Science.gov

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. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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…

  20. 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

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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).

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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

  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. 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.

  8. 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

  9. 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.

  10. 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

  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. 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.

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  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. 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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. [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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  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. 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

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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.

  2. Enhanced Inhibition of Prostate Tumor Growth by Dual Targeting the Androgen Receptor and the Regulatory Subunit Type Iα of Protein Kinase A in Vivo

    PubMed Central

    Eder, Iris E.; Egger, Martina; Neuwirt, Hannes; Seifarth, Christof; Maddalo, Danilo; Desiniotis, Andreas; Schäfer, Georg; Puhr, Martin; Bektic, Jasmin; Cato, Andrew C. B.; Klocker, Helmut

    2013-01-01

    Progression to castration resistance is a major problem in the treatment of advanced prostate cancer and is likely to be driven by activation of several molecular pathways, including androgen receptor (AR) and cyclic AMP-dependent protein kinase A (PKA). In this study, we examined the therapeutic efficacy of a combined inhibition of the AR and the regulatory subunit type Iα (RIα) of protein kinase A with second generation antisense oligonucleotides (ODNs) in androgen-sensitive LNCaP and castration-resistant LNCaPabl tumors in vivo. We found that targeting the AR alone inhibited LNCaP, as well as LNCaPabl tumors. Combined inhibition resulted in an improved response over single targeting and even a complete tumor remission in LNCaPabl. Western blot analysis revealed that both ODNs were effective in reducing their target proteins when administered alone or in combination. In addition, treatment with the ODNs was associated with an induction of apoptosis. Our data suggest that dual targeting of the AR and PKARIα is more effective in inhibiting LNCaP and LNCaPabl tumor growth than single treatment and may give a treatment benefit, especially in castration-resistant prostate cancers. PMID:23736698

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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

  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. 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

  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. 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.

  18. 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

  19. 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.

  20. 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

  1. 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…

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. A Comparison of Target Detection and Rifle Marksmanship During Live and Simulator Firing with and without Caffeine Consumption

    DTIC Science & Technology

    2003-01-01

    and rifle marksmanship during live and simulator firing with and without caffeine consumption * Allan A. Keefe PeterTikuisis DISTRIBUTION STATEMENT A...20030610 i󈧧 A comparison of target detection and rifle marksmanship during live and simulator firing with and without caffeine consumption Allan A. Keefe...help realise the research potential of the SAT. DRDC Toronto TR 2003-003 Resume’_ _ _ Cette 6tude comparait les effets de l’ingestion de caffine sur la

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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...

  2. 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.

  3. Effective expansion of forkhead box P3⁺ regulatory T cells via early secreted antigenic target 6 and antigen 85 complex B from Mycobacterium tuberculosis.

    PubMed

    Wu, Ying-E; Du, Zhong-Ren; Cai, Ying-Mu; Peng, Wen-Guang; Zheng, Gao-Zhe; Zheng, Geng-Long; Wu, Li-Biao; Li, Ke

    2015-04-01

    The expansion of CD4+ CD25+ forkhead box (FOX)P3+ regulatory T (Treg) cells has been observed in patients with Mycobacterium (M.) tuberculosis; however, the mechanism of expansion remains to be elucidated. The aim of the present study was to examine the role of the early secreted antigenic target 6(ESAT‑6) and antigen 85 complex B (Ag85B) from M. tuberculosis on Treg cell expansion. To investigate the sensitivity of peripheral blood cultures to the M. tuberculosis ESAT‑6 and Ag85B antigens, the proportion of circulating CD4+ CD25+ FOXP3+ Treg cells was determined using flow cytometry and the levels of FOXP3 mRNA were determined using reverse transcription quantitative polymerase chain reaction. The mRNA levels of FOXP3 and the proportion of circulating CD4+ CD25+ FOXP3+ Treg cells were increased in multiplicitous drug‑resistant tuberculosis patients compared with those in healthy controls and patients with latent tuberculosis (TB) infection (LTBI) (P<0.001). The mycobacterial antigens ESAT‑6 and Ag85B increased the expansion of the CD4+ CD25+ FOXP3+ Treg cells and the mRNA levels of FOXP3 in healthy controls and LTBI patients compared with the effect of Bacillus Calmette‑Guerin (P<0.05). Additionally, the mRNA levels of FOXP3 were elevated in the LTBI patients following stimulations with the mycobacterial antigens (P=0.012). Therefore, the M. tuberculosis antigens ESAT‑6 and Ag85B induced CD4+ CD25+ FOXP3+ Treg‑cell expansion, particularly in patients with LTBI. These findings indicated that CD4+ CD25+ FOXP3+ Treg cells may have a primary role in the failure of the host immune system to eradicate M. tuberculosis.

  4. 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.

  5. 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).

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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…

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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

  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

    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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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

  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. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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).

  20. 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.

  1. 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

  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. 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.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. [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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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…

  4. 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.

  5. 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

  6. 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).

  7. 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.

  8. The Regulatory Plan

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-20

    ... [The Regulatory Plan and Unified Agenda of Federal Regulatory and Deregulatory Actions] #7; #7; The Regulatory Plan #7; #7; ] OPEN GOVERNMENT AND EVIDENCE-BASED REGULATION There is a close connection, even an inextricable relationship, between open government and evidence- based regulation. If regulatory choices are based on careful analysis of...

  9. 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.

  10. 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.

  11. 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.

  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. 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

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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

  1. Importance of protocol target definition on the ability to spare normal tissue: An IMRT and 3D-CRT planning comparison for intraorbital tumors

    SciTech Connect

    Hein, Patrick A.; Gladstone, David J.; Bellerive, Marc R.; Hug, Eugen B. . E-mail: Eugen.B.Hug@hitchcock.org

    2005-08-01

    Purpose: We selected five intraorbital tumor sites that are frequently found in clinical practice in children diagnosed with orbital rhabdomyosarcoma and performed three-dimensional conformal radiotherapy (3D-CRT) and intensity-modulated photon radiotherapy (IMRT) planning. Results of target coverage and doses to critical structures were compared. The goal of this study was to evaluate and to document realistic expectations as to organ-sparing capabilities of modern radiation therapy planning technologies with a focus on lens-sparing irradiation. Furthermore, we investigated potential added benefits of IMRT compared with 3D-CRT and the influence of protocol volume criteria definitions on the ability to obtain normal tissue dose sparing using the orbit as an example of a complex anatomic site. Methods and Materials: The five intraorbital tumor sites were placed retrobulbar, temporal, nasal, in the upper inner and upper outer quadrant, the latter two more complex in shape. Gross tumor volume (GTV), clinical target volume (CTV), and planning target volume (PTV) were defined in image-fused computed tomography and magnetic resonance data sets. 3D-CRT and IMRT photon plans, using equal beam angles and collimation for direct comparison, were designed to 45 Gy prescription dose according to Intergroup Rhabdomyosarcoma Study Group-D9602 (IRSG-D9602) protocol (Intergroup Rhabdomyosarcoma Study V [IRS-V] protocol) for Stage I, Clinical Group 3 orbital rhabdomyosarcoma. To compare the impact of changed target definitions in IMRT planning, additional IMRT plans were generated using modified volume and dose coverage criteria. The minimum dose constraint (95%) of the PTV was substituted by a required minimum volume coverage (95%) with the prescribed dose. Dose-volume histograms (DVHs) were obtained, including target volumes, lens, optic nerves, optic chiasm, lacrimal gland, bony orbit, pituitary gland, frontal and temporal lobes. Results: Protocol target volume coverage criteria

  2. COMPARISON OF MERCURY BLOOD PRESSURE READINGS TO OSCILLOMETRIC AND CENTRAL BLOOD PRESSURE IN PREDICTING TARGET ORGAN DAMAGE IN YOUTH

    PubMed Central

    Urbina, Elaine M; Khoury, Philip R; McCoy, Connie E; Daniels, Stephen R; Dolan, Lawrence M; Kimball, Thomas R

    2015-01-01

    Objective Hypertension (HT) is an important risk factor for target organ damage (TOD). New methods for measuring BP are replacing mercury sphygmomanometry in many clinics. We examined the utility of different BP measurement techniques in predicting subclinical TOD in adolescents and young adults. Methods Subjects in a study of the CV effects of obesity and type 2 diabetes (T2DM) were evaluated (N=677, 18 ± 3.3 years, 35% male, 60% non-Caucasian, 30% T2DM). We measured adiposity, lab, left ventricular mass, carotid intima-media thickness & pulse wave. BP was measured 3 times with mercury sphygmomanometery (BPm) an oscillometric device (BPo) and central aortic BP (BPc) was derived with arterial tonometry. Subjects were stratified as normotensive (N), pre-hypertensive (P) or hypertensive (H). Results The prevalence of HT this cohort with mean BMI of 31 was highest with BPo (16%), followed by BPm (11%) and BPc (9%), p≤0.001. BPm was most consistent in differentiating left ventricular mass and pulse wave velocity among subjects in the P group as compared to the N & H groups. Mercury BP was also more sensitive and specific in predicting greater left ventricular mass, pulse wave velocity and carotid thickness than the other BP measurement techniques in logistic regression. Conclusions We conclude that mercury sphygmomanometry should remain the gold standard for evaluation of HT and the risk for TOD in adolescents and young adults. PMID:25647284

  3. Additional Targeted Biopsy in Clinically Suspected Prostate Cancer: Prospective Randomized Comparison between Contrast-Enhanced Ultrasound and Sonoelastography Guidance.

    PubMed

    Koh, Jieun; Jung, Dae Chul; Oh, Young Taik; Yoo, Moon Gyu; Noh, Songmi; Han, Kyung Hwa; Rha, Koon-Ho; Choi, Young Deuk; Hong, Sung Joon

    2015-11-01

    Our aim was to improve the detection of prostate cancer by evaluating whether contrast-enhanced ultrasound (CEUS) or sonoelastography (SE) is more helpful in guiding targeted biopsy (TB) performed before systematic biopsy (SB). A total of 52 patients suspected of having prostate cancer were prospectively included and randomly assigned to either the CEUS or SE group. Different, independent radiologists performed TB and twelve-core SB. Within each group, cancer detection rates based on core number were compared between SB and TB. We evaluated the effect of TB on core-based cancer detection rates between the CEUS and SE groups. Cancer detection was higher in overall TB cores 16.4% (28/171) than SB cores 11.4% (71/624) in both groups. In the SE group, TB cores revealed higher cancer detection than did SB cores from 4.49% (14/312) to 12.86% (9/70) (p = 0.01). Compared with CEUS, SE may improve detection rates when considering additional TB guidance methods.

  4. Sequence Variation in Amplification Target Genes and Standards Influences Interlaboratory Comparison of BK Virus DNA Load Measurement

    PubMed Central

    Solis, Morgane; Meddeb, Mariam; Sueur, Charlotte; Domingo-Calap, Pilar; Soulier, Eric; Chabaud, Angeline; Perrin, Peggy; Moulin, Bruno; Bahram, Seiamak; Stoll-Keller, Françoise; Caillard, Sophie; Barth, Heidi

    2015-01-01

    International guidelines define a BK virus (BKV) load of ≥4 log10 copies/ml as presumptive of BKV-associated nephropathy (BKVN) and a cutoff for therapeutic intervention. To investigate whether BKV DNA loads (BKVL) are comparable between laboratories, 2 panels of 15 and 8 clinical specimens (urine, whole blood, and plasma) harboring different BKV genotypes were distributed to 20 and 27 French hospital centers in 2013 and 2014, respectively. Although 68% of the reported results fell within the acceptable range of the expected result ±0.5 log10, the interlaboratory variation ranged from 1.32 to 5.55 log10. Polymorphisms specific to BKV genotypes II and IV, namely, the number and position of mutations in amplification target genes and/or deletion in standards, arose as major sources of interlaboratory disagreements. The diversity of DNA purification methods also contributed to the interlaboratory variability, in particular for urine samples. Our data strongly suggest that (i) commercial external quality controls for BKVL assessment should include all major BKV genotypes to allow a correct evaluation of BKV assays, and (ii) the BKV sequence of commercial standards should be provided to users to verify the absence of mismatches with the primers and probes of their BKV assays. Finally, the optimization of primer and probe design and standardization of DNA extraction methods may substantially decrease interlaboratory variability and allow interinstitutional studies to define a universal cutoff for presumptive BKVN and, ultimately, ensure adequate patient care. PMID:26468499

  5. Intracellular distribution of the vitamin D receptor in the brain: comparison with classic target tissues and redistribution with development.

    PubMed

    Eyles, D W; Liu, P Y; Josh, P; Cui, X

    2014-05-30

    Apart from its role in regulating calcium there is growing evidence that vitamin D is a neuroactive steroid capable of regulating multiple pathways important for both brain development and mature brain function. Vitamin D induces its genomic effects through its nuclear receptor the vitamin D receptor (VDR). Although there is abundant evidence for this receptor's presence in the mammalian brain from studies employing immunohistochemistry, Western blot or quantitative RNA studies there remains some dispute regarding the validity of these studies. In this study we provide unambiguous confirmation for the VDR in adult rodent brain using proteomic techniques. However Western blot experiments show that compared to more classic target organs such as the gut and kidney, VDR expression is quantitatively lower in the brain. In addition we have examined VDR subcellular distribution in the gut, kidney and brain from both embryonic and adult tissues. We show that in all embryonic tissues VDR distribution is mostly nuclear, however by adulthood it appears that at least in the gut and kidney, VDR presence in the plasma membrane is more prominent perhaps reflecting some change in VDR function with the maturation of these tissues. Finally the subcellular distribution of VDR in the embryo did not appear to be altered by vitamin D deficiency indicating that perhaps there are other mechanisms at play in vivo to stabilize this receptor in the absence of its ligand.

  6. Performance evaluation of Sanger sequencing for the diagnosis of primary hyperoxaluria and comparison with targeted next generation sequencing

    PubMed Central

    Williams, Emma L; Bagg, Eleanor A L; Mueller, Michael; Vandrovcova, Jana; Aitman, Timothy J; Rumsby, Gill

    2015-01-01

    Definitive diagnosis of primary hyperoxaluria (PH) currently utilizes sequential Sanger sequencing of the AGXT, GRPHR, and HOGA1 genes but efficacy is unproven. This analysis is time-consuming, relatively expensive, and delays in diagnosis and inappropriate treatment can occur if not pursued early in the diagnostic work-up. We reviewed testing outcomes of Sanger sequencing in 200 consecutive patient samples referred for analysis. In addition, the Illumina Truseq custom amplicon system was evaluated for paralleled next-generation sequencing (NGS) of AGXT,GRHPR, and HOGA1 in 90 known PH patients. AGXT sequencing was requested in all patients, permitting a diagnosis of PH1 in 50%. All remaining patients underwent targeted exon sequencing of GRHPR and HOGA1 with 8% diagnosed with PH2 and 8% with PH3. Complete sequencing of both GRHPR and HOGA1 was not requested in 25% of patients referred leaving their diagnosis in doubt. NGS analysis showed 98% agreement with Sanger sequencing and both approaches had 100% diagnostic specificity. Diagnostic sensitivity of Sanger sequencing was 98% and for NGS it was 97%. NGS has comparable diagnostic performance to Sanger sequencing for the diagnosis of PH and, if implemented, would screen for all forms of PH simultaneously ensuring prompt diagnosis at decreased cost. PMID:25629080

  7. Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM).

    PubMed

    Schiffmann, Christian; Hansen, Rasmus; Baumann, Sven; Kublik, Anja; Nielsen, Per Halkjær; Adrian, Lorenz; von Bergen, Martin; Jehmlich, Nico; Seifert, Jana

    2014-01-01

    Targeted absolute protein quantification yields valuable information about physiological adaptation of organisms and is thereby of high interest. Especially for this purpose, two proteomic mass spectrometry-based techniques namely selective reaction monitoring (SRM) and precursor reaction monitoring (PRM) are commonly applied. The objective of this study was to establish an optimal quantification assay for proteins with the focus on those involved in housekeeping functions and putative reductive dehalogenase proteins from the strictly anaerobic bacterium Dehalococcoides mccartyi strain CBDB1. This microbe is small and slow-growing; hence, it provides little biomass for comprehensive proteomic analysis. We therefore compared SRM and PRM techniques. Eleven peptides were successfully quantified by both methods. In addition, six peptides were solely quantified by SRM and four by PRM, respectively. Peptides were spiked into a background of Escherichia coli lysate and the majority of peptides were quantifiable down to 500 amol absolute on column by both methods. Peptide quantification in CBDB1 lysate resulted in the detection of 15 peptides using SRM and 14 peptides with the PRM assay. Resulting quantification of five dehalogenases revealed copy numbers of <10 to 115 protein molecules per cell indicating clear differences in abundance of RdhA proteins during growth on hexachlorobenzene. Our results indicated that both methods show comparable sensitivity and that the combination of the mass spectrometry assays resulted in higher peptide coverage and thus more reliable protein quantification.

  8. Comparison of short-lived medical isotopes activation by laser thin target induced protons and conventional cyclotron proton beams

    NASA Astrophysics Data System (ADS)

    Murray, Joseph; Dudnikova, Galina; Liu, Tung-Chang; Papadopoulos, Dennis; Sagdeev, Roald; Su, J. J.; UMD MicroPET Team

    2014-10-01

    Production diagnostic or therapeutic nuclear medicines are either by nuclear reactors or by ion accelerators. In general, diagnostic nuclear radioisotopes have a very short half-life varying from tens of minutes for PET tracers and few hours for SPECT tracers. Thus supplies of PET and SPECT radiotracers are limited by regional production facilities. For example 18F-fluorodeoxyglucose (FDG) is the most desired tracer for positron emission tomography because its 110 minutes half-life is sufficient long for transport from production facilities to nearby users. From nuclear activation to completing image taking must be done within 4 hours. Decentralized production of diagnostic radioisotopes will be idea to make high specific activity radiotracers available to researches and clinicians. 11 C, 13 N, 15 O and 18 F can be produced in the energy range from 10-20 MeV by protons. Protons of energies up to tens of MeV generated by intense laser interacting with hydrogen containing targets have been demonstrated by many groups in the past decade. We use 2D PIC code for proton acceleration, Geant4 Monte Carlo code for nuclei activation to compare the yields and specific activities of short-lived isotopes produced by cyclotron proton beams and laser driven protons.

  9. 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.

  10. Human T-Cell Leukemia Virus Type 1 Integration Target Sites in the Human Genome: Comparison with Those of Other Retroviruses▿ ‡

    PubMed Central

    Derse, David; Crise, Bruce; Li, Yuan; Princler, Gerald; Lum, Nicole; Stewart, Claudia; McGrath, Connor F.; Hughes, Stephen H.; Munroe, David J.; Wu, Xiaolin

    2007-01-01

    Retroviral integration into the host genome is not entirely random, and integration site preferences vary among different retroviruses. Human immunodeficiency virus (HIV) prefers to integrate within active genes, whereas murine leukemia virus (MLV) prefers to integrate near transcription start sites and CpG islands. On the other hand, integration of avian sarcoma-leukosis virus (ASLV) shows little preference either for genes, transcription start sites, or CpG islands. While host cellular factors play important roles in target site selection, the viral integrase is probably the major viral determinant. It is reasonable to hypothesize that retroviruses with similar integrases have similar preferences for target site selection. Although integration profiles are well defined for members of the lentivirus, spumaretrovirus, alpharetrovirus, and gammaretrovirus genera, no members of the deltaretroviruses, for example, human T-cell leukemia virus type 1 (HTLV-1), have been evaluated. We have mapped 541 HTLV-1 integration sites in human HeLa cells and show that HTLV-1, like ASLV, does not specifically target transcription units and transcription start sites. Comparing the integration sites of HTLV-1 with those of ASLV, HIV, simian immunodeficiency virus, MLV, and foamy virus, we show that global and local integration site preferences correlate with the sequence/structure of virus-encoded integrases, supporting the idea that integrase is the major determinant of retroviral integration site selection. Our results suggest that the global integration profiles of other retroviruses could be predicted from phylogenetic comparisons of the integrase proteins. Our results show that retroviruses that engender different insertional mutagenesis risks can have similar integration profiles. PMID:17409138

  11. Comparison of Efficacy of Regional and Extensive Clinical Target Volumes in Postoperative Radiotherapy for Esophageal Squamous Cell Carcinoma

    SciTech Connect

    Qiao Xueying; Wang Wei; Zhou Zhiguo; Gao Xianshu; Chang, Joe Y.

    2008-02-01

    Purpose: To compare and analyze the effect of different clinical target volumes (CTVs) on survival rate after postoperative radiotherapy (RT) for esophageal squamous cell carcinoma (SCC). Methods and Materials: We studied 102 patients who underwent postoperative RT after radical resection for esophageal SCC (T3/4 or N1). The radiation dose was {>=}50 Gy. In the extensive portal group (E group, 43 patients), the CTV encompassed the bilateral supraclavicular region, all mediastinal lymph nodes, the anastomosis site, and the left gastric and pericardial lymphatic. In the regional portal group (R group, 59 patients), the CTV was confined to tumor bed and the lymph nodes in the immediate region of the primary lesion. The 1-, 3-, and 5-year survival rates were compared between the groups, and multivariate/univariate analysis for factors predicting survival was studied. Results: For the entire group, the 1-, 3- and 5-year survival rates were 76.3%, 50.5%, and 42.9%, respectively (median survival, 30 months). The 1-, 3-, and 5-year survival rates were 76.5%, 52.1%, and 41.3%, respectively, in the E group and 76.2%, 49.2%, and 44.6%, respectively, in the R group (not significant). According to the multivariate analysis, N stage, number of lymph nodes with metastatic disease, and tumor length were the independent prognostic factors for survival. Conclusions: Using a regional portal in postoperative RT for esophageal SCC is not associated with compromised survival compared with extensive portal RT and therefore should be considered. N stage, number of affected lymph nodes, and tumor length predict poor survival.

  12. 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

  13. 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.

  14. 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.

  15. Comparison of three transgenic Bt rice lines for insecticidal protein expression and resistance against a target pest, Chilo suppressalis (Lepidoptera: Crambidae).

    PubMed

    Wang, Ya-Nan; Ke, Kai-Qie; Li, Yun-He; Han, Lan-Zhi; Liu, Yan-Min; Hua, Hong-Xia; Peng, Yu-Fa

    2016-02-01

    Two transgenic rice lines (T2A-1 and T1C-19b) expressing cry2A and cry1C genes, respectively, were developed in China, targeting lepidopteran pests including Chilo suppressalis (Walker) (Lepidoptera: Crambidae). The seasonal expression of Cry proteins in different tissues of the rice lines and their resistance to C. suppressalis were assessed in comparison to a Bt rice line expressing a cry1Ab/Ac fusion gene, Huahui 1, which has been granted a biosafety certificate. In general, levels of Cry proteins were T2A-1 > Huahui 1 > T1C-19b among rice lines, and leaf > stem > root among rice tissues. The expression patterns of Cry protein in the rice line plants were similar: higher level at early stages than at later stages with an exception that high Cry1C level in T1C-19b stems at the maturing stage. The bioassay results revealed that the three transgenic rice lines exhibited significantly high resistance against C. suppressalis larvae throughout the rice growing season. According to Cry protein levels in rice tissues, the raw and corrected mortalities of C. suppressalis caused by each Bt rice line were the highest in the seedling and declined through the jointing stage with an exception for T1C-19b providing an excellent performance at the maturing stage. By comparison, T1C-19b exhibited more stable and greater resistance to C. suppressalis larvae than T2A-1, being close to Huahui 1. The results suggest cry1C is an ideal Bt gene for plant transformation for lepidopteran pest control, and T1C-19b is a promising Bt rice line for commercial use for tolerating lepidopteran rice pests.

  16. Building the connectivity map of epigenetics: Chromatin profiling by quantitative targeted mass spectrometry

    PubMed Central

    Creech, Amanda L.; Taylor, Jordan E.; Maier, Verena K.; Wu, Xiaoyun; Feeney, Caitlin M.; Udeshi, Namrata D.; Peach, Sally E.; Boehm, Jesse S.; Lee, Jeannie T.; Carr, Steven A.; Jaffe, Jacob D.

    2014-01-01

    Epigenetic control of genome function is an important regulatory mechanism in diverse processes such as lineage commitment and environmental sensing, and in disease etiologies ranging from neuropsychiatric disorders to cancer. Here we report a robust, high-throughput targeted, quantitative mass spectrometry (MS) method to rapidly profile modifications of the core histones of chromatin that compose the epigenetic landscape, enabling comparisons among cells with differing genetic backgrounds, genomic perturbations, and drug treatments. PMID:25448295

  17. Comparison of surface matching and target matching for image-guided pelvic radiation therapy for both supine and prone patient positions.

    PubMed

    Zhao, Hui; Wang, Brian; Sarkar, Vikren; Rassiah-Szegedi, Prema; Huang, Y Jessica; Szegedi, Martin; Huang, Long; Gonzalez, Victor; Salter, Bill

    2016-05-01

    We investigate the difference between surface matching and target matching for pelvic radiation image guidance. The uniqueness of our study is that all patients have multiple CT-on-rails (CTOR) scans to compare to corresponding AlignRT images. Ten patients receiving pelvic radiation were enrolled in this study. Two simulation CT scans were performed in supine and prone positions for each patient. Body surface contours were generated in treatment planning system and exported to AlignRT to serve as reference images. During treatment day, the patient was aligned to treatment isocenter with room lasers, and then scanned with both CTOR and AlignRT. Image-guidance shifts were calculated for both modalities by comparison to the simulation CT and the differences between them were analyzed for both supine and prone positions, respectively. These procedures were performed for each patient once per week for five weeks. The difference of patient displacement between AlignRT and CTOR was analyzed. For supine position, five patients had an average difference of displacement between AlignRT and CTOR along any direction (vertical, longitudinal, and lateral) greater than 0.5 cm, and one patient greater than 1 cm. Four patients had a maximum difference greater than 1 cm. For prone position, seven patients had an average difference greater than 0.5 cm, and three patients greater than 1 cm. Nine patients had a maximum difference greater than 1 cm. The difference of displacement between AlignRT and CTOR was greater for the prone position than for the supine position. For the patients studied here, surface matching does not appear to be an advisable image-guidance approach for pelvic radiation therapy for patients with either supine or prone position. There appears to be a potential for large alignment discrepancies (up to 2.25 cm) between surface matching and target matching. PACS number(s): 87.55.-x.

  18. Comparison of surface matching and target matching for image-guided pelvic radiation therapy for both supine and prone patient positions.

    PubMed

    Zhao, Hui; Wang, Brian; Sarkar, Vikren; Rassiah-Szegedi, Prema; Huang, Y Jessica; Szegedi, Martin; Huang, Long; Gonzalez, Victor; Salter, Bill

    2016-05-08

    We investigate the difference between surface matching and target matching for pelvic radiation image guidance. The uniqueness of our study is that all patients have multiple CT-on-rails (CTOR) scans to compare to corresponding AlignRT images. Ten patients receiving pelvic radiation were enrolled in this study. Two simulation CT scans were performed in supine and prone positions for each patient. Body surface contours were generated in treatment planning system and exported to AlignRT to serve as reference images. During treatment day, the patient was aligned to treatment isocenter with room lasers, and then scanned with both CTOR and AlignRT. Image-guidance shifts were calculated for both modalities by com-parison to the simulation CT and the differences between them were analyzed for both supine and prone positions, respectively. These procedures were performed for each patient once per week for five weeks. The difference of patient displace-ment between AlignRT and CTOR was analyzed. For supine position, five patients had an average difference of displacement between AlignRT and CTOR along any direction (vertical, longitudinal, and lateral) greater than 0.5 cm, and one patient greater than 1 cm. Four patients had a maximum difference greater than 1 cm. For prone position, seven patients had an average difference greater than 0.5 cm, and three patients greater than 1 cm. Nine patients had a maximum difference greater than 1 cm. The difference of displacement between AlignRT and CTOR was greater for the prone position than for the supine position. For the patients studied here, surface matching does not appear to be an advisable image-guidance approach for pelvic radiation therapy for patients with either supine or prone position. There appears to be a potential for large alignment discrepancies (up to 2.25 cm) between surface matching and target matching.

  19. Steroidogenic acute regulatory (StAR) protein and cholesterol side-chain cleavage (P450scc) as molecular and cellular targets for 17alpha-ethynylestradiol in salmon previtellogenic oocytes.

    PubMed

    Vang, Siv-Hege; Kortner, Trond M; Arukwe, Augustine

    2007-12-01

    Gonadal steroids are known to modulate both the synthesis and the release of gonadotropins by the pituitary and influence several brain functions that are apparently responsible for gender-specific differences in the regulation of the hypothalamus-pituitary-gonadal (HPG) axis. It is believed that the true rate-limiting step in acute steroid production is the movement of cholesterol across the mitochondrial membrane by the steroidogenic acute regulatory (StAR) protein and subsequent conversion to pregnenolone by P450-mediated cholesterol side chain cleavage (P450 scc). In the present study, we have evaluated the effects of 17alpha-ethynylestradiol (EE2) on salmon previtellogenic oocytes using an in vitro culture system and molecular, histological, and physiological methods. The in vitro culture technique was based on an agarose floating method recently validated for xenoestrogens in our laboratory. Tissue was cultured in a humidified incubator at 10 degrees C for 3, 7, and 14 days with different concentrations of EE2 [0 (control), 0.01, 0.1, and 1 microM] dissolved in ethanol (0.1%). The StAR, P450 scc, P450 arom isoforms, and insulin-like growth factor 2 (IGF-2) mRNA expressions were performed using validated real-time polymerase chain reaction (PCR) with specific primers, and immunohistochemistry of the StAR and P450 scc proteins was performed using antisera prepared against synthetic peptide for both proteins and estradiol-17beta (E2); testosterone (T) and 11-ketotestosterone (11-KT) tissue levels were performed using enzyme immunoassay (EIA). Our data show that EE2 produced time- and concentration-specific effects on the StAR protein, P450 scc, P450 arom isoforms, and IGF-2 gene expressions in salmon gonadal tissues. Cellular expression of the StAR and P450 scc proteins was mainly demonstrated in follicular cells of the oocyte membrane, showing time- and EE2 concentration-dependent differences in staining intensities. Tissue levels of E2, T, and 11-KT in salmon

  20. 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.

  1. Using Inequality Measures to Incorporate Environmental Justice into Regulatory Analyses

    EPA Science Inventory

    Abstract: Formally evaluating how specific policy measures influence environmental justice is challenging, especially in the context of regulatory analyses in which quantitative comparisons are the norm. However, there is a large literature on developing and applying quantitative...

  2. YTRP: a repository for yeast transcriptional regulatory pathways

    PubMed Central

    Yang, Tzu-Hsien; Wang, Chung-Ching; Wang, Yu-Chao; Wu, Wei-Sheng

    2014-01-01

    Regulatory targets of transcription factors (TFs) can be identified by the TF perturbation experiments, which reveal the expression changes owing to the perturbation (deletion or overexpression) of TFs. But the identified targets of a given TF consist of both direct and indirect regulatory targets. It has been shown that most of the TFPE-identified regulatory targets are indirect, indicating that TF-gene regulation is mainly through transcriptional regulatory pathways (TRPs) consisting of intermediate TFs. Without identification of these TRPs, it is not easy to understand how a TF regulates its indirect targets. Because there is no such database depositing the potential TRPs for Saccharomyces cerevisiae now, this motivates us to construct the YTRP (Yeast Transcriptional Regulatory Pathway) database. For each TF-gene regulatory pair under different experimental conditions, all possible TRPs in two underlying networks (constructed using experimentally verified TF-gene binding pairs and TF-gene regulatory pairs from the literature) for the specified experimental conditions were automatically enumerated by TRP mining procedures developed from the graph theory. The enumerated TRPs of a TF-gene regulatory pair provide experimentally testable hypotheses for the molecular mechanisms behind a TF and its regulatory target. YTRP is available online at http://cosbi3.ee.ncku.edu.tw/YTRP/. We believe that the TRPs deposited in this database will greatly improve the usefulness of TFPE data for yeast biologists to study the regulatory mechanisms between a TF and its knocked-out targets. Database URL: http://cosbi3.ee.ncku.edu.tw/YTRP/ PMID:24608172

  3. Small regulatory RNAs in Archaea.

    PubMed

    Babski, Julia; Maier, Lisa-Katharina; Heyer, Ruth; Jaschinski, Katharina; Prasse, Daniela; Jäger, Dominik; Randau, Lennart; Schmitz, Ruth A; Marchfelder, Anita; Soppa, Jörg

    2014-01-01

    Small regulatory RNAs (sRNAs) are universally distributed in all three domains of life, Archaea, Bacteria, and Eukaryotes. In bacteria, sRNAs typically function by binding near the translation start site of their target mRNAs and thereby inhibit or activate translation. In eukaryotes, miRNAs and siRNAs typically bind to the 3'-untranslated region (3'-UTR) of their target mRNAs and influence translation efficiency and/or mRNA stability. In archaea, sRNAs have been identified in all species investigated using bioinformatic approaches, RNomics, and RNA-Seq. Their size can vary significantly between less than 50 to more than 500 nucleotides. Differential expression of sRNA genes has been studied using northern blot analysis, microarrays, and RNA-Seq. In addition, biological functions have been unraveled by genetic approaches, i.e., by characterization of designed mutants. As in bacteria, it was revealed that archaeal sRNAs are involved in many biological processes, including metabolic regulation, adaptation to extreme conditions, stress responses, and even in regulation of morphology and cellular behavior. Recently, the first target mRNAs were identified in archaea, including one sRNA that binds to the 5'-region of two mRNAs in Methanosarcina mazei Gö1 and a few sRNAs that bind to 3'-UTRs in Sulfolobus solfataricus, three Pyrobaculum species, and Haloferax volcanii, indicating that archaeal sRNAs appear to be able to target both the 5'-UTR or the 3'-UTRs of their respective target mRNAs. In addition, archaea contain tRNA-derived fragments (tRFs), and one tRF has been identified as a major ribosome-binding sRNA in H. volcanii, which downregulates translation in response to stress. Besides regulatory sRNAs, archaea contain further classes of sRNAs, e.g., CRISPR RNAs (crRNAs) and snoRNAs.

  4. Regulatory RNAs in Planarians.

    PubMed

    Pawlicka, Kamila; Perrigue, Patrick M; Barciszewski, Jan

    2016-01-01

    The full scope of regulatory RNA evolution and function in epigenetic processes is still not well understood. The development of planarian flatworms to be used as a simple model organism for research has shown a great potential to address gaps in the knowledge in this field of study. The genomes of planarians encode a wide array of regulatory RNAs that function in gene regulation. Here, we review planarians as a suitable model organism for the identification and function of regulatory RNAs.

  5. Regulatory Information By Sector

    EPA Pesticide Factsheets

    Find environmental regulatory, compliance, & enforcement information for various business, industry and government sectors, listed by NAICS code. Sectors include agriculture, automotive, petroleum manufacturing, oil & gas extraction & other manufacturing

  6. Comparison and Consensus Guidelines for Delineation of Clinical Target Volume for CT- and MR-Based Brachytherapy in Locally Advanced Cervical Cancer

    SciTech Connect

    Viswanathan, Akila N.; Gaffney, David K.; Beriwal, Sushil; Bhatia, Sudershan K.; Lee Burnett, Omer; D'Souza, David P.; Patil, Nikhilesh; Haddock, Michael G.; Jhingran, Anuja; Jones, Ellen L.; Kunos, Charles A.; Lee, Larissa J.; Mayr, Nina A.; Petersen, Ivy; Petric, Primoz; Portelance, Lorraine; Small, William; Strauss, Jonathan B.; and others

    2014-10-01

    Objective: To create and compare consensus clinical target volume (CTV) contours for computed tomography (CT) and 3-Tesla (3-T) magnetic resonance (MR) image-based cervical-cancer brachytherapy. Methods and Materials: Twenty-three experts in gynecologic radiation oncology contoured the same 3 cervical cancer brachytherapy cases: 1 stage IIB near-complete response (CR) case with a tandem and ovoid, 1 stage IIB partial response (PR) case with tandem and ovoid with needles, and 1 stage IB2 CR case with a tandem and ring applicator. The CT contours were completed before the MRI contours. These were analyzed for consistency and clarity of target delineation using an expectation maximization algorithm for simultaneous truth and performance level estimation (STAPLE), with κ statistics as a measure of agreement between participants. The conformity index was calculated for each of the 6 data sets. Dice coefficients were generated to compare the CT and MR contours of the same case. Results: For all 3 cases, the mean tumor volume was smaller on MR than on CT (P<.001). The κ and conformity index estimates were slightly higher for CT, indicating a higher level of agreement on CT. The Dice coefficients were 89% for the stage IB2 case with a CR, 74% for the stage IIB case with a PR, and 57% for the stage IIB case with a CR. Conclusion: In a comparison of MR-contoured with CT-contoured CTV volumes, the higher level of agreement on CT may be due to the more distinct contrast medium visible on the images at the time of brachytherapy. MR at the time of brachytherapy may be of greatest benefit in patients with large tumors with parametrial extension that have a partial or complete response to external beam. On the basis of these results, a 95% consensus volume was generated for CT and for MR. Online contouring atlases are available for instruction at (http://www.nrgoncology.org/Resources/ContouringAtlases/GYNCervicalBrachytherapy.aspx)

  7. Regulatory pathways in the European Union.

    PubMed

    Kohler, Manuela

    2011-01-01

    In principle, there are three defined procedures to obtain approval for a medicinal product in the European Union. As discussed in this overview of the procedures, the decision on which regulatory pathway to use will depend on the nature of the active substance, the target indication(s), the history of product and/or the marketing strategy.

  8. A comparison of quantitative-competitive and realtime PCR assays using an identical target sequence to detect Epstein-Barr virus viral load in the peripheral blood.

    PubMed

    Xu, Shushen; Green, Michael; Kingsley, Laurence; Webber, Steven; Rowe, David

    2006-11-01

    Monitoring the load of Epstein-Barr virus (EBV) in the peripheral blood by quantitative PCR has been accepted as a useful tool for predicting the onset of EBV related diseases, confirming an EBV disease diagnosis and following the response to treatment interventions. In the present study, the use of a realtime polymerase chain reaction (rt-PCR) assay developed for unpurified cell preparations was examined and the results of the realtime assay were compared to an EBV quantitative-competitive PCR assay (QC-PCR). Both assays use the same target sequence and the same method for determining the standard value for the copy number of EBV genomes present. A comparison of 572 PCR results reveals that the realtime assay gave 5-10-fold higher values than the QC-PCR. Fifty-one results (8.9%) were discordant between the two sets of data. The most commonly encountered discordant result was detection of low amounts of EBV DNA by the rt-PCR assay that were not detected in specimens by QC-PCR. The two assays had a high degree of correlation across the range of load detection allowing clinically relevant threshold values determined in the QC-PCR assay to be inferred for the rt-PCR assay. External normalization of the rt-PCR assay was determined to be an important tool for monitoring the quality and/or quantity of human DNA in the starting material. rt-PCR assays with unpurified cell lysates compare favorably with quantitative-competitive assays and when normalized offer real advantages in specimen preparation, assay manipulations and reproducibility over both quantitative-competitive assays and realtime assays that require purified nucleic acid inputs.

  9. A comparison between radiation therapists and medical specialists in the use of kilovoltage cone-beam computed tomography scans for potential lung cancer radiotherapy target verification and adaptation

    SciTech Connect

    Watt, Sandie Carolyn; Vinod, Shalini K.; Dimigen, Marion; Descallar, Joseph; Zogovic, Branimere; Atyeo, John; Wallis, Sian; Holloway, Lois C.

    2016-04-01

    Target volume matching using cone-beam computed tomography (CBCT) is the preferred treatment verification method for lung cancer in many centers. However, radiation therapists (RTs) are trained in bony matching and not soft tissue matching. The purpose of this study was to determine whether RTs were equivalent to radiation oncologists (ROs) and radiologists (RDs) in alignment of the treatment CBCT with the gross tumor volume (GTV) defined at planning and in delineating the GTV on the treatment CBCT, as may be necessary for adaptive radiotherapy. In this study, 10 RTs, 1 RO, and 1 RD performed a manual tumor alignment and correction of the planning GTV to a treatment CBCT to generate an isocenter correction distance for 15 patient data sets. Participants also contoured the GTV on the same data sets. The isocenter correction distance and the contoured GTVs from the RTs were compared with the RD and RO. The mean difference in isocenter correction distances was 0.40 cm between the RO and RD, 0.51 cm between the RTs, and RO and 0.42 cm between the RTs and RD. The 95% CIs were smaller than the equivalence limit of 0.5 cm, indicating that the RTs were equivalent to the RO and RD. For GTV delineation comparisons, the RTs were not found to be equivalent to the RD or RO. The alignment of the planning defined GTV and treatment CBCT using soft tissue matching by the RTs has been shown to be equivalent to those by the RO and RD. However, tumor delineation by the RTs on the treatment CBCT was not equivalent to that of the RO and RD. Thus, it may be appropriate for RTs to undertake soft tissue alignment based on CBCT; however, further investigation may be necessary before RTs undertake delineation for adaptive radiotherapy purposes.

  10. Pleiotropy constrains the evolution of protein but not regulatory sequences in a transcription regulatory network influencing complex social behaviors

    PubMed Central

    Molodtsova, Daria; Harpur, Brock A.; Kent, Clement F.; Seevananthan, Kajendra; Zayed, Amro

    2014-01-01

    It is increasingly apparent that genes and networks that influence complex behavior are evolutionary conserved, which is paradoxical considering that behavior is labile over evolutionary timescales. How does adaptive change in behavior arise if behavior is controlled by conserved, pleiotropic, and likely evolutionary constrained genes? Pleiotropy and connectedness are known to constrain the general rate of protein evolution, prompting some to suggest that the evolution of complex traits, including behavior, is fuelled by regulatory sequence evolution. However, we seldom have data on the strength of selection on mutations in coding and regulatory sequences, and this hinders our ability to study how pleiotropy influences coding and regulatory sequence evolution. Here we use population genomics to estimate the strength of selection on coding and regulatory mutations for a transcriptional regulatory network that influences complex behavior of honey bees. We found that replacement mutations in highly connected transcription factors and target genes experience significantly stronger negative selection relative to weakly connected transcription factors and targets. Adaptively evolving proteins were significantly more likely to reside at the periphery of the regulatory network, while proteins with signs of negative selection were near the core of the network. Interestingly, connectedness and network structure had minimal influence on the strength of selection on putative regulatory sequences for both transcription factors and their targets. Our study indicates that adaptive evolution of complex behavior can arise because of positive selection on protein-coding mutations in peripheral genes, and on regulatory sequence mutations in both transcription factors and their targets throughout the network. PMID:25566318

  11. Influence of macrocyclic chelators on the targeting properties of (68)Ga-labeled synthetic affibody molecules: comparison with (111)In-labeled counterparts.

    PubMed

    Strand, Joanna; Honarvar, Hadis; Perols, Anna; Orlova, Anna; Selvaraju, Ram Kumar; Karlström, Amelie Eriksson; Tolmachev, Vladimir

    2013-01-01

    Affibody molecules are a class of small (7 kDa) non-immunoglobulin scaffold-based affinity proteins, which have demonstrated substantial potential as probes for radionuclide molecular imaging. The use of positron emission tomography (PET) would further increase the resolution and quantification accuracy of Affibody-based imaging. The rapid in vivo kinetics of Affibody molecules permit the use of the generator-produced radionuclide (68)Ga (T1/2=67.6 min). Earlier studies have demonstrated that the chemical nature of chelators has a substantial influence on the biodistribution properties of Affibody molecules. To determine an optimal labeling approach, the macrocyclic chelators 1,4,7,10-tetraazacylododecane-1,4,7,10-tetraacetic acid (DOTA), 1,4,7-triazacyclononane-N,N,N-triacetic acid (NOTA) and 1-(1,3-carboxypropyl)-1,4,7- triazacyclononane-4,7-diacetic acid (NODAGA) were conjugated to the N-terminus of the synthetic Affibody molecule ZHER2:S1 targeting HER2. Affibody molecules were labeled with (68)Ga, and their binding specificity and cellular processing were evaluated. The biodistribution of (68)Ga-DOTA-ZHER2:S1, (68)Ga-NOTA-ZHER2:S1 and (68)Ga-NODAGA-ZHER2:S1, as well as that of their (111)In-labeled counterparts, was evaluated in BALB/C nu/nu mice bearing HER2-expressing SKOV3 xenografts. The tumor uptake for (68)Ga-DOTA-ZHER2:S1 (17.9 ± 0.7%IA/g) was significantly higher than for both (68)Ga-NODAGA-ZHER2:S1 (16.13 ± 0.67%IA/g) and (68)Ga-NOTA-ZHER2:S1 (13 ± 3%IA/g) at 2 h after injection. (68)Ga-NODAGA-ZHER2:S1 had the highest tumor-to-blood ratio (60 ± 10) in comparison with both (68)Ga-DOTA-ZHER2:S1 (28 ± 4) and (68)Ga-NOTA-ZHER2:S1 (42 ± 11). The tumor-to-liver ratio was also higher for (68)Ga-NODAGA-ZHER2:S1 (7 ± 2) than the DOTA and NOTA conjugates (5.5 ± 0.6 vs.3.3 ± 0.6). The influence of chelator on the biodistribution and targeting properties was less pronounced for (68)Ga than for (111)In. The results of this study demonstrate that

  12. 78 FR 44279 - Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-23

    ... Regulatory Flexibility Act, 5 U.S.C. sections 601 to 612 (1988). FOR FURTHER INFORMATION CONTACT: Robert... mandated for the regulatory flexibility agendas required by the Regulatory Flexibility Act (5 U.S.C. 602... regulatory flexibility agenda, in accordance with the Regulatory Flexibility Act, because they are likely...

  13. Revealing global regulatory perturbations across human cancers

    PubMed Central

    Goodarzi, Hani; Elemento, Olivier; Tavazoie, Saeed

    2010-01-01

    Summary The discovery of pathways and regulatory networks whose perturbation contributes to neoplastic transformation remains a fundamental challenge for cancer biology. We show that such pathway perturbations, and the cis-regulatory elements through which they operate, can be efficiently extracted from global gene-expression profiles. Our approach utilizes information-theoretic analysis of expression levels, pathways, and genomic sequences. Analysis across a diverse set of human cancers reveals the majority of previously known cancer pathways. Through de novo motif discovery we associate these pathways with transcription-factor binding sites and miRNA targets, including those of E2F, NF-Y, p53, and let-7. Follow-up experiments confirmed that these predictions correspond to functional in vivo regulatory interactions. Strikingly, the majority of the perturbations, associated with putative cis-regulatory elements, fall outside of known cancer pathways. Our study provides a systems-level dissection of regulatory perturbations in cancer—an essential component of a rational strategy for therapeutic intervention and drug-target discovery. PMID:20005852

  14. Pharmacologic agents targeting autophagy

    PubMed Central

    Vakifahmetoglu-Norberg, Helin; Xia, Hong-guang; Yuan, Junying

    2015-01-01

    Autophagy is an important intracellular catabolic mechanism critically involved in regulating tissue homeostasis. The implication of autophagy in human diseases and the need to understand its regulatory mechanisms in mammalian cells have stimulated research efforts that led to the development of high-throughput screening protocols and small-molecule modulators that can activate or inhibit autophagy. Herein we review the current landscape in the development of screening technology as well as the molecules and pharmacologic agents targeting the regulatory mechanisms of autophagy. We also evaluate the potential therapeutic application of these compounds in different human pathologies. PMID:25654545

  15. Cis-regulatory mutations in human disease

    PubMed Central

    2009-01-01

    Cis-acting regulatory sequences are required for the proper temporal and spatial control of gene expression. Variation in gene expression is highly heritable and a significant determinant of human disease susceptibility. The diversity of human genetic diseases attributed, in whole or in part, to mutations in non-coding regulatory sequences is on the rise. Improvements in genome-wide methods of associating genetic variation with human disease and predicting DNA with cis-regulatory potential are two of the major reasons for these recent advances. This review will highlight select examples from the literature that have successfully integrated genetic and genomic approaches to uncover the molecular basis by which cis-regulatory mutations alter gene expression and contribute to human disease. The fine mapping of disease-causing variants has led to the discovery of novel cis-acting regulatory elements that, in some instances, are located as far away as 1.5 Mb from the target gene. In other cases, the prior knowledge of the regulatory landscape surrounding the gene of interest aided in the selection of enhancers for mutation screening. The success of these studies should provide a framework for following up on the large number of genome-wide association studies that have identified common variants in non-coding regions of the genome that associate with increased risk of human diseases including, diabetes, autism, Crohn's, colorectal cancer, and asthma, to name a few. PMID:19641089

  16. Cis-regulatory mutations in human disease.

    PubMed

    Epstein, Douglas J

    2009-07-01

    Cis-acting regulatory sequences are required for the proper temporal and spatial control of gene expression. Variation in gene expression is highly heritable and a significant determinant of human disease susceptibility. The diversity of human genetic diseases attributed, in whole or in part, to mutations in non-coding regulatory sequences is on the rise. Improvements in genome-wide methods of associating genetic variation with human disease and predicting DNA with cis-regulatory potential are two of the major reasons for these recent advances. This review will highlight select examples from the literature that have successfully integrated genetic and genomic approaches to uncover the molecular basis by which cis-regulatory mutations alter gene expression and contribute to human disease. The fine mapping of disease-causing variants has led to the discovery of novel cis-acting regulatory elements that, in some instances, are located as far away as 1.5 Mb from the target gene. In other cases, the prior knowledge of the regulatory landscape surrounding the gene of interest aided in the selection of enhancers for mutation screening. The success of these studies should provide a framework for following up on the large number of genome-wide association studies that have identified common variants in non-coding regions of the genome that associate with increased risk of human diseases including, diabetes, autism, Crohn's, colorectal cancer, and asthma, to name a few.

  17. Comparison of active, passive and magnetic targeting to tumors of multifunctional paclitaxel/SPIO-loaded nanoparticles for tumor imaging and therapy.

    PubMed

    Schleich, Nathalie; Po, Chrystelle; Jacobs, Damien; Ucakar, Bernard; Gallez, Bernard; Danhier, Fabienne; Préat, Véronique

    2014-11-28

    Multifunctional nanoparticles combining therapy and imaging have the potential to improve cancer treatment by allowing personalized therapy. Herein, we aimed to compare in vivo different strategies in terms of targeting capabilities: (1) passive targeting via the EPR effect, (2) active targeting of αvβ3 integrin via RGD grafting, (3) magnetic targeting via a magnet placed on the tumor and (4) the combination of magnetic targeting and active targeting of αvβ3 integrin. For a translational approach, PLGA-based nanoparticles loaded with paclitaxel and superparamagnetic iron oxides were used. Electron Spin Resonance spectroscopy and Magnetic Resonance Imaging (MRI) were used to both quantify and visualize the accumulation of multifunctional nanoparticles into the tumors. We demonstrate that compared to untargeted or single targeted nanoparticles, the combination of both active strategy and magnetic targeting drastically enhanced (i) nanoparticle accumulation into the tumor tissue with an 8-fold increase compared to passive targeting (1.12% and 0.135% of the injected dose, respectively), (ii) contrast in MRI (imaging purpose) and (iii) anti-cancer efficacy with a median survival time of 22 days compared to 13 for the passive targeting (therapeutic purpose). Double targeting of nanoparticles to tumors by different mechanisms could be a promising translational approach for the management of therapeutic treatment and personalized therapy.

  18. Regulatory guidance document

    SciTech Connect

    1994-05-01

    The Office of Civilian Radioactive Waste Management (OCRWM) Program Management System Manual requires preparation of the OCRWM Regulatory Guidance Document (RGD) that addresses licensing, environmental compliance, and safety and health compliance. The document provides: regulatory compliance policy; guidance to OCRWM organizational elements to ensure a consistent approach when complying with regulatory requirements; strategies to achieve policy objectives; organizational responsibilities for regulatory compliance; guidance with regard to Program compliance oversight; and guidance on the contents of a project-level Regulatory Compliance Plan. The scope of the RGD includes site suitability evaluation, licensing, environmental compliance, and safety and health compliance, in accordance with the direction provided by Section 4.6.3 of the PMS Manual. Site suitability evaluation and regulatory compliance during site characterization are significant activities, particularly with regard to the YW MSA. OCRWM`s evaluation of whether the Yucca Mountain site is suitable for repository development must precede its submittal of a license application to the Nuclear Regulatory Commission (NRC). Accordingly, site suitability evaluation is discussed in Chapter 4, and the general statements of policy regarding site suitability evaluation are discussed in Section 2.1. Although much of the data and analyses may initially be similar, the licensing process is discussed separately in Chapter 5. Environmental compliance is discussed in Chapter 6. Safety and Health compliance is discussed in Chapter 7.

  19. Steroidogenic acute regulatory (StAR) protein and cholesterol side-chain cleavage (P450scc)-regulated steroidogenesis as an organ-specific molecular and cellular target for endocrine disrupting chemicals in fish.

    PubMed

    Arukwe, Augustine

    2008-12-01

    Biologically active steroids are synthesised de novo in specialised cells of several organs, including the adrenal gland, testis, ovary, brain, placenta and adipose tissue. Regardless of organ or tissue, the rate-limiting step in steroid hormone synthesis is the movement of cholesterol across the mitochondrial membrane (i.e. from the outer to the inner membrane) mediated by the steroidogenic acute regulatory (StAR) protein. Subsequent conversion of cholesterol to pregnenolone by cytochrome P450 side-chain cleavage (P450scc) represents the initiation of steroidogenesis. Chemically mediated disruption of StAR and P450scc expression may represent the first step in the sequence of related event cascades underlying xenoestrogen-induced toxicity and transmittable disturbances to the whole organism level. This may include, but is not limited to, alterations in sexual differentiation, growth, reproduction, development and metabolism. Despite the integral role of StAR and P450scc in acute steroidogenesis, and popular demand from regulatory agencies, bioassays for evaluating the effect of endocrine-disrupting chemicals have the potential to overlook chemicals that may modulate estrogenic responses through mechanisms that do not involve direct binding to estrogen receptors (ERs). In addition to their effect as direct ER agonists, the effects of endocrine disruptors may be evaluated and interpreted as interference with steroidogenesis and with the steroidal regulation of the normal development and function of juvenile, male and female individuals. Knowledge of these effects is scarce, indicating that relatively little is known about the mechanisms or mode-of-action of chemical alterations to steroidogenesis and their potential toxicity for wildlife species. In addition, analytical methods for the complete adaptation of these responses as biomarkers of response and effect are yet to be properly validated.

  20. Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion

    PubMed Central

    Smith, Carol; Stringer, Anne M.; Mao, Chunhong; Palumbo, Michael J.

    2016-01-01

    ABSTRACT Salmonella enterica pathogenicity island 1 (SPI-1) encodes proteins required for invasion of gut epithelial cells. The timing of invasion is tightly controlled by a complex regulatory network. The transcription factor (TF) HilD is the master regulator of this process and senses environmental signals associated with invasion. HilD activates transcription of genes within and outside SPI-1, including six other TFs. Thus, the transcriptional program associated with host cell invasion is controlled by at least 7 TFs. However, very few of the regulatory targets are known for these TFs, and the extent of the regulatory network is unclear. In this study, we used complementary genomic approaches to map the direct regulatory targets of all 7 TFs. Our data reveal a highly complex and interconnected network that includes many previously undescribed regulatory targets. Moreover, the network extends well beyond the 7 TFs, due to the inclusion of many additional TFs and noncoding RNAs. By comparing gene expression profiles of regulatory targets for the 7 TFs, we identified many uncharacterized genes that are likely to play direct roles in invasion. We also uncovered cross talk between SPI-1 regulation and other regulatory pathways, which, in turn, identified gene clusters that likely share related functions. Our data are freely available through an intuitive online browser and represent a valuable resource for the bacterial research community. PMID:27601571

  1. Select Biosolids Regulatory Processes

    EPA Pesticide Factsheets

    Historical Regulatory Development and activities EPA has undertaken to respond to statutory obligations, respond to the National Academy of Sciences, understand pollutants that may occur in sewage sludge, and address dioxins in sewage sludge.

  2. Regulatory T cell memory

    PubMed Central

    Rosenblum, Michael D.; Way, Sing Sing; Abbas, Abul K.

    2016-01-01

    Memory for antigen is a defining feature of adaptive immunity. Antigen-specific lymphocyte populations show an increase in number and function after antigen encounter and more rapidly re-expand upon subsequent antigen exposure. Studies of immune memory have primarily focused on effector B cells and T cells with microbial specificity, using prime challenge models of infection. However, recent work has also identified persistently expanded populations of antigen-specific regulatory T cells that protect against aberrant immune responses. In this Review, we consider the parallels between memory effector T cells and memory regulatory T cells, along with the functional implications of regulatory memory in autoimmunity, antimicrobial host defence and maternal fetal tolerance. In addition, we discuss emerging evidence for regulatory T cell memory in humans and key unanswered questions in this rapidly evolving field. PMID:26688349

  3. 3 CFR - Regulatory Compliance

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... protecting the air we breathe and the water we drink. Consistent regulatory enforcement also levels the... can lead the Government to hold itself more accountable, encouraging agencies to identify and...

  4. 3 CFR - Regulatory Review

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... in general—should be revisited. I therefore direct the Director of OMB, in consultation with... delay; clarify the role of the behavioral sciences in formulating regulatory policy; and identify...

  5. Assessing the regulatory picture

    SciTech Connect

    Not Available

    1994-02-01

    This article addresses the safety of the nation's drinking water supply and discusses compliance of the Clean Water Act. Right now, the shape of the regulatory future is uncertain. The results of the D-DBP regulatory negotiation are imminent. Congress is ready to begin debating reauthorization of the Safe Drinking Water Act, and utilities are trying to comply with the regulations while trying not to price water out of the reach of some of their customers.

  6. NRC regulatory initiatives

    SciTech Connect

    Johnson, T.C.

    1989-11-01

    The US Nuclear Regulatory Commission (NRC) is addressing several low-level waste disposal issues that will be important to waste generators and to States and Compacts developing new disposal capacity. These issues include Greater-Than-Class C (GTCC) waste, mixed waste, below regulatory concern (BRC) waste, and the low-level waste data base. This paper discusses these issues and their current status.

  7. A comparison of Agrobacterium-mediated transformation and protoplast-mediated transformation with CRISPR-Cas9 and bipartite gene targeting substrates, as effective gene targeting tools for Aspergillus carbonarius.

    PubMed

    Weyda, István; Yang, Lei; Vang, Jesper; Ahring, Birgitte K; Lübeck, Mette; Lübeck, Peter S

    2017-04-01

    In recent years, versatile genetic tools have been developed and applied to a number of filamentous fungi of industrial importance. However, the existing techniques have limitations when it comes to achieve the desired genetic modifications, especially for efficient gene targeting. In this study, we used Aspergillus carbonarius as a host strain due to its potential as a cell factory, and compared three gene targeting techniques by disrupting the ayg1 gene involved in the biosynthesis of conidial pigment in A. carbonarius. The absence of the ayg1 gene leads to phenotypic change in conidia color, which facilitated the analysis on the gene targeting frequency. The examined transformation techniques included Agrobacterium-mediated transformation (AMT) and protoplast-mediated transformation (PMT). Furthermore, the PMT for the disruption of the ayg1 gene was carried out with bipartite gene targeting fragments and the recently adapted CRISPR-Cas9 system. All three techniques were successful in generating Δayg1 mutants, but showed different efficiencies. The most efficient method for gene targeting was AMT, but further it was shown to be dependent on the choice of Agrobacterium strain. However, there are different advantages and disadvantages of all three gene targeting methods which are discussed, in order to facilitate future approaches for fungal strain improvements.

  8. Comparison of Gull Feces-specific Assays Targeting the 16S rRNA Gene of Catellicoccus Marimammalium and Streptococcus spp.

    EPA Science Inventory

    Two novel gull-specific qPCR assays were developed using 16S rRNA gene sequences from gull fecal clone libraries: a SYBR-green-based assay targeting Streptococcus spp. (i.e., gull3) and a TaqMan qPCR assay targeting Catellicoccus marimammalium (i.e., gull4). The main objectives ...

  9. SU-E-J-231: Comparison of 3D Angiogram and MRI in Delineating the AVM Target for Frameless Stereotactic Radiosurgery

    SciTech Connect

    Avkshtol, V; Tanny, S; Reddy, K; Chen, C; Parsai, E

    2014-06-01

    Purpose: Stereotactic radiation therapy (SRT) provides an excellent alternative to embolization and surgical excision for the management of appropriately selected cerebral arteriovenous malformations (AVMs). The currently accepted standard for delineating AVMs is planar digital subtraction angiography (DSA). DSA can be used to acquire a 3D data set that preserves osseous structures (3D-DA) at the time of the angiography for SRT planning. Magnetic resonance imaging (MRI) provides an alternative noninvasive method of visualizing the AVM nidus with comparable spatial resolution. We utilized 3D-DA and T1 post-contrast MRI data to evaluate the differences in SRT target volumes. Methods: Four patients underwent 3D-DA and high-resolution MRI. 3D T1 post-contrast images were obtained in all three reconstruction planes. A planning CT was fused with MRI and 3D-DA data sets. The AVMs were contoured utilizing one of the image sets at a time. Target volume, centroid, and maximum and minimum dimensions were analyzed for each patient. Results: Targets delineated using post-contrast MRI demonstrated a larger mean volume. AVMs >2 cc were found to have a larger difference between MRI and 3D-DA volumes. Larger AVMs also demonstrated a smaller relative uncertainty in contour centroid position (1 mm). AVM targets <2 cc had smaller absolute differences in volume, but larger differences in contour centroid position (2.5 mm). MRI targets demonstrated a more irregular shape compared to 3D-DA targets. Conclusions: Our preliminary data supports the use of MRI alone to delineate AVM targets >2 cc. The greater centroid stability for AVMs >2 cc ensures accurate target localization during image fusion. The larger MRI target volumes did not result in prohibitively greater volumes of normal brain tissue receiving the prescription dose. The larger centroid instability for AVMs <2 cc precludes the use of MRI alone for target delineation. We recommend incorporating a 3D-DA for these patients.

  10. Comparison of Continuous-Wave CO2 Lidar Calibration by use of Earth-Surface Targets in Laboratory and Airborne Measurements

    NASA Technical Reports Server (NTRS)

    Jarzembski, Maurice A.; Srivastava, Vandana

    1998-01-01

    Backscatter of several Earth surfaces was characterized in the laboratory as a function of incidence angle with a focused continuous-wave 9.1 micro meter CO2 Doppler lidar for use as possible calibration targets. Some targets showed negligible angular dependence, while others showed a slight increase with decreasing angle. The Earth-surface signal measured over the complex Californian terrain during a 1995 NASA airborne mission compared well with laboratory data. Distributions of the Earth's surface signal shows that the lidar efficiency can be estimated with a fair degree of accuracy, preferably with uniform Earth-surface targets during flight for airborne or space-based lidar.

  11. 75 FR 61530 - Issuance of Regulatory Guides

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-05

    ... Engineering, Office of Nuclear Regulatory Research, U.S. Nuclear Regulatory Commission, Washington, DC 20555... From the Federal Register Online via the Government Publishing Office NUCLEAR REGULATORY COMMISSION Issuance of Regulatory Guides AGENCY: Nuclear Regulatory Commission. ACTION: Notice. SUMMARY:...

  12. Comparison of pencil beam–based homogeneous vs inhomogeneous target dose planning for stereotactic body radiotherapy of peripheral lung tumors through Monte Carlo–based recalculation

    SciTech Connect

    Ohtakara, Kazuhiro; Hoshi, Hiroaki

    2015-10-01

    This study was conducted to ascertain whether homogeneous target dose planning is suitable for stereotactic body radiotherapy (SBRT) of peripheral lung cancer under appropriate breath-holding. For 20 peripheral lung tumors, paired dynamic conformal arc plans were generated by only adjusting the leaf margin to the planning target volume (PTV) edge for fulfilling the conditions such that the prescription isodose surface (IDS) encompassing exactly 95% of the PTV (PTV D{sub 95}) corresponds to 95% and 80% IDS, normalized to 100% at the PTV isocenter under a pencil beam (PB) algorithm with radiologic path length correction. These plans were recalculated using the x-ray voxel Monte Carlo (XVMC) algorithm under otherwise identical conditions, and then compared. Lesions abutting the parietal pleura or not were defined as edge or island tumors, respectively, and the influences of the target volume and its location relative to the chest wall on the target dose were examined. The median (range) leaf margin required for the 95% and 80% plans was 3.9 mm (1.3 to 5.0) and −1.2 mm (−1.8 to 0.1), respectively. Notably, the latter was significantly correlated negatively with PTV. In the 80% plans, the PTV D{sub 95} was slightly higher under XVMC, whereas the PTV D{sub 98} was significantly lower, irrespective of the dose calculation algorithm used. Other PTV and all gross tumor volume doses were significantly higher, while the lung doses outside the PTV were slightly lower. The target doses increased as a function of PTV and were significantly lower for island tumors than for edge tumors. In conclusion, inhomogeneous target dose planning using smaller leaf margin for a larger tumor volume was deemed suitable in ensuring more sufficient target dose while slightly reducing lung dose. In addition, more inhomogeneous target dose planning using <80% IDS (e.g., 70%) for PTV covering would be preferable for island tumors.

  13. Rationales for regulatory activity

    SciTech Connect

    Perhac, R.M.

    1997-02-01

    The author provides an outline which touches on the types of concerns about risk evaluation which are addressed in the process of establishing regulatory guides. Broadly he says regulatory activity serves three broad constituents: (1) Paternalism (private risk); (2) Promotion of social welfare (public risks); (3) Protection of individual rights (public risks). He then discusses some of the major issues encountered in reaching a decision on what is an acceptable level of risk within each of these areas, and how one establishes such a level.

  14. Comparison between target margins derived from 4DCT scans and real-time tumor motion tracking: Insights from lung tumor patients treated with robotic radiosurgery

    SciTech Connect

    Descovich, Martina McGuinness, Christopher; Kannarunimit, Danita; Chen, Josephine; Pinnaduwage, Dilini; Pouliot, Jean; Kased, Norbert; Gottschalk, Alexander R.; Yom, Sue S.

    2015-03-15

    Purpose: A unique capability of the CyberKnife system is dynamic target tracking. However, not all patients are eligible for this approach. Rather, their tumors are tracked statically using the vertebral column for alignment. When using static tracking, the internal target volume (ITV) is delineated on the four-dimensional (4D) CT scan and an additional margin is added to account for setup uncertainty [planning target volume (PTV)]. Treatment margins are difficult to estimate due to unpredictable variations in tumor motion and respiratory pattern during the course of treatment. The inability to track the target and detect changes in respiratory characteristics might result in geographic misses and local tumor recurrences. The purpose of this study is to develop a method to evaluate the adequacy of ITV-to-PTV margins for patients treated in this manner. Methods: Data from 24 patients with lesions in the upper lobe (n = 12), middle lobe (n = 3), and lower lobe (n = 9) were included in this study. Each patient was treated with dynamic tracking and underwent 4DCT scanning at the time of simulation. Data including the 3D coordinates of the target over the course of treatment were extracted from the treatment log files and used to determine actual target motion in the superior–inferior (S–I), anterior–posterior (A–P), and left–right (L–R) directions. Different approaches were used to calculate anisotropic and isotropic margins, assuming that the tumor moves as a rigid body. Anisotropic margins were calculated by separating target motion in the three anatomical directions, and a uniform margin was calculated by shifting the gross tumor volume contours in the 3D space and by computing the percentage of overlap with the PTV. The analysis was validated by means of a theoretical formulation. Results: The three methods provided consistent results. A uniform margin of 4.5 mm around the ITV was necessary to assure 95% target coverage for 95% of the fractions included

  15. Comparison of line x-ray emission from solid and porous nano-layer coated targets irradiated by double laser pulses

    SciTech Connect

    Fazeli, R.; Mahdieh, M. H.

    2015-11-15

    Enhancement of line x-ray emission from both solid and porous iron targets induced by irradiation of single and double laser pulses is studied numerically. The line emission from laser produced plasma is calculated within the extreme ultra-violet lithography wavelength range of 13.5–13.7 nm. The effects of pre-pulse intensity and delay time between two pulses (pre-pulse and main pulse) are examined. The results show that using double pulses irradiation in the conditions of porous target can reduce the x-ray enhancement. According to the results, the use of both pre-pulse and porous target leads to efficient absorption of the laser energy. Calculations also show that such enhanced laser absorption can ionize atoms of the target material to very high degrees of ionization, leading to decrease of the density of appropriate ions that are responsible for line emission in the selected wavelength region. By increasing the target porosity, x-ray yield was more reduced.

  16. Adaptive infrared target detection

    NASA Astrophysics Data System (ADS)

    McBride, Jonah C.; Stevens, Mark R.; Eaton, Ross S.; Snorrason, Magnus S.

    2004-09-01

    Automatic Target Recognition (ATR) algorithms are extremely sensitive to differences between the operating conditions under which they are trained and the extended operating conditions (EOCs) in which the fielded algorithms are tested. These extended operating conditions can cause a target's signature to be drastically different from training exemplars/models. For example, a target's signature can be influenced by: the time of day, the time of year, the weather, atmospheric conditions, position of the sun or other illumination sources, the target surface and material properties, the target composition, the target geometry, sensor characteristics, sensor viewing angle and range, the target surroundings and environment, and the target and scene temperature. Recognition rates degrade if an ATR is not trained for a particular EOC. Most infrared target detection techniques are based on a very simple probabilistic theory. This theory states that a pixel should be assigned the label of "target" if a set of measurements (features) is more likely to have come from an assumed (or learned) distribution of target features than from the distribution of background features. However, most detection systems treat these learned distributions as static and they are not adapted to changing EOCs. In this paper, we present an algorithm for assigning a pixel the label of target or background based on a statistical comparison of the distributions of measurements surrounding that pixel in the image. This method provides a feature-level adaptation to changing EOCs. Results are demonstrated on infrared imagery containing several military vehicles.

  17. A comparative analytical assay of gene regulatory networks inferred using microarray and RNA-seq datasets

    PubMed Central

    Izadi, Fereshteh; Zarrini, Hamid Najafi; Kiani, Ghaffar; Jelodar, Nadali Babaeian

    2016-01-01

    A Gene Regulatory Network (GRN) is a collection of interactions between molecular regulators and their targets in cells governing gene expression level. Omics data explosion generated from high-throughput genomic assays such as microarray and RNA-Seq technologies and the emergence of a number of pre-processing methods demands suitable guidelines to determine the impact of transcript data platforms and normalization procedures on describing associations in GRNs. In this study exploiting publically available microarray and RNA-Seq datasets and a gold standard of transcriptional interactions in Arabidopsis, we performed a comparison between six GRNs derived by RNA-Seq and microarray data and different normalization procedures. As a result we observed that compared algorithms were highly data-specific and Networks reconstructed by RNA-Seq data revealed a considerable accuracy against corresponding networks captured by microarrays. Topological analysis showed that GRNs inferred from two platforms were similar in several of topological features although we observed more connectivity in RNA-Seq derived genes network. Taken together transcriptional regulatory networks obtained by Robust Multiarray Averaging (RMA) and Variance-Stabilizing Transformed (VST) normalized data demonstrated predicting higher rate of true edges over the rest of methods used in this comparison. PMID:28293077

  18. The regulatory horizon

    NASA Technical Reports Server (NTRS)

    Cook, ED

    1987-01-01

    The author briefly discusses the FAA's position as it relates to cockpit resource management. For example, if Cockpit Resource Management (CRM) is a positive concept, why isn't everyone required to implement it? The regulatory practice of the FAA is discussed and questions and answers are presented.

  19. Toxicogenomics in Regulatory Ecotoxicology

    EPA Science Inventory

    The potential utility of toxicogenomics in toxicological research and regulatory activities has been the subject of scientific discussions, and as with any new technology, there is a wide range of opinion. The purpose of this feature article is to consider roles of toxicogenomic...

  20. Comparison of the RECIST 1.0 and RECIST 1.1 in patients treated with targeted agents: a pooled analysis and review

    PubMed Central

    Kim, Jung Han

    2016-01-01

    Patients treated with targeted agents were not included in the data warehouse when the RECIST 1.1 was revised in 2009. We conducted this pooled analysis to investigate the impact of the RECIST 1.1 on the assessment of tumor response in cancer patients treated with targeted agents. We surveyed MEDLINE, EMBASE and PubMed for articles with terms of the RECIST 1.0 or RECIST 1.1. We searched for all the references of relevant articles and reviews using the ‘related articles’ feature in the PubMed. There were six articles in the literature comparing the clinical impacts of the RECIST 1.0 and RECIST 1.1 in patients treated with targeted agents for advanced or metastatic cancer. A total of 322 patients were recruited from the six trials; 217 with non-small cell lung cancer, 23 with thyroid cancer, 20 with gastrointestinal stromal tumor, and 62 with renal cell carcinoma. Because of new lymph node criteria, eight patients (2.5%) had no target lesions when adopting the RECIST 1.1. The number of target lesions by the RECIST 1.1 was significantly lower than that by the RECIST 1.0 (P < 0.001). However, the RECIST 1.1 showed high concordance with the RECIST 1.0 in the assessment of best tumor responses (k = 0.908). Seventeen patients (5.6%) showed discrepancy in the best tumor response between the RECIST 1.0 and RECIST 1.1. This pooled study demonstrates that the RECIST 1.1 shows the highly concordant response assessment with the RECIST 1.0 in patients treated with targeted agents. PMID:26885610

  1. Assessment of experimental d-PIGE γ-ray production cross sections for 12C, 14N and 16O and comparison with absolute thick target yields

    NASA Astrophysics Data System (ADS)

    Csedreki, L.; Halász, Z.; Kiss, Á. Z.

    2016-08-01

    Measured differential cross sections for deuteron induced γ-ray emission from the reactions 12C(d,pγ)13C, (Eγ = 3089 keV), 14N(d,pγ)15N (Eγ = 8310 keV) and 16O(d,pγ)17O (Eγ = 871 keV) available in the literature were assessed. In order to cross check the assessed γ-ray production cross section data, thick target γ-yields calculated from the differential cross sections were compared with available measured thick target yields. Recommended differential cross section data for each reaction were deduced for particle induced γ-ray emission (PIGE) applications.

  2. RSAT 2015: Regulatory Sequence Analysis Tools

    PubMed Central

    Medina-Rivera, Alejandra; Defrance, Matthieu; Sand, Olivier; Herrmann, Carl; Castro-Mondragon, Jaime A.; Delerce, Jeremy; Jaeger, Sébastien; Blanchet, Christophe; Vincens, Pierre; Caron, Christophe; Staines, Daniel M.; Contreras-Moreira, Bruno; Artufel, Marie; Charbonnier-Khamvongsa, Lucie; Hernandez, Céline; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

    2015-01-01

    RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/. PMID:25904632

  3. RSAT 2015: Regulatory Sequence Analysis Tools.

    PubMed

    Medina-Rivera, Alejandra; Defrance, Matthieu; Sand, Olivier; Herrmann, Carl; Castro-Mondragon, Jaime A; Delerce, Jeremy; Jaeger, Sébastien; Blanchet, Christophe; Vincens, Pierre; Caron, Christophe; Staines, Daniel M; Contreras-Moreira, Bruno; Artufel, Marie; Charbonnier-Khamvongsa, Lucie; Hernandez, Céline; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

    2015-07-01

    RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/.

  4. Intra-Animal Comparison between Three-dimensional Molecularly Targeted US and Three-dimensional Dynamic Contrast-enhanced US for Early Antiangiogenic Treatment Assessment in Colon Cancer1

    PubMed Central

    Wang, Huaijun; Lutz, Amelie M.; Hristov, Dimitre; Tian, Lu; Willmann, Jürgen K.

    2017-01-01

    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 micro-bubbles, 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

  5. Comparison of a Targeted Intervention Program Delivered Face-to-Face and by Personal Videoconferencing for Primary and Middle School Students with Mathematical Learning Difficulties

    ERIC Educational Resources Information Center

    Kestel, Eugénie

    2014-01-01

    This paper describes part of a mixed-methods study comparing the effectiveness of an individual, conceptual instruction based, tuition program delivered face-to-face and by personal videoconferencing (PVC) for 30 upper primary and middle school students with mathematical learning difficulties (MLDs). The experimental intervention targeted number…

  6. Toxicogenomics and the Regulatory Framework

    EPA Science Inventory

    Toxicogenomics presents regulatory agencies with the opportunity to revolutionize their analyses by enabling the collection of information on a broader range of responses than currently considered in traditional regulatory decision making. Analyses of genomic responses are expec...

  7. Differential network analysis reveals dysfunctional regulatory networks in gastric carcinogenesis

    PubMed Central

    Cao, Mu-Shui; Liu, Bing-Ya; Dai, Wen-Tao; Zhou, Wei-Xin; Li, Yi-Xue; Li, Yuan-Yuan

    2015-01-01

    Gastric Carcinoma is one of the most common cancers in the world. A large number of differentially expressed genes have been identified as being associated with gastric cancer progression, however, little is known about the underlying regulatory mechanisms. To address this problem, we developed a differential networking approach that is characterized by including a nascent methodology, differential coexpression analysis (DCEA), and two novel quantitative methods for differential regulation analysis. We first applied DCEA to a gene expression dataset of gastric normal mucosa, adenoma and carcinoma samples to identify gene interconnection changes during cancer progression, based on which we inferred normal, adenoma, and carcinoma-specific gene regulation networks by using linear regression model. It was observed that cancer genes and drug targets were enriched in each network. To investigate the dynamic changes of gene regulation during carcinogenesis, we then designed two quantitative methods to prioritize differentially regulated genes (DRGs) and gene pairs or links (DRLs) between adjacent stages. It was found that known cancer genes and drug targets are significantly higher ranked. The top 4% normal vs. adenoma DRGs (36 genes) and top 6% adenoma vs. carcinoma DRGs (56 genes) proved to be worthy of further investigation to explore their association with gastric cancer. Out of the 16 DRGs involved in two top-10 DRG lists of normal vs. adenoma and adenoma vs. carcinoma comparisons, 15 have been reported to be gastric cancer or cancer related. Based on our inferred differential networking information and known signaling pathways, we generated testable hypotheses on the roles of GATA6, ESRRG and their signaling pathways in gastric carcinogenesis. Compared with established approaches which build genome-scale GRNs, or sub-networks around differentially expressed genes, the present one proved to be better at enriching cancer genes and drug targets, and prioritizing

  8. Functional footprinting of regulatory DNA

    PubMed Central

    Vierstra, Jeff; Reik, Andreas; Chang, Kai-Hsin; Stehling-Sun, Sandra; Zhou, Yuan-Yue; Hinkley, Sarah J.; Paschon, David E.; Zhang, L.; Psatha, Nikoletta; Bendana, Yuri R.; O'Neill, Colleen M.; Song, Alex H.; Mich, Andrea; Liu, Pei-Qi; Lee, Gary; Bauer, Daniel E.; Holmes, Michael C.; Orkin, Stuart H.; Papayannopoulou, Thalia; Stamatoyannopoulos, George; Rebar, Edward J.; Gregory, Philip D.; Urnov, Fyodor D.; Stamatoyannopoulos, John A.

    2017-01-01

    Regulatory regions harbor multiple transcription factor recognition sites; however, the contribution of individual sites to regulatory function remains challenging to define. We describe a facile approach that exploits the error-prone nature of genome editing-induced double-strand break repair to map functional elements within regulatory DNA at nucleotide resolution. We demonstrate the approach on a human erythroid enhancer, revealing single TF recognition sites that gate the majority of downstream regulatory function. PMID:26322838

  9. Nuclear Regulatory Commission information digest

    SciTech Connect

    None,

    1990-03-01

    The Nuclear Regulatory Commission information digest provides summary information regarding the US Nuclear Regulatory Commission, its regulatory responsibilities, and areas licensed by the commission. This is an annual publication for the general use of the NRC Staff and is available to the public. The digest is divided into two parts: the first presents an overview of the US Nuclear Regulatory Commission and the second provides data on NRC commercial nuclear reactor licensees and commercial nuclear power reactors worldwide.

  10. Overcoming regulatory and economic challenges facing pharmacogenomics.

    PubMed

    Cohen, Joshua P

    2012-09-15

    The number of personalized medicines and companion diagnostics in use in the United States has gradually increased over the past decade, from a handful of medicines and tests in 2001 to several dozen in 2011. However, the numbers have not reached the potential hoped for when the human genome project was completed in 2001. Significant clinical, regulatory, and economic barriers exist and persist. From a regulatory perspective, therapeutics and companion diagnostics are ideally developed simultaneously, with the clinical significance of the diagnostic established using data from the clinical development program of the corresponding therapeutic. Nevertheless, this is not (yet) happening. Most personalized medicines are personalized post hoc, that is, a companion diagnostic is developed separately and approved after the therapeutic. This is due in part to a separate and more complex regulatory process for diagnostics coupled with a lack of clear regulatory guidance. More importantly, payers have placed restrictions on reimbursement of personalized medicines and their companion diagnostics, given the lack of evidence on the clinical utility of many tests. To achieve increased clinical adoption of diagnostics and targeted therapies through more favorable reimbursement and incorporation in clinical practice guidelines, regulators will need to provide unambiguous guidance and manufacturers will need to bring more and better clinical evidence to the market place.

  11. Comparison of RNAi Sequences in Insect-Resistant Plants to Expressed Sequences of a Beneficial Lady Beetle: A Closer Look at Off-Target Considerations

    PubMed Central

    Allen, Margaret L.

    2017-01-01

    Sequences obtained from transcriptomes of the lady beetle Coleomegilla maculata were compared to those designed for incorporation into crops. Searches of the transcriptomes identified sequences as the most likely to be closely similar to the sequences described in RNAi plant incorporated products. Some proposed prime RNAi pest management targets were also used to identify predicted orthologs from C. maculata. The lady beetle sequences were aligned with sequences from corn rootworms and Colorado potato beetles and, as appropriate in the case of targets, regions of similarity were compared with the genetic model organism for beetles, Tribolium castaneum. Some high levels of nucleotide identity were identified, particularly with an actin-derived sequence from Colorado potato beetle. This actin-derived sequence shared identical sequences with the lady beetle and a parasitic wasp. PMID:28257058

  12. Comparison of RNAi Sequences in Insect-Resistant Plants to Expressed Sequences of a Beneficial Lady Beetle: A Closer Look at Off-Target Considerations.

    PubMed

    Allen, Margaret L

    2017-03-01

    Sequences obtained from transcriptomes of the lady beetle Coleomegilla maculata were compared to those designed for incorporation into crops. Searches of the transcriptomes identified sequences as the most likely to be closely similar to the sequences described in RNAi plant incorporated products. Some proposed prime RNAi pest management targets were also used to identify predicted orthologs from C. maculata. The lady beetle sequences were aligned with sequences from corn rootworms and Colorado potato beetles and, as appropriate in the case of targets, regions of similarity were compared with the genetic model organism for beetles, Tribolium castaneum. Some high levels of nucleotide identity were identified, particularly with an actin-derived sequence from Colorado potato beetle. This actin-derived sequence shared identical sequences with the lady beetle and a parasitic wasp.

  13. Cognitive regulatory control therapies.

    PubMed

    Bowins, Brad

    2013-01-01

    Cognitive regulatory control processes play an essential but typically unappreciated role in maintaining mental health. The purpose of the current paper is to identify this role and demonstrate how cognitive-behavioral and related techniques can compensate for impairments. Impaired cognitive regulation contributes to the overly intense emotional states present in anxiety disorders, depression, and personality disorders; progression of adaptive hypomania to mania; expression of psychosis in the conscious and awake state; dominance of immature defense mechanisms in borderline and other personality disorders. A wide variety of standard (monitoring, reappraisal, response inhibition, relaxation training) and more novel (suppression therapy, willful detachment, cost-benefit analysis, normalization, mature defense mechanism training) cognitive-behavioral and related techniques can be applied to compensate for cognitive regulatory control impairments, and their success probably aligns with this capacity.

  14. Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification.

    PubMed

    Kobayashi, Masakazu; Retra, Kim; Figaroa, Francis; Hollander, Johan G; Ab, Eiso; Heetebrij, Robert J; Irth, Hubertus; Siegal, Gregg

    2010-09-01

    Fragment-based drug discovery (FBDD) has become a widely accepted tool that is complementary to high-throughput screening (HTS) in developing small-molecule inhibitors of pharmaceutical targets. Because a fragment campaign can only be as successful as the hit matter found, it is critical that the first stage of the process be optimized. Here the authors compare the 3 most commonly used methods for hit discovery in FBDD: high concentration screening (HCS), solution ligand-observed nuclear magnetic resonance (NMR), and surface plasmon resonance (SPR). They selected the commonly used saturation transfer difference (STD) NMR spectroscopy and the proprietary target immobilized NMR screening (TINS) as representative of the array of possible NMR methods. Using a target typical of FBDD campaigns, the authors find that HCS and TINS are the most sensitive to weak interactions. They also find a good correlation between TINS and STD for tighter binding ligands, but the ability of STD to detect ligands with affinity weaker than 1 mM K(D) is limited. Similarly, they find that SPR detection is most suited to ligands that bind with K(D) better than 1 mM. However, the good correlation between SPR and potency in a bioassay makes this a good method for hit validation and characterization studies.

  15. A deposit scale mineral prospectivity analysis: A comparison of various knowledge-driven approaches for porphyry copper targeting in Seridune, Iran

    NASA Astrophysics Data System (ADS)

    Abedi, Maysam; Mostafavi Kashani, Seyed Bagher; Norouzi, Gholam-Hossain; Yousefi, Mahyar

    2017-04-01

    In this paper, an application of a knowledge-driven mineral prospectivity mapping (MPM) approach so-called ;the evidential belief functions (EBFs) using Dempster-Shafer's rule of combination; is proposed. This technique is used to weight and integrate a large scale exploration dataset in order to localize prospects for definition of further exploration drilling sites. In this study, exploration datasets of Seridune copper deposit in the Kerman province, SE Iran used for the methodology. In this regard, geophysical evidence layers extracted from interpretation of magnetic and electrical surveys, geological evidence layers derived via the geological datasets (i.e. lithology, fault and alteration), and geochemical evidence maps were generated and integrated for MPM. Furthermore, various MPM approaches including outranking, index overlay and fuzzy logic methods were examined for comparison with the introduced method. To evaluate and compare the efficiency of the methods, the productivity of the drilled boreholes (Cu concentration multiplied by its ore thickness along each drilled borehole) was used to validate the generated prospectivity models. The results showed higher efficiency of the Dempster-Shafer's model in comparison with the prospectivity models generated using other MPM approaches.

  16. Deciphering the Transcriptional-Regulatory Network of Flocculation in Schizosaccharomyces pombe

    PubMed Central

    Kwon, Eun-Joo Gina; Laderoute, Amy; Chatfield-Reed, Kate; Vachon, Lianne; Karagiannis, Jim; Chua, Gordon

    2012-01-01

    In the fission yeast Schizosaccharomyces pombe, the transcriptional-regulatory network that governs flocculation remains poorly understood. Here, we systematically screened an array of transcription factor deletion and overexpression strains for flocculation and performed microarray expression profiling and ChIP–chip analysis to identify the flocculin target genes. We identified five transcription factors that displayed novel roles in the activation or inhibition of flocculation (Rfl1, Adn2, Adn3, Sre2, and Yox1), in addition to the previously-known Mbx2, Cbf11, and Cbf12 regulators. Overexpression of mbx2+ and deletion of rfl1+ resulted in strong flocculation and transcriptional upregulation of gsf2 +/pfl1+ and several other putative flocculin genes (pfl2+–pfl9+). Overexpression of the pfl+ genes singly was sufficient to trigger flocculation, and enhanced flocculation was observed in several combinations of double pfl+ overexpression. Among the pfl1+ genes, only loss of gsf2+ abrogated the flocculent phenotype of all the transcription factor mutants and prevented flocculation when cells were grown in inducing medium containing glycerol and ethanol as the carbon source, thereby indicating that Gsf2 is the dominant flocculin. In contrast, the mild flocculation of adn2+ or adn3+ overexpression was likely mediated by the transcriptional activation of cell wall–remodeling genes including gas2+, psu1+, and SPAC4H3.03c. We also discovered that Mbx2 and Cbf12 displayed transcriptional autoregulation, and Rfl1 repressed gsf2+ expression in an inhibitory feed-forward loop involving mbx2+. These results reveal that flocculation in S. pombe is regulated by a complex network of multiple transcription factors and target genes encoding flocculins and cell wall–remodeling enzymes. Moreover, comparisons between the flocculation transcriptional-regulatory networks of Saccharomyces cerevisiae and S. pombe indicate substantial rewiring of transcription factors and cis-regulatory

  17. A comparison of different regulatory approaches, analysis of the relative benefits of command and control, reflexive law and social licensing in ensuring oil industry compliance with environmentally sustainable practices and obligations

    NASA Astrophysics Data System (ADS)

    Ghanaati, Sahar

    This paper explores the relative benefits of command and control, reflexive law and social licensing in ensuring oil industry compliance with environmentally sustainable practices and obligations. Recognizing why oil sands and their development are significant, the background and development are reviewed first, and then the focus is shifted to look at its economics including the benefits, uncertainties and environmental costs of development. This paper examines how lawmakers in Canada have failed to meet their respective obligation. Drawing on environmental provisions, case law and legal scholars’ articles, books and reports, this paper examines the very problematic issue of oil sands regulation. It proposes to provide an in depth analysis of each regulatory forms and their application to the oil sands. It concludes that in order to solve the oil sands regulation challenges, a collaborative stringent enforcement of regulation from both federal and provincial governments, oil industry and public Pressure is required.

  18. 75 FR 61531 - Issuance of Regulatory Guide

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-05

    ... E. Norris, Component Integrity Branch, Division of Engineering, Office of Nuclear Regulatory... From the Federal Register Online via the Government Publishing Office NUCLEAR REGULATORY COMMISSION Issuance of Regulatory Guide AGENCY: Nuclear Regulatory Commission. ACTION: Notice. SUMMARY:...

  19. Regulatory approaches to worker protection in nanotechnology industry in the USA and European union.

    PubMed

    Murashov, Vladimir; Schulte, Paul; Geraci, Charles; Howard, John

    2011-01-01

    A number of reports have been published regarding the applicability of existing regulatory frameworks to protect consumers and the environment from potentially adverse effects related to introduction of nanomaterials into commerce in the United States and the European Union. However, a detailed comparison of the regulatory approaches to worker safety and health in the USA and in the EU is lacking. This report aims to fill this gap by reviewing regulatory frameworks designed to protect workers and their possible application to nanotechnology.

  20. Abeta targets of the biosimilar antibodies of Bapineuzumab, Crenezumab, Solanezumab in comparison to an antibody against N‑truncated Abeta in sporadic Alzheimer disease cases and mouse models.

    PubMed

    Bouter, Yvonne; Lopez Noguerola, Jose Socrates; Tucholla, Petra; Crespi, Gabriela A N; Parker, Michael W; Wiltfang, Jens; Miles, Luke A; Bayer, Thomas A

    2015-11-01

    Solanezumab and Crenezumab are two humanized antibodies targeting Amyloid-β (Aβ) which are currently tested in multiple clinical trials for the prevention of Alzheimer's disease. However, there is a scientific discussion ongoing about the target engagement of these antibodies. Here, we report the immunohistochemical staining profiles of biosimilar antibodies of Solanezumab, Crenezumab and Bapineuzumab in human formalin-fixed, paraffin-embedded tissue and human fresh frozen tissue. Furthermore, we performed a direct comparative immunohistochemistry analysis of the biosimilar versions of the humanized antibodies in different mouse models including 5XFAD, Tg4-42, TBA42, APP/PS1KI, 3xTg. The staining pattern with these humanized antibodies revealed a surprisingly similar profile. All three antibodies detected plaques, cerebral amyloid angiopathy and intraneuronal Aβ in a similar fashion. Remarkably, Solanezumab showed a strong binding affinity to plaques. We also reaffirmed that Bapineuzumab does not recognize N-truncated or modified Aβ, while Solanezumab and Crenezumab do detect N-terminally modified Aβ peptides Aβ4-42 and pyroglutamate Aβ3-42. In addition, we compared the results with the staining pattern of the mouse NT4X antibody that recognizes specifically Aβ4-42 and pyroglutamate Aβ3-42, but not full-length Aβ1-42. In contrast to the biosimilar antibodies of Solanezumab, Crenezumab and Bapineuzumab, the murine NT4X antibody shows a unique target engagement. NT4X does barely cross-react with amyloid plaques in human tissue. It does, however, detect cerebral amyloid angiopathy in human tissue. In Alzheimer mouse models, NT4X detects intraneuronal Aβ and plaques comparable to the humanized antibodies. In conclusion, the biosimilar antibodies Solanezumab, Crenezumab and Bapineuzumab strongly react with amyloid plaques, which are in contrast to the NT4X antibody that hardly recognizes plaques in human tissue. Therefore, NT4X is the first of a new class of

  1. Evolving Robust Gene Regulatory Networks

    PubMed Central

    Noman, Nasimul; Monjo, Taku; Moscato, Pablo; Iba, Hitoshi

    2015-01-01

    Design and implementation of robust network modules is essential for construction of complex biological systems through hierarchical assembly of ‘parts’ and ‘devices’. The robustness of gene regulatory networks (GRNs) is ascribed chiefly to the underlying topology. The automatic designing capability of GRN topology that can exhibit robust behavior can dramatically change the current practice in synthetic biology. A recent study shows that Darwinian evolution can gradually develop higher topological robustness. Subsequently, this work presents an evolutionary algorithm that simulates natural evolution in silico, for identifying network topologies that are robust to perturbations. We present a Monte Carlo based method for quantifying topological robustness and designed a fitness approximation approach for efficient calculation of topological robustness which is computationally very intensive. The proposed framework was verified using two classic GRN behaviors: oscillation and bistability, although the framework is generalized for evolving other types of responses. The algorithm identified robust GRN architectures which were verified using different analysis and comparison. Analysis of the results also shed light on the relationship among robustness, cooperativity and complexity. This study also shows that nature has already evolved very robust architectures for its crucial systems; hence simulation of this natural process can be very valuable for designing robust biological systems. PMID:25616055

  2. Comparison of internal target volumes defined on 3-dimensional, 4-dimensonal, and cone-beam CT images of non-small-cell lung cancer

    PubMed Central

    Li, Fengxiang; Li, Jianbin; Ma, Zhifang; Zhang, Yingjie; Xing, Jun; Qi, Huanpeng; Shang, Dongping

    2016-01-01

    Purpose The purpose of this study was to compare the positional and volumetric differences of internal target volumes defined on three-dimensional computed tomography (3DCT), four-dimensional CT (4DCT), and cone-beam CT (CBCT) images of non-small-cell lung cancer (NSCLC). Materials and methods Thirty-one patients with NSCLC sequentially underwent 3DCT and 4DCT simulation scans of the thorax during free breathing. The first CBCT was performed and registered to the planning CT using the bony anatomy registration during radiotherapy. The gross tumor volumes were contoured on the basis of 3DCT, maximum intensity projection (MIP) of 4DCT, and CBCT. CTV3D (clinical target volume), internal target volumes, ITVMIP and ITVCBCT, were defined with a 7 mm margin accounting for microscopic disease. ITV10 mm and ITV5 mm were defined on the basis of CTV3D: ITV10 mm with a 5 mm margin in left–right (LR), anterior–posterior (AP) directions and 10 mm in cranial–caudal (CC) direction; ITV5 mm with an isotropic internal margin (IM) of 5 mm. The differences in the position, size, Dice’s similarity coefficient (DSC) and inclusion relation of different volumes were evaluated. Results The median size ratios of ITV10 mm, ITV5 mm, and ITVMIP to ITVCBCT were 2.33, 1.88, and 1.03, respectively, for tumors in the upper lobe and 2.13, 1.76, and 1.1, respectively, for tumors in the middle-lower lobe. The median DSCs of ITV10 mm, ITV5 mm, ITVMIP, and ITVCBCT were 0.6, 0.66, and 0.83 for all patients. The median percentages of ITVCBCT not included in ITV10 mm, ITV5 mm, and ITVMIP were 0.1%, 1.63%, and 15.21%, respectively, while the median percentages of ITV10 mm, ITV5 mm, and ITVMIP not included in ITVCBCT were 57.08%, 48.89%, and 20.04%, respectively. Conclusion The use of the individual ITV derived from 4DCT merely based on bony registration in radiotherapy may result in a target miss. The ITVs derived from 3DCT with isotropic margins have a good coverage of the ITV from CBCT, but the

  3. Comparison of the (p,xn) cross sections from /sup 238/U, /sup 235/U, and /sup 232/Th targets irradiated with 200-MeV protons

    SciTech Connect

    Chu, Y.Y.; Zhou, M.L.

    1982-01-01

    We have measured absolute cross sections for (p,xn) reactions (x ranges from 0 to 8) from /sup 238/U, /sup 235/U, and /sup 232/Th targets irradiated with 200-MeV protons at the Brookhaven AGS Linac injector. Chemical yields were determined by using /sup 239/Np and /sup 233/Pa as tracers. Yield patterns obtained in this work can be compared to the experimental results and theoretical calculations from earlier work, and they are consistent within the framework of intranuclear cascade followed by neutron evaporation and fission competition.

  4. Proposed HEW Day Care Requirements. Regulatory Analysis Draft.

    ERIC Educational Resources Information Center

    Department of Health , Education, and Welfare, Washington., DC. Office of the Secretary.

    The purpose of this analysis is to provide decision makers with a careful comparison of alternate regulatory approaches and requirements for federal day care programs. The proposed day care regulations and this analysis cover about one-fifth of federal funding for day care and an even smaller segment of the total day care market. Proposed…

  5. Formation of Regulatory Modules by Local Sequence Duplication

    PubMed Central

    Nourmohammad, Armita; Lässig, Michael

    2011-01-01

    Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here we show that a large fraction of neighboring transcription factor binding sites in the fly genome have formed from a common sequence origin by local duplications. This mode of evolution is found to produce regulatory information: duplications can seed new sites in the neighborhood of existing sites. Duplicate seeds evolve subsequently by point mutations, often towards binding a different factor than their ancestral neighbor sites. These results are based on a statistical analysis of 346 cis-regulatory modules in the Drosophila melanogaster genome, and a comparison set of intergenic regulatory sequence in Saccharomyces cerevisiae. In fly regulatory modules, pairs of binding sites show significantly enhanced sequence similarity up to distances of about 50 bp. We analyze these data in terms of an evolutionary model with two distinct modes of site formation: (i) evolution from independent sequence origin and (ii) divergent evolution following duplication of a common ancestor sequence. Our results suggest that pervasive formation of binding sites by local sequence duplications distinguishes the complex regulatory architecture of higher eukaryotes from the simpler architecture of unicellular organisms. PMID:21998564

  6. Biotin/Folate-decorated Human Serum Albumin Nanoparticles of Docetaxel: Comparison of Chemically Conjugated Nanostructures and Physically Loaded Nanoparticles for Targeting of Breast Cancer.

    PubMed

    Nateghian, Navid; Goodarzi, Navid; Amini, Mohsen; Atyabi, Fatemeh; Khorramizadeh, Mohammad Reza; Dinarvand, Rassoul

    2016-01-01

    Docetaxel (DTX) is a widely used chemotherapeutic agent with very low water solubility. Conjugation of DTX to human serum albumin (HSA) is an effective way to increase its water solubility. Attachment of folic acid (FA) or biotin as targeting moieties to DTX-HSA conjugates may lead to active targeting and specific uptake by cancer cells with overexpressed FA or biotin receptors. In this study, FA or biotin molecules were attached to DTX-HSA conjugates by two different methods. In one method, FA or biotin molecules were attached to remaining NH2 residues of HSA in DTX-HSA conjugate by covalent bonds. In the second method, HSA-FA or HSA-biotin conjugates were synthesized separately and then combined by DTX-HSA conjugate in proper ratio to prepare nanoparticles containing DTX-HSA plus HSA-FA or HSA-biotin. Cell viability of different nanoparticle was evaluated on MDA-MB-231 (folate receptor positive), A549 (folate receptor negative), and 4T1 (biotin receptor positive) and showed superior cytotoxicity compared with free docetaxel (Taxotere). In vivo studies of DTX-HSA-FA and DTX-HSA-biotin conjugates in BULB/c mice, tumorized by 4T1 cell line, showed the conjugates prepared in this study were more powerful in the reduction in tumor size and increasing the survival rate when compared to free docetaxel.

  7. Comparison of the selective targeting efficacy of Salmonella typhimurium A1-R and VNP20009 on the Lewis lung carcinoma in nude mice.

    PubMed

    Zhang, Yong; Zhang, Nan; Zhao, Ming; Hoffman, Robert M

    2015-06-10

    Salmonella typhimurium A1-R is auxotrophic for arg and leu, which attenuates growth in normal tissue but allows high tumor targeting and virulence. A1-R is effective against metastatic human prostate, breast, and pancreatic cancer as well as osteosarcoma, fibrosarcoma, and glioma in clinically-relevant mouse models. VNP20009 is also a genetically-modified strain of Salmonella typhimurium that has been tested in Phase I clinical trials, but is more attenuated than S. typhimurium A1-R and in addition of multiple amino-acid auxotrophs, is purine auxotropic with the purI mutation. In the present study, mouse Lewis lung carcinoma-bearing nude mouse models were treated with S. typhimurium A1-R or VNP20009. S. typhimurium A1-R and VNP20009 were both eliminated from the liver and spleen approximately 3-5 days after administration via the tail vein. However, A1-R showed higher tumor targeting and inhibited the Lewis lung carcinoma to a greater extent than VNP20009, with less body weight loss. The mice tolerated S. typhimurium A1-R to at a least 2-fold higher dose than VNP20009 when the bacteria were administered iv. The results of the present study suggest that S. typhimurium A1-R has greater clinical potential than VNP20009.

  8. Dose finding when the target dose is on a plateau of a dose-response curve: comparison of fully sequential designs.

    PubMed

    Ivanova, Anastasia; Xiao, Changfu

    2013-01-01

    Consider the problem of estimating a dose with a certain response rate. Many multistage dose-finding designs for this problem were originally developed for oncology studies where the mean dose-response is strictly increasing in dose. In non-oncology phase II dose-finding studies, the dose-response curve often plateaus in the range of interest, and there are several doses with the mean response equal to the target. In this case, it is usually of interest to find the lowest of these doses because higher doses might have higher adverse event rates. It is often desirable to compare the response rate at the estimated target dose with a placebo and/or active control. We investigate which of the several known dose-finding methods developed for oncology phase I trials is the most suitable when the dose-response curve plateaus. Some of the designs tend to spread the allocation among the doses on the plateau. Others, such as the continual reassessment method and the t-statistic design, concentrate allocation at one of the doses with the t-statistic design selecting the lowest dose on the plateau more frequently.

  9. Comparison of real-time PCR assays for detection of pathogenic Leptospira spp. in blood and identification of variations in target sequences.

    PubMed

    Bourhy, Pascale; Bremont, Sylvie; Zinini, Farida; Giry, Claude; Picardeau, Mathieu

    2011-06-01

    Leptospirosis is considered an underdiagnosed disease. Although several PCR-based methods are currently in use, there is little information on their comparability. In this study, four quantitative real-time PCR (qPCR) assays (SYBR green and TaqMan chemistries) targeting the secY, lfb1, and lipL32 genes were evaluated as diagnostic assays. In our hands, these assays can detect between 10(2) and 10(3) bacteria/ml of pure culture, whole-blood, plasma, and serum samples. In three independent experiments, we found a slightly higher sensitivity of the PCR assays in plasma than in whole blood and serum. We also evaluated the specificity of the PCR assays on reference Leptospira strains, including newly described Leptospira species, and clinical isolates. No amplification was detected for DNA obtained from saprophytic or intermediate Leptospira species. However, among the pathogens, we identified sequence polymorphisms in target genes that result in primer and probe mismatches and affect qPCR assay performance. In conclusion, most of these assays are sensitive and specific tools for routine diagnosis of leptospirosis. However, it is important to continually evaluate and, if necessary, modify the primers and/or probes used to ensure effective detection of the circulating Leptospira isolates.

  10. A comparison of the reliability of two gene targets in loop-mediated isothermal amplification assays for detecting leptospiral DNA in canine urine.

    PubMed

    Gentilini, Fabio; Zanoni, Renato Giulio; Zambon, Elisa; Turba, Maria Elena

    2017-01-01

    We compared 2 novel loop-mediated isothermal amplification (LAMP) assays that target either the 16S ribosomal RNA ( rrs) gene or the gene encoding a 32-kDa leptospiral lipoprotein ( lipL32) in order to assess the effect of the target on the accuracy of the LAMP assays. The most sensitive assay was the rrs assay with a limit of detection (LOD) of 1.2 × 10(1) genome equivalents per reaction. The novel lipL32 assay showed an LOD of 1.2 × 10(2) genome equivalents per reaction. Both assays showed adequate specificity when tested against a collection of bacteria commonly found in voided canine urine. However, when field samples were assayed, the rrs assays gave many false-positive results and a poor positive predictive value of 8.33%. In conclusion, even if the LAMP assay is used in low prevalence areas, the lipL32 assay would be preferable. Conversely, the higher analytical sensitivity of the rrs assay could be effectively used as a screening test in endemic areas with high disease prevalence, followed by confirmation of the positive results using the lipL32 assay.

  11. WE-AB-BRA-01: 3D-2D Image Registration for Target Localization in Spine Surgery: Comparison of Similarity Metrics Against Robustness to Content Mismatch

    SciTech Connect

    De Silva, T; Ketcha, M; Siewerdsen, J H; Uneri, A; Reaungamornrat, S; Vogt, S; Kleinszig, G; Lo, S F; Wolinsky, J P; Gokaslan, Z L; Aygun, N

    2015-06-15

    Purpose: In image-guided spine surgery, mapping 3D preoperative images to 2D intraoperative images via 3D-2D registration can provide valuable assistance in target localization. However, the presence of surgical instrumentation, hardware implants, and soft-tissue resection/displacement causes mismatches in image content, confounding existing registration methods. Manual/semi-automatic methods to mask such extraneous content is time consuming, user-dependent, error prone, and disruptive to clinical workflow. We developed and evaluated 2 novel similarity metrics within a robust registration framework to overcome such challenges in target localization. Methods: An IRB-approved retrospective study in 19 spine surgery patients included 19 preoperative 3D CT images and 50 intraoperative mobile radiographs in cervical, thoracic, and lumbar spine regions. A neuroradiologist provided truth definition of vertebral positions in CT and radiography. 3D-2D registration was performed using the CMA-ES optimizer with 4 gradient-based image similarity metrics: (1) gradient information (GI); (2) gradient correlation (GC); (3) a novel variant referred to as gradient orientation (GO); and (4) a second variant referred to as truncated gradient correlation (TGC). Registration accuracy was evaluated in terms of the projection distance error (PDE) of the vertebral levels. Results: Conventional similarity metrics were susceptible to gross registration error and failure modes associated with the presence of surgical instrumentation: for GI, the median PDE and interquartile range was 33.0±43.6 mm; similarly for GC, PDE = 23.0±92.6 mm respectively. The robust metrics GO and TGC, on the other hand, demonstrated major improvement in PDE (7.6 ±9.4 mm and 8.1± 18.1 mm, respectively) and elimination of gross failure modes. Conclusion: The proposed GO and TGC similarity measures improve registration accuracy and robustness to gross failure in the presence of strong image content mismatch. Such

  12. Comparison of the effects of couplings to breakup channels in reactions induced by {sup 6}Li and {sup 6}He on the same {sup 64}Zn target

    SciTech Connect

    Fernández-García, J. P. Di Pietro, A.; Figuera, P.; Fisichella, M.; Lattuada, M.; Musumarra, A.; Pellegriti, M. G.; Scuderi, V.; Torresi, D.; Moro, A. M.; Zadro, M.

    2015-10-15

    The experimental elastic scattering angular distributions for the weakly bound nuclei {sup 6,7}Li and for the halo nucleus {sup 6}He on the same {sup 64}Zn target at several energies around the Coulomb barrier were measured at the Laboratori Nazionali del Sud (LNS, Italy) and at the Cyclotron Research Center, Louvain La Neuve (Belgium), respectively. The measured elastic scattering angular distributions of these three systems at the same center of mass energy have been compared. The experimental data of the {sup 6,7}Li+ {sup 64}Zn systems have been analyzed within the CDCC method, while the {sup 6}He+{sup 64}Zn data have been compared with both both CDCC and CRC calculations.

  13. Reduced variability and execution time to reach a target with a needle GPS system: Comparison between physicians, residents and nurse anaesthetists.

    PubMed

    Fevre, Marie-Cécile; Vincent, Caroline; Picard, Julien; Vighetti, Arnaud; Chapuis, Claire; Detavernier, Maxime; Allenet, Benoît; Payen, Jean-François; Bosson, Jean-Luc; Albaladejo, Pierre

    2016-09-19

    Ultrasound (US) guided needle positioning is safer than anatomical landmark techniques for central venous access. Hand-eye coordination and execution time depend on the professional's ability, previous training and personal skills. Needle guidance positioning systems (GPS) may theoretically reduce execution time and facilitate needle positioning in specific targets, thus improving patient comfort and safety. Three groups of healthcare professionals (41 anaesthesiologists and intensivists, 41 residents in anaesthesiology and intensive care, 39 nurse anaesthetists) were included and required to perform 3 tasks (positioning the tip of a needle in three different targets in a silicon phantom) by using successively a conventional US-guided needle positioning and a needle GPS. We measured execution times to perform the tasks, hand-eye coordination and the number of repositioning occurrences or errors in handling the needle or the probe. Without the GPS system, we observed a significant inter-individual difference for execution time (P<0.05), hand-eye coordination and the number of errors/needle repositioning between physicians, residents and nurse anaesthetists. US training and video gaming were found to be independent factors associated with a shorter execution time. Use of GPS attenuated the inter-individual and group variability. We observed a reduced execution time and improved hand-eye coordination in all groups as compared to US without GPS. Neither US training, video gaming nor demographic personal or professional factors were found to be significantly associated with reduced execution time when GPS was used. US associated with GPS systems may improve safety and decrease execution time by reducing inter-individual variability between professionals for needle-handling procedures.

  14. Comparison and Consensus Guidelines for Delineation of Clinical Target Volume for CT- and MR-Based Brachytherapy in Locally Advanced Cervical Cancer

    PubMed Central

    Viswanathan, Akila N.; Erickson, Beth; Gaffney, David K.; Bosch, Walter

    2014-01-01

    Purpose/Objective To create and compare consensus clinical target volume (CTV) contours for computed tomography (CT) and 3 Tesla (3T) magnetic resonance (MR) image-based cervical-cancer brachytherapy Materials/Methods Twenty-three gynecologic radiation oncology experts contoured the same 3 cervical-cancer brachytherapy cases: one Stage IIB near-complete response (CR) case with a tandem and ovoid, one Stage IIB partial response (PR) case with ovoid with needles and one Stage IB2 CR case with a ring applicator. CT contours were completed before MRI contours. These were analyzed for consistency and clarity of target delineation using an expectation maximization algorithm for simultaneous truth and performance level estimation (STAPLE), with kappa statistics as a measure of agreement between participants. The conformity index (CI) was calculated for each of the six data sets. Dice coefficients were generated to compare CT and MR contours of the same case. Results For all 3 cases, the mean tumor volume was smaller on MR than on CT (p<0.001). Kappa and CI estimates were slightly higher for CT, indicating a higher level of agreement on CT. DICE coefficients were 89% for the Stage IB2 case with a CR, 74% for the Stage IIB case with a PR, and 57% for the Stage IIB case with a CR. Conclusion When comparing MR- to CT-contoured CTV volumes, the higher level of agreement on CT may be due to the more distinct contrast visible on the images at the time of brachytherapy. The largest difference at the time of brachytherapy was in the case with parametrial extension at diagnosis that had a near-complete response, due to the appearance of the parametria on CT but not on MR. Based on these results, a 95% consensus volume was generated for CT and for MR. Online contouring atlases are available for instruction at http://www.nrgoncology.org/Resources/ContouringAtlases.aspx. PMID:25304792

  15. Comparison of Gull Feces-Specific Assays Targeting the 16S rRNA Genes of Catellicoccus marimammalium and Streptococcus spp.

    PubMed Central

    Ryu, Hodon; Griffith, John F.; Khan, Izhar U. H.; Hill, Stephen; Edge, Thomas A.; Toledo-Hernandez, Carlos; Gonzalez-Nieves, Joel

    2012-01-01

    Two novel gull-specific quantitative PCR (qPCR) assays were developed using 16S rRNA gene sequences from gull fecal clone libraries: a SYBR green assay targeting Streptococcus spp. (gull3) and a hydrolysis TaqMan assay targeting Catellicoccus marimammalium (gull4). The objectives of this study were to compare the host specificity of a previous C. marimammalium qPCR assay (gull2) with that of the new markers and to examine the presence of the three gull markers in environmental water samples from different geographic locations. Most of the gull fecal samples tested (n = 255) generated positive signals with the gull2 and gull4 assays (i.e., >86%), whereas only 28% were positive with gull3. Low prevalence and abundance of tested gull markers (0.6 to 15%) were observed in fecal samples from six nonavian species (n = 180 fecal samples), whereas the assays cross-reacted to some extent (13 to 31%) with other (nongull) avian fecal samples. The gull3 assay was positive against fecal samples from 11 of 15 avian species, including gull. Of the presumed gull-impacted water samples (n = 349), 86%, 59%, and 91% were positive with the gull2, the gull3, and the gull4 assays, respectively. Approximately 5% of 239 non-gull-impacted water samples were positive with the gull2 and the gull4 assays, whereas 21% were positive witg the gull3 assay. While the relatively high occurrence of gull2 and gull4 markers in waters impacted by gull feces suggests that these assays could be used in environmental monitoring studies, the data also suggest that multiple avian-specific assays will be needed to accurately assess the contribution of different avian sources in recreational waters. PMID:22226950

  16. Comparison of Measurements of the Uterus and Cervix Obtained by Magnetic Resonance and Transabdominal Ultrasound Imaging to Identify the Brachytherapy Target in Patients With Cervix Cancer

    SciTech Connect

    Dyk, Sylvia van; Kondalsamy-Chennakesavan, Srinivas; Schneider, Michal; Bernshaw, David; Narayan, Kailash

    2014-03-15

    Purpose: To compare measurements of the uterus and cervix obtained with magnetic resonance imaging (MRI) and transabdominal ultrasound to determine whether ultrasound can identify the brachytherapy target and be used to guide conformal brachytherapy planning and treatment for cervix cancer. Methods and Materials: Consecutive patients undergoing curative treatment with radiation therapy between January 2007 and March 2012 were included in the study. Intrauterine applicators were inserted into the uterine canal while patients were anesthetized. Images were obtained by MRI and transabdominal ultrasound in the longitudinal axis of the uterus with the applicator in treatment position. Measurements were taken at the anterior and posterior surface of the uterus at 2.0-cm intervals along the applicator, from the external os to the tip of the applicator. Data were analyzed using Bland Altman plots examining bias and 95% limits of agreement. Results: A total of 192 patients contributed 1668 measurements of the cervix and uterus. Mean (±SD) differences of measurements between imaging modalities at the anterior and posterior uterine surface ranged from 1.5 (±3.353) mm to 3.7 (±3.856) mm, and −1.46 (±3.308) mm to 0.47 (±3.502) mm, respectively. The mean differences were less than 3 mm in the cervix. The mean differences were less than 1.5 mm at all measurement points on the posterior surface. Conclusion: Differences in the measurements of the cervix and uterus obtained by MRI and ultrasound were within clinically acceptable limits. Transabdominal ultrasound can be substituted for MRI in defining the target volume for conformal brachytherapy treatment of cervix cancer.

  17. Alpha particle induced reactions on natCr up to 39 MeV: Experimental cross-sections, comparison with theoretical calculations and thick target yields for medically relevant 52gFe production

    NASA Astrophysics Data System (ADS)

    Hermanne, A.; Adam Rebeles, R.; Tárkányi, F.; Takács, S.

    2015-08-01

    Thin natCr targets were obtained by electroplating, using 23.75 μm Cu foils as backings. In five stacked foil irradiations, followed by high resolution gamma spectroscopy, the cross sections for production of 52gFe, 49,51cumCr, 52cum,54,56cumMn and 48cumV in Cr and 61Cu,68Ga in Cu were measured up to 39 MeV incident α-particle energy. Reduced uncertainty is obtained by simultaneous remeasurement of the natCu(α,x)67,66Ga monitor reactions over the whole energy range. Comparisons with the scarce literature values and results from the TENDL-2013 on-line library, based on the theoretical code family TALYS-1.6, were made. A discussion of the production routes for 52gFe with achievable yields and contamination rates was made.

  18. Targeted percutaneous microwave ablation at the pulmonary lesion combined with mediastinal radiotherapy with or without concurrent chemotherapy in locally advanced non-small cell lung cancer evaluation in a randomized comparison study.

    PubMed

    Xu, Xinglu; Ye, Xin; Liu, Gang; Zhang, Tingping

    2015-09-01

    Concurrent chemoradiotherapy is the standard treatment for patients with locally advanced lung cancer. The most common dose-limiting adverse effect of thoracic radiotherapy (RT) is radiation pneumonia (RP). A randomized comparison study was designed to investigate targeted percutaneous microwave ablation at pulmonary lesion combined with mediastinal RT with or without chemotherapy (ablation group) in comparison with RT (target volume includes pulmonary tumor and mediastinal node) with or without chemotherapy (RT group) for the treatment of locally advanced non-small cell lung cancers (NSCLCs). From 2009 to 2012, patients with stage IIIA or IIIB NSCLCs who refused to undergo surgery or were not suitable for surgery were enrolled. Patients were randomly assigned to the RT group (n = 47) or ablation group (n = 51). Primary outcomes were the incidence of RP and curative effectiveness (complete response, partial response, and stable disease); secondary outcome was the 2-year overall survival (OS). Fifteen patients (31.9%) in the RT and two (3.9%) in the ablation group experienced RP (P < 0.001). The ratio of effective cases was 85.1 versus 80.4% for mediastinal lymph node (P = 0.843) and 83.0 versus 100% for pulmonary tumors (P = 0.503), respectively, for the RT and ablation groups. Kaplan-Meier analysis demonstrated 2-year OS rate of NSCLC patients in ablation group was higher than RT group, but no statistical difference (log-rank test, P = 0.297). Percutaneous microwave ablation followed by RT for inoperable stage III NSCLCs may result in a lower rate of RP and better local control than radical RT treatments.

  19. California environmental regulatory climate: Linking regulation to specific concerns

    SciTech Connect

    Rauh, T.N.

    1996-12-31

    This paper focuses on three areas of change which are aimed at recognizing and taking advantage of the benefits offered by the tremendous body of information and knowledge now available in the realm of environmental protection and regulation: Comprehensive re-evaluation and reform of California`s hazardous waste management regulatory program through the Department of Toxic Substances Control`s (DTSC) Regulatory Structure Update (RSU), which is designed to eliminate unnecessary regulatory burden while retaining requirements needed to protect the citizens and environment of California; Consolidation of governmental oversight functions in the areas of hazardous materials and hazardous waste at the local level through certified unified program agencies (CUPAs), providing for more effective and efficient utilization of limited governmental resources; Development of environmental management standards and systems and compliance assurance plans and programs to shift regulatory emphasis away from pre-operational regulatory agency command and control review and approval towards self-responsibility and self-evaluation on the part of California businesses with regulatory agencies emphasizing compliance assistance and enforcement targeted at bad actors. Together, these program reforms and redirections, when fully implemented, will substantially alter and improve the environmental regulatory climate for California business, while effectively protecting the environment and health of all Californians.

  20. [Comparison of two access portals of an employee assistance program at an insurance corporation targeted to reduce stress levels of employees].

    PubMed

    Burnus, M; Benner, V; Kirchner, D; Drabik, A; Stock, St

    2012-03-01

    Support programmes for stress reduction were offered independently in two departments (650 employees in total) of an insurance group. Both departments, referred to as comparison group 1 and 2 (CG1 and CG2), offered an Employee Assistance Programme (EAP) featuring individual consultations. The employees were addressed through different channels of communication, such as staff meetings, superiors and email. In CG1, a staff adviser additionally called on all employees at their workplace and showed them a brief relaxing technique in order to raise awareness of stress reduction. By contacting employees personally it was also intended to reduce the inhibition threshold for the following individual talks. In CG2 individual talks were done face-to-face, whereas CG1 used telephone counselling. By using the new access channel with an additional personal contact at the workplace, an above average percentage of employees in CG1 could be motivated to participate in the following talks. The rate of participants was five times as high as in CG1, with lower costs for the consultation in each case.

  1. Distant cis Regulatory Elements in Human Skeletal Muscle Differentiation

    PubMed Central

    McCord, Rachel Patton; Zhou, Vicky W.; Yuh, Tiffany; Bulyk, Martha L.

    2011-01-01

    Identifying gene regulatory elements and their target genes in human cells remains a significant challenge. Despite increasing evidence of physical interactions between distant regulatory elements and gene promoters in mammalian cells, many studies consider only promoter-proximal regulatory regions. We identify putative cis-regulatory modules (CRMs) in human skeletal muscle differentiation by combining myogenic TF binding data before and after differentiation with histone modification data in myoblasts. CRMs that are distant (>20 kb) from muscle gene promoters are common and are more likely than proximal promoter regions to show differentiation-specific changes in myogenic TF binding. We find that two of these distant CRMs, known to activate transcription in differentiating myoblasts, interact physically with gene promoters (PDLIM3 and ACTA1) during differentiation. Our results highlight the importance of considering distal CRMs in investigations of mammalian gene regulation and support the hypothesis that distant CRM-promoter looping contacts are a general mechanism of gene regulation. PMID:21907276

  2. Meeting Regulatory Needs.

    PubMed

    Weber, Michael Fred

    2017-02-01

    The world is experiencing change at an unprecedented pace, as reflected in social, cultural, economic, political, and technological advances around the globe. Regulatory agencies, like the U.S. Nuclear Regulatory Commission (NRC), must also transform in response to and in preparation for these changes. In 2014, the NRC staff commenced Project Aim 2020 to transform the agency by enhancing efficiency, agility, and responsiveness, while accomplishing NRC's safety and security mission. Following Commission review and approval in 2015, the NRC began implementing the approved strategies, including strategic workforce planning to provide confidence that NRC will have employees with the right skills and talents at the right time to accomplish the agency's mission. Based on the work conducted so far, ensuring an adequate pipeline of radiation protection professionals is a significant need that NRC shares with states and other government agencies, private industry, academia, as well as international counterparts. NRC is working to ensure that sufficient radiation protection professionals will be available to fulfill its safety and security mission and leverage the work of the National Council on Radiation Protection and Measurements, the Conference of Radiation Control Program Directors, the Health Physics Society, the Organization of Agreement States, the International Atomic Energy Agency, the Nuclear Energy Agency, and others.

  3. Clinical research: regulatory issues.

    PubMed

    Wermeling, D P

    1999-02-01

    The regulatory issues faced by institutions performing clinical research are described. Many institutions do not have on staff an expert who understands the regulatory issues involved in managing investigational new drug research and who knows the institution's obligations under the federal rules. Because pharmacists understand the FDA regulations that apply to the management of drugs in clinical research, institutions are asking pharmacists to expand their role and manage clinical research offices. Many authorities govern various aspects of investigational drug research. FDA has published regulations for good clinical practice (GCP), and the International Conference on Harmonisation is developing an international standard for the proper management of clinical trials. The guidelines published by the Joint Commission on Accreditation of Healthcare Organizations aim to protect patients who are in the institution to receive health care and also participate in clinical trials. The Social Security Administration Acts specifically state that only items and services that are reasonable and necessary for the diagnosis and treatment of injury or disease can be billed to the government; research-related billings are excluded from coverage. Proper management of drug research is crucial to the success of a research program that is integrated with patient care.

  4. Regulatory considerations for biosimilars.

    PubMed

    Nellore, Ranjani

    2010-01-01

    Currently there is considerable interest in the legislative debate around generic biological drugs or "biosimilars" in the EU and US due to the large, lucrative market that it offers to the industry. While some countries have issued a few regulatory guidelines as well as product specific requirements, there is no general consensus as to a single, simple mechanism similar to the bioequivalence determination that leads to approval of generic small molecules all over the world. The inherent complex nature of the molecules, along with complicated manufacturing and analytical techniques to characterize them make it difficult to rely on a single human pharmacokinetic study for assurance of safety and efficacy. In general, the concept of comparability has been used for evaluation of the currently approved "similar" biological where a step by step assessment on the quality, preclinical and clinical aspects is made. In India, the focus is primarily on the availability and affordability of life-saving drugs. In this context every product needs to be evaluated on its own merit irrespective of the innovator brand. The formation of the National Biotechnology Regulatory Authority may provide a step in the right direction for regulation of these complex molecules. However, in order to have an efficient machinery for initial approval and ongoing oversight with a country-specific focus, cooperation with international authorities for granting approvals and continuous risk-benefit review is essential. Several steps are still needed for India to be perceived as a country that leads the world in providing quality biological products.

  5. Comparison of real-time PCR and conventional PCR with two DNA targets for detection of Leishmania (Leishmania) infantum infection in human and dog blood samples.

    PubMed

    Mohammadiha, A; Mohebali, M; Haghighi, A; Mahdian, R; Abadi, A R; Zarei, Z; Yeganeh, F; Kazemi, B; Taghipour, N; Akhoundi, B

    2013-01-01

    Zoonotic visceral leishmaniasis (VL) is endemic in northwestern Iran. Real-time PCR, conventional PCR, and the direct agglutination test (DAT) were used to diagnose Leishmania infantum infection in blood samples from 100 domestic dogs and 100 humans. Based on clinical evaluation, 82 humans and 72 dogs from the endemic area were categorized as having asymptomatic infection, DAT positive with no clinical signs of VL, or symptomatic infection, DAT positive with at least one sign of VL. Eighteen human samples containing no Leishmania antibodies (DAT(-)) and 28 dog DAT(-) sera from non-endemic areas with no history of VL constituted negative controls. All 46 DAT(-) samples were also negative by Dipstick rK39. Bone marrow material was used for parasitological examinations in symptomatic VL, and peripheral blood samples were used for detection of L. infantum infection using conventional PCR and real-time PCR in non-symptomatic subjects. Two DNA targets (ITS1 kDNA) were used for conventional PCR. L. infantum antibodies in sera were detected by DAT. Parasitemia was measured by real-time PCR targeting kDNA using Taqman Assay. All 72 (100%) symptomatic (38/38) and asymptomatic (34/34) dog DAT(+)samples, 45 of 48 (93.8%) symptomatic human DAT(+) samples, and 32 of 34 (94.1%) human asymptomatic cases were identified by real-time PCR. The mean (59.19 vs 12.38 parasite equivalents/mL of blood) and median (16.15 vs 1 parasite equivalents/mL of blood) ranges of parasitemia were higher in dogs than in humans (P<0.05). The highest agreement was obtained between real-time PCR and DAT (99% in dogs and 95% in humans). Sensitivity of 100% and 93.9%, specificity of 96.4% and 100%, positive predictive values of 98.6% and 100%, and negative predictive values of 100% and 78.3% were found by real-time PCR for dog and human samples, respectively.

  6. Learning regulatory programs that accurately predict differential expression with MEDUSA.

    PubMed

    Kundaje, Anshul; Lianoglou, Steve; Li, Xuejing; Quigley, David; Arias, Marta; Wiggins, Chris H; Zhang, Li; Leslie, Christina

    2007-12-01

    Inferring gene regulatory networks from high-throughput genomic data is one of the central problems in computational biology. In this paper, we describe a predictive modeling approach for studying regulatory networks, based on a machine learning algorithm called MEDUSA. MEDUSA integrates promoter sequence, mRNA expression, and transcription factor occupancy data to learn gene regulatory programs that predict the differential expression of target genes. Instead of using clustering or correlation of expression profiles to infer regulatory relationships, MEDUSA determines condition-specific regulators and discovers regulatory motifs that mediate the regulation of target genes. In this way, MEDUSA meaningfully models biological mechanisms of transcriptional regulation. MEDUSA solves the problem of predicting the differential (up/down) expression of target genes by using boosting, a technique from statistical learning, which helps to avoid overfitting as the algorithm searches through the high-dimensional space of potential regulators and sequence motifs. Experimental results demonstrate that MEDUSA achieves high prediction accuracy on held-out experiments (test data), that is, data not seen in training. We also present context-specific analysis of MEDUSA regulatory programs for DNA damage and hypoxia, demonstrating that MEDUSA identifies key regulators and motifs in these processes. A central challenge in the field is the difficulty of validating reverse-engineered networks in the absence of a gold standard. Our approach of learning regulatory programs provides at least a partial solution for the problem: MEDUSA's prediction accuracy on held-out data gives a concrete and statistically sound way to validate how well the algorithm performs. With MEDUSA, statistical validation becomes a prerequisite for hypothesis generation and network building rather than a secondary consideration.

  7. Comparison of active and passive targeting of doxorubicin for somatostatin receptor 2 positive tumor models by octreotide-modified HPMA copolymer-doxorubicin conjugates.

    PubMed

    He, Shuang; Zhou, Zhou; Li, Lian; Yang, Qingqing; Yang, Yang; Guan, Shan; Zhang, Jian; Zhu, Xi; Jin, Yun; Huang, Yuan

    2016-01-01

    Somatostatin receptor 2 (SSTR2), specifically over-expressed on many tumor cells, is a potential receipt for active targeting in cancer therapy. In the present study, octreotide (Oct), which had high affinity to SSTR2, was attached to N-(2-hydroxypropyl) methacrylamide (HPMA) polymeric system to enhance the antitumor efficiency of the anticancer drug doxorubicin (DOX). Two kinds of cell lines (HepG2 and A549), which overexpress SSTR2, were chosen as cell models. Compared with non-modified conjugates, Oct-modified conjugates exhibited superior cytotoxicity and intracellular uptake on both HepG2 and A549 cell lines. This might be due to the mechanism of receptor-mediated endocytosis. Subsequently, the in vivo biodistribution and antitumor activity evaluations showed that Oct modification significantly improved the tumor accumulation and antitumor efficacy of HPMA copolymer conjugates in SSTR2 over-expressed Kunming mice bearing H22 tumor xenografts. In summary, Oct-modified HPMA polymer-DOX conjugates might be a promising system for the treatment of SSTR2 over-expressed cancers.

  8. A Cross-model Comparison of Global Long-term Technology Diffusion under a 2°C Climate Change Control Target

    SciTech Connect

    van der Zwaan, Bob; Rosler, Hilke; Kober, Tom; Aboumahboub, Tino; Calvin, Katherine V.; Gernaat, David; Marangoni, Giacomo; McCollum, David

    2013-11-04

    We investigate the long-term global energy technology diffusion patterns required to reach a stringent climate change target with a maximum average atmospheric temperature increase of 2°C. If the anthropogenic temperature increase is to be limited to 2°C, total CO2 emissions have to be reduced massively, so as to reach substantial negative values during the second half of the century. Particularly power sector CO2 emissions should become negative from around 2050 onwards according to most models used for this analysis in order to compensate for GHG emissions in other sectors where abatement is more costly. The annual additional capacity deployment intensity (expressed in GW/yr) for solar and wind energy until 2030 needs to be around that recently observed for coal-based power plants, and will have to be several times higher in the period 2030–2050. Relatively high agreement exists across models in terms of the aggregated low-carbon energy system cost requirements on the supply side until 2050, which amount to about 50 trillion US$.

  9. Development of numerical model to investigate the laser driven shock waves from aluminum target into ambient air at atmospheric pressure and its comparison with experiment

    NASA Astrophysics Data System (ADS)

    Shiva, S. Sai; Leela, Ch.; Chaturvedi, S.; Sijoy, C. D.; Kiran, P. Prem

    2017-01-01

    A one-dimensional, three-temperature (electron, ion and thermal radiation) numerical model was developed to study the laser induced shock wave (LISW) propagation from aluminum target in ambient air at atmospheric pressure. The hydrodynamic equations of mass, momentum and energy are solved by using an implicit scheme in Lagrangian form. The model considers the laser absorption to take place via inverse-bremsstrahlung due to electron-ion (e-i) process. The flux limited electron thermal energy transport due e-i and e-n thermal energy relaxation equations are solved implicitly. The experimental characterization of spatio-temporal evolution of the LISW in air generated by focusing a second harmonic (532 nm, 7ns) of Nd:YAG laser on to surface of Al is performed using shadowgraphy technique with a temporal resolution of 1.5 ns. The velocity of SW observed in the experiments over 0.2 µs-8 µs time scales was compared with the numerical results to understand the SW transition from planar to spherical evolution.

  10. MODIS Collection 6 aerosol products: Comparison between Aqua's e-Deep Blue, Dark Target, and "merged" data sets, and usage recommendations

    NASA Astrophysics Data System (ADS)

    Sayer, A. M.; Munchak, L. A.; Hsu, N. C.; Levy, R. C.; Bettenhausen, C.; Jeong, M.-J.

    2014-12-01

    The Moderate Resolution Imaging Spectroradiometer (MODIS) Atmospheres data product suite includes three algorithms applied to retrieve midvisible aerosol optical depth (AOD): the Enhanced Deep Blue (DB) and Dark Target (DT) algorithms over land, and a DT over-water algorithm. All three have been refined in the recent "Collection 6" (C6) MODIS reprocessing. In particular, DB has been expanded to cover vegetated land surfaces as well as brighter desert/urban areas. Additionally, a new "merged" data set which draws from all three algorithms is included in the C6 products. This study is intended to act as a point of reference for new and experienced MODIS data users with which to understand the global and regional characteristics of the C6 DB, DT, and merged data sets, based on MODIS Aqua data. This includes validation against Aerosol Robotic Network (AERONET) observations at 111 sites, focused toward regional and categorical (surface/aerosol type) analysis. Neither algorithm consistently outperforms the other, although in many cases the retrieved AOD and the level of its agreement with AERONET are very similar. In many regions the DB, DT, and merged data sets are all suitable for quantitative applications, bearing in mind that they cannot be considered independent, while in other cases one algorithm does consistently outperform the other. Usage recommendations and caveats are thus somewhat complicated and regionally dependent.

  11. Comparison of sample preparation strategies for target analysis of total thyroid hormones levels in serum by liquid chromatography-quadrupole time-of-flight-mass spectrometry.

    PubMed

    Álvarez, E; Madrid, Y; Marazuela, M D

    2017-03-01

    This paper describes a novel method based on liquid chromatography quadrupole time-of-flight-mass spectrometry (LC-QTOF-MS) for target analysis of total THs in serum. Several sample preparation strategies have been evaluated to reduce matrix effect (namely, HybridSPE cartridges, supported liquid extraction, SLE and solid phase extraction, SPE). Deproteinization and further clean-up with mixed-mode SPE was selected as the best strategy for sample preparation, since achieved the cleanest extracts and reduced ionization suppression effects (between -11 and -24%). Method validation was performed by the analysis of control human serum samples. Criteria for confirming THs identity in serum extracts were based on retention times, accurate masses, isotopic pattern and MS/MS fragmentation pattern. Moreover, the quantitation capabilities of the LC-QTOF-MS method were also evaluated in terms of linearity, precision, accuracy and sensitivity by the application of matrix-matched calibration. Additionally, the developed LC-QTOF-MS method successfully provides qualitative information on endogenous components responsible of ion suppression (e.g. lysophosphatidylcholines), via post acquisition data analysis. This demonstrates the significant advantage of using LC-QTOF-MS, as it allows retrospective querying of the acquired data without the need of re-injecting/re-processing the samples.

  12. Heat and noxious chemical sensor, chicken TRPA1, as a target of bird repellents and identification of its structural determinants by multispecies functional comparison.

    PubMed

    Saito, Shigeru; Banzawa, Nagako; Fukuta, Naomi; Saito, Claire T; Takahashi, Kenji; Imagawa, Toshiaki; Ohta, Toshio; Tominaga, Makoto

    2014-03-01

    Nociceptive receptors enable animals to sense tissue-damaging stimuli, thus playing crucial roles in survival. Due to evolutionary diversification, responses of nociceptive receptors to specific stimuli can vary among species. Multispecies functional comparisons of nociceptive receptors help elucidate their evolutionary process and molecular basis for activation. The transient receptor potential ankyrin 1 (TRPA1) ion channel serves as a nociceptive receptor for chemical and thermal stimuli that is heat-activated in reptiles and frogs while potentially cold-activated in rodents. Here, we characterized channel properties of avian TRPA1 in chicken. Chicken TRPA1 was activated by noxious chemicals that also activate TRPA1 in other vertebrates. Regarding thermal sensitivity, chicken TRPA1 was activated by heat stimulation, but not cold, thus thermal sensitivity of avian TRPA1 does not coincide with rodent TRPA1, although both are homeotherms. Furthermore, in chicken sensory neurons, TRPA1 was highly coexpressed with TRPV1, another nociceptive heat and chemical receptor, similar to mammals and frogs. These results suggest that TRPA1 acted as a noxious chemical and heat receptor, and was coexpressed with TRPV1 in the ancestral terrestrial vertebrate. The acquisition of TRPV1 as a novel heat receptor in the ancestral terrestrial vertebrate is likely to have affected the functional evolution of TRPA1 regarding thermal sensitivity and led to the diversification among diverse vertebrate species. Additionally, we found for the first time that chicken TRPA1 is activated by methyl anthranilate (MA) and its structurally related chemicals used as nonlethal bird repellents. MA-induced responses were abolished by a TRPA1 antagonist in somatosensory neurons, indicating that TRPA1 acts as a MA receptor in chicken. Furthermore, TRPA1 responses to MA varied among five diverse vertebrate species. Utilizing species diversity and mutagenesis experiments, three amino acids were identified

  13. How important is the choice of the nutrient profile model used to regulate broadcast advertising of foods to children? A comparison using a targeted data set

    PubMed Central

    Scarborough, P; Payne, C; Agu, C G; Kaur, A; Mizdrak, A; Rayner, M; Halford, J C G; Boyland, E

    2013-01-01

    Background/Objective: The World Health Assembly recommends that children's exposure to marketing of unhealthy foods should be reduced. Nutrient profile models have been developed that define ‘unhealthy' to support regulation of broadcast advertising of foods to children. The level of agreement between these models is not clear. The objective of this study was to measure the agreement between eight nutrient profile models that have been proposed for the regulation of marketing to children over (a) how many and (b) what kind of foods should be permitted to be advertised during television viewed by children. Subjects/Methods: A representative data set of commercials for foods broadcast during television viewed by children in the UK was collected in 2008. The data set consisted of 11 763 commercials for 336 different products or brands. This data set was supplemented with nutrition data from company web sites, food packaging and a food composition table, and the nutrient profile models were applied. Results: The percentage of commercials that would be permitted by the different nutrient profile models ranged from 2.1% (0.4%, 3.7%) to 47.4% (42.1%, 52.6%). Half of the pairwise comparisons between models yielded kappa statistics less than 0.2, indicating that there was little agreement between models. Conclusions: Policy makers considering the regulation of broadcast advertising to children should carefully consider the choice of nutrient profile model to support the regulation, as this choice will have considerable influence on the outcome of the regulation. PMID:23801095

  14. Regulatory roles of phosphorylation in model and pathogenic fungi

    PubMed Central

    Albataineh, Mohammad T.; Kadosh, David

    2015-01-01

    Over the past 20 years, considerable advances have been made toward our understanding of how post-translational modifications affect a wide variety of biological processes, including morphology and virulence, in medically important fungi. Phosphorylation stands out as a key molecular switch and regulatory modification that plays a critical role in controlling these processes. In this article, we first provide a comprehensive and up-to-date overview of the regulatory roles that both Ser/Thr and non-Ser/Thr kinases and phosphatases play in model and pathogenic fungi. Next, we discuss the impact of current global approaches that are being used to define the complete set of phosphorylation targets (phosphoproteome) in medically important fungi. Finally, we provide new insights and perspectives into the potential use of key regulatory kinases and phosphatases as targets for the development of novel and more effective antifungal strategies. PMID:26705834

  15. Sputter target

    DOEpatents

    Gates, Willard G.; Hale, Gerald J.

    1980-01-01

    The disclosure relates to an improved sputter target for use in the deposition of hard coatings. An exemplary target is given wherein titanium diboride is brazed to a tantalum backing plate using a gold-palladium-nickel braze alloy.

  16. Perchlorate Regulatory Determination Fact Sheets

    EPA Pesticide Factsheets

    Fact sheets have been developed for the perchlorate regulatory determination corresponding to the following stages published in the Federal Register: Final, Supplemental request for comments, and Preliminary.

  17. NMR structure of the HIV-1 regulatory protein Vpr in H2O/trifluoroethanol. Comparison with the Vpr N-terminal (1-51) and C-terminal (52-96) domains.

    PubMed

    Wecker, K; Morellet, N; Bouaziz, S; Roques, B P

    2002-08-01

    The human immunodeficiency virus type 1, HIV-1, genome encodes a highly conserved regulatory gene product, Vpr (96 amino acids), which is incorporated into virions in quantities equivalent to those of the viral Gag protein. In infected cells, Vpr is believed to function during the early stages of HIV-1 replication (such as transcription of the proviral genome and migration of preintegration nuclear complex), blocks cells in G2 phase and triggers apoptosis. Vpr also plays a critical role in long-term AIDS disease by inducing viral infection in nondividing cells such as monocytes and macrophages. To gain deeper insight of the structure-function relationship of Vpr, the intact protein (residues 1-96) was synthesized. Its three-dimensional structure was analysed using circular dichroism and two-dimensional 1H- and 15N-NMR and refined by restrained molecular dynamics. In addition, 15N relaxation parameters (T1, T2) and heteronuclear 1H-15N NOEs were measured. The structure of the protein is characterized by a well-defined gamma turn(14-16)-alpha helix(17-33)-turn(34-36), followed by a alpha helix(40-48)-loop(49-54)-alpha helix(55-83) domain and ends with a very flexible C-terminal sequence. This structural determination of the whole intact Vpr molecule provide insights into the biological role played by this protein during the virus life cycle, as such amphipathic helices are believed to be involved in protein-lipid bilayers, protein-protein and/or protein-nucleic acid interactions.

  18. 75 FR 54210 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-03

    ...-2010-032] Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of... Transactions August 30, 2010. On June 17, 2010, the Financial Industry Regulatory Authority, Inc....

  19. Comparison of catch and lake trout bycatch in commercial trap nets and gill nets targeting lake whitefish in northern Lake Huron

    USGS Publications Warehouse

    Johnson, James E.; Ebener, Mark P.; Gebhardt, Kenneth; Bergstedt, Roger

    2004-01-01

    We compared seasonal lake whitefish catch rates, lake trout bycatch, and gearinduced lake trout mortality between commercial trap nets and gill nets in north-central Lake Huron. Onboard monitors recorded catches from 260 gill net and 96 trap net lifts from October 1998 through December 1999. Catch rates for lake whitefish were highest in fall for both gear types, reflecting proximity of spawning sites to the study area. Lake whitefish catch rates were also relatively high in spring but low in both gear types in summer. Lake trout were the principal bycatch species in both gears. The lake trout bycatch was lowest in both gear types in fall, highest in gill nets in spring, and highest in trap nets in summer. The ratio of lake trout to legal whitefish (the target species) was highest in summer and lowest in fall in both gear types. The high lake trout ratio in summer was due principally to low catch rates of lake whitefish. All but 3 of 186 live lake trout removed from trap net pots survived for at least two days of observation in laboratory tanks. Therefore, we estimated that post-release survival of trap netted lake trout that had not been entangled in the mesh was 98.4%. In addition, we accounted for stress-induced mortality for lake trout that were live at capture but entangled in the mesh of either gear type. Resulting estimates of lake trout survival were higher in trap nets (87.8%) than in gill nets (39.6%). The number of lake trout killed per lift was highest during summer in trap nets and during spring in gill nets. In trap nets, 85% of dead lake trout were observed to be entangled in the mesh of the pot or tunnels. Survival rates of lake trout in gill nets were higher in our study than reported by others, probably because our nets were hand lifted in a small boat. Our trap net-induced mortality estimates on lake trout were higher than those reported by others because we adjusted our estimates to account for post-release mortality caused by handling and

  20. Evaluation of the cone beam CT for internal target volume localization in lung stereotactic radiotherapy in comparison with 4D MIP images

    SciTech Connect

    Wang, Lu; Chen, Xiaoming; Lin, Mu-Han; Lin, Teh; Fan, Jiajin; Jin, Lihui; Ma, Charlie M.; Xue, Jun

    2013-11-15

    Purpose: To investigate whether the three-dimensional cone-beam CT (CBCT) is clinically equivalent to the four-dimensional computed tomography (4DCT) maximum intensity projection (MIP) reconstructed images for internal target volume (ITV) localization in image-guided lung stereotactic radiotherapy.Methods: A ball-shaped polystyrene phantom with built-in cube, sphere, and cone of known volumes was attached to a motor-driven platform, which simulates a sinusoidal movement with changeable motion amplitude and frequency. Target motion was simulated in the patient in a superior-inferior (S-I) direction with three motion periods and 2 cm peak-to-peak amplitudes. The Varian onboard Exact-Arms kV CBCT system and the GE LightSpeed four-slice CT integrated with the respiratory-position-management 4DCT scanner were used to scan the moving phantom. MIP images were generated from the 4DCT images. The clinical equivalence of the two sets of images was evaluated by comparing the extreme locations of the moving objects along the motion direction, the centroid position of the ITV, and the ITV volumes that were contoured automatically by Velocity or calculated with an imaging gradient method. The authors compared the ITV volumes determined by the above methods with those theoretically predicted by taking into account the physical object dimensions and the motion amplitudes. The extreme locations were determined by the gradient method along the S-I axis through the center of the object. The centroid positions were determined by autocenter functions. The effect of motion period on the volume sizes was also studied.Results: It was found that the extreme locations of the objects determined from the two image modalities agreed with each other satisfactorily. They were not affected by the motion period. The average difference between the two modalities in the extreme locations was 0.68% for the cube, 1.35% for the sphere, and 0.5% for the cone, respectively. The maximum difference in the

  1. Intertemporal Regulatory Tasks and Responsibilities for Greenhouse Gas Reductions

    ERIC Educational Resources Information Center

    Deason, Jeffrey A.; Friedman, Lee S.

    2010-01-01

    Jurisdictions are in the process of establishing regulatory systems to control greenhouse gas emissions. Short-term and sometimes long-term emissions reduction goals are established, as California does for 2020 and 2050, but little attention has yet been focused on annual emissions targets for the intervening years. We develop recommendations for…

  2. Targeted Endovascular Temporary Vessel Occlusion with a Reverse Thermosensitive Polymer for Near-Bloodless Partial Nephrectomy: Comparison to Standard Surgical Clamping Techniques

    SciTech Connect

    Flacke, Sebastian; Harty, Niall J.; Laskey, Daniel H.; Moinzadeh, Alireza; Benn, James A.; Villani, Rosanna; Kalra, Aarti; Libertino, John A.; Madras, Peter N.

    2012-10-15

    Purpose: To determine whether reversible blood flow interruption to a randomly chosen target region of the kidney may be achieved with the injection of a reverse thermoplastic polymer through an angiographic catheter, thereby facilitating partial nephrectomy without compromising blood flow to the remaining kidney or adding risks beyond those encountered by the use of hilar clamping. Methods: Fifteen pigs underwent partial nephrectomy after blood flow interruption by vascular cross-clamping or injection of polymer (Lumagel Trade-Mark-Sign ) into a segmental artery. Five animals were euthanized after surgery (three open and two laparoscopic resection, cross-clamping n = 2), and 10 (open resection, cross-clamping n = 4) were euthanized after 6 weeks' survival. Blood specimens were obtained periodically, and angiogram and necropsy were performed at 6 weeks. Results: Selective renal ischemia was achieved in all cases. Surgical resection time averaged 9 and 24.5 min in the open and laparoscopic groups, respectively. Estimated blood loss was negligible with the exception of one case where an accessory renal artery was originally overlooked. Reversal of the polymer to a liquid state was consistent angiographically and visually in all cases. Time to complete flow return averaged 7.4 and 2 min for polymer and clamping, respectively. Angiography at 6 weeks revealed no evidence of vascular injury. Laboratory data and necropsies revealed no differences between animals undergoing vascular clamping or polymer injection. Conclusion: Lumagel was as effective as vascular clamping in producing a near bloodless operative field for partial nephrectomy while maintaining flow to the uninvolved portion of the affected kidney.

  3. The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation.

    PubMed

    Schwartz, John C; Gibson, Mark S; Heimeier, Dorothea; Koren, Sergey; Phillippy, Adam M; Bickhart, Derek M; Smith, Timothy P L; Medrano, Juan F; Hammond, John A

    2017-04-01

    Natural killer (NK) cells are a diverse population of lymphocytes with a range of biological roles including essential immune functions. NK cell diversity is in part created by the differential expression of cell surface receptors which modulate activation and function, including multiple subfamilies of C-type lectin receptors encoded within the NK complex (NKC). Little is known about the gene content of the NKC beyond rodent and primate lineages, other than it appears to be extremely variable between mammalian groups. We compared the NKC structure between mammalian species using new high-quality draft genome assemblies for cattle and goat; re-annotated sheep, pig, and horse genome assemblies; and the published human, rat, and mouse lemur NKC. The major NKC genes are largely in the equivalent positions in all eight species, with significant independent expansions and deletions between species, allowing us to propose a model for NKC evolution during mammalian radiation. The ruminant species, cattle and goats, have independently evolved a second KLRC locus flanked by KLRA and KLRJ, and a novel KLRH-like gene has acquired an activating tail. This novel gene has duplicated several times within cattle, while other activating receptor genes have been selectively disrupted. Targeted genome enrichment in cattle identified varying levels of allelic polymorphism between the NKC genes concentrated in the predicted extracellular ligand-binding domains. This novel recombination and allelic polymorphism is consistent with NKC evolution under balancing selection, suggesting that this diversity influences individual immune responses and may impact on differential outcomes of pathogen infection and vaccination.

  4. Cross-species pharmacokinetic comparison from mouse to man of a second-generation antisense oligonucleotide, ISIS 301012, targeting human apolipoprotein B-100.

    PubMed

    Yu, Rosie Z; Kim, Tae-Won; Hong, An; Watanabe, Tanya A; Gaus, Hans J; Geary, Richard S

    2007-03-01

    The pharmacokinetics of a 2'-O-(2-methoxyethyl)-modified oligonucleotide, ISIS 301012 [targeting human apolipoprotein B-100 (apoB-100)], was characterized in mouse, rat, monkey, and human. Plasma pharmacokinetics following parental administration was similar across species, exhibiting a rapid distribution phase with t(1/2alpha) of several hours and a prolonged elimination phase with t(1/2beta) of days. The prolonged elimination phase represents equilibrium between tissues and circulating drug due to slow elimination from tissues. Absorption was nearly complete following s.c. injection, with bioavailability ranging from 80 to 100% in monkeys. Plasma clearance scaled well across species as a function of body weight alone, and this correlation was improved when corrected for plasma protein binding. In all of the animal models studied, the highest tissue concentrations of ISIS 301012 were observed in kidney and liver. Urinary excretion was less than 3% in monkeys and human in the first 24 h. ISIS 301012 is highly bound to plasma proteins, probably preventing rapid removal by renal filtration. However, following 25 mg/kg s.c. administration in mouse and 5-mg/kg i.v. bolus administration in rat, plasma concentrations of ISIS 301012 exceeded their respective protein binding capacity. Thus, urinary excretion increased to 16% or greater within the first 24 h. Albeit slow, urinary excretion of ISIS 301012 and its shortened metabolites is the ultimate elimination pathway of this compound, as demonstrated by 32% of dose recovered in total excreta by 14 days in a rat mass balance study. The pharmacokinetics of ISIS 301012 in human is predictable from the pharmacokinetics measured in animals. The pharmacokinetic properties of ISIS 301012 provide guidance for clinical development and support infrequent dose administration.

  5. Amino Acid and Biogenic Amine Profile Deviations in an Oral Glucose Tolerance Test: A Comparison between Healthy and Hyperlipidaemia Individuals Based on Targeted Metabolomics

    PubMed Central

    Li, Qi; Gu, Wenbo; Ma, Xuan; Liu, Yuxin; Jiang, Lidan; Feng, Rennan; Liu, Liyan

    2016-01-01

    Hyperlipidemia (HLP) is characterized by a disturbance in lipid metabolism and is a primary risk factor for the development of insulin resistance (IR) and a well-established risk factor for cardiovascular disease and atherosclerosis. The aim of this work was to investigate the changes in postprandial amino acid and biogenic amine profiles provoked by an oral glucose tolerance test (OGTT) in HLP patients using targeted metabolomics. We used ultra-high-performance liquid chromatography-triple quadrupole mass spectrometry to analyze the serum amino acid and biogenic amine profiles of 35 control and 35 HLP subjects during an OGTT. The amino acid and biogenic amine profiles from 30 HLP subjects were detected as independent samples to validate the changes in the metabolites. There were differences in the amino acid and biogenic amine profiles between the HLP individuals and the healthy controls at baseline and after the OGTT. The per cent changes of 13 metabolites from fasting to the 2 h samples during the OGTT in the HLP patients were significantly different from those of the healthy controls. The lipid parameters were associated with the changes in valine, isoleucine, creatine, creatinine, dimethylglycine, asparagine, serine, and tyrosine (all p < 0.05) during the OGTT in the HLP group. The postprandial changes in isoleucine and γ-aminobutyric acid (GABA) during the OGTT were positively associated with the homeostasis model assessment of insulin resistance (HOMA-IR; all p < 0.05) in the HLP group. Elevated oxidative stress and disordered energy metabolism during OGTTs are important characteristics of metabolic perturbations in HLP. Our findings offer new insights into the complex physiological regulation of metabolism during the OGTT in HLP. PMID:27338465

  6. Comparison of effect-site concentration of remifentanil for tracheal intubation with the lightwand and laryngoscopy during propofol target-controlled infusion

    PubMed Central

    Kim, Jin-Soo; Kim, Dae-Hee; Min, Sang-Kee; Kim, Kyung-Mi

    2011-01-01

    Background Target-controlled infusion (TCI) of propofol and remifentanil can provide satisfactory intubating conditions without a neuromuscular blocking agent. We compared the effect-site concentration of remifentanil required for intubation with the lightwand and the Macintosh laryngoscope during propofol TCI without a neuromuscular blocking agent in adult patients. Methods Forty-nine patients were randomly assigned to the lightwand group (n = 25) or the direct laryngoscope group (n = 24). Anesthesia was induced by propofol TCI with an effect-site concentration of 5.4 µg/ml. Two minutes after start of propofol TCI, remifentanil was administered at the predetermined effect-site concentration. The effect-site concentration of remifentanil was determined using Dixon's up-and-down method (0.5 ng/ml as a step size). The first patient in each group was tested at 4.5 ng/ml of remifentanil. Tracheal intubation was performed 2 min after the start of remifentanil TCI. Acceptable intubation was defined as an excellent or good intubating conditions. Results Using a modified Dixon's up and down method, the EC50 ± SD of remifentanil in the lightwand and laryngoscope groups was 4.75 ± 0.71 ng/ml and 5.08 ± 0.52 ng/ml, respectively; there was no statistically significant difference between the groups (P = 0.373). Conclusions The effect-site concentration of remifentanil for acceptable intubation with the lightwand and Macintosh laryngoscope in 50% of adults did not differ during propofol TCI without a neuromuscular blocking agent. PMID:21738840

  7. Toxicogenomics in regulatory ecotoxicology

    USGS Publications Warehouse

    Ankley, Gerald T.; Daston, George P.; Degitz, Sigmund J.; Denslow, Nancy D.; Hoke, Robert A.; Kennedy, Sean W.; Miracle, Ann L.; Perkins, Edward J.; Snape, Jason; Tillitt, Donald E.; Tyler, Charles R.; Versteeg, Donald

    2006-01-01

    Recently, we have witnessed an explosion of different genomic approaches that, through a combination of advanced biological, instrumental, and bioinformatic techniques, can yield a previously unparalleled amount of data concerning the molecular and biochemical status of organisms. Fueled partially by large, well-publicized efforts such as the Human Genome Project, genomic research has become a rapidly growing topical area in multiple biological disciplines. Since 1999, when the term “toxicogenomics” was coined to describe the application of genomics to toxicology (1), a rapid increase in publications on the topic has occurred (Figure 1). The potential utility of toxicogenomics in toxicological research and regulatory activities has been the subject of scientific discussions and, as with any new technology, has evoked a wide range of opinion (2–6).

  8. Regulatory T cells.

    PubMed

    Thompson, Claire; Powrie, Fiona

    2004-08-01

    Regulatory T (TR) cells are a subset of T cells that function to control immune responses. Different populations of TR cells have been described, including thymically derived CD4(+)CD25+ TR cells and Tr1 cells induced in the periphery through exposure to antigen. A transcription factor, Foxp3, has been identified that is essential for CD4(+)CD25+ TR cell development and function. There is now evidence that transforming growth factor-beta might play a role in this pathway. CD4(+)CD25+ TR cells proliferate extensively in vivo in an antigen-specific manner, and can respond to both self and foreign peptides. By suppressing excessive immune responses, TR cells play a key role in the maintenance of self-tolerance, thus preventing autoimmune disease, as well as inhibiting harmful inflammatory diseases such as asthma and inflammatory bowel disease.

  9. Multigenome DNA sequence conservation identifies Hox cis-regulatory elements

    PubMed Central

    Kuntz, Steven G.; Schwarz, Erich M.; DeModena, John A.; De Buysscher, Tristan; Trout, Diane; Shizuya, Hiroaki; Sternberg, Paul W.; Wold, Barbara J.

    2008-01-01

    To learn how well ungapped sequence comparisons of multiple species can predict cis-regulatory elements in Caenorhabditis elegans, we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how prediction quality varied with different genomes and parameters in our comparisons. Specifically, we sequenced ∼0.5% of the C. brenneri and C. sp. 3 PS1010 genomes, and compared five Caenorhabditis genomes (C. elegans, C. briggsae, C. brenneri, C. remanei, and C. sp. 3 PS1010) to find regulatory elements in 22.8 kb of noncoding sequence from the ceh-13/lin-39 Hox subcluster. We developed the MUSSA program to find ungapped DNA sequences with N-way transitive conservation, applied it to the ceh-13/lin-39 locus, and transgenically assayed 21 regions with both high and low degrees of conservation. This identified 10 functional regulatory elements whose activities matched known ceh-13/lin-39 expression, with 100% specificity and a 77% recovery rate. One element was so well conserved that a similar mouse Hox cluster sequence recapitulated the native nematode expression pattern when tested in worms. Our findings suggest that ungapped sequence comparisons can predict regulatory elements genome-wide. PMID:18981268

  10. Regulatory Considerations for Biosimilars

    PubMed Central

    Nellore, Ranjani

    2010-01-01

    Currently there is considerable interest in the legislative debate around generic biological drugs or “biosimilars” in the EU and US due to the large, lucrative market that it offers to the industry. While some countries have issued a few regulatory guidelines as well as product specific requirements, there is no general consensus as to a single, simple mechanism similar to the bioequivalence determination that leads to approval of generic small molecules all over the world. The inherent complex nature of the molecules, along with complicated manufacturing and analytical techniques to characterize them make it difficult to rely on a single human pharmacokinetic study for assurance of safety and efficacy. In general, the concept of comparability has been used for evaluation of the currently approved “similar” biological where a step by step assessment on the quality, preclinical and clinical aspects is made. In India, the focus is primarily on the availability and affordability of life-saving drugs. In this context every product needs to be evaluated on its own merit irrespective of the innovator brand. The formation of the National Biotechnology Regulatory Authority may provide a step in the right direction for regulation of these complex molecules. However, in order to have an efficient machinery for initial approval and ongoing oversight with a country-specific focus, cooperation with international authorities for granting approvals and continuous risk-benefit review is essential. Several steps are still needed for India to be perceived as a country that leads the world in providing quality biological products. PMID:21829775

  11. Regulatory Streamlining and Improvement

    SciTech Connect

    Mark A. Carl

    2006-07-11

    The Interstate Oil and Gas Compact Commission (IOGCC) engaged in numerous projects outlined under the scope of work discussed in the United States Department of Energy (DOE) grant number DE-FC26-04NT15456 awarded to the IOGCC. Numerous projects were completed that were extremely valuable to state oil and gas agencies as a result of work performed utilizing resources provided by the grant. There are numerous areas in which state agencies still need assistance. This additional assistance will need to be addressed under future scopes of work submitted annually to DOE's Project Officer for this grant. This report discusses the progress of the projects outlined under the grant scope of work for the 2005-2006 areas of interest, which are as follows: Area of Interest No. 1--Regulatory Streamlining and Improvement: This area of interest continues to support IOGCC's regulatory streamlining efforts that include the identification and elimination of unnecessary duplications of efforts between and among state and federal programs dealing with exploration and production on public lands. Area of Interest No. 2--Technology: This area of interest seeks to improve efficiency in states through the identification of technologies that can reduce costs. Area of Interest No. 3--Training and Education: This area of interest is vital to upgrading the skills of regulators and industry alike. Within the National Energy Policy, there are many appropriate training and education opportunities. Education was strongly endorsed by the President's National Energy Policy Development group. Acting through the governors offices, states are very effective conduits for the dissemination of energy education information. While the IOGCC favors the development of a comprehensive, long-term energy education plan, states are also supportive of immediate action on important concerns, such as energy prices, availability and conservation. Area of Interest No. 4--Resource Assessment and Development: This area

  12. Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks.

    PubMed

    Narang, Vipin; Ramli, Muhamad Azfar; Singhal, Amit; Kumar, Pavanish; de Libero, Gennaro; Poidinger, Michael; Monterola, Christopher

    2015-01-01

    Human gene regulatory networks (GRN) can be difficult to interpret due to a tangle of edges interconnecting thousands of genes. We constructed a general human GRN from extensive transcription factor and microRNA target data obtained from public databases. In a subnetwork of this GRN that is active during estrogen stimulation of MCF-7 breast cancer cells, we benchmarked automated algorithms for identifying core regulatory genes (transcription factors and microRNAs). Among these algorithms, we identified K-core decomposition, pagerank and betweenness centrality algorithms as the most effective for discovering core regulatory genes in the network evaluated based on previously known roles of these genes in MCF-7 biology as well as in their ability to explain the up or down expression status of up to 70% of the remaining genes. Finally, we validated the use of K-core algorithm for organizing the GRN in an easier to interpret layered hierarchy where more influential regulatory genes percolate towards the inner layers. The integrated human gene and miRNA network and software used in this study are provided as supplementary materials (S1 Data) accompanying this manuscript.

  13. Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain

    PubMed Central

    Schrider, Daniel R.; Kern, Andrew D.

    2015-01-01

    The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely missed by searching for sequence conservation across species. Here we present an analysis based on variation data among human genomes that utilizes a supervised machine learning approach for the identification of human-specific purifying selection in the genome. Using only allele frequency information from the complete low-coverage 1000 Genomes Project data set in conjunction with a support vector machine trained from known functional and nonfunctional portions of the genome, we are able to accurately identify portions of the genome constrained by purifying selection. Our method identifies previously known human-specific gains or losses of function and uncovers many novel candidates. Candidate targets for gain and loss of function along the human lineage include numerous putative regulatory regions of genes essential for normal development of the central nervous system, including a significant enrichment of gain of function events near neurotransmitter receptor genes. These results are consistent with regulatory turnover being a key mechanism in the evolution of human-specific characteristics of brain development. Finally, we show that the majority of the genome is unconstrained by natural selection currently, in agreement with what has been estimated from phylogenetic methods but in sharp contrast to estimates based on transcriptomics or other high-throughput functional methods. PMID:26590212

  14. Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain.

    PubMed

    Schrider, Daniel R; Kern, Andrew D

    2015-11-19

    The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely missed by searching for sequence conservation across species. Here we present an analysis based on variation data among human genomes that utilizes a supervised machine learning approach for the identification of human-specific purifying selection in the genome. Using only allele frequency information from the complete low-coverage 1000 Genomes Project data set in conjunction with a support vector machine trained from known functional and nonfunctional portions of the genome, we are able to accurately identify portions of the genome constrained by purifying selection. Our method identifies previously known human-specific gains or losses of function and uncovers many novel candidates. Candidate targets for gain and loss of function along the human lineage include numerous putative regulatory regions of genes essential for normal development of the central nervous system, including a significant enrichment of gain of function events near neurotransmitter receptor genes. These results are consistent with regulatory turnover being a key mechanism in the evolution of human-specific characteristics of brain development. Finally, we show that the majority of the genome is unconstrained by natural selection currently, in agreement with what has been estimated from phylogenetic methods but in sharp contrast to estimates based on transcriptomics or other high-throughput functional methods.

  15. Therapeutic target database update 2014: a resource for targeted therapeutics.

    PubMed

    Qin, Chu; Zhang, Cheng; Zhu, Feng; Xu, Feng; Chen, Shang Ying; Zhang, Peng; Li, Ying Hong; Yang, Sheng Yong; Wei, Yu Quan; Tao, Lin; Chen, Yu Zong

    2014-01-01

    Here we describe an update of the Therapeutic Target Database (http://bidd.nus.edu.sg/group/ttd/ttd.asp) for better serving the bench-to-clinic communities and for enabling more convenient data access, processing and exchange. Extensive efforts from the research, industry, clinical, regulatory and management communities have been collectively directed at the discovery, investigation, application, monitoring and management of targeted therapeutics. Increasing efforts have been directed at the development of stratified and personalized medicines. These efforts may be facilitated by the knowledge of the efficacy targets and biomarkers of targeted therapeutics. Therefore, we added search tools for using the International Classification of Disease ICD-10-CM and ICD-9-CM codes to retrieve the target, biomarker and drug information (currently enabling the search of almost 900 targets, 1800 biomarkers and 6000 drugs related to 900 disease conditions). We added information of almost 1800 biomarkers for 300 disease conditions and 200 drug scaffolds for 700 drugs. We significantly expanded Therapeutic Target Database data contents to cover >2300 targets (388 successful and 461 clinical trial targets), 20 600 drugs (2003 approved and 3147 clinical trial drugs), 20,000 multitarget agents against almost 400 target-pairs and the activity data of 1400 agents against 300 cell lines.

  16. Targeting growth factor supply in keratopathy treatment: comparison between maternal peripheral blood and cord blood as sources for the preparation of topical eye drops

    PubMed Central

    Versura, Piera; Buzzi, Marina; Giannaccare, Giuseppe; Terzi, Adriana; Fresina, Michela; Velati, Claudio; Campos, Emilio C.

    2016-01-01

    Background Epitheliotrophic growth factors (GF) can be supplied topically to patients with severe keratopathy through a variety of blood-derived products. We compared GF content in adult peripheral blood serum (PB-S) and cord blood serum (CB-S) as potential sources of GF. To limit inter-individual variability the assessment was performed in maternal-child pairs at the time of delivery. Material and methods The amounts of epidermal GF (EGF), insulin-like GF (IGF), transforming GF-beta (TGF-β), vascular endothelial GF (VEGF) in CB units collected from the umbilical vein and PB from mothers (each group n=30) were estimated by enzyme-linked immunosorbent assays. Obstetric characteristics and haematological data were recorded from the archives of the Emilia Romagna Cord Blood Bank. Statistical evaluations were performed by Wilcoxon’s test and correlations between variables were determined using Spearman’s (ρ) coefficient; p-values <0.05 were considered statistically significant. Results EGF, TGF-β and VEGF levels were significantly higher in CB-S than in PB-S (median 1,254.4 vs 646.0 pg/mL, 51.3 vs 38.4 μg/mL and 686.8 vs 30 pg/mL, respectively; all p<0.0001) whereas IGF content was significantly higher in PB-S than in CB-S (159.9 vs 53.5 pg/mL, respectively; p<0.0001). In CB-S, the CD34+ cell concentration appeared to be related to EGF, IGF and TGF-β levels whereas white blood cell count appeared to be related to EGF and TGF-β levels. VEGF levels showed no relation to the haematological parameters considered. Platelet counts were not related to GF level in either CB or PB. Discussion The GF content in the two blood sources was different, with CB containing larger amounts. Each GF selectively regulates cellular processes involved in corneal healing, so the use of PB or CB should be targeted to supply specific GF on the basis of the type and severity of the keratopathy. PMID:26192781

  17. Identification of early target genes of aflatoxin B1 in human hepatocytes, inter-individual variability and comparison with other genotoxic compounds

    SciTech Connect

    Josse, Rozenn; Dumont, Julie; Fautrel, Alain; Robin, Marie-Anne; Guillouzo, André

    2012-01-15

    Gene expression profiling has recently emerged as a promising approach to identify early target genes and discriminate genotoxic carcinogens from non-genotoxic carcinogens and non-carcinogens. However, early gene changes induced by genotoxic compounds in human liver remain largely unknown. Primary human hepatocytes and differentiated HepaRG cells were exposed to aflatoxin B1 (AFB1) that induces DNA damage following enzyme-mediated bioactivation. Gene expression profile changes induced by a 24 h exposure of these hepatocyte models to 0.05 and 0.25 μM AFB1 were analyzed by using oligonucleotide pangenomic microarrays. The main altered signaling pathway was the p53 pathway and related functions such as cell cycle, apoptosis and DNA repair. Direct involvement of the p53 protein in response to AFB1 was verified by using siRNA directed against p53. Among the 83 well-annotated genes commonly modulated in two pools of three human hepatocyte populations and HepaRG cells, several genes were identified as altered by AFB1 for the first time. In addition, a subset of 10 AFB1-altered genes, selected upon basis of their function or tumor suppressor role, was tested in four human hepatocyte populations and in response to other chemicals. Although they exhibited large variable inter-donor fold-changes, several of these genes, particularly FHIT, BCAS3 and SMYD3, were found to be altered by various direct and other indirect genotoxic compounds and unaffected by non-genotoxic compounds. Overall, this comprehensive analysis of early gene expression changes induced by AFB1 in human hepatocytes identified a gene subset that included several genes representing potential biomarkers of genotoxic compounds. -- Highlights: ► Gene expression profile changes induced by aflatoxin B1 in human hepatocytes. ► AFB1 modulates various genes including tumor suppressor genes and proto-oncogenes. ► Important inter-individual variations in the response to AFB1. ► Some genes also altered by other

  18. Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters.

    PubMed

    Santini, Simona; Boore, Jeffrey L; Meyer, Axel

    2003-06-01

    Comparisons of DNA sequences among evolutionarily distantly related genomes permit identification of conserved functional regions in noncoding DNA. Hox genes are highly conserved in vertebrates, occur in clusters, and are uninterrupted by other genes. We aligned (PipMaker) the nucleotide sequences of the HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human, and mouse, which are separated by approximately 500 million years of evolution. In support of our approach, several identified putative regulatory elements known to regulate the expression of Hox genes were recovered. The majority of the newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac database). The regulatory intergenic regions located between the genes that are expressed most anteriorly in the embryo are longer and apparently more evolutionarily conserved than those at the other end of Hox clusters. Different presumed regulatory sequences are retained in either the Aalpha or Abeta duplicated Hox clusters in the fish lineages. This suggests that the conserved elements are involved in different gene regulatory networks and supports the duplication-deletion-complementation model of functional divergence of duplicated genes.

  19. Regulatory Foci and Organizational Commitment

    ERIC Educational Resources Information Center

    Markovits, Yannis; Ullrich, Johannes; van Dick, Rolf; Davis, Ann J.

    2008-01-01

    We use regulatory focus theory to derive specific predictions regarding the differential relationships between regulatory focus and commitment. We estimated a structural equation model using a sample of 520 private and public sector employees and found in line with our hypotheses that (a) promotion focus related more strongly to affective…

  20. 75 FR 79763 - Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-20

    ...The Regulatory Flexibility Act of 1980 and Executive Order (EO) 12866 require the semi-annual issuance of an inventory of rulemaking actions under development throughout the Department with a view to offering summarized information about forthcoming regulatory actions for public...

  1. Microbial regulatory and metabolic networks.

    PubMed

    Cho, Byung-Kwan; Charusanti, Pep; Herrgård, Markus J; Palsson, Bernhard O

    2007-08-01

    Reconstruction of transcriptional regulatory and metabolic networks is the foundation of large-scale microbial systems and synthetic biology. An enormous amount of information including the annotated genomic sequences and the genomic locations of DNA-binding regulatory proteins can be used to define metabolic and regulatory networks in cells. In particular, advances in experimental methods to map regulatory networks in microbial cells have allowed reliable data-driven reconstruction of these networks. Recent work on metabolic engineering and experimental evolution of microbes highlights the key role of global regulatory networks in controlling specific metabolic processes and the need to consider the integrated function of multiple types of networks for both scientific and engineering purposes.

  2. Regulatory component analysis: a semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge

    PubMed Central

    Wang, Chen; Xuan, Jianhua; Shih, Ie-Ming; Clarke, Robert; Wang, Yue

    2011-01-01

    With the advent of high-throughput biotechnology capable of monitoring genomic signals, it becomes increasingly promising to understand molecular cellular mechanisms through systems biology approaches. One of the active research topics in systems biology is to infer gene transcriptional regulatory networks using various genomic data; this inference problem can be formulated as a linear model with latent signals associated with some regulatory proteins called transcription factors (TFs). As common statistical assumptions may not hold for genomic signals, typical latent variable algorithms such as independent component analysis (ICA) are incapable to reveal underlying true regulatory signals. Liao et al. [1] proposed to perform inference using an approach named network component analysis (NCA), the optimization of which is achieved by a least-squares fitting approach with biological knowledge constraints. However, the incompleteness of biological knowledge and its inconsistency with gene expression data are not considered in the original NCA solution, which could greatly affect the inference accuracy. To overcome these limitations, we propose a linear extraction scheme, namely regulatory component analysis (RCA), to infer underlying regulatory signals even with partial biological knowledge. Numerical simulations show a significant improvement of our proposed RCA over NCA, not only when signal-to-noise-ratio (SNR) is low, but also when the given biological knowledge is incomplete and inconsistent to gene expression data. Furthermore, real biological experiments on E. coli are performed for regulatory network inference in comparison with several typical linear latent variable methods, which again demonstrates the effectiveness and improved performance of the proposed algorithm. PMID:22685363

  3. Cancer-Associated Myeloid Regulatory Cells

    PubMed Central

    De Vlaeminck, Yannick; González-Rascón, Anna; Goyvaerts, Cleo; Breckpot, Karine

    2016-01-01

    Myeloid cells are critically involved in the pathophysiology of cancers. In the tumor microenvironment (TME), they comprise tumor-associated macrophages (TAMs), neutrophils (TANs), dendritic cells, and myeloid-derived suppressor cells, which are further subdivided into a monocytic subset and a granulocytic subset. Some of these myeloid cells, in particular TAMs and TANs, are divided into type 1 or type 2 cells, according to the paradigm of T helper type 1 or type 2 cells. Type 1-activated cells are generally characterized as cells that aid tumor rejection, while all other myeloid cells are shown to favor tumor progression. Moreover, these cells are often at the basis of resistance to various therapies. Much research has been devoted to study the biology of myeloid cells. This endeavor has proven to be challenging, as the markers used to categorize myeloid cells in the TME are not restricted to particular subsets. Also from a functional and metabolic point of view, myeloid cells share many features. Finally, myeloid cells are endowed with a certain level of plasticity, which further complicates studying them outside their environment. In this article, we challenge the exclusive use of cell markers to unambiguously identify myeloid cell subsets in the TME. We further propose to divide myeloid cells into myeloid regulatory or stimulatory cells according to their pro- or antitumor function, because we contend that for therapeutic purposes it is not targeting the cell subsets but rather targeting their protumor traits; hence, myeloid regulatory cells will push antitumor immunotherapy to the next level. PMID:27065074

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

    PubMed

    Banf, Michael; Rhee, Seung Y

    2017-02-01

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

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

    PubMed Central

    Banf, Michael; Rhee, Seung Y.

    2017-01-01

    A gene regulatory network links transcription factors to their target genes and represents a map of transcriptional regulation. Much progress has been made in deciphering gene regulatory networks computationally. However, gene regulatory network inference for most eukaryotic organisms remain challenging. To improve the accuracy of gene regulatory network inference and facilitate candidate selection for experimentation, we developed an algorithm called GRACE (Gene Regulatory network inference ACcuracy Enhancement). GRACE exploits biological a priori and heterogeneous data integration to generate high- confidence network predictions for eukaryotic organisms using Markov Random Fields in a semi-supervised fashion. GRACE uses a novel optimization scheme to integrate regulatory evidence and biological relevance. It is particularly suited for model learning with sparse regulatory gold standard data. We show GRACE’s potential to produce high confidence regulatory networks compared to state of the art approaches using Drosophila melanogaster and Arabidopsis thaliana data. In an A. thaliana developmental gene regulatory network, GRACE recovers cell cycle related regulatory mechanisms and further hypothesizes several novel regulatory links, including a putative control mechanism of vascular structure formation due to modifications in cell proliferation. PMID:28145456

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

    DOE PAGES

    Banf, Michael; Rhee, Seung Y.

    2017-02-01

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

  7. 75 FR 40000 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-13

    ... COMMISSION Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving Proposed Rule Change Relating to the Restated Certificate of Incorporation of Financial Industry Regulatory Authority, Inc. July 2, 2010. On May 21, 2010, Financial Industry Regulatory Authority, Inc....

  8. 75 FR 30453 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-01

    ... COMMISSION Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving..., Financial Industry Regulatory Authority, Inc. (``FINRA'') (f/k/a National Association of Securities Dealers... National Association of Securities Dealers, Inc., the Financial Industry Regulatory Authority, Inc., or...

  9. A cis-Regulatory Signature for Chordate Anterior Neuroectodermal Genes

    PubMed Central

    Christiaen, Lionel; Joly, Jean-Stéphane

    2010-01-01

    One of the striking findings of comparative developmental genetics was that expression patterns of core transcription factors are extraordinarily conserved in bilaterians. However, it remains unclear whether cis-regulatory elements of their target genes also exhibit common signatures associated with conserved embryonic fields. To address this question, we focused on genes that are active in the anterior neuroectoderm and non-neural ectoderm of the ascidian Ciona intestinalis. Following the dissection of a prototypic anterior placodal enhancer, we searched all genomic conserved non-coding elements for duplicated motifs around genes showing anterior neuroectodermal expression. Strikingly, we identified an over-represented pentamer motif corresponding to the binding site of the homeodomain protein OTX, which plays a pivotal role in the anterior development of all bilaterian species. Using an in vivo reporter gene assay, we observed that 10 of 23 candidate cis-regulatory elements containing duplicated OTX motifs are active in the anterior neuroectoderm, thus showing that this cis-regulatory signature is predictive of neuroectodermal enhancers. These results show that a common cis-regulatory signature corresponding to K50-Paired homeodomain transcription factors is found in non-coding sequences flanking anterior neuroectodermal genes in chordate embryos. Thus, field-specific selector genes impose architectural constraints in the form of combinations of short tags on their target enhancers. This could account for the strong evolutionary conservation of the regulatory elements controlling field-specific selector genes responsible for body plan formation. PMID:20419150

  10. Deciphering RNA Regulatory Elements Involved in the Developmental and Environmental Gene Regulation of Trypanosoma brucei.

    PubMed

    Gazestani, Vahid H; Salavati, Reza

    2015-01-01

    Trypanosoma brucei is a vector-borne parasite with intricate life cycle that can cause serious diseases in humans and animals. This pathogen relies on fine regulation of gene expression to respond and adapt to variable environments, with implications in transmission and infectivity. However, the involved regulatory elements and their mechanisms of actions are largely unknown. Here, benefiting from a new graph-based approach for finding functional regulatory elements in RNA (GRAFFER), we have predicted 88 new RNA regulatory elements that are potentially involved in the gene regulatory network of T. brucei. We show that many of these newly predicted elements are responsive to both transcriptomic and proteomic changes during the life cycle of the parasite. Moreover, we found that 11 of predicted elements strikingly resemble previously identified regulatory elements for the parasite. Additionally, comparison with previously predicted motifs on T. brucei suggested the superior performance of our approach based on the current limited knowledge of regulatory elements in T. brucei.

  11. Understanding genetic regulatory networks

    NASA Astrophysics Data System (ADS)

    Kauffman, Stuart

    2003-04-01

    Random Boolean networks (RBM) were introduced about 35 years ago as first crude models of genetic regulatory networks. RBNs are comprised of N on-off genes, connected by a randomly assigned regulatory wiring diagram where each gene has K inputs, and each gene is controlled by a randomly assigned Boolean function. This procedure samples at random from the ensemble of all possible NK Boolean networks. The central ideas are to study the typical, or generic properties of this ensemble, and see 1) whether characteristic differences appear as K and biases in Boolean functions are introducted, and 2) whether a subclass of this ensemble has properties matching real cells. Such networks behave in an ordered or a chaotic regime, with a phase transition, "the edge of chaos" between the two regimes. Networks with continuous variables exhibit the same two regimes. Substantial evidence suggests that real cells are in the ordered regime. A key concept is that of an attractor. This is a reentrant trajectory of states of the network, called a state cycle. The central biological interpretation is that cell types are attractors. A number of properties differentiate the ordered and chaotic regimes. These include the size and number of attractors, the existence in the ordered regime of a percolating "sea" of genes frozen in the on or off state, with a remainder of isolated twinkling islands of genes, a power law distribution of avalanches of gene activity changes following perturbation to a single gene in the ordered regime versus a similar power law distribution plus a spike of enormous avalanches of gene changes in the chaotic regime, and the existence of branching pathway of "differentiation" between attractors induced by perturbations in the ordered regime. Noise is serious issue, since noise disrupts attractors. But numerical evidence suggests that attractors can be made very stable to noise, and meanwhile, metaplasias may be a biological manifestation of noise. As we learn more

  12. Regulatory T Cells and Their Role in Animal Disease.

    PubMed

    Veiga-Parga, T

    2016-07-01

    In humans and mouse models, Foxp3(+) regulatory T cells are known to control all aspects of immune responses. However, only limited information exists on these cells' role in diseases of other animals. In this review, we cover the most important features and different types of regulatory T cells, which include those that are thymus-derived and peripherally induced, the mechanisms by which they control immune responses by targeting effector T cells and antigen-presenting cells, and most important, their role in animal health and diseases including cancer, infections, and other conditions such as hypersensitivities and autoimmunity. Although the literature regarding regulatory T cells in domestic animal species is still limited, multiple articles have recently emerged and are discussed. Moreover, we also discuss the evidence suggesting that regulatory T cells might limit the magnitude of effector responses, which can have either a positive or negative result, depending on the context of animal and human disease. In addition, the issue of plasticity is discussed because plasticity in regulatory T cells can result in the loss of their protective function in some microenvironments during disease. Lastly, the manipulation of regulatory T cells is discussed in assessing the possibility of their use as a treatment in the future.

  13. Conservation of trans-acting networks during mammalian regulatory evolution

    PubMed Central

    Stergachis, Andrew B.; Neph, Shane; Sandstrom, Richard; Haugen, Eric; Reynolds, Alex P.; Zhang, Miaohua; Byron, Rachel; Canfield, Theresa; Stelhing-Sun, Sandra; Lee, Kristen; Thurman, Robert E.; Vong, Shinny; Bates, Daniel; Neri, Fidencio; Diegel, Morgan; Giste, Erika; Dunn, Douglas; Hansen, R. Scott; Johnson, Audra K.; Sabo, Peter J.; Wilken, Matthew S.; Reh, Thomas A.; Treuting, Piper M.; Kaul, Rajinder; Groudine, Mark; Bender, M.A.; Borenstein, Elhanan; Stamatoyannopoulos, John A.

    2014-01-01

    The fundamental body plan and major physiological axes have been highly conserved during mammalian evolution, despite constraint of only a fraction of the human genome sequence. To quantify cis- vs. trans-regulatory contributions to mammalian regulatory evolution, we performed genomic DNase I footprinting of the mouse genome across 25 cell and tissue types, collectively defining >8.6 million TF occupancy sites at nucleotide resolution. Here we show that mouse TF footprints encode a regulatory lexicon of >600 motifs that is >95% similar with that recognized in vivo by human TFs. However, only ~20% of mouse TF footprints have human orthologues. Despite substantial turnover of the cis-regulatory landscape around each TF gene, nearly half of all pairwise regulatory interactions connecting mouse TF genes have been maintained in orthologous human cell types through evolutionary innovation of TF recognition sequences. Strikingly, the higher-level organization of mouse TF-to-TF connections into cellular network architectures is nearly identical with human. Our results suggest that evolutionary selection on mammalian gene regulation is targeted chiefly at the level of trans-regulatory circuitry. PMID:25409825

  14. Lawmakers target PURPA for repeal

    SciTech Connect

    Burkhart, L.A.

    1995-07-01

    This article is a review of current legislative initiatives to repeal certain sections of the Public Utilities Regulatory Policy Act (PURPA). Targeted for repeal is Section 210 of PURPA, which mandates purchases from qualifying facilities at avoided-cost rates. Pros and cons of this proposed repeal are reviewed, with Administration officials lining up against the repeal and industry casting their vote for repeal of this and other sections of PURPA.

  15. Internationalization of regulatory requirements.

    PubMed

    Juillet, Y

    2003-02-01

    The aim of harmonisation of medicines regulatory requirements is to allow the patient quicker access to new drugs and to avoid animal and human duplications. Harmonisation in the European Union (EU) is now completed, and has led to the submission of one dossier in one language study leading to European marketing authorizations, thanks in particular to efficacy guidelines published at the European level. With the benefit of the European experience since 1989, more than 40 guidelines have been harmonised amongst the EU, Japan and the USA through the International Conference on Harmonisation (ICH). ICH is a unique process gathering regulators and industry experts from the three regions. Its activity is built on expertise and trust. The Common Technical Document (CTD), an agreed common format for application in the three regions, is a logical follow-up to the ICH first phase harmonising the content of the dossier. The CTD final implementation in July 2003 will have considerable influence on the review process and on the exchange of information in the three regions.

  16. 21 CFR 500.88 - Regulatory method.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... § 500.88 Regulatory method. (a) The sponsor shall submit for evaluation and validation a regulatory... method validation data. (c) FDA will publish in the Federal Register the complete regulatory method...

  17. Inferring transcription factor collaborations in gene regulatory networks

    PubMed Central

    2014-01-01

    Background Living cells are realized by complex gene expression programs that are moderated by regulatory proteins called transcription factors (TFs). The TFs control the differential expression of target genes in the context of transcriptional regulatory networks (TRNs), either individually or in groups. Deciphering the mechanisms of how the TFs control the expression of target genes is a challenging task, especially when multiple TFs collaboratively participate in the transcriptional regulation. Results We model the underlying regulatory interactions in terms of the directions (activation or repression) and their logical roles (necessary and/or sufficient) with a modified association rule mining approach, called mTRIM. The experiment on Yeast discovered 670 regulatory interactions, in which multiple TFs express their functions on common target genes collaboratively. The evaluation on yeast genetic interactions, TF knockouts and a synthetic dataset shows that our algorithm is significantly better than the existing ones. Conclusions mTRIM is a novel method to infer TF collaborations in transcriptional regulation networks. mTRIM is available at http://www.msu.edu/~jinchen/mTRIM. PMID:24565025

  18. Characterizing regulatory path motifs in integrated networks using perturbational data

    PubMed Central

    2010-01-01

    We introduce Pathicular http://bioinformatics.psb.ugent.be/software/details/Pathicular, a Cytoscape plugin for studying the cellular response to perturbations of transcription factors by integrating perturbational expression data with transcriptional, protein-protein and phosphorylation networks. Pathicular searches for 'regulatory path motifs', short paths in the integrated physical networks which occur significantly more often than expected between transcription factors and their targets in the perturbational data. A case study in Saccharomyces cerevisiae identifies eight regulatory path motifs and demonstrates their biological significance. PMID:20230615

  19. Estimating Gene Regulatory Networks with pandaR.

    PubMed

    Schlauch, Daniel; Paulson, Joseph N; Young, Albert; Glass, Kimberly; Quackenbush, John

    2017-03-11

    PANDA (Passing Attributes betweenNetworks forData Assimilation) is a gene regulatory network inference method that begins with amodel of transcription factor-target gene interactions and usesmessage passing to update the network model given available transcriptomic and protein-protein interaction data. PANDA is used to estimate networks for each experimental group and the network models are then compared between groups to explore transcriptional processes that distinguish the groups. We present pandaR (bioconductor.org/packages/pandaR), a Bioconductor package that implements PANDA and provides a framework for exploratory data analysis on gene regulatory networks.

  20. Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference

    PubMed Central

    Kilicoglu, Halil; Shin, Dongwook; Rindflesch, Thomas C.

    2014-01-01

    Gene regulatory networks are a crucial aspect of systems biology in describing molecular mechanisms of the cell. Various computational models rely on random gene selection to infer such networks from microarray data. While incorporation of prior knowledge into data analysis has been deemed important, in practice, it has generally been limited to referencing genes in probe sets and using curated knowledge bases. We investigate the impact of augmenting microarray data with semantic relations automatically extracted from the literature, with the view that relations encoding gene/protein interactions eliminate the need for random selection of components in non-exhaustive approaches, producing a more accurate model of cellular behavior. A genetic algorithm is then used to optimize the strength of interactions using microarray data and an artificial neural network fitness function. The result is a directed and weighted network providing the individual contribution of each gene to its target. For testing, we used invasive ductile carcinoma of the breast to query the literature and a microarray set containing gene expression changes in these cells over several time points. Our model demonstrates significantly better fitness than the state-of-the-art model, which relies on an initial random selection of genes. Comparison to the component pathways of the KEGG Pathways in Cancer map reveals that the resulting networks contain both known and novel relationships. The p53 pathway results were manually validated in the literature. 60% of non-KEGG relationships were supported (74% for highly weighted interactions). The method was then applied to yeast data and our model again outperformed the comparison model. Our results demonstrate the advantage of combining gene interactions extracted from the literature in the form of semantic relations with microarray analysis in generating contribution-weighted gene regulatory networks. This methodology can make a significant contribution to

  1. [Biotherapy targeting the immune system].

    PubMed

    Frenzel, Laurent

    2015-01-01

    The use of monoclonal antibody targeted therapy has changed the management of several diseases, including in hematology and immunology. The panel of the present available biotherapies allows a specific action at various stages of the immune response. Indeed, some of these molecules can target the naive T cell at the immunological synapse or the way of TH1, TH17 and regulatory T cell. Others may be more specific for the B cell and immunoglobulin. Some will even be active on both B and T cells.

  2. Conservation and evolution of cis-regulatory systems in ascomycete fungi

    SciTech Connect

    Gasch, Audrey P.; Moses, Alan M.; Chiang, Derek Y.; Fraser, Hunter B.; Berardini, Mark; Eisen, Michael B.

    2004-03-15

    Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by examining the cis-regulatory elements that govern the expression of coregulated genes. We first identified groups of coregulated Saccharomyces cerevisiae genes enriched for genes with known upstream or downstream cis-regulatory sequences. Reasoning that many of these gene groups are coregulated in related species as well, we performed similar analyses on orthologs of coregulated S. cerevisiae genes in 13 other ascomycete species. We find that many species-specific gene groups are enriched for the same flanking regulatory sequences as those found in the orthologous gene groups from S. cerevisiae, indicating that those regulatory systems have been conserved in multiple ascomycete species. In addition to these clear cases of regulatory conservation, we find examples of cis-element evolution that suggest multiple modes of regulatory diversification, including alterations in transcription factor-binding specificity, incorporation of new gene targets into an existing regulatory system, and cooption of regulatory systems to control a different set of genes. We investigated one example in greater detail by measuring the in vitro activity of the S. cerevisiae transcription factor Rpn4p and its orthologs from Candida albicans and Neurospora crassa. Our results suggest that the DNA binding specificity of these proteins has coevolved with the sequences found upstream of the Rpn4p target genes and suggest that Rpn4p has a different function in N. crassa.

  3. A new approach for modelling gene regulatory networks using fuzzy petri nets.

    PubMed

    Hamed, Raed I; Ahson, S I; Parveen, R

    2010-02-04

    Gene Regulatory Networks are models of genes and gene interactions at the expression level. The advent of microarray technology has challenged computer scientists to develop better algorithms for modeling the underlying regulatory relationship in between the genes. Fuzzy system has an ability to search microarray datasets for activator/repressor regulatory relationship. In this paper, we present a fuzzy reasoning model based on the Fuzzy Petri Net. The model considers the regulatory triplets by means of predicting changes in expression level of the target based on input expression level. This method eliminates possible false predictions from the classical fuzzy model thereby allowing a wider search space for inferring regulatory relationship. Through formalization of fuzzy reasoning, we propose an approach to construct a rulebased reasoning system. The experimental results show the proposed approach is feasible and acceptable to predict changes in expression level of the target gene.

  4. Virulence-targeted Antibacterials: Concept, Promise, and Susceptibility to Resistance Mechanisms.

    PubMed

    Ruer, Ségolène; Pinotsis, Nikos; Steadman, David; Waksman, Gabriel; Remaut, Han

    2015-10-01

    In view of the relentless increase in antibiotic resistance in human pathogens, efforts are needed to safeguard our future therapeutic options against infectious diseases. In addition to regulatory changes in our antibiotic use, this will have to include the development of new therapeutic compounds. One area that has received growing attention in recent years is the possibility to treat or prevent infections by targeting the virulence mechanisms that render bacteria pathogenic. Antivirulence targets include bacterial adherence, secretion of toxic effector molecules, bacterial persistence through biofilm formation, quorum sensing and immune evasion. Effective small-molecule compounds have already been identified that suppress such processes. In this review, we discuss the susceptibility of such compounds to the development of resistance, by comparison with known resistance mechanisms observed for classical bacteriostatic or bacteriolytic antibiotics, and by review of available experimental case studies. Unfortunately, appearance of resistance mechanisms has already been demonstrated for some, showing that the quest of new, lasting drugs remains complicated.

  5. LIQUID TARGET

    DOEpatents

    Martin, M.D.; Salsig, W.W. Jr.

    1959-01-13

    A liquid handling apparatus is presented for a liquid material which is to be irradiated. The apparatus consists essentially of a reservoir for the liquid, a target element, a drain tank and a drain lock chamber. The target is in the form of a looped tube, the upper end of which is adapted to be disposed in a beam of atomic particles. The lower end of the target tube is in communication with the liquid in the reservoir and a means is provided to continuously circulate the liquid material to be irradiated through the target tube. Means to heat the reservoir tank is provided in the event that a metal is to be used as the target material. The apparatus is provided with suitable valves and shielding to provide maximum safety in operation.

  6. Lepidopteran HMG-CoA reductase is a potential selective target for pest control

    PubMed Central

    Li, Yuan-mei; Huang, Juan; Tobe, Stephen S.

    2017-01-01

    As a consequence of the negative impacts on the environment of some insecticides, discovery of eco-friendly insecticides and target has received global attention in recent years. Sequence alignment and structural comparison of the rate-limiting enzyme HMG-CoA reductase (HMGR) revealed differences between lepidopteran pests and other organisms, which suggested insect HMGR could be a selective insecticide target candidate. Inhibition of JH biosynthesis in vitro confirmed that HMGR inhibitors showed a potent lethal effect on the lepidopteran pest Manduca sexta, whereas there was little effect on JH biosynthesis in Apis mellifera and Diploptera punctata. The pest control application of these inhibitors demonstrated that they can be insecticide candidates with potent ovicidal activity, larvicidal activity and insect growth regulatory effects. The present study has validated that Lepidopteran HMGR can be a potent selective insecticide target, and the HMGR inhibitors (especially type II statins) could be selective insecticide candidates and lead compounds. Furthermore, we demonstrated that sequence alignment, homology modeling and structural comparison may be useful for determining potential enzymes or receptors which can be eco-friendly pesticide  targets. PMID:28133568

  7. Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort.

    PubMed

    Vockley, Christopher M; Guo, Cong; Majoros, William H; Nodzenski, Michael; Scholtens, Denise M; Hayes, M Geoffrey; Lowe, William L; Reddy, Timothy E

    2015-08-01

    We report a novel high-throughput method to empirically quantify individual-specific regulatory element activity at the population scale. The approach combines targeted DNA capture with a high-throughput reporter gene expression assay. As demonstration, we measured the activity of more than 100 putative regulatory elements from 95 individuals in a single experiment. In agreement with previous reports, we found that most genetic variants have weak effects on distal regulatory element activity. Because haplotypes are typically maintained within but not between assayed regulatory elements, the approach can be used to identify causal regulatory haplotypes that likely contribute to human phenotypes. Finally, we demonstrate the utility of the method to functionally fine map causal regulatory variants in regions of high linkage disequilibrium identified by expression quantitative trait loci (eQTL) analyses.

  8. Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort

    PubMed Central

    Vockley, Christopher M.; Guo, Cong; Majoros, William H.; Nodzenski, Michael; Scholtens, Denise M.; Hayes, M. Geoffrey; Lowe, William L.; Reddy, Timothy E.

    2015-01-01

    We report a novel high-throughput method to empirically quantify individual-specific regulatory element activity at the population scale. The approach combines targeted DNA capture with a high-throughput reporter gene expression assay. As demonstration, we measured the activity of more than 100 putative regulatory elements from 95 individuals in a single experiment. In agreement with previous reports, we found that most genetic variants have weak effects on distal regulatory element activity. Because haplotypes are typically maintained within but not between assayed regulatory elements, the approach can be used to identify causal regulatory haplotypes that likely contribute to human phenotypes. Finally, we demonstrate the utility of the method to functionally fine map causal regulatory variants in regions of high linkage disequilibrium identified by expression quantitative trait loci (eQTL) analyses. PMID:26084464

  9. State/Federal Regulatory Considerations

    EPA Pesticide Factsheets

    This page contains presentations from the Brown to Green: Make the Connection to Renewable Energy workshop held in Santa Fe, New Mexico, during December 10-11, 2008, regarding State/Federal Regulatory Considerations.

  10. Current Regulations and Regulatory Actions

    EPA Pesticide Factsheets

    This site will provide basic information on clean air permitting under the title V operating permits program, provide access to state and regional permitting programs, and maintain access to proposed and final regulatory requirements.

  11. 77 FR 7972 - Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-13

    ... Identifier No. 396 National Standards to 1105-AB34 Prevent, Detect, and Respond to Prison Rape (Reg Plan Seq... Prevent, Detect, and Respond to Prison Rape Regulatory Plan: This entry is Seq. No. 85 in part II of...

  12. Electronic Commerce Removing Regulatory Impediments

    DTIC Science & Technology

    1992-05-01

    AD-A252 691 ELECTRONIC COMMERCE Removing Regulatory Impediments ~DuiG A% ELECTE I JUL1 8 1992 0 C D Daniel J. Drake John A. Ciucci ... - ""N ST AT KE...Management Institute 6400 Goldsboro Road Bethesda, Maryland 20817-5886 92 LMI Executive Summary ELECTRONIC COMMERCE : REMOVING REGULATORY IMPEDIMENTS... Electronic Commerce techniques, such as electronic mail and electronic data interchange (EDI), enable Government agencies to conduct business without the

  13. Regulatory facility guide for Ohio

    SciTech Connect

    Anderson, S.S.; Bock, R.E.; Francis, M.W.; Gove, R.M.; Johnson, P.E.; Kovac, F.M.; Mynatt, J.O.; Rymer, A.C.

    1994-02-28

    The Regulatory Facility Guide (RFG) has been developed for the DOE and contractor facilities located in the state of Ohio. It provides detailed compilations of international, federal, and state transportation-related regulations applicable to shipments originating at destined to Ohio facilities. This RFG was developed as an additional resource tool for use both by traffic managers who must ensure that transportation operations are in full compliance with all applicable regulatory requirements and by oversight personnel who must verify compliance activities.

  14. Regulatory Network Structure as a Dominant Determinant of Transcription Factor Evolutionary Rate

    PubMed Central

    Coulombe-Huntington, Jasmin; Xia, Yu

    2012-01-01

    The evolution of transcriptional regulatory networks has thus far mostly been studied at the level of cis-regulatory elements. To gain a complete understanding of regulatory network evolution we must also study the evolutionary role of trans-factors, such as transcription factors (TFs). Here, we systematically assess genomic and network-level determinants of TF evolutionary rate in yeast, and how they compare to those of generic proteins, while carefully controlling for differences of the TF protein set, such as expression level. We found significantly distinct trends relating TF evolutionary rate to mRNA expression level, codon adaptation index, the evolutionary rate of physical interaction partners, and, confirming previous reports, to protein-protein interaction degree and regulatory in-degree. We discovered that for TFs, the dominant determinants of evolutionary rate lie in the structure of the regulatory network, such as the median evolutionary rate of target genes and the fraction of species-specific target genes. Decomposing the regulatory network by edge sign, we found that this modular evolution of TFs and their targets is limited to activating regulatory relationships. We show that fast evolving TFs tend to regulate other TFs and niche-specific processes and that their targets show larger evolutionary expression changes than targets of other TFs. We also show that the positive trend relating TF regulatory in-degree and evolutionary rate is likely related to the species-specificity of the transcriptional regulation modules. Finally, we discuss likely causes for TFs' different evolutionary relationship to the physical interaction network, such as the prevalence of transient interactions in the TF subnetwork. This work suggests that positive and negative regulatory networks follow very different evolutionary rules, and that transcription factor evolution is best understood at a network- or systems-level. PMID:23093926

  15. Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells.

    PubMed

    Freire-Pritchett, Paula; Schoenfelder, Stefan; Várnai, Csilla; Wingett, Steven W; Cairns, Jonathan; Collier, Amanda J; García-Vílchez, Raquel; Furlan-Magaril, Mayra; Osborne, Cameron S; Fraser, Peter J; Rugg-Gunn, Peter J; Spivakov, Mikhail

    2017-03-23

    Long-range cis-regulatory elements such as enhancers coordinate cell-specific transcriptional programmes by engaging in DNA looping interactions with target promoters. Deciphering the interplay between the promoter connectivity and activity of cis-regulatory elements during lineage commitment is crucial for understanding developmental transcriptional control. Here, we use Promoter Capture Hi-C to generate a high-resolution atlas of chromosomal interactions involving ~22,000 gene promoters in human pluripotent and lineage-committed cells, identifying putative target genes for known and predicted enhancer elements. We reveal extensive dynamics of cis-regulatory contacts upon lineage commitment, including the acquisition and loss of promoter interactions. This spatial rewiring occurs preferentially with predicted changes in the activity of cis-regulatory elements, and is associated with changes in target gene expression. Our results provide a global and integrated view of promoter interactome dynamics during lineage commitment of human pluripotent cells.

  16. Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors.

    PubMed

    Zabidi, Muhammad A; Stark, Alexander

    2016-12-01

    Gene expression is regulated by genomic enhancers that recruit transcription factors and cofactors to activate transcription from target core promoters. Over the past years, thousands of enhancers and core promoters in animal genomes have been annotated, and we have learned much about the domain structure in which regulatory genomes are organized in animals. Enhancer-core-promoter targeting occurs at several levels, including regulatory domains, DNA accessibility, and sequence-encoded core-promoter specificities that are likely mediated by different regulatory proteins. We review here current knowledge about enhancer-core-promoter targeting, regulatory communication between enhancers and core promoters, and the protein factors involved. We conclude with an outlook on open questions that we find particularly interesting and that will likely lead to additional insights in the upcoming years.

  17. The limits of regulatory toxicology

    SciTech Connect

    Carrington, Clark D.; Bolger, P. Michael

    2010-03-01

    The Acceptable Daily Intake (ADI) has been used by regulatory and public health organizations (e.g., the U.S. Food and Drug and Administration, and the World Health Organization) for chemicals for more than 50 years. The ADI concept was also initially employed at the U.S. Environmental Protection Agency at its inception in 1971, although with the adoption of newer terminology, it later became known as the Reference Dose (RfD). It is clear from the literature that both were first devised as instruments of regulatory policy. In the intervening years, it has become common to use language that implies that these standards are statements of scientific fact. Similarly, some of the discretionary or default values that are used to derive regulatory standards are represented as scientific assumptions when in fact they also represent regulatory policy. This confusion impedes both the best use of the available science and informed public participation in policy making. In addition, the misconception of the ADI or the RfD as statements of scientific fact may impede the consideration of alternative means to reduce exposure to chemicals that may be harmful, including regulatory measures that do not involve prescribing a regulatory concentration limit.

  18. Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters

    SciTech Connect

    Santini, Simona; Boore, Jeffrey L.; Meyer, Axel

    2003-12-31

    Due to their high degree of conservation, comparisons of DNA sequences among evolutionarily distantly-related genomes permit to identify functional regions in noncoding DNA. Hox genes are optimal candidate sequences for comparative genome analyses, because they are extremely conserved in vertebrates and occur in clusters. We aligned (Pipmaker) the nucleotide sequences of HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human and mouse (over 500 million years of evolutionary distance). We identified several highly conserved intergenic sequences, likely to be important in gene regulation. Only a few of these putative regulatory elements have been previously described as being involved in the regulation of Hox genes, while several others are new elements that might have regulatory functions. The majority of these newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac). The conserved intergenic regions located between the most rostrally expressed genes in the developing embryo are longer and better retained through evolution. We document that presumed regulatory sequences are retained differentially in either A or A clusters resulting from a genome duplication in the fish lineage. This observation supports both the hypothesis that the conserved elements are involved in gene regulation and the Duplication-Deletion-Complementation model.

  19. Targeted Endoscopic Imaging

    PubMed Central

    Li, Meng; Wang, Thomas D

    2011-01-01

    Summary Endoscopy has undergone explosive technological growth in over recent years, and with the emergence of targeted imaging, its truly transformative power and impact in medicine lies just over the horizon. Today, our ability to see inside the digestive tract with medical endoscopy is headed toward exciting crossroads. The existing paradigm of making diagnostic decisions based on observing structural changes and identifying anatomical landmarks may soon be replaced by visualizing functional properties and imaging molecular expression. In this novel approach, the presence of intracellular and cell surface targets unique to disease are identified and used to predict the likelihood of mucosal transformation and response to therapy. This strategy can result in the development of new methods for early cancer detection, personalized therapy, and chemoprevention. This targeted approach will require further development of molecular probes and endoscopic instruments, and will need support from the FDA for streamlined regulatory oversight. Overall, this molecular imaging modality promises to significantly broaden the capabilities of the gastroenterologist by providing a new approach to visualize the mucosa of the digestive tract in a manner that has never been seen before. PMID:19423025

  20. Better by design: business preferences for environmental regulatory reform.

    PubMed

    Taylor, Christopher M; Pollard, Simon J T; Rocks, Sophie A; Angus, Andrew J

    2015-04-15

    We present the preferences for environmental regulatory reform expressed by 30 UK businesses and industry bodies from 5 sectors. While five strongly preferred voluntary regulation, seven expressed doubts about its effectiveness, and 18 expressed no general preference between instrument types. Voluntary approaches were valued for flexibility and lower burdens, but direct regulation offered stability and a level playing field. Respondents sought regulatory frameworks that: are coherent; balance clarity, prescription and flexibility; are enabled by positive regulatory relationships; administratively efficient; targeted according to risk magnitude and character; evidence-based and that deliver long-term market stability for regulatees. Anticipated differences in performance between types of instrument can be undermined by poor implementation. Results underline the need for policy makers and regulators to tailor an effective mix of instruments for a given sector, and to overcome analytical, institutional and political barriers to greater coherence, to better coordinate existing instruments and tackle new environmental challenges as they emerge.

  1. In silico regulatory analysis for exploring human disease progression

    PubMed Central

    Holloway, Dustin T; Kon, Mark; DeLisi, Charles

    2008-01-01

    Background An important goal in bioinformatics is to unravel the network of transcription factors (TFs) and their targets. This is important in the human genome, where many TFs are involved in disease progression. Here, classification methods are applied to identify new targets for 152 transcriptional regulators using publicly-available targets as training examples. Three types of sequence information are used: composition, conservation, and overrepresentation. Results Starting with 8817 TF-target interactions we predict an additional 9333 targets for 152 TFs. Randomized classifiers make few predictions (~2/18660) indicating that our predictions for many TFs are significantly enriched for true targets. An enrichment score is calculated and used to filter new predictions. Two case-studies for the TFs OCT4 and WT1 illustrate the usefulness of our predictions: • Many predicted OCT4 targets fall into the Wnt-pathway. This is consistent with known biology as OCT4 is developmentally related and Wnt pathway plays a role in early development. • Beginning with 15 known targets, 354 predictions are made for WT1. WT1 has a role in formation of Wilms' tumor. Chromosomal regions previously implicated in Wilms' tumor by cytological evidence are statistically enriched in predicted WT1 targets. These findings may shed light on Wilms' tumor progression, suggesting that the tumor progresses either by loss of WT1 or by loss of regions harbouring its targets. • Targets of WT1 are statistically enriched for cancer related functions including metastasis and apoptosis. Among new targets are BAX and PDE4B, which may help mediate the established anti-apoptotic effects of WT1. • Of the thirteen TFs found which co-regulate genes with WT1 (p ≤ 0.02), 8 have been previously implicated in cancer. The regulatory-network for WT1 targets in genomic regions relevant to Wilms' tumor is provided. Conclusion We have assembled a set of features for the targets of human TFs and used them to

  2. Powerplant productivity improvements and regulatory incentives

    SciTech Connect

    Hardy, D; Brown, D

    1980-10-27

    The purpose of this study was to examine the benefits to be gained from increased powerplant productivity and to validate and demonstrate the use of incentives within the regulatory process to promote the improvement of powerplant productivity. The system-wide costs savings to be gained from given productivity improvement scenarios are estimated in both the short and long term. Numerous reports and studies exist which indicate that productivity improvements at the powerplant level are feasible and cost effective. The efforts of this study widen this focus and relate system-wide productivity improvements with system-wide cost savings. The initial thrust of the regulatory section of this study is to validate the existence of reasonable incentive procedures which would enable regulatory agencies to better motivate electric utilities to improve productivity on both the powerplant and system levels. The voluntary incentive format developed in this study was designed to facilitate the link between profit and efficiency which is typically not clear in most regulated market environments. It is concluded that at the present time, many electric utilities in this country could significantly increase the productivity of their base load units, and the adoption of an incentive program of the general type recommended in this study would add to rate of return regulation the needed financial incentives to enable utilities to make such improvements without losing long-run profit. In light of the upcoming oil import target levels and mandatory cutbacks of oil and gas as boiler fuels for electric utilities, the use of incentive programs to encourage more efficient utilization of coal and nuclear base load capacity will become far more inviting over the next two decades.

  3. 21 CFR 500.88 - Regulatory method.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... § 500.88 Regulatory method. (a) The sponsor shall submit for evaluation and validation a regulatory... method validation data. (c) FDA will publish in the Federal Register the complete regulatory method for... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Regulatory method. 500.88 Section 500.88 Food...

  4. Burglar Target Selection

    PubMed Central

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

    2015-01-01

    Objectives: 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. Methods: 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. Results: 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. Conclusions: 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. PMID:25866418

  5. Integrated module and gene-specific regulatory inference implicates upstream signaling networks.

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  7. A gene regulatory network controlling the embryonic specification of endoderm.

    PubMed

    Peter, Isabelle S; Davidson, Eric H

    2011-05-29

    Specification of endoderm is the prerequisite for gut formation in the embryogenesis of bilaterian organisms. Modern lineage labelling studies have shown that in the sea urchin embryo model system, descendants of the veg1 and veg2 cell lineages produce the endoderm, and that the veg2 lineage also gives rise to mesodermal cell types. It is known that Wnt/β-catenin signalling is required for endoderm specification and Delta/Notch signalling is required for mesoderm specification. Some direct cis-regulatory targets of these signals have been found and various phenomenological patterns of gene expression have been observed in the pre-gastrular endomesoderm. However, no comprehensive, causal explanation of endoderm specification has been conceived for sea urchins, nor for any other deuterostome. Here we propose a model, on the basis of the underlying genomic control system, that provides such an explanation, built at several levels of biological organization. The hardwired core of the control system consists of the cis-regulatory apparatus of endodermal regulatory genes, which determine the relationship between the inputs to which these genes are exposed and their outputs. The architecture of the network circuitry controlling the dynamic process of endoderm specification then explains, at the system level, a sequence of developmental logic operations, which generate the biological process. The control system initiates non-interacting endodermal and mesodermal gene regulatory networks in veg2-derived cells and extinguishes the endodermal gene regulatory network in mesodermal precursors. It also generates a cross-regulatory network that specifies future anterior endoderm in veg2 descendants and institutes a distinct network specifying posterior endoderm in veg1-derived cells. The network model provides an explanatory framework that relates endoderm specification to the genomic regulatory code.

  8. Gene regulatory networks modelling using a dynamic evolutionary hybrid

    PubMed Central

    2010-01-01

    Background Inference of gene regulatory networks is a key goal in the quest for understanding fundamental cellular processes and revealing underlying relations among genes. With the availability of gene expression data, computational methods aiming at regulatory networks reconstruction are facing challenges posed by the data's high dimensionality, temporal dynamics or measurement noise. We propose an approach based on a novel multi-layer evolutionary trained neuro-fuzzy recurrent network (ENFRN) that is able to select potential regulators of target genes and describe their regulation type. Results The recurrent, self-organizing structure and evolutionary training of our network yield an optimized pool of regulatory relations, while its fuzzy nature avoids noise-related problems. Furthermore, we are able to assign scores for each regulation, highlighting the confidence in the retrieved relations. The approach was tested by applying it to several benchmark datasets of yeast, managing to acquire biologically validated relations among genes. Conclusions The results demonstrate the effectiveness of the ENFRN in retrieving biologically valid regulatory relations and providing meaningful insights for better understanding the dynamics of gene regulatory networks. The algorithms and methods described in this paper have been implemented in a Matlab toolbox and are available from: http://bioserver-1.bioacademy.gr/DataRepository/Project_ENFRN_GRN/. PMID:20298548

  9. 75 FR 16202 - Notice of Issuance of Regulatory Guide

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-31

    ..., Regulatory Guide Development Branch, Division of Engineering, Office of Nuclear Regulatory Research. BILLING... From the Federal Register Online via the Government Publishing Office NUCLEAR REGULATORY COMMISSION Notice of Issuance of Regulatory Guide AGENCY: Nuclear Regulatory Commission. ACTION: Notice...

  10. 76 FR 14107 - Notice of Issuance of Regulatory Guide

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-15

    .... Boyce, Chief, Regulatory Guide Development Branch, Division of Engineering, Office of Nuclear Regulatory... From the Federal Register Online via the Government Publishing Office NUCLEAR REGULATORY COMMISSION Notice of Issuance of Regulatory Guide AGENCY: Nuclear Regulatory Commission. ACTION: Notice...

  11. 75 FR 1658 - Withdrawal of Regulatory Guide 7.5

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-12

    .... Valentin, Chief, Regulatory Guide Development Branch, Division of Engineering, Office of Nuclear Regulatory... From the Federal Register Online via the Government Publishing Office NUCLEAR REGULATORY COMMISSION Withdrawal of Regulatory Guide 7.5 AGENCY: Nuclear Regulatory Commission. ACTION: Withdrawal...

  12. Structural Code for DNA Recognition Revealed in Crystal Structures of Papillomavirus E2-DNA Targets

    NASA Astrophysics Data System (ADS)

    Rozenberg, Haim; Rabinovich, Dov; Frolow, Felix; Hegde, Rashmi S.; Shakked, Zippora

    1998-12-01

    Transcriptional regulation in papillomaviruses depends on sequence-specific binding of the regulatory protein E2 to several sites in the viral genome. Crystal structures of bovine papillomavirus E2 DNA targets reveal a conformational variant of B-DNA characterized by a roll-induced writhe and helical repeat of 10.5 bp per turn. A comparison between the free and the protein-bound DNA demonstrates that the intrinsic structure of the DNA regions contacted directly by the protein and the deformability of the DNA region that is not contacted by the protein are critical for sequence-specific protein/DNA recognition and hence for gene-regulatory signals in the viral system. We show that the selection of dinucleotide or longer segments with appropriate conformational characteristics, when positioned at correct intervals along the DNA helix, can constitute a structural code for DNA recognition by regulatory proteins. This structural code facilitates the formation of a complementary protein-DNA interface that can be further specified by hydrogen bonds and nonpolar interactions between the protein amino acids and the DNA bases.

  13. Regulatory physiology discipline science plan

    NASA Technical Reports Server (NTRS)

    1991-01-01

    The focus of the Regulatory Physiology discipline of the Space Physiology and Countermeasures Program is twofold. First, to determine and study how microgravity and associated factors of space flight affect the regulatory mechanisms by which humans adapt and achieve homeostasis and thereby regulate their ability to respond to internal and external signals; and, second, to study selected physiological systems that have been demonstrated to be influenced by gravity. The Regulatory Physiology discipline, as defined here, is composed of seven subdisciplines: (1) Circadian Rhythms, (2) Endocrinology, (3) Fluid and Electrolyte Regulation, (4) Hematology, (5) Immunology, (6) Metabolism and Nutrition, and (7) Temperature Regulation. The purpose of this Discipline Science Plan is to provide a conceptual strategy for NASA's Life Sciences Division research and development activities in the area of regulatory physiology. It covers the research areas critical to NASA's programmatic requirements for the Extended-Duration Orbiter, Space Station Freedom, and exploration mission science activities. These science activities include ground-based and flight; basic, applied, and operational; and animal and human research and development. This document summarizes the current status of the program, outlines available knowledge, establishes goals and objectives, identifies science priorities, and defines critical questions in regulatory physiology. It contains a general plan that will be used by both NASA Headquarters Program Offices and the field centers to review and plan basic, applied, and operational intramural and extramural research and development activities in this area.

  14. 75 FR 11166 - Joint Meeting of the Nuclear Regulatory Commission and the Federal Energy Regulatory Commission...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-10

    ... Federal Energy Regulatory Commission Joint Meeting of the Nuclear Regulatory Commission and the Federal Energy Regulatory Commission; Notice of Joint Meeting of the Nuclear Regulatory Commission and the... the Nuclear Regulatory Commission (NRC) will hold a joint meeting on Tuesday, March 16, 2010 at...

  15. Applying Attractor Dynamics to Infer Gene Regulatory Interactions Involved in Cellular Differentiation.

    PubMed

    Ghaffarizadeh, Ahmadreza; Podgorski, Gregory J; Flann, Nicholas S

    2017-02-27

    The dynamics of gene regulatory networks (GRNs) guide cellular differentiation. Determining the ways regulatory genes control expression of their targets is essential to understand and control cellular differentiation. The way a regulatory gene controls its target can be expressed as a gene regulatory function. Manual derivation of these regulatory functions is slow, error-prone and difficult to update as new information arises. Automating this process is a significant challenge and the subject of intensive effort. This work presents a novel approach to discovering biologically plausible gene regulatory interactions that control cellular differentiation. This method integrates known cell type expression data, genetic interactions, and knowledge of the effects of gene knockouts to determine likely GRN regulatory functions. We employ a genetic algorithm to search for candidate GRNs that use a set of transcription factors that control differentiation within a lineage. Nested canalyzing functions are used to constrain the search space to biologically plausible networks. The method identifies an ensemble of GRNs whose dynamics reproduce the gene expression pattern for each cell type within a particular lineage. The method's effectiveness was tested by inferring consensus GRNs for myeloid and pancreatic cell differentiation and comparing the predicted gene regulatory interactions to manually derived interactions. We identified many regulatory interactions reported in the literature and also found differences from published reports. These discrepancies suggest areas for biological studies of myeloid and pancreatic differentiation. We also performed a study that used defined synthetic networks to evaluate the accuracy of the automated search method and found that the search algorithm was able to discover the regulatory interactions in these defined networks with high accuracy. We suggest that the GRN functions derived from the methods described here can be used to fill

  16. 77 FR 30928 - Target Date Disclosure

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-24

    ...-30929] [FR Doc No: 2012-12386] DEPARTMENT OF LABOR Employee Benefits Security Administration 29 CFR Part 2550 RIN 1210-AB38 Target Date Disclosure AGENCY: Employee Benefits Security Administration, Labor... Security Administration is reopening the period for public comment on proposed regulatory...

  17. The two faces of regulatory T cells in cancer

    PubMed Central

    Blatner, Nichole R; Gounari, Fotini; Khazaie, Khashayarsha

    2013-01-01

    Regulatory T cells (Tregs) that expand in human colon cancer express retinoid-related orphan receptor γt (RORγt) and exert potent T-cell suppressive functions while mediating pro-inflammatory effects. Similar Tregs expand and drive a vicious cycle of inflammation in murine polyposis. Targeting RORγt in Tregs interrupts such a cycle and protects mice against polyposis, suggesting that a similar intervention may provide therapeutic benefits to colon cancer patients. PMID:23762787

  18. The Cellular and Molecular Mechanisms of Immuno-Suppression by Human Type 1 Regulatory T Cells

    PubMed Central

    Gregori, Silvia; Goudy, Kevin S.; Roncarolo, Maria Grazia

    2011-01-01

    The immuno-regulatory mechanisms of IL-10-producing type 1 regulatory T (Tr1) cells have been widely studied over the years. However, several recent discoveries have shed new light on the cellular and molecular mechanisms that human Tr1 cells use to control immune responses and induce tolerance. In this review we outline the well known and newly discovered regulatory properties of human Tr1 cells and provide an in-depth comparison of the known suppressor mechanisms of Tr1 cells with FOXP3+ Treg. We also highlight the role that Tr1 cells play in promoting and maintaining tolerance in autoimmunity, allergy, and transplantation. PMID:22566914

  19. Tackling Targets.

    ERIC Educational Resources Information Center

    Further Education Unit, London (England).

    This document is designed to help British training and enterprise councils (TECs) and further education (FE) colleges develop and implement strategies for achieving the National Targets for Education and Training (NTET), which were developed by the Confederation of British Industry in 1992 and endorsed by the British government. The findings from…

  20. On Target.

    ERIC Educational Resources Information Center

    Barbalich, Andrea

    1991-01-01

    Campus public relations professionals offer advice for improving the effectiveness of public relations efforts by (1) setting behavioral goals; (2) targeting audiences carefully; (3) focusing appeals by making messages explicit; (4) connecting the public relations message with larger societal issues; and (5) reaching internal as well as external…

  1. The rise of regulatory RNA

    PubMed Central

    Morris, K.V.; Mattick, J.S.

    2015-01-01

    Discoveries over the last decade portend a paradigm shift in molecular biology. Evidence suggests that RNA is not only functional as a messenger between DNA and protein but also in the regulation of genome organization and gene expression, which is increasingly elaborated in complex organisms. Regulatory RNAs appear to operate at many levels, but in particular to play an important role in the epigenetic processes that control differentiation and development. These discoveries suggest a central role for RNA in human evolution and ontogeny. Here we survey the emergence of the previously unsuspected world of regulatory RNAs from an historical perspective. PMID:24776770

  2. Glycoconjugate Vaccines: The Regulatory Framework.

    PubMed

    Jones, Christopher

    2015-01-01

    Most vaccines, including the currently available glycoconjugate vaccines, are administered to healthy infants, to prevent future disease. The safety of a prospective vaccine is a key prerequisite for approval. Undesired side effects would not only have the potential to damage the individual infant but also lead to a loss of confidence in the respective vaccine-or vaccines in general-on a population level. Thus, regulatory requirements, particularly with regard to safety, are extremely rigorous. This chapter highlights regulatory aspects on carbohydrate-based vaccines with an emphasis on analytical approaches to ensure the consistent quality of successive manufacturing lots.

  3. 75 FR 18245 - Public Federal Regulatory Enforcement Fairness Hearing Region IX Regulatory Fairness Board

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-09

    ... From the Federal Register Online via the Government Publishing Office SMALL BUSINESS ADMINISTRATION Public Federal Regulatory Enforcement Fairness Hearing Region IX Regulatory Fairness Board.... Small Business Administration (SBA) Region IX Regulatory Fairness Board and the SBA Office of...

  4. 77 FR 55517 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving a...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-10

    ... COMMISSION Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving a.... Introduction On May 24, 2012, Financial Industry Regulatory Authority, Inc. (``FINRA'') filed with the... General Counsel, Securities Industry and Financial Markets Association, dated June 26, 2012...

  5. 76 FR 20757 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Granting...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-13

    ... From the Federal Register Online via the Government Publishing Office SECURITIES AND EXCHANGE COMMISSION Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Granting... February 4, 2011, the Financial Industry Regulatory Authority, Inc. (``FINRA'') filed with the...

  6. 75 FR 62439 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving a...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-08

    ...-2010-043] Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving..., 2010. I. Introduction On August 6, 2010, the Financial Industry Regulatory Authority, Inc. (``FINRA..., 2010 (``Wiesenberg Letter''); Letter from Manisha Kimmel, Executive Director, Financial...

  7. 76 FR 72736 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Granting...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-25

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  8. 75 FR 17456 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving...

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    ... From the Federal Register Online via the Government Publishing Office SECURITIES AND EXCHANGE COMMISSION Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving... January 21, 2010, Financial Industry Regulatory Authority, Inc. (``FINRA'') filed with the Securities...

  9. 77 FR 47470 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of...

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    ... From the Federal Register Online via the Government Publishing Office SECURITIES AND EXCHANGE COMMISSION Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of Withdrawal... FINRA Rulebook August 2, 2012. On April 22, 2009, the Financial Industry Regulatory Authority,...

  10. 75 FR 74766 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of Filing...

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    ... COMMISSION Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of Filing and..., Financial Industry Regulatory Authority, Inc. (``FINRA'') filed with the Securities and Exchange Commission... class of its securities, another waiver will not be granted. Notwithstanding the significant...

  11. 78 FR 17969 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of...

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    ... Associate General Counsel, Securities Industry and Financial Markets Association to Elizabeth M. Murphy... COMMISSION Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of..., 2013. On February 1, 2013, the Financial Industry Regulatory Authority, Inc. (``FINRA'') filed with...

  12. 78 FR 72951 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving...

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    2013-12-04

    ... disclosure requirement believing it will help customers ``assess the risks and financial impact associated... COMMISSION Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Order Approving... Financial Industry Regulatory Authority, Inc. (``FINRA'') filed with the Securities and ]...

  13. A novel microRNA-1207-3p/FNDC1/FN1/AR regulatory pathway in prostate cancer

    PubMed Central

    Das, Dibash K.; Ogunwobi, Olorunseun O.

    2017-01-01

    Prostate cancer (PCa) is the second most common cause of cancer-specific deaths in the U.S. Unfortunately, the underlying molecular mechanisms for its development and progression remain unclear. Studies have established that microRNAs (miRNAs) are dysregulated in PCa. The intron-derived microRNA-1207-3p (miR-1207-3p) is encoded at the non-protein coding gene locus PVT1 on the 8q24 human chromosomal region, an established PCa susceptibility locus. However, miR-1207-3p in PCa had not previously been investigated. Therefore, we explored if miR-1207-3p plays any regulatory role in PCa. We discovered that miR-1207-3p is significantly underexpressed in PCa cell lines in comparison to normal prostate epithelial cells, and that increased expression of microRNA-1207-3p in PCa cells significantly inhibits proliferation, migration, and induces apoptosis via direct molecular targeting of fibronectin type III domain containing 1 (FNDC1). Our studies also revealed significant overexpression of FNDC1, fibronectin (FN1) and the androgen receptor (AR) in human PCa cell lines as well as tissues, and FNDC1, FN1, and AR positively correlate with aggressive PCa. These findings, recently published in Experimental Cell Research, are the first to describe a novel miR-1207-3p/FNDC1/FN1/AR novel regulatory pathway in PCa. PMID:28251177

  14. Dimensional comparison theory.

    PubMed

    Möller, Jens; Marsh, Herb W

    2013-07-01

    Although social comparison (Festinger, 1954) and temporal comparison (Albert, 1977) theories are well established, dimensional comparison is a largely neglected yet influential process in self-evaluation. Dimensional comparison entails a single individual comparing his or her ability in a (target) domain with his or her ability in a standard domain (e.g., "How good am I in math compared with English?"). This article reviews empirical findings from introspective, path-analytic, and experimental studies on dimensional comparisons, categorized into 3 groups according to whether they address the "why," "with what," or "with what effect" question. As the corresponding research shows, dimensional comparisons are made in everyday life situations. They impact on domain-specific self-evaluations of abilities in both domains: Dimensional comparisons reduce self-concept in the worse off domain and increase self-concept in the better off domain. The motivational basis for dimensional comparisons, their integration with recent social cognitive approaches, and the interdependence of dimensional, temporal, and social comparisons are discussed.

  15. 75 FR 79799 - Regulatory Agenda

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    2010-12-20

    ... Hinchman, Senior Counsel, Office of Legal Policy, Department of Justice, Room 4252, 950 Pennsylvania Avenue... Department of Justice