons. We hypothesized that targeted HIV screening, when fully implemented and using maximally broad risk criteria, could detect nearly as many cases as universal screening with many fewer tests. This single-center cluster-randomized trial compared universal and targeted patient selection for HIV screening in a lower prevalence urban emergency department. Patients were excluded for age (<18 and >64 years), known HIV infection, or previous approach for HIV testing that day. Targeted screening was offered for any risk indicator identified from charts, staff referral, or self-disclosure. Universal screening was offered regardless of risk. Baseline seroprevalence was estimated from consecutive deidentified blood samples. There were 9572 eligible visits during which the patient was approached. For universal screening, 40.8% (1915/4692) consented with 6 being newly diagnosed [0.31%, 95% confidence interval (CI): 0.13% to 0.65%]. For targeted screening, 37% (1813/4880) had no testing indication. Of the 3067 remaining, 47.4% (1454) consented with 3 being newly diagnosed (0.22%, 95% CI: 0.06% to 0.55%). Estimated seroprevalence was 0.36% (95% CI: 0.16% to 0.70%). Targeted screening had a higher proportion consenting (47.4% vs. 40.8%, P < 0.002), but a lower proportion of ED encounters with testing (29.7% vs. 40.7%, P < 0.002). Targeted screening, even when fully implemented with maximally permissive selection, offered no important increase in positivity rate or decrease in tests performed. Universal screening diagnosed more cases, because more were tested, despite a modestly lower consent rate.

  17. Immune Cell Regulatory Pathways Unexplored as Host-Directed Therapeutic Targets for Mycobacterium tuberculosis: An Opportunity to Apply Precision Medicine Innovations to Infectious Diseases

    PubMed Central

    Mahon, Robert N.; Hafner, Richard

    2015-01-01

    The lack of novel antimicrobial drugs in development for tuberculosis treatment has provided an impetus for the discovery of adjunctive host-directed therapies (HDTs). Several promising HDT candidates are being evaluated, but major advancement of tuberculosis HDTs will require understanding of the master or “core” cell signaling pathways that control intersecting immunologic and metabolic regulatory mechanisms, collectively described as “immunometabolism.” Core regulatory pathways conserved in all eukaryotic cells include poly (ADP-ribose) polymerases (PARPs), sirtuins, AMP-activated protein kinase (AMPK), and mechanistic target of rapamycin (mTOR) signaling. Critical interactions of these signaling pathways with each other and their roles as master regulators of immunometabolic functions will be addressed, as well as how Mycobacterium tuberculosis is already known to influence various other cell signaling pathways interacting with them. Knowledge of these essential mechanisms of cell function regulation has led to breakthrough targeted treatment advances for many diseases, most prominently in oncology. Leveraging these exciting advances in precision medicine for the development of innovative next-generation HDTs may lead to entirely new paradigms for treatment and prevention of tuberculosis and other infectious diseases. PMID:26409283

  18. Genome-Wide Characterization of cis-Acting DNA Targets Reveals the Transcriptional Regulatory Framework of Opaque2 in Maize[OPEN

    PubMed Central

    Li, Chaobin; Qiao, Zhenyi; Qi, Weiwei; Wang, Qian; Yuan, Yue; Yang, Xi; Tang, Yuanping; Mei, Bing; Lv, Yuanda; Zhao, Han; Xiao, Han; Song, Rentao

    2015-01-01

    Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we studied the transcriptome of o2 mutants using RNA sequencing (RNA-Seq) and determined O2 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). The RNA-Seq analysis revealed 1605 differentially expressed genes (DEGs) and 383 differentially expressed long, noncoding RNAs. The DEGs cover a wide range of functions related to nutrient reservoir activity, nitrogen metabolism, stress resistance, etc. ChIP-Seq analysis detected 1686 O2 DNA binding sites distributed over 1143 genes. Overlay of the RNA-Seq and ChIP-Seq results revealed 35 O2-modulated target genes. We identified four O2 binding motifs; among them, TGACGTGG appears to be the most conserved and strongest. We confirmed that, except for the 16- and 18-kD zeins, O2 directly regulates expression of all other zeins. O2 directly regulates two transcription factors, genes linked to carbon and amino acid metabolism and abiotic stress resistance. We built a hierarchical regulatory model for O2 that provides an understanding of its pleiotropic biological effects. PMID:25691733

  19. Regulatory T Cells, a Potent Immunoregulatory Target for CAM Researchers: Modulating Tumor Immunity, Autoimmunity and Alloreactive Immunity (III)

    PubMed Central

    Vojdani, Aristo; Erde, Jonathan

    2006-01-01

    Regulatory T (Treg) cells are the major arbiter of immune responses, mediating actions through the suppression of inflammatory and destructive immune reactions. Inappropriate Treg cell frequency or functionality potentiates the pathogenesis of myriad diseases with ranging magnitudes of severity. Lack of suppressive capability hinders restraint on immune responses involved in autoimmunity and alloreactivity, while excessive suppressive capacity effectively blocks processes necessary for tumor destruction. Although the etiology of dysfunctional Treg cell populations is under debate, the ramifications, and their mechanisms, are increasingly brought to light in the medical community. Methods that compensate for aberrant immune regulation may not address the underlying complications; however, they hold promise for the alleviation of debilitating immune system-related disorders. The dominant immunoregulatory nature of Treg cells, coupled with recent mechanistic knowledge of natural immunomodulatory compounds, highlights the importance of Treg cells to practitioners and researchers of complementary and alternative medicine (CAM). PMID:16951715

  20. Advanced regulatory control and coordinated plant-wide control strategies for IGCC targeted towards improving power ramp-rates

    SciTech Connect

    Mahapatra, P.; Zitney, S.

    2012-01-01

    As part of ongoing R&D activities at the National Energy Technology Laboratory's (NETL) Advanced Virtual Energy Simulation Training & Research (AVESTAR™) Center, this paper highlights strategies for enhancing low-level regulatory control and system-wide coordinated control strategies implemented in a high-fidelity dynamic simulator for an Integrated Gasification Combined Cycle (IGCC) power plant with carbon capture. The underlying IGCC plant dynamic model contains 20 major process areas, each of which is tightly integrated with the rest of the power plant, making individual functionally-independent processes prone to routine disturbances. Single-loop feedback control although adequate to meet the primary control objective for most processes, does not take into account in advance the effect of these disturbances, making the entire power plant undergo large offshoots and/or oscillations before the feedback action has an opportunity to impact control performance. In this paper, controller enhancements ranging from retuning feedback control loops, multiplicative feed-forward control and other control techniques such as split-range control, feedback trim and dynamic compensation, applicable on various subsections of the integrated IGCC plant, have been highlighted and improvements in control responses have been given. Compared to using classical feedback-based control structure, the enhanced IGCC regulatory control architecture reduces plant settling time and peak offshoots, achieves faster disturbance rejection, and promotes higher power ramp-rates. In addition, improvements in IGCC coordinated plant-wide control strategies for “Gasifier-Lead”, “GT-Lead” and “Plantwide” operation modes have been proposed and their responses compared. The paper is concluded with a brief discussion on the potential IGCC controller improvements resulting from using advanced process control, including model predictive control (MPC), as a supervisory control layer.

  1. Regulation of the small regulatory RNA MicA by ribonuclease III: a target-dependent pathway

    PubMed Central

    Viegas, Sandra C.; Silva, Inês J.; Saramago, Margarida; Domingues, Susana; Arraiano, Cecília M.

    2011-01-01

    MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the control of free MicA levels in the cell. We purified both Salmonella enzymes and demonstrated that in vitro RNase III is only active over MicA when in complex with its targets (whether ompA or lamB mRNAs). In vivo, MicA is demonstrated to be cleaved by RNase III in a coupled way with ompA mRNA. On the other hand, RNase E is able to cleave unpaired MicA and does not show a marked dependence on its 5′ phosphorylation state. The main conclusion of this work is the existence of two independent pathways for MicA turnover. Each pathway involves a distinct endoribonuclease, having a different role in the context of the fine-tuned regulation of porin levels. Cleavage of MicA by RNase III in a target-dependent fashion, with the concomitant decay of the mRNA target, strongly resembles the eukaryotic RNAi system, where RNase III-like enzymes play a pivotal role. PMID:21138960

  2. Regulation of the small regulatory RNA MicA by ribonuclease III: a target-dependent pathway.

    PubMed

    Viegas, Sandra C; Silva, Inês J; Saramago, Margarida; Domingues, Susana; Arraiano, Cecília M

    2011-04-01

    MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the control of free MicA levels in the cell. We purified both Salmonella enzymes and demonstrated that in vitro RNase III is only active over MicA when in complex with its targets (whether ompA or lamB mRNAs). In vivo, MicA is demonstrated to be cleaved by RNase III in a coupled way with ompA mRNA. On the other hand, RNase E is able to cleave unpaired MicA and does not show a marked dependence on its 5' phosphorylation state. The main conclusion of this work is the existence of two independent pathways for MicA turnover. Each pathway involves a distinct endoribonuclease, having a different role in the context of the fine-tuned regulation of porin levels. Cleavage of MicA by RNase III in a target-dependent fashion, with the concomitant decay of the mRNA target, strongly resembles the eukaryotic RNAi system, where RNase III-like enzymes play a pivotal role.

  3. Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks

    NASA Astrophysics Data System (ADS)

    Nishtala, Sneha; Neelamraju, Yaseswini; Janga, Sarath Chandra

    2016-05-01

    RNA-binding proteins (RBPs) are pivotal in orchestrating several steps in the metabolism of RNA in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Here, we employed CLIP (cross-linking immunoprecipitation)-seq datasets for 60 human RBPs and RIP-ChIP (RNP immunoprecipitation-microarray) data for 69 yeast RBPs to construct a network of genome-wide RBP- target RNA interactions for each RBP. We show in humans that majority (~78%) of the RBPs are strongly associated with their target transcripts at transcript level while ~95% of the studied RBPs were also found to be strongly associated with expression levels of target transcripts when protein expression levels of RBPs were employed. At transcript level, RBP - RNA interaction data for the yeast genome, exhibited a strong association for 63% of the RBPs, confirming the association to be conserved across large phylogenetic distances. Analysis to uncover the features contributing to these associations revealed the number of target transcripts and length of the selected protein-coding transcript of an RBP at the transcript level while intensity of the CLIP signal, number of RNA-Binding domains, location of the binding site on the transcript, to be significant at the protein level. Our analysis will contribute to improved modelling and prediction of post-transcriptional networks.

  4. TTS Mapping: integrative WEB tool for analysis of triplex formation target DNA Sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome

    PubMed Central

    2009-01-01

    Background DNA triplexes can naturally occur, co-localize and interact with many other regulatory DNA elements (e.g. G-quadruplex (G4) DNA motifs), specific DNA-binding proteins (e.g. transcription factors (TFs)), and micro-RNA (miRNA) precursors. Specific genome localizations of triplex target DNA sites (TTSs) may cause abnormalities in a double-helix DNA structure and can be directly involved in some human diseases. However, genome localization of specific TTSs, their interconnection with regulatory DNA elements and physiological roles in a cell are poor defined. Therefore, it is important to identify comprehensive and reliable catalogue of specific potential TTSs (pTTSs) and their co-localization patterns with other regulatory DNA elements in the human genome. Results "TTS mapping" database is a web-based search engine developed here, which is aimed to find and annotate pTTSs within a region of interest of the human genome. The engine provides descriptive statistics of pTTSs in a given region and its sequence context. Different annotation tracks of TTS-overlapping gene region(s), G4 motifs, CpG Island, miRNA precursors, miRNA targets, transcription factor binding sites (TFBSs), Single Nucleotide Polymorphisms (SNPs), small nucleolar RNAs (snoRNA), and repeat elements are also mapped based onto a sequence location provided by UCSC genome browser, G4 database http://www.quadruplex.org and several other datasets. The results pages provide links to UCSC genome browser annotation tracks and relative DBs. BLASTN program was included to check the uniqueness of a given pTTS in the human genome. Recombination- and mutation-prone genes (e.g. EVI-1, MYC) were found to be significantly enriched by TTSs and multiple co-occurring with our regulatory DNA elements. TTS mapping reveals that a high-complementary and evolutionarily conserved polypurine and polypyrimidine DNA sequence pair linked by a non-conserved short DNA sequence can form miR-483 transcribed from intron 2 of

  5. TTS mapping: integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome.

    PubMed

    Jenjaroenpun, Piroon; Kuznetsov, Vladimir A

    2009-12-03

    DNA triplexes can naturally occur, co-localize and interact with many other regulatory DNA elements (e.g. G-quadruplex (G4) DNA motifs), specific DNA-binding proteins (e.g. transcription factors (TFs)), and micro-RNA (miRNA) precursors. Specific genome localizations of triplex target DNA sites (TTSs) may cause abnormalities in a double-helix DNA structure and can be directly involved in some human diseases. However, genome localization of specific TTSs, their interconnection with regulatory DNA elements and physiological roles in a cell are poor defined. Therefore, it is important to identify comprehensive and reliable catalogue of specific potential TTSs (pTTSs) and their co-localization patterns with other regulatory DNA elements in the human genome. "TTS mapping" database is a web-based search engine developed here, which is aimed to find and annotate pTTSs within a region of interest of the human genome. The engine provides descriptive statistics of pTTSs in a given region and its sequence context. Different annotation tracks of TTS-overlapping gene region(s), G4 motifs, CpG Island, miRNA precursors, miRNA targets, transcription factor binding sites (TFBSs), Single Nucleotide Polymorphisms (SNPs), small nucleolar RNAs (snoRNA), and repeat elements are also mapped based onto a sequence location provided by UCSC genome browser, G4 database http://www.quadruplex.org and several other datasets. The results pages provide links to UCSC genome browser annotation tracks and relative DBs. BLASTN program was included to check the uniqueness of a given pTTS in the human genome. Recombination- and mutation-prone genes (e.g. EVI-1, MYC) were found to be significantly enriched by TTSs and multiple co-occurring with our regulatory DNA elements. TTS mapping reveals that a high-complementary and evolutionarily conserved polypurine and polypyrimidine DNA sequence pair linked by a non-conserved short DNA sequence can form miR-483 transcribed from intron 2 of IGF2 gene and bound

  6. Functional screening of guide RNAs targeting the regulatory and structural HIV-1 viral genome for a cure of AIDS.

    PubMed

    Yin, Chaoran; Zhang, Ting; Li, Fang; Yang, Fan; Putatunda, Raj; Young, Won-Bin; Khalili, Kamel; Hu, Wenhui; Zhang, Yonggang

    2016-05-15

    There is an urgent need for the development of HIV-1 genome eradication strategies that lead to a permanent cure for HIV-1/AIDS. We previously reported that four guide RNAs (gRNAs) targeting HIV-1 long terminal repeats (LTR) effectively eradicated the entire HIV-1 genome. In this study, we sought to identify the best gRNAs targeting HIV-1 LTR and viral structural region and optimize gRNA pairing that can efficiently eradicate the HIV-1 genome. Highly specific gRNAs were designed using bioinformatics tools, and their capacity of guiding CRISPR-associated system 9 to cleave HIV-1 proviral DNA was evaluated using high-throughput HIV-1 luciferase reporter assay and rapid Direct-PCR genotyping. The target seed sequences for each gRNA were cloned into lentiviral vectors. HEK293T cells were cotransfected with a pEcoHIV-NL4-3-firefly-luciferase reporter vector (1 : 20) over lentiviral vectors carrying CRISPR-associated system 9 and single gRNA or various combinations of gRNAs. The EcoHIV DNA cleaving efficiency was evaluated by Direct-PCR genotyping, and the EcoHIV transcription/replication activity was examined by a luciferase reporter assay. Most of the designed gRNAs are effective to eliminate the predicted HIV-1 genome sequence between the selected two target sites. This is evidenced by the presence of PCR genotypic deletion/insertion and the decrease of luciferase reporter activity. In particular, a combination of viral structural gRNAs with LTR gRNAs provided a higher efficiency of genome eradication and an easier approach for PCR genotyping. Our screening strategy can specifically and effectively identify gRNAs targeting HIV-1 LTR and structural region to excise proviral HIV-1 from the host genome.

  7. Comparison of FDA Approved Kinase Targets to Clinical Trial Ones: Insights from Their System Profiles and Drug-Target Interaction Networks

    PubMed Central

    Xu, Jingyu; Wang, Panpan; Yang, Hong; Li, Yinghong; Yu, Chunyan; Tian, Yubin

    2016-01-01

    Kinase is one of the most productive classes of established targets, but the majority of approved drugs against kinase were developed only for cancer. Intensive efforts were therefore exerted for releasing its therapeutic potential by discovering new therapeutic area. Kinases in clinical trial could provide great opportunities for treating various diseases. However, no systematic comparison between system profiles of established targets and those of clinical trial ones was conducted. The reveal of probable difference or shift of trend would help to identify key factors defining druggability of established targets. In this study, a comparative analysis of system profiles of both types of targets was conducted. Consequently, the systems profiles of the majority of clinical trial kinases were identified to be very similar to those of established ones, but percentages of established targets obeying the system profiles appeared to be slightly but consistently higher than those of clinical trial targets. Moreover, a shift of trend in the system profiles from the clinical trial to the established targets was identified, and popular kinase targets were discovered. In sum, this comparative study may help to facilitate the identification of the druggability of established drug targets by their system profiles and drug-target interaction networks. PMID:27547755

  8. Regulatory T cell-mediated resolution of lung injury: identification of potential target genes via expression profiling

    PubMed Central

    Aggarwal, Neil R.; D'Alessio, Franco R.; Tsushima, Kenji; Sidhaye, Venkataramana K.; Cheadle, Christopher; Grigoryev, Dmitry N.; Barnes, Kathleen C.

    2010-01-01

    In animal models of acute lung injury (ALI), gene expression studies have focused on the acute phase of illness, with little emphasis on resolution. In this study, the acute phase of intratracheal lipopolysaccharide (IT LPS)-induced lung injury was similar in wild-type (WT) and recombinase-activating gene-1-deficient (Rag-1−/−) lymphocyte-deficient mice, but resolution was impaired and resolution-phase lung gene expression remained different from baseline only in Rag-1−/− mice. By focusing on groups of genes involved in similar biological processes (gene ontologies) pertinent to inflammation and the immune response, we identified 102 genes at days 4 and 10 after IT LPS with significantly different expression between WT and Rag-1−/− mice. After adoptive transfer of isolated CD4+CD25+Foxp3+ regulatory T cells (Tregs) to Rag-1−/− mice at the time of IT LPS, resolution was similar to that in WT mice. Of the 102 genes distinctly changed in either WT or Rag-1−/− mice from our 7 gene ontologies, 19 genes reverted from the Rag-1−/− to the WT pattern of expression after adoptive transfer of Tregs, implicating those 19 genes in Treg-mediated resolution of ALI. PMID:20028937

  9. Therapeutic targeting of regulatory T cells enhances tumor-specific CD8+ T cell responses in Epstein–Barr virus associated nasopharyngeal carcinoma

    SciTech Connect

    Fogg, Mark; Murphy, John R.; Lorch, Jochen; Posner, Marshall; Wang, Fred

    2013-07-05

    Epstein–Barr virus (EBV) is associated with multiple malignancies including nasopharyngeal carcinoma (NPC). In nasopharynx cancer, CD8+ T cells specific for EBV Nuclear Antigen-1 (EBNA-1) and Latent Membrane Protein 2 (LMP2) are important components of anti-tumor immunity since both are consistently expressed in NPC. We have previously shown that EBNA-1-specific CD8+ T cell responses were suppressed in NPC patients compared to healthy controls. We now find that CD8+ T cell responses specific for LMP2 are also abnormal in NPC patients, and both EBNA-1- and LMP2-specific responses are suppressed by regulatory T cells (Treg). EBNA-1 and LMP2-specific CD8+ T cell responses, as well as immune control of EBV-infected cells in vitro, could be restored by the depletion of Tregs and by use of a clinically approved drug targeting Tregs. Thus, in vivo modulation of Tregs may be an effective means of enhancing these anti-tumor immune responses in NPC patients. - Highlights: • Viral proteins are tumor antigens in Epstein–Barr virus associated Nasopharyngeal Carcinoma. • CD8+ T cell responses against EBV proteins EBNA-1 and LMP2 are suppressed in NPC patients. • T regulatory cells are responsible for suppressing EBV immunity in NPC patients. • Depletion of Tregs with Ontak can rescue EBV-specific CD8+ T cell responses in NPC patients. • This clinically approved drug may be effective for enhancing anti-tumor immunity in NPC patients.

  10. miR-145 mediates the antiproliferative and gene regulatory effects of vitamin D3 by directly targeting E2F3 in gastric cancer cells

    PubMed Central

    Chang, Su'e; Gao, Ling; Yang, Yang; Tong, Dongdong; Guo, Bo; Liu, Liying; Li, Zongfang; Song, Tusheng; Huang, Chen

    2015-01-01

    VitaminD3 signaling is involved in inhibiting the development and progression of gastric cancer (GC), while the active vitamin D metabolite 1-alpha,25-dihydroxyvitamin D3 (1,25(OH)2D3)-mediated gene regulatory mechanisms in GC remain unclear. We found that miR-145 is induced by 1,25(OH)2D3 in a dose- and vitamin D receptor (VDR)-dependent manner in GC cells. Inhibition of miR-145 reverses the antiproliferative effect of 1,25(OH)2D3. Furthermore, miR-145 expression was lower in tumors compared with matched normal samples and correlated with increased the E2F3 transcription factor protein staining. Overexpression of miR-145 inhibited colony formation, cell viability and induced cell arrest in S-phase in GC cells by targeting E2F3 and CDK6. miR-145 inhibition consistently abrogates the 1,25(OH)2D3-mediated suppression of E2F3, CDK6, CDK2 and CCNA2 genes. Altogether, our results indicate that miR-145 mediates the antiproliferative and gene regulatory effects of vitamin D3 in GC cells and might hold promise for prognosis and therapeutic strategies for GC treatment. PMID:25762621

  11. Expanded roles of leucine-responsive regulatory protein in transcription regulation of the Escherichia coli genome: Genomic SELEX screening of the regulation targets

    PubMed Central

    Saito, Natsumi; Maeda, Michihisa; Tanaka, Kan; Ishihama, Akira

    2015-01-01

    Leucine-responsive regulatory protein (Lrp) is a transcriptional regulator for the genes involved in transport, biosynthesis and catabolism of amino acids in Escherichia coli. In order to identify the whole set of genes under the direct control of Lrp, we performed Genomic SELEX screening and identified a total of 314 Lrp-binding sites on the E. coli genome. As a result, the regulation target of Lrp was predicted to expand from the hitherto identified genes for amino acid metabolism to a set of novel target genes for utilization of amino acids for protein synthesis, including tRNAs, aminoacyl-tRNA synthases and rRNAs. Northern blot analysis indicated alteration of mRNA levels for at least some novel targets, including the aminoacyl-tRNA synthetase genes. Phenotype MicroArray of the lrp mutant indicated significant alteration in utilization of amino acids and peptides, whilst metabolome analysis showed variations in the concentration of amino acids in the lrp mutant. From these two datasets we realized a reverse correlation between amino acid levels and cell growth rate: fast-growing cells contain low-level amino acids, whilst a high level of amino acids exists in slow-growing cells. Taken together, we propose that Lrp is a global regulator of transcription of a large number of the genes involved in not only amino acid transport and metabolism, but also amino acid utilization. PMID:28348809

  12. Comparison of Different INC Physical Models of MCNPX to Compute Spallation Neutronics of LBE Target

    NASA Astrophysics Data System (ADS)

    Feghhi, Seyed Amir Hossein; Gholamzadeh, Zohreh; Tenreiro, Claudio; Alipoor, Zahra

    2015-04-01

    Spallation particles can utilize in different fields such as neutron scattering studies, external source for burning spent fuel as well as running subcritical reactors. Different computational particle transport codes are widely used to model spallation process into the heavy targets. Among these codes, MCNPX 2.6.0 comprises various intra nuclear cascade models for spallation calculations. Impact of different intra nuclear cascade models on calculation of neutronic parameters of LBE target has been evaluated in this work. Escaped neutron yield, energy deposition and residual nuclei production in the spallation target has been calculated using the physical models. A comparison between the computational and experimental has been carried out to validate the computational data. The simulation data showed there is a good conformity between the obtained data from Bertini/Drenser and Isabel/Drenser. The data achieved by Bertini/Abla and Isabel/Abla models are close to each other for the studied parameters as well. Among the studied models, CEM showed more discrepancies with experimental and other computational data. According to the obtained data, INCL4/Drenser, INCL4/Abla and Isabel/Drenser models can meet more agreements with experimental data.

  13. Misclassification Errors in Unsupervised Classification Methods. Comparison Based on the Simulation of Targeted Proteomics Data

    PubMed Central

    Andreev, Victor P; Gillespie, Brenda W; Helfand, Brian T; Merion, Robert M

    2016-01-01

    Unsupervised classification methods are gaining acceptance in omics studies of complex common diseases, which are often vaguely defined and are likely the collections of disease subtypes. Unsupervised classification based on the molecular signatures identified in omics studies have the potential to reflect molecular mechanisms of the subtypes of the disease and to lead to more targeted and successful interventions for the identified subtypes. Multiple classification algorithms exist but none is ideal for all types of data. Importantly, there are no established methods to estimate sample size in unsupervised classification (unlike power analysis in hypothesis testing). Therefore, we developed a simulation approach allowing comparison of misclassification errors and estimating the required sample size for a given effect size, number, and correlation matrix of the differentially abundant proteins in targeted proteomics studies. All the experiments were performed in silico. The simulated data imitated the expected one from the study of the plasma of patients with lower urinary tract dysfunction with the aptamer proteomics assay Somascan (SomaLogic Inc, Boulder, CO), which targeted 1129 proteins, including 330 involved in inflammation, 180 in stress response, 80 in aging, etc. Three popular clustering methods (hierarchical, k-means, and k-medoids) were compared. K-means clustering performed much better for the simulated data than the other two methods and enabled classification with misclassification error below 5% in the simulated cohort of 100 patients based on the molecular signatures of 40 differentially abundant proteins (effect size 1.5) from among the 1129-protein panel. PMID:27524871

  14. The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors.

    PubMed

    Willingham, Stephen B; Volkmer, Jens-Peter; Gentles, Andrew J; Sahoo, Debashis; Dalerba, Piero; Mitra, Siddhartha S; Wang, Jian; Contreras-Trujillo, Humberto; Martin, Robin; Cohen, Justin D; Lovelace, Patricia; Scheeren, Ferenc A; Chao, Mark P; Weiskopf, Kipp; Tang, Chad; Volkmer, Anne Kathrin; Naik, Tejaswitha J; Storm, Theresa A; Mosley, Adriane R; Edris, Badreddin; Schmid, Seraina M; Sun, Chris K; Chua, Mei-Sze; Murillo, Oihana; Rajendran, Pradeep; Cha, Adriel C; Chin, Robert K; Kim, Dongkyoon; Adorno, Maddalena; Raveh, Tal; Tseng, Diane; Jaiswal, Siddhartha; Enger, Per Øyvind; Steinberg, Gary K; Li, Gordon; So, Samuel K; Majeti, Ravindra; Harsh, Griffith R; van de Rijn, Matt; Teng, Nelson N H; Sunwoo, John B; Alizadeh, Ash A; Clarke, Michael F; Weissman, Irving L

    2012-04-24

    CD47, a "don't eat me" signal for phagocytic cells, is expressed on the surface of all human solid tumor cells. Analysis of patient tumor and matched adjacent normal (nontumor) tissue revealed that CD47 is overexpressed on cancer cells. CD47 mRNA expression levels correlated with a decreased probability of survival for multiple types of cancer. CD47 is a ligand for SIRPα, a protein expressed on macrophages and dendritic cells. In vitro, blockade of CD47 signaling using targeted monoclonal antibodies enabled macrophage phagocytosis of tumor cells that were otherwise protected. Administration of anti-CD47 antibodies inhibited tumor growth in orthotopic immunodeficient mouse xenotransplantation models established with patient tumor cells and increased the survival of the mice over time. Anti-CD47 antibody therapy initiated on larger tumors inhibited tumor growth and prevented or treated metastasis, but initiation of the therapy on smaller tumors was potentially curative. The safety and efficacy of targeting CD47 was further tested and validated in immune competent hosts using an orthotopic mouse breast cancer model. These results suggest all human solid tumor cells require CD47 expression to suppress phagocytic innate immune surveillance and elimination. These data, taken together with similar findings with other human neoplasms, show that CD47 is a commonly expressed molecule on all cancers, its function to block phagocytosis is known, and blockade of its function leads to tumor cell phagocytosis and elimination. CD47 is therefore a validated target for cancer therapies.

  15. The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors

    PubMed Central

    Willingham, Stephen B.; Volkmer, Jens-Peter; Gentles, Andrew J.; Sahoo, Debashis; Dalerba, Piero; Mitra, Siddhartha S.; Wang, Jian; Contreras-Trujillo, Humberto; Martin, Robin; Cohen, Justin D.; Lovelace, Patricia; Scheeren, Ferenc A.; Chao, Mark P.; Weiskopf, Kipp; Tang, Chad; Volkmer, Anne Kathrin; Naik, Tejaswitha J.; Storm, Theresa A.; Mosley, Adriane R.; Edris, Badreddin; Schmid, Seraina M.; Sun, Chris K.; Chua, Mei-Sze; Murillo, Oihana; Rajendran, Pradeep; Cha, Adriel C.; Chin, Robert K.; Kim, Dongkyoon; Adorno, Maddalena; Raveh, Tal; Tseng, Diane; Jaiswal, Siddhartha; Enger, Per Øyvind; Steinberg, Gary K.; Li, Gordon; So, Samuel K.; Majeti, Ravindra; Harsh, Griffith R.; van de Rijn, Matt; Teng, Nelson N. H.; Sunwoo, John B.; Alizadeh, Ash A.; Clarke, Michael F.; Weissman, Irving L.

    2012-01-01

    CD47, a “don't eat me” signal for phagocytic cells, is expressed on the surface of all human solid tumor cells. Analysis of patient tumor and matched adjacent normal (nontumor) tissue revealed that CD47 is overexpressed on cancer cells. CD47 mRNA expression levels correlated with a decreased probability of survival for multiple types of cancer. CD47 is a ligand for SIRPα, a protein expressed on macrophages and dendritic cells. In vitro, blockade of CD47 signaling using targeted monoclonal antibodies enabled macrophage phagocytosis of tumor cells that were otherwise protected. Administration of anti-CD47 antibodies inhibited tumor growth in orthotopic immunodeficient mouse xenotransplantation models established with patient tumor cells and increased the survival of the mice over time. Anti-CD47 antibody therapy initiated on larger tumors inhibited tumor growth and prevented or treated metastasis, but initiation of the therapy on smaller tumors was potentially curative. The safety and efficacy of targeting CD47 was further tested and validated in immune competent hosts using an orthotopic mouse breast cancer model. These results suggest all human solid tumor cells require CD47 expression to suppress phagocytic innate immune surveillance and elimination. These data, taken together with similar findings with other human neoplasms, show that CD47 is a commonly expressed molecule on all cancers, its function to block phagocytosis is known, and blockade of its function leads to tumor cell phagocytosis and elimination. CD47 is therefore a validated target for cancer therapies. PMID:22451913

  16. Transcriptome profiling of degU expression reveals unexpected regulatory patterns in Bacillus megaterium and discloses new targets for optimizing expression.

    PubMed

    Borgmeier, Claudia; Biedendieck, Rebekka; Hoffmann, Kristina; Jahn, Dieter; Meinhardt, Friedhelm

    2011-11-01

    The first whole transcriptome assessment of a Bacillus megaterium strain provides unanticipated insights into the degSU regulon considered to be of central importance for exo-enzyme production. Regulatory patterns as well as the transcription of degSU itself deviate from the model organism Bacillus subtilis; the number of DegU-regulated secretory enzymes is rather small. Targets for productivity optimization, besides degSU itself, arise from the unexpected DegU-dependent induction of the transition-state regulator AbrB during exponential growth. Induction of secretion-assisting factors, such as the translocase subunit SecY or the signal peptidase SipM, promote hypersecretion. B. megaterium DegSU transcriptional control is advantageous for production purposes, since the degU32 constitutively active mutant conferred hypersecretion of a heterologous Bacillus amyloliquefaciens amylase without the detrimental rise, as for B. subtilis and Bacillus licheniformis, in extracellular proteolytic activities.

  17. Murine Hyperglycemic Vasculopathy and Cardiomyopathy: Whole-Genome Gene Expression Analysis Predicts Cellular Targets and Regulatory Networks Influenced by Mannose Binding Lectin

    PubMed Central

    Zou, Chenhui; La Bonte, Laura R.; Pavlov, Vasile I.; Stahl, Gregory L.

    2012-01-01

    Hyperglycemia, in the absence of type 1 or 2 diabetes, is an independent risk factor for cardiovascular disease. We have previously demonstrated a central role for mannose binding lectin (MBL)-mediated cardiac dysfunction in acute hyperglycemic mice. In this study, we applied whole-genome microarray data analysis to investigate MBL’s role in systematic gene expression changes. The data predict possible intracellular events taking place in multiple cellular compartments such as enhanced insulin signaling pathway sensitivity, promoted mitochondrial respiratory function, improved cellular energy expenditure and protein quality control, improved cytoskeleton structure, and facilitated intracellular trafficking, all of which may contribute to the organismal health of MBL null mice against acute hyperglycemia. Our data show a tight association between gene expression profile and tissue function which might be a very useful tool in predicting cellular targets and regulatory networks connected with in vivo observations, providing clues for further mechanistic studies. PMID:22375142

  18. Targeting CD28, CTLA-4 and PD-L1 Costimulation Differentially Controls Immune Synapses and Function of Human Regulatory and Conventional T-Cells

    PubMed Central

    Hulin, Philippe; Coulon, Flora; Mary, Caroline; Ville, Simon; Vie, Henri; Clémenceau, Béatrice; Blancho, Gilles; Vanhove, Bernard

    2013-01-01

    CD28, CTLA-4 and PD-L1, the three identified ligands for CD80/86, are pivotal positive and negative costimulatory molecules that, among other functions, control T cell motility and formation of immune synapse between T cells and antigen-presenting cells (APCs). What remains incompletely understood is how CD28 leads to the activation of effector T cells (Teff) but inhibition of suppression by regulatory T cells (Tregs), while CTLA-4 and PD-L1 inhibit Teff function but are crucial for the suppressive function of Tregs. Using alloreactive human T cells and blocking antibodies, we show here by live cell dynamic microscopy that CD28, CTLA-4, and PD-L1 differentially control velocity, motility and immune synapse formation in activated Teff versus Tregs. Selectively antagonizing CD28 costimulation increased Treg dwell time with APCs and induced calcium mobilization which translated in increased Treg suppressive activity, in contrast with the dampening effect on Teff responses. The increase in Treg suppressive activity after CD28 blockade was also confirmed with polyclonal Tregs. Whereas CTLA-4 played a critical role in Teff by reversing TCR-induced STOP signals, it failed to affect motility in Tregs but was essential for formation of the Treg immune synapse. Furthermore, we identified a novel role for PD-L1-CD80 interactions in suppressing motility specifically in Tregs. Thus, our findings reveal that the three identified ligands of CD80/86, CD28, CTLA-4 and PD-L1, differentially control immune synapse formation and function of the human Teff and Treg cells analyzed here. Individually targeting CD28, CTLA-4 and PD-L1 might therefore represent a valuable therapeutic strategy to treat immune disorders where effector and regulatory T cell functions need to be differentially targeted. PMID:24376655

  19. Validating the GTP-cyclohydrolase 1-feedback regulatory complex as a therapeutic target using biophysical and in vivo approaches

    PubMed Central

    Hussein, D; Starr, A; Heikal, L; McNeill, E; Channon, K M; Brown, P R; Sutton, B J; McDonnell, J M; Nandi, M

    2015-01-01

    Background and Purpose 6R-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) is an essential cofactor for nitric oxide biosynthesis. Substantial clinical evidence indicates that intravenous BH4 restores vascular function in patients. Unfortunately, oral BH4 has limited efficacy. Therefore, orally bioavailable pharmacological activators of endogenous BH4 biosynthesis hold significant therapeutic potential. GTP-cyclohydrolase 1 (GCH1), the rate limiting enzyme in BH4 synthesis, forms a protein complex with GCH1 feedback regulatory protein (GFRP). This complex is subject to allosteric feed-forward activation by L-phenylalanine (L-phe). We investigated the effects of L-phe on the biophysical interactions of GCH1 and GFRP and its potential to alter BH4 levels in vivo. Experimental Approach Detailed characterization of GCH1–GFRP protein–protein interactions were performed using surface plasmon resonance (SPR) with or without L-phe. Effects on systemic and vascular BH4 biosynthesis in vivo were investigated following L-phe treatment (100 mg·kg−1, p.o.). Key Results GCH1 and GFRP proteins interacted in the absence of known ligands or substrate but the presence of L-phe doubled maximal binding and enhanced binding affinity eightfold. Furthermore, the complex displayed very slow association and dissociation rates. In vivo, L-phe challenge induced a sustained elevation of aortic BH4, an effect absent in GCH1(fl/fl)-Tie2Cre mice. Conclusions and Implications Biophysical data indicate that GCH1 and GFRP are constitutively bound. In vivo, data demonstrated that L-phe elevated vascular BH4 in an endothelial GCH1 dependent manner. Pharmacological agents which mimic the allosteric effects of L-phe on the GCH1–GFRP complex have the potential to elevate endothelial BH4 biosynthesis for numerous cardiovascular disorders. PMID:26014146

  20. Method comparison of ultrasound and kilovoltage x-ray fiducial marker imaging for prostate radiotherapy targeting.

    PubMed

    Fuller, Clifton David; Thomas, Charles R; Schwartz, Scott; Golden, Nanalei; Ting, Joe; Wong, Adrian; Erdogmus, Deniz; Scarbrough, Todd J

    2006-10-07

    majority of all individual US and FM directional measures may be expected to agree with each other within a range of 1-1.5 cm. Since neither system represents a gold standard, clinical judgment must dictate whether such a difference is of import. As IMRT protocols seek dose escalation and PTV reduction predicated on US- and FM-guided imaging, future studies are needed to address these potential clinically relevant issues regarding the interchangeability and accuracy of novel positional verification techniques. Comparison series with multiple image-guidance systems are needed to refine comparisons between targeting methods. However, we do not advocate interchangeability of US and FM localization methods.

  1. Genome-Wide Analyses of Nkx2-1 Binding to Transcriptional Target Genes Uncover Novel Regulatory Patterns Conserved in Lung Development and Tumors

    PubMed Central

    Tagne, Jean-Bosco; Gupta, Sumeet; Gower, Adam C.; Shen, Steven S.; Varma, Saaket; Lakshminarayanan, Meenakshi; Cao, Yuxia; Spira, Avrum; Volkert, Thomas L.; Ramirez, Maria I.

    2012-01-01

    The homeodomain transcription factor Nkx2-1 is essential for normal lung development and homeostasis. In lung tumors, it is considered a lineage survival oncogene and prognostic factor depending on its expression levels. The target genes directly bound by Nkx2-1, that could be the primary effectors of its functions in the different cellular contexts where it is expressed, are mostly unknown. In embryonic day 11.5 (E11.5) mouse lung, epithelial cells expressing Nkx2-1 are predominantly expanding, and in E19.5 prenatal lungs, Nkx2-1-expressing cells are predominantly differentiating in preparation for birth. To evaluate Nkx2-1 regulated networks in these two cell contexts, we analyzed genome-wide binding of Nkx2-1 to DNA regulatory regions by chromatin immunoprecipitation followed by tiling array analysis, and intersected these data to expression data sets. We further determined expression patterns of Nkx2-1 developmental target genes in human lung tumors and correlated their expression levels to that of endogenous NKX2-1. In these studies we uncovered differential Nkx2-1 regulated networks in early and late lung development, and a direct function of Nkx2-1 in regulation of the cell cycle by controlling the expression of proliferation-related genes. New targets, validated in Nkx2-1 shRNA transduced cell lines, include E2f3, Cyclin B1, Cyclin B2, and c-Met. Expression levels of Nkx2-1 direct target genes identified in mouse development significantly correlate or anti-correlate to the levels of endogenous NKX2-1 in a dosage-dependent manner in multiple human lung tumor expression data sets, supporting alternative roles for Nkx2-1 as a transcriptional activator or repressor, and direct regulator of cell cycle progression in development and tumors. PMID:22242187

  2. A comparison of adverse event and fracture efficacy data for strontium ranelate in regulatory documents and the publication record

    PubMed Central

    Bolland, Mark J; Grey, Andrew

    2014-01-01

    Objective Recently, the European Medicines Agency reported that strontium ranelate increases myocardial infarction risk in postmenopausal women, 8.5 years after it was registered for use in osteoporosis. Unreported serious adverse events in clinical trials for other pharmaceuticals have been described in recent years. We assessed reporting of adverse events and fracture efficacy of strontium. Methods We compared data on adverse effects (myocardial infarction, venous thromboembolism and pulmonary embolism) and fracture efficacy of strontium in publicly available regulatory documents with data in publications retrieved from searching PubMed. Results We identified 5 regulatory documents and 9 primary publications of 7 randomised, placebo-controlled trials of strontium that reported relevant data. We identified several areas of concern in these reports: the increased risk of myocardial infarction with strontium was not identified in a pivotal phase 3 clinical trial despite specific regulatory review of cardiovascular events; data on myocardial infarction were not included in any primary publication; increased risks of venous thromboembolism and pulmonary embolism with strontium were not reported in either of the phase 3 clinical trials; data on venous thromboembolism were reported in only 5 of 9 primary publications, data on pulmonary embolism in only 2 of 9 primary publications, and either was discussed in <50% of subsequent review articles. There were differences in participant numbers, fracture cases and venous thromboembolism cases between regulatory documents and primary publications. Based on all available data from primary publications and regulatory documents, the number of fractures prevented by strontium use is similar to the number of extra cases of venous thromboembolism, pulmonary embolism and myocardial infarction caused by strontium use. Conclusions The risks of strontium use are similar to the benefits. Full disclosure of the clinical trial data and

  3. Comparison of Folate Receptor Targeted Optical Contrast Agents for Intraoperative Molecular Imaging

    PubMed Central

    De Jesus, Elizabeth; Keating, Jane J.; Kularatne, Sumith A.; Jiang, Jack; Judy, Ryan; Predina, Jarrod; Nie, Shuming; Low, Philip; Singhal, Sunil

    2015-01-01

    Background. Intraoperative imaging can identify cancer cells in order to improve resection; thus fluorescent contrast agents have emerged. Our objective was to do a preclinical comparison of two fluorescent dyes, EC17 and OTL38, which both target folate receptor but have different fluorochromes. Materials. HeLa and KB cells lines were used for in vitro and in vivo comparisons of EC17 and OTL38 brightness, sensitivity, pharmacokinetics, and biodistribution. In vivo experiments were then performed in mice. Results. The peak excitation and emission wavelengths of EC17 and OTL38 were 470/520 nm and 774/794 nm, respectively. In vitro, OTL38 required increased incubation time compared to EC17 for maximum fluorescence; however, peak signal-to-background ratio (SBR) was 1.4-fold higher compared to EC17 within 60 minutes (p < 0.001). Additionally, the SBR for detecting smaller quantity of cells was improved with OTL38. In vivo, the mean improvement in SBR of tumors visualized using OTL38 compared to EC17 was 3.3 fold (range 1.48–5.43). Neither dye caused noticeable toxicity in animal studies. Conclusions. In preclinical testing, OTL38 appears to have superior sensitivity and brightness compared to EC17. This coincides with the accepted belief that near infrared (NIR) dyes tend to have less autofluorescence and scattering issues than visible wavelength fluorochromes. PMID:26491562

  4. Single-cell analyses of regulatory network perturbations using enhancer-targeting TALEs suggest novel roles for PU.1 during haematopoietic specification

    PubMed Central

    Wilkinson, Adam C.; Kawata, Viviane K. S.; Schütte, Judith; Gao, Xuefei; Antoniou, Stella; Baumann, Claudia; Woodhouse, Steven; Hannah, Rebecca; Tanaka, Yosuke; Swiers, Gemma; Moignard, Victoria; Fisher, Jasmin; Hidetoshi, Shimauchi; Tijssen, Marloes R.; de Bruijn, Marella F. T. R.; Liu, Pentao; Göttgens, Berthold

    2014-01-01

    Transcription factors (TFs) act within wider regulatory networks to control cell identity and fate. Numerous TFs, including Scl (Tal1) and PU.1 (Spi1), are known regulators of developmental and adult haematopoiesis, but how they act within wider TF networks is still poorly understood. Transcription activator-like effectors (TALEs) are a novel class of genetic tool based on the modular DNA-binding domains of Xanthomonas TAL proteins, which enable DNA sequence-specific targeting and the manipulation of endogenous gene expression. Here, we report TALEs engineered to target the PU.1-14kb and Scl+40kb transcriptional enhancers as efficient new tools to perturb the expression of these key haematopoietic TFs. We confirmed the efficiency of these TALEs at the single-cell level using high-throughput RT-qPCR, which also allowed us to assess the consequences of both PU.1 activation and repression on wider TF networks during developmental haematopoiesis. Combined with comprehensive cellular assays, these experiments uncovered novel roles for PU.1 during early haematopoietic specification. Finally, transgenic mouse studies confirmed that the PU.1-14kb element is active at sites of definitive haematopoiesis in vivo and PU.1 is detectable in haemogenic endothelium and early committing blood cells. We therefore establish TALEs as powerful new tools to study the functionality of transcriptional networks that control developmental processes such as early haematopoiesis. PMID:25252941

  5. Differential PI3Kδ signaling in CD4+ T cell subsets enables selective targeting of T regulatory cells to enhance cancer immunotherapy.

    PubMed

    Ahmad, Shamim; Abu-Eid, Rasha; Shrimali, Rajeev K; Webb, Mason; Verma, Vivek; Doroodchi, Atbin; Berrong, Zuzana; Samara, Raed N; Rodriguez, Paulo C; Mkrtichyan, Mikayel; Khleif, Samir N

    2017-01-20

    To modulate T cell function for cancer therapy one challenge is to selectively attenuate regulatory but not conventional CD4+ T cell subsets (Treg and Tconv). In this study we show how a functional dichotomy in Class IA PI3K isoforms in these two subsets of CD4+ T cells be exploited to target Treg while leaving Tconv intact. Studies employing isoform-specific PI3K inhibitors and a PI3Kδ-deficient mouse strain revealed that PI3Kα and PI3Kβ were functionally redundant with PI3Kδ in Tconv. Conversely, PI3Kδ was functionally critical in Treg, acting there to control TCR signaling, cell proliferation and survival. Notably, in a murine model of lung cancer, co-administration of a PI3Kδ-specific inhibitor with a tumor-specific vaccine decreased numbers of suppressive Treg and increased numbers of vaccine-induced CD8 T-cells within the tumor microenvironment, eliciting potent anti-tumor efficacy. Overall, our results offer a mechanistic rationale to employ PI3Kδ inhibitors to selectively target Treg and improve cancer immunotherapy.

  6. The comparison of extraction of energy in two-cascade and one-cascade targets

    SciTech Connect

    Dolgoleva, G. V.; Ponomarev, I. V.

    2016-01-15

    The paper is devoted to numerical designing of cylindrical microtargets on the basis of shock-free compression. When designing microtargets for the controlled thermonuclear fusion, the core tasks are to select geometry and make-up of layers, and the law of energy embedding as well, which allow receiving of “burning” of deuterium- tritium mix, that is, the existence of thermonuclear reactions of working area. Yet, the energy yield as a result of thermonuclear reactions has to be more than the embedded energy (the coefficient of amplification is more than a unit). So, an important issue is the value of the embedded energy. The purpose of the present paper is to study the extraction of energy by working DT area in one-cascade and two-cascade targets. A bigger extraction of energy will contribute to a better burning of DT mix and a bigger energy yield as a result of thermonuclear reactions. The comparison of analytical results to numerical calculations is carried out. The received results show advantages of a two-cascade target compared to a one-cascade one.

  7. Transient antibody targeting of CD45RC induces transplant tolerance and potent antigen-specific regulatory T cells

    PubMed Central

    Picarda, Elodie; Bézie, Séverine; Boucault, Laetitia; Autrusseau, Elodie; Kilens, Stéphanie; Martinet, Bernard; Daguin, Véronique; Donnart, Audrey; Charpentier, Eric; Anegon, Ignacio

    2017-01-01

    Rat and human CD4+ and CD8+ Tregs expressing low levels of CD45RC have strong immunoregulatory properties. We describe here that human CD45 isoforms are nonredundant and identify distinct subsets of cells. We show that CD45RC is not expressed by CD4+ and CD8+ Foxp3+ Tregs, while CD45RA/RB/RO are. Transient administration of a monoclonal antibody (mAb) targeting CD45RC in a rat cardiac allotransplantation model induced transplant tolerance associated with inhibition of allogeneic humoral responses but maintained primary and memory responses against cognate antigens. Anti-CD45RC mAb induced rapid death of CD45RChigh T cells through intrinsic cell signaling but preserved and potentiated CD4+ and CD8+ CD45RClow/– Tregs, which are able to adoptively transfer donor-specific tolerance to grafted recipients. Anti-CD45RC treatment results in distinct transcriptional signature of CD4+ and CD8+ CD45RClow/– Tregs. Finally, we demonstrate that anti-human CD45RC treatment inhibited graft-versus-host disease (GVHD) in immune-humanized NSG mice. Thus, short-term anti-CD45RC is a potent therapeutic candidate to induce transplantation tolerance in human. PMID:28194440

  8. Targeting Extracellular Domains D4 and D7 of Vascular Endothelial Growth Factor Receptor 2 Reveals Allosteric Receptor Regulatory Sites

    PubMed Central

    Hyde, Caroline A. C.; Giese, Alexandra; Stuttfeld, Edward; Abram Saliba, Johan; Villemagne, Denis; Schleier, Thomas; Binz, H. Kaspar

    2012-01-01

    Vascular endothelial growth factors (VEGFs) activate three receptor tyrosine kinases, VEGFR-1, -2, and -3, which regulate angiogenic and lymphangiogenic signaling. VEGFR-2 is the most prominent receptor in angiogenic signaling by VEGF ligands. The extracellular part of VEGF receptors consists of seven immunoglobulin homology domains (Ig domains). Earlier studies showed that domains 2 and 3 (D23) mediate ligand binding, while structural analysis of dimeric ligand/receptor complexes by electron microscopy and small-angle solution scattering revealed additional homotypic contacts in membrane-proximal Ig domains D4 and D7. Here we show that D4 and D7 are indispensable for receptor signaling. To confirm the essential role of these domains in signaling, we isolated VEGFR-2-inhibitory “designed ankyrin repeat proteins” (DARPins) that interact with D23, D4, or D7. DARPins that interact with D23 inhibited ligand binding, receptor dimerization, and receptor kinase activation, while DARPins specific for D4 or D7 did not prevent ligand binding or receptor dimerization but effectively blocked receptor signaling and functional output. These data show that D4 and D7 allosterically regulate VEGFR-2 activity. We propose that these extracellular-domain-specific DARPins represent a novel generation of receptor-inhibitory drugs for in vivo applications such as targeting of VEGFRs in medical diagnostics and for treating vascular pathologies. PMID:22801374

  9. Targeting extracellular domains D4 and D7 of vascular endothelial growth factor receptor 2 reveals allosteric receptor regulatory sites.

    PubMed

    Hyde, Caroline A C; Giese, Alexandra; Stuttfeld, Edward; Abram Saliba, Johan; Villemagne, Denis; Schleier, Thomas; Binz, H Kaspar; Ballmer-Hofer, Kurt

    2012-10-01

    Vascular endothelial growth factors (VEGFs) activate three receptor tyrosine kinases, VEGFR-1, -2, and -3, which regulate angiogenic and lymphangiogenic signaling. VEGFR-2 is the most prominent receptor in angiogenic signaling by VEGF ligands. The extracellular part of VEGF receptors consists of seven immunoglobulin homology domains (Ig domains). Earlier studies showed that domains 2 and 3 (D23) mediate ligand binding, while structural analysis of dimeric ligand/receptor complexes by electron microscopy and small-angle solution scattering revealed additional homotypic contacts in membrane-proximal Ig domains D4 and D7. Here we show that D4 and D7 are indispensable for receptor signaling. To confirm the essential role of these domains in signaling, we isolated VEGFR-2-inhibitory "designed ankyrin repeat proteins" (DARPins) that interact with D23, D4, or D7. DARPins that interact with D23 inhibited ligand binding, receptor dimerization, and receptor kinase activation, while DARPins specific for D4 or D7 did not prevent ligand binding or receptor dimerization but effectively blocked receptor signaling and functional output. These data show that D4 and D7 allosterically regulate VEGFR-2 activity. We propose that these extracellular-domain-specific DARPins represent a novel generation of receptor-inhibitory drugs for in vivo applications such as targeting of VEGFRs in medical diagnostics and for treating vascular pathologies.

  10. Self-System Therapy as an Intervention for Self-Regulatory Dysfunction in Depression: A Randomized Comparison with Cognitive Therapy

    ERIC Educational Resources Information Center

    Strauman, Timothy J.; Vieth, Angela Z.; Merrill, Kari A.; Kolden, Gregory G.; Woods, Teresa E.; Klein, Marjorie H.; Papadakis, Alison A.; Schneider, Kristin L.; Kwapil, Lori

    2006-01-01

    Self-system therapy (SST) is a new therapy based on regulatory focus theory (E. T. Higgins, 1997) for depressed individuals unable to pursue promotion goals effectively. The authors conducted a randomized trial comparing SST with cognitive therapy (CT) in a sample of 45 patients with a range of depressive symptoms to test 2 hypotheses: that SST…

  11. Self-System Therapy as an Intervention for Self-Regulatory Dysfunction in Depression: A Randomized Comparison with Cognitive Therapy

    ERIC Educational Resources Information Center

    Strauman, Timothy J.; Vieth, Angela Z.; Merrill, Kari A.; Kolden, Gregory G.; Woods, Teresa E.; Klein, Marjorie H.; Papadakis, Alison A.; Schneider, Kristin L.; Kwapil, Lori

    2006-01-01

    Self-system therapy (SST) is a new therapy based on regulatory focus theory (E. T. Higgins, 1997) for depressed individuals unable to pursue promotion goals effectively. The authors conducted a randomized trial comparing SST with cognitive therapy (CT) in a sample of 45 patients with a range of depressive symptoms to test 2 hypotheses: that SST…

  12. A cis-regulatory antisense RNA represses translation in Vibrio cholerae through extensive complementarity and proximity to the target locus.

    PubMed

    Chang, Howard; Replogle, John Michael; Vather, Naomi; Tsao-Wu, Maya; Mistry, Ronak; Liu, Jane M

    2015-01-01

    As with all facultative pathogens, Vibrio cholerae must optimize its cellular processes to adapt to different environments with varying carbon sources and to environmental stresses. More specifically, in order to metabolize mannitol, V. cholerae must regulate the synthesis of MtlA, a mannitol transporter protein produced exclusively in the presence of mannitol. We previously showed that a cis-acting small RNA (sRNA) expressed by V. cholerae, MtlS, appears to post-transcriptionally downregulate the expression of mtlA and is produced in the absence of mannitol. We hypothesized that since it is complementary to the 5' untranslated region (UTR) of mtlA mRNA, MtlS may affect synthesis of MtlA by forming an mtlA-MtlS complex that blocks translation of the mRNA through occlusion of its ribosome binding site. To test this hypothesis, we used in vitro translation assays in order to examine the role MtlS plays in mtlA regulation and found that MtlS is sufficient to suppress translation of transcripts harboring the 5' UTR of mtlA. However, in a cellular context, the 5' UTR of mtlA is not sufficient for targeted repression by endogenous MtlS; additional segments from the coding region of mtlA play a role in the ability of the sRNA to regulate translation of mtlA mRNA. Additionally, proximity of transcription sites between the sRNA and mRNA significantly affects the efficacy of MtlS.

  13. Comparison of adenovirus fiber, protein IX, and hexon capsomeres as scaffolds for vector purification and cell targeting

    SciTech Connect

    Campos, Samuel K.; Barry, Michael A. . E-mail: mab@bcm.edu

    2006-06-05

    The direct genetic modification of adenoviral capsid proteins with new ligands is an attractive means to confer targeted tropism to adenoviral vectors. Although several capsid proteins have been reported to tolerate the genetic fusion of foreign peptides and proteins, direct comparison of cell targeting efficiencies through the different capsomeres has been lacking. Likewise, direct comparison of with one or multiple ligands has not been performed due to a lack of capsid-compatible ligands available for retargeting. Here we utilize a panel of metabolically biotinylated Ad vectors to directly compare targeted transduction through the fiber, protein IX, and hexon capsomeres using a variety of biotinylated ligands including antibodies, transferrin, EGF, and cholera toxin B. These results clearly demonstrate that cell targeting with a variety of high affinity receptor-binding ligands is only effective when transduction is redirected through the fiber protein. In contrast, protein IX and hexon-mediated targeting by the same set of ligands failed to mediate robust vector targeting, perhaps due to aberrant trafficking at the cell surface or inside targeted cells. These data suggest that vector targeting by genetic incorporation of high affinity ligands will likely be most efficient through modification of the adenovirus fiber rather than the protein IX and hexon capsomeres. In contrast, single-step monomeric avidin affinity purification of Ad vectors using the metabolic biotinylation system is most effective through capsomeres like protein IX and hexon.

  14. Routine gastric residual volume measurement and energy target achievement in the PICU: a comparison study.

    PubMed

    Tume, Lyvonne N; Bickerdike, Anna; Latten, Lynne; Davies, Simon; Lefèvre, Madeleine H; Nicolas, Gaëlle W; Valla, Frédéric V

    2017-09-18

    Critically ill children frequently fail to achieve adequate energy intake, and some care practices, such as the measurement of gastric residual volume (GRV), may contribute to this problem. We compared outcomes in two similar European Paediatric Intensive Care Units (PICUs): one which routinely measures GRV (PICU-GRV) to one unit that does not (PICU-noGRV). An observational pilot comparison study was undertaken. Eighty-seven children were included in the study, 42 (PICU-GRV) and 45 (PICU-noGRV). There were no significant differences in the percentage of energy targets achieved in the first 4 days of PICU admission although PICU-noGRV showed more consistent delivery of median (and IQR) energy targets and less under and over feeding for PICU-GRV and PICU-noGRV: day 1 37 (14-72) vs 44 (0-100), day 2 97 (53-126) vs 100 (100-100), day 3 84 (45-112) vs 100 (100-100) and day 4 101 (63-124) vs 100 (100-100). The incidence of vomiting was higher in PICU-GRV. No necrotising enterocolitis was confirmed in either unit, and ventilator-acquired pneumonia rates were not significantly different (7.01 vs 12 5.31 per 1000 ventilator days; p = 0.70) between PICU-GRV and PICU-noGRV units. The practice of routine gastric residual measurement did not significantly impair energy targets in the first 4 days of PICU admission. However, not measuring GRV did not increase vomiting, ventilator-acquired pneumonia or necrotising enterocolitis, which is the main reason clinicians cite for measuring GRV. What is known: • The practice of routinely measuring gastric residual volume is widespread in critical care units • This practice is increasingly being questioned in critically ill patients, both as a practice that increases • The likelihood of delivering inadequate enteral nutrition amounts and as a tool to assess feeding tolerance What is new: • Not routinely measuring gastric residual volume did not increase adverse events of ventilator acquired pneumonia, necrotising enterocolitis

  15. Comparison of Current Regulatory Status for Gene-Based Vaccines in the U.S., Europe and Japan.

    PubMed

    Nakayama, Yoshikazu; Aruga, Atsushi

    2015-03-18

    Gene-based vaccines as typified by plasmid DNA vaccines and recombinant viral-vectored vaccines are expected as promising solutions against infectious diseases for which no effective prophylactic vaccines exist such as HIV, dengue virus, Ebola virus and malaria, and for which more improved vaccines are needed such as tuberculosis and influenza virus. Although many preclinical and clinical trials have been conducted to date, no DNA vaccines or recombinant viral-vectored vaccines expressing heterologous antigens for human use have yet been licensed in the U.S., Europe or Japan. In this research, we describe the current regulatory context for gene-based prophylactic vaccines against infectious disease in the U.S., Europe, and Japan. We identify the important considerations, in particular, on the preclinical assessments that would allow these vaccines to proceed to clinical trials, and the differences on the regulatory pathway for the marketing authorization in each region.

  16. Identification of chemical hazards for terrestrial plants in the regulatory context: comparison of OECD and ISO guidelines.

    PubMed

    Tarazona, Jose V; Cesnaitis, Romanas; Herranz-Montes, Francisco Javier; Versonnen, Bram

    2013-11-01

    Standardized test protocols are used in the regulatory context for identifying the hazardous properties of chemicals, wastes, and contaminated materials. This paper compares the relevance of two guidelines measuring effects on terrestrial plants, the OECD TG 208 and the ISO TG 22030 and presents the scientific basis for a recent decision of the European Chemicals Agency (ECHA) under the European chemicals regulation REACH. If there are no specific phytotoxicity alerts, both guidelines are considered suitable for assessing long-term hazards, providing that a sufficient number of species is included in the OECD protocol, the recommended minimum number is six, which offer a reasonably broad selection of species to account for interspecies sensitivity. The proposed methodology, based on a combination of probabilistic assessments using Monte Carlo analysis, can be adapted for supporting similar decisions under specific regulatory processes; for example, for assessing contaminated soils or pesticides' applications.

  17. Comparison of Current Regulatory Status for Gene-Based Vaccines in the U.S., Europe and Japan

    PubMed Central

    Nakayama, Yoshikazu; Aruga, Atsushi

    2015-01-01

    Gene-based vaccines as typified by plasmid DNA vaccines and recombinant viral-vectored vaccines are expected as promising solutions against infectious diseases for which no effective prophylactic vaccines exist such as HIV, dengue virus, Ebola virus and malaria, and for which more improved vaccines are needed such as tuberculosis and influenza virus. Although many preclinical and clinical trials have been conducted to date, no DNA vaccines or recombinant viral-vectored vaccines expressing heterologous antigens for human use have yet been licensed in the U.S., Europe or Japan. In this research, we describe the current regulatory context for gene-based prophylactic vaccines against infectious disease in the U.S., Europe, and Japan. We identify the important considerations, in particular, on the preclinical assessments that would allow these vaccines to proceed to clinical trials, and the differences on the regulatory pathway for the marketing authorization in each region. PMID:26344953

  18. Method comparison of ultrasound and kilovoltage x-ray fiducial marker imaging for prostate radiotherapy targeting

    NASA Astrophysics Data System (ADS)

    Fuller, Clifton David; Thomas, Charles R., Jr.; Schwartz, Scott; Golden, Nanalei; Ting, Joe; Wong, Adrian; Erdogmus, Deniz; Scarbrough, Todd J.

    2006-10-01

    all individual US and FM directional measures may be expected to agree with each other within a range of 1-1.5 cm. Since neither system represents a gold standard, clinical judgment must dictate whether such a difference is of import. As IMRT protocols seek dose escalation and PTV reduction predicated on US- and FM-guided imaging, future studies are needed to address these potential clinically relevant issues regarding the interchangeability and accuracy of novel positional verification techniques. Comparison series with multiple image-guidance systems are needed to refine comparisons between targeting methods. However, we do not advocate interchangeability of US and FM localization methods. Portions of this data were presented at the American Society of Clinical Oncology/American Society for Therapeutic Radiology and Oncology/Society of Surgical Oncology 2006 Prostate Cancer Symposium, San Francisco, CA, USA.

  19. A comparison of stereopsis testing between red/green targets and polarized targets in children with normal binocular vision.

    PubMed

    Yamada, Tomohiko; Scheiman, Mitchell; Mitchell, G Lynn

    2008-03-01

    Measurement of stereopsis is important in assessing a patient's binocular status. Several measurement methods are available, most commonly using polarized targets. Recently, less expensive red/green targets have become available. In this study, we compare polarized versus red/green methods, using random dot and contour targets. Sixty children with no strabismus, amblyopia, or high refractive error and normal ocular health were recruited. Stereopsis measurements were taken using the red/green and polarized versions of the Random Dot Letter "E"/RDE Test, Random Dot Butterfly/Stereo Butterfly Test, Stereo Circles/Wirt Circles, Stereo Numbers, and Stereo Animals tests. Observed agreement was used to assess agreement between results. Wilcoxon signed-rank tests were used to compare an individual's response with both targets. There was greater than 95% agreement using any of the Random Dot-based tests and the Stereo Animals tests. However, agreement was less than 60% with the Stereo Numbers test and less than 35% with the Stereo Circles/Wirt Circles test. The red/green versions of the Random Dot-based tests and the Stereo Animals test appear to be a cost-effective alternative to their polarized equivalents. Our data, however, show that the red/green versions tend to underestimate the level of stereopsis when using the Stereo Numbers and Stereo Circles/Wirt Circles tests compared to their polarized equivalents.

  20. Synthesis of the Danish Experience with Combating Nutrient Pollution of Surface Waters: The Old Regulatory Approach and a New Targeted Approach Utilising the Natural Attenuation Capacity in Landscapes

    NASA Astrophysics Data System (ADS)

    Kronvang, Brian; Windolf, Jørgen; Blicher-Mathiesen, Gitte; Tornbjerg, Henrik; Højberg, Anker; Rieman, Bo

    2016-04-01

    Excess nitrogen (N) and phosphorus (P) emissions to surface waters are a high priority environmental problem worldwide for protection of water resources in times of population growth and climate change. As clean water is a scarce resource the struggle for reducing nutrient emissions are an ongoing issue for many countries and regions. Since the mid1980s a wide range of national regulatory general measures have been implemented to reduce land based nitrogen (N) and phosphorus (P) loadings of the Danish aquatic environment. These measures have addressed both point source emissions and emissions from diffuse sources especially from agricultural production. Following nearly 4 decades of combating nutrient pollution our surface waters such as lakes and estuaries are only slowly responding on the 50% reduction in N and 56% reduction in P. Therefore, the implementation of the EU Water Framework Directive in Danish surface waters still call for further reductions of N and P loadings. Introduction of a new paradigm of targeted implemented measures was the proposed outcome of a Commission on Nature and Agriculture established by the Danish Government in 2013. Their White Book points to the need of increased growth and better environment through more targeted and efficient regulation using advanced technological mitigation methods that are implemented intelligently according to the local natural attenuation capacity for nutrients in the landscape. As a follow up a national consensus model for N was established chaining existing leaching, 3D groundwater and surface water models. The new model concept enables a calculation of the N dynamics and attenuation capacity within a scale of 15 km2. Moreover, several research projects have been conducted to investigate the effect of a suite of targeted mitigation measures such as restored natural wetlands, constructed wetlands, controlled drainage and intelligent buffer zones. The outcome of six Danish management plans for nutrient load

  1. Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis).

    PubMed

    Hebert, Francois Olivier; Renaut, Sébastien; Bernatchez, Louis

    2013-10-01

    Latest technological developments in evolutionary biology bring new challenges in documenting the intricate genetic architecture of species in the process of divergence. Sympatric populations of lake whitefish represent one of the key systems to investigate this issue. Despite the value of random genotype-by-sequencing methods and decreasing cost of sequencing technologies, it remains challenging to investigate variation in coding regions, especially in the case of recently duplicated genomes as in salmonids, as this greatly complicates whole genome resequencing. We thus designed a sequence capture array targeting 2773 annotated genes to document the nature and the extent of genomic divergence between sympatric dwarf and normal whitefish. Among the 2728 genes successfully captured, a total of 2182 coding and 10,415 noncoding putative single-nucleotide polymorphisms (SNPs) were identified after applying a first set of basic filters. A genome scan with a quality-refined selection of 2203 SNPs identified 267 outlier SNPs in 210 candidate genes located in genomic regions potentially involved in whitefish divergence and reproductive isolation. We found highly heterogeneous FST estimates among SNP loci. There was an overall low level of coding polymorphism, with a predominance of noncoding mutations among outliers. The heterogeneous patterns of divergence among loci confirm the porous nature of genomes during speciation with gene flow. Considering that few protein-coding mutations were identified as highly divergent, our results, along with previous transcriptomic studies, imply that changes in regulatory regions most likely had a greater role in the process of whitefish population divergence than protein-coding mutations. This study is the first to demonstrate the efficiency of large-scale targeted resequencing for a nonmodel species with such a large and unsequenced genome.

  2. Scenario-targeted toxicity assessment through multiple endpoint bioassays in a soil posing unacceptable environmental risk according to regulatory screening values.

    PubMed

    Rodriguez-Ruiz, A; Etxebarria, J; Boatti, L; Marigómez, I

    2015-09-01

    Lanestosa is a chronically polluted site (derelict mine) where the soil (Lanestosa (LA) soil) exceeds screening values (SVs) of regulatory policies in force (Basque Country; Europe) for Zn, Pb and Cd. A scenario-targeted toxicity assessment was carried out on the basis of a multi-endpoint bioassay approach. Acute and chronic toxicity bioassays were conducted with selected test species (Vibrio fischeri, Dictyostelium discoideum, Lactuca sativa, Raphanus sativus and Eisenia fetida) in combination with chemical analysis of soils and elutriates and with bioaccumulation studies in earthworms. Besides, the toxicity profile was compared with that of the mine runoff (RO) soil and of a fresh artificially polluted soil (LAAPS) resembling LA soil pollutant profile. Extractability studies in LA soil revealed that Pb, Zn and Cd were highly available for exchange and/or release into the environment. Indeed, Pb and Zn were accumulated in earthworms and LA soil resulted to be toxic. Soil respiration, V. fischeri, vegetative and developmental cycles of D. discoideum and survival and juvenile production of E. fetida were severely affected. These results confirmed that LA soil had unacceptable environmental risk and demanded intervention. In contrast, although Pb and Zn concentrations in RO soil revealed also unacceptable risk, both metal extractability and toxicity were much lower than in LA soil. Thus, within the polluted site, the need for intervention varied between areas that posed dissimilar risk. Besides, since LAAPS, with a high exchangeable metal fraction, was the most toxic, ageing under in situ natural conditions seemingly contributed to attenuate LA soil risk. As a whole, combining multi-endpoint bioassays with scenario-targeted analysis (including leaching and ageing) provides reliable risk assessment in soils posing unacceptable environmental risk according to SVs, which is useful to optimise the required intervention measures.

  3. Sox2 regulatory region 2 sequence works as a DNA nuclear targeting sequence enhancing the efficiency of an exogenous gene expression in ES cells.

    PubMed

    Funabashi, Hisakage; Takatsu, Makoto; Saito, Mikako; Matsuoka, Hideaki

    2010-10-01

    In this report, the effects of two DNA nuclear targeting sequence (DTS) candidates on the gene expression efficiency in ES cells were investigated. Reporter plasmids containing the simian virus 40 (SV40) promoter/enhancer sequence (SV40-DTS), a DTS for various types of cells but not being reported yet for ES cells, and the 81 base pairs of Sox2 regulatory region 2 (SRR2) where two transcriptional factors in ES cells, Oct3/4 and Sox2, are bound (SRR2-DTS), were introduced into cytoplasm in living cells by femtoinjection. The gene expression efficiencies of each plasmid in mouse insulinoma cell line MIN6 cells and mouse ES cells were then evaluated. Plasmids including SV40-DTS and SRR2-DTS exhibited higher gene expression efficiency comparing to plasmids without these DTSs, and thus it was concluded that both sequences work as a DTS in ES cells. In addition, it was suggested that SRR2-DTS works as an ES cell-specific DTS. To the best of our knowledge, this is the first report to confirm the function of DTSs in ES cells.

  4. Therapeutic targeting of regulatory T cells enhances tumor-specific CD8+ T cell responses in Epstein–Barr virus associated nasopharyngeal carcinoma

    PubMed Central

    Fogg, Mark; Murphy, John R.; Lorch, Jochen; Posner, Marshall; Wang, Fred

    2013-01-01

    Epstein–Barr virus (EBV) is associated with multiple malignancies including nasopharyngeal carcinoma (NPC). In nasopharynx cancer, CD8+ T cells specific for EBV Nuclear Antigen-1 (EBNA-1) and Latent Membrane Protein 2 (LMP2) are important components of anti-tumor immunity since both are consistently expressed in NPC. We have previously shown that EBNA-1-specific CD8+ T cell responses were suppressed in NPC patients compared to healthy controls. We now find that CD8+ T cell responses specific for LMP2 are also abnormal in NPC patients, and both EBNA-1- and LMP2-specific responses are suppressed by regulatory T cells (Treg). EBNA-1 and LMP2-specific CD8+ T cell responses, as well as immune control of EBV-infected cells in vitro, could be restored by the depletion of Tregs and by use of a clinically approved drug targeting Tregs. Thus, in vivo modulation of Tregs may be an effective means of enhancing these anti-tumor immune responses in NPC patients. PMID:23601786

  5. Expression profiling of the developing and mature Nrl-/- mouse retina: identification of retinal disease candidates and transcriptional regulatory targets of Nrl.

    PubMed

    Yoshida, Shigeo; Mears, Alan J; Friedman, James S; Carter, Todd; He, Shirley; Oh, Edwin; Jing, Yuezhou; Farjo, Rafal; Fleury, Gilles; Barlow, Carrolee; Hero, Alfred O; Swaroop, Anand

    2004-07-15

    The rod photoreceptor-specific neural retina leucine zipper protein Nrl is essential for rod differentiation and plays a critical role in regulating gene expression. In the mouse retina, rods account for 97% of the photoreceptors; however, in the absence of Nrl (Nrl-/-), no rods are present and a concomitant increase in cones is observed. A functional all-cone mouse retina represents a unique opportunity to investigate, at the molecular level, differences between the two photoreceptor subtypes. Using mouse GeneChips (Affymetrix), we have generated expression profiles of the wild-type and Nrl-/- retina at three time-points representing distinct stages of photoreceptor differentiation. Comparative data analysis revealed 161 differentially expressed genes; of which, 78 exhibited significantly lower and 83 higher expression in the Nrl-/- retina. Hierarchical clustering was utilized to predict the function of these genes in a temporal context. The differentially expressed genes primarily encode proteins associated with signal transduction, transcriptional regulation, intracellular transport and other processes, which likely correspond to differences between rods and cones and/or retinal remodeling in the absence of rods. A significant number of these genes may serve as candidates for diseases involving rod or cone dysfunction. Chromatin immunoprecipitation assay showed that in addition to the rod phototransduction genes, Nrl might modulate the promoters of many functionally diverse genes in vivo. Our studies provide molecular insights into differences between rod and cone function, yield interesting candidates for retinal diseases and assist in identifying transcriptional regulatory targets of Nrl.

  6. Identification of 4-arylidene curcumin analogues as novel proteasome inhibitors for potential anticancer agents targeting 19S regulatory particle associated deubiquitinase.

    PubMed

    Yue, Xin; Zuo, Yinglin; Ke, Hongpeng; Luo, Jiaming; Lou, Lanlan; Qin, Wenjing; Wang, Youqiao; Liu, Ziyi; Chen, Daoyuan; Sun, Haixia; Zheng, Weichao; Zhu, Cuige; Wang, Ruimin; Wen, Gesi; Du, Jun; Zhou, Binhua; Bu, Xianzhang

    2017-08-01

    The proteasomal 19S regulatory particle (RP) associated deubiquitinases (DUBs) have attracted much attention owing to their potential as a therapeutic target for cancer therapy. Identification of new entities against 19S RP associated DUBs and illustration of the underlying mechanisms is crucial for discovery of novel proteasome blockers. In this study, a series of 4-arylidene curcumin analogues were identified as potent proteasome inhibitor by preferentially blocking deubiquitinase function of proteasomal 19S RP with moderate 20S CP inhibition. The most active compound 33 exhibited a major inhibitory effect on 19S RP-associated ubiquitin-specific proteases 14, along with a minor effect on ubiquitin C-terminal hydrolase 5, which resulted in dysfunction of proteasome, and subsequently accumulated ubiquitinated proteins (such as IκB) in several cancer cells. Remarkably, though both 19S RP and 20S CP inhibition induced significantly endoplasmic reticulum stress and triggered caspase-12/9 pathway activation to promote cancer cell apoptosis, the 19S RP inhibition by 33 avoided slow onset time, Bcl-2 overexpression, and PERK-phosphorylation, which contribute to the deficiencies of clinical drug Bortezomib. These systematic studies provided insights in the development of novel proteasome inhibitors for cancer treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Comparison of Artificial Neural Networks and ARIMA statistical models in simulations of target wind time series

    NASA Astrophysics Data System (ADS)

    Kolokythas, Kostantinos; Vasileios, Salamalikis; Athanassios, Argiriou; Kazantzidis, Andreas

    2015-04-01

    The wind is a result of complex interactions of numerous mechanisms taking place in small or large scales, so, the better knowledge of its behavior is essential in a variety of applications, especially in the field of power production coming from wind turbines. In the literature there is a considerable number of models, either physical or statistical ones, dealing with the problem of simulation and prediction of wind speed. Among others, Artificial Neural Networks (ANNs) are widely used for the purpose of wind forecasting and, in the great majority of cases, outperform other conventional statistical models. In this study, a number of ANNs with different architectures, which have been created and applied in a dataset of wind time series, are compared to Auto Regressive Integrated Moving Average (ARIMA) statistical models. The data consist of mean hourly wind speeds coming from a wind farm on a hilly Greek region and cover a period of one year (2013). The main goal is to evaluate the models ability to simulate successfully the wind speed at a significant point (target). Goodness-of-fit statistics are performed for the comparison of the different methods. In general, the ANN showed the best performance in the estimation of wind speed prevailing over the ARIMA models.

  8. Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β-catenin recruitment to cis-regulatory modules

    PubMed Central

    Nakamura, Yukio; de Paiva Alves, Eduardo; Veenstra, Gert Jan C.; Hoppler, Stefan

    2016-01-01

    Key signalling pathways, such as canonical Wnt/β-catenin signalling, operate repeatedly to regulate tissue- and stage-specific transcriptional responses during development. Although recruitment of nuclear β-catenin to target genomic loci serves as the hallmark of canonical Wnt signalling, mechanisms controlling stage- or tissue-specific transcriptional responses remain elusive. Here, a direct comparison of genome-wide occupancy of β-catenin with a stage-matched Wnt-regulated transcriptome reveals that only a subset of β-catenin-bound genomic loci are transcriptionally regulated by Wnt signalling. We demonstrate that Wnt signalling regulates β-catenin binding to Wnt target genes not only when they are transcriptionally regulated, but also in contexts in which their transcription remains unaffected. The transcriptional response to Wnt signalling depends on additional mechanisms, such as BMP or FGF signalling for the particular genes we investigated, which do not influence β-catenin recruitment. Our findings suggest a more general paradigm for Wnt-regulated transcriptional mechanisms, which is relevant for tissue-specific functions of Wnt/β-catenin signalling in embryonic development but also for stem cell-mediated homeostasis and cancer. Chromatin association of β-catenin, even to functional Wnt-response elements, can no longer be considered a proxy for identifying transcriptionally Wnt-regulated genes. Context-dependent mechanisms are crucial for transcriptional activation of Wnt/β-catenin target genes subsequent to β-catenin recruitment. Our conclusions therefore also imply that Wnt-regulated β-catenin binding in one context can mark Wnt-regulated transcriptional target genes for different contexts. PMID:27068107

  9. Comparison of optimization-algorithm based feature extraction from time data or time-frequency data for target recognition purposes

    NASA Astrophysics Data System (ADS)

    Strifors, H. C.; Abrahamson, S.; Andersson, T.; Gaunaurd, G. C.

    2006-05-01

    Ultra-wideband ground penetrating radar (GPR) systems have proved useful for extracting and displaying information for target recognition purposes. Target signatures whether in the time, frequency, or joint time-frequency domains, will substantially depend on the target's burial conditions such as the type of soil, burial depth, and the soil's moisture content. That dependence can be utilized for target recognition purposes as we have demonstrated previously. The signature template of each target was computed in the time-frequency domain from the returned echo when the target was buried at a known depth in the soil with a known moisture content. Then, for any returned echo the relative difference between the similarly computed target signature and a selected signature template was computed. A global optimization method together with our (approximate) target translation method (TTM) that signature difference, chosen as object function, was minimized by adjusting the depth and moisture content, now taken to be unknown parameters. The template that gave the smallest value of the minimized object function for the returned echo was taken as target classification and the corresponding values of the depth and moisture parameters as estimates of the target's burial conditions. This optimization technique can also be applied to time-series data, avoiding the need for time-frequency analysis. It is then of interest to evaluate the relative merits of time data and time-frequency data for target recognition. Such a comparison is here preformed using signals returned from dummy mines buried underground. The results of the analysis serve to assess the intrinsic worth of data in the time domain and in the time-frequency domain for identifying subsurface targets using a GPR. The targets are buried in a test field at the Swedish Explosive Ordnance Disposal and Demining Center (SWEDEC) at Eksjo, Sweden.

  10. Regulatory mechanisms in cell-mediated immune responses. VIII. Differential expression of I-region determinants by suppressor cells and their targets in suppression of mixed leukocyte reactions

    PubMed Central

    1979-01-01

    The phenotypic expression of I-region determinants on cells producing and responding to MLR suppressor factor (MLR-TsF) was established in these studies. Alloantigen-activated MLR suppressor T cells (MLR-Ts), which produce MLR-TsF bearing gene products of the I-C subregion, were exposed to anti-I subregion sera and complement (C) before in vitro culture for MLR-TsF production. Suppressor activity was prevented by removal of cells bearing I-C determinants, whereas elimination of cells expressing I-A/B determinants had no effect. Interestingly, cytotoxic elimination of cells displaying I-J determinants also prevented MLR-TsF production. Admixture of anti-I-J and I-C antiserum-treated cells for MLR-TsF production failed to reconstitute suppressor activity, indicating that I-C and I-J gene products are expressed on a single population of cells critical to MLR suppression, rather than on distinct interacting subpopulations. Anti-I-C serum activity specific for I-C+ MLR-Ts was removed by adsorption with nylon wool-nonadherent splenic T cells and concanavalin A-activated thymocytes; adsorption with splenic B cells from anti-Thy-1,2 serum and C-treated spleen failed to remove relevant anti-I-C activity. These data suggest that regulatory I-C molecules, like I-J molecules, are preferentially expressed on T lymphocytes. Expression of I-C, or other I-region molecules on responder cell targets of MLR-TsF activity was also investigated. Responder cells were pretreated with anti-I subregion- specific sera in blocking or complement-dependent cytotoxic protocols before addition to MLR with MLR-TsF. Neither blocking nor the cytotoxic removal of cells bearing I-C or other I-region determinants from MLR responder populations interfered with MLR-TsF suppression. Because it has previously been demonstrated that MLR-TsF interacts optimally with activated, I-C syngeneic target cells, blocking and cytotoxic studies with anti-I subregion sera were also performed with responder cells

  11. [Comparison of manual infusion of propofol and target-controlled infusion: effectiveness, safety and acceptability].

    PubMed

    Mazzarella, B; Melloni, C; Montanini, S; Novelli, G P; Peduto, V A; Santandrea, E; Vincenti, E; Zattoni, J

    1999-10-01

    Diprifusor TCI is a newly developed target-controlled system for the infusion of propofol. Purpose of this study is to evaluate the acceptability, efficacy and safety of Diprifusor TCI in comparison with the manually controlled technique. This multicentre, randomised, parallel group study was carried out in 160 patients undergoing surgical procedures of 10 min to 4 h duration in 8 centres. In each centre 20 male or female patients, aged > or = 18 years, ASA I-III were randomised to treatment with either Diprifusor TCI (TCI group--80 patients) or manually controlled infusion (MI group--80 patients). Assessments included hemodynamics; adverse events, including accidents, actual or possible; recovery times; anesthetist ratings of quality of induction and maintenance, and of ease of control and use of technique. Ratings were summed up in a global quality score (study end-point). Induction doses were significantly lower (median values 1.4 vs 1.9 mg/kg) and maintenance infusion rate significantly higher (median values 10.2 vs 8.8 mg/kg/h) in the TCI group; anesthetists ratings obtained maximum scores in most patients of either group, but more frequently in the TCI group, with significant differences for ease of control (good 91.2% TCI vs 74.7% IM; adequate 8.8 vs 21.5%; poor 0 vs 3.8%), and of use of technique (good 91.2% TCI vs 60.8% IM; adequate 8.8 vs 39.2%); the global quality score showed a significant advantage for the TCI system (median value 12 vs 11). The TCI technique is effective and safe, and has a better acceptability than the manually controlled infusion technique.

  12. Novel vaccines targeting dendritic cells by coupling allergoids to nonoxidized mannan enhance allergen uptake and induce functional regulatory T cells through programmed death ligand 1.

    PubMed

    Sirvent, Sofía; Soria, Irene; Cirauqui, Cristina; Cases, Bárbara; Manzano, Ana I; Diez-Rivero, Carmen M; Reche, Pedro A; López-Relaño, Juan; Martínez-Naves, Eduardo; Cañada, F Javier; Jiménez-Barbero, Jesús; Subiza, Javier; Casanovas, Miguel; Fernández-Caldas, Enrique; Subiza, José Luis; Palomares, Oscar

    2016-08-01

    Allergen immunotherapy (AIT) is the only curative treatment for allergy. AIT faces pitfalls related to efficacy, security, duration, and patient compliance. Novel vaccines overcoming such inconveniences are in demand. We sought to study the immunologic mechanisms of action for novel vaccines targeting dendritic cells (DCs) generated by coupling glutaraldehyde-polymerized grass pollen allergoids to nonoxidized mannan (PM) compared with glutaraldehyde-polymerized allergoids (P) or native grass pollen extracts (N). Skin prick tests and basophil activation tests with N, P, or PM were performed in patients with grass pollen allergy. IgE-blocking experiments, flow cytometry, confocal microscopy, cocultures, suppression assays, real-time quantitative PCR, ELISAs, and ELISpot assays were performed to assess allergen capture by human DCs and T-cell responses. BALB/c mice were immunized with PM, N, or P. Antibody levels, cytokine production by splenocytes, and splenic forkhead box P3 (FOXP3)(+) regulatory T (Treg) cells were quantified. Experiments with oxidized PM were also performed. PM displays in vivo hypoallergenicity, induces potent blocking antibodies, and is captured by human DCs much more efficiently than N or P by mechanisms depending on mannose receptor- and dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin-mediated internalization. PM endorses human DCs to generate functional FOXP3(+) Treg cells through programmed death ligand 1. Immunization of mice with PM induces a shift to nonallergic responses and increases the frequency of splenic FOXP3(+) Treg cells. Mild oxidation impairs these effects in human subjects and mice, demonstrating the essential role of preserving the carbohydrate structure of mannan. Allergoids conjugated to nonoxidized mannan represent suitable vaccines for AIT. Our findings might also be of the utmost relevance to development of therapeutic interventions in other immune tolerance-related diseases. Copyright

  13. The adrenal cortex and steroidogenesis as cellular and molecular targets for toxicity: critical omissions from regulatory endocrine disrupter screening strategies for human health?

    PubMed

    Harvey, Philip W; Everett, David J

    2003-01-01

    Current testing strategies to assess the endocrine disrupting properties of chemicals have omitted examination of the adrenal gland and do not adequately cover the process of steroidogenesis. Steroidogenesis is critical for adrenocortical function as well as that of the testes and ovaries, and presents multiple molecular targets for toxicity, ranging from general effects on all steroidogenic tissues (e.g. via StAR protein or CYP11A1 cholesterol side-chain cleavage) through to specific targets affecting only adrenocortical function (e.g. CYP11beta/18 and glucocorticoid synthesis). Numerous chemicals of environmental relevance are now being shown to affect adrenocortical function both in vivo in aquatic species and in vitro in human cell lines, and given the vital role of the adrenal gland to human health and development, there is a strong case for including dedicated assessment techniques in screening batteries for endocrine-disrupting chemicals, not least to assist in general data interpretation (e.g. whether adrenal hypertrophy is due to stress or to a more sinister adrenocortical insufficiency). Cell lines such as H295R (derived from a human adrenocortical adenocarcinoma) currently exist that will allow assessment of cortisol production and most of the major enzymes and functional proteins in the steroidogenic pathway (e.g. StAR; CYP11A1/scc; CYP11beta/18; CYP17; CYP19; CYP21; 3beta-hydroxysteroid dehydrogenase). Adequate assessment of adrenocortical function, as with any component of the integrated endocrine system, probably also will require the development of specific in vivo methodology to include effects on hypothalamo-pituitary function. Finally, although there is currently no direct evidence that environmental exposure to endocrine-disrupting (oestrogenic) chemicals has actually caused adverse human health effects, lessons have been learned on their potential from the diethylstilboestrol case. Similar evidence exists from aminoglutethimide and etomidate on

  14. Direct Comparison of a Natural Loss-Of-Function Single Nucleotide Polymorphism with a Targeted Deletion in the Ncf1 Gene Reveals Different Phenotypes

    PubMed Central

    Sareila, Outi; Hagert, Cecilia; Rantakari, Pia; Poutanen, Matti; Holmdahl, Rikard

    2015-01-01

    The genetic targeting of mouse models has given insight into complex processes. However, phenotypes of genetically targeted mice are susceptible to artifacts due to gene manipulation, which may lead to misinterpretation of the observations. To directly address these issues, we have compared the immunological phenotypes of Ncf1 knockout mice with Ncf1m1J mice possessing a naturally occurring intronic loss-of-function SNP in their Ncf1 gene. Neutrophil cytosolic factor 1 (NCF1) is the key regulatory component of the phagocytic NADPH oxidase 2 (NOX2) complex. Defects in NCF1 lead to lower production of reactive oxygen species (ROS) associated with autoimmune diseases in humans. In mice, collagen induced arthritis (CIA) and psoriatic arthritis are autoimmune disorders known to be regulated by Ncf1, and they were utilized in the present study to compare the Ncf1 knockout with Ncf1m1J mice. Targeted Ncf1 knockout mice were generated on a pure C57BL/6N genetic background, and thereafter crossed with B10.Q.Ncf1m1J mice. The targeting silenced the Ncf1 gene as intended, and both the B6N;B10.Q.Ncf1m1J mice as well as the knockout littermates had reduced ROS production compared to wild type mice. Both also exhibited enhanced STAT1 (signal transducer and activator of transcription 1) protein expression as an indicator of pronounced interferon signature reported recently for Ncf1 deficient mice. Surprisingly, female Ncf1 knockout mice were protected from CIA whereas the Ncf1m1J females developed severe disease. Ovariectomization retrieved the susceptibility of Ncf1 knockout females pointing to a sex hormone regulated protection against CIA in these mice. The data partly explains the discrepancy of the phenotypes reported earlier utilizing the Ncf1m1J mice or Ncf1 knockout mice. These observations indicate that even a targeted knockout mutation may lead to a different biological outcome in comparison to the natural loss-of-function mutation of the same gene. PMID:26528554

  15. Genome-Wide Investigation Using sRNA-Seq, Degradome-Seq and Transcriptome-Seq Reveals Regulatory Networks of microRNAs and Their Target Genes in Soybean during Soybean mosaic virus Infection

    PubMed Central

    Yu, Kangfu; Wang, Aiming

    2016-01-01

    MicroRNAs (miRNAs) play key roles in a variety of cellular processes through regulation of their target gene expression. Accumulated experimental evidence has demonstrated that infections by viruses are associated with the altered expression profile of miRNAs and their mRNA targets in the host. However, the regulatory network of miRNA-mRNA interactions during viral infection remains largely unknown. In this study, we performed small RNA (sRNA)-seq, degradome-seq and as well as a genome-wide transcriptome analysis to profile the global gene and miRNA expression in soybean following infections by three different Soybean mosaic virus (SMV) isolates, L (G2 strain), LRB (G2 strain) and G7 (G7 strain). sRNA-seq analyses revealed a total of 253 soybean miRNAs with a two-fold or greater change in abundance compared with the mock-inoculated control. 125 transcripts were identified as the potential cleavage targets of 105 miRNAs and validated by degradome-seq analyses. Genome-wide transcriptome analysis showed that total 2679 genes are differentially expressed in response to SMV infection including 71 genes predicted as involved in defense response. Finally, complex miRNA-mRNA regulatory networks were derived using the RNAseq, small RNAseq and degradome data. This work represents a comprehensive, global approach to examining virus-host interactions. Genes responsive to SMV infection are identified as are their potential miRNA regulators. Additionally, regulatory changes of the miRNAs themselves are described and the regulatory relationships were supported with degradome data. Taken together these data provide new insights into molecular SMV-soybean interactions and offer candidate miRNAs and their targets for further elucidation of the SMV infection process. PMID:26963095

  16. Comparison of regulatory method estimated drinking water exposure concentrations with monitoring results from surface drinking water supplies.

    PubMed

    Jackson, Scott; Hendley, Paul; Jones, Russell; Poletika, Nick; Russell, Mark

    2005-11-02

    Crop-protection compounds are useful tools that enhance the quality of the food we enjoy. However, crop-protection products can enter aquatic systems either by direct or by indirect application. To better understand the possible frequency and magnitude of exposure to water resources, the regulatory community has developed a set of relatively straightforward models for estimating exposure to these water systems. The focus of this research was to compare how well the estimates of exposure to drinking water based on model calculations relate to actual monitoring data. Physical/chemical property data were entered in the EPA's exposure model FIRST and into PRZM/EXAMS. The predictions from FIRST and PRZM/EXAMS were then compared to actual monitoring data from a USGS/EPA cooperative program, which monitored for pesticides in vulnerable surface drinking water supplies during 1999 and 2000. Results from this examination indicate the exposure from the models can overpredict concentrations found in water by several orders of magnitude. An overprediction factor is presented that corrects model predictions to more closely approximate concentrations found in reservoirs (p = 0.05).

  17. Global Comparison of Warring Groups in 2002–2007: Fatalities from Targeting Civilians vs. Fighting Battles

    PubMed Central

    Hicks, Madelyn Hsiao-Rei; Lee, Uih Ran; Sundberg, Ralph; Spagat, Michael

    2011-01-01

    Background Warring groups that compete to dominate a civilian population confront contending behavioral options: target civilians or battle the enemy. We aimed to describe degrees to which combatant groups concentrated lethal behavior into intentionally targeting civilians as opposed to engaging in battle with opponents in contemporary armed conflict. Methodology/Principal Findings We identified all 226 formally organized state and non-state groups (i.e. actors) that engaged in lethal armed conflict during 2002–2007: 43 state and 183 non-state. We summed civilians killed by an actor's intentional targeting with civilians and combatants killed in battles in which the actor was involved for total fatalities associated with each actor, indicating overall scale of armed conflict. We used a Civilian Targeting Index (CTI), defined as the proportion of total fatalities caused by intentional targeting of civilians, to measure the concentration of lethal behavior into civilian targeting. We report actor-specific findings and four significant trends: 1.) 61% of all 226 actors (95% CI 55% to 67%) refrained from targeting civilians. 2.) Logistic regression showed actors were more likely to have targeted civilians if conflict duration was three or more years rather than one year. 3.) In the 88 actors that targeted civilians, multiple regressions showed an inverse correlation between CTI values and the total number of fatalities. Conflict duration of three or more years was associated with lower CTI values than conflict duration of one year. 4.) When conflict scale and duration were accounted for, state and non-state actors did not differ. We describe civilian targeting by actors in prolonged conflict. We discuss comparable patterns found in nature and interdisciplinary research. Conclusions/Significance Most warring groups in 2002–2007 did not target civilians. Warring groups that targeted civilians in small-scale, brief conflict concentrated more lethal behavior into

  18. Comparison of a grid-based filter to a Kalman filter for the state estimation of a maneuvering target

    NASA Astrophysics Data System (ADS)

    Silbert, Mark; Mazzuchi, Thomas; Sarkani, Shahram

    2011-09-01

    Providing accurate state estimates of a maneuvering target is an important problem. This problem occurs when tracking maneuvering boats or even people wandering around. In our earlier paper, a specialized grid-based filter (GBF) was introduced as an effective method to produce accurate state estimates of a target moving in two dimensions, while requiring only a two-dimensional grid. The paper showed that this GBF produces accurate state estimates because the filter can capture the kinematic constraints of the target directly, and thus account for them in the estimation process. In this paper, the relative performance of a GBF to a Kalman filter is investigated. The state estimates (position and velocity) from a GBF are compared to those from a Kalman filter, against a maneuvering target. This study will employ the comparison paradigm presented by Kirubarajan and Bar-Shalom. The paradigm incrementally increases the maneuverability of a target to determine how the two different track filters compare as the target becomes more maneuverable. The intent of this study is to determine how maneuverable the target must be to gain the benefit from a GBF over a Kalman filter. The paper will discuss the target motion model, the GBF implementation, and the Kalman filter used for the study. Our results show that the GBF outperforms a Kalman filter, especially as the target becomes more maneuverable. A disadvantage of the GBF is that it is more computational than a Kalman filter. The paper will discuss the grid and sample sizing needed to obtain quality estimates from a GBF. It will be shown that the sizes are much smaller than what may be expected and is quite stable over a large range of sizes. Furthermore, this GBF can exploit parallelization of the computations, making the processing time significantly less.

  19. Comparison of PCR assays targeting the multi-copy targets B1 gene and 529 bp repetitive element for detection of Toxoplasma gondii in swine muscle.

    PubMed

    Veronesi, Fabrizia; Santoro, Azzurra; Milardi, Giovanni Luigi; Diaferia, Manuela; Branciari, Raffaella; Miraglia, Dino; Cioffi, Attilia; Gabrielli, Simona; Ranucci, David

    2017-05-01

    The comparison of the sensitivities of two molecular assays designed to target the multi-copy sequences of the Toxoplasma gondii genomic B1 region and 529 bp-RE respectively, in detecting T. gondii in swine muscle was assessed. Diaphragm pillars were obtained from 498 slaughtered pigs managed in intensive farms in Central Italy. Genomic DNA was extracted from the tissues and T. gondii-B1 and 529 bp-RE sequences were amplified by specific PCR protocols. Toxoplasma gondii DNA was detected in 165 samples (33.13%). There was a good correlation (κ = 0.77) between the results obtained targeting the two different genetic markers, however the 529 bp RE-PCR assay overall detected a significantly higher (P < 0.05) number of T. gondii-positive samples (150 samples) than the B1-PCR protocol (134). Our results show that: i) standardized B1 and 529 bp-RE PCRs applied to muscle tissues can detect a high rate of T. gondii-infection; ii) a multi-target PCR approach is recommended for the accurate diagnosis of infection in swine and can also be used in food testing. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Comparisons of Reflectance Targets at the Above Water Radiometry Workshop on Long Island Sound, August 4 - 6, 2010

    NASA Astrophysics Data System (ADS)

    Johnson, B.; Fargion, G. S.; Saunders, R. D.; Ondrusek, M. E.

    2012-12-01

    On August 4-5, 2010, members from the satellite remote sensing community participated in a workshop off the coast of Long Island, New York. The participant's objective was to interpret and implement recently published protocols for measuring normalized, water-leaving spectral radiances by above-water in situ radiometry and compare the results. Each research team applied the protocols to the measurement of the water's surface and three reflectance standard targets supplied by NIST - a white and a gray diffuse reflectance target and a blue ground-glass target. The reflectance values of the water's surface and the test targets were derived and analyzed by each team. We report on the workshop detailing the methods for comparison of the participant's results of the test targets. The workshop served as a preparation for the vigorous validation activities that occurred following the launch of the Visible Infrared Imager Radiometer Suite (VIIRS). Above water, in situ, radiometric measurements using uncalibrated radiometers and standard diffuse reflectance targets are one method used by researchers to validate the VIIRS data products. The Joint Polar Satellite System (JPSS) office provided support to NIST for this work (NA12AANEG0230).

  1. Comparison of provider and plan-based targeting strategies for disease management.

    PubMed

    Annis, Ann M; Holtrop, Jodi Summers; Tao, Min; Chang, Hsiu-Ching; Luo, Zhehui

    2015-05-01

    We aimed to describe and contrast the targeting methods and engagement outcomes for health plan-delivered disease management with those of a provider-delivered care management program. Health plan epidemiologists partnered with university health services researchers to conduct a quasi-experimental, mixed-methods study of a 2-year pilot. We used semi-structured interviews to assess the characteristics of program-targeting strategies, and calculated target and engagement rates from clinical encounter data. Five physician organizations (POs) with 51 participating practices implemented care management. Health plan member lists were sent monthly to the practices to accept patients, and then the practices sent back data reports regarding targeting and engagement in care management. Among patients accepted by the POs, we compared those who were targeted and engaged by POs with those who met health plan targeting criteria. The health plan's targeting process combined claims algorithms and employer group preferences to identify candidates for disease management; on the other hand, several different factors influenced PO practices' targeting approaches, including clinical and personal knowledge of the patients, health assessment information, and availability of disease-relevant programs. Practices targeted a higher percentage of patients for care management than the health plan (38% vs 16%), where only 7% of these patients met the targeting criteria of both. Practices engaged a higher percentage of their targeted patients than the health plan (50% vs 13%). The health plan's claims-driven targeting approach and the clinically based strategies of practices both provide advantages; an optimal model may be to combine the strengths of each approach to maximize benefits in care management.

  2. Comparison of Orientation and Rotational Motion of Skeletal Muscle Cross-bridges Containing Phosphorylated and Dephosphorylated Myosin Regulatory Light Chain*

    PubMed Central

    Midde, Krishna; Rich, Ryan; Marandos, Peter; Fudala, Rafal; Li, Amy; Gryczynski, Ignacy; Borejdo, Julian

    2013-01-01

    Calcium binding to thin filaments is a major element controlling active force generation in striated muscles. Recent evidence suggests that processes other than Ca2+ binding, such as phosphorylation of myosin regulatory light chain (RLC) also controls contraction of vertebrate striated muscle (Cooke, R. (2011) Biophys. Rev. 3, 33–45). Electron paramagnetic resonance (EPR) studies using nucleotide analog spin label probes showed that dephosphorylated myosin heads are highly ordered in the relaxed fibers and have very low ATPase activity. This ordered structure of myosin cross-bridges disappears with the phosphorylation of RLC (Stewart, M. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 430–435). The slower ATPase activity in the dephosporylated moiety has been defined as a new super-relaxed state (SRX). It can be observed in both skeletal and cardiac muscle fibers (Hooijman, P., Stewart, M. A., and Cooke, R. (2011) Biophys. J. 100, 1969–1976). Given the importance of the finding that suggests a novel pathway of regulation of skeletal muscle, we aim to examine the effects of phosphorylation on cross-bridge orientation and rotational motion. We find that: (i) relaxed cross-bridges, but not active ones, are statistically better ordered in muscle where the RLC is dephosporylated compared with phosphorylated RLC; (ii) relaxed phosphorylated and dephosphorylated cross-bridges rotate equally slowly; and (iii) active phosphorylated cross-bridges rotate considerably faster than dephosphorylated ones during isometric contraction but the duty cycle remained the same, suggesting that both phosphorylated and dephosphorylated muscles develop the same isometric tension at full Ca2+ saturation. A simple theory was developed to account for this fact. PMID:23319584

  3. Comparison of quantitative PCR assays for Escherichia coli targeting ribosomal RNA and single copy genes

    EPA Science Inventory

    Aims: Compare specificity and sensitivity of quantitative PCR (qPCR) assays targeting single and multi-copy gene regions of Escherichia coli. Methods and Results: A previously reported assay targeting the uidA gene (uidA405) was used as the basis for comparing the taxono...

  4. Comparison of quantitative PCR assays for Escherichia coli targeting ribosomal RNA and single copy genes

    EPA Science Inventory

    Aims: Compare specificity and sensitivity of quantitative PCR (qPCR) assays targeting single and multi-copy gene regions of Escherichia coli. Methods and Results: A previously reported assay targeting the uidA gene (uidA405) was used as the basis for comparing the taxono...

  5. Comparison of bulk and pitcher-catcher targets for laser-driven neutron production

    NASA Astrophysics Data System (ADS)

    Willingale, L.; Petrov, G. M.; Maksimchuk, A.; Davis, J.; Freeman, R. R.; Joglekar, A. S.; Matsuoka, T.; Murphy, C. D.; Ovchinnikov, V. M.; Thomas, A. G. R.; Van Woerkom, L.; Krushelnick, K.

    2011-08-01

    Laser-driven d(d, n)-3He beam-target fusion neutron production from bulk deuterated plastic (CD) targets is compared with a pitcher-catcher target scheme using an identical laser and detector arrangement. For laser intensities in the range of (1-3) × 1019 W cm-2, it was found that the bulk targets produced a high yield (5 × 104 neutrons per steradian) beamed preferentially in the laser propagation direction. Numerical modeling shows the importance of considering the temperature adjusted stopping powers to correctly model the neutron production. The bulk CD targets have a high background target temperature leading to a reduced stopping power for the deuterons, which increases the probability of generating neutrons by fusion. Neutron production from the pitcher-catcher targets was not as efficient since it does not benefit from the reduced stopping power in the cold catcher target. Also, the inhibition of the deuteron acceleration by a proton rich contamination layer significantly reduces the pitcher-catcher neutron production.

  6. Comparison of small molecules and oligonucleotides that target a toxic, non-coding RNA.

    PubMed

    Costales, Matthew G; Rzuczek, Suzanne G; Disney, Matthew D

    2016-06-01

    Potential RNA targets for chemical probes and therapeutic modalities are pervasive in the transcriptome. Oligonucleotide-based therapeutics are commonly used to target RNA sequence. Small molecules are emerging as a modality to target RNA structures selectively, but their development is still in its infancy. In this work, we compare the activity of oligonucleotides and several classes of small molecules that target the non-coding r(CCUG) repeat expansion (r(CCUG)(exp)) that causes myotonic dystrophy type 2 (DM2), an incurable disease that is the second-most common cause of adult onset muscular dystrophy. Small molecule types investigated include monomers, dimers, and multivalent compounds synthesized on-site by using RNA-templated click chemistry. Oligonucleotides investigated include phosphorothioates that cleave their target and vivo-morpholinos that modulate target RNA activity via binding. We show that compounds assembled on-site that recognize structure have the highest potencies amongst small molecules and are similar in potency to a vivo-morpholino modified oligonucleotide that targets sequence. These studies are likely to impact the design of therapeutic modalities targeting other repeats expansions that cause fragile X syndrome and amyotrophic lateral sclerosis, for example.

  7. Experimental comparison of carbon and beryllium as divertor target materials in JET

    NASA Astrophysics Data System (ADS)

    Campbell, D. J.; JET Team

    1997-02-01

    The performance of carbon (CFC) and beryllium as divertor target materials has been investigated in the JET pumped divertor under a wide range of experimental conditions. In general, the characteristics of L- and H-mode plasmas on the two targets were very similar. The impurity content in the two cases was also similar and it is believed that carbon sputtered from plasma-facing components in the main chamber played a significant role in beryllium target experiments. The success of the target design was confirmed by the absence of carbon blooms and beryllium melting on tile edges. However, in a specific melt experiment designed to assess the behaviour of plasmas on molten and melted beryllium, little evidence of vapour shielding of the target was found and melt damage to a depth of 3 mm was observed.

  8. Comparison of relative effectiveness of video with serial visual presentation for target reconnaissance from UASs

    NASA Astrophysics Data System (ADS)

    Skirlo, Frank E.; Matthews, Anthony J.; Friedman, Melvin; Mark, Brian L.

    2016-05-01

    Reconnaissance from an unmanned aerial systems (UAS) is often done using video presentation. An alternate method is Serial Visual Presentation (SVP). In SVP, a static image remains in view until replaced by a new image at a rate equivalent to the live video. Mardell et al. have shown, in a forested environment, that a higher fraction of targets (people lost in the forest), are found with SVP than with video presentation. Here Mardell's experiment is repeated for military targets in forested terrain at a fixed altitude. We too find a higher fraction of targets are found using SVP rather than video presentation. Typically it takes five seconds to cover a video field of view and at 30 frames per second. This implies that, for scenes where the target is not moving, 150 video images have nearly identical information (from a reconnaissance point of view) as a single SVP image. This is highly significant since transmission bandwidth is a limiting factor for most UASs. Finding targets in video or in SVP is an arduous task. For that reason we also compare aided target detection performance (Aided SVP) and unaided target detection performance on SVP images.

  9. Comparison of ({alpha},n) thick-target neutron yields and spectra from ORIGEN-S and SOURCES

    SciTech Connect

    Brown, T.H.; Wilson, W.B.; Perry, R.T.

    1998-12-31

    Both ORIGEN-S and SOURCES generate thick-target neutron yields and energy spectra from ({alpha}, n) reactions in homogeneous material containing alpha-emitting and ({alpha},n) target elements by simulating reaction physics, using alpha-emission energy spectra, elemental stopping cross sections, ({alpha}, n) target elements by simulating reaction physics, using alpha-emission energy spectra, elemental stopping cross sections, ({alpha}, n) cross sections for target nuclei, and branching fractions to product-nuclide energy levels. This methodology results in accurate yield and spectra. ORIGEN-S has two options for calculating yields and spectra. The UO{sub 2} option (default) estimates yields and spectra assuming the input alpha emitters to be infinitely dilute in UO{sub 2}. The borosilicate-glass option estimates yields from the total input material composition and generates spectra purportedly representative of spectra generated by {sup 238}Pu, {sup 241}Am, {sup 242}Cm, and {sup 244}Cm infinitely dilute in borosilicate glass, even if none of these four alpha emitters are present in the input material composition. Because yields from the borosilicate-glass option in ORIGEN-S are based on entire input material composition and are reasonably accurate, the same is often assumed to be true for spectra. The input/output functionality of the borosilicate-glass option, along with ambiguity in ORIGEN-S documentation, gives the incorrect impression that spectra representative of input compositions are generated. This impression is reinforced by wide usage of the SCALE code system and its ORIGEN-S module and their sponsorship by the US Nuclear Regulatory Commission.

  10. A comparison between computer-controlled and set work rate exercise based on target heart rate

    NASA Technical Reports Server (NTRS)

    Pratt, Wanda M.; Siconolfi, Steven F.; Webster, Laurie; Hayes, Judith C.; Mazzocca, Augustus D.; Harris, Bernard A., Jr.

    1991-01-01

    Two methods are compared for observing the heart rate (HR), metabolic equivalents, and time in target HR zone (defined as the target HR + or - 5 bpm) during 20 min of exercise at a prescribed intensity of the maximum working capacity. In one method, called set-work rate exercise, the information from a graded exercise test is used to select a target HR and to calculate a corresponding constant work rate that should induce the desired HR. In the other method, the work rate is controlled by a computer algorithm to achieve and maintain a prescribed target HR. It is shown that computer-controlled exercise is an effective alternative to the traditional set work rate exercise, particularly when tight control of cardiovascular responses is necessary.

  11. A comparison between computer-controlled and set work rate exercise based on target heart rate

    NASA Technical Reports Server (NTRS)

    Pratt, Wanda M.; Siconolfi, Steven F.; Webster, Laurie; Hayes, Judith C.; Mazzocca, Augustus D.; Harris, Bernard A., Jr.

    1991-01-01

    Two methods are compared for observing the heart rate (HR), metabolic equivalents, and time in target HR zone (defined as the target HR + or - 5 bpm) during 20 min of exercise at a prescribed intensity of the maximum working capacity. In one method, called set-work rate exercise, the information from a graded exercise test is used to select a target HR and to calculate a corresponding constant work rate that should induce the desired HR. In the other method, the work rate is controlled by a computer algorithm to achieve and maintain a prescribed target HR. It is shown that computer-controlled exercise is an effective alternative to the traditional set work rate exercise, particularly when tight control of cardiovascular responses is necessary.

  12. Comparison of monostatic and bistatic bearing estimation performance for low RCS targets

    NASA Astrophysics Data System (ADS)

    Boyle, Robert J.; Wasylkiwskyj, Wasyl

    1994-07-01

    Bistatic radars, specifically forward-scatter radars, are proposed as an alternative to standard monostatic radars against targets whose radar cross sections (RCS) have been reduced by passive means. Forward-scatter radars operate by detecting echoes from a targets forward-scatter RCS, which is insensitive to effects of passive RCS reduction techniques. However, the performance of the forward-scatter radar is compromised when the angular separation between the interference, which propagates directly from the transmitter to the receiver, and the target return is less than the Rayleigh resolution limit of the receiving antenna. This research presents the results of a parametric study of the ability of a forward-scatter radar to detect and measure the bearing of a large target, whose RCS is reduced via passive means. Super-resolution array processing techniques, particularly root-MUSIC (multiple signal classification), are used to overcome the traditional limitations resulting from the Rayleigh resolution limit of the antenna. The study compares the received power and the bearing measurement accuracy of the forward-scatter radar to that of an 'equivalent' monostatic radar system. The results indicate that forward-scatter radars enjoy advantages in detection and bearing measurement when the backscatter RCS of the target has been reduced and when the target is close to the baseline. The results also indicate that, through the use of super-resolution array processing, the capability of the forward-scatter radar to accurately measure the bearing of the target is dependent upon the amount of interference from the direct wave (i.e., the wave which propagates from the transmitter directly to the receiver) and the correlation between the direct wave and the target echo. Good bearing estimates can be achieved if the correlation coefficient is less than 0.95. Bearing measurements may be improved by suppressing the direct wave by either sidelobe control or null steering

  13. Calibration Targets of the Southwest: Albedo and Homogeneity Comparisons Using AVIRIS Data

    NASA Technical Reports Server (NTRS)

    Pavri, Betina; Green, Robert

    1998-01-01

    Various locations in the southwestern U.S. are used to calibrate remote sensing instruments. This study shows how some of these targets compare in terms of albedo and homogeneity, and records the variation of these factors for a single location (Ivanpah Playa) over a period of one year. Results indicate that there is a great deal of variation among these targets in albedo, spectral flatness, and surface uniformity, and that these factors can change throughout the year.

  14. Comparison of Standard Light Water Reactor Cross-Section Libraries using the United States Nuclear Regulatory Commission Boiling Water Reactor Benchmark Problem

    NASA Astrophysics Data System (ADS)

    Kulesza, Joel A.; Arzu Alpan, F.

    2016-02-01

    This paper describes a comparison of contemporary and historical light water reactor shielding and pressure vessel dosimetry cross-section libraries for a boiling water reactor calculational benchmark problem. The calculational benchmark problem was developed at Brookhaven National Laboratory by the request of the U. S. Nuclear Regulatory Commission. The benchmark problem was originally evaluated by Brookhaven National Laboratory using the Oak Ridge National Laboratory discrete ordinates code DORT and the BUGLE-93 cross-section library. In this paper, the Westinghouse RAPTOR-M3G three-dimensional discrete ordinates code was used. A variety of cross-section libraries were used with RAPTOR-M3G including the BUGLE93, BUGLE-96, and BUGLE-B7 cross-section libraries developed at Oak Ridge National Laboratory and ALPAN-VII.0 developed at Westinghouse. In comparing the calculated fast reaction rates using the four aforementioned cross-section libraries in the pressure vessel capsule, for six dosimetry reaction rates, a maximum relative difference of 8% was observed. As such, it is concluded that the results calculated by RAPTOR-M3G are consistent with the benchmark and further that the different vintage BUGLE cross-section libraries investigated are largely self-consistent.

  15. Cancer targeting potential of some ligand-anchored poly(propylene imine) dendrimers: a comparison.

    PubMed

    Kesharwani, Prashant; Tekade, Rakesh K; Gajbhiye, Virendra; Jain, Keerti; Jain, Narendra K

    2011-06-01

    The present investigation was aimed at developing and comparing the cancer-targeting potential of ligand-anchored dendrimers. Folate-, dextran-, and galactose-anchored poly(propylene imine) dendrimers were synthesized and characterized. Dendritic formulations were evaluated for ex vivo cytotoxicity on HeLa and SiHa cell lines. Flow cytometry studies were performed on the HeLa cell line. An ex vivo MTT assay on HeLa cells indicated IC(50) values of 0.05, 0.2, 0.8, and 0.08 μM for folate, dextran, and galactose formulations, and for free paclitaxel (PTX), respectively. An analogous observation was carried out in SiHa cells, where IC(50) values of 0.6, 0.8, 10, and 6 μM were observed by folate, dextran, and galactose formulations, and free PTX, respectively. The outcome of the MTT assay and flow cytometry suggested the order of targeting potential of various ligands under investigation as folate > dextran > galactose. The outcome is deemed to be of scientific value and is believed to assist drug delivery scientists during selection of targeting ligands. The cancer targeting potential of folate, dextran and galactose functionalized polypropyleneimine (PPI) dendrimers was studied by this group of investigators, reporting the order of targeting potential as folate > dextran > galactose. Copyright © 2011 Elsevier Inc. All rights reserved.

  16. Comparison of treecodes for computing electrostatic potentials in charged particle systems with disjoint targets and sources.

    PubMed

    Boateng, Henry A; Krasny, Robert

    2013-09-30

    In molecular simulations, it is sometimes necessary to compute the electrostatic potential at M target sites due to a disjoint set of N charged source particles. Direct summation requires O(MN) operations, which is prohibitively expensive when M and N are large. Here, we consider two alternative tree-based methods that reduce the cost. The standard particle-cluster treecode partitions the N sources into an octree and applies a far-field approximation, whereas a recently developed cluster-particle treecode instead partitions the M targets into an octree and applies a near-field approximation. We compare the two treecodes with direct summation and document their accuracy, CPU run time, and memory usage. We find that the particle-cluster treecode is faster when N > M, that is, when the sources outnumber the targets, and conversely, the cluster-particle treecode is faster when M > N, that is, when the targets outnumber the sources. Hence, the two treecodes provide useful tools for computing electrostatic potentials in charged particle systems with disjoint targets and sources.

  17. Performance and strategy comparisons of human listeners and logistic regression in discriminating underwater targets.

    PubMed

    Yang, Lixue; Chen, Kean

    2015-11-01

    To improve the design of underwater target recognition systems based on auditory perception, this study compared human listeners with automatic classifiers. Performances measures and strategies in three discrimination experiments, including discriminations between man-made and natural targets, between ships and submarines, and among three types of ships, were used. In the experiments, the subjects were asked to assign a score to each sound based on how confident they were about the category to which it belonged, and logistic regression, which represents linear discriminative models, also completed three similar tasks by utilizing many auditory features. The results indicated that the performances of logistic regression improved as the ratio between inter- and intra-class differences became larger, whereas the performances of the human subjects were limited by their unfamiliarity with the targets. Logistic regression performed better than the human subjects in all tasks but the discrimination between man-made and natural targets, and the strategies employed by excellent human subjects were similar to that of logistic regression. Logistic regression and several human subjects demonstrated similar performances when discriminating man-made and natural targets, but in this case, their strategies were not similar. An appropriate fusion of their strategies led to further improvement in recognition accuracy.

  18. Comparison of three image segmentation techniques for target volume delineation in positron emission tomography.

    PubMed

    Drever, Laura A; Roa, Wilson; McEwan, Alexander; Robinson, Don

    2007-03-09

    Incorporation of positron emission tomography (PET) data into radiotherapy planning is currently under investigation for numerous sites including lung, brain, head and neck, breast, and prostate. Accurate tumor-volume quantification is essential to the proper utilization of the unique information provided by PET. Unfortunately,target delineation within PET currently remains a largely unaddressed problem. We therefore examined the ability of three segmentation methods-thresholding, Sobel edge detection, and the watershed approach-to yield accurate delineation of PET target cross-sections. A phantom study employing well-defined cylindrical and spherical volumes and activity distributions provided an opportunity to assess the relative efficacy with which the three approaches could yield accurate target delineation in PET. Results revealed that threshold segmentation can accurately delineate target cross-sections, but that the Sobel and watershed techniques both consistently fail to correctly identify the size of experimental volumes. The usefulness of threshold-based segmentation is limited, however, by the dependence of the correct threshold (that which returns the correct area at each image slice) on target size.

  19. Comparison of two kinds of nanomedicine for targeted gene therapy: premodified or postmodified gene delivery systems

    PubMed Central

    Jiang, Zhaoshun; Sun, Cong; Yin, Zhaohui; Zhou, Fang; Ge, Linfu; Liu, Ximin; Kong, Fansheng

    2012-01-01

    Background The applications of ligand-polyethylene glycol (PEG)-modified nanocarriers have now emerged, as well as recognized strategies to provide the vectors with active targeting properties. In this research, premodification and postmodification were compared using the same ligand, ie, a novel conjugated mannan-containing PEG and L-α-phosphatidylethanolamine (PE). Methods Premodified and postmodified solid lipid nanoparticles were prepared and the characteristics of the two kinds of vehicles were evaluated. The modified vectors were then administered intravenously to rats and the in vivo targeting behavior of the complexes was investigated in liver macrophages. Results By carefully formulating the carriers with an optimal ratio of mannan-containing PEG-PE, postmodified vehicles displayed more efficient gene expression in rat Kupffer cells both in vitro and in vivo. Conclusion Postmodified gene carriers are superior to premodified gene vectors, although the latter is also promising for targeted gene delivery. This discovery could guide our future research. PMID:22619539

  20. Plasmodial sugar transporters as anti-malarial drug targets and comparisons with other protozoa

    PubMed Central

    2011-01-01

    Glucose is the primary source of energy and a key substrate for most cells. Inhibition of cellular glucose uptake (the first step in its utilization) has, therefore, received attention as a potential therapeutic strategy to treat various unrelated diseases including malaria and cancers. For malaria, blood forms of parasites rely almost entirely on glycolysis for energy production and, without energy stores, they are dependent on the constant uptake of glucose. Plasmodium falciparum is the most dangerous human malarial parasite and its hexose transporter has been identified as being the major glucose transporter. In this review, recent progress regarding the validation and development of the P. falciparum hexose transporter as a drug target is described, highlighting the importance of robust target validation through both chemical and genetic methods. Therapeutic targeting potential of hexose transporters of other protozoan pathogens is also reviewed and discussed. PMID:21676209

  1. Comparison of Active and Passive Targeting of Docetaxel for Prostate Cancer Therapy by HPMA copolymer-RGDfK Conjugates

    PubMed Central

    Ray, Abhijit; Larson, Nate; Pike, Daniel B.; Grüner, Michele; Naik, Sachin; Bauer, Hillevi; Malugin, Alexander; Greish, Khaled; Ghandehari, Hamidreza

    2011-01-01

    N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer-docetaxel-RGDfK conjugate was synthesized, characterized, and evaluated in vitro and in vivo in comparison with untargeted low and high molecular weight HPMA copolymer-docetaxel conjugates. The targeted conjugate was designed to have a hydrodynamic diameter below renal threshold to allow elimination post treatment. All conjugates demonstrated the ability to inhibit the growth of DU145 and PC3 human prostate cancer cells and the HUVEC at low nanomolar concentrations. The targeted conjugate showed active binding to αvβ3 integrins in both HUVEC and DU145 cells, whereas the untargeted conjugate demonstrated no evidence of specific binding. Efficacy at two concentrations (20 mg/kg and 40 mg/kg) was evaluated in nu/nu mice bearing DU145 tumor xenografts treated with a single dose of conjugates and compared with controls. RGDfK targeted and high molecular weight nontargeted conjugates exhibited the highest antitumor efficacy as evaluated by tumor regression. These results demonstrate that αvβ3 integrin targeted polymeric conjugates with improved water solubility, reduced toxicity and ease of elimination post treatment in vivo are promising candidates for prostate cancer therapy. PMID:21599008

  2. A comparison of 1-D and 2-D algorithms for radar target classification

    NASA Astrophysics Data System (ADS)

    Novak, Leslie M.

    The use of high-resolution radar measurement data from four ground vehicles (bulldozer, Dodge Power Wagon, Dodge Van, and Camaro) to evaluate the performance of several 1D and 2D classifiers is discussed. The 1D classifiers use high-resolution range profiles to classify targets; the 2D classifier uses high-resolution inverse synthetic aperture radar (ISAR) images to classify targets. Classification performance results using the 1D and 2D algorithms are presented, and it is shown that the 2D algorithm performed best.

  3. Comparison of hematin-targeting properties of pynacrine, an acridine analog of the benzonaphthyridine antimalarial pyronaridine.

    PubMed

    Sereekhajornjaru, Narumon; Somboon, Chanat; Rattanajak, Roonglawan; Denny, William A; Wilairat, Prapin; Auparakkitanon, Saranya

    2014-12-01

    The hematin-targeting properties of pynacrine, an acridine analog of the schizontocidal antimalarial drug, pyronaridine, were evaluated to probe the role of the latter's benzonaphthyridine moiety. Pynacrine was as active as pyronaridine in inhibiting glutathione-induced hematin degradation and in enhancing hematin-mediated membrane lysis. It formed a 1:2 complex with hematin but was 50-fold less effective in inhibiting β-hematin formation. However, pynacrine was as potent as pyronaridine in inhibiting intra-erythrocytic Plasmodium falciparum growth in culture, suggesting that it has other off-target(s) effects. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. A comparison of optical and electromagnetic computer-assisted navigation systems for fluoroscopic targeting.

    PubMed

    Ricci, William M; Russell, Thomas A; Kahler, David M; Terrill-Grisoni, Lauralan; Culley, Patrick

    2008-03-01

    Freehand targeting using fluoroscopic guidance is routine for placement of interlocking screws associated with intramedullary nailing and for insertion of screws for reconstruction of pelvic and acetabular injuries. New technologies that use fluoroscopy with the assistance of computer guidance have the potential to improve accuracy and reduce radiation exposure to patient and surgeon. We sought to compare 2 fluoroscopic navigation tracking technologies, optical and electromagnetic versus standard freehand fluoroscopic targeting in a standardized model. Three experienced orthopaedic trauma surgeons placed 3.2-mm guide pins through test foam blocks that simulate cancellous bone. The entry site for each pin was within a circular (18-mm) entry zone. On the opposite surface of the test block (130-mm across), the target was a 1-mm-diameter radioopaque spherical ball marker. Each surgeon placed 10 pins using freehand targeting (control group) navigation using Medtronic iON StealthStation (Optical A), navigation using BrainLAB VectorVision (Optical B), or navigation using GE Medical Systems InstaTrak 3500 system (EM). Data were collected for accuracy (the distance from the exit site of the guidewire to the target spherical ball marker), fluoroscopy time (seconds), and total number of individual fluoroscopy images taken. The 2 optical systems and the electromagnetic system provided significantly improved accuracy compared to freehand technique. The average distance from the target was significantly (3.5 times) greater for controls (7.1 mm) than for each of the navigated systems (Optical A = 2.1 mm, Optical B = 1.9 mm EM = 2.4 mm; P < .05). Accuracy was similar for the 3 navigated systems, (P > 0.05). The ability to place guidewires in a 5-mm safe zone surrounding the target sphere was also significantly improved with the optical systems and the EM system (99% of wires in the safe zone) compared to controls (47% in the safe zone) (P < 0.002). Safe zone placement was similar

  5. Triatoma dimidiata Infestation in Chagas Disease Endemic Regions of Guatemala: Comparison of Random and Targeted Cross-Sectional Surveys

    PubMed Central

    King, Raymond J.; Cordon-Rosales, Celia; Cox, Jonathan; Kitron, Uriel D.

    2011-01-01

    targeted surveys in both regions. Sensitivity did not differ between surveys, but the positive predictive value was significantly greater in the random surveys. Conclusions/Significance Surprisingly, targeted surveys were not more effective at determining T. dimidiata prevalence or at directing control to high risk villages in comparison to random surveys. We recommend that random surveys should be selected over targeted surveys whenever possible, particularly when the focus is on directing disease control and elimination and when risk factor association has not been evaluated for all regions under investigation. PMID:21532742

  6. Comparison of "E-Rater"[R] Automated Essay Scoring Model Calibration Methods Based on Distributional Targets

    ERIC Educational Resources Information Center

    Zhang, Mo; Williamson, David M.; Breyer, F. Jay; Trapani, Catherine

    2012-01-01

    This article describes two separate, related studies that provide insight into the effectiveness of "e-rater" score calibration methods based on different distributional targets. In the first study, we developed and evaluated a new type of "e-rater" scoring model that was cost-effective and applicable under conditions of absent human rating and…

  7. Comparison of Item Targeting Strategies for Pass/Fail Computer Adaptive Tests.

    ERIC Educational Resources Information Center

    Bergstrom, Betty A.; Gershon, Richard

    The most useful method of item selection for making pass-fail decisions with a Computerized Adaptive Test (CAT) was studied. Medical technology students (n=86) took a computer adaptive test in which items were targeted to the ability of the examinee. The adaptive algorithm that selected items and estimated person measures used the Rasch model and…

  8. Contingency management and levodopa-carbidopa for cocaine treatment: a comparison of three behavioral targets.

    PubMed

    Schmitz, Joy M; Lindsay, Jan A; Stotts, Angela L; Green, Charles E; Moeller, F Gerard

    2010-06-01

    New data support use of levodopa pharmacotherapy with behavioral contingency management (CM) as one efficacious combination in cocaine dependence disorder treatment. A potential mechanism of the combined treatment effects may be related to dopamine-induced enhancement of the saliency of contingently delivered reinforcers. Evidence to support this mechanism was sought by evaluating levodopa-enhancing effects across distinct CM conditions that varied in behavioral targets. A total of 136 treatment-seeking, cocaine dependent subjects participated in this 12-week, randomized, placebo-controlled trial of levodopa (vs. placebo) administered in combination with one of three behavioral CM conditions. In the CM-URINE condition, subjects received cash-valued vouchers contingent on cocaine-negative urine toxicology results. In the CM-ATTEND condition, the same voucher schedule was contingent on attending thrice weekly clinic visits. In the CM-MEDICATION condition, the same voucher schedule was contingent on Medication Event Monitoring Systems- and riboflavin-based evidence of pill-taking behavior. Primary outcomes associated with each CM target behavior were analyzed using generalized linear mixed models for repeated outcomes. CM responding in the CM-ATTEND and CM-MEDICATION conditions showed orderly effects, with each condition producing corresponding changes in targeted behaviors, regardless of medication condition. In contrast, CM responding in the CM-URINE condition was moderated by medication, with levodopa-treated subjects more likely to submit cocaine-negative urines. These findings specify the optimal target behavior for CM when used in combination with levodopa pharmacotherapy.

  9. DSL prescriptive targets for bone conduction devices: adaptation and comparison to clinical fittings.

    PubMed

    Hodgetts, William E; Scollie, Susan D

    2017-07-01

    To develop an algorithm that prescribes targets for bone conduction frequency response shape, compression, and output limiting, along with a clinical method that ensures accurate transforms between assessment and verification stages of the clinical workflow. Technical report of target generation and validation. We recruited 39 adult users of unilateral percutaneous bone conduction hearing aids with a range of unilateral, bilateral, mixed and conductive hearing losses across the sample. The initial algorithm over-prescribed output compared to the user's own settings in the low frequencies, but provided a good match to user settings in the high frequencies. Corrections to the targets were derived and implemented as a low-frequency cut aimed at improving acceptance of the wearer's own voice during device use. The DSL-BCD prescriptive algorithm is compatible with verification of devices and fine-tuning to target for percutaneous bone conduction hearing devices that can be coupled to a skull simulator. Further study is needed to investigate the appropriateness of this prescriptive algorithm for other input levels, and for other clinical populations including those with single-sided deafness, bilateral devices, children and users of transcutaneous bone conduction hearing aids.

  10. Monitoring benthic aIgal communides: A comparison of targeted and coefficient sampling methods

    USGS Publications Warehouse

    Edwards, Matthew S.; Tinker, M. Tim

    2009-01-01

    Choosing an appropriate sample unit is a fundamental decision in the design of ecological studies. While numerous methods have been developed to estimate organism abundance, they differ in cost, accuracy and precision.Using both field data and computer simulation modeling, we evaluated the costs and benefits associated with two methods commonly used to sample benthic organisms in temperate kelp forests. One of these methods, the Targeted Sampling method, relies on different sample units, each "targeted" for a specific species or group of species while the other method relies on coefficients that represent ranges of bottom cover obtained from visual esti-mates within standardized sample units. Both the field data and the computer simulations suggest that both methods yield remarkably similar estimates of organism abundance and among-site variability, although the Coefficient method slightly underestimates variability among sample units when abundances are low. In contrast, the two methods differ considerably in the effort needed to sample these communities; the Targeted Sampling requires more time and twice the personnel to complete. We conclude that the Coefficent Sampling method may be better for environmental monitoring programs where changes in mean abundance are of central concern and resources are limiting, but that the Targeted sampling methods may be better for ecological studies where quantitative relationships among species and small-scale variability in abundance are of central concern.

  11. Identification of microRNAs and Their Target Genes Explores miRNA-Mediated Regulatory Network of Cytoplasmic Male Sterility Occurrence during Anther Development in Radish (Raphanus sativus L.)

    PubMed Central

    Zhang, Wei; Xie, Yang; Xu, Liang; Wang, Yan; Zhu, Xianwen; Wang, Ronghua; Zhang, Yang; Muleke, Everlyne M.; Liu, Liwang

    2016-01-01

    MicroRNAs (miRNAs) are a type of endogenous non-coding small RNAs that play critical roles in plant growth and developmental processes. Cytoplasmic male sterility (CMS) is typically a maternally inherited trait and widely used in plant heterosis utilization. However, the miRNA-mediated regulatory network of CMS occurrence during anther development remains largely unknown in radish. In this study, a comparative small RNAome sequencing was conducted in floral buds of CMS line ‘WA’ and its maintainer line ‘WB’ by high-throughput sequencing. A total of 162 known miRNAs belonging to 25 conserved and 24 non-conserved miRNA families were isolated and 27 potential novel miRNA families were identified for the first time in floral buds of radish. Of these miRNAs, 28 known and 14 potential novel miRNAs were differentially expressed during anther development. Several target genes for CMS occurrence-related miRNAs encode important transcription factors and functional proteins, which might be involved in multiple biological processes including auxin signaling pathways, signal transduction, miRNA target silencing, floral organ development, and organellar gene expression. Moreover, the expression patterns of several CMS occurrence-related miRNAs and their targets during three stages of anther development were validated by qRT-PCR. In addition, a potential miRNA-mediated regulatory network of CMS occurrence during anther development was firstly proposed in radish. These findings could contribute new insights into complex miRNA-mediated genetic regulatory network of CMS occurrence and advance our understanding of the roles of miRNAs during CMS occurrence and microspore formation in radish and other crops. PMID:27499756

  12. Identification of microRNAs and Their Target Genes Explores miRNA-Mediated Regulatory Network of Cytoplasmic Male Sterility Occurrence during Anther Development in Radish (Raphanus sativus L.).

    PubMed

    Zhang, Wei; Xie, Yang; Xu, Liang; Wang, Yan; Zhu, Xianwen; Wang, Ronghua; Zhang, Yang; Muleke, Everlyne M; Liu, Liwang

    2016-01-01

    MicroRNAs (miRNAs) are a type of endogenous non-coding small RNAs that play critical roles in plant growth and developmental processes. Cytoplasmic male sterility (CMS) is typically a maternally inherited trait and widely used in plant heterosis utilization. However, the miRNA-mediated regulatory network of CMS occurrence during anther development remains largely unknown in radish. In this study, a comparative small RNAome sequencing was conducted in floral buds of CMS line 'WA' and its maintainer line 'WB' by high-throughput sequencing. A total of 162 known miRNAs belonging to 25 conserved and 24 non-conserved miRNA families were isolated and 27 potential novel miRNA families were identified for the first time in floral buds of radish. Of these miRNAs, 28 known and 14 potential novel miRNAs were differentially expressed during anther development. Several target genes for CMS occurrence-related miRNAs encode important transcription factors and functional proteins, which might be involved in multiple biological processes including auxin signaling pathways, signal transduction, miRNA target silencing, floral organ development, and organellar gene expression. Moreover, the expression patterns of several CMS occurrence-related miRNAs and their targets during three stages of anther development were validated by qRT-PCR. In addition, a potential miRNA-mediated regulatory network of CMS occurrence during anther development was firstly proposed in radish. These findings could contribute new insights into complex miRNA-mediated genetic regulatory network of CMS occurrence and advance our understanding of the roles of miRNAs during CMS occurrence and microspore formation in radish and other crops.

  13. Interventions targeting mental health self-stigma: A review and comparison.

    PubMed

    Yanos, Philip T; Lucksted, Alicia; Drapalski, Amy L; Roe, David; Lysaker, Paul

    2015-06-01

    With growing awareness of the impact of mental illness self-stigma, interest has arisen in the development of interventions to combat it. The present article briefly reviews and compares interventions targeting self-stigma to clarify the similarities and important differences between the interventions. We conducted a narrative review of published literature on interventions targeting self-stigma. Six intervention approaches (Healthy Self-Concept, Self-Stigma Reduction Program, Ending Self-Stigma, Narrative Enhancement and Cognitive Therapy, Coming Out Proud, and Anti-Stigma Photo-Voice Intervention) were identified and are discussed, and data is reviewed on format, group-leader backgrounds, languages, number of sessions, primary mechanisms of action, and the current state of data on their efficacy. We conclude with a discussion of common elements and important distinctions between the interventions and a consideration of which interventions might be best suited to particular populations or settings. (c) 2015 APA, all rights reserved).

  14. Interventions Targeting Mental Health Self-Stigma: A Review and Comparison

    PubMed Central

    Yanos, Philip T.; Lucksted, Alicia; Drapalski, Amy L.; Roe, David; Lysaker, Paul

    2014-01-01

    Objective With growing awareness of the impact of mental illness self-stigma, interest has arisen in the development of interventions to combat it. The present article briefly reviews and compares interventions targeting self-stigma to clarify the similarities and important differences between the interventions. Methods We conducted a narrative review of published literature on interventions targeting self-stigma. Results Six intervention approaches (Healthy Self-Concept, Self-Stigma Reduction Program, Ending Self-Stigma, Narrative Enhancement and Cognitive Therapy, Coming Out Proud, and Anti-Stigma Photo-Voice Intervention) were identified and are discussed, and data is reviewed on format, group-leader backgrounds, languages, number of sessions, primary mechanisms of action, and the current state of data on their efficacy. Conclusions and Implications for Practice We conclude with a discussion of common elements and important distinctions between the interventions and a consideration of which interventions might be best suited to particular populations or settings. PMID:25313530

  15. CTH analyses of steel rod penetration into aluminum and concrete targets with comparisons to experimental data

    SciTech Connect

    Kmetyk, L.N.; Yarrington, P.

    1994-10-01

    Calculational results are presented here for a class of intermediate-velocity penetration problems. The problems of interest involve penetration of moderate-strength target materials by high-strength projectiles. Two series of metal penetration experiments and a series of concrete slab perforation tests were simulated in this study. The computer code used for the calculations was the CTH code, which employs a recently-developed ``boundary layer`` algorithm for treating penetration problems such as these.

  16. Comparison of various radiation therapy techniques in breast cancer where target volume includes mammaria interna region.

    PubMed

    Dogan, Mehmet Hakan; Zincircioglu, Seyit Burhanedtin; Zorlu, Faruk

    2009-01-01

    In breast cancer radiotherapy, the internal mammary lymphatic chain is treated in the target volume in a group of patients with high-risk criteria. Because of the variability of the anatomic region and structures in the irradiation field, there are a number of different techniques in breast radiotherapy. While irradiating the target volume, we also consider minimizing the dose to critical structures such as heart, lung, and contralateral breast tissue. In this study, we evaluated the dose distribution of different radiotherapy techniques in patients with left-sided breast cancer who had breast-conserving surgery. A three-dimensional computerized planning system (3DCPS) was used for each patient to compare wide-field, oblique photon-electron, and perpendicular photon-electron techniques in terms of dose homogeneities in the target volume; the doses received by the contralateral breast, heart, and lung; and the coverage of the internal mammary chain. Data from 3DCPS were controlled by the Rando-phantom and thermoluminescence dosimetry. Critical structures were irradiated with acceptable dose percentages in addition to the internal mammary chain with both wide-field and photon-electron techniques. We detected more frequent hot spots in the oblique photon-electron technique than in the other techniques, and this situation necessitated changing the junctions. The wide-field technique was easy to perform and exposed less radiation dose to the heart than photon-electron techniques. In conclusion, we suggest the use of the wide-field technique in breast irradiation when the internal mammary area is in the target volume.

  17. Comparison of Various Radiation Therapy Techniques in Breast Cancer Where Target Volume Includes Mammaria Interna Region

    SciTech Connect

    Dogan, Mehmet Hakan; Zincircioglu, Seyit Burhanedtin Zorlu, Faruk

    2009-04-01

    In breast cancer radiotherapy, the internal mammary lymphatic chain is treated in the target volume in a group of patients with high-risk criteria. Because of the variability of the anatomic region and structures in the irradiation field, there are a number of different techniques in breast radiotherapy. While irradiating the target volume, we also consider minimizing the dose to critical structures such as heart, lung, and contralateral breast tissue. In this study, we evaluated the dose distribution of different radiotherapy techniques in patients with left-sided breast cancer who had breast-conserving surgery. A three-dimensional computerized planning system (3DCPS) was used for each patient to compare wide-field, oblique photon-electron, and perpendicular photon-electron techniques in terms of dose homogeneities in the target volume; the doses received by the contralateral breast, heart, and lung; and the coverage of the internal mammary chain. Data from 3DCPS were controlled by the Rando-phantom and thermoluminescence dosimetry. Critical structures were irradiated with acceptable dose percentages in addition to the internal mammary chain with both wide-field and photon-electron techniques. We detected more frequent hot spots in the oblique photon-electron technique than in the other techniques, and this situation necessitated changing the junctions. The wide-field technique was easy to perform and exposed less radiation dose to the heart than photon-electron techniques. In conclusion, we suggest the use of the wide-field technique in breast irradiation when the internal mammary area is in the target volume.

  18. Application of Sequence Comparison Methods to Multisensor Data Fusion and Target Recognition

    DTIC Science & Technology

    1993-06-18

    Discussion ...................... C-20 C.7 Equations for Direction Cosine Matrix ( DCM ) Generation . C-26 C.7.1 DCM for Sensor-to-Inertial Frame...Transformation C-26 C.7.2 DCM for Target Lift-to-Inertial Frame Transformation C-30 Vita ........... .......................................... VITA- I...5-5 CRLB (Cramrr-Rao lower bound) .............................. 2-85 DCM (direction cosine matrix) ................................. C-26 DOF

  19. Performance Comparison of Feature Extraction Algorithms for Target Detection and Classification

    DTIC Science & Technology

    2013-01-01

    Succi, D. Clapp, R. Gampert, and G. Prado, “ Footstep detection and tracking,” Unattended Ground Sensor Technologies and Applications III, vol. 4393... Detection and Classification⋆ Soheil Bahrampour1 Asok Ray2 Soumalya Sarkar2 Thyagaraju Damarla3 Nasser M. Nasrabadi3 Keywords: Feature Extraction...rithm, symbolic dynamic filtering (SDF), is investigated for target detection and classification by using unmanned ground sensors (UGS). In SDF, sensor

  20. The heart rate VO2 relationship of aerobic dance: a comparison of target heart rate methods.

    PubMed

    Scharff-Olson, M; Williford, H N; Smith, F H

    1992-12-01

    The purpose of this study was to examine the relationship between heart rate (HR) and oxygen consumption (VO2) for aerobic dance exercise. Therefore, eleven females completed 20 minutes of aerobic dance with continuous monitoring of HR and VO2. These physiological responses were analyzed with correlation/regression techniques. The results showed that for aerobic dance to produce a response in excess of 50% of VO2 max, the target HR must be approximately 80% of the age-predicted HR max or greater. In contrast, previously reported data for treadmill running shows that 50% of VO2 max is achieved at approximately 65% of age-predicted HR max in females. The maximum heart rate reserve (Karvonen) method was also found to underestimate the actual VO2 of AD. With the Karvonen method, the target heart rate must approximate 65% of maximum HR reserve in order to elicit a VO2 response which is representative of 50% of VO2 max. These data support recent research which illustrates that target heart rate prescriptions derived from treadmill testing may fail to accurately place AD participants in the recommended training zone.

  1. Human-computer interaction in radiotherapy target volume delineation: a prospective, multi-institutional comparison of user input devices.

    PubMed

    2011-10-01

    The purpose of this study was the prospective comparison of objective and subjective effects of target volume region of interest (ROI) delineation using mouse-keyboard and pen-tablet user input devices (UIDs). The study was designed as a prospective test/retest sequence, with Wilcoxon signed rank test for matched-pair comparison. Twenty-one physician-observers contoured target volume ROIs on four standardized cases (representative of brain, prostate, lung, and head and neck malignancies) twice: once using QWERTY keyboard/scroll-wheel mouse UID and once with pen-tablet UID (DTX2100, Wacom Technology Corporation, Vancouver, WA, USA). Active task time, ROI manipulation task data, and subjective survey data were collected. One hundred twenty-nine target volume ROI sets were collected, with 62 paired pen-tablet/mouse-keyboard sessions. Active contouring time was reduced using the pen-tablet UID, with mean ± SD active contouring time of 26 ± 23 min, compared with 32 ± 25 with the mouse (p ≤ 0.01). Subjective estimation of time spent was also reduced from 31 ± 26 with mouse to 27 ± 22 min with the pen (p = 0.02). Task analysis showed ROI correction task reduction (p = 0.045) and decreased panning and scrolling tasks (p < 0.01) with the pen-tablet; drawing, window/level changes, and zoom commands were unchanged (p = n.s.) Volumetric analysis demonstrated no detectable differences in ROI volume nor intra- or inter-observer volumetric coverage. Fifty-two of 62 (84%) users preferred the tablet for each contouring task; 5 of 62 (8%) denoted no preference, and 5 of 62 (8%) chose the mouse interface. The pen-tablet UID reduced active contouring time and reduced correction of ROIs, without substantially altering ROI volume/coverage.

  2. Receptor binding assay for the detection of paralytic shellfish poisoning toxins: comparison to the mouse bioassay and applicability under regulatory use.

    PubMed

    Ruberu, Shiyamalie R; Langlois, Gregg W; Masuda, Melisa; Kittredge, Clive; Perera, S Kusum; Kudela, Raphael M

    2017-09-08

    The receptor-binding assay (RBA) method for the detection of paralytic shellfish poisoning (PSP) toxins was evaluated for its overall performance in comparison with the mouse bioassay (MBA). An initial study to evaluate the effects of filtering shellfish extracts prior to running the RBA indicated no significant difference between filtered and unfiltered extracts on the determined saxitoxin (STX) concentrations. Next, we tested the RBA assay on 295 naturally contaminated mussel tissue samples, ranging in concentrations from 320 µg STX equiv. kg(-1) to 13,000 µg STX equiv. kg(-1) by MBA. An overall trend was observed with the RBA giving higher results (256 µg STX equiv. kg(-1) on average) than the MBA; however, at low concentrations (< 500 µg STX equiv. kg(-1)) the RBA results were marginally lower. A third study was conducted using spiked mussel tissue analysed by three independent laboratories, two of which performed the RBA and one the MBA. This multi-laboratory study again showed the RBA to give higher results than the MBA; however, it also revealed that STX determination was accurate by the RBA, unlike the MBA. To optimise the assay for efficient usage under regulatory practice, three suggestions have been made: the use of an initial screening plate to separate those samples that exceed the alert level; use of rapid PSP test kits in the field and in the laboratory for screening negative samples and for early detection of toxicity; and use of an alternate commercially available porcine membrane in place of the laboratory-prepared rat membrane homogenate. The large number of samples analysed and the diversity of the tests conducted in this study further support the RBA as an affordable rapid method for STX detection that is also free of the routine sacrifice of live animals.

  3. Enterococci as Indicators of Lake Michigan Recreational Water Quality: Comparison of Two Methodologies and Their Impacts on Public Health Regulatory Events

    PubMed Central

    Kinzelman, Julie; Ng, Clement; Jackson, Emma; Gradus, Stephen; Bagley, Robert

    2003-01-01

    The frequency of poor-water-quality advisories issued in Milwaukee and Racine, Wisconsin, in the absence of identifiable sources of contamination brought into question the reliability of the present indicator organism, Escherichia coli. Enteroccoci have been suggested as an alternative to E. coli for freshwater monitoring due to their direct correlation to swimmer-associated gastroenteritis. The purpose of this research was threefold: (i) to explore enterococci as an alternative to E. coli for monitoring freshwater Lake Michigan beaches, (ii) to evaluate the impact of the two indicators on regulatory decisions, and (iii) to compare membrane filtration m-enterococcus agar with indoxyl-β-d-glucoside to a chemical substrate technique (Enterolert) for the recovery of enterococci. Recreational water samples from Milwaukee (n = 305) and Racine (n = 153) were analyzed for the enumeration of E. coli and enterococci using IDEXX Colilert-18 and Enterolert. Correlation between the indicators was low (R2 = 0.60 and 0.69). Based on U.S. Environmental Protection Agency bacterial indicator threshold levels of risk for full body immersion, using enterococci would have resulted in 56 additional unsafe-recreational-water-quality advisories compared to the total from using E. coli and the substrate-based methods. A comparison of the two enterococcal methods (n = 124) yielded similar results (R2 = 0.62). This was further confounded by the frequent inability to verify enterococci from those wells producing fluorescence by the defined substrate test using conventional microbiological methods. These results suggest that further research is necessary regarding the use of defined substrate technology interchangeably with the U.S. Environmental Protection Agency-approved membrane filtration test for the detection of enterococci from fresh surface water. PMID:12513981

  4. Measurement and comparison of taekwondo and yongmudo turning kick impact force for two target heights.

    PubMed

    O'Sullivan, David; Chung, Chulsoo; Lee, Kikwang; Kim, Euihwan; Kang, Sungchul; Kim, Taewhan; Shin, Insik

    2009-11-01

    The primary purpose of this research was to compare the impact characteristics of Taekwondo (TKD) and Yongmudo (YMD) player's turning kick according to the target height. 5 highly skilled YMD and 5 TKD players participated in this study. To measure the impact force, two accelerometers were fixed to a PVC pipe in a sandbag. Each participant performed 10 turning kicks trunk and face height in random order. Only the trial with the most accurate (most central impact) measurement was used in the statistical analysis (p < 0.05).There was a significant difference for impact force according to the target height approximately 6400 ± 898 N, 6393 ± 1382 N for the mid section and 5419 ± 659 N, 5475 ± 1293 N for the high section of TKD and YMD groups, but not between groups. The swing phase for the TKD group was significantly shorter than the YMD group's. The TKD groups' recovery phase of the trunk height turning kick was significantly shorter. There was a difference in the players' center of mass (COM) movement as the TKD players' moved significantly more forward, suggesting that the TKD players tended to slide towards the target during the execution of the kick. In conclusion, as the turning kick was performed quicker by the TKD players with a similar impact force and more forward motion, it is evaluated to be a better technique of turning kicking. Key PointsThis impact force measuring device had a significantly smaller standard deviation then that of impact force measuring devices.There was a significant difference between the impact forces according to the height approximately 6400 ± 898N, 6393 ± 1382N for the mid section and 5419 ± 659N, 5475 ± 1293N for the high section of TKD and YMD groups.The turning kick was performed quicker by the TKD players with a similar impact force and more forward motion.

  5. [The optimal blood glucose target in critically ill patient: comparison of two intensive insulin therapy protocols].

    PubMed

    Raurell Torredà, Marta; del Llano Serrano, César; Almirall Solsona, Dolors; Catalan Ibars, Rosa María; Nicolás Arfelis, José María

    2014-03-04

    Recent studies in critically ill patients receiving insulin intravenous therapy (IIT) have shown an increased incidence of severe hypoglycemia, while intermittent subcutaneous insulin «sliding scales» (conventional insulin therapy [CIT]) is associated with hyperglycemia. The objective of this study is to assess whether glycemic control range IIT can affect glucose levels and their variability and to compare it with CIT. Prospective comparative cohort study in intensive care unit, with 2 study periods: Period 1, IIT with glycemic target range 110-140 mg/dL, and Period 2, IIT of 140-180 mg/dL. In both periods CIT glycemic target was 110-180 mg/dL. We assessed severe hypoglycemia (< 50 mg/dL), moderate hypoglycemia (51-79 mg/dL), hyperglycemia (> 216 mg/L) and the variability of blood glucose. We studied 221 patients with 12.825 blood glucose determinations. Twenty-six and 17% of patients required IIT for glycemic control in Period 1 and 2, respectively. Hypoglycemia was associated with a discontinuous nutritional intake, glycemic target 110-140 mg/dL and low body mass index (BMI) (P = .002). Hyperglycemia was exclusively associated with a history of diabetes mellitus (OR 2.6 [95% CI 1.6 to 4.5]). Glycemic variability was associated with a discontinuous nutritional intake, low BMI, CIT insulinization, diabetes mellitus, elderly and high APACHE II (P < .001). The use of IIT is useful to reduce the variability of blood glucose. Although the 140-180 mg/dL range would be more secure as to presenting greater variability and hyperglycemia, the 110-140 mg/dL range is most suitable. Copyright © 2012 Elsevier España, S.L. All rights reserved.

  6. Pyrimidine metabolism in schistosomes: A comparison with other parasites and the search for potential chemotherapeutic targets.

    PubMed

    El Kouni, Mahmoud H

    2017-11-01

    Schistosomes are responsible for the parasitic disease schistosomiasis, an acute and chronic parasitic ailment that affects >240 million people in 70 countries worldwide. It is the second most devastating parasitic disease after malaria. At least 200,000 deaths per year are associated with the disease. In the absence of the availability of vaccines, chemotherapy is the main stay for combating schistosomiasis. The antischistosomal arsenal is currently limited to a single drug, Praziquantel, which is quite effective with a single-day treatment and virtually no host-toxicity. Recently, however, the question of reduced activity of Praziquantel has been raised. Therefore, the search for alternative antischistosomal drugs merits the study of new approaches of chemotherapy. The rational design of a drug is usually based on biochemical and physiological differences between pathogens and host. Pyrimidine metabolism is an excellent target for such studies. Schistosomes, unlike most of the host tissues, require a very active pyrimidine metabolism for the synthesis of DNA and RNA. This is essential for the production of the enormous numbers of eggs deposited daily by the parasite to which the granulomas response precipitates the pathogenesis of schistosomiasis. Furthermore, there are sufficient differences between corresponding enzymes of pyrimidine metabolism from the host and the parasite that can be exploited to design specific inhibitors or "subversive substrates" for the parasitic enzymes. Specificities of pyrimidine transport also diverge significantly between parasites and their mammalian host. This review deals with studies on pyrimidine metabolism in schistosomes and highlights the unique characteristic of this metabolism that could constitute excellent potential targets for the design of safe and effective antischistosomal drugs. In addition, pyrimidine metabolism in schistosomes is compared with that in other parasites where studies on pyrimidine metabolism have

  7. Measurement and Comparison of Taekwondo and Yongmudo Turning Kick Impact Force for Two Target Heights

    PubMed Central

    O’Sullivan, David; Chung, Chulsoo; Lee, Kikwang; Kim, Euihwan; Kang, Sungchul; Kim, Taewhan; Shin, Insik

    2009-01-01

    The primary purpose of this research was to compare the impact characteristics of Taekwondo (TKD) and Yongmudo (YMD) player’s turning kick according to the target height. 5 highly skilled YMD and 5 TKD players participated in this study. To measure the impact force, two accelerometers were fixed to a PVC pipe in a sandbag. Each participant performed 10 turning kicks trunk and face height in random order. Only the trial with the most accurate (most central impact) measurement was used in the statistical analysis (p < 0.05).There was a significant difference for impact force according to the target height approximately 6400 ± 898 N, 6393 ± 1382 N for the mid section and 5419 ± 659 N, 5475 ± 1293 N for the high section of TKD and YMD groups, but not between groups. The swing phase for the TKD group was significantly shorter than the YMD group’s. The TKD groups’ recovery phase of the trunk height turning kick was significantly shorter. There was a difference in the players’ center of mass (COM) movement as the TKD players’ moved significantly more forward, suggesting that the TKD players tended to slide towards the target during the execution of the kick. In conclusion, as the turning kick was performed quicker by the TKD players with a similar impact force and more forward motion, it is evaluated to be a better technique of turning kicking. Key Points This impact force measuring device had a significantly smaller standard deviation then that of impact force measuring devices. There was a significant difference between the impact forces according to the height approximately 6400 ± 898N, 6393 ± 1382N for the mid section and 5419 ± 659N, 5475 ± 1293N for the high section of TKD and YMD groups. The turning kick was performed quicker by the TKD players with a similar impact force and more forward motion. PMID:24474880

  8. Shock generation comparison with planar and hemispherical targets in shock ignition relevant experiment

    NASA Astrophysics Data System (ADS)

    Baton, S. D.; Le Bel, E.; Brygoo, S.; Ribeyre, X.; Rousseaux, C.; Breil, J.; Koenig, M.; Batani, D.; Raffestin, D.

    2017-09-01

    We performed an experiment on the "Ligne d'Intégration Laser" facility to produce strong shocks with plasma conditions relevant for the Shock Ignition approach to Inertial Confinement Fusion. Two kinds of targets have been used: planar and hemispherical. We observe an increase in the shock velocity in hemispherical geometry, which entails a fairly planar shock despite the Gaussian focal spot. Numerical results reproduce the shock dynamics in the two cases in a successful way, indicating, for laser intensities around 1.5 × 1015 W/cm2 at 3ω, an ablation pressure of (90 ± 20) Mbar and (120 ± 20) Mbar in planar and hemispherical geometry, respectively.

  9. A Comparison of Fully Polarimetric X-Band ISAR Imagery of Scaled Model Tactical Targets

    DTIC Science & Technology

    2006-05-01

    scaled X- band radar data with 6-inch full-scale range resolution. In order to investigate the reproduction of X-band data using scale models, fully...polarimetric high-resolution radar signature data has been collected on several targets which include a high-fidelity in-house built 1/16th scale T72...It will be shown that the T72 data sets compare well across the three different radar platforms. It has also been found that there are persistent

  10. The Mars Science Laboratory APXS calibration target: Comparison of Martian measurements with the terrestrial calibration

    NASA Astrophysics Data System (ADS)

    Campbell, J. L.; King, P. L.; Burkemper, L.; Berger, J. A.; Gellert, R.; Boyd, N. I.; Perrett, G. M.; Pradler, I.; Thompson, L.; Edgett, K. S.; Yingst, R. A.

    2014-03-01

    The Mars Science Laboratory Curiosity rover carries a basalt calibration target for monitoring the performance of the alpha particle X-ray spectrometer. The spectrum acquired on Sol 34 shows increased contributions from Mg, S, Cl and Fe relative to laboratory spectra recorded before launch. Mars Hand Lens Imager images confirm changes in the appearance of the surface. Spectra taken on Sols 179 and 411 indicate some loss of the deposited material. The observations suggest deposition of a surface film likely consisting of dust mobilized by impingement of the sky crane's terminal descent engine plumes with surface fines during Curiosity's landing. New APXS software has been used to model the thin film that coated the calibration target on landing. The results suggest that a film of about 100 nm thickness, and containing predominantly MgO, Fe2O3, SO3, Cl and Na2O could give rise to the observed spectral changes. If this film is also present on the alpha particle sources within the APXS, then its effect is negligible and the terrestrial calibration remains appropriate.

  11. Comparison of Two Inexpensive Rapid Prototyping Methods for Manufacturing Filament Target Ultrasound Phantoms.

    PubMed

    Füzesi, Krisztián; Gyöngy, Miklós

    2017-03-01

    Current use of 3-D printers to manufacture ultrasound phantoms is limited to relatively expensive photopolymer jetting printers. The present work investigates the feasibility of using two common and inexpensive 3-D printer technologies, fused deposition modeling (FDM) and digital light processing (DLP), to print custom filament target phantoms. Acoustic characteristics obtained from printed solid blocks indicated that the printing materials-acrylonitrile butadiene styrene and polylactic acid for FDM and a photopolymer for DLP printing-were appropriate for use as scatterers. A regular grid of filaments was printed to study printing accuracy. As a proof of concept of the phantom manufacturing process, a complex pattern of filament targets was placed in de-ionized water to create a phantom, which was then imaged using an ultrasound imager. The pattern was clearly identifiable, although multiple reflections were observed, which underscores the importance of future work to enhance printing resolution. This goal is deemed possible using improvement of the DLP printing setup. Copyright © 2016 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

  12. RF magnetron sputtering of a hydroxyapatite target: A comparison study on polytetrafluorethylene and titanium substrates

    NASA Astrophysics Data System (ADS)

    Surmenev, Roman A.; Surmeneva, Maria A.; Grubova, Irina Yu.; Chernozem, Roman V.; Krause, Bärbel; Baumbach, Tilo; Loza, Kateryna; Epple, Matthias

    2017-08-01

    A pure hydroxyapatite (HA) target was used to prepare the biocompatible coating of HA on the surface of a polytetrafluorethylene (PTFE) substrate, which was placed on the same substrate holder with technically pure titanium (Ti) in the single deposition runs by radio-frequency (RF) magnetron sputtering. The XPS, XRD and FTIR analyses of the obtained surfaces showed that for all substrates, instead of the HA coating deposition, the coating of a mixture of calcium carbonate and calcium fluoride was grown. According to SEM investigations, the surface of PTFE was etched, and the surface topography of uncoated Ti was preserved after the depositions. The FTIR results reveal no phosphate bonds; only calcium tracks were observed in the EDX-spectra on the surface of the coated PTFE substrates. Phosphate oxide (V), which originated from the target, could be removed using a vacuum pump system, or no phosphate-containing bonds could be formed on the substrate surface because of the severe substrate bombardment process, which prevented the HA coating deposition. The observed results may be connected with the surface re-sputtering effect of the growing film by high-energy negatively charged ions (most probably oxygen or fluorine), which are accelerated in the cathode dark sheath.

  13. Comparison of EKF, pseudomeasurement, and particle filters for a bearing-only target tracking problem

    NASA Astrophysics Data System (ADS)

    Lin, Xiangdong; Kirubarajan, Thiagalingam; Bar-Shalom, Yaakov; Maskell, Simon

    2002-08-01

    In this paper we consider a nonlinear bearing-only target tracking problem using three different methods and compare their performances. The study is motivated by a ground surveillance problem where a target is tracked from an airborne sensor at an approximately known altitude using depression angle observations. Two nonlinear suboptimal estimators, namely, the extended Kalman Filter (EKF) and the pseudomeasurement tracking filter are applied in a 2-D bearing-only tracking scenario. The EKF is based on the linearization of the nonlinearities in the dynamic and/or the measurement equations. The pseudomeasurement tracking filter manipulates the original nonlinear measurement algebraically to obtain the linear-like structures measurement. Finally, the particle filter, which is a Monte Carlo integration based optimal nonlinear filter and has been presented in the literature as a better alternative to linearization via EKF, is used on the same problem. The performances of these three different techniques in terms of accuracy and computational load are presented in this paper. The results demonstrate the limitations of these algorithms on this deceptively simple tracking problem.

  14. Comparison of hydrodynamic simulations with two-shockwave drive target experiments

    NASA Astrophysics Data System (ADS)

    Karkhanis, Varad; Ramaprabhu, Praveen; Buttler, William

    2015-11-01

    We consider hydrodynamic continuum simulations to mimic ejecta generation in two-shockwave target experiments, where metallic surface is loaded by two successive shock waves. Time of second shock in simulations is determined to match experimental amplitudes at the arrival of the second shock. The negative Atwood number A --> - 1 of ejecta simulations leads to two successive phase inversions of the interface corresponding to the passage of the shocks from heavy to light media in each instance. Metallic phase of ejecta (solid/liquid) depends on shock loading pressure in the experiment, and we find that hydrodynamic simulations quantify the liquid phase ejecta physics with a fair degree of accuracy, where RM instability is not suppressed by the strength effect. In particular, we find that our results of free surface velocity, maximum ejecta velocity, and maximum ejecta areal density are in excellent agreement with their experimental counterparts, as well as ejecta models. We also comment on the parametric space for hydrodynamic simulations in which they can be used to compare with the target experiments. This work was supported in part by the (U.S.) Department of Energy (DOE) under Contract No. DE-AC52-06NA2-5396.

  15. Comparison of hydrodynamic simulations with two-shockwave drive target experiments

    NASA Astrophysics Data System (ADS)

    Karkhanis, Varad; Ramaprabhu, Praveen; Buttler, William

    2015-11-01

    We consider hydrodynamic continuum simulations to mimic ejecta generation in two-shockwave target experiments, where metallic surface is loaded by two successive shock waves. Time of second shock in simulations is determined to match experimental amplitudes at the arrival of the second shock. The negative Atwood number (A --> - 1) of ejecta simulations leads to two successive phase inversions of the interface corresponding to the passage of the shocks from heavy to light media in each instance. Metallic phase of ejecta (solid/liquid) depends on shock loading pressure in the experiment, and we find that hydrodynamic simulations quantify the liquid phase ejecta physics with a fair degree of accuracy, where RM instability is not suppressed by the strength effect. In particular, we find that our results of free surface velocity, maximum ejecta velocity, and maximum ejecta areal density are in excellent agreement with their experimental counterparts, as well as ejecta models. We also comment on the parametric space for hydrodynamic simulations in which they can be used to compare with the target experiments.

  16. Dosimetric Comparison of Split Field and Fixed Jaw Techniques for Large IMRT Target Volumes in the Head and Neck

    SciTech Connect

    Srivastava, Shiv P.; Das, Indra J.; Kumar, Arvind; Johnstone, Peter A.S.

    2011-04-01

    Some treatment planning systems (TPSs), when used for large-field (>14 cm) intensity-modulated radiation therapy (IMRT), create split fields that produce excessive multiple-leaf collimator segments, match-line dose inhomogeneity, and higher treatment times than nonsplit fields. A new method using a fixed-jaw technique (FJT) forces the jaw to stay at a fixed position during optimization and is proposed to reduce problems associated with split fields. Dosimetric comparisons between split-field technique (SFT) and FJT used for IMRT treatment is presented. Five patients with head and neck malignancies and regional target volumes were studied and compared with both techniques. Treatment planning was performed on an Eclipse TPS using beam data generated for Varian 2100C linear accelerator. A standard beam arrangement consisting of nine coplanar fields, equally spaced, was used in both techniques. Institutional dose-volume constraints used in head and neck cancer were kept the same for both techniques. The dosimetric coverage for the target volumes between SFT and FJT for head and neck IMRT plan is identical within {+-}1% up to 90% dose. Similarly, the organs at risk (OARs) have dose-volume coverage nearly identical for all patients. When the total monitor unit (MU) and segments were analyzed, SFT produces statistically significant higher segments (17.3 {+-} 6.3%) and higher MU (13.7 {+-} 4.4%) than the FJT. There is no match line in FJT and hence dose uniformity in the target volume is superior to the SFT. Dosimetrically, SFT and FJT are similar for dose-volume coverage; however, the FJT method provides better logistics, lower MU, shorter treatment time, and better dose uniformity. The number of segments and MU also has been correlated with the whole body radiation dose with long-term complications. Thus, FJT should be the preferred option over SFT for large target volumes.

  17. Dosimetric comparison of split field and fixed jaw techniques for large IMRT target volumes in the head and neck.

    PubMed

    Srivastava, Shiv P; Das, Indra J; Kumar, Arvind; Johnstone, Peter A S

    2011-01-01

    Some treatment planning systems (TPSs), when used for large-field (>14 cm) intensity-modulated radiation therapy (IMRT), create split fields that produce excessive multiple-leaf collimator segments, match-line dose inhomogeneity, and higher treatment times than nonsplit fields. A new method using a fixed-jaw technique (FJT) forces the jaw to stay at a fixed position during optimization and is proposed to reduce problems associated with split fields. Dosimetric comparisons between split-field technique (SFT) and FJT used for IMRT treatment is presented. Five patients with head and neck malignancies and regional target volumes were studied and compared with both techniques. Treatment planning was performed on an Eclipse TPS using beam data generated for Varian 2100C linear accelerator. A standard beam arrangement consisting of nine coplanar fields, equally spaced, was used in both techniques. Institutional dose-volume constraints used in head and neck cancer were kept the same for both techniques. The dosimetric coverage for the target volumes between SFT and FJT for head and neck IMRT plan is identical within ± 1% up to 90% dose. Similarly, the organs at risk (OARs) have dose-volume coverage nearly identical for all patients. When the total monitor unit (MU) and segments were analyzed, SFT produces statistically significant higher segments (17.3 ± 6.3%) and higher MU (13.7 ± 4.4%) than the FJT. There is no match line in FJT and hence dose uniformity in the target volume is superior to the SFT. Dosimetrically, SFT and FJT are similar for dose-volume coverage; however, the FJT method provides better logistics, lower MU, shorter treatment time, and better dose uniformity. The number of segments and MU also has been correlated with the whole body radiation dose with long-term complications. Thus, FJT should be the preferred option over SFT for large target volumes. Copyright © 2011 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights

  18. CREB is a regulatory target for the protein kinase Akt/PKB in the differentiation of pancreatic ductal cells into islet {beta}-cells mediated by hepatocyte growth factor

    SciTech Connect

    Li, Xin-Yu; Zhan, Xiao-Rong; Liu, Xiao-Min; Wang, Xiao-Chen

    2011-01-14

    Research highlights: {yields} CREB is a regulatory target for the protein kinase Akt/PKB in pancreatic duct cells. {yields} Activation of the PI3K/AKT/CREB pathway plays a critical role in the HGF-mediated differentiation of pancreatic duct cells in vivo. {yields} CREB was causally linked to the expression of transcription factors during PDEC differentiation induced by HGF. -- Abstract: We have previously reported that the PI3K/Akt signaling pathway is involved in hepatocyte growth factor (HGF)-induced differentiation of adult rat pancreatic ductal epithelial cells (PDECs) into islet {beta}-cells in vitro. The transcription factor CREB is one of the downstream key effectors of the PI3K/Akt signaling pathway. Recent studies showing that CREB is required for the survival of certain cell types prompted us to examine whether CREB is a nuclear target for activation via the HGF-dependent Ser/Thr kinase Akt/PKB in the differentiation of pancreatic duct cell into islet {beta}-cells. In this study, we first attempted to examine whether HGF modulates the Akt-dependent activation of target gene CREB and then investigated whether CREB activity affects the differentiation of HGF-induced PDECs. Finally, we studied the role of CREB in modulating the expression of transcription factors in PDECs during the differentiation of HGF-induced PDECs. Our results demonstrated that CREB is a regulatory target for the protein kinase Akt/PKB in the differentiation of pancreatic ductal cells into islet {beta}-cells mediated by HGF.

  19. Sézary Syndrome and Atopic Dermatitis: Comparison of Immunological Aspects and Targets

    PubMed Central

    Saulite, Ieva; Hoetzenecker, Wolfram; Weidinger, Stephan; Cozzio, Antonio; Guenova, Emmanuella; Wehkamp, Ulrike

    2016-01-01

    Sézary syndrome (SS), an aggressive form of erythrodermic pruritic cutaneous T cell lymphoma (CTCL), from an immunological perspective characterized by increased Th2 cytokine levels, elevated serum IgE and impaired cellular immunity. Not only the clinical appearance but also the hallmark immunological characteristics of SS often share striking similarities with acute flares of atopic dermatitis (AD), a common benign chronic inflammatory skin disease. Given the overlap of several immunological features, the application of similar or even identical therapeutic approaches in certain stages of both diseases may come into consideration. The aim of this review is to compare currently accepted immunological aspects and possible therapeutic targets in AD and SS. PMID:27294147

  20. Comparison of point target detection algorithms for space-based scanning infrared sensors

    NASA Astrophysics Data System (ADS)

    Namoos, Omar M.; Schulenburg, Nielson W.

    1995-09-01

    The tracking of resident space objects (RSO) by space-based sensors can lead to engagements that result in stressing backgrounds. These backgrounds, including hard earth, earth limb, and zodiacal, pose various difficulties for signal processing algorithms designed to detect and track the target with a minimum of false alarms. Simulated RSO engagements were generated using the Strategic Scene Generator Model and a sensor model to create focal plane scenes. Using this data, the performance of several detection algorithms has been quantified for space, earth limb and cluttered hard earth backgrounds. These algorithms consist of an adaptive spatial filter, a transversal (matched) filters, and a median variance (nonlinear) filter. Signal-to-clutter statistics of the filtered scenes are compared to those of the unfiltered scene. False alarm and detection results are included. Based on these findings, a suggested processing software architectures design is hypothesized.

  1. Ginsenoside Rc from Panax ginseng exerts anti-inflammatory activity by targeting TANK-binding kinase 1/interferon regulatory factor-3 and p38/ATF-2.

    PubMed

    Yu, Tao; Yang, Yanyan; Kwak, Yi-Seong; Song, Gwan Gyu; Kim, Mi-Yeon; Rhee, Man Hee; Cho, Jae Youl

    2017-04-01

    Ginsenoside Rc (G-Rc) is one of the major protopanaxadiol-type saponins isolated from Panax ginseng, a well-known medicinal herb with many beneficial properties including anticancer, anti-inflammatory, antiobesity, and antidiabetic effects. In this study, we investigated the effects of G-Rc on inflammatory responses in vitro and examined the mechanisms of these effects. The in vitro inflammation system used lipopolysaccharide-treated macrophages, tumor necrosis factor-α/interferon-γ-treated synovial cells, and HEK293 cells transfected with various inducers of inflammation. G-Rc significantly inhibited the expression of macrophage-derived cytokines, such as tumor necrosis factor-α and interleukin-1β. G-Rc also markedly suppressed the activation of TANK-binding kinase 1/IκB kinase ε/interferon regulatory factor-3 and p38/ATF-2 signaling in activated RAW264.7 macrophages, human synovial cells, and HEK293 cells. G-Rc exerts its anti-inflammatory actions by suppressing TANK-binding kinase 1/IκB kinase ε/interferon regulatory factor-3 and p38/ATF-2 signaling.

  2. A comparison of information functions and search strategies for sensor planning in target classification.

    PubMed

    Zhang, Guoxian; Ferrari, Silvia; Cai, Chenghui

    2012-02-01

    This paper investigates the comparative performance of several information-driven search strategies and decision rules using a canonical target classification problem. Five sensor models are considered: one obtained from classical estimation theory and four obtained from Bernoulli, Poisson, binomial, and mixture-of-binomial distributions. A systematic approach is presented for deriving information functions that represent the expected utility of future sensor measurements from mutual information, Rènyi divergence, Kullback-Leibler divergence, information potential, quadratic entropy, and the Cauchy-Schwarz distance. The resulting information-driven strategies are compared to direct-search, alert-confirm, task-driven (TS), and log-likelihood-ratio (LLR) search strategies. Extensive numerical simulations show that quadratic entropy typically leads to the most effective search strategy with respect to correct-classification rates. In the presence of prior information, the quadratic-entropy-driven strategy also displays the lowest rate of false alarms. However, when prior information is absent or very noisy, TS and LLR strategies achieve the lowest false-alarm rates for the Bernoulli, mixture-of-binomial, and classical sensor models.

  3. The comparison of the efficacy of radiofrequency nucleoplasty and targeted disc decompression in lumbar radiculopathy

    PubMed Central

    Adakli, Barıs; Turhan, K. Sanem Cakar; Asik, Ibrahim

    2015-01-01

    Chronic low back pain is a common clinical condition causing medical, socioeconomic, and treatment difficulties. In our study, we aimed to compare early and long-term efficacy of lumbar radiofrequency thermocoagulation (RFTC) nucleoplasty and targeted disc decompression (TDD) in patients with lumbar radiculopathy in whom previous conventional therapy had failed. The medical records of 37 patients undergoing TDD and 36 patients undergoing lumbar RFTC nucleoplasty were retrospectively examined and assigned to the Group D and Group N, respectively. In all patients Visual Analogue Scale (VAS) and Functional Rating Index (FRI) were recorded before treatment and after one, six and twelve months after the procedure. The North American Spine Society Satisfaction Scale (NASSSS) was also recoreded twelve months after the therapeutic procedure. Statistically significant postprocedural improvement in VAS and FRI was evident in both groups. VAS scores after one, six, and twelve month were slightly higher in Group N, compared to Group D. The overall procedure-related patient satisfaction ratio was 67.5% in the Group D, compared to 75% in the Group N. Regardless of the different mechanism of action, both methods are effective therapies for lumbar radiculopathy, with TDD showing long-term lower pain scores. PMID:26042514

  4. Comparison and analysis of point target reference spectrum of FMCW synthetic aperture imaging sensor

    NASA Astrophysics Data System (ADS)

    Liu, Yue; Deng, Yun-Kai; Wang, Robert; Jia, Xiao-Xue; Han, Xiao-Dong

    2012-12-01

    Frequency-modulated continuous-wave (FMCW) synthetic aperture imaging sensor (SAIS) combines FMCW technology and SAIS techniques which makes a lightweight, high-resolution, and cost-effective imaging sensor. FMCW SAIS systems are going to play an important role in airborne and spaceborne earth observation fields. However, the stop-and-go approximation used in conventional pulsed SAIR (e.g., synthetic aperture radar—SAR) is no longer valid due to the long signal duration time or low wave propagation speed. To exploit the potentialities of an accurate signal model under FMCW SAIS circumstances, this article presents the relationship and remarkable differences between the analytical FMCW SAIS point target reference spectrum model and the traditional ones in pulsed SAR and Synthetic Aperture Acoustic imaging system, and validates the significance of the additional range-azimuth coupling term and range walk term in FMCW SAIS spectrum introduced by the variation of slant range during the long pulse durations, and highlight the limitations of other two spectra. Finally, the simulation experiments are carried out to compare the performance of the aforementioned spectrum formulations.

  5. A Global Comparison of the Human and T. brucei Degradomes Gives Insights about Possible Parasite Drug Targets

    PubMed Central

    Mashiyama, Susan T.; Koupparis, Kyriacos; Caffrey, Conor R.; McKerrow, James H.; Babbitt, Patricia C.

    2012-01-01

    We performed a genome-level computational study of sequence and structure similarity, the latter using crystal structures and models, of the proteases of Homo sapiens and the human parasite Trypanosoma brucei. Using sequence and structure similarity networks to summarize the results, we constructed global views that show visually the relative abundance and variety of proteases in the degradome landscapes of these two species, and provide insights into evolutionary relationships between proteases. The results also indicate how broadly these sequence sets are covered by three-dimensional structures. These views facilitate cross-species comparisons and offer clues for drug design from knowledge about the sequences and structures of potential drug targets and their homologs. Two protease groups (“M32” and “C51”) that are very different in sequence from human proteases are examined in structural detail, illustrating the application of this global approach in mining new pathogen genomes for potential drug targets. Based on our analyses, a human ACE2 inhibitor was selected for experimental testing on one of these parasite proteases, TbM32, and was shown to inhibit it. These sequence and structure data, along with interactive versions of the protein similarity networks generated in this study, are available at http://babbittlab.ucsf.edu/resources.html. PMID:23236535

  6. A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets.

    PubMed

    Mashiyama, Susan T; Koupparis, Kyriacos; Caffrey, Conor R; McKerrow, James H; Babbitt, Patricia C

    2012-01-01

    We performed a genome-level computational study of sequence and structure similarity, the latter using crystal structures and models, of the proteases of Homo sapiens and the human parasite Trypanosoma brucei. Using sequence and structure similarity networks to summarize the results, we constructed global views that show visually the relative abundance and variety of proteases in the degradome landscapes of these two species, and provide insights into evolutionary relationships between proteases. The results also indicate how broadly these sequence sets are covered by three-dimensional structures. These views facilitate cross-species comparisons and offer clues for drug design from knowledge about the sequences and structures of potential drug targets and their homologs. Two protease groups ("M32" and "C51") that are very different in sequence from human proteases are examined in structural detail, illustrating the application of this global approach in mining new pathogen genomes for potential drug targets. Based on our analyses, a human ACE2 inhibitor was selected for experimental testing on one of these parasite proteases, TbM32, and was shown to inhibit it. These sequence and structure data, along with interactive versions of the protein similarity networks generated in this study, are available at http://babbittlab.ucsf.edu/resources.html.

  7. REGULATORY T CELL SUPPRESSION IS POTENTIATED BY TARGET T CELLS IN A CELL CONTACT, IL-35- AND IL-10-DEPENDENT MANNER1

    PubMed Central

    Collison, Lauren W.; Pillai, Meenu R.; Chaturvedi, Vandana; Vignali, Dario A. A.

    2009-01-01

    Regulatory T cells (Treg) are believed to suppress conventional T cell (Tconv) proliferation in vitro in a contact-dependent, cytokine-independent manner, based in part on experiments in which Treg and Tconv are separated by a permeable membrane. We show that the production of interleukin-35 (IL-35), a novel inhibitory cytokine expressed by natural Treg, increases substantially following contact with Tconv. Surprisingly, Treg were able to mediate potent suppression of Tconv across a permeable membrane when placed in direct contact with Tconv in the upper chamber of a Transwell™ plate. Suppression was IL-35- and IL-10-dependent, and Tconv activation was required for maximal potentiation of Treg suppression. These data suggest that it is the ‘induction’ of suppression, rather than the ‘function’ of Treg that is obligatorily contact-dependent. PMID:19414764

  8. Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region

    PubMed Central

    Overlöper, Aaron; Kraus, Alexander; Gurski, Rosemarie; Wright, Patrick R; Georg, Jens; Hess, Wolfgang R; Narberhaus, Franz

    2014-01-01

    The small RNA AbcR1 regulates the expression of ABC transporters in the plant pathogen Agrobacterium tumefaciens, the plant symbiont Sinorhizobium meliloti, and the human pathogen Brucella abortus. A combination of proteomic and bioinformatic approaches suggested dozens of AbcR1 targets in A. tumefaciens. Several of these newly discovered targets are involved in the uptake of amino acids, their derivatives, and sugars. Among the latter is the periplasmic sugar-binding protein ChvE, a component of the virulence signal transduction system. We examined 16 targets and their interaction with AbcR1 in close detail. In addition to the previously described mRNA interaction site of AbcR1 (M1), the CopraRNA program predicted a second functional module (M2) as target-binding site. Both M1 and M2 contain single-stranded anti-SD motifs. Using mutated AbcR1 variants, we systematically tested by band shift experiments, which sRNA region is responsible for mRNA binding and gene regulation. On the target site, we find that AbcR1 interacts with some mRNAs in the translation initiation region and with others far into their coding sequence. Our data show that AbcR1 is a versatile master regulator of nutrient uptake systems in A. tumefaciens and related bacteria. PMID:24921646

  9. Imaging of Her2-Targeted Magnetic Nanoparticles for Breast Cancer Detection: Comparison of SQUID-detected Magnetic Relaxometry and MRI

    PubMed Central

    Adolphi, Natalie L.; Butler, Kimberly S.; Lovato, Debbie M.; Tessier, T. E.; Trujillo, Jason E.; Hathaway, Helen J.; Fegan, Danielle L.; Monson, Todd C.; Stevens, Tyler E.; Huber, Dale L.; Ramu, Jaivijay; Milne, Michelle L.; Altobelli, Stephen A.; Bryant, Howard C.; Larson, Richard S.; Flynn, Edward R.

    2013-01-01

    Both magnetic relaxometry and magnetic resonance imaging (MRI) can be used to detect and locate targeted magnetic nanoparticles, non-invasively and without ionizing radiation. Magnetic relaxometry offers advantages in terms of its specificity (only nanoparticles are detected) and the linear dependence of the relaxometry signal on the number of nanoparticles present. In this study, detection of single-core iron oxide nanoparticles by Superconducting Quantum Interference Device (SQUID)-detected magnetic relaxometry and standard 4.7 T MRI are compared. The nanoparticles were conjugated to a Her2 monoclonal antibody and targeted to Her2-expressing MCF7/Her2-18 breast cancer cells); binding of the nanoparticles to the cells was assessed by magnetic relaxometry and iron assay. The same nanoparticle-labeled cells, serially diluted, were used to assess the detection limits and MR relaxivities. The detection limit of magnetic relaxometry was 125,000 nanoparticle-labeled cells at 3 cm from the SQUID sensors. T2-weighted MRI yielded a detection limit of 15,600 cells in a 150 μl volume, with r1 = 1.1 mM−1s−1 and r2 = 166 mM−1s−1. Her2-targeted nanoparticles were directly injected into xenograft MCF7/Her2-18 tumors in nude mice, and magnetic relaxometry imaging and 4.7 T MRI were performed, enabling direct comparison of the two techniques. Co-registration of relaxometry images and MRI of mice resulted in good agreement. A method for obtaining accurate quantification of microgram quantities of iron in the tumors and liver by relaxometry was also demonstrated. These results demonstrate the potential of SQUID-detected magnetic relaxometry imaging for the specific detection of breast cancer and the monitoring of magnetic nanoparticle-based therapies. PMID:22539401

  10. Imaging of Her2-targeted magnetic nanoparticles for breast cancer detection: comparison of SQUID-detected magnetic relaxometry and MRI.

    PubMed

    Adolphi, Natalie L; Butler, Kimberly S; Lovato, Debbie M; Tessier, T E; Trujillo, Jason E; Hathaway, Helen J; Fegan, Danielle L; Monson, Todd C; Stevens, Tyler E; Huber, Dale L; Ramu, Jaivijay; Milne, Michelle L; Altobelli, Stephen A; Bryant, Howard C; Larson, Richard S; Flynn, Edward R

    2012-01-01

    Both magnetic relaxometry and magnetic resonance imaging (MRI) can be used to detect and locate targeted magnetic nanoparticles, noninvasively and without ionizing radiation. Magnetic relaxometry offers advantages in terms of its specificity (only nanoparticles are detected) and the linear dependence of the relaxometry signal on the number of nanoparticles present. In this study, detection of single-core iron oxide nanoparticles by superconducting quantum interference device (SQUID)-detected magnetic relaxometry and standard 4.7 T MRI are compared. The nanoparticles were conjugated to a Her2 monoclonal antibody and targeted to Her2-expressing MCF7/Her2-18 (breast cancer cells); binding of the nanoparticles to the cells was assessed by magnetic relaxometry and iron assay. The same nanoparticle-labeled cells, serially diluted, were used to assess the detection limits and MR relaxivities. The detection limit of magnetic relaxometry was 125 000 nanoparticle-labeled cells at 3 cm from the SQUID sensors. T(2)-weighted MRI yielded a detection limit of 15 600 cells in a 150 µl volume, with r(1) = 1.1 mm(-1) s(-1) and r(2) = 166 mm(-1) s(-1). Her2-targeted nanoparticles were directly injected into xenograft MCF7/Her2-18 tumors in nude mice, and magnetic relaxometry imaging and 4.7 T MRI were performed, enabling direct comparison of the two techniques. Co-registration of relaxometry images and MRI of mice resulted in good agreement. A method for obtaining accurate quantification of microgram quantities of iron in the tumors and liver by relaxometry was also demonstrated. These results demonstrate the potential of SQUID-detected magnetic relaxometry imaging for the specific detection of breast cancer and the monitoring of magnetic nanoparticle-based therapies. Copyright © 2012 John Wiley & Sons, Ltd.

  11. Comparison of universal and targeted screening for thyroid dysfunction in pregnant Egyptian women.

    PubMed

    Ahmed, Iman Z; Eid, Yara M; El Orabi, Hussein; Ibrahim, Hani Refat

    2014-08-01

    To compare universal vs targeted screening for thyroid dysfunction and to estimate the prevalence of hypothyroidism in pregnant Egyptian women. A total of 168 of pregnant women who attended the outpatient obstetric clinic at Ain Shams University Hospital (Cairo, Egypt) for antenatal care between September 2011 and December 2011 were enrolled. Based on the detailed data collection and results of laboratory testing, they were subdivided into the high- and low-risk group for thyroid disease according to the most recent Endocrine Society clinical practice guidelines, as well as into groups by trimester for application of American Thyroid Association guidelines. The group values were subjected to statistical analysis for estimating the prevalence of clinical and subclinical hypothyroidism and for identifying significant differences. Of the 168 patients, 104 were classified into the low-risk group and 64 into the high-risk group. Using the trimesteric and normal population cutoff values for thyroid functions, the prevalence of hypothyroidism was found to be 56% (n=94) and 44.6% (n=75) respectively. No statistically significant differences were found between the high- and low-risk group regarding prevalence of either clinical or subclinical hypothyroidism, and no significant differences were found regarding the prevalence of hypothyroidism in the first, second, or third trimester. Use of the most recent Endocrine Society clinical practice guidelines led to missed detection of clinical or subclinical hypothyroidism in 34.5% of pregnant women. Universal screening of pregnant women for thyroid dysfunction should thus be adopted throughout Egypt. © 2014 European Society of Endocrinology.

  12. Large-scale targeted sequencing comparison highlights extreme genetic heterogeneity in nephronophthisis-related ciliopathies

    PubMed Central

    Schueler, Markus; Halbritter, Jan; Phelps, Ian G.; Braun, Daniela A.; Otto, Edgar A.; Porath, Jonathan D.; Gee, Heon Yung; Shendure, Jay; O’Roak, Brian J.; Lawson, Jennifer A.; Soliman, Neveen A.; Nabhan, Marwa M.; Doherty, Dan; Hildebrandt, Friedhelm

    2016-01-01

    The term nephronophthisis-related ciliopathies (NPHP-RC) describes a group of rare autosomal-recessive cystic kidney diseases, characterized by broad genetic and clinical heterogeneity. NPHP-RC is frequently associated with extrarenal manifestations and accounts for the majority of genetically caused chronic kidney disease (CKD) during childhood and adolescence. Generation of a molecular diagnosis has been impaired by this broad genetic heterogeneity. However, recently developed high-throughput exon sequencing techniques represent powerful and efficient tools to screen large cohorts for dozens of causative genes. Therefore, we performed massively multiplexed targeted sequencing using the modified molecular inversion probe (MIPs) strategy in an international cohort of 384 patients diagnosed with NPHP-RC. As a result, we established the molecular diagnoses in 81/384 unrelated individuals (21.1%). We detected 127 likely disease-causing mutations in 18 of 34 evaluated NPHP-RC genes, 22 of which were novel. We further compared a subgroup of current findings to the results of a previous study in which we used an array-based microfluidic PCR technology in the same cohort. While 78 likely disease-causing mutations were previously detected by the array-based microfluidic PCR, the MIPs approach identified 94 likely pathogenic mutations. Compared to the previous approach, MIPs re-detected 66 out of 78 variants and 28 previously unidentified variants, for a total of 94 variants. In summary, we demonstrate that the modified MIPs technology is a useful approach to screen large cohorts for a multitude of established NPHP genes in order to identify the underlying molecular cause. Combined application of two independent library preparation and sequencing techniques, however, may still be indicated for Mendelian diseases with extensive genetic heterogeneity in order to further increase diagnostic sensitivity. PMID:26673778

  13. [Regulatory mechanism of hormones of the pituitary-target gland axes in kidney-Yang deficiency based on a support vector machine model].

    PubMed

    Xiufeng, Wang; Lei, Zhang; Rongbo, Huang; Qinghua, Wu; Jianxin, Min; Na, Ma; Laicheng, Luo

    2015-04-01

    To study the development mechanism of kidney-Yang deficiency through the establishment of support vector machine models of relevant hormones of the pituitary-target gland axes in rats with kidney-Yang deficiency syndrome. The kidney-Yang deficiency rat model was created by intramuscular injection of hydrocortisone, and contents of the hormones of the pituitary-thyroid axis: thyroid stimulating hormone (TSH), 3,3',5-triiodothyronine (T3) and thyroxine (T4); hormones of the pituitary-adrenal gland axis: adrenocorticotropic hormone (ACTH) and cortisol (CORT); and hormones of the pituitary-gonadal axis: luteinizing hormone (LH), follicle-stimulating hormone (FSH), and testosterone (T), were determined in the early, middle, and advanced stages. Ten support vector regression (SVR) models of the hormones were established to analyze the mutual relationships among the hormones of the three axes. The feedback control action of the pituitary-adrenal axis began to lose efficacy from the middle stage of kidney-Yang deficiency. The contents all hormones of the three pituitary-target gland axes decreased in the advanced stage. Relative errors of the jackknife test of the SVR models all were less than 10%. Imbalances in mutual regulation among the hormones of the pituitary-target gland axes, especially loss of effectiveness of the pituitary-adrenal axis, is one pathogenesis of kidney-Yang deficiency. The SVR model can accurately reflect the complicated non-linear relationships among pituitary-target gland axes in rats with of kidney-Yang deficiency.

  14. Mutant Thyroid Hormone Receptors (TRs) Isolated from Distinct Cancer Types Display Distinct Target Gene Specificities: a Unique Regulatory Repertoire Associated with Two Renal Clear Cell Carcinomas

    PubMed Central

    Rosen, Meghan D.; Chan, Ivan H.

    2011-01-01

    Thyroid hormone receptors (TRs) are hormone-regulated transcription factors that regulate a diverse array of biological activities, including metabolism, homeostasis, and development. TRs also serve as tumor suppressors, and aberrant TR function (via mutation, deletion, or altered expression) is associated with a spectrum of both neoplastic and endocrine diseases. A particularly high frequency of TR mutations has been reported in renal clear cell carcinoma (RCCC) and in hepatocellular carcinoma (HCC). We have shown that HCC-TR mutants regulate only a fraction of the genes targeted by wild-type TRs but have gained the ability to regulate other, unique, targets. We have suggested that this altered gene recognition may contribute to the neoplastic phenotype. Here, to determine the generality of this phenomenon, we examined a distinct set of TR mutants associated with RCCC. We report that two different TR mutants, isolated from independent RCCC tumors, possess greatly expanded target gene specificities that extensively overlap one another, but only minimally overlap that of the wild-type TRs, or those of two HCC-TR mutants. Many of the genes targeted by either or both RCCC-TR mutants have been previously implicated in RCCC and include a series of metallothioneins, solute carriers, and genes involved in glycolysis and energy metabolism. We propose as a hypothesis that TR mutations from RCCC and HCC may play tissue-specific roles in carcinogenesis, and that the divergent target gene recognition patterns of TR mutants isolated from the two different types of tumors may arise from different selective pressures during development of RCCC vs. HCC. PMID:21622534

  15. Mutant thyroid hormone receptors (TRs) isolated from distinct cancer types display distinct target gene specificities: a unique regulatory repertoire associated with two renal clear cell carcinomas.

    PubMed

    Rosen, Meghan D; Chan, Ivan H; Privalsky, Martin L

    2011-08-01

    Thyroid hormone receptors (TRs) are hormone-regulated transcription factors that regulate a diverse array of biological activities, including metabolism, homeostasis, and development. TRs also serve as tumor suppressors, and aberrant TR function (via mutation, deletion, or altered expression) is associated with a spectrum of both neoplastic and endocrine diseases. A particularly high frequency of TR mutations has been reported in renal clear cell carcinoma (RCCC) and in hepatocellular carcinoma (HCC). We have shown that HCC-TR mutants regulate only a fraction of the genes targeted by wild-type TRs but have gained the ability to regulate other, unique, targets. We have suggested that this altered gene recognition may contribute to the neoplastic phenotype. Here, to determine the generality of this phenomenon, we examined a distinct set of TR mutants associated with RCCC. We report that two different TR mutants, isolated from independent RCCC tumors, possess greatly expanded target gene specificities that extensively overlap one another, but only minimally overlap that of the wild-type TRs, or those of two HCC-TR mutants. Many of the genes targeted by either or both RCCC-TR mutants have been previously implicated in RCCC and include a series of metallothioneins, solute carriers, and genes involved in glycolysis and energy metabolism. We propose as a hypothesis that TR mutations from RCCC and HCC may play tissue-specific roles in carcinogenesis, and that the divergent target gene recognition patterns of TR mutants isolated from the two different types of tumors may arise from different selective pressures during development of RCCC vs. HCC.

  16. The Pseudomonas aeruginosa PAO1 Two-Component Regulator CarSR Regulates Calcium Homeostasis and Calcium-Induced Virulence Factor Production through Its Regulatory Targets CarO and CarP

    PubMed Central

    Guragain, Manita; King, Michelle M.; Williamson, Kerry S.; Pérez-Osorio, Ailyn C.; Akiyama, Tatsuya; Khanam, Sharmily

    2016-01-01

    ABSTRACT Pseudomonas aeruginosa is an opportunistic human pathogen that causes severe, life-threatening infections in patients with cystic fibrosis (CF), endocarditis, wounds, or artificial implants. During CF pulmonary infections, P. aeruginosa often encounters environments where the levels of calcium (Ca2+) are elevated. Previously, we showed that P. aeruginosa responds to externally added Ca2+ through enhanced biofilm formation, increased production of several secreted virulence factors, and by developing a transient increase in the intracellular Ca2+ level, followed by its removal to the basal submicromolar level. However, the molecular mechanisms responsible for regulating Ca2+-induced virulence factor production and Ca2+ homeostasis are not known. Here, we characterized the genome-wide transcriptional response of P. aeruginosa to elevated [Ca2+] in both planktonic cultures and biofilms. Among the genes induced by CaCl2 in strain PAO1 was an operon containing the two-component regulator PA2656-PA2657 (here called carS and carR), while the closely related two-component regulators phoPQ and pmrAB were repressed by CaCl2 addition. To identify the regulatory targets of CarSR, we constructed a deletion mutant of carR and performed transcriptome analysis of the mutant strain at low and high [Ca2+]. Among the genes regulated by CarSR in response to CaCl2 are the predicted periplasmic OB-fold protein, PA0320 (here called carO), and the inner membrane-anchored five-bladed β-propeller protein, PA0327 (here called carP). Mutations in both carO and carP affected Ca2+ homeostasis, reducing the ability of P. aeruginosa to export excess Ca2+. In addition, a mutation in carP had a pleotropic effect in a Ca2+-dependent manner, altering swarming motility, pyocyanin production, and tobramycin sensitivity. Overall, the results indicate that the two-component system CarSR is responsible for sensing high levels of external Ca2+ and responding through its regulatory targets that

  17. Gene expression profiling of whole blood: Comparison of target preparation methods for accurate and reproducible microarray analysis

    PubMed Central

    Vartanian, Kristina; Slottke, Rachel; Johnstone, Timothy; Casale, Amanda; Planck, Stephen R; Choi, Dongseok; Smith, Justine R; Rosenbaum, James T; Harrington, Christina A

    2009-01-01

    Background Peripheral blood is an accessible and informative source of transcriptomal information for many human disease and pharmacogenomic studies. While there can be significant advantages to analyzing RNA isolated from whole blood, particularly in clinical studies, the preparation of samples for microarray analysis is complicated by the need to minimize artifacts associated with highly abundant globin RNA transcripts. The impact of globin RNA transcripts on expression profiling data can potentially be reduced by using RNA preparation and labeling methods that remove or block globin RNA during the microarray assay. We compared four different methods for preparing microarray hybridization targets from human whole blood collected in PAXGene tubes. Three of the methods utilized the Affymetrix one-cycle cDNA synthesis/in vitro transcription protocol but varied treatment of input RNA as follows: i. no treatment; ii. treatment with GLOBINclear; or iii. treatment with globin PNA oligos. In the fourth method cDNA targets were prepared with the Ovation amplification and labeling system. Results We find that microarray targets generated with labeling methods that reduce globin mRNA levels or minimize the impact of globin transcripts during hybridization detect more transcripts in the microarray assay compared with the standard Affymetrix method. Comparison of microarray results with quantitative PCR analysis of a panel of genes from the NF-kappa B pathway shows good correlation of transcript measurements produced with all four target preparation methods, although method-specific differences in overall correlation were observed. The impact of freezing blood collected in PAXGene tubes on data reproducibility was also examined. Expression profiles show little or no difference when RNA is extracted from either fresh or frozen blood samples. Conclusion RNA preparation and labeling methods designed to reduce the impact of globin mRNA transcripts can significantly improve the

  18. Regulatory T cells and COPD.

    PubMed

    Dancer, Rachel; Sansom, David M

    2013-12-01

    While the innate immune system has long been implicated in the pathogenesis of COPD, a role for the acquired immune system is less well studied. The increasing recognition that COPD shares features with autoimmune disease has led to interest in a potential role for regulatory T cells, which are intimately involved in the control of autoimmunity. The suggestion that regulatory T cell numbers are increased in patients with COPD may indicate their dysfunction or resistance to suppression by target cells. Investigation of regulatory T cells may therefore be of importance in understanding the inflammation and tissue damage that occurs in patients with COPD who cease smoking.

  19. The small regulatory RNA FasX enhances group A Streptococcus virulence and inhibits pilus expression via serotype-specific targets.

    PubMed

    Danger, Jessica L; Cao, Tram N; Cao, Tran H; Sarkar, Poulomee; Treviño, Jeanette; Pflughoeft, Kathryn J; Sumby, Paul

    2015-04-01

    Bacterial pathogens commonly show intra-species variation in virulence factor expression and often this correlates with pathogenic potential. The group A Streptococcus (GAS) produces a small regulatory RNA (sRNA), FasX, which regulates the expression of pili and the thrombolytic agent streptokinase. As GAS serotypes are polymorphic regarding (a) FasX abundance, (b) the fibronectin, collagen, T-antigen (FCT) region of the genome, which contains the pilus genes (nine different FCT-types), and (c) the streptokinase-encoding gene (ska) sequence (two different alleles), we sought to test whether FasX regulates pilus and streptokinase expression in a serotype-specific manner. Parental, fasX mutant and complemented derivatives of serotype M1 (ska-2, FCT-2), M2 (ska-1, FCT-6), M6 (ska-2, FCT-1) and M28 (ska-1, FCT-4) isolates were compared. While FasX reduced pilus expression in each serotype, the molecular basis differed, as FasX bound, and inhibited the translation of, different FCT-region mRNAs. FasX enhanced streptokinase expression in each serotype, although the degree of regulation varied. Finally, we established that the regulation afforded by FasX enhances GAS virulence, assessed by a model of bacteremia using human plasminogen-expressing mice. Our data are the first to identify and characterize serotype-specific regulation by an sRNA in GAS, and to show an sRNA directly contributes to GAS virulence.

  20. Celastrol, a Chinese herbal compound, controls autoimmune inflammation by altering the balance of pathogenic and regulatory T cells in the target organ

    PubMed Central

    Astry, Brian; Venkatesha, Shivaprasad H.; Laurence, Arian; Christensen-Quick, Aaron; Garzinodemo, Alfredo; Frieman, Matthew B; O’Shea, John J.; Moudgil, Kamal D.

    2015-01-01

    Inflammation is an integral component of autoimmune arthritis. The balance of pathogenic T helper 17 (Th17) and protective T regulatory (Treg) cells can influence disease severity, and its resetting offers an attractive approach to control autoimmunity. We determined the frequency of Th17 and Treg in the joints of rats with adjuvant arthritis (AA), a model of rheumatoid arthritis (RA). We also investigated the impact of Celastrol, a bioactive compound from the traditional Chinese medicine Celastrus that can suppress AA, on Th17/Treg balance in the joints. Celastrol treatment reduced Th17 cells but increased Treg in the joints, and it inhibited Th17 differentiation but promoted Treg differentiation in vitro by blocking the activation of pSTAT3. Furthermore, Celastrol limited the production of Th17-differentiating cytokines and chemokines (CCL3, CCL5). Thus, Celastrol suppressed arthritis in part by altering Th17/Treg ratio in inflamed joints, and it should be tested as a potential adjunct/alternative for RA therapy. PMID:25660987

  1. The Diabetes Drug Target MitoNEET Governs a Novel Trafficking Pathway to Rebuild an Fe-S Cluster into Cytosolic Aconitase/Iron Regulatory Protein 1*

    PubMed Central

    Ferecatu, Ioana; Gonçalves, Sergio; Golinelli-Cohen, Marie-Pierre; Clémancey, Martin; Martelli, Alain; Riquier, Sylvie; Guittet, Eric; Latour, Jean-Marc; Puccio, Hélène; Drapier, Jean-Claude; Lescop, Ewen; Bouton, Cécile

    2014-01-01

    In eukaryotes, mitochondrial iron-sulfur cluster (ISC), export and cytosolic iron-sulfur cluster assembly (CIA) machineries carry out biogenesis of iron-sulfur (Fe-S) clusters, which are critical for multiple essential cellular pathways. However, little is known about their export out of mitochondria. Here we show that Fe-S assembly of mitoNEET, the first identified Fe-S protein anchored in the mitochondrial outer membrane, strictly depends on ISC machineries and not on the CIA or CIAPIN1. We identify a dedicated ISC/export pathway in which augmenter of liver regeneration, a mitochondrial Mia40-dependent protein, is specific to mitoNEET maturation. When inserted, the Fe-S cluster confers mitoNEET folding and stability in vitro and in vivo. The holo-form of mitoNEET is resistant to NO and H2O2 and is capable of repairing oxidatively damaged Fe-S of iron regulatory protein 1 (IRP1), a master regulator of cellular iron that has recently been involved in the mitochondrial iron supply. Therefore, our findings point to IRP1 as the missing link to explain the function of mitoNEET in the control of mitochondrial iron homeostasis. PMID:25012650

  2. T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements

    PubMed Central

    Kanhere, Aditi; Hertweck, Arnulf; Bhatia, Urvashi; Gökmen, M. Refik; Perucha, Esperanza; Jackson, Ian; Lord, Graham M.; Jenner, Richard G.

    2012-01-01

    T-bet and GATA3 regulate the CD4+ T cell Th1/Th2 cell fate decision but little is known about the interplay between these factors outside of the murine Ifng and Il4/Il5/Il13 loci. Here we show that T-bet and GATA3 bind to multiple distal sites at immune regulatory genes in human effector T cells. These sites display markers of functional elements, act as enhancers in reporter assays and are associated with a requirement for T-bet and GATA3. Furthermore, we demonstrate that both factors bind distal sites at Tbx21 and that T-bet directly activates its own expression. We also show that in Th1 cells, GATA3 is distributed away from Th2 genes, instead occupying T-bet binding sites at Th1 genes, and that T-bet is sufficient to induce GATA3 binding at these sites. We propose these aspects of T-bet and GATA3 function are important for Th1/Th2 differentiation and for understanding transcription factor interactions in other T cell lineage decisions. PMID:23232398

  3. Host MicroRNA miR-197 Plays a Negative Regulatory Role in the Enterovirus 71 Infectious Cycle by Targeting the RAN Protein

    PubMed Central

    Tang, Wen-Fang; Huang, Ru-Ting; Chien, Kun-Yi; Huang, Jo-Yun; Lau, Kean-Seng; Jheng, Jia-Rong; Chiu, Cheng-Hsun; Wu, Tzong-Yuan; Chen, Chung-Yung

    2015-01-01

    ABSTRACT Enterovirus 71 (EV71), a member of Picornaviridae, is associated with severe central nervous system complications. In this study, we identified a cellular microRNA (miRNA), miR-197, whose expression was downregulated by viral infection in a time-dependent manner. In miR-197 mimic-transfected cells, EV71 replication was inhibited, whereas the internal ribosome entry site (IRES) activity was decreased in EV71 strains with or without predicted miR-197 target sites, indicating that miR-197 targets host proteins to modulate viral replication. We thus used a quantitative proteomics approach, aided by the TargetScan algorithm, to identify putative target genes of miR-197. Among them, RAN was selected and validated as a genuine target in a 3′ untranslated region (UTR) reporter assay. Reduced production of RAN by RNA interference markedly reduced the synthesis of EV71-encoded viral proteins and virus titers. Furthermore, reintroduction of nondegradable RAN into these knockdown cells rescued viral protein synthesis. miR-197 levels were modulated by EV71 to maintain RAN mRNA translatability at late times postinfection since we demonstrated that cap-independent translation exerted by its intrinsic IRES activity was occurring at times when translation attenuation was induced by EV71. EV71-induced downregulation of miR-197 expression increased the expression of RAN, which supported the nuclear transport of the essential viral proteins 3D/3CD and host protein hnRNP K for viral replication. Our data suggest that downregulation of cellular miRNAs may constitute a newly identified mechanism that sustains the expression of host proteins to facilitate viral replication. IMPORTANCE Enterovirus 71 (EV71) is a picornavirus with a positive-sense single-stranded RNA that globally inhibits the cellular translational system, mainly by cleaving cellular eukaryotic translation initiation factor 4G (eIF4G) and poly(A)-binding protein (PABP), which inhibits the association of the

  4. Accuracy of targeted wire guided tube thoracostomy in comparison to classical surgical chest tube placement - A clinical study.

    PubMed

    Protic, Alen; Barkovic, Igor; Ivancic, Aldo; Kricka, Ozren; Zuvic-Butorac, Marta; Sustic, Alan

    2015-11-01

    Chest tube malfunction, after the tube thoracostomy, is often the result of an inappropriate chest tube tip position. The aim of this study was to analyse the precision of chest tube placement using the targeted wire guide technique (TWG technique) with curve dilator and to compare it to the classical surgical technique (CS technique). In this clinical study 80 patients with an indication for thoracic drainage, due to pneumothorax or pleural effusion were included. Experimental group contained 39 patients whose chest tube was placed using the TWG technique. The control group contained 41 patients whose chest tube was placed using the CS technique. The comparison of the outcomes of the two techniques applied suggests that the TWG technique was significantly more successful in achieving adequate (precise) chest tube placement, irrespective of patient diagnosis (TWG vs. CS in all patients, 78.4% vs. 36.6%, p<0.001). In the pleural effusion group, TWG and CS had success rates of 78.2% and 37.5% (p=0.005), respectively, while in pneumothorax group, TWG and CS had success rates of 78.6% and 35.3% (p=0.029), respectively. Using a curved dilator and the TWG technique for the thoracic drainage procedure we found statistically significant advantage to the TWG technique in comparison to the CS technique (78% vs. 37%) regarding precise chest tube placement within the pleural cavity. Introducing the materials and technique used in this clinical trial into clinical practice may improve the quality of thoracic drainage, including residual volume of air and/or fluid, poor functioning of the chest tube, and, as a consequence of both, prolonged hospitalisation. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Genome-Wide Mapping of Targets of Maize Histone Deacetylase HDA101 Reveals Its Function and Regulatory Mechanism during Seed Development[OPEN

    PubMed Central

    Yang, Hua; Liu, Xinye; Xin, Mingming; Du, Jinkun; Hu, Zhaorong; Peng, HuiRu; Sun, Qixin; Ni, Zhongfu; Yao, Yingyin

    2016-01-01

    Histone deacetylases (HDACs) regulate histone acetylation levels by removing the acetyl group from lysine residues. The maize (Zea mays) HDAC HDA101 influences several aspects of development, including kernel size; however, the molecular mechanism by which HDA101 affects kernel development remains unknown. In this study, we find that HDA101 regulates the expression of transfer cell-specific genes, suggesting that their misregulation may be associated with the defects in differentiation of endosperm transfer cells and smaller kernels observed in hda101 mutants. To investigate HDA101 function during the early stages of seed development, we performed genome-wide mapping of HDA101 binding sites. We observed that, like mammalian HDACs, HDA101 mainly targets highly and intermediately expressed genes. Although loss of HDA101 can induce histone hyperacetylation of its direct targets, this often does not involve variation in transcript levels. A small subset of inactive genes that must be negatively regulated during kernel development is also targeted by HDA101 and its loss leads to hyperacetylation and increased expression of these inactive genes. Finally, we report that HDA101 interacts with members of different chromatin remodeling complexes, such as NFC103/MSI1 and SNL1/SIN3-like protein corepressors. Taken together, our results reveal a complex genetic network regulated by HDA101 during seed development and provide insight into the different mechanisms of HDA101-mediated regulation of transcriptionally active and inactive genes. PMID:26908760

  6. Comparison of Continuous Wave CO2 Doppler Lidar Calibration Using Earth Surface Targets in Laboratory and Airborne Measurements

    NASA Technical Reports Server (NTRS)

    Jarzembski, Maurice A.; Srivastava, Vandana

    1999-01-01

    Routine backscatter, beta, measurements by an airborne or space-based lidar from designated earth surfaces with known and fairly uniform beta properties can potentially offer lidar calibration opportunities. This can in turn be used to obtain accurate atmospheric aerosol and cloud beta measurements on large spatial scales. This is important because achieving a precise calibration factor for large pulsed lidars then need not rest solely on using a standard hard target procedure. Furthermore, calibration from designated earth surfaces would provide an inflight performance evaluation of the lidar. Hence, with active remote sensing using lasers with high resolution data, calibration of a space-based lidar using earth's surfaces will be extremely useful. The calibration methodology using the earth's surface initially requires measuring beta of various earth surfaces simulated in the laboratory using a focused continuous wave (CW) CO2 Doppler lidar and then use these beta measurements as standards for the earth surface signal from airborne or space-based lidars. Since beta from the earth's surface may be retrieved at different angles of incidence, beta would also need to be measured at various angles of incidences of the different surfaces. In general, Earth-surface reflectance measurements have been made in the infrared, but the use of lidars to characterize them and in turn use of the Earth's surface to calibrate lidars has not been made. The feasibility of this calibration methodology is demonstrated through a comparison of these laboratory measurements with actual earth surface beta retrieved from the same lidar during the NASA/Multi-center Airborne Coherent Atmospheric Wind Sensor (MACAWS) mission on NASA's DC8 aircraft from 13 - 26 September, 1995. For the selected earth surface from the airborne lidar data, an average beta for the surface was established and the statistics of lidar efficiency was determined. This was compared with the actual lidar efficiency

  7. Comparison of Continuous Wave CO2 Doppler Lidar Calibration Using Earth Surface Targets in Laboratory and Airborne Measurements

    NASA Technical Reports Server (NTRS)

    Jarzembski, Maurice A.; Srivastava, Vandana

    1999-01-01

    Routine backscatter, beta, measurements by an airborne or space-based lidar from designated earth surfaces with known and fairly uniform beta properties can potentially offer lidar calibration opportunities. This can in turn be used to obtain accurate atmospheric aerosol and cloud beta measurements on large spatial scales. This is important because achieving a precise calibration factor for large pulsed lidars then need not rest solely on using a standard hard target procedure. Furthermore, calibration from designated earth surfaces would provide an inflight performance evaluation of the lidar. Hence, with active remote sensing using lasers with high resolution data, calibration of a space-based lidar using earth's surfaces will be extremely useful. The calibration methodology using the earth's surface initially requires measuring beta of various earth surfaces simulated in the laboratory using a focused continuous wave (CW) CO2 Doppler lidar and then use these beta measurements as standards for the earth surface signal from airborne or space-based lidars. Since beta from the earth's surface may be retrieved at different angles of incidence, beta would also need to be measured at various angles of incidences of the different surfaces. In general, Earth-surface reflectance measurements have been made in the infrared, but the use of lidars to characterize them and in turn use of the Earth's surface to calibrate lidars has not been made. The feasibility of this calibration methodology is demonstrated through a comparison of these laboratory measurements with actual earth surface beta retrieved from the same lidar during the NASA/Multi-center Airborne Coherent Atmospheric Wind Sensor (MACAWS) mission on NASA's DC8 aircraft from 13 - 26 September, 1995. For the selected earth surface from the airborne lidar data, an average beta for the surface was established and the statistics of lidar efficiency was determined. This was compared with the actual lidar efficiency

  8. Improving acne keloidalis nuchae with targeted ultraviolet B treatment: a prospective, randomized, split-scalp comparison study

    PubMed Central

    Okoye, G.A.; Rainer, B.M.; Leung, S.G.; Suh, H.S.; Kim, J.H.; Nelson, A.M.; Garza, L.A.; Chien, A.L.; Kang, S.

    2014-01-01

    Background Acne keloidalis nuchae (AKN) is a chronic scarring folliculitis with fibrotic papules on the occipital scalp. Its treatment is limited and unsatisfactory. Objectives To determine if targeted ultraviolet B (tUVB) phototherapy will (1) improve the clinical appearance of AKN and (2) induce extracellular matrix remodeling in affected lesions. Methods Eleven patients with AKN were enrolled in a prospective, randomized, split-scalp comparison study. One randomly selected side of the scalp was treated with tUVB up to three times weekly for eight weeks. After week 8, both sides were treated for eight additional weeks. Assessment included lesion counts in two 3×3 cm regions of interest (ROI), one on each side of the scalp (ROI-1: tUVB week 0–16, ROI-2: tUVB week 9–16), patient self-assessment, and analysis of MMP-1, MMP-9, TGF-β1, and Col1a1 mRNA expression by qRT-PCR. Results Before treatment, the mean lesion count was similar between tUVB-treated and untreated sides (14.8 vs. 15.0). After eight weeks of tUVB, the mean lesion count decreased significantly to 9.4±1.2 (P=0.03), with no change on the untreated side. With continued treatment, the mean lesion count in ROI-1 decreased further to 7±1.5 (P=0.04) after 16 weeks of tUVB. Conclusion Targeted UVB significantly improved clinical appearance of AKN, led to patient satisfaction, and was well tolerated. PMID:24863570

  9. Prioritization of gene regulatory interactions from large-scale modules in yeast

    PubMed Central

    Lee, Ho-Joon; Manke, Thomas; Bringas, Ricardo; Vingron, Martin

    2008-01-01

    Background The identification of groups of co-regulated genes and their transcription factors, called transcriptional modules, has been a focus of many studies about biological systems. While methods have been developed to derive numerous modules from genome-wide data, individual links between regulatory proteins and target genes still need experimental verification. In this work, we aim to prioritize regulator-target links within transcriptional modules based on three types of large-scale data sources. Results Starting with putative transcriptional modules from ChIP-chip data, we first derive modules in which target genes show both expression and function coherence. The most reliable regulatory links between transcription factors and target genes are established by identifying intersection of target genes in coherent modules for each enriched functional category. Using a combination of genome-wide yeast data in normal growth conditions and two different reference datasets, we show that our method predicts regulatory interactions with significantly higher predictive power than ChIP-chip binding data alone. A comparison with results from other studies highlights that our approach provides a reliable and complementary set of regulatory interactions. Based on our results, we can also identify functionally interacting target genes, for instance, a group of co-regulated proteins related to cell wall synthesis. Furthermore, we report novel conserved binding sites of a glycoprotein-encoding gene, CIS3, regulated by Swi6-Swi4 and Ndd1-Fkh2-Mcm1 complexes. Conclusion We provide a simple method to prioritize individual TF-gene interactions from large-scale transcriptional modules. In comparison with other published works, we predict a complementary set of regulatory interactions which yields a similar or higher prediction accuracy at the expense of sensitivity. Therefore, our method can serve as an alternative approach to prioritization for further experimental studies. PMID

  10. Single-domain antibody-based and linker-free bispecific antibodies targeting FcγRIII induce potent antitumor activity without recruiting regulatory T cells.

    PubMed

    Rozan, Caroline; Cornillon, Amélie; Pétiard, Corinne; Chartier, Martine; Behar, Ghislaine; Boix, Charlotte; Kerfelec, Brigitte; Robert, Bruno; Pèlegrin, André; Chames, Patrick; Teillaud, Jean-Luc; Baty, Daniel

    2013-08-01

    Antibody-dependent cell-mediated cytotoxicity, one of the most prominent modes of action of antitumor antibodies, suffers from important limitations due to the need for optimal interactions with Fcγ receptors. In this work, we report the design of a new bispecific antibody format, compact and linker-free, based on the use of llama single-domain antibodies that are capable of circumventing most of these limitations. This bispecific antibody format was created by fusing single-domain antibodies directed against the carcinoembryonic antigen and the activating FcγRIIIa receptor to human Cκ and CH1 immunoglobulin G1 domains, acting as a natural dimerization motif. In vitro and in vivo characterization of these Fab-like bispecific molecules revealed favorable features for further development as a therapeutic molecule. They are easy to produce in Escherichia coli, very stable, and elicit potent lysis of tumor cells by human natural killer cells at picomolar concentrations. Unlike conventional antibodies, they do not engage inhibitory FcγRIIb receptor, do not compete with serum immunoglobulins G for receptor binding, and their cytotoxic activity is independent of Fc glycosylation and FcγRIIIa polymorphism. As opposed to anti-CD3 bispecific antitumor antibodies, they do not engage regulatory T cells as these latter cells do not express FcγRIII. Studies in nonobese diabetic/severe combined immunodeficient gamma mice xenografted with carcinoembryonic antigen-positive tumor cells showed that Fab-like bispecific molecules in the presence of human peripheral blood mononuclear cells significantly slow down tumor growth. This new compact, linker-free bispecific antibody format offers a promising approach for optimizing antibody-based therapies.

  11. Identification of the transcriptional regulatory sequences of human calponin promoter and their use in targeting a conditionally replicating herpes vector to malignant human soft tissue and bone tumors.

    PubMed

    Yamamura, H; Hashio, M; Noguchi, M; Sugenoya, Y; Osakada, M; Hirano, N; Sasaki, Y; Yoden, T; Awata, N; Araki, N; Tatsuta, M; Miyatake, S I; Takahashi, K

    2001-05-15

    The calponin (basic or h1) gene, normally expressed in maturated smooth muscle cells, is aberrantly expressed in a variety of human soft tissue and bone tumors. In this study, we show that expression of the calponin gene in human soft tissue and bone tumor cells is regulated at the transcriptional level by the sequence between positions -260 and -219 upstream of the translation initiation site. A novel conditionally replicating herpes simplex virus-1 vector (d12.CALP) in which the calponin promoter drives expression of ICP4, a major trans-activating factor for viral genes was constructed and tested as an experimental treatment for malignant human soft tissue and bone tumors. In cell culture, d12.CALP at low multiplicity of infection (0.001 plaque-forming unit/cell) selectively killed calponin-positive human synovial sarcoma, leiomyosarcoma, and osteosarcoma cells. For in vivo studies, 10 animals harboring SK-LMS-1 human leiomyosarcoma cells were randomly divided and treated twice on days 0 and 9 intraneoplastically with either 1 x 10(7) plaque-forming units of d12.CALP/100 mm(3) of tumor volume or with medium alone. The viral treatment group showed stable and significant inhibition of tumorigenicity with apparent cure in four of five mice by day 35. Replication of viral DNA demonstrated by PCR amplification and expression of the inserted LacZ gene visualized by 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside histochemistry was associated with oncolysis of d12.CALP-treated tumors, while sparing normal vascular smooth muscle cells. In mice harboring two SK-LMS-1 tumors, replication of d12.CALP was detected in a nontreated tumor distant from the site of virus inoculation. These results indicate that replication-competent virus vectors controlled by the calponin transcriptional regulatory sequence may be a new therapeutic strategy for treatment of malignant human soft tissue and bone tumors.

  12. Exogenous interleukin-33 targets myeloid-derived suppressor cells and generates periphery-induced Foxp3+ regulatory T cells in skin-transplanted mice

    PubMed Central

    Gajardo, Tania; Morales, Rodrigo A; Campos-Mora, Mauricio; Campos-Acuña, Javier; Pino-Lagos, Karina

    2015-01-01

    Interleukin-33 (IL-33) has been a focus of study because of its variety of functions shaping CD4+ T-cell biology. In the present work, we evaluated the modulatory effect of IL-33 on suppressor cells in an in vivo transplantation model. C57BL/6 wild-type mice were grafted with syngeneic or allogeneic skin transplants and treated with exogenous IL-33 daily. After 10 days of treatment, we analysed draining lymph node cellularity and found in allogeneic animals an increment in myeloid-derived suppressor cells, which co-express MHC-II, and become enriched upon IL-33 treatment. In line with this observation, inducible nitric oxide synthase and arginase 1 expression were also increased in allogeneic animals upon IL-33 administration. In addition, IL-33 treatment up-regulated the number of Foxp3+ regulatory T (Treg) cells in the allogeneic group, complementing the healthier integrity of the allografts and the increased allograft survival. Moreover, we demonstrate that IL-33 promotes CD4+ T-cell expansion and conversion of CD4+ Foxp3− T cells into CD4+ Foxp3+ Treg cells in the periphery. Lastly, the cytokine pattern of ex vivo-stimulated draining lymph nodes indicates that IL-33 dampens interferon-γ and IL-17 production, stimulating IL-10 secretion. Altogether, our work complements previous studies on the immune-modulatory activity of IL-33, showing that this cytokine affects myeloid-derived suppressor cells at the cell number and gene expression levels. More importantly, our research demonstrates for the first time that IL-33 allows for in vivo Foxp3+ Treg cell conversion and favours an anti-inflammatory or tolerogenic state by skewing cytokine production. Therefore, our data suggest a potential use of IL-33 to prevent allograft rejection, bringing new therapeutics to the transplantation field. PMID:25988395

  13. Yeast Edc3 Targets RPS28B mRNA for Decapping by Binding to a 3′ Untranslated Region Decay-Inducing Regulatory Element

    PubMed Central

    Li, Chunfang; Roy, Bijoyita

    2014-01-01

    mRNA decapping commits a transcript to complete turnover in eukaryotic cells. In yeast, general mRNA decapping requires the Dcp1/Dcp2 decapping enzyme and a set of decapping activators, including Pat1, Dhh1, Edc3, and the Lsm1-7 complex. The exact function and mode of action of each of these decapping activators in mRNA decapping largely remain elusive. Here, we analyzed the role of Edc3 in the decay of yeast RPS28B mRNA, a pathway triggered by a negative-feedback autoregulatory mechanism. We show that Edc3-mediated RPS28B mRNA decay requires either of two orthologous proteins, Rps28a and Rps28b, expressed from the RPS28A and RPS28B genes, respectively. Contrary to a generally accepted model, we found that Rps28b does not bind to the 3′-untranslated region (UTR) regulatory element in RPS28B mRNA. Instead, Edc3 is directly involved in binding the element, and Rps28b binds Edc3 and regulates its activity. Decay of RPS28B mRNA requires the Lsm and YjeF-N domains of Edc3, but surprisingly, decay of YRA1 pre-mRNA, the only other known substrate of Edc3, requires only the Lsm domain. Collectively, our experiments reveal a new role for Edc3 in mRNA substrate recognition and suggest that this activity is subject to intricate regulation by additional factors, including the Rps28 ribosomal protein. PMID:24492965

  14. Regulatory effects of intermittent noxious stimulation on spinal cord injury-sensitive microRNAs and their presumptive targets following spinal cord contusion.

    PubMed

    Strickland, Eric R; Woller, Sarah A; Garraway, Sandra M; Hook, Michelle A; Grau, James W; Miranda, Rajesh C

    2014-01-01

    Uncontrollable nociceptive stimulation adversely affects recovery in spinally contused rats. Spinal cord injury (SCI) results in altered microRNA (miRNA) expression both at, and distal to the lesion site. We hypothesized that uncontrollable nociception further influences SCI-sensitive miRNAs and associated gene targets, potentially explaining the progression of maladaptive plasticity. Our data validated previously described sensitivity of miRNAs to SCI alone. Moreover, following SCI, intermittent noxious stimulation decreased expression of miR124 in dorsal spinal cord 24 h after stimulation and increased expression of miR129-2 in dorsal, and miR1 in ventral spinal cord at 7 days. We also found that brain-derived neurotrophic factor (BDNF) mRNA expression was significantly down-regulated 1 day after SCI alone, and significantly more so, after SCI followed by tailshock. Insulin-like growth factor-1 (IGF-1) mRNA expression was significantly increased at both 1 and 7 days post-SCI, and significantly more so, 7 days post-SCI with shock. MiR1 expression was positively and significantly correlated with IGF-1, but not BDNF mRNA expression. Further, stepwise linear regression analysis indicated that a significant proportion of the changes in BDNF and IGF-1 mRNA expression were explained by variance in two groups of miRNAs, implying co-regulation. Collectively, these data show that uncontrollable nociception which activates sensorimotor circuits distal to the injury site, influences SCI-miRNAs and target mRNAs within the lesion site. SCI-sensitive miRNAs may well mediate adverse consequences of uncontrolled sensorimotor activation on functional recovery. However, their sensitivity to distal sensory input also implicates these miRNAs as candidate targets for the management of SCI and neuropathic pain.

  15. Neutron scattering with deuterium labeling reveals the nature of complexes formed by Ca{sup 2+}-binding proteins and their regulatory targets

    SciTech Connect

    Trewhella, J.

    1994-12-01

    Small-angle neutron scattering with deuterium labeling is extremely useful for studying the structures of complex biomolecular assemblies in solution. The different neutron scattering properties of their isotopes of hydrogen combines with the ability to uniformly label biomolecules with deuterium allow one to characterize the structures and relative dispositions of the individual components of an assembly using methods of {open_quotes}contrast variation.{close_quotes} We have applied these techniques to studies of the evolutionarily related dumbbell-shaped Ca{sup 2+}-binding proteins calmodulin and troponin C and their interactions with the target proteins whose activities they regulate. Ca{sup 2+} is one of the simplest of nature`s messengers used in the communication pathways between physiological stimulus and cellular response. The signaling mechanism generally involves Ca{sup 2+} binding to a protein and inducing a conformational change that transmits a signal to modify the activity of a specific target protein. Ca{sup 2+} is thus important in the regulation of a diverse array of intracellular responses, including neurotransmitter release, muscle contraction, the degradation of glycogen to glucose to generate energy, microtubule assembly, membrane phosphorylation, etc. It is the conformational language of the Ca{sup 2+} induced signal transduction that we have sought to understand because of its central importance to biochemical regulation and, hence, to healthy cellular function.

  16. Ca2+-activated nucleotidase 1, a novel target gene for the transcriptional repressor DREAM (downstream regulatory element antagonist modulator), is involved in protein folding and degradation.

    PubMed

    Calì, Tito; Fedrizzi, Laura; Ottolini, Denis; Gomez-Villafuertes, Rosa; Mellström, Britt; Naranjo, Jose R; Carafoli, Ernesto; Brini, Marisa

    2012-05-25

    DREAM is a Ca(2+)-dependent transcriptional repressor highly expressed in neuronal cells. A number of genes have already been identified as the target of its regulation. Targeted analysis performed on cerebella from transgenic mice expressing a dominant active DREAM mutant (daDREAM) showed a drastic reduction of the amount of transcript of Ca(2+)-activated nucleotidase 1 (CANT1), an endoplasmic reticulum (ER)-Golgi resident Ca(2+)-dependent nucleoside diphosphatase that has been suggested to have a role in glucosylation reactions related to the quality control of proteins in the ER and the Golgi apparatus. CANT1 down-regulation was also found in neuroblastoma SH-SY5Y cells stably overexpressing wild type (wt) DREAM or daDREAM, thus providing a simple cell model to investigate the protein maturation pathway. Pulse-chase experiments demonstrated that the down-regulation of CANT1 is associated with reduced protein secretion and increased degradation rates. Importantly, overexpression of wtDREAM or daDREAM augmented the expression of the EDEM1 gene, which encodes a key component of the ER-associated degradation pathway, suggesting an alternative pathway to enhanced protein degradation. Restoring CANT1 levels in neuroblastoma clones recovered the phenotype, thus confirming a key role of CANT1, and of the regulation of its gene by DREAM, in the control of protein synthesis and degradation.

  17. In silico analysis of regulatory networks underlines the role of miR-10b-5p and its target BDNF in huntington's disease.

    PubMed

    Müller, Sören

    2014-01-01

    Non-coding RNAs (ncRNAs) play various roles during central nervous system development. MicroRNAs (miRNAs) are a class of ncRNAs that exert their function together with argonaute proteins by post-transcriptional gene silencing of messenger RNAs (mRNAs). Several studies provide evidence for alterations in miRNA expression in patients with neurodegenerative diseases. Among these is huntington's disease (HD), a dominantly inherited fatal disorder characterized by deregulation of neuronal-specific mRNAs as well as miRNAs. Recently, next-generation sequencing (NGS) miRNA profiles from human HD and neurologically normal control brain tissues were reported. Five consistently upregulated miRNAs affect the expression of genes involved in neuronal differentiation, neurite outgrowth, cell death and survival. We re-analyzed the NGS data publicly available in array express and detected nineteen additional differentially expressed miRNAs. Subsequently, we connected these miRNAs to genes implicated in HD development and network analysis pointed to miRNA-mediated downregulation of twenty-two genes with roles in the pathogenesis as well as treatment of the disease. In silico prediction and reporter systems prove that levels of BDNF, a central node in the miRNA-mRNA regulatory network, can be post-transcriptionally controlled by upregulated miR-10b-5p and miR-30a-5p. Reduced BDNF expression is associated with neuronal dysfunction and death in HD. Moreover, the 3'UTR of CREB1 harbors a predicted binding site for these two miRNAs. CREB1 is similarly downregulated in HD and overexpression decreased susceptibility to 3-nitropropionic-induced toxicity in a cell model. In contradiction to these observations, it is presumed that miR-10b-5p upregulation in HD exerts a neuroprotective role in response to the mutation in the huntingtin gene. Therefore, the function of miR-10b-5p and especially its effect on BDNF expression in HD requires further academic research.

  18. GPC1 exosome and its regulatory miRNAs are specific markers for the detection and target therapy of colorectal cancer.

    PubMed

    Li, Jian; Chen, Yuxiang; Guo, Xiong; Zhou, Lin; Jia, Zeming; Peng, Zha; Tang, Yaping; Liu, Weidong; Zhu, Bin; Wang, Lei; Ren, Caiping

    2017-02-24

    Colorectal cancer (CRC) is the second leading cause of cancer-related deaths worldwide. However, a biomarker for a sensitive and simple diagnostic test and highly effective target therapy of CRC is still clinically unavailable. This study is to investigate the evidence and significance of plasma GPC1 positive exosomes as a biomarker of CRC. Results showed that GPC1(+) exosomes were successfully isolated from tissues and plasma. The percentage of GPC1(+) exosomes and the GPC1 protein expression in exosomes from tumour tissues and plasma of CRC patients before surgical treatment was significantly elevated compared to that in the peritumoural tissues and the plasma of healthy controls. miR-96-5p and miR-149 expression in tumour tissues and plasma of CRC patients as well as in the GPC1(+) exosomes from CRC patients were significantly decreased compared to that in the peritumoural tissues and the plasma of healthy controls. Two months after surgical treatment, levels of all tested markers significantly normalized. Overexpression of miR-96-5p and miR-149 significantly decreased GPC1 expression in HT-29 and HCT-116 cells, xenograft tumours, plasma in mice bearing HT-29 and HCT-116 tumours, and the secretion of GPC1(+) exosomes from the HT-29 and HCT-116 cells and xenograft tumours. Overexpression of miR-96-5p and miR-149 significantly decreased cell viability and increased cell apoptosis in HT-29 and HCT-116 cells, and inhibited the growth of xenograft HT-29 and HCT-116 tumours. In conclusion, the increased plasma GPC1(+) exosomes and reduced plasma miR-96-5p and miR-149 expression are specific markers for the diagnosis of CRC and targets for the therapy of CRC.

  19. Regulatory Snapshots: integrative mining of regulatory modules from expression time series and regulatory networks.

    PubMed

    Gonçalves, Joana P; Aires, Ricardo S; Francisco, Alexandre P; Madeira, Sara C

    2012-01-01

    Explaining regulatory mechanisms is crucial to understand complex cellular responses leading to system perturbations. Some strategies reverse engineer regulatory interactions from experimental data, while others identify functional regulatory units (modules) under the assumption that biological systems yield a modular organization. Most modular studies focus on network structure and static properties, ignoring that gene regulation is largely driven by stimulus-response behavior. Expression time series are key to gain insight into dynamics, but have been insufficiently explored by current methods, which often (1) apply generic algorithms unsuited for expression analysis over time, due to inability to maintain the chronology of events or incorporate time dependency; (2) ignore local patterns, abundant in most interesting cases of transcriptional activity; (3) neglect physical binding or lack automatic association of regulators, focusing mainly on expression patterns; or (4) limit the discovery to a predefined number of modules. We propose Regulatory Snapshots, an integrative mining approach to identify regulatory modules over time by combining transcriptional control with response, while overcoming the above challenges. Temporal biclustering is first used to reveal transcriptional modules composed of genes showing coherent expression profiles over time. Personalized ranking is then applied to prioritize prominent regulators targeting the modules at each time point using a network of documented regulatory associations and the expression data. Custom graphics are finally depicted to expose the regulatory activity in a module at consecutive time points (snapshots). Regulatory Snapshots successfully unraveled modules underlying yeast response to heat shock and human epithelial-to-mesenchymal transition, based on regulations documented in the YEASTRACT and JASPAR databases, respectively, and available expression data. Regulatory players involved in functionally enriched

  20. Regulatory Forum.

    PubMed

    Peden, W Michael

    2016-12-01

    Revision of the International Council for Harmonization (ICH) S1 guidance for rat carcinogenicity studies to be more selective of compounds requiring a 2-year rat carcinogenicity study has been proposed following extensive evaluation of rat carcinogenicity and chronic toxicity studies by industry and drug regulatory authorities. To inform the ICH S1 expert working group in their potential revision of ICH S1, a prospective evaluation study was initiated in 2013, in which sponsors would assess the pharmacologic and toxicologic findings present in the chronic toxicity studies and predict a positive or negative carcinogenicity outcome using a weight of evidence argument (a carcinogenicity assessment document [CAD]). The Scientific and Regulatory Policy Committee was asked by the Society of Toxicology Pathology (STP) executive committee to track these changes with ICH S1 and inform the STP membership of status changes. This commentary is intended to provide a brief summary of recent changes to the CAD guidance and highlight the importance of STP membership participation in the process of CAD submissions.

  1. Label-Free Raman Microspectral Analysis for Comparison of Cellular Uptake and Distribution between Non-Targeted and EGFR-Targeted Biodegradable Polymeric Nanoparticles

    PubMed Central

    Chernenko, Tatyana; Buyukozturk, Fulden; Miljkovic, Milos; Carrier, Rebecca; Diem, Max; Amiji, Mansoor

    2013-01-01

    Active targeted delivery of nanoparticle-encapsulated agents to tumor cells in vivo is expected to enhance therapeutic effect with significantly less non-specific toxicity. Active targeting is based on surface modification of nanoparticles with ligands that bind with extracellular targets and enhance payload delivery in the cells. In this study, we have used label-free Raman micro-spectral analysis and kinetic modeling to study cellular interactions and intracellular delivery of C6-ceramide using a non-targeted and an epidermal growth factor receptor (EGFR) targeted biodegradable polymeric nano-delivery systems, in EGFR-expressing human ovarian adenocarcinoma (SKOV3) cells. The results show that EGFR peptide-modified nanoparticles were rapidly internalized in SKOV3 cells leading to significant intracellular accumulation as compared to non-specific uptake by the non-targeted nanoparticles. Raman micro-spectral analysis enables visualization and quantification of the carrier system, drug-load, and responses of the biological systems interrogated, without exogenous staining and labeling procedures. PMID:24298430

  2. Anti-regulatory T cells.

    PubMed

    Andersen, Mads Hald

    2017-04-01

    Our initial understanding of immune-regulatory cells was based on the discovery of suppressor cells that assure peripheral T-cell tolerance and promote immune homeostasis. Research has particularly focused on the importance of regulatory T cells (Tregs) for immune modulation, e.g. directing host responses to tumours or inhibiting autoimmunity development. However, recent studies report the discovery of self-reactive pro-inflammatory T cells-termed anti-regulatory T cells (anti-Tregs)-that target immune-suppressive cells. Thus, regulatory cells can now be defined as both cells that suppress immune reactions as well as effector cells that counteract the effects of suppressor cells and support immune reactions. Self-reactive anti-Tregs have been described that specifically recognize human leukocyte antigen-restricted epitopes derived from proteins that are normally expressed by regulatory immune cells, including indoleamine 2,3-dioxygenase (IDO), tryptophan 2,6-dioxygenase (TDO), programmed death-ligand 1 (PD-L1), and forkhead box P3 (Foxp3). These proteins are highly expressed in professional antigen-presenting cells under various physiological conditions, such as inflammation and stress. Therefore, self-reactive T cells that recognize such targets may be activated due to the strong activation signal given by their cognate targets. The current review describes the existing knowledge regarding these self-reactive anti-Tregs, providing examples of antigen-specific anti-Tregs and discussing their possible roles in immune homeostasis and their potential future clinical applications.

  3. H1N1 influenza virus induces narcolepsy-like sleep disruption and targets sleep–wake regulatory neurons in mice

    PubMed Central

    Tesoriero, Chiara; Codita, Alina; Zhang, Ming-Dong; Cherninsky, Andrij; Karlsson, Håkan; Grassi-Zucconi, Gigliola; Bertini, Giuseppe; Harkany, Tibor; Ljungberg, Karl; Liljeström, Peter; Hökfelt, Tomas G. M.; Bentivoglio, Marina; Kristensson, Krister

    2016-01-01

    An increased incidence in the sleep-disorder narcolepsy has been associated with the 2009–2010 pandemic of H1N1 influenza virus in China and with mass vaccination campaigns against influenza during the pandemic in Finland and Sweden. Pathogenetic mechanisms of narcolepsy have so far mainly focused on autoimmunity. We here tested an alternative working hypothesis involving a direct role of influenza virus infection in the pathogenesis of narcolepsy in susceptible subjects. We show that infection with H1N1 influenza virus in mice that lack B and T cells (Recombinant activating gene 1-deficient mice) can lead to narcoleptic-like sleep–wake fragmentation and sleep structure alterations. Interestingly, the infection targeted brainstem and hypothalamic neurons, including orexin/hypocretin-producing neurons that regulate sleep–wake stability and are affected in narcolepsy. Because changes occurred in the absence of adaptive autoimmune responses, the findings show that brain infections with H1N1 virus have the potential to cause per se narcoleptic-like sleep disruption. PMID:26668381

  4. H1N1 influenza virus induces narcolepsy-like sleep disruption and targets sleep-wake regulatory neurons in mice.

    PubMed

    Tesoriero, Chiara; Codita, Alina; Zhang, Ming-Dong; Cherninsky, Andrij; Karlsson, Håkan; Grassi-Zucconi, Gigliola; Bertini, Giuseppe; Harkany, Tibor; Ljungberg, Karl; Liljeström, Peter; Hökfelt, Tomas G M; Bentivoglio, Marina; Kristensson, Krister

    2016-01-19

    An increased incidence in the sleep-disorder narcolepsy has been associated with the 2009-2010 pandemic of H1N1 influenza virus in China and with mass vaccination campaigns against influenza during the pandemic in Finland and Sweden. Pathogenetic mechanisms of narcolepsy have so far mainly focused on autoimmunity. We here tested an alternative working hypothesis involving a direct role of influenza virus infection in the pathogenesis of narcolepsy in susceptible subjects. We show that infection with H1N1 influenza virus in mice that lack B and T cells (Recombinant activating gene 1-deficient mice) can lead to narcoleptic-like sleep-wake fragmentation and sleep structure alterations. Interestingly, the infection targeted brainstem and hypothalamic neurons, including orexin/hypocretin-producing neurons that regulate sleep-wake stability and are affected in narcolepsy. Because changes occurred in the absence of adaptive autoimmune responses, the findings show that brain infections with H1N1 virus have the potential to cause per se narcoleptic-like sleep disruption.

  5. Multi-modal Mn-Zn ferrite nanocrystals for magnetically-induced cancer targeted hyperthermia: a comparison of passive and active targeting effects.

    PubMed

    Xie, Jun; Yan, Caiyun; Yan, Yu; Chen, Ling; Song, Lina; Zang, Fengchao; An, Yanli; Teng, Gaojun; Gu, Ning; Zhang, Yu

    2016-10-14

    The high performance and increased tumor-targeting accumulation of magnetic nanocrystals (MNCs) are the most important considerations in cancer targeted magnetic hyperthermia (TMH). To achieve these goals, our study was firstly done using well-established fluorescence/magnetic Mn-Zn ferrite MNCs (core size: 14 nm) as multi-modal imaging contrast agents and highly-efficient "heat generators", which were coated with a biocompatible PEG-phospholipid (DSPE-PEG2000) and further modified by a cyclic tripeptide of arginine-glycine-aspartic acid (RGD). By using a mouse model bearing breast carcinoma (4T1), we then systematically compared PEGylated MNCs (MNCs@PEG)- and RGD-PEGylated MNCs (MNCs@RGD)-mediated tumor targeting abilities by intravenous administration. The MNCs@PEG-based passive targeting could successfully accumulate at the tumor due to the enhanced permeability and retention (EPR) effects, but the non-targeted localization might make the MNCs@PEG "leaking" from larger pores of tumor fenestrated vascular networks. Our designed MNCs@RGD, simultaneously functionalized with PEG and RGD ligands, might promote a synergistic effect including efficient tumor vasculature active targeting and EPR-mediated passive targeting, improving total MNC concentration and retention time in tumor tissues. By combining fluorescence/magnetic resonance (MR)/thermal multi-modal imaging-guided diagnostics and continuous TMH treatment under an alternating current magnetic field (ACMF, 2.58 kA m(-1), 390 kHz), the tumor surface could be heated to approximately 43-44 °C based on the MNC-mediated repeated injections. Sufficient temperature elevation induced the apoptosis of tumor cells, and inhibited the tumor angiogenesis. Compared with MNCs@PEG, the active MNCs@RGD-based tumor targeting MR image was significantly more efficient due to both the higher and long-lasting tumor accumulation, but its antitumor efficacy was not obviously improved in the TMH treatments. To achieve a singularly

  6. In vitro comparison of a novel facilitated ultrasound targeting technology vs standard technique for percutaneous renal biopsy.

    PubMed

    Menhadji, Ashleigh; Nguyen, Vien; Cho, Jane; Chu, Ringo; Osann, Kathyrn; Bucur, Philip; Patel, Puja; Lusch, Achim; McDougall, Elspeth; Landman, Jaime

    2013-09-01

    To improve the understanding of the epidemiology of renal cortical neoplasms through pretreatment biopsy, we evaluated a facilitated ultrasound targeting (FUT) technology. The technology allows a needle to be passed through the transducer probe and guided along a virtual dotted line on the monitor. We compared the FUT with standard percutaneous biopsy (PB) technique. Forty-eight participants with various levels of training were recruited. Participants performed ultrasound-guided biopsies on phantom models using FUT and the standard biopsy technique in a randomized sequence. The phantom models consisted of pimento olives embedded in an opaque mold of Metamucil and Knox gelatin. Patients were given up to 10 attempts to achieve 3 complete specimens from the olives. Patients rated each biopsy technique. Results were stratified by level of experience. The mean time to obtain 3 complete biopsy specimens was significantly faster for FUT compared with the standard technique (140 seconds vs 246 seconds, P = .0001). The mean number of attempts needed to obtain 3 specimens was significantly less with FUT compared with the standard technique (4.3 vs 5.6 attempts, P = .0007). Patients reported that FUT was significantly easier to use compared with the standard technique (P = .0005). No significant order effect was observed. In this in vitro comparison, FUT increased the efficiency and efficacy of PB for users of all experience levels. FUT may allow urologists with limited PB experience to perform the procedure reliably and easily. Clinical evaluation of this technology is actively in progress. Copyright © 2013 Elsevier Inc. All rights reserved.

  7. Comparison of the packaging and labeling of Target ClearRx with conventional prescription drug packaging and labeling.

    PubMed

    Soller, R William; Lightwood, James M

    2007-01-01

    To compare consumer preferences for Target pharmacy's clearrx packaging and labeling with conventional prescription drug packaging and labeling. Prospective, hands-on comparison of packaging and labeling formats. Two suburban shopping malls in northern California in February and March 2006. Volunteer participants from local communities. Self-administered questionnaire. Participants were asked to compare ClearRx bottles with conventional cylindrical prescription bottles (both labeled as containing fluoxetine). They also were asked their opinions on three ClearRx bottles (labeled as containing albuterol, amoxicillin, or atenolol) with different color rings corresponding to three fictitious family members. Consumer preference for ClearRx or conventional packaging and labeling, consumer ability to differentiate between two types of packaging and labeling, consumer perception of safety design, and reasons for consumer preferences. The majority of consumers (85%) preferred ClearRx packaging and labeling over the conventional format (10%; 5% uncertain; P < 0.0005). Consumers described distinct differences between the packaging and labeling formats, citing ClearRx as better designed for safety, easier to read, and having better organized warnings with larger type size. The ClearRx patient information card was rated by the majority of consumers as easy or very easy to access (91%; P < 0.0005), important or very important to retain as a reference during use (94%; P < 0.0005), and helpful for improving medication safety (91% agree or strongly agree; P < 0.0005). Features designed to avoid medication mix-ups (i.e., color rings, large type face for medication name) allowed consumers to easily distinguish among bottles of ClearRx. These findings were consistent across various demographic categories. ClearRx represents an important advance in meeting consumer needs for patient-centered designs in prescription packaging and labeling.

  8. Identification of orthologous target pairs with shared active compounds and comparison of organism-specific activity patterns.

    PubMed

    Dimova, Dilyana; Stumpfe, Dagmar; Bajorath, Jürgen

    2015-11-01

    A systematic search for active small molecules shared by orthologous targets was carried out, leading to the identification of 803 compound-based orthologous target pairs covering a total of 938 orthologues, 358 unique targets and 98 organisms. Many orthologous target pairs were found to have substantial compound coverage, enabling the introduction of an orthologous target pairs classification including 'organism cliffs' and 'potency-retaining' pairs. A total of 158 orthologous target pairs involving human orthologues were identified, which were typically associated with drug discovery-relevant targets, organism combinations and compound data. Orthologous target pairs with human orthologues included 83 potency-retaining orthologous target pairs covering a variety of targets and organisms. On the basis of these orthologous target pairs, the compound search was further extended and 1149 potent compounds were identified that only had reported activities for non-human orthologues of 48 therapeutic targets, but not their human counterparts, hence providing a large pool of candidate compounds for further evaluation. The complete set of orthologous target pairs identified in our analysis, the orthologous target pairs classification including associated data and all candidate compounds are made freely available.

  9. Regulatory Physiology

    NASA Technical Reports Server (NTRS)

    Lane, Helen W.; Whitson, Peggy A.; Putcha, Lakshmi; Baker, Ellen; Smith, Scott M.; Stewart, Karen; Gretebeck, Randall; Nimmagudda, R. R.; Schoeller, Dale A.; Davis-Street, Janis

    1999-01-01

    As noted elsewhere in this report, a central goal of the Extended Duration Orbiter Medical Project (EDOMP) was to ensure that cardiovascular and muscle function were adequate to perform an emergency egress after 16 days of spaceflight. The goals of the Regulatory Physiology component of the EDOMP were to identify and subsequently ameliorate those biochemical and nutritional factors that deplete physiological reserves or increase risk for disease, and to facilitate the development of effective muscle, exercise, and cardiovascular countermeasures. The component investigations designed to meet these goals focused on biochemical and physiological aspects of nutrition and metabolism, the risk of renal (kidney) stone formation, gastrointestinal function, and sleep in space. Investigations involved both ground-based protocols to validate proposed methods and flight studies to test those methods. Two hardware tests were also completed.

  10. Regulatory Anatomy

    PubMed Central

    2015-01-01

    This article proposes the term “safety logics” to understand attempts within the European Union (EU) to harmonize member state legislation to ensure a safe and stable supply of human biological material for transplants and transfusions. With safety logics, I refer to assemblages of discourses, legal documents, technological devices, organizational structures, and work practices aimed at minimizing risk. I use this term to reorient the analytical attention with respect to safety regulation. Instead of evaluating whether safety is achieved, the point is to explore the types of “safety” produced through these logics as well as to consider the sometimes unintended consequences of such safety work. In fact, the EU rules have been giving rise to complaints from practitioners finding the directives problematic and inadequate. In this article, I explore the problems practitioners face and why they arise. In short, I expose the regulatory anatomy of the policy landscape. PMID:26139952

  11. Glucose adsorption to chitosan membranes increases proliferation of human chondrocyte via mammalian target of rapamycin complex 1 and sterol regulatory element-binding protein-1 signaling.

    PubMed

    Chang, Shun-Fu; Huang, Kuo-Chin; Cheng, Chin-Chang; Su, Yu-Ping; Lee, Ko-Chao; Chen, Cheng-Nan; Chang, Hsin-I

    2017-10-01

    Osteoarthritis (OA) is currently still an irreversible degenerative disease of the articular cartilage. Recent, dextrose (d-glucose) intraarticular injection prolotherapy for OA patients has been reported to benefit the chondrogenic stimulation of damaged cartilage. However, the detailed mechanism of glucose's effect on cartilage repair remains unclear. Chitosan, a naturally derived polysaccharide, has recently been investigated as a surgical or dental dressing to control breeding. Therefore, in this study, glucose was adsorbed to chitosan membranes (CTS-Glc), and the study aimed to investigate whether CTS-Glc complex membranes could regulate the proliferation of human OA chondrocytes and to explore the underlying mechanism. Human OA and SW1353 chondrocytes were used in this study. The experiments involving the transfection of cells used SW1353 chondrocytes. A specific inhibitor and siRNAs were used to investigate the mechanism underlying the CTS-Glc-regulated proliferation of human chondrocytes. We found that CTS-Glc significantly increased the proliferation of both human OA and SW1353 chondrocytes comparable to glucose- or chitosan-only stimulation. The role of mammalian target of rapamycin complex 1 (mTORC1) signaling, including mTOR, raptor, and S6k proteins, has been demonstrated in the regulation of CTS-Glc-increased human chondrocyte proliferation. mTORC1 signaling increased the expression levels of maturated SREBP-1 and FASN and then induced the expressions of cell cycle regulators, that is, cyclin D, cyclin-dependent kinase-4 and -6 in human chondrocytes. This study elucidates the detailed mechanism behind the effect of CTS-Glc complex membranes in promoting chondrocyte proliferation and proposes a possible clinical application of the CTS-Glc complex in the dextrose intraarticular injection of OA prolotherapy in the future to attenuate the pain and discomfort of OA patients. © 2017 Wiley Periodicals, Inc.

  12. MiR-1 Overexpression Enhances Ca2+ release and Promotes Cardiac Arrhythmogenesis by Targeting PP2A Regulatory Subunit B56α and Causing CaMKII-Dependent Hyperphosphorylation of RyR2

    PubMed Central

    Terentyev, Dmitry; Belevych, Andriy E.; Terentyeva, Radmila; Martin, Mickey M.; Malana, Geraldine E.; Kuhn, Donald E.; Abdellatif, Maha; Feldman, David S; Elton, Terry S.; Gyorke, Sandor

    2015-01-01

    MicroRNAs are small endogenous noncoding RNAs that regulate protein expression by hybridization to imprecise complementary sequences of target mRNAs. Changes in abundance of muscle-specific microRNA, miR-1, have been implicated in cardiac disease, including arrhythmia and heart failure. However, the specific molecular targets and cellular mechanisms involved in the action of miR-1 in the heart are only beginning to emerge. In this study we investigated the effects of increased expression of miR-1 on excitation-contraction coupling and Ca2+ cycling in rat ventricular myocytes using methods of electrophysiology, Ca2+ imaging and quantitative immunoblotting. Adenoviral-mediated overexpression of miR-1 in myocytes resulted in a marked increase in the amplitude of the inward Ca2+ current, flattening of Ca2+ transients voltage dependency and enhanced frequency of spontaneous Ca2+ sparks while reducing the sarcoplasmic reticulum Ca2+ content as compared with control. In the presence of isoproterenol, rhythmically paced, miR-1-overexpressing myocytes exhibited spontaneous arrhythmogenic oscillations of intracellular Ca2+, events that occurred rarely in control myocytes under the same conditions. The effects of miR-1 were completely reversed by the CaMKII inhibitor KN93. Although phosphorylation of phospholamban was not altered, miR-1 overexpression increased phosphorylation of the ryanodine receptor (RyR2) at S2814 (CaMKII) but not at S2808 (PKA). Overexpression of miR-1 was accompanied by a selective decrease in expression of the protein phosphatase PP2A regulatory subunit B56α involved in PP2A targeting to specialized subcellular domains. We conclude that miR-1 enhances cardiac excitation-contraction coupling by selectively increasing phosphorylation of the L-type and RyR2 channels via disrupting localization of PP2A activity to these channels. PMID:19131648

  13. Comparison of nucleic acid targets prepared from total RNA or poly(A) RNA for DNA oligonucleotide microarray hybridization.

    PubMed

    Petersen, Kjell; Oyan, Anne Margrete; Rostad, Kari; Olsen, Sue; Bø, Trond Hellem; Salvesen, Helga B; Gjertsen, Bjørn Tore; Bruserud, Oystein; Halvorsen, Ole Johan; Akslen, Lars Andreas; Steen, Vidar M; Jonassen, Inge; Kalland, Karl-Henning

    2007-07-01

    The aim of this work was to compare DNA microarray results using either total RNA or affinity-purified poly(A) RNA from the same biological sample for target preparation. The high-density oligonucleotide microarrays of both Agilent Technologies (based on two-color detection) and Applied Biosystems (based on single-color detection) were evaluated. Real-time quantitative PCR was used to quantify messenger RNA (mRNA) and ribosomal RNA (rRNA) at different stages of target preparations. Poly(A) RNA versus total RNA target hybridizations exhibited slightly lower correlation coefficients than did self versus self hybridizations (i.e., poly(A) RNA targets vs. poly(A) RNA targets or total RNA targets vs. total RNA targets). Only a small fraction of all transcripts appeared to be significantly over- or underrepresented when total RNA targets or poly(A) RNA targets from the same biological sample were compared. Therefore, the conclusion is that poly(A) affinity purification from total RNA can be omitted during target preparation for routine mRNA expression analysis using high-density oligonucleotide microarrays. Among consistently overrepresented transcripts in total RNA targets were histone mRNAs known to lack poly(A) tails. Therefore, structurally exceptional RNA species can be identified by comparing targets derived from either poly(A) RNA or total RNA using microarray hybridization.

  14. Radio-frequency electromagnetic field (RF-EMF) exposure levels in different European outdoor urban environments in comparison with regulatory limits.

    PubMed

    Urbinello, Damiano; Joseph, Wout; Huss, Anke; Verloock, Leen; Beekhuizen, Johan; Vermeulen, Roel; Martens, Luc; Röösli, Martin

    2014-07-01

    Concerns of the general public about potential adverse health effects caused by radio-frequency electromagnetic fields (RF-EMFs) led authorities to introduce precautionary exposure limits, which vary considerably between regions. It may be speculated that precautionary limits affect the base station network in a manner that mean population exposure unintentionally increases. The objectives of this multicentre study were to compare mean exposure levels in outdoor areas across four different European cities and to compare with regulatory RF-EMF exposure levels in the corresponding areas. We performed measurements in the cities of Amsterdam (the Netherlands, regulatory limits for mobile phone base station frequency bands: 41-61 V/m), Basel (Switzerland, 4-6 V/m), Ghent (Belgium, 3-4.5 V/m) and Brussels (Belgium, 2.9-4.3 V/m) using a portable measurement device. Measurements were conducted in three different types of outdoor areas (central and non-central residential areas and downtown), between 2011 and 2012 at 12 different days. On each day, measurements were taken every 4s for approximately 15 to 30 min per area. Measurements per urban environment were repeated 12 times during 1 year. Arithmetic mean values for mobile phone base station exposure ranged between 0.22 V/m (Basel) and 0.41 V/m (Amsterdam) in all outdoor areas combined. The 95th percentile for total RF-EMF exposure varied between 0.46 V/m (Basel) and 0.82 V/m (Amsterdam) and the 99th percentile between 0.81 V/m (Basel) and 1.20 V/m (Brussels). All exposure levels were far below international reference levels proposed by ICNIRP (International Commission on Non-Ionizing Radiation Protection). Our study did not find indications that lowering the regulatory limit results in higher mobile phone base station exposure levels. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. [Comparison of anticoagulant effects of regulatory proline-containing oligopeptides. Specificity of glyprolines, semax, and selank and potential of their practical application].

    PubMed

    Liapina, L A; Pastorova, V E; Obergan, T Iu; Samonina, G E; Ashmarin, I P; Miasoedov, N F

    2006-01-01

    Experimental and theoretical demonstration of different effect of certain regulatory peptides (RPs) on blood coagulation is available. The problem of the role of RPs in hemostatic processes becomes particularly significant since, first, the peptides are widespread in nature both in animal and plant tissues, second, there is a relationship between the peptide structure and function and, third, both natural and synthetic peptides are used in practical medicine to correct functions of some factors of the hemostatic system. Many peptide inhibitors of the primary and plasma hemostasis potentiating anticoagulant effects in the body have been described.

  16. KEY COMPARISON: CCQM-K61: Quantitation of a linearised plasmid DNA, based on a matched standard in a matrix of non-target DNA

    NASA Astrophysics Data System (ADS)

    Ellison, Stephen L. R.; Holden, Marcia J.; Woolford, Alison; Haynes, Ross J.; Salit, Marc L.; Burns, Malcolm; Parkes, Helen; Cherdchu, Chainarong; Corbisier, Philippe; Emslie, Kerry R.; Gao, Yunhua; Gioria, Sabrina; Griffiths, Kate R.; Kawaharasaki, Mamoru; Konopelko, Leonid A.; Kustikov, Yury A.; Park, Sang-Ryoul; Phunbua, Nittaya; Vonsky, Maxim S.; Wang, Jing; Yang, Inchul

    2009-01-01

    Key comparison CCQM-K61 was performed to demonstrate and document the capability of interested national metrology institutes in the determination of the quantity of specific DNA target in an aqueous solution. The study provides support for the following measurement claim: "Quantitation of a linearised plasmid DNA, based on a matched standard in a matrix of non-target DNA". The comparison was an activity of the Bioanalysis Working Group (BAWG) of the Comité Consultatif pour la Quantité de Matière and was coordinated by NIST (Gaithersburg, USA) and LGC (Teddington, UK). The following laboratories (in alphabetical order) participated in this key comparison. DMSC (Thailand); IRMM (European Union); KRISS (Republic of Korea); LGC (UK); NIM (China); NIST (USA); NMIA (Australia); NMIJ (Japan); VNIIM (Russian Federation) Good agreement was observed between the reported results of all nine of the participants. Uncertainty estimates did not account fully for the dispersion of results even after allowance for possible inhomogeneity in calibration materials. Preliminary studies suggest that the effects of fluorescence threshold setting might contribute to the excess dispersion, and further study of this topic is suggested Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

  17. Text-mining assisted regulatory annotation

    PubMed Central

    Aerts, Stein; Haeussler, Maximilian; van Vooren, Steven; Griffith, Obi L; Hulpiau, Paco; Jones, Steven JM; Montgomery, Stephen B; Bergman, Casey M

    2008-01-01

    Background Decoding transcriptional regulatory networks and the genomic cis-regulatory logic implemented in their control nodes is a fundamental challenge in genome biology. High-throughput computational and experimental analyses of regulatory networks and sequences rely heavily on positive control data from prior small-scale experiments, but the vast majority of previously discovered regulatory data remains locked in the biomedical literature. Results We develop text-mining strategies to identify relevant publications and extract sequence information to assist the regulatory annotation process. Using a vector space model to identify Medline abstracts from papers likely to have high cis-regulatory content, we demonstrate that document relevance ranking can assist the curation of transcriptional regulatory networks and estimate that, minimally, 30,000 papers harbor unannotated cis-regulatory data. In addition, we show that DNA sequences can be extracted from primary text with high cis-regulatory content and mapped to genome sequences as a means of identifying the location, organism and target gene information that is critical to the cis-regulatory annotation process. Conclusion Our results demonstrate that text-mining technologies can be successfully integrated with genome annotation systems, thereby increasing the availability of annotated cis-regulatory data needed to catalyze advances in the field of gene regulation. PMID:18271954

  18. In vivo erythrocyte micronucleus assay III. Validation and regulatory acceptance of automated scoring and the use of rat peripheral blood reticulocytes, with discussion of non-hematopoietic target cells and a single dose-level limit test.

    PubMed

    Hayashi, Makoto; MacGregor, James T; Gatehouse, David G; Blakey, David H; Dertinger, Stephen D; Abramsson-Zetterberg, Lilianne; Krishna, Gopala; Morita, Takeshi; Russo, Antonella; Asano, Norihide; Suzuki, Hiroshi; Ohyama, Wakako; Gibson, Dave

    2007-02-03

    The in vivo micronucleus assay working group of the International Workshop on Genotoxicity Testing (IWGT) discussed new aspects in the in vivo micronucleus (MN) test, including the regulatory acceptance of data derived from automated scoring, especially with regard to the use of flow cytometry, the suitability of rat peripheral blood reticulocytes to serve as the principal cell population for analysis, the establishment of in vivo MN assays in tissues other than bone marrow and blood (for example liver, skin, colon, germ cells), and the biological relevance of the single-dose-level test. Our group members agreed that flow cytometric systems to detect induction of micronucleated immature erythrocytes have advantages based on the presented data, e.g., they give good reproducibility compared to manual scoring, are rapid, and require only small quantities of peripheral blood. Flow cytometric analysis of peripheral blood reticulocytes has the potential to allow monitoring of chromosome damage in rodents and also other species as part of routine toxicology studies. It appears that it will be applicable to humans as well, although in this case the possible confounding effects of splenic activity will need to be considered closely. Also, the consensus of the group was that any system that meets the validation criteria recommended by the IWGT (2000) should be acceptable. A number of different flow cytometric-based micronucleus assays have been developed, but at the present time the validation data are most extensive for the flow cytometric method using anti-CD71 fluorescent staining especially in terms of inter-laboratory collaborative data. Whichever method is chosen, it is desirable that each laboratory should determine the minimum sample size required to ensure that scoring error is maintained below the level of animal-to-animal variation. In the second IWGT, the potential to use rat peripheral blood reticulocytes as target cells for the micronucleus assay was discussed

  19. A Comparison of Recruitment Methods for an mHealth Intervention Targeting Mothers: Lessons from the Growing Healthy Program

    PubMed Central

    Litterbach, Eloise-Kate V; Denney-Wilson, Elizabeth A; Russell, Catherine G; Taki, Sarah; Ong, Kok-Leong; Elliott, Rosalind M; Lymer, Sharyn J; Campbell, Karen J

    2016-01-01

    Background Mobile health (mHealth) programs hold great promise for increasing the reach of public health interventions. However, mHealth is a relatively new field of research, presenting unique challenges for researchers. A key challenge is understanding the relative effectiveness and cost of various methods of recruitment to mHealth programs. Objective The objectives of this study were to (1) compare the effectiveness of various methods of recruitment to an mHealth intervention targeting healthy infant feeding practices, and (2) explore factors influencing practitioner referral to the intervention. Methods The Growing healthy study used a quasi-experimental design with an mHealth intervention group and a concurrent nonrandomized comparison group. Eligibility criteria included: expectant parents (>30 weeks of gestation) or parents with an infant <3 months old, ability to read and understand English, own a mobile phone, ≥18 years old, and living in Australia. Recruitment to the mHealth program consisted of: (1) practitioner-led recruitment through Maternal and Child Health nurses, midwives, and nurses in general practice; (2) face-to-face recruitment by researchers; and (3) online recruitment. Participants’ baseline surveys provided information regarding how participants heard about the study, and their sociodemographic details. Costs per participant recruited were calculated by taking into account direct advertising costs and researcher time/travel costs. Practitioner feedback relating to the recruitment process was obtained through a follow-up survey and qualitative interviews. Results A total of 300 participants were recruited to the mHealth intervention. The cost per participant recruited was lowest for online recruitment (AUD $14) and highest for practice nurse recruitment (AUD $586). Just over half of the intervention group (50.3%, 151/300) were recruited online over a 22-week period compared to practitioner recruitment (29.3%, 88/300 over 46 weeks) and

  20. A Comparison of Recruitment Methods for an mHealth Intervention Targeting Mothers: Lessons from the Growing Healthy Program.

    PubMed

    Laws, Rachel A; Litterbach, Eloise-Kate V; Denney-Wilson, Elizabeth A; Russell, Catherine G; Taki, Sarah; Ong, Kok-Leong; Elliott, Rosalind M; Lymer, Sharyn J; Campbell, Karen J

    2016-09-15

    Mobile health (mHealth) programs hold great promise for increasing the reach of public health interventions. However, mHealth is a relatively new field of research, presenting unique challenges for researchers. A key challenge is understanding the relative effectiveness and cost of various methods of recruitment to mHealth programs. The objectives of this study were to (1) compare the effectiveness of various methods of recruitment to an mHealth intervention targeting healthy infant feeding practices, and (2) explore factors influencing practitioner referral to the intervention. The Growing healthy study used a quasi-experimental design with an mHealth intervention group and a concurrent nonrandomized comparison group. Eligibility criteria included: expectant parents (>30 weeks of gestation) or parents with an infant <3 months old, ability to read and understand English, own a mobile phone, ≥18 years old, and living in Australia. Recruitment to the mHealth program consisted of: (1) practitioner-led recruitment through Maternal and Child Health nurses, midwives, and nurses in general practice; (2) face-to-face recruitment by researchers; and (3) online recruitment. Participants' baseline surveys provided information regarding how participants heard about the study, and their sociodemographic details. Costs per participant recruited were calculated by taking into account direct advertising costs and researcher time/travel costs. Practitioner feedback relating to the recruitment process was obtained through a follow-up survey and qualitative interviews. A total of 300 participants were recruited to the mHealth intervention. The cost per participant recruited was lowest for online recruitment (AUD $14) and highest for practice nurse recruitment (AUD $586). Just over half of the intervention group (50.3%, 151/300) were recruited online over a 22-week period compared to practitioner recruitment (29.3%, 88/300 over 46 weeks) and face-to-face recruitment by researchers

  1. A nuclear gene, erd1, encoding a chloroplast-targeted Clp protease regulatory subunit homolog is not only induced by water stress but also developmentally up-regulated during senescence in Arabidopsis thaliana.

    PubMed

    Nakashima, K; Kiyosue, T; Yamaguchi-Shinozaki, K; Shinozaki, K

    1997-10-01

    A cDNA, ERD1, isolated from one-hour-dehydrated plants of Arabidopsis thaliana L. encodes a putative protein that is similar to the regulatory ATPase subunit (ClpA) of the Clp protease and contains a putative chloroplast-targeting transit-peptide at the N-terminus. A chimeric gene with the putative plastid-targeting sequence of the erd1 gene fused to the synthetic green-fluorescent protein (sGFP) gene was constructed and introduced into Arabidopsis protoplasts. The N-terminal region of the ERD1 protein directed the sGFP protein into the plastids of the protoplasts, and functioned as a transit peptide. Northern blot analysis indicated that expression of the erd1 gene was induced not only by water stress, such as dehydration and high salinity, but also by natural senescence and dark-induced etiolation. The erd1 gene was not strongly induced by exogenous abscisic acid. A chimeric gene with the 0.9 kb promoter region of the erd1 gene fused to the beta-glucuronidase (GUS) reporter gene was constructed, and tobacco plants transformed with the construct. The GUS reporter gene driven by the erd1 promoter was induced by dehydration and high salt stress at significant levels in the transgenic plants. The GUS gene was strongly expressed in older leaves without dehydration, and was induced by dark-induced etiolation. Furthermore, GUS activity was reduced by cytokinin treatment during dark-induced etiolation. These results indicate that expression of the erd1 gene is developmentally up-regulated by senescence as well as by water stress.

  2. Characteristics of Movement-Induced Dose Reduction in Target Volume: A Comparison Between Photon and Proton Beam Treatment

    SciTech Connect

    Yoon, Myonggeun; Shin, Dongho; Kwak, Jungwon; Park, Soah; Lim, Young Kyung; Kim, Dongwook; Park, Sung Yong Lee, Se Byeong; Shin, Kyung Hwan; Kim, Tae Hyun; Cho, Kwan Ho

    2009-10-01

    We compared the main characteristics of movement-induced dose reduction during photon and proton beam treatment, based on an analysis of dose-volume histograms. To simulate target movement, a target contour was delineated in a scanned phantom and displaced by 3 to 20 mm. Although the dose reductions to the target in the 2 treatment systems were similar for transverse (perpendicular to beam direction) target motion, they were completely different for longitudinal (parallel to beam direction) target motion. While both modalities showed a relationship between the degree of target shift and the reduction in dose coverage, dose reduction showed a strong directional dependence in proton beam treatment. Clinical simulation of target movement for a prostate cancer patient showed that, although coverage and conformity indices for a 6-mm lateral movement of the prostate were reduced by 9% and 16%, respectively, for proton beam treatment, they were reduced by only 1% and 7%, respectively, for photon treatment. This difference was greater for a 15-mm target movement in the lateral direction, which lowered the coverage and conformity indices by 34% and 54%, respectively, for proton beam treatment, but changed little during photon treatment. In addition, we found that the equivalent uniform dose (EUD) and homogeneity index show similar characteristics during target movement. These results suggest that movement-induced dose reduction differs significantly between photon and proton beam treatment. Attention should be paid to the target margin in proton beam treatment due to the distinct characteristics of heavy ion beams.

  3. SRD: a Staphylococcus regulatory RNA database

    PubMed Central

    Sassi, Mohamed; Augagneur, Yoann; Mauro, Tony; Ivain, Lorraine; Chabelskaya, Svetlana; Hallier, Marc; Sallou, Olivier; Felden, Brice

    2015-01-01

    An overflow of regulatory RNAs (sRNAs) was identified in a wide range of bacteria. We designed and implemented a new resource for the hundreds of sRNAs identified in Staphylococci, with primary focus on the human pathogen Staphylococcus aureus. The “Staphylococcal Regulatory RNA Database” (SRD, http://srd.genouest.org/) compiled all published data in a single interface including genetic locations, sequences and other features. SRD proposes novel and simplified identifiers for Staphylococcal regulatory RNAs (srn) based on the sRNA's genetic location in S. aureus strain N315 which served as a reference. From a set of 894 sequences and after an in-depth cleaning, SRD provides a list of 575 srn exempt of redundant sequences. For each sRNA, their experimental support(s) is provided, allowing the user to individually assess their validity and significance. RNA-seq analysis performed on strains N315, NCTC8325, and Newman allowed us to provide further details, upgrade the initial annotation, and identified 159 RNA-seq independent transcribed sRNAs. The lists of 575 and 159 sRNAs sequences were used to predict the number and location of srns in 18 S. aureus strains and 10 other Staphylococci. A comparison of the srn contents within 32 Staphylococcal genomes revealed a poor conservation between species. In addition, sRNA structure predictions obtained with MFold are accessible. A BLAST server and the intaRNA program, which is dedicated to target prediction, were implemented. SRD is the first sRNA database centered on a genus; it is a user-friendly and scalable device with the possibility to submit new sequences that should spread in the literature. PMID:25805861

  4. Buried targets in layered media: A combined finite element/physical acoustics model and comparison to data on a half buried 2:1 cylinder.

    PubMed

    Williams, Kevin L

    2016-12-01

    Previously, a combined finite element/physical acoustics model for proud targets [K. L. Williams, S. G. Kargl, E. I. Thorsos, D. S. Burnett, J. L. Lopes, M. Zampolli, and P. L. Marston, J. Acoust. Soc. Am. 127, 3356-3371 (2010)] was compared to both higher fidelity finite element models and to experimental data for a proud 2:1 aluminum cylinder. Here that expression is generalized to address the case of a target buried in a layered media. The result is compared to data acquired for the same 2:1 cylinder but half buried in a mud layer that covers the sand sediment (considered here as infinite in extent below the mud layer). The generalized expression reduces to both the previous proud result and to the result for a target buried in an infinite medium under the appropriate limiting conditions. The model/data comparisons shown include both the previous proud model and data results along with the ones for the half buried cylinder. The comparison quantifies the reduction in target strength as a function of frequency in the half buried case relative to the proud case.

  5. Development and evaluation of a four-tube real time multiplex PCR assay covering fourteen respiratory viruses, and comparison to its corresponding single target counterparts.

    PubMed

    Jansen, Rogier R; Schinkel, Janke; Koekkoek, Sylvie; Pajkrt, Dasja; Beld, Marcel; de Jong, Menno D; Molenkamp, Richard

    2011-07-01

    Multiplex real time PCR is increasingly used to diagnose respiratory viruses and has shown to be superior to traditional methods, like culture and antigen detection. However, comprehensive data on sensitivity, specificity and performance of the multiplex PCR compared to the single target PCR's is limited for most published respiratory multiplex real time PCR assays. Development and extensive analysis of an internally controlled multiplex real time rt-PCR for detection of respiratory viruses. The assay was validated in comparison to single-target PCR's using plasmid targets and prospectively collected nasopharyngeal aspirates. Using plasmid targets the multiplex format was found to be as least as sensitive and specific as the single-target PCR and no competition was observed when different targets were present at different amounts in one tube. Clinical validation showed high concordance for all viruses tested except for samples with low levels of enterovirus. This multiplex showed excellent specificities for all 14 respiratory viruses and sensitivity was high except for clinical samples with low levels of enterovirus. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Target-dependence of sensory neurons: an ultrastructural comparison of axotomised dorsal root ganglion neurons with allowed or denied reinnervation of peripheral targets.

    PubMed

    Johnson, I P; Sears, T A

    2013-01-03

    Evidence is emerging for a role of rough endoplasmic reticulum (RER) in the form of stress granules, the unfolded protein response and protein bodies in the response of neurons to injury and in neurodegenerative diseases. Here, we have studied the role of the peripheral target in regulating the RER and polyribosomes of Nissl bodies in axotomised adult cat dorsal root ganglion (DRG) neurons where axonal regeneration and peripheral target reinnervation was either allowed or denied. Retrograde labelling with horseradish peroxidise was used as an independent marker to enable selection of only those DRG neuronal cell bodies with axons in the injured intercostal nerves. Indications of polyribosomal dispersal were seen by 6h following axotomy, and by 24h the normal orderly arrangement of lamellae of RER in Nissl bodies had become disorganised. These ultrastructural changes preceded light microscopical chromatolysis by 1-3d. The retrograde response was maximal 8-32 d after axotomy. Clusters of debris-laden satellite cells/macrophages were present at this time but no ultrastructural evidence of neuronal apoptosis or necrosis was seen and there were no differences in the initial retrograde response according to the type of injury. By 64 d following axotomy with reinnervation, approximately half the labelled DRG neurons showed restoration of the orderly arrangement of RER and polyribosomes in their Nissl bodies. This was not seen after axotomy with reinnervation denied. We propose that the target-dependent changes in Nissl body ultrastructure described here are part of a continuum that can modify neuronal protein synthesis directed towards growth, maintenance or death of the neuron. This represents a possible structural basis for mediating the varied effects of neurotrophic interactions.

  7. Gender Representation on Gender-Targeted Television Channels: A Comparison of Female- and Male-Targeted TV Channels in the Netherlands.

    PubMed

    Daalmans, Serena; Kleemans, Mariska; Sadza, Anne

    2017-01-01

    The current study investigated the differences in the representation of gender on male- and female-targeted channels with regard to recognition (i.e., the actual presence of men and women) and respect (i.e., the nature of that representation or portrayal). To this end, the presence of men and women on two female- and two male-targeted Dutch channels (N = 115 programs, N = 1091 persons) were compared via content analysis. The expectation that men's channels would portray a less equal and more traditional image of gender than women's channels was generally supported by the results. Regardless of genre as well as country of origin of the program, women were underrepresented on men's channels, while gender distribution on women's channels was more equal. The representation of women in terms of age and occupation was more stereotypical on men's channels than on women's channels, whereas men were represented in more contra-stereotypical ways (e.g., performing household tasks) on women's channels. Since television viewing contributes to the learning and maintenance of stereotyped perceptions, the results imply that it is important to strengthen viewers' defenses against the effects of gender stereotyping when watching gendered television channels, for instance through media literacy programs in schools.

  8. Regional Differences in Gallbladder Cancer Pathogenesis: Insights from a Comparison of Cell Cycle-Regulatory, PI3K, and Pro-Angiogenic Protein Expression

    PubMed Central

    Butte, Jean M.; Torres, Javiera; Veras, Emanuela F.; Matsuo, Kenichi; Gönen, Mithat; D’Angelica, Michael I.; Waugh, Enrique; Meneses, Manuel; Inayama, Yoshiyaki; Fong, Yuman; DeMatteo, Ronald P.; De La Fuente, Hernan; Endo, Itaru; Klimstra, David S.; Jarnagin, William R.

    2014-01-01

    Background The variable incidence of gallbladder cancer (GBCA) suggests regional pathogenetic differences. This study compares cell cycle-regulatory, angiogenesis-related, and PI3K pathway protein expression in GBCAs from three continents. Methods Immunohistochemical expression of several proteins was assessed, correlated with clinicopathologic variables, and compared among centers from Chile (Fundación Arturo López Pérez [FALP]), Japan (Yokohama City University [YCU]), and the United States (Memorial Sloan-Kettering Cancer Center [MSKCC]). Hierarchical clustering was used to partition the data based on protein-expression and treatment center. Results Tissue from 117 patients (MSKCC = 76; FALP = 22; YCU = 19) was analyzed. Mdm2 overexpression was seen only at MSKCC (p < 0.0001). Absence of p21 (p = 0.03) and VEGFR2 (p = 0.018) were more common and p27 expression was less frequent (p = 0.047) in tumors from YCU. Ki-67 labeling index in YCU tumors (median = 10) was two-thirds lower than at other centers. On hierarchical clustering analysis, all YCU patients (p = 0.017) and those with early tumors (p = 0.017) clustered separately from MSKCC. Median disease-specific survival after curative intent (R0) resection was 27 months and was similar among centers (p = 0.9). Median disease-specific survival of patients with early tumors was 28.4 months and was higher at YCU (not reached, p = 0.06). Conclusions Cell cycle-regulatory protein expression patterns of YCU tumors differed from those treated at FALP and MSKCC. The differential clustering of protein expression and survival in patients with early tumors suggest regional differences in pathogenesis and disease biology. PMID:23212762

  9. Regulatory fit messages and physical activity motivation.

    PubMed

    Pfeffer, Ines

    2013-04-01

    Targeted communication about health behaviors seems to be more effective than mass communication in which undifferentiated audiences receive identical messages. Regulatory focus is psychological variable that can be used to build two target groups: promotion-focused or prevention-focused people. It is hypothesized that targeting messages to an individual's regulatory focus creates regulatory fit and is more successful to promote a physically active lifestyle than nonfit messages. Two different print messages promoting a physically active lifestyle derived from regulatory focus theory (promotion message vs. prevention message) were randomly assigned to N = 98 participants after measuring their regulatory focus. It was examined whether regulatory fit between the regulatory focus and the assigned print message would lead to more positive evaluations in the dependent variables inclination toward the message (preference for the message), intention to perform the behavior, prospective and retrospective feelings associated with the behavior (positive and negative), and perceived value of the behavior directly after reading the message. Hierarchical linear regression analyses revealed that regulatory fit led to stronger intentions in the prevention-message condition and more prospective positive and retrospective positive feelings associated with the behavior in the promotion-message condition in contrast to the nonfit conditions. Prospective positive feelings associated with the behavior mediated the effect of regulatory fit on intention. The results partly provided support for the regulatory fit concept. Matching print messages to the regulatory focus of individuals seems to be a useful approach to enhance physical activity motivation. Future studies should include an objective measure of physical activity behavior.

  10. Comparison of four radiofrequency ablation systems at two target volumes in an ex vivo bovine liver model

    PubMed Central

    Rathke, Hendrik; Hamm, Bernd; Güttler, Felix; Rathke, Joern; Rump, Jens; Teichgräber, Ulf; de Bucourt, Maximilian

    2014-01-01

    PURPOSE We aimed to validate actually achieved macroscopic ablation volumes in relation to calculated target volumes using four different radiofrequency ablation (RFA) systems operated with default settings and protocols for 3 cm and 5 cm target volumes in ex vivo bovine liver. MATERIALS AND METHODS Sixty-four cuboid liver specimens were ablated with four commercially available RFA systems (Radionics Cool-tip, AngioDynamic 1500X, Boston Scientific RF 3000, Celon CelonPower LAB): 16 specimens for each system; eight for 3 cm, and eight for 5 cm. Ablation diameters were measured, volumes were calculated, and RFA times were recorded. RESULTS For the 3 cm target ablation volume, all tested RFA systems exceeded the mathematically calculated volume of 14.14 cm3. For the 3 cm target ablation volume, mean ablation volume and mean ablation time for each RFA system were as follows: 28.5±6.5 cm3, 12.0±0.0 min for Radionics Cool-tip; 17.1±4.9 cm3, 9.36±0.63 min for AngioDynamic 1500X; 29.7±11.7 cm3, 4.60±0.50 min for Boston Scientific RF 3000; and 28.8±7.0 cm3, 20.85±0.86 min for Celon Celon-Power LAB. For the 5 cm target ablation volume, Radionics Cool-tip (48.3±9.9 cm3, 12.0±0.0 min) and AngioDynamic 1500X (39.4±16.2 cm3, 19.59±1.13 min) did not reach the mathematically calculated target ablation volume (65.45 cm3), whereas Boston Scientific RF 3000 (71.8±14.5 cm3, 9.15±2.93 min) and Celon CelonPower LAB (93.9±28.1 cm3, 40.21±1.78 min) exceeded it. CONCLUSION While all systems reached the 3 cm target ablation volume, results were variable for the 5 cm target ablation volume. Only Boston Scientific RF 3000 and Celon CelonPower LAB created volumes above the target, whereas Radionics Cool-tip and AngioDynamic 1500X remained below the target volume. For the 3 cm target ablation volume, AngioDynamic 1500X with 21% deviation was closest to the target volume. For the 5 cm target volume Boston Scientific RF 3000 with 10% deviation was closest. PMID:24509185

  11. Comparison of four radiofrequency ablation systems at two target volumes in an ex vivo bovine liver model.

    PubMed

    Rathke, Hendrik; Hamm, Bernd; Güttler, Felix; Rathke, Joern; Rump, Jens; Teichgräber, Ulf; de Bucourt, Maximilian

    2014-01-01

    We aimed to validate actually achieved macroscopic ablation volumes in relation to calculated target volumes using four different radiofrequency ablation (RFA) systems operated with default settings and protocols for 3 cm and 5 cm target volumes in ex vivo bovine liver. Sixty-four cuboid liver specimens were ablated with four commercially available RFA systems (Radionics Cool-tip, AngioDynamic 1500X, Boston Scientific RF 3000, Celon CelonPower LAB): 16 specimens for each system; eight for 3 cm, and eight for 5 cm. Ablation diameters were measured, volumes were calculated, and RFA times were recorded. For the 3 cm target ablation volume, all tested RFA systems exceeded the mathematically calculated volume of 14.14 cm3. For the 3 cm target ablation volume, mean ablation volume and mean ablation time for each RFA system were as follows: 28.5 ± 6.5 cm3, 12.0 ± 0.0 min for Radionics Cool-tip; 17.1 ± 4.9 cm3, 9.36 ± 0.63 min for AngioDynamic 1500X; 29.7 ± 11.7 cm3, 4.60 ± 0.50 min for Boston Scientific RF 3000; and 28.8 ± 7.0 cm3, 20.85 ± 0.86 min for Celon CelonPower LAB. For the 5 cm target ablation volume, Radionics Cool-tip (48.3 ± 9.9 cm3, 12.0 ± 0.0 min) and AngioDynamic 1500X (39.4 ± 16.2 cm3, 19.59 ± 1.13 min) did not reach the mathematically calculated target ablation volume (65.45 cm3), whereas Boston Scientific RF 3000 (71.8 ± 14.5 cm3, 9.15 ± 2.93 min) and Celon CelonPower LAB (93.9 ± 28.1 cm3, 40.21 ± 1.78 min) exceeded it. While all systems reached the 3 cm target ablation volume, results were variable for the 5 cm target ablation volume. Only Boston Scientific RF 3000 and Celon CelonPower LAB created volumes above the target, whereas Radionics Cool-tip and AngioDynamic 1500X remained below the target volume. For the 3 cm target ablation volume, AngioDynamic 1500X with 21% deviation was closest to the target volume. For the 5 cm target volume Boston Scientific RF 3000 with 10% deviation was closest.

  12. Horizontal and vertical targeting: a population-based comparison of public eldercare services in urban and rural areas of Sweden.

    PubMed

    Lagergren, Mårten; Fagerström, Cecilia; Sjölund, Britt-Marie; Berglund, Johan; Fratiglioni, Laura; Nordell, Eva; von Strauss, Eva; Wimo, Anders; Elmståhl, Sölve

    2016-02-01

    The concepts of target efficiency can be used to assess the extent to which service provision is in line with the needs of the population. Horizontal target efficiency denotes the extent to which those deemed to need a service receive it and vertical target efficiency is the corresponding extent to which those who receive services actually need them. The aim of this study was to assess the target efficiency of the Swedish eldercare system and to establish whether target efficiencies differ in different geographical areas such as large urban, midsize urban and rural areas. Vertical efficiency was measured by studying those people who received eldercare services and was expressed as a percentage of those who received services who were functionally dependent. To measure horizontal target efficiency, data collected at baseline in the longitudinal population study SNAC (Swedish National study on Aging and Care) during the years 2001-2004 were used. The horizontal efficiency was calculated as the percentage of functionally dependent persons who received services. Functional dependency was measured as having difficulty with instrumental activities of daily living (IADL) and/or personal activities of daily living (PADL). Services included long-term municipal eldercare services (LTC). Horizontal target efficiency for the public LTC system was reasonably high in all three geographical areas, when using dependency in PADL as the measure of need (70-90 %), but efficiency was lower when the less restrictive measure of IADL dependency was used (40-50 %). In both cases, the target efficiency was markedly higher in the large urban and the rural areas than in the midsize urban areas. Vertical target efficiency showed the same pattern-it was almost 100 % in all areas for IADL dependency, but only 50-60 % for PADL dependency. Household composition differed in the areas studied as did the way public long-term care was provided to people living alone as compared to those co-habiting.

  13. Comparison of the calcium release channel of cardiac and skeletal muscle sarcoplasmic reticulum by target inactivation analysis

    SciTech Connect

    McGrew, S.G.; Inui, Makoto; Chadwick, C.C.; Boucek, R.J. Jr.; Jung, C.Y.; Fleischer, S. )

    1989-02-07

    The calcium release channel of sarcoplasmic reticulum which triggers muscle contraction in excitation-contraction coupling has recently been isolated. The channel has been found to be morphologically identical with the feet structures of the junctional face membrane of terminal cisternae and consists of an oligomer of a unique high molecular weight polypeptide. In this study, the authors compare the target size of the calcium release channel from heart and skeletal muscle using target inactivation analysis. The target molecular weights of the calcium release channel estimated by measuring ryanodine binding after irradiation are similar for heart (139,000) and skeletal muscle (143,000) and are smaller than the monomeric unit (estimated to be about 360,000). The target size, estimated by measuring polypeptide remaining after irradiation, was essentially the same for heart and skeletal muscle, 1,061,000 and 1,070,000, respectively, indicating an oligomeric association of protomers. Thus, the calcium release channel of both cardiac and skeletal muscle reacts uniquely with regard to target inactivation analysis in that (1) the size by ryanodine binding is smaller than the monomeric unit and (2) a single hit leads to destruction of more than one polypeptide, by measuring polypeptide remaining. The target inactivation analysis studies indicate that heart and skeletal muscle receptors are structurally very similar.

  14. An in silico comparison between margin-based and probabilistic target-planning approaches in head and neck cancer patients.

    PubMed

    Fontanarosa, Davide; van der Laan, Hans Paul; Witte, Marnix; Shakirin, Georgy; Roelofs, Erik; Langendijk, Johannes A; Lambin, Philippe; van Herk, Marcel

    2013-12-01

    To apply target probabilistic planning (TPP) approach to intensity modulated radiotherapy (IMRT) plans for head and neck cancer (HNC) patients. Twenty plans of HNC patients were re-planned replacing the simultaneous integrated boost IMRT optimization objectives for minimum dose on the boost target and the elective volumes with research probabilistic objectives: the latter allow for explicit handling of systematic and random geometric uncertainties, enabling confidence level based probabilistic treatment planning. Monte-Carlo evaluations of geometrical errors were performed, with endpoints D98%, D2% and Dmean, calculated at a confidence level of 90%. The dose distribution was expanded outside the patient to prevent large bilateral elective treatment volumes ending up in air for probabilistic shifts. TPP resulted in more regular isodoses and in reduced dose, on average, to organs at risk (OAR), up to more than 6Gy, while maintaining target coverage and keeping the maximum dose to limiting structures within requirements. In particular, when the surrounding OARs overlap with the planning target volume (PTV) but not with the clinical target volume (CTV), better results were achieved. The TPP approach was evaluated in HNC patients, and proven to be an efficient tool for managing uncertainties. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  15. Comparison of Standard Light Water Reactor Cross-Section Libraries using the United States Nuclear Regulatory Commission Pressurized Water Reactor Standard Core Loading Benchmark Problem

    NASA Astrophysics Data System (ADS)

    Arzu Alpan, F.; Kulesza, Joel A.

    2016-02-01

    This paper compares contemporary and historical light water reactor shielding and pressure vessel dosimetry cross-section libraries for a pressurized water reactor calculational benchmark problem with a standard out-in core loading. The calculational benchmark problem was developed at Brookhaven National Laboratory by the request of the U. S. Nuclear Regulatory Commission and used the Oak Ridge National Laboratory two-dimensional discrete ordinates code DORT and the BUGLE-93 cross-section library for the calculations. In this paper, a Westinghouse three-dimensional discrete ordinates code with parallel processing, the RAPTOR-M3G code was used. A variety of cross section libraries were used with RAPTOR-M3G including the BUGLE-93, BUGLE-96, and BUGLE-B7 cross-section libraries developed at Oak Ridge National Laboratory, and the broad-group ALPAN-VII.0 cross-section library developed at Westinghouse. In comparing the calculation-to-calculation reaction rates using the BUGLE-93 cross-section library at the thermal shield, pressure vessel, and cavity capsules, for eleven dosimetry reaction rates, a maximum relative difference of 5% was observed, with the exception of 65Cu(n,2n) in the pressure vessel capsule that had a 90% relative difference with respect to the reference results. It is thought that the 65Cu(n,2n) reaction rate reported in the reference for the pressure vessel capsule is not correct. In considering the libraries developed after BUGLE-93, a maximum relative difference of 12% was observed in reaction rates, with respect to the reference results, for 237Np(n,f) in the cavity capsule using BUGLE-B7.

  16. Outlier and target detection in aerial hyperspectral imagery: a comparison of traditional and percentage occupancy hit or miss transform techniques

    NASA Astrophysics Data System (ADS)

    Young, Andrew; Marshall, Stephen; Gray, Alison

    2016-05-01

    The use of aerial hyperspectral imagery for the purpose of remote sensing is a rapidly growing research area. Currently, targets are generally detected by looking for distinct spectral features of the objects under surveillance. For example, a camouflaged vehicle, deliberately designed to blend into background trees and grass in the visible spectrum, can be revealed using spectral features in the near-infrared spectrum. This work aims to develop improved target detection methods, using a two-stage approach, firstly by development of a physics-based atmospheric correction algorithm to convert radiance into re ectance hyperspectral image data and secondly by use of improved outlier detection techniques. In this paper the use of the Percentage Occupancy Hit or Miss Transform is explored to provide an automated method for target detection in aerial hyperspectral imagery.

  17. Investigation of mixed ion fields in the forward direction for 220.5 MeV/u helium ion beams: comparison between water and PMMA targets.

    PubMed

    Aricò, G; Gehrke, T; Jakubek, J; Gallas, R; Berke, S; Jäkel, O; Mairani, A; Ferrari, A; Martišíková, M

    2017-10-03

    Currently there is a rising interest in helium ion beams for radiotherapy. For benchmarking of the physical beam models used in treatment planning, there is a need for experimental data on the composition and spatial distribution of mixed ion fields. Of particular interest are the attenuation of the primary helium ion fluence and the build-up of secondary hydrogen ions due to nuclear interactions. The aim of this work was to provide such data with an enhanced precision. Moreover, the validity and limits of the mixed ion field equivalence between water and PMMA targets were investigated. Experiments with a 220.5 MeV/u helium ion pencil beam were performed at the Heidelberg Ion-Beam Therapy Center in Germany. The compact detection system used for ion tracking and identification was solely based on Timepix position-sensitive semiconductor detectors. In comparison to standard techniques, this system is two orders of magnitude smaller, and provides higher precision and flexibility. The numbers of outgoing helium and hydrogen ions per primary helium ion as well as the lateral particle distributions were quantitatively investigated in the forward direction behind water and PMMA targets with 5.2-18 cm water equivalent thickness (WET). Comparing water and PMMA targets with the same WET, we found that significant differences in the amount of outgoing helium and hydrogen ions and in the lateral particle distributions arise for target thicknesses above 10 cm WET. The experimental results concerning hydrogen ions emerging from the targets were reproduced reasonably well by Monte Carlo simulations using the FLUKA code. Concerning the amount of outgoing helium ions, significant differences of 3-15% were found between experiments and simulations. We conclude that if PMMA is used in place of water in dosimetry, differences in the dose distributions could arise close to the edges of the field, in particular for deep seated targets.

  18. Planning Study Comparison of Real-Time Target Tracking and Four-Dimensional Inverse Planning for Managing Patient Respiratory Motion

    SciTech Connect

    Zhang Peng; Hugo, Geoffrey D.; Yan Di

    2008-11-15

    Purpose: Real-time target tracking (RT-TT) and four-dimensional inverse planning (4D-IP) are two potential methods to manage respiratory target motion. In this study, we evaluated each method using the cumulative dose-volume criteria in lung cancer radiotherapy. Methods and Materials: Respiration-correlated computed tomography scans were acquired for 4 patients. Deformable image registration was applied to generate a displacement mapping for each phase image of the respiration-correlated computed tomography images. First, the dose distribution for the organs of interest obtained from an idealized RT-TT technique was evaluated, assuming perfect knowledge of organ motion and beam tracking. Inverse planning was performed on each phase image separately. The treatment dose to the organs of interest was then accumulated from the optimized plans. Second, 4D-IP was performed using the probability density function of respiratory motion. The beam arrangement, prescription dose, and objectives were consistent in both planning methods. The dose-volume and equivalent uniform dose in the target volume, lung, heart, and spinal cord were used for the evaluation. Results: The cumulative dose in the target was similar for both techniques. The equivalent uniform dose of the lung, heart, and spinal cord was 4.6 {+-} 2.2, 11 {+-} 4.4, and 11 {+-} 6.6 Gy for RT-TT with a 0-mm target margin, 5.2 {+-} 3.1, 12 {+-} 5.9, and 12 {+-} 7.8 Gy for RT-TT with a 2-mm target margin, and 5.3 {+-} 2.3, 11.9 {+-} 5.0, and 12 {+-} 5.6 Gy for 4D-IP, respectively. Conclusion: The results of our study have shown that 4D-IP can achieve plans similar to those achieved by RT-TT. Considering clinical implementation, 4D-IP could be a more reliable and practical method to manage patient respiration-induced motion.

  19. A TPD and AR based comparison of accelerator neutron irradiation fields between (7)Li and W targets for BNCT.

    PubMed

    Tanaka, Kenichi; Endo, Satoru; Yonai, Shunsuke; Baba, Mamoru; Hoshi, Masaharu

    2014-06-01

    The characteristics of moderator assembly dimension was investigated for the usage of (7)Li(p,n) neutrons by 2.3-2.8MeV protons and W(p,n) neutrons by 50MeV protons. The indexes were the treatable protocol depth (TPD) and advantage depth (AD). Consequently, a configuration for W target with the Fe filter, Fluental moderator, Pb reflector showed the TPD of 5.8cm and AD of 9.3cm. Comparable indexes were found for the Li target in a geometry with the MgF2 moderator and Teflon reflector.

  20. Intra-Animal Comparison between Three-dimensional Molecularly Targeted US and Three-dimensional Dynamic Contrast-enhanced US for Early Antiangiogenic Treatment Assessment in Colon Cancer.

    PubMed

    Wang, Huaijun; Lutz, Amelie M; Hristov, Dimitre; Tian, Lu; Willmann, Jürgen K

    2017-02-01

    Purpose To perform an intra-animal comparison between (a) three-dimensional (3D) molecularly targeted ultrasonography (US) by using clinical-grade vascular endothelial growth factor receptor 2 (VEGFR2)-targeted microbubbles and (b) 3D dynamic contrast material-enhanced (DCE) US by using nontargeted microbubbles for assessment of antiangiogenic treatment effects in a murine model of human colon cancer. Materials and Methods Twenty-three mice with human colon cancer xenografts were randomized to receive either single-dose antiangiogenic treatment (bevacizumab, n = 14) or control treatment (saline, n = 9). At baseline and 24 hours after treatment, animals were imaged with a clinical US system equipped with a clinical matrix array transducer by using the following techniques: (a) molecularly targeted US with VEGFR2-targeted microbubbles, (b) bolus DCE US with nontargeted microbubbles, and (c) destruction-replenishment DCE US with nontargeted microbubbles. VEGFR2-targeted US signal, peak enhancement, area under the time-intensity curve, time to peak, relative blood volume (rBV), relative blood flow, and blood flow velocity were quantified. VEGFR2 expression and percentage area of blood vessels were assessed ex vivo with quantitative immunofluorescence and correlated with corresponding in vivo US parameters. Statistical analysis was performed with Wilcoxon signed rank tests and rank sum tests, as well as Pearson correlation analysis. Results Molecularly targeted US signal with VEGFR2-targeted microbubbles, peak enhancement, and rBV significantly decreased (P ≤ .03) after a single antiangiogenic treatment compared with those in the control group; similarly, ex vivo VEGFR2 expression (P = .03) and percentage area of blood vessels (P = .03) significantly decreased after antiangiogenic treatment. Three-dimensional molecularly targeted US signal correlated well with VEGFR2 expression (r = 0.86, P = .001), and rBV (r = 0.71, P = .01) and relative blood flow (r = 0.78, P

  1. A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo

    NASA Technical Reports Server (NTRS)

    Davidson, Eric H.; Rast, Jonathan P.; Oliveri, Paola; Ransick, Andrew; Calestani, Cristina; Yuh, Chiou-Hwa; Minokawa, Takuya; Amore, Gabriele; Hinman, Veronica; Arenas-Mena, Cesar; Otim, Ochan; Brown, C. Titus; Livi, Carolina B.; Lee, Pei Yun; Revilla, Roger; Schilstra, Maria J.; Clarke, Peter J C.; Rust, Alistair G.; Pan, Zhengjun; Arnone, Maria I.; Rowen, Lee; Cameron, R. Andrew; McClay, David R.; Hood, Leroy; Bolouri, Hamid

    2002-01-01

    We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.caltech.edu/mirsky/endomeso.htm (End-mes Gene Network Update) for the latest version. The network contains over 40 genes at present, many newly uncovered in the course of this work, and most encoding DNA-binding transcriptional regulatory factors. The architecture of the network was approached initially by construction of a logic model that integrated the extensive experimental evidence now available on endomesoderm specification. The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network. Five kinds of perturbation have been applied: (1) use of morpholino antisense oligonucleotides targeted to many of the key regulatory genes in the network; (2) transformation of other regulatory factors into dominant repressors by construction of Engrailed repressor domain fusions; (3) ectopic expression of given regulatory factors, from genetic expression constructs and from injected mRNAs; (4) blockade of the beta-catenin/Tcf pathway by introduction of mRNA encoding the intracellular domain of cadherin; and (5) blockade of the Notch signaling pathway by introduction of mRNA encoding the extracellular domain of the Notch receptor. The network model predicts the cis-regulatory inputs that link each gene into the network. Therefore, its architecture is testable by cis-regulatory analysis. Strongylocentrotus purpuratus and Lytechinus variegatus genomic BAC recombinants that include a large number of the genes in the network have been sequenced and annotated. Tests of the cis-regulatory predictions of

  2. A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo

    NASA Technical Reports Server (NTRS)

    Davidson, Eric H.; Rast, Jonathan P.; Oliveri, Paola; Ransick, Andrew; Calestani, Cristina; Yuh, Chiou-Hwa; Minokawa, Takuya; Amore, Gabriele; Hinman, Veronica; Arenas-Mena, Cesar; hide

    2002-01-01

    We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.caltech.edu/mirsky/endomeso.htm (End-mes Gene Network Update) for the latest version. The network contains over 40 genes at present, many newly uncovered in the course of this work, and most encoding DNA-binding transcriptional regulatory factors. The architecture of the network was approached initially by construction of a logic model that integrated the extensive experimental evidence now available on endomesoderm specification. The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network. Five kinds of perturbation have been applied: (1) use of morpholino antisense oligonucleotides targeted to many of the key regulatory genes in the network; (2) transformation of other regulatory factors into dominant repressors by construction of Engrailed repressor domain fusions; (3) ectopic expression of given regulatory factors, from genetic expression constructs and from injected mRNAs; (4) blockade of the beta-catenin/Tcf pathway by introduction of mRNA encoding the intracellular domain of cadherin; and (5) blockade of the Notch signaling pathway by introduction of mRNA encoding the extracellular domain of the Notch receptor. The network model predicts the cis-regulatory inputs that link each gene into the network. Therefore, its architecture is testable by cis-regulatory analysis. Strongylocentrotus purpuratus and Lytechinus variegatus genomic BAC recombinants that include a large number of the genes in the network have been sequenced and annotated. Tests of the cis-regulatory predictions of

  3. Regulatory myeloid cells in transplantation.

    PubMed

    Rosborough, Brian R; Raïch-Regué, Dàlia; Turnquist, Heth R; Thomson, Angus W

    2014-02-27

    Regulatory myeloid cells (RMC) are emerging as novel targets for immunosuppressive (IS) agents and hold considerable promise as cellular therapeutic agents. Herein, we discuss the ability of regulatory macrophages, regulatory dendritic cells, and myeloid-derived suppressor cells to regulate alloimmunity, their potential as cellular therapeutic agents, and the IS agents that target their function. We consider protocols for the generation of RMC and the selection of donor- or recipient-derived cells for adoptive cell therapy. Additionally, the issues of cell trafficking and antigen (Ag) specificity after RMC transfer are discussed. Improved understanding of the immunobiology of these cells has increased the possibility of moving RMC into the clinic to reduce the burden of current IS agents and to promote Ag-specific tolerance. In the second half of this review, we discuss the influence of established and experimental IS agents on myeloid cell populations. IS agents believed historically to act primarily on T cell activation and proliferation are emerging as important regulators of RMC function. Better insights into the influence of IS agents on RMC will enhance our ability to develop cell therapy protocols to promote the function of these cells. Moreover, novel IS agents may be designed to target RMC in situ to promote Ag-specific immune regulation in transplantation and to usher in a new era of immune modulation exploiting cells of myeloid origin.

  4. Second order optimization for the inference of gene regulatory pathways.

    PubMed

    Das, Mouli; Murthy, Chivukula A; De, Rajat K

    2014-02-01

    With the increasing availability of experimental data on gene interactions, modeling of gene regulatory pathways has gained special attention. Gradient descent algorithms have been widely used for regression and classification applications. Unfortunately, results obtained after training a model by gradient descent are often highly variable. In this paper, we present a new second order learning rule based on the Newton's method for inferring optimal gene regulatory pathways. Unlike the gradient descent method, the proposed optimization rule is independent of the learning parameter. The flow vectors are estimated based on biomass conservation. A set of constraints is formulated incorporating weighting coefficients. The method calculates the maximal expression of the target gene starting from a given initial gene through these weighting coefficients. Our algorithm has been benchmarked and validated on certain types of functions and on some gene regulatory networks, gathered from literature. The proposed method has been found to perform better than the gradient descent learning. Extensive performance comparison with the extreme pathway analysis method has underlined the effectiveness of our proposed methodology.

  5. Comparison of the structure function F2 as measured by charged lepton and neutrino scattering from iron targets

    NASA Astrophysics Data System (ADS)

    Kalantarians, N.; Keppel, C.; Christy, M. E.

    2017-09-01

    A comparison study of world data for the structure function F2 for iron, as measured by both charged lepton and neutrino scattering experiments, is presented. Consistency of results for both charged lepton and neutrino scattering is observed for the full global data set in the valence regime. Consistency is also observed at low x for the various neutrino data sets, as well as for the charged lepton data sets, independently. However, data from the two probes exhibit differences on the order of 15% in the shadowing-antishadowing transition region where the Bjorken scaling variable x is <0.15 . This observation is indicative that neutrino probes of nucleon structure might be sensitive to different nuclear effects than charged lepton probes. Details and results of the data comparison are presented here.

  6. Comparison of the structure function F2 as measured by charged lepton and neutrino scattering from iron targets

    DOE PAGES

    Kalantarians, N.; Keppel, C.; Christy, M. E.

    2017-09-12

    A comparison study of world data for the structure function F2 for Iron, as measured by both charged lepton and neutrino scattering experiments, is presented. Consistency of results for both charged lepton and neutrino scattering is observed for the full global data set in the valence regime. Consistency is also observed at low x for the various neutrino data sets, as well as for the charged lepton data sets, independently. However, data from the two probes exhibit differences on the order of 15% in the shadowing/anti-shadowing transition region where the Bjorken scaling variable x is < 0.15. This observation ismore » indicative that neutrino probes of nucleon structure might be sensitive to different nuclear effects than charged lepton probes. Details and results of the data comparison are here presented.« less

  7. A Preliminary Controlled Comparison of Programs Designed to Reduce Risk of Eating Disorders Targeting Perfectionism and Media Literacy

    ERIC Educational Resources Information Center

    Wilksch, Simon M.; Durbridge, Mitchell R.; Wade, Tracey D.

    2008-01-01

    The study aims to find out whether programs targeting perfectionism and media literacy are more effective than control classes in reducing eating disorder risk factors. Finding reveals that perfectionism programs are well suited to individuals of mid- to late adolescent age and shows the importune of making prevention programs developmentally…

  8. Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets.

    PubMed

    Chen, Zhi; Li, Hong-lin; Zhang, Qi-jun; Bao, Xiao-guang; Yu, Kun-qian; Luo, Xiao-min; Zhu, Wei-liang; Jiang, Hua-liang

    2009-12-01

    This study was conducted to compare the efficiencies of two virtual screening approaches, pharmacophore-based virtual screening (PBVS) and docking-based virtual screening (DBVS) methods. All virtual screens were performed on two data sets of small molecules with both actives and decoys against eight structurally diverse protein targets, namely angiotensin converting enzyme (ACE), acetylcholinesterase (AChE), androgen receptor (AR), D-alanyl-D-alanine carboxypeptidase (DacA), dihydrofolate reductase (DHFR), estrogen receptors alpha (ERalpha), HIV-1 protease (HIV-pr), and thymidine kinase (TK). Each pharmacophore model was constructed based on several X-ray structures of protein-ligand complexes. Virtual screens were performed using four screening standards, the program Catalyst for PBVS and three docking programs (DOCK, GOLD and Glide) for DBVS. Of the sixteen sets of virtual screens (one target versus two testing databases), the enrichment factors of fourteen cases using the PBVS method were higher than those using DBVS methods. The average hit rates over the eight targets at 2% and 5% of the highest ranks of the entire databases for PBVS are much higher than those for DBVS. The PBVS method outperformed DBVS methods in retrieving actives from the databases in our tested targets, and is a powerful method in drug discovery.

  9. Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets

    PubMed Central

    Chen, Zhi; Li, Hong-lin; Zhang, Qi-jun; Bao, Xiao-guang; Yu, Kun-qian; Luo, Xiao-min; Zhu, Wei-liang; Jiang, Hua-liang

    2009-01-01

    Aim: This study was conducted to compare the efficiencies of two virtual screening approaches, pharmacophore-based virtual screening (PBVS) and docking-based virtual screening (DBVS) methods. Methods: All virtual screens were performed on two data sets of small molecules with both actives and decoys against eight structurally diverse protein targets, namely angiotensin converting enzyme (ACE), acetylcholinesterase (AChE), androgen receptor (AR), D-alanyl-D-alanine carboxypeptidase (DacA), dihydrofolate reductase (DHFR), estrogen receptors α (ERα), HIV-1 protease (HIV-pr), and thymidine kinase (TK). Each pharmacophore model was constructed based on several X-ray structures of protein-ligand complexes. Virtual screens were performed using four screening standards, the program Catalyst for PBVS and three docking programs (DOCK, GOLD and Glide) for DBVS. Results: Of the sixteen sets of virtual screens (one target versus two testing databases), the enrichment factors of fourteen cases using the PBVS method were higher than those using DBVS methods. The average hit rates over the eight targets at 2% and 5% of the highest ranks of the entire databases for PBVS are much higher than those for DBVS. Conclusion: The PBVS method outperformed DBVS methods in retrieving actives from the databases in our tested targets, and is a powerful method in drug discovery. PMID:19935678

  10. Targeted fluorescence imaging enhanced by 2D materials: a comparison between 2D MoS2 and graphene oxide.

    PubMed

    Xie, Donghao; Ji, Ding-Kun; Zhang, Yue; Cao, Jun; Zheng, Hu; Liu, Lin; Zang, Yi; Li, Jia; Chen, Guo-Rong; James, Tony D; He, Xiao-Peng

    2016-08-04

    Here we demonstrate that 2D MoS2 can enhance the receptor-targeting and imaging ability of a fluorophore-labelled ligand. The 2D MoS2 has an enhanced working concentration range when compared with graphene oxide, resulting in the improved imaging of both cell and tissue samples.

  11. Comparison of the probability of target attainment of anidulafungin against Candida spp. in patients with acute leukaemia.

    PubMed

    Doan, Tan N; Kong, David C M; Patel, Kashyap; Walker, Patricia; Spencer, Andrew; Kirkpatrick, Carl M J

    2014-11-01

    This study aimed to investigate the probability of target attainment (PTA) of various anidulafungin dosing regimens against Candida spp. in patients with acute leukaemia. A Monte Carlo simulation was performed using a previously published population pharmacokinetic model. The following dosing scenarios were evaluated: 200 mg loading dose (LD) on Day 1 then 100 mg daily (manufacturer's recommended dosing regimen); 200 mg LD on Day 1 then 100 mg every 48 h (q48 h); and 200 mg q48 h, 200 mg every 72 h (q72 h) and 300 mg q72 h. For each dosing regimen, free drug concentrations were calculated to evaluate the effect of 99% protein binding. The PTA at various pharmacodynamic (PD) targets was determined as the percentage of subjects who achieved a free drug area under the plasma concentration-time curve over the minimum inhibitory concentration ratio (ƒAUC/MIC) or a free drug maximum plasma concentration over the minimum inhibitory concentration ratio (ƒC(max)/MIC) above the PD targets. PTA expectation values were then calculated for each dosing regimen. The currently recommended dosing regimen of anidulafungin was not optimal for invasive candidiasis in patients with acute leukaemia. Alternate dosing strategies with higher doses and extended dosing intervals (intermittent dosing) achieved better target attainment. This is the first study to optimise therapy with anidulafungin using Monte Carlo simulation. These results provide a rationale in support of future clinical investigation of intermittent dosing of anidulafungin.

  12. Comparison of large-angle production of charged pions with incident protons on cylindrical long and short targets

    SciTech Connect

    Apollonio, M.; Chimenti, P.; Giannini, G.; Artamonov, A.; Giani, S.; Gilardoni, S.; Gorbunov, P.; Grant, A.; Grossheim, A.; Ivanchenko, A.; Ivanchenko, V.; Kayis-Topaksu, A.; Panman, J.; Papadopoulos, I.; Tcherniaev, E.; Tsukerman, I.; Wiebusch, C.; Zucchelli, P.; Bagulya, A.; Grichine, V.

    2009-12-15

    The HARP Collaboration has presented measurements of the double-differential {pi}{sup {+-}} production cross section in the range of momentum 100 MeV/c{<=}p{<=}800 MeV/c and angle 0.35 rad{<=}{theta}{<=}2.15 rad with proton beams hitting thin nuclear targets. In many applications the extrapolation to long targets is necessary. In this article the analysis of data taken with long (one interaction length) solid cylindrical targets made of carbon, tantalum, and lead is presented. The data were taken with the large-acceptance HARP detector in the T9 beam line of the CERN proton synchrotron. The secondary pions were produced by beams of protons with momenta of 5, 8, and 12GeV/c. The tracking and identification of the produced particles were performed using a small-radius cylindrical time projection chamber placed inside a solenoidal magnet. Incident protons were identified by an elaborate system of beam detectors. Results are obtained for the double-differential yields per target nucleon d{sup 2}{sigma}/dpd{theta}. The measurements are compared with predictions of the MARS and GEANT4 Monte Carlo simulations.

  13. Screening trematodes for novel intervention targets: a proteomic and immunological comparison of Schistosoma haematobium, Schistosoma bovis and Echinostoma caproni

    PubMed Central

    HIGÓN, MELISSA; COWAN, GRAEME; NAUSCH, NORMAN; CAVANAGH, DAVID; OLEAGA, ANA; TOLEDO, RAFAEL; STOTHARD, J. RUSSELL; ANTÚNEZ, ORETO; MARCILLA, ANTONIO; BURCHMORE, RICHARD; MUTAPI, FRANCISCA

    2011-01-01

    SUMMARY With the current paucity of vaccine targets for parasitic diseases, particularly those in childhood, the aim of this study was to compare protein expression and immune cross-reactivity between the trematodes Schistosoma haematobium, S. bovis and Echinostoma caproni in the hope of identifying novel intervention targets. Native adult parasite proteins were separated by 2-dimensional gel electrophoresis and identified through electrospray ionisation tandem mass spectrometry to produce a reference gel. Proteins from differential gel electrophoresis analyses of the three parasite proteomes were compared and screened against sera from hamsters infected with S. haematobium and E. caproni following 2-dimensional Western blotting. Differential protein expression between the three species was observed with circa 5% of proteins from S. haematobium showing expression up-regulation compared to the other two species. There was 91% similarity between the proteomes of the two Schistosoma species and 81% and 78·6% similarity between S. haematobium and S. bovis versus E. caproni, respectively. Although there were some common cross-species antigens, species-species targets were revealed which, despite evolutionary homology, could be due to phenotypic plasticity arising from different host-parasite relationships. Nevertheless, this approach helps to identify novel intervention targets which could be used as broad-spectrum candidates for future use in human and veterinary vaccines. PMID:21729355

  14. Comparison of an 'intuitive' NHS hearing aid prescription method with DSL 4.1 targets for amplification.

    PubMed

    Parsons, Jonathan O; Clark, Charles R

    2002-09-01

    This study aimed to evaluate current practice in a National Health Service Trust in setting hearing aid output to meet amplification targets prescribed by desired sensation level (DSL) using a range of NHS hearing aids. A consecutive sample of 33 patients was drawn from the hearing aid waiting list of the Royal Devon & Exeter Hospital (RD&E). The age range was 33-83 years. Patients not giving written consent and those with complex hearing losses were excluded. At review, pure-tone audiogram, uncomfortable loudness levels, real-ear coupler difference, user gain and maximum output were recorded. Data were entered into DSL 4.1 prescription software. Wilcoxon tests were used to compare the measured user gain and maximum output with DSL 4.1-generated targets. The results demonstrate significant differences (p<0.05) at 0.25, 0.5, 0.75, 1.5, 2, 3, 4 and 6 kHz between target and measured values for user gain. This study reveals that the routine intuitive method for prescribing hearing aids at the RD&E is not effective in meeting targets for amplified speech as prescribed by DSL.

  15. Comparison of the pharmacological profiles of murine antisense oligonucleotides targeting apolipoprotein B and microsomal triglyceride transfer protein

    PubMed Central

    Lee, Richard G.; Fu, Wuxia; Graham, Mark J.; Mullick, Adam E.; Sipe, Donna; Gattis, Danielle; Bell, Thomas A.; Booten, Sheri; Crooke, Rosanne M.

    2013-01-01

    Therapeutic agents that suppress apolipoprotein B (apoB) and microsomal triglyceride transfer protein (MTP) levels/activity are being developed in the clinic to benefit patients who are unable to reach target LDL-C levels with maximally tolerated lipid-lowering drugs. To compare and contrast the metabolic consequences of reducing these targets, murine-specific apoB or MTP antisense oligonucleotides (ASOs) were administered to chow-fed and high fat-fed C57BL/6 or to chow-fed and Western diet-fed LDLr−/− mice for periods ranging from 2 to 12 weeks, and detailed analyses of various factors affecting fatty acid metabolism were performed. Administration of these drugs significantly reduced target hepatic mRNA and protein, leading to similar reductions in hepatic VLDL/triglyceride secretion. MTP ASO treatment consistently led to increases in hepatic triglyceride accumulation and biomarkers of hepatotoxicity relative to apoB ASO due in part to enhanced expression of peroxisome proliferator activated receptor γ target genes and the inability to reduce hepatic fatty acid synthesis. Thus, although both drugs effectively lowered LDL-C levels in mice, the apoB ASO produced a more positive liver safety profile. PMID:23220583

  16. Genome-wide map of regulatory interactions in the human genome

    PubMed Central

    Heidari, Nastaran; Phanstiel, Douglas H.; He, Chao; Grubert, Fabian; Jahanbani, Fereshteh; Kasowski, Maya; Zhang, Michael Q.

    2014-01-01

    Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer–promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus. PMID:25228660

  17. Genome-wide map of regulatory interactions in the human genome.

    PubMed

    Heidari, Nastaran; Phanstiel, Douglas H; He, Chao; Grubert, Fabian; Jahanbani, Fereshteh; Kasowski, Maya; Zhang, Michael Q; Snyder, Michael P

    2014-12-01

    Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer-promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus. © 2014 Heidari et al.; Published by Cold Spring Harbor Laboratory Press.

  18. Professional and Regulatory Search

    EPA Pesticide Factsheets

    Professional and Regulatory search are designed for people who use EPA web resources to do their job. You will be searching collections where information that is not relevant to Environmental and Regulatory professionals.

  19. Poisson approach to clustering analysis of regulatory sequences.

    PubMed

    Wang, Haiying; Zheng, Huiru; Hu, Jinglu

    2008-01-01

    The presence of similar patterns in regulatory sequences may aid users in identifying co-regulated genes or inferring regulatory modules. By modelling pattern occurrences in regulatory regions with Poisson statistics, this paper presents a log likelihood ratio statistics-based distance measure to calculate pair-wise similarities between regulatory sequences. We employed it within three clustering algorithms: hierarchical clustering, Self-Organising Map, and a self-adaptive neural network. The results indicate that, in comparison to traditional clustering algorithms, the incorporation of the log likelihood ratio statistics-based distance into the learning process may offer considerable improvements in the process of regulatory sequence-based classification of genes.

  20. Comparison of anterior cingulate vs. insular cortex as targets for real-time fMRI regulation during pain stimulation

    PubMed Central

    Emmert, Kirsten; Breimhorst, Markus; Bauermann, Thomas; Birklein, Frank; Van De Ville, Dimitri; Haller, Sven

    2014-01-01

    Real-time functional magnetic resonance imaging (rt-fMRI) neurofeedback allows learning voluntary control over specific brain areas by means of operant conditioning and has been shown to decrease pain perception. To further increase the effect of rt-fMRI neurofeedback on pain, we directly compared two different target regions of the pain network, notably the anterior insular cortex (AIC) and the anterior cingulate cortex (ACC). Participants for this prospective study were randomly assigned to two age-matched groups of 14 participants each (7 females per group) for AIC and ACC feedback. First, a functional localizer using block-design heat pain stimulation was performed to define the pain-sensitive target region within the AIC or ACC. Second, subjects were asked to down-regulate the BOLD activation in four neurofeedback runs during identical pain stimulation. Data analysis included task-related and functional connectivity analysis. At the behavioral level, pain ratings significantly decreased during feedback vs. localizer runs, but there was no difference between AIC and ACC groups. Concerning neuroimaging, ACC and AIC showed consistent involvement of the caudate nucleus for subjects that learned down-regulation (17/28) in both task-related and functional connectivity analysis. The functional connectivity toward the caudate nucleus is stronger for the ACC while the AIC is more heavily connected to the ventrolateral prefrontal cortex. Consequently, the ACC and AIC are suitable targets for real-time fMRI neurofeedback during pain perception as they both affect the caudate nucleus, although functional connectivity indicates that the direct connection seems to be stronger with the ACC. Additionally, the caudate, an important area involved in pain perception and suppression, could be a good rt-fMRI target itself. Future studies are needed to identify parameters characterizing successful regulators and to assess the effect of repeated rt-fMRI neurofeedback on pain

  1. Comparison of the toxicity of two chelated copper algaecides and copper sulfate to non-target fish.

    PubMed

    Closson, K R; Paul, E A

    2014-12-01

    New pesticide products are reviewed by the United States Environmental Protection Agency for possible effects to non-target aquatic organisms. The required toxicity data are for the active ingredient only, and fail to include toxicity of the mixture of other ingredients found in these pesticides. These ingredients may increase the toxicity of the active ingredient to non-target organisms. Our study compares the toxicity of two formulations of chelated copper algaecides with each other, and to a copper sulfate algaecide. We were particularly interested in the effects of a surfactant that is present in one of the formulations. We found that copper becomes less toxic to fish (e.g. fathead minnow 48-h LC50 = 0.90 mg/L) when it is chelated, providing an additional margin of safety to non-target fish compared to copper sulfate. However, inclusion of a surfactant to the formulation resulted in increased toxicity (e.g. fathead minnow 48-h LC50 = 0.30 mg/L).

  2. An objective method for bed capacity planning in a hospital department - a comparison with target ratio methods.

    PubMed

    Nguyen, J M; Six, P; Chaussalet, T; Antonioli, D; Lombrail, P; Le Beux, P

    2007-01-01

    To propose an objective approach in order to determine the number of beds required for a hospital department by considering how recruitment fluctuates over time. To compare this approach with classical bed capacity planning techniques. A simulated data-based evaluation of the impact that the variability in hospital department activity produces upon the performance of methods used for determining the number of beds required. The evaluation criteria included productive efficiency measured by the bed occupancy rate, accessibility measured by the transfer rate of patients due to lack of available beds and a proxy of clinical effectiveness, by the proportion of days during which there is no possibility for unscheduled admission. When the variability of the number of daily patients increases, the Target Occupancy Rate favors productive efficiency at the expense of accessibility and proxy clinical effectiveness. On the contrary, when the variability of the department activity is marginal, the Target Activity Rate penalizes the proxy of clinical effectiveness, and the Target Occupancy Rate underoptimizes productive efficiency. The method we propose led to a superior performance in terms of accessibility and proxy of clinical effectiveness at the expense of productive efficiency. Such a situation is suitable for intensive care units. In the case of other departments, a weighting procedure should be used to improve productive efficiency. This approach could be considered as the first step of a family of methods for quantitative healthcare planning.

  3. Variation in adverse drug reactions listed in product information for antidepressants and anticonvulsants, between the USA and Europe: a comparison review of paired regulatory documents

    PubMed Central

    Cornelius, Victoria R; Liu, Kun; Peacock, Janet; Sauzet, Odile

    2016-01-01

    Objective To compare consistency of adverse drug reaction (ADR) data in publicly available product information documents for brand drugs, between the USA and Europe. To assess the usefulness of information for prescribers and patients. Design A comparison review of product information documents for antidepressants and anticonvulsants concurrently marketed by the same pharmaceutical company in the USA and Europe. Setting For each drug, data were extracted from the US Product Inserts and the European Summary of Product Characteristics documents between 09/2013 and 01/2015. Participants Individuals contributing ADR information to product information documents. Main outcomes measures All ADRs reported in product information sections 5 and 6 (USA), and 4·4 and 4·8 (Europe). Results Twelve brand drugs—24 paired documents—were included. On average, there were 77 more ADRs reported in the USA compared with in the European product information document, with a median number of 201 ADRs (range: 65–425) and 114 (range: 56–265), respectively. More product information documents in the USA reported information on the source of evidence (10 vs 5) and risk (9 vs 5) for greater than 80% of ADRs included in the document. There was negligible information included regarding duration, severity, reversibility or recurrence of ADRs. On average, only 29% of ADR terms were reported in both paired documents. Conclusions Product information documents contained a large number of ADRs, but lacked contextual data and information important to patients and prescribers, such as duration, severity and reversibility. The ADR profile was found to be inconsistently reported between the USA and Europe, for the same drug. Identifying, selecting, summarising and presenting multidimensional harm data should be underpinned by practical evidence-based guidelines. In order for prescribers to provide considered risk-benefit advice across competing drug therapies to patients, they need access to

  4. Variation in adverse drug reactions listed in product information for antidepressants and anticonvulsants, between the USA and Europe: a comparison review of paired regulatory documents.

    PubMed

    Cornelius, Victoria R; Liu, Kun; Peacock, Janet; Sauzet, Odile

    2016-03-20

    To compare consistency of adverse drug reaction (ADR) data in publicly available product information documents for brand drugs, between the USA and Europe. To assess the usefulness of information for prescribers and patients. A comparison review of product information documents for antidepressants and anticonvulsants concurrently marketed by the same pharmaceutical company in the USA and Europe. For each drug, data were extracted from the US Product Inserts and the European Summary of Product Characteristics documents between 09/2013 and 01/2015. Individuals contributing ADR information to product information documents. All ADRs reported in product information sections 5 and 6 (USA), and 4·4 and 4·8 (Europe). Twelve brand drugs--24 paired documents--were included. On average, there were 77 more ADRs reported in the USA compared with in the European product information document, with a median number of 201 ADRs (range: 65-425) and 114 (range: 56-265), respectively. More product information documents in the USA reported information on the source of evidence (10 vs 5) and risk (9 vs 5) for greater than 80% of ADRs included in the document. There was negligible information included regarding duration, severity, reversibility or recurrence of ADRs. On average, only 29% of ADR terms were reported in both paired documents. Product information documents contained a large number of ADRs, but lacked contextual data and information important to patients and prescribers, such as duration, severity and reversibility. The ADR profile was found to be inconsistently reported between the USA and Europe, for the same drug. Identifying, selecting, summarising and presenting multidimensional harm data should be underpinned by practical evidence-based guidelines. In order for prescribers to provide considered risk-benefit advice across competing drug therapies to patients, they need access to comprehensible and reliable ADR information. Published by the BMJ Publishing Group Limited

  5. Drug lag and key regulatory barriers in the emerging markets.

    PubMed

    Wileman, Harriet; Mishra, Arun

    2010-04-01

    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.

  6. 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

  7. Comparison of virtual reality versus physical reality on movement characteristics of persons with Parkinson's disease: effects of moving targets.

    PubMed

    Wang, Ching-Yi; Hwang, Wen-Juh; Fang, Jing-Jing; Sheu, Ching-Fan; Leong, Iat-Fai; Ma, Hui-Ing

    2011-08-01

    To compare the performance of reaching for stationary and moving targets in virtual reality (VR) and physical reality in persons with Parkinson's disease (PD). A repeated-measures design in which all participants reached in physical reality and VR under 5 conditions: 1 stationary ball condition and 4 conditions with the ball moving at different speeds. University research laboratory. Persons with idiopathic PD (n=29) and age-matched controls (n=25). Not applicable. Success rates and kinematics of arm movement (movement time, amplitude of peak velocity, and percentage of movement time for acceleration phase). In both VR and physical reality, the PD group had longer movement time (P<.001) and lower peak velocity (P<.001) than the controls when reaching for stationary balls. When moving targets were provided, the PD group improved more than the controls did in movement time (P<.001) and peak velocity (P<.001), and reached a performance level similar to that of the controls. Except for the fastest moving ball condition (0.5-s target viewing time), which elicited worse performance in VR than in physical reality, most cueing conditions in VR elicited performance generally similar to those in physical reality. Although slower than the controls when reaching for stationary balls, persons with PD increased movement speed in response to fast moving balls in both VR and physical reality. This suggests that with an appropriate choice of cueing speed, VR is a promising tool for providing visual motion stimuli to improve movement speed in persons with PD. More research on the long-term effect of this type of VR training program is needed. Copyright © 2011 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  8. Trunk-arm coordination in reaching for moving targets in people with Parkinson's disease: comparison between virtual and physical reality.

    PubMed

    Ma, Hui-Ing; Hwang, Wen-Juh; Wang, Ching-Yi; Fang, Jing-Jing; Leong, Iat-Fai; Wang, Tsui-Ying

    2012-10-01

    We used a trunk-assisted prehension task to examine the effect of task (reaching for stationary vs. moving targets) and environmental constraints (virtual reality [VR] vs. physical reality) on the temporal control of trunk and arm motions in people with Parkinson's disease (PD). Twenty-four participants with PD and 24 age-matched controls reached for and grasped a ball that was either stationary or moving along a ramp 120% of arm length away. In a similar VR task, participants reached for a virtual ball that was either stationary or moving. Movement speed was measured as trunk and arm movement times (MTs); trunk-arm coordination was measured as onset interval and offset interval between trunk and arm motions, as well as a summarized index-desynchrony score. In both VR and physical reality, the PD group had longer trunk and arm MTs than the control group when reaching for stationary balls (p<.001). When reaching for moving balls in VR and physical reality, however, the PD group had lower trunk and arm MTs, onset intervals, and desynchrony scores (p<.001). For the PD group, VR induced shorter trunk MTs, shorter offset intervals, and lower desynchrony scores than did physical reality when reaching for moving balls (p<.001). These findings suggest that using real moving targets in trunk-assisted prehension tasks improves the speed and synchronization of trunk and arm motions in people with PD, and that using virtual moving targets may induce a movement termination strategy different from that used in physical reality.

  9. Comparison of the nutritional content of products, with and without nutrient claims, targeted at children in Brazil.

    PubMed

    Rodrigues, Vanessa Mello; Rayner, Mike; Fernandes, Ana Carolina; Oliveira, Renata Carvalho de; Proença, Rossana Pacheco da Costa; Fiates, Giovanna Medeiros Rataichesck

    2016-06-01

    Many children's food products highlight positive attributes on their front-of-package labels in the form of nutrient claims. This cross-sectional study investigated all retailed packaged foods (n 5620) in a major Brazilian supermarket, in order to identify the availability of products targeted at children, and to compare the nutritional content of products with and without nutrient claims on labels. Data on energy, carbohydrate, protein, fibre, Na and total and SFA content, along with the presence and type of nutrient claims, were obtained in-store from labels of all products. Products targeted at children were identified, divided into eight food groups and compared for their nutritional content per 100 g/ml and the presence of nutrient claims using the Mann-Whitney U test (P<0·05). Of the 535 food products targeted at children (9·5 % of all products), 270 (50·5 %) displayed nutrient claims on their labels. Children's products with nutrient claims had either a similar or worse nutritional content than their counterparts without nutrient claims. The major differences among groups were found in Group 8 (e.g. sauces and ready meals), in which children's products bearing nutrient claims had higher energy, carbohydrate, Na and total and SFA content per 100 g/ml than products without nutrient claims (P<0·05). This suggests that, to prevent misleading parents who are seeking healthier products for their children, the regulation on the use of nutrient claims should be revised, so that only products with appropriate nutrient profiles are allowed to display them.

  10. Implant-assisted magnetic drug targeting in permeable microvessels: Comparison of two-fluid statistical transport model with experiment

    NASA Astrophysics Data System (ADS)

    ChiBin, Zhang; XiaoHui, Lin; ZhaoMin, Wang; ChangBao, Wang

    2017-03-01

    In experiments and theoretical analyses, this study examines the capture efficiency (CE) of magnetic drug carrier particles (MDCPs) for implant-assisted magnetic drug targeting (IA-MDT) in microvessels. It also proposes a three-dimensional statistical transport model of MDCPs for IA-MDT in permeable microvessels, which describes blood flow by the two-fluid (Casson and Newtonian) model. The model accounts for the permeable effect of the microvessel wall and the coupling effect between the blood flow and tissue fluid flow. The MDCPs move randomly through the microvessel, and their transport state is described by the Boltzmann equation. The regulated changes and factors affecting the CE of the MDCPs in the assisted magnetic targeting were obtained by solving the theoretical model and by experimental testing. The CE was negatively correlated with the blood flow velocity, and positively correlated with the external magnetic field intensity and microvessel permeability. The predicted CEs of the MDCPs were consistent with the experimental results. Additionally, under the same external magnetic field, the predicted CE was 5-8% higher in the IA-MDT model than in the model ignoring the permeability effect of the microvessel wall.

  11. Targeted gene delivery to the enteric nervous system using AAV: a comparison across serotypes and capsid mutants.

    PubMed

    Benskey, Matthew J; Kuhn, Nathan C; Galligan, James J; Garcia, Joanna; Boye, Shannon E; Hauswirth, William W; Mueller, Christian; Boye, Sanford L; Manfredsson, Fredric P

    2015-03-01

    Recombinant adeno-associated virus (AAV) vectors are one of the most widely used gene transfer systems in research and clinical trials. AAV can transduce a wide range of biological tissues, however to date, there has been no investigation on targeted AAV transduction of the enteric nervous system (ENS). Here, we examined the efficiency, tropism, spread, and immunogenicity of AAV transduction in the ENS. Rats received direct injections of various AAV serotypes expressing green fluorescent protein (GFP) into the descending colon. AAV serotypes tested included; AAV 1, 2, 5, 6, 8, or 9 and the AAV2 and AAV8 capsid mutants, AAV2-Y444F, AAV2-tripleY-F, AAV2-tripleY-F+T-V, AAV8-Y733F, and AAV8-doubeY-F+T-V. Transduction, as determined by GFP-positive cells, occurred in neurons and enteric glia within the myenteric and submucosal plexuses of the ENS. AAV6 and AAV9 showed the highest levels of transduction within the ENS. Transduction efficiency scaled with titer and time, was translated to the murine ENS, and produced no vector-related immune response. A single injection of AAV into the colon covered an area of ~47 mm(2). AAV9 primarily transduced neurons, while AAV6 transduced enteric glia and neurons. This is the first report on targeted AAV transduction of neurons and glia in the ENS.

  12. Comparison of thermal (FLIR) and television images. [in natural and man-made target detection and identification

    NASA Technical Reports Server (NTRS)

    Brickner, Michael S.; Staveland, Lowell E.

    1989-01-01

    The human eye is sensitive to electromagnetic radiation in the 0.4 to 0.7 micron band (light). Thermal imaging (TI) systems are sensitive to heat radiation in the infrared band (3-5 or 8-14 microns) and are capable of transforming the distribution of relative temperatures in a scene into a visible TV image. The present experiment was designed to investigate the impact of the difference between TIs and regular TV images on the detection and identification of natural and man-made targets. Parallel TV and TI videotapes were recorded during helicopter flights. Fifteen subjects who viewed both the TV and the TI images (separately), were asked to detect predefined targets and to identify features pointed out to them by the experimenter. In general, performance with TVs was superior to performance with TIs in terms of response times and errors. However, subjects required significantly less time to detect man-made objects with TIs than with TVs. The correlation between the performance of the same task with the two kinds of images was very low. The results are discussed in terms of image quality and in terms of humans' internal representations of natural categories.

  13. Photosensitizer delivery to vulnerable atherosclerotic plaque: comparison of macrophage-targeted conjugate versus free chlorin(e6).

    PubMed

    Tawakol, Ahmed; Castano, Ana P; Anatelli, Florencia; Bashian, Gregory; Stern, Jeremy; Zahra, Touqir; Gad, Faten; Chirico, Stephanie; Ahmadi, Atosa; Fischman, Alan J; Muller, James E; Hamblin, Michael R

    2006-01-01

    We have previously shown that a conjugate (MA-ce6) between maleylated serum albumin and the photosensitizer chlorin(e6) (ce6) is targeted in vitro to macrophages via class A scavenger receptors. We now report on the ability of this conjugate to localize in macrophage-rich atherosclerotic plaques in vivo. Both the conjugate and the free photosensitizer ce6 are studied after injection into New Zealand White rabbits that are rendered atherosclerotic by a combination of aortic endothelial injury and cholesterol feeding into normal rabbits. Rabbits are sacrificed at 6 and 24 h after injection and intravascular fluorescence spectroscopy is carried out by fiber-based fluorimetry in intact blood-filled arteries. Surface spectrofluorimetry of numbered excised aortic segments together with injured and normal iliac arteries is carried out, and quantified ce6 content by subsequent extraction and quantitative fluorescence determination of the arterial segments and also of nontarget organs. There is good agreement between the various techniques for quantifying ce6 localization, and high contrast between arteries from atherosclerotic and normal rabbits is obtained. Fluorescence correlates with the highest burden of plaque in the aorta and the injured iliac artery. The highest accumulation in plaques is obtained using MA-ce6 at 24 h. Free ce6 gives better accumulation at 6 h compared to 24 h. The liver, spleen, lung, and gall bladder have the highest uptake in nontarget organs. Macrophage-targeted photosensitizer conjugates may have applications in both detecting and treating inflamed vulnerable plaque.

  14. Targeting GTPases in Parkinson’s disease: comparison to the historic path of kinase drug discovery and perspectives

    PubMed Central

    Hong, Lin; Sklar, Larry A.

    2014-01-01

    Neurological diseases have placed heavy social and financial burdens on modern society. As the life expectancy of humans is extended, neurological diseases, such as Parkinson’s disease, have become increasingly common among senior populations. Although the enigmas of Parkinson’s diseases await resolution, more vivid pictures on the cause, progression, and control of the illness are emerging after years of research. On the molecular level, GTPases are implicated in the etiology of Parkinson’s disease and are rational pharmaceutical targets for their control. However, targeting individual GTPases, which belong to a superfamily of proteins containing multiple members with a conserved guanine nucleotide binding domain, has proven to be challenging. In contrast, pharmaceutical pursuit of inhibition of kinases, which constitute another superfamily of proteins with more than 500 members, has been fairly successful. We reviewed the breakthroughs in the history of kinase drug discovery to provide guidance for the GTPase field. We summarize recent progress made in the regulation of GTPase activity. We also present an efficient and cost effective approach to drug screening, which uses multiplex flow cytometry and mixture-based positional scanning libraries. These methods allow simultaneous measurements of both the activity and the selectivity of the screened library. Several GTPase activator clusters were identified which showed selectivity against different GTPase subfamilies. While the clusters need to be further deconvoluted to identify individual active compounds, the method described here and the structure information gathered create a foundation for further developments to build upon. PMID:24926233

  15. A preliminary controlled comparison of programs designed to reduce risk of eating disorders targeting perfectionism and media literacy.

    PubMed

    Wilksch, Simon M; Durbridge, Mitchell R; Wade, Tracey D

    2008-08-01

    The primary objective was to compare the efficacy of two eight-lesson programs, targeting perfectionism and media literacy compared to control classes in reducing eating disorder risk. Students from six classes (N = 127, mean age 15.0 years, SD 0.4) and two schools participated. Linear mixed-model analyses were conducted by group (3: perfectionism, media literacy, control), time (2: postprogram, 3-month follow-up) and eating disorder risk status (2: high, low), with baseline observations included as a covariate. An interaction effect favoring the perfectionism program at 3-month follow-up was found for concern over mistakes (effect size 0.45). A main effect for group, also favoring the perfectionism program, was found for personal standards (effect size 0.44). High-risk participants (i.e., those with high levels of shape and weight concern at baseline) benefited most from the perfectionism program with reliable change indices indicating favorable rates of improvement beyond chance on all of the variables, whereas the media literacy and control participants experienced a comparable rate of change during the course of the study. Targeting perfectionism represents a promising prevention option that requires further investigation in children of mid-adolescence age, and further investigation is required to determine the demographic most likely to benefit from media literacy.

  16. Photosensitizer delivery to vulnerable atherosclerotic plaque: comparison of macrophage-targeted conjugate versus free chlorine(e6)

    NASA Astrophysics Data System (ADS)

    Tawakol, Ahmed; Castano, Ana P.; Anatelli, Florencia; Bashian, Gregory; Stern, Jeremy; Zahra, Touqir; Gad, Faten; Chirico, Stephanie; Ahmadi, Atosa; Fischman, Alan J.; Muller, James E.; Hamblin, Michael R.

    2006-03-01

    We have previously shown that a conjugate (MA-ce6) between maleylated serum albumin and the photosensitizer chlorin(e6) (ce6) is targeted in vitro to macrophages via class A scavenger receptors. We now report on the ability of this conjugate to localize in macrophage-rich atherosclerotic plaques in vivo. Both the conjugate and the free photosensitizer ce6 are studied after injection into New Zealand White rabbits that are rendered atherosclerotic by a combination of aortic endothelial injury and cholesterol feeding into normal rabbits. Rabbits are sacrificed at 6 and 24 h after injection and intravascular fluorescence spectroscopy is carried out by fiber-based fluorimetry in intact blood-filled arteries. Surface spectrofluorimetry of numbered excised aortic segments together with injured and normal iliac arteries is carried out, and quantified ce6 content by subsequent extraction and quantitative fluorescence determination of the arterial segments and also of nontarget organs. There is good agreement between the various techniques for quantifying ce6 localization, and high contrast between arteries from atherosclerotic and normal rabbits is obtained. Fluorescence correlates with the highest burden of plaque in the aorta and the injured iliac artery. The highest accumulation in plaques is obtained using MA-ce6 at 24 h. Free ce6 gives better accumulation at 6 h compared to 24 h. The liver, spleen, lung, and gall bladder have the highest uptake in nontarget organs. Macrophage-targeted photosensitizer conjugates may have applications in both detecting and treating inflamed vulnerable plaque.

  17. Comparison of thermal (FLIR) and television images. [in natural and man-made target detection and identification

    NASA Technical Reports Server (NTRS)

    Brickner, Michael S.; Staveland, Lowell E.

    1989-01-01

    The human eye is sensitive to electromagnetic radiation in the 0.4 to 0.7 micron band (light). Thermal imaging (TI) systems are sensitive to heat radiation in the infrared band (3-5 or 8-14 microns) and are capable of transforming the distribution of relative temperatures in a scene into a visible TV image. The present experiment was designed to investigate the impact of the difference between TIs and regular TV images on the detection and identification of natural and man-made targets. Parallel TV and TI videotapes were recorded during helicopter flights. Fifteen subjects who viewed both the TV and the TI images (separately), were asked to detect predefined targets and to identify features pointed out to them by the experimenter. In general, performance with TVs was superior to performance with TIs in terms of response times and errors. However, subjects required significantly less time to detect man-made objects with TIs than with TVs. The correlation between the performance of the same task with the two kinds of images was very low. The results are discussed in terms of image quality and in terms of humans' internal representations of natural categories.

  18. Comparison of Sputum and Nasopharyngeal Aspirate Samples and of the PCR Gene Targets lytA and Spn9802 for Quantitative PCR for Rapid Detection of Pneumococcal Pneumonia

    PubMed Central

    Herrmann, Björn; Abdeldaim, Guma; Olcén, Per; Holmberg, Hans; Mölling, Paula

    2014-01-01

    We aimed to compare sputum and nasopharyngeal aspirate (NpA) samples and the PCR gene targets lytA and Spn9802 in quantitative PCR (qPCR) assays for rapid detection of pneumococcal etiology in community-acquired pneumonia (CAP). Seventy-eight adult patients hospitalized for radiologically confirmed CAP had both good-quality sputum and NpA specimens collected at admission. These samples were subjected to lytA qPCR and Spn9802 qPCR assays with analytical times of <3 h. Thirty-two patients had CAP with a pneumococcal etiology, according to conventional diagnostic criteria. The following qPCR positivity rates were noted in CAP cases with and without pneumococcal etiology: 96% and 15% (sputum lytA assay), 96% and 17% (sputum Spn9802 assay), 81% and 11% (NpA lytA assay), and 81% and 20% (NpA Spn9802 assay), respectively. The mean lytA and Spn9802 DNA levels were significantly higher in qPCR-positive sputum samples from cases with pneumococcal etiology than in qPCR-positive sputum samples from CAP cases without pneumococcal etiology or qPCR-positive NpA samples from cases with pneumococcal etiology (P < 0.02 for all comparisons). For detection of pneumococcal etiology, receiver operating characteristic curve analysis showed that sputum specimens were superior to NpA specimens as the sample type (P < 0.02 for both gene targets) and lytA tended to be superior to Spn9802 as the gene target. The best-performing test, the sputum lytA qPCR assay, showed high sensitivity (94%) and specificity (96%) with a cutoff value of 105 DNA copies/ml. In CAP patients with good sputum production, this test has great potential to be used for the rapid detection of pneumococcal etiology and to target penicillin therapy. PMID:24153121

  19. Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks

    PubMed Central

    Yan, Koon-Kiu; Fang, Gang; Bhardwaj, Nitin; Alexander, Roger P.; Gerstein, Mark

    2010-01-01

    The genome has often been called the operating system (OS) for a living organism. A computer OS is described by a regulatory control network termed the call graph, which is analogous to the transcriptional regulatory network in a cell. To apply our firsthand knowledge of the architecture of software systems to understand cellular design principles, we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology and evolution. We show that both networks have a fundamentally hierarchical layout, but there is a key difference: The transcriptional regulatory network possesses a few global regulators at the top and many targets at the bottom; conversely, the call graph has many regulators controlling a small set of generic functions. This top-heavy organization leads to highly overlapping functional modules in the call graph, in contrast to the relatively independent modules in the regulatory network. We further develop a way to measure evolutionary rates comparably between the two networks and explain this difference in terms of network evolution. The process of biological evolution via random mutation and subsequent selection tightly constrains the evolution of regulatory network hubs. The call graph, however, exhibits rapid evolution of its highly connected generic components, made possible by designers’ continual fine-tuning. These findings stem from the design principles of the two systems: robustness for biological systems and cost effectiveness (reuse) for software systems. PMID:20439753

  20. Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.

    PubMed

    Yan, Koon-Kiu; Fang, Gang; Bhardwaj, Nitin; Alexander, Roger P; Gerstein, Mark

    2010-05-18

    The genome has often been called the operating system (OS) for a living organism. A computer OS is described by a regulatory control network termed the call graph, which is analogous to the transcriptional regulatory network in a cell. To apply our firsthand knowledge of the architecture of software systems to understand cellular design principles, we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology and evolution. We show that both networks have a fundamentally hierarchical layout, but there is a key difference: The transcriptional regulatory network possesses a few global regulators at the top and many targets at the bottom; conversely, the call graph has many regulators controlling a small set of generic functions. This top-heavy organization leads to highly overlapping functional modules in the call graph, in contrast to the relatively independent modules in the regulatory network. We further develop a way to measure evolutionary rates comparably between the two networks and explain this difference in terms of network evolution. The process of biological evolution via random mutation and subsequent selection tightly constrains the evolution of regulatory network hubs. The call graph, however, exhibits rapid evolution of its highly connected generic components, made possible by designers' continual fine-tuning. These findings stem from the design principles of the two systems: robustness for biological systems and cost effectiveness (reuse) for software systems.

  1. Interrogating transcriptional regulatory sequences in Tol2-mediated Xenopus transgenics.

    PubMed

    Loots, Gabriela G; Bergmann, Anne; Hum, Nicholas R; Oldenburg, Catherine E; Wills, Andrea E; Hu, Na; Ovcharenko, Ivan; Harland, Richard M

    2013-01-01

    Identifying gene regulatory elements and their target genes in vertebrates remains a significant challenge. It is now recognized that transcriptional regulatory sequences are critical in orchestrating dynamic controls of tissue-specific gene expression during vertebrate development and in adult tissues, and that these elements can be positioned at great distances in relation to the promoters of the genes they control. While significant progress has been made in mapping DNA binding regions by combining chromatin immunoprecipitation and next generation sequencing, functional validation remains a limiting step in improving our ability to correlate in silico predictions with biological function. We recently developed a computational method that synergistically combines genome-wide gene-expression profiling, vertebrate genome comparisons, and transcription factor binding-site analysis to predict tissue-specific enhancers in the human genome. We applied this method to 270 genes highly expressed in skeletal muscle and predicted 190 putative cis-regulatory modules. Furthermore, we optimized Tol2 transgenic constructs in Xenopus laevis to interrogate 20 of these elements for their ability to function as skeletal muscle-specific transcriptional enhancers during embryonic development. We found 45% of these elements expressed only in the fast muscle fibers that are oriented in highly organized chevrons in the Xenopus laevis tadpole. Transcription factor binding site analysis identified >2 Mef2/MyoD sites within ~200 bp regions in 6 of the validated enhancers, and systematic mutagenesis of these sites revealed that they are critical for the enhancer function. The data described herein introduces a new reporter system suitable for interrogating tissue-specific cis-regulatory elements which allows monitoring of enhancer activity in real time, throughout early stages of embryonic development, in Xenopus.

  2. Interrogating Transcriptional Regulatory Sequences in Tol2-Mediated Xenopus Transgenics

    PubMed Central

    Loots, Gabriela G.; Bergmann, Anne; Hum, Nicholas R.; Oldenburg, Catherine E.; Wills, Andrea E.; Hu, Na; Ovcharenko, Ivan; Harland, Richard M.

    2013-01-01

    Identifying gene regulatory elements and their target genes in vertebrates remains a significant challenge. It is now recognized that transcriptional regulatory sequences are critical in orchestrating dynamic controls of tissue-specific gene expression during vertebrate development and in adult tissues, and that these elements can be positioned at great distances in relation to the promoters of the genes they control. While significant progress has been made in mapping DNA binding regions by combining chromatin immunoprecipitation and next generation sequencing, functional validation remains a limiting step in improving our ability to correlate in silico predictions with biological function. We recently developed a computational method that synergistically combines genome-wide gene-expression profiling, vertebrate genome comparisons, and transcription factor binding-site analysis to predict tissue-specific enhancers in the human genome. We applied this method to 270 genes highly expressed in skeletal muscle and predicted 190 putative cis-regulatory modules. Furthermore, we optimized Tol2 transgenic constructs in Xenopus laevis to interrogate 20 of these elements for their ability to function as skeletal muscle-specific transcriptional enhancers during embryonic development. We found 45% of these elements expressed only in the fast muscle fibers that are oriented in highly organized chevrons in the Xenopus laevis tadpole. Transcription factor binding site analysis identified >2 Mef2/MyoD sites within ∼200 bp regions in 6 of the validated enhancers, and systematic mutagenesis of these sites revealed that they are critical for the enhancer function. The data described herein introduces a new reporter system suitable for interrogating tissue-specific cis-regulatory elements which allows monitoring of enhancer activity in real time, throughout early stages of embryonic development, in Xenopus. PMID:23874664

  3. Comparison of planning target volumes based on three-dimensional and four-dimensional CT imaging of thoracic esophageal cancer.

    PubMed

    Wang, Wei; Li, Jianbin; Zhang, Yingjie; Shao, Qian; Xu, Min; Fan, Tingyong; Wang, Jinzhi

    2016-01-01

    To investigate the definition of planning target volumes (PTVs) based on four-dimensional computed tomography (4DCT) compared with conventional PTV definition and PTV definition using asymmetrical margins for thoracic primary esophageal cancer. Forty-three patients with esophageal cancer underwent 3DCT and 4DCT simulation scans during free breathing. The motions of primary tumors located in the proximal (group A), middle (group B), and distal (group C) thoracic esophagus were obtained from the 4DCT scans. PTV3D was defined on 3DCT using the tumor motion measured based on 4DCT, PTV conventional (PTVconv) was defined on 3DCT by adding a 1.0 cm margin to the clinical target volume, and PTV4D was defined as the union of the target volumes contoured on the ten phases of the 4DCT images. The centroid positions, volumetric differences, and dice similarity coefficients were evaluated for all PTVs. The median centroid shifts between PTV3D and PTV4D and between PTVconv and PTV4D in all three dimensions were <0.3 cm for the three groups. The median size ratios of PTV4D to PTV3D were 0.80, 0.88, and 0.71, and PTV4D to PTVconv were 0.67, 0.73, and 0.76 (χ (2)=-3.18, -2.98, and -3.06; P=0.001, 0.003, and 0.002) for groups A, B, and C, respectively. The dice similarity coefficients were 0.87, 0.90, and 0.81 between PTV4D and PTV3D and 0.80, 0.84, and 0.83 between PTV4D and PTVconv (χ (2) =-3.18, -2.98, and -3.06; P=0.001, 0.003, and 0.002) for groups A, B, and C, respectively. The difference between the degree of inclusion of PTV4D in PTV3D and that of PTV4D in PTVconv was <2% for all groups. Compared with PTVconv, the amount of irradiated normal tissue for PTV3D was decreased by 11.81% and 11.86% in groups A and B, respectively, but was increased by 2.93% in group C. For proximal and middle esophageal cancer, 3DCT-based PTV using asymmetrical margins provides good coverage of PTV4D; however, for distal esophageal cancer, 3DCT-based PTV using conventional margins provides ideal

  4. Petrology and geochemistry of target rocks from the Bosumtwi impact structure, Ghana, and comparison with Ivory Coast tektites

    NASA Astrophysics Data System (ADS)

    Koeberl, Christian; Reimold, Wolf Uwe; Blum, Joel D.; Chamberlain, C. Page

    1998-06-01

    The 10.5 km diameter Bosumtwi crater in Ghana, West Africa, is the most likely source crater for the Ivory Coast tektites, as the tektites and the crater have the same age (1.07 Ma), and there are close similarities between the isotopic and chemical compositions of the tektites and crater rocks. The crater is excavated in 2.1-2.2 Ga old metasediments and metavolcanics of the Birimian Supergroup. Here we present the first integrated petrographic and geochemical study of rocks from the Bosumtwi impact crater. A variety of target rocks from the Bosumtwi impact structure were selected to represent the major rock types that have been described before, resulting in four groups: shale, phyllite-graywacke, and two different types of granites (from dispersed dikes and from the so-called Pepiakese intrusion at the northeastern side of the crater). These rocks were analyzed for their major and trace element composition and their petrographic characteristics. In addition, representative samples were also analyzed for their O, Sr, and Nd isotopic compositions. The target rocks do not show any unambiguous evidence of shock metamorphism (i.e., planar deformation features, PDFs). Distinct impact-characteristic shock effects (PDFs) were identified only in clasts within suevite-derived melt fragments. The compositional range of the target rocks is significantly wider than that of the Ivory Coast tektites, but overlap the tektite compositions. A best-fit line for the Bosumtwi crater rocks in a Rb-Sr isotope evolution diagram yields an "age" of 1.98 Ga, and an initial 87Sr/ 86Sr ratio of 0.701, which is close to results previously obtained for granitoid intrusions in the Birimian of Ghana. Our Nd isotopic data yield depleted mantle model ages ranging from 2.16 to 2.64 Ga, and ɛ Nd values of -17.2 to -25.9‰. Harmonic least-squares (HMX) mixing calculations were able to reproduce the composition of Ivory Coast tektites from a mixture of Bosumtwi country rocks that include about 70

  5. Comparison of radiofrequency body coils for MRI at 3 Tesla: a simulation study using parallel transmission on various anatomical targets

    PubMed Central

    Wu, Xiaoping; Zhang, Xiaotong; Tian, Jinfeng; Schmitter, Sebastian; Hanna, Brian; Strupp, John; Pfeuffer, Josef; Hamm, Michael; Wang, Dingxin; Nistler, Juergen; He, Bin; Vaughan, J. Thomas; Ugurbil, Kamil; Van de Moortele, Pierre-Francois

    2015-01-01

    The performance of multichannel transmit coil layouts and parallel transmission (pTx) radiofrequency (RF) pulse design was evaluated with respect to transmit B1 (B1+) homogeneity and Specific Absorption Rate (SAR) at 3 Tesla for a whole body coil. Five specific coils were modeled and compared: a 32-rung birdcage body coil (driven either in a fixed quadrature mode or a two-channel transmit mode), two single-ring stripline arrays (with either 8 or 16 elements), and two multi-ring stripline arrays (with 2 or 3 identical rings, stacked in the z-axis and each comprising eight azimuthally distributed elements). Three anatomical targets were considered, each defined by a 3D volume representative of a meaningful region of interest (ROI) in routine clinical applications. For a given anatomical target, global or local SAR controlled pTx pulses were designed to homogenize RF excitation within the ROI. At the B1+ homogeneity achieved by the quadrature driven birdcage design, pTx pulses with multichannel transmit coils achieved up to ~8 fold reduction in local and global SAR. When used for imaging head and cervical spine or imaging thoracic spine, the double-ring array outperformed all coils including the single-ring arrays. While the advantage of the double-ring array became much less pronounced for pelvic imaging with a substantially larger ROI, the pTx approach still provided significant gains over the quadrature birdcage coil. For all design scenarios, using the 3-ring array did not necessarily improve the RF performance. Our results suggest that pTx pulses with multichannel transmit coils can reduce local and global SAR substantially for body coils while attaining improved B1+ homogeneity, particularly for a “z-stacked” double-ring design with coil elements arranged on two transaxial rings. PMID:26332290

  6. Comparison of inert supports in laser desorption/ionization mass spectrometry of peptides: pencil lead, porous silica gel, DIOS-chip and NALDI target.

    PubMed

    Shenar, Nawar; Cantel, Sonia; Martinez, Jean; Enjalbal, Christine

    2009-08-01

    In the search for alternative inert surfaces replacing silicon chips in Desorption/Ionization On porous Silicon (DIOS)-like mass spectrometry analyses, nanostructured silicon-based NALDI chips were evaluated in Laser Desorption/Ionization (LDI) of peptides. Comparisons were made using commercially available DIOS chips (MassPREP-DIOS-target), amorphous carbon powder from lead pencil and porous silica gel used for chromatographic purposes as reference supports. A set of synthetic model peptides presenting variable amino acid sequences of various lengths was analyzed under all conditions. The LDI responses of the four 'matrix-free' techniques were compared, especially in terms of peptide detection sensitivity and overall experiment robustness. Copyright (c) 2009 John Wiley & Sons, Ltd.

  7. Modeling of hysteresis in gene regulatory networks.

    PubMed

    Hu, J; Qin, K R; Xiang, C; Lee, T H

    2012-08-01

    Hysteresis, observed in many gene regulatory networks, has a pivotal impact on biological systems, which enhances the robustness of cell functions. In this paper, a general model is proposed to describe the hysteretic gene regulatory network by combining the hysteresis component and the transient dynamics. The Bouc-Wen hysteresis model is modified to describe the hysteresis component in the mammalian gene regulatory networks. Rigorous mathematical analysis on the dynamical properties of the model is presented to ensure the bounded-input-bounded-output (BIBO) stability and demonstrates that the original Bouc-Wen model can only generate a clockwise hysteresis loop while the modified model can describe both clockwise and counter clockwise hysteresis loops. Simulation studies have shown that the hysteresis loops from our model are consistent with the experimental observations in three mammalian gene regulatory networks and two E.coli gene regulatory networks, which demonstrate the ability and accuracy of the mathematical model to emulate natural gene expression behavior with hysteresis. A comparison study has also been conducted to show that this model fits the experiment data significantly better than previous ones in the literature. The successful modeling of the hysteresis in all the five hysteretic gene regulatory networks suggests that the new model has the potential to be a unified framework for modeling hysteresis in gene regulatory networks and provide better understanding of the general mechanism that drives the hysteretic function.

  8. Performance Scores in General Practice: A Comparison between the Clinical versus Medication-Based Approach to Identify Target Populations

    PubMed Central

    Saint-Lary, Olivier; Boisnault, Philippe; Naiditch, Michel; Szidon, Philippe; Duhot, Didier; Bourgueil, Yann; Pelletier-Fleury, Nathalie

    2012-01-01

    Context From one country to another, the pay-for-performance mechanisms differ on one significant point: the identification of target populations, that is, populations which serve as a basis for calculating the indicators. The aim of this study was to compare clinical versus medication-based identification of populations of patients with diabetes and hypertension over the age of 50 (for men) or 60 (for women), and any consequences this may have on the calculation of P4P indicators. Methods A comparative, retrospective, observational study was carried out with clinical and prescription data from a panel of general practitioners (GPs), the Observatory of General Medicine (OMG) for the year 2007. Two indicators regarding the prescription for statins and aspirin in these populations were calculated. Results We analyzed data from 21.690 patients collected by 61 GPs via electronic medical files. Following the clinical-based approach, 2.278 patients were diabetic, 8,271 had hypertension and 1.539 had both against respectively 1.730, 8.511 and 1.304 following the medication-based approach (% agreement = 96%, kappa = 0.69). The main reasons for these differences were: forgetting to code the morbidities in the clinical approach, not taking into account the population of patients who were given life style and diet rules only or taking into account patients for whom morbidities other than hypertension could justify the use of antihypertensive drugs in the medication-based approach. The mean (confidence interval) per doctor was 33.7% (31.5–35.9) for statin indicator and 38.4% (35.4–41.4) for aspirin indicator when the target populations were identified on the basis of clinical criteria whereas they were 37.9% (36.3–39.4) and 43.8% (41.4–46.3) on the basis of treatment criteria. Conclusion The two approaches yield very “similar” scores but these scores cover different realities and offer food for thought on the possible usage of these indicators in the

  9. Targeted delivery of a model immunomodulator to the lymphatic system: comparison of alkyl ester versus triglyceride mimetic lipid prodrug strategies.

    PubMed

    Han, Sifei; Quach, Tim; Hu, Luojuan; Wahab, Anisa; Charman, William N; Stella, Valentino J; Trevaskis, Natalie L; Simpson, Jamie S; Porter, Christopher J H

    2014-03-10

    A lipophilic prodrug approach has been used to promote the delivery of a model immunomodulator, mycophenolic acid (MPA), to the lymphatic system after oral administration. Lymphatic transport was employed to facilitate enhanced drug uptake into lymphocytes, as recent studies demonstrate that targeted drug delivery to lymph resident lymphocytes may enhance immunomodulatory effects. Two classes of lymph-directing prodrugs were synthesised. Alkyl chain derivatives (octyl mycophenolate, MPA-C8E; octadecyl mycophenolate, MPA-C18E; and octadecyl mycophenolamide, MPA-C18AM), to promote passive partitioning into lipids in lymphatic transport pathways, and a triglyceride mimetic prodrug (1,3-dipalmitoyl-2-mycophenoloyl glycerol, 2-MPA-TG) to facilitate metabolic integration into triglyceride deacylation-reacylation pathways. Lymphatic transport, lymphocyte uptake and plasma pharmacokinetics were assessed in mesenteric lymph and carotid artery cannulated rats following intraduodenal infusion of lipid-based formulations containing MPA or MPA prodrugs. Patterns of prodrug hydrolysis in rat digestive fluid, and cellular re-esterification in vivo, were evaluated to examine the mechanisms responsible for lymphatic transport. Poor enzyme stability and low absorption appeared to limit lymphatic transport of the alkyl derivatives, although two of the three alkyl chain prodrugs - MPA-C18AM (6-fold) and MPA-C18E (13-fold) still increased lymphatic drug transport when compared to MPA. In contrast, 2-MPA-TG markedly increased lymphatic drug transport (80-fold) and drug concentrations in lymphocytes (103-fold), and this was achieved via biochemical incorporation into triglyceride deacylation-reacylation pathways. The prodrug was hydrolysed rapidly to 2-mycophenoloyl glycerol (2-MPA-MG) in the presence of rat digestive fluid, and 2-MPA-MG was subsequently re-esterified in the enterocyte with oleic acid (most likely originating from the co-administered formulation) prior to accessing the

  10. Comparison of O-polysaccharide and hemolysin co-regulated protein as target antigens for serodiagnosis of melioidosis

    PubMed Central

    Pumpuang, Apinya; Dunachie, Susanna J.; Phokrai, Phornpun; Jenjaroen, Kemajittra; Sintiprungrat, Kitisak; Boonsilp, Siriphan; Brett, Paul J.; Burtnick, Mary N.

    2017-01-01

    Background Melioidosis is a severe disease caused by Burkholderia pseudomallei. Clinical manifestations are diverse and acute infections require immediate treatment with effective antibiotics. While culture is the current diagnostic standard, it is time-consuming and has low sensitivity. In endemic areas, inaccessibility to biosafety level 3 facilities and a lack of good serodiagnostic tools can impede diagnosis and disease surveillance. Recent studies have suggested that O-polysaccharide (OPS) and hemolysin co-regulated protein 1 (Hcp1) are promising target antigens for serodiagnosis of melioidosis. Methodology/Principle findings We evaluated rapid ELISAs using crude antigens, purified OPS and Hcp1 to measure antibody levels in three sets of sera: (i) 419 serum samples from melioidosis patients, Thai and U.S. healthy donors, (ii) 120 serum samples from patients with other bacterial infections, and (iii) 423 serum samples from 200 melioidosis patients obtained upon admission and at 12 and 52 weeks post-recovery. We observed significantly higher antibody levels using the crude antigen prepared from wild type B. pseudomallei K96243 compared to that of an OPS-mutant. The areas under receiver operator characteristics (AUROCCs) for diagnosis were compared for individual Hcp1-ELISA or OPS-ELISA or combined Hcp1/OPS-ELISA. For Thai donors, AUROCCs were highest and comparable between the Hcp1-ELISA and the combined Hcp1/OPS-ELISA (0.95 versus 0.94). For U.S. donors, the AUROCC was highest for the combined Hcp1/OPS-ELISA (0.96). Significantly higher seropositivity was observed in diabetic patients compared to those without diabetes for both the Hcp1-ELISA (87.3% versus 69.7%) and OPS-ELISA (88.1% versus 60.6%). Although antibody levels for Hcp1 were highest upon admission, the titers declined by week 52 post-recovery. Conclusions/Significance Hcp1 and OPS are promising candidates for serodiagnosis of melioidosis in different groups of patients. The Hcp1-ELISA performed

  11. Evaluation and comparison of two commercially available targeted next-generation sequencing platforms to assist oncology decision making

    PubMed Central

    Weiss, Glen J; Hoff, Brandi R; Whitehead, Robert P; Sangal, Ashish; Gingrich, Susan A; Penny, Robert J; Mallery, David W; Morris, Scott M; Thompson, Eric J; Loesch, David M; Khemka, Vivek

    2015-01-01

    Background It is widely acknowledged that there is value in examining cancers for genomic aberrations via next-generation sequencing (NGS). How commercially available NGS platforms compare with each other, and the clinical utility of the reported actionable results, are not well known. During the course of the current study, the Foundation One (F1) test generated data on a combination of somatic mutations, insertion and deletion polymorphisms, chromosomal abnormalities, and deoxyribonucleic acid (DNA) copy number changes at ~250× coverage, while the Paradigm Cancer Diagnostic (PCDx) test generated the same type of data at >5,000× coverage, plus provided messenger RNA (mRNA) expression levels. We sought to compare and evaluate paired formalin-fixed paraffin-embedded tumor tissue using these two platforms. Methods Samples from patients with advanced solid tumors were submitted to both the F1 and PCDx vendors for NGS analysis. Turnaround time (TAT) was calculated. Biomarkers were considered clinically actionable if they had a published association with treatment response in humans and were assigned to the following categories: commercially available drug (CA), clinical trial drug (CT), or neither option (hereafter referred to as “None”). Results The demographics of the 21 unique patient tumor samples included ten men and eleven women, with a median age of 56 years. Due to insufficient archival tissue from the same collection period, in one case, we used samples from different collections. PCDx reported first results faster than F1 in 20 cases. When received at both vendors on the same day, PCDx reported first results for 14 of 15 cases, with a median TAT of 9 days earlier than F1 (P<0.0001). Categorization of CA compared to CT and none significantly favored PCDx (P=0.012). Conclusion In the current analysis, commercially available NGS platforms provided clinically relevant actionable targets (CA or CT) in 47%–67% of diverse cancer types. In the samples

  12. Steroidogenic acute regulatory (StAR) protein and cholesterol side-chain cleavage (P450scc) as molecular and cellular targets for 17alpha-ethynylestradiol in salmon previtellogenic oocytes.

    PubMed

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