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Sample records for regulatory targets comparisons

  1. A comparison of regulatory impacts to real target impacts

    SciTech Connect

    Ammerman, D.J.

    1998-05-01

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

  2. Targeting regulatory T cells in tumors.

    PubMed

    Liu, Chang; Workman, Creg J; Vignali, Dario A A

    2016-07-01

    Regulatory T (Treg ) cells play a crucial role in maintaining peripheral tolerance and preventing autoimmunity. However, they also represent a major barrier to effective antitumor immunity and immunotherapy. Consequently, there has been considerable interest in developing approaches that can selectively or preferentially target Treg cells in tumors, while not impacting their capacity to maintain peripheral immune homeostasis. In this review, we describe our current understanding of the mechanisms underlying the recruitment, expansion, and suppressive activity of tumor-associated Treg cells, and discuss the approaches used and the challenges encountered in the immunotherapeutic targeting of Treg cells. In addition, we summarize the primary clinical targets and some emerging data on exciting new potential Treg cell-restricted targets. We propose that discovering and understanding mechanisms that are preferentially used by Treg cells within the tumor microenvironment will lead to strategies that selectively target Treg cell-mediated suppression of antitumor immunity while maintaining peripheral immune tolerance. PMID:26787424

  3. Target activation by regulatory RNAs in bacteria

    PubMed Central

    Papenfort, Kai; Vanderpool, Carin K.

    2015-01-01

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

  4. Companion diagnostics for targeted cancer drugs - clinical and regulatory aspects.

    PubMed

    Olsen, Dana; Jørgensen, Jan Trøst

    2014-01-01

    Companion diagnostics (CDx) holds the promise of improving the predictability of the oncology drug development process and become an important tool for the oncologist in relation to the choice of treatment for the individual patient. A number of drug-diagnostic co-development programs have already been completed successfully, and in the clinic, the use of several targeted cancer drugs is now guided by a CDx. This central role of the CDx assays has attracted the attention of the regulators, and especially the US Food and Drug Administration has been at the forefront in relation to developing regulatory strategies for CDx and the drug-diagnostic co-development project. For an increasing number of cancer patients the treatment selection will depend on the result generated by a CDx assay, and consequently this type of assay has become critical for the care and safety of the patients. In order to secure that the CDx assays have a high degree of analytical and clinical validity, they must undergo an extensive non-clinical and clinical testing before release for routine patient management. This review will give a brief introduction to some of the scientific and medical challenges related to the CDx development with specific emphasis on the regulatory requirements in different regions of the world. PMID:24904822

  5. Microinterventions targeting regulatory focus and regulatory fit selectively reduce dysphoric and anxious mood.

    PubMed

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

    2015-09-01

    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

  6. T Cell Signaling Targets for Enhancing Regulatory or Effector Function

    PubMed Central

    Pan, Fan; Fan, Huimin; Liu, Zhongmin; Jiang, Shuiping

    2015-01-01

    To respond to infection, resting or naïve T cells must undergo activation, clonal expansion, and differentiation into specialized functional subsets of effector T cells. However, to prevent excessive or self-destructive immune responses, regulatory T cells (Tregs) are instrumental in suppressing the activation and function of effector cells, including effector T cells. The transcription factor Forkhead box P3 (Foxp3) regulates the expression of genes involved in the development and function of Tregs. Foxp3 interacts with other transcription factors and with epigenetic elements such as histone deacetylases (HDACs) and histone acetyltransferases. Treg suppressive function can be increased by exposure to HDAC inhibitors. The individual contributions of different HDAC family members to Treg function and their respective mechanisms of action, however, remain unclear. A study showed that HDAC6, HDAC9, and Sirtuin-1 had distinct effects on Foxp3 expression and function, suggesting that selectively targeting HDACs individually or in combination may enhance Treg stability and suppressive function. Another study showed that the receptor programmed death 1 (PD-1), a well-known inhibitor of T cell activation, halted cell cycle progression in effector T cells by inhibiting the transcription of the gene encoding the substrate-recognition component (Skp2) of the ubiquitin ligase SCFSkp2. Together, these findings reveal new signaling targets for enhancing Treg or effector T cell function that may be helpful in designing future therapies, either to increase Treg suppressive function in transplantation and autoimmune diseases or to block PD-1 function, thus increasing the magnitude of antiviral or antitumor immune responses of effector T cells. PMID:22855503

  7. Tregalizumab – A Monoclonal Antibody to Target Regulatory T Cells

    PubMed Central

    König, Martin; Rharbaoui, Faiza; Aigner, Silke; Dälken, Benjamin; Schüttrumpf, Jörg

    2016-01-01

    Regulatory T cells (Tregs) represent a subpopulation of CD4+ T cells, which are essential for the maintenance of immunological tolerance. The absence or dysfunction of Tregs can lead to autoimmunity and allergies. The restoration of functional Tregs and/or Treg cell numbers represents a novel and attractive approach for the treatment of autoimmune diseases, e.g., rheumatoid arthritis (RA). The CD4 cell surface receptor is a target for modulation of T cell function. Monoclonal antibodies (mAbs) against CD4 have previously been tested for the treatment of autoimmune diseases, including RA. Furthermore, in model systems, anti-CD4 antibodies are able to induce tolerance and mediate immunomodulatory effects through a variety of mechanisms. Despite the availability of innovative and effective therapies for RA, many patients still have persistently active disease or experience adverse events that can limit use. A growing body of evidence suggests that Treg modulation could offer a new therapeutic strategy in RA and other autoimmune disorders. Here, we describe tregalizumab (BT-061), which is a novel, non-depleting IgG1 mAb that binds to a unique epitope of CD4. Tregalizumab represents the first humanized anti-CD4 mAb that selectively induces Treg activation. PMID:26834751

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

    PubMed Central

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

    2012-01-01

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

  9. 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. PMID:27190026

  10. Regulatory network analysis of transcription factors, microRNAs, target genes and host genes in human multiple myeloma.

    PubMed

    Huang, Zhuoyan; Xu, Zhiwen; Kunhao Wang, Kunhao Wang; Wang, Ning; Wang, Shang

    2015-11-01

    In recent years, molecular biologists have achieved great advance in micro RNA (miRNA) and gene investigation about the pathogenesis of multiple myeloma (MM). Existing research data of the transcription factors (TFs) and miRNAs is disperse and unorganized, which prevents researchers from investigating the mechanism and analyze regulatory pathways of MM systematically. In our research, regulatory interactions among miRNAs, TFs, host genes and target genes were imported to construct regulatory networks at three levels, including the abnormally expressed network and the related network as well as the global network. The abnormally expressed network was primary investigated cause it was an experimentally validated topological network, and it systematically explained the regulatory mechanism of MM. Its outstanding significance lies in that if we correct each abnormally expressed gene and miRNA to normal expression level by transcriptional control adjustment, thus the whole genetic expression network will return to normal state, and MM may not relapse. Additionally, analyses and comparisons to upstream as well as downstream of abnormally expressed miRNAs and genes in three networks highlighted some important regulators and key signaling pathways. For example, STAT3 and hsa-miR-125b, PIAS3 and hsa-miR-21 respectively formed self adaptation feedback regulations. The current research proposed a novel perspective to systematically explained the regulatory mechanism of MM and may contribute to further research and therapy of carcinomas. PMID:26687742

  11. A comparison of crop and non-crop plants as sensitive indicator species for regulatory testing.

    PubMed

    McKelvey, Robert A; Wright, John P; Honegger, Joy L

    2002-12-01

    The effectiveness of regulatory non-target plant testing using crop species to predict the phytotoxicicity of herbicides to non-crop species was evaluated for eleven herbicides. These herbicides were representative of eight chemical classes and six modes of action. Data for non-crop plants from pre-emergence and post-emergence efficacy screening studies were compared with those for the most sensitive crop species defined by regulatory tests conducted to meet US EPA requirements. Testing under pre-emergence conditions for ten compounds indicated that for five of the compounds (K-815910, trifluralin, pyridyloxy A, pyridyloxy B and cyanazine), the most sensitive crop species was more sensitive than all the non-crop species evaluated. For metsulfuron-methyl, chlorimuron-ethyl, hexazinone and bromacil, only one of the non-crop species evaluated was more sensitive than the most sensitive crop species from regulatory tests. Data for the tenth compound, chloroacetamide, showed that four of 32 non-crop species tested in efficacy screens had at least one rate at which greater visual effects were observed than were observed for the most sensitive crop response in a regulatory test. The results of post-emergence exposure comparisons for five of the compounds (pyridyloxy A, cloransulam-methyl, chlorimuron-ethyl, cyanazine and hexazinone) indicated that the most sensitive crop species were more sensitive than all the non-crop species evaluated. Data for pyridyloxy B, metsulfuron-methyl and bromacil indicated that only one of the non-crop species evaluated was more sensitive than the most sensitive crop species. For trifluralin, three of the eight non-crop species were more sensitive than the most sensitive crop species. Data for K-815910 indicated that four of the fourteen non-crop species tested were marginally more sensitive than the most sensitive crop, but were within the same range of sensitivity. These results indicate that the current regulatory test batteries and methods

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

    PubMed

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

    2016-01-01

    Phosphorylation and proteolysis are among the most common post-translational modifications (PTMs), and play critical roles in various biological processes. More recent discoveries imply that the crosstalks between these two PTMs are involved in many diseases. In this work, we construct a post-translational regulatory network (PTRN) consists of phosphorylation and proteolysis processes, which enables us to investigate the regulatory interplays between these two PTMs. With the PTRN, we identify some functional network motifs that are significantly enriched with drug targets, some of which are further found to contain multiple proteins targeted by combinatorial drugs. These findings imply that the network motifs may be used to predict targets when designing new drugs. Inspired by this, we propose a novel computational approach called NetTar for predicting drug targets using the identified network motifs. Benchmarking results on real data indicate that our approach can be used for accurate prediction of novel proteins targeted by known drugs. PMID:26853265

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

    PubMed Central

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

    2016-01-01

    Phosphorylation and proteolysis are among the most common post-translational modifications (PTMs), and play critical roles in various biological processes. More recent discoveries imply that the crosstalks between these two PTMs are involved in many diseases. In this work, we construct a post-translational regulatory network (PTRN) consists of phosphorylation and proteolysis processes, which enables us to investigate the regulatory interplays between these two PTMs. With the PTRN, we identify some functional network motifs that are significantly enriched with drug targets, some of which are further found to contain multiple proteins targeted by combinatorial drugs. These findings imply that the network motifs may be used to predict targets when designing new drugs. Inspired by this, we propose a novel computational approach called NetTar for predicting drug targets using the identified network motifs. Benchmarking results on real data indicate that our approach can be used for accurate prediction of novel proteins targeted by known drugs. PMID:26853265

  14. Identification of bacterial sRNA regulatory targets using ribosome profiling

    PubMed Central

    Wang, Jing; Rennie, William; Liu, Chaochun; Carmack, Charles S.; Prévost, Karine; Caron, Marie-Pier; Massé, Eric; Ding, Ye; Wade, Joseph T.

    2015-01-01

    Bacteria express large numbers of non-coding, regulatory RNAs known as ‘small RNAs’ (sRNAs). sRNAs typically regulate expression of multiple target messenger RNAs (mRNAs) through base-pairing interactions. sRNA:mRNA base-pairing often results in altered mRNA stability and/or altered translation initiation. Computational identification of sRNA targets is challenging due to the requirement for only short regions of base-pairing that can accommodate mismatches. Experimental approaches have been applied to identify sRNA targets on a genomic scale, but these focus only on those targets regulated at the level of mRNA stability. Here, we utilize ribosome profiling (Ribo-seq) to experimentally identify regulatory targets of the Escherichia coli sRNA RyhB. We not only validate a majority of known RyhB targets using the Ribo-seq approach, but also discover many novel ones. We further confirm regulation of a selection of known and novel targets using targeted reporter assays. By mutating nucleotides in the mRNA of a newly discovered target, we demonstrate direct regulation of this target by RyhB. Moreover, we show that Ribo-seq distinguishes between mRNAs regulated at the level of RNA stability and those regulated at the level of translation. Thus, Ribo-seq represents a powerful approach for genome-scale identification of sRNA targets. PMID:26546513

  15. Identification of bacterial sRNA regulatory targets using ribosome profiling.

    PubMed

    Wang, Jing; Rennie, William; Liu, Chaochun; Carmack, Charles S; Prévost, Karine; Caron, Marie-Pier; Massé, Eric; Ding, Ye; Wade, Joseph T

    2015-12-01

    Bacteria express large numbers of non-coding, regulatory RNAs known as 'small RNAs' (sRNAs). sRNAs typically regulate expression of multiple target messenger RNAs (mRNAs) through base-pairing interactions. sRNA:mRNA base-pairing often results in altered mRNA stability and/or altered translation initiation. Computational identification of sRNA targets is challenging due to the requirement for only short regions of base-pairing that can accommodate mismatches. Experimental approaches have been applied to identify sRNA targets on a genomic scale, but these focus only on those targets regulated at the level of mRNA stability. Here, we utilize ribosome profiling (Ribo-seq) to experimentally identify regulatory targets of the Escherichia coli sRNA RyhB. We not only validate a majority of known RyhB targets using the Ribo-seq approach, but also discover many novel ones. We further confirm regulation of a selection of known and novel targets using targeted reporter assays. By mutating nucleotides in the mRNA of a newly discovered target, we demonstrate direct regulation of this target by RyhB. Moreover, we show that Ribo-seq distinguishes between mRNAs regulated at the level of RNA stability and those regulated at the level of translation. Thus, Ribo-seq represents a powerful approach for genome-scale identification of sRNA targets. PMID:26546513

  16. CyTargetLinker: A Cytoscape App to Integrate Regulatory Interactions in Network Analysis

    PubMed Central

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

    2013-01-01

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

  17. Tissue resident regulatory T cells: novel therapeutic targets for human disease

    PubMed Central

    Zhou, Xiaohui; Tang, Jiayou; Cao, Hao; Fan, Huimin; Li, Bin

    2015-01-01

    Over the past decade, the ability of regulatory T cells (Tregs) to suppress multiple types of immune cells has received tremendous attention. Mounting evidence has revealed that tissue resident Tregs control non-immunological processes of their target tissues and contribute to a plethora of human diseases. The identification of novel tissue-specific Tregs has highlighted their heterogeneity and complexity. This review summarizes the recent findings for visceral adipose tissue CD4+Foxp3+ regulatory T cells (VAT Tregs), muscle Tregs, bone Tregs and skin memory Tregs, with a focus on their unique functions in local tissues. This interpretation of the roles of tissue-specific Tregs and of their involvement in disease progression provides new insight into the discovery of potential therapeutic targets of human diseases. PMID:25891216

  18. 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

  19. 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. PMID:27382281

  20. 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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2015-01-01

    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. PMID:26680438

  3. 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.

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

    PubMed

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

    2016-07-01

    Secreted by viable embryos, PIF is expressed by the placenta and found in maternal circulation. It promotes implantation and trophoblast invasion, achieving systemic immune homeostasis. Synthetic PIF successfully transposes endogenous PIF features to non-pregnant immune and transplant models. PIF affects innate and activated PBMC cytokines and genes expression. We report that PIF targets similar proteins in CD14+, CD4+ and CD8+ cells instigating integrated immune regulation. PIF-affinity chromatography followed by mass-spectrometry, pathway and heatmap analysis reveals that SET-apoptosis inhibitor, vimentin, myosin-9 and calmodulin are pivotal for immune regulation. PIF acts on macrophages down-stream of LPS (lipopolysaccharide-bacterial antigen) CD14/TLR4/MD2 complex, targeting myosin-9, thymosin-α1 and 14-3-3eta. PIF mainly targets platelet aggregation in CD4+, and skeletal proteins in CD8+ cells. Pathway analysis demonstrates that PIF targets and regulates SET, tubulin, actin-b, and S100 genes expression. PIF targets systemic immunity and has a short circulating half-life. Collectively, PIF targets identified; protective, immune regulatory and cytoskeleton proteins reveal mechanisms involved in the observed efficacy against immune disorders. PMID:26944449

  5. Early kinetic window of target T cell susceptibility to CD25+ regulatory T cell activity.

    PubMed

    Sojka, Dorothy K; Hughson, Angela; Sukiennicki, Teresa L; Fowell, Deborah J

    2005-12-01

    Peripheral tolerance is maintained in part by thymically derived CD25+CD4+ T cells (regulatory T cells (Tregs)). Their mechanism of action has not been well characterized. Therefore, to get a better understanding of Treg action, we investigated the kinetics of murine Treg activity in vitro. Tregs were suppressive within a surprisingly narrow kinetic window: necessary and sufficient only in the first 6-10 h of culture. Visualization of this time frame, using a sensitive single-cell assay for IL-2, revealed the early elaboration of target cell IL-2 producers in the first 6 h despite the presence of CD25+CD4+ Tregs. However, after 6 h, a rapid rise in the number of IL-2 producers in the absence of Tregs was dramatically abrogated by the presence of Tregs. Importantly, the timing of suppression was dictated by the kinetics of target T cell activation suggesting that early target T cell signals may alter susceptibility to suppression. Modulating target T cell activation signals with provision of CD28, IL-2, or high Ag dose all abrogated suppression of proliferation late in culture. However, only CD28 signals enabled target T cells to resist the early Treg-induced down-regulation of IL-2. Therefore the quality of early target T cell activation signals, in particular engagement of CD28, represents an important control point in the balance between vulnerability and resistance to Treg suppression. PMID:16301632

  6. Close sequence comparisons are sufficient to identify human cis-regulatory elements.

    PubMed

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

    2006-07-01

    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. To address this problem, we identified evolutionarily conserved noncoding regions in primate, mammalian, and more distant comparisons using a uniform approach (Gumby) that facilitates unbiased assessment of the impact of evolutionary distance on predictive power. We benchmarked computational 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 an in vivo enhancer assay in transgenic mice. Human regulatory elements were identified with acceptable sensitivity (53%-80%) and true-positive rate (27%-67%) by comparison with one to five other eutherian mammals or six other simian primates. More distant comparisons (marsupial, avian, amphibian, and fish) failed to identify many of the empirically defined functional noncoding elements. Our results highlight the practical utility of close sequence comparisons, and the loss of sensitivity entailed by more distant comparisons. We derived an intuitive relationship between ancient and recent noncoding sequence conservation from whole-genome comparative analysis that explains most of the observations from empirical benchmarking. 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 in vivo testing at embryonic time points. PMID:16769978

  7. 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.

  8. Regulatory T Cells, a Potent Immunoregulatory Target for CAM Researchers: The Ultimate Antagonist (I)

    PubMed Central

    Vojdani, Aristo; Erde, Jonathan

    2006-01-01

    Over the past decade, great interest has been given to regulatory T (Treg) cells. A vast body of evidence has shown the existence and highlighted the importance of Treg cells in the active suppression of immune system responses. This form of immunoregulation is the dominant means utilized by the immune system to reach a harmony between reciprocal response processes in order to ensure adequate host defense with minimal host detriment. Therapeutically targeting Treg cells is a direct and powerful means to manipulate the immune system to achieve beneficial effects on various disease pathologies, including allergy, autoimmunity and cancer, as well as the facilitation of organ transplantation. This powerful target for immunoregulation is of much concern to practitioners and researchers of complementary and alternative medicine because it allows a great deal of control and certainty in dealing with the prevalence of debilitating immune system-related disorders for which there has been little remedy outside of Western Medicine. PMID:16550220

  9. Memory of tolerance and induction of regulatory T cells by erythrocyte-targeted antigens

    PubMed Central

    Grimm, Alizée J.; Kontos, Stephan; Diaceri, Giacomo; Quaglia-Thermes, Xavier; Hubbell, Jeffrey A.

    2015-01-01

    New approaches based on induction of antigen-specific immunological tolerance are being explored for treatment of autoimmunity and prevention of immunity to protein drugs. Antigens associated with apoptotic debris are known to be processed tolerogenically in vivo. Our group is exploring an approach toward antigen-specific tolerization using erythrocyte-binding antigens, based on the premise that as the erythrocytes circulate, age and are cleared, the erythrocyte surface-bound antigen payload will be cleared tolerogenically along with the eryptotic debris. Here, we characterized the phenotypic signatures of CD8+ T cells undergoing tolerance in response to soluble and erythrocyte-targeted antigen. Signaling through programmed death-1/programmed death ligand-1 (PD-1/PD-L1), but not through cytotoxic T lymphocyte antigen 4 (CTLA4), was shown to be required for antigen-specific T cell deletion, anergy and expression of regulatory markers. Generation of CD25+FOXP3+ regulatory T cells in response to erythrocyte-targeted antigens but not soluble antigen at an equimolar dose was observed, and these cells were required for long-term maintenance of immune tolerance in both the CD4+ and CD8+ T cell compartments. Evidence of infectious tolerance was observed, in that tolerance to a one antigenic epitope was able to regulate responses to other epitopes in the same protein antigen. PMID:26511151

  10. 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

  11. p38β, A novel regulatory target of Pokemon in hepatic cells.

    PubMed

    Chen, Zhe; Liu, Feng; Zhang, Nannan; Cao, Deliang; Liu, Min; Tan, Ying; Jiang, Yuyang

    2013-01-01

    Pokemon is an important proto-oncogene involved in various biological processes and cancer development, such as cell differentiation, tumorigenesis and metastasis. Pokemon is recognized as a transcription factor localized upstream of several oncogenes, regulating their expression. p38MAPKs act as key regulatory factors in cellular signaling pathways associated with inflammatory responses, cell proliferation, differentiation and survival. p38β, a member of p38MAPK family, is closely correlated with tumorigenesis, but the mechanism of activation remains unclear. In this study, we found overexpression of Pokemon promoted the growth, migration and invasion of HepG2 cells. However, a p38 inhibitor SB202190 efficiently attenuated the promoting effect of Pokemon in the HepG2 cells. Targeted expression or silencing of Pokemon changed cellular p38β protein level and phosphorylation of downstream ATF2 in the p38 signaling pathway. Both dual luciferase report assay and ChIP assay suggested that p38β is a novel regulatory target of the transcription factor Pokemon and positively regulated by Pokemon in hepatic cells. PMID:23807508

  12. Regulatory network of microRNAs, target genes, transcription factors and host genes in endometrial cancer.

    PubMed

    Xue, Lu-Chen; Xu, Zhi-Wen; Wang, Kun-Hao; Wang, Ning; Zhang, Xiao-Xu; Wang, Shang

    2015-01-01

    Genes and microRNAs (miRNAs) have important roles in human oncology. However, most of the biological factors are reported in disperse form which makes it hard to discover the pathology. In this study, genes and miRNAs involved in human endometrial cancer(EC) were collected and formed into regulatory networks following their interactive relations, including miRNAs targeting genes, transcription factors (TFs) regulating miRNAs and miRNAs included in their host genes. Networks are constructed hierarchically at three levels: differentially expressed, related and global. Among the three, the differentially expressed network is the most important and fundamental network that contains the key genes and miRNAs in EC. The target genes, TFs and miRNAs are differentially expressed in EC so that any mutation in them may impact on EC development. Some key pathways in networks were highlighted to analyze how they interactively influence other factors and carcinogenesis. Upstream and downstream pathways of the differentially expressed genes and miRNAs were compared and analyzed. The purpose of this study was to partially reveal the deep regulatory mechanisms in EC using a new method that combines comprehensive genes and miRNAs together with their relationships. It may contribute to cancer prevention and gene therapy of EC. PMID:25684474

  13. Stress-induced endogenous siRNAs targeting regulatory intron sequences in Brachypodium

    PubMed Central

    Wang, Hsiao-Lin V.; Dinwiddie, Brandon L.; Lee, Herman

    2015-01-01

    Exposure to abiotic stresses triggers global changes in the expression of thousands of eukaryotic genes at the transcriptional and post-transcriptional levels. Small RNA (smRNA) pathways and splicing both function as crucial mechanisms regulating stress-responsive gene expression. However, examples of smRNAs regulating gene expression remain largely limited to effects on mRNA stability, translation, and epigenetic regulation. Also, our understanding of the networks controlling plant gene expression in response to environmental changes, and examples of these regulatory pathways intersecting, remains limited. Here, to investigate the role of smRNAs in stress responses we examined smRNA transcriptomes of Brachypodium distachyon plants subjected to various abiotic stresses. We found that exposure to different abiotic stresses specifically induced a group of novel, endogenous small interfering RNAs (stress-induced, UTR-derived siRNAs, or sutr-siRNAs) that originate from the 3′ UTRs of a subset of coding genes. Our bioinformatics analyses predicted that sutr-siRNAs have potential regulatory functions and that over 90% of sutr-siRNAs target intronic regions of many mRNAs in trans. Importantly, a subgroup of these sutr-siRNAs target the important intron regulatory regions, such as branch point sequences, that could affect splicing. Our study indicates that in Brachypodium, sutr-siRNAs may affect splicing by masking or changing accessibility of specific cis-elements through base-pairing interactions to mediate gene expression in response to stresses. We hypothesize that this mode of regulation of gene expression may also serve as a general mechanism for regulation of gene expression in plants and potentially in other eukaryotes. PMID:25480817

  14. 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

  15. 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. PMID:18585108

  16. Rotavirus NSP1 Mediates Degradation of Interferon Regulatory Factors through Targeting of the Dimerization Domain

    PubMed Central

    Arnold, Michelle M.; Barro, Mario

    2013-01-01

    Rotavirus nonstructural protein NSP1 can inhibit expression of interferon (IFN) and IFN-stimulated gene products by inducing proteasome-mediated degradation of IFN-regulatory factors (IRFs), including IRF3, IRF5, and IRF7. All IRF proteins share an N-terminal DNA-binding domain (DBD), and IRF3, IRF5, and IRF7 contain a similar C-proximal IRF association domain (IAD) that mediates IRF dimerization. An autoinhibitory domain (ID) at the extreme C terminus interacts with the IAD, burying residues necessary for IRF dimerization. Phosphorylation of serine/threonine residues in the ID induces charge repulsions that unmask the IAD, enabling IRF dimerization and subsequent nuclear translocation. To define the region of IRF proteins targeted for degradation by NSP1, we generated IRF3 and IRF7 truncation mutants and transiently expressed each with simian SA11-4F NSP1. These assays indicated that the IAD represented a necessary and sufficient target for degradation. Because NSP1 did not mediate degradation of truncated forms of the IAD, NSP1 likely requires a structurally intact IAD for recognition and targeting of IRF proteins. IRF9, which contains an IAD-like region that directs interactions with signal inducer and activator of transcription (STAT) proteins, was also targeted for degradation by NSP1, while IRF1, which lacks an IAD, was not. Analysis of mutant forms of IRF3 unable to undergo dimerization or that were constitutively dimeric showed that both were targeted for degradation by NSP1. These results indicate that SA11-4F NSP1 can induce degradation of inactive and activated forms of IAD-containing IRF proteins (IRF3 to IRF9), allowing a multipronged attack on IFN-based pathways that promote antiviral innate and adaptive immune responses. PMID:23824805

  17. 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

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

    PubMed

    Ishihama, Akira; Shimada, Tomohiro; Yamazaki, Yukiko

    2016-03-18

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

  19. 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. PMID:20937913

  20. Lessons from Domestication: Targeting Cis-Regulatory Elements for Crop Improvement.

    PubMed

    Swinnen, Gwen; Goossens, Alain; Pauwels, Laurens

    2016-06-01

    Domestication of wild plant species has provided us with crops that serve our human nutritional needs. Advanced DNA sequencing has propelled the unveiling of underlying genetic changes associated with domestication. Interestingly, many changes reside in cis-regulatory elements (CREs) that control the expression of an unmodified coding sequence. Sequence variation in CREs can impact gene expression levels, but also developmental timing and tissue specificity of expression. When genes are involved in multiple pathways or active in several organs and developmental stages CRE modifications are favored in contrast to mutations in coding regions, due to the lack of detrimental pleiotropic effects. Therefore, learning from domestication, we propose that CREs are interesting targets for genome editing to create new alleles for plant breeding. PMID:26876195

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

    PubMed

    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

  2. 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

  3. 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

  4. 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

  5. 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

  6. Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species

    PubMed Central

    Laurençon, Anne; Dubruille, Raphaëlle; Efimenko, Evgeni; Grenier, Guillaume; Bissett, Ryan; Cortier, Elisabeth; Rolland, Vivien; Swoboda, Peter; Durand, Bénédicte

    2007-01-01

    Background Regulatory factor X (RFX) transcription factors play a key role in ciliary assembly in nematode, Drosophila and mouse. Using the tremendous advantages of comparative genomics in closely related species, we identified novel genes regulated by dRFX in Drosophila. Results We first demonstrate that a subset of known ciliary genes in Caenorhabditis elegans and Drosophila are regulated by dRFX and have a conserved RFX binding site (X-box) in their promoters in two highly divergent Drosophila species. We then designed an X-box consensus sequence and carried out a genome wide computer screen to identify novel genes under RFX control. We found 412 genes that share a conserved X-box upstream of the ATG in both species, with 83 genes presenting a more restricted consensus. We analyzed 25 of these 83 genes, 16 of which are indeed RFX target genes. Two of them have never been described as involved in ciliogenesis. In addition, reporter construct expression analysis revealed that three of the identified genes encode proteins specifically localized in ciliated endings of Drosophila sensory neurons. Conclusion Our X-box search strategy led to the identification of novel RFX target genes in Drosophila that are involved in sensory ciliogenesis. We also established a highly valuable Drosophila cilia and basal body dataset. These results demonstrate the accuracy of the X-box screen and will be useful for the identification of candidate genes for human ciliopathies, as several human homologs of RFX target genes are known to be involved in diseases, such as Bardet-Biedl syndrome. PMID:17875208

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

    PubMed

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

    2008-07-22

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

  8. 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

  9. 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

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

    PubMed

    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

    2015-10-01

    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

  11. Interferon Regulatory Factor 4 (IRF-4) Targets IRF-5 to Regulate Epstein-Barr Virus Transformation*

    PubMed Central

    Xu, Dongsheng; Meyer, Florencia; Ehlers, Erica; Blasnitz, Laura; Zhang, Luwen

    2011-01-01

    The cellular interferon regulatory factor-4 (IRF-4), which is a member of IRF family, is involved in the development of multiple myeloma and Epstein-Barr virus (EBV)-mediated transformation of B lymphocytes. However, the molecular mechanism of IRF-4 in cellular transformation is unknown. We have found that knockdown of IRF-4 leads to high expression of IRF-5, a pro-apoptotic member in the IRF family. Overexpression of IRF-4 represses IRF-5 expression. Reduction of IRF-4 leads to growth inhibition, and the restoration of IRF-4 by exogenous plasmids correlates with the growth recovery and reduces IRF-5 expression. In addition, IRF-4 negatively regulates IRF-5 promoter reporter activities and binds to IRF-5 promoters in vivo and in vitro. Knockdown of IRF-5 rescues IRF-4 knockdown-mediated growth inhibition, and IRF-5 overexpression alone is sufficient to induce cellular growth inhibition of EBV-transformed cells. Therefore, IRF-5 is one of the targets of IRF-4, and IRF-4 regulates the growth of EBV-transformed cells partially through IRF-5. This work provides insight on how IRFs interact with one another to participate in viral pathogenesis and transformation. PMID:21454650

  12. miRNA-target gene regulatory networks: A Bayesian integrative approach to biomarker selection with application to kidney cancer.

    PubMed

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

    2015-06-01

    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

  13. 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

  14. Tissue-specific targeting of cell fate regulatory genes by E2f factors.

    PubMed

    Julian, L M; Liu, Y; Pakenham, C A; Dugal-Tessier, D; Ruzhynsky, V; Bae, S; Tsai, S-Y; Leone, G; Slack, R S; Blais, A

    2016-04-01

    Cell cycle proteins are important regulators of diverse cell fate decisions, and in this capacity have pivotal roles in neurogenesis and brain development. The mechanisms by which cell cycle regulation is integrated with cell fate control in the brain and other tissues are poorly understood, and an outstanding question is whether the cell cycle machinery regulates fate decisions directly or instead as a secondary consequence of proliferative control. Identification of the genes targeted by E2 promoter binding factor (E2f) transcription factors, effectors of the pRb/E2f cell cycle pathway, will provide essential insights into these mechanisms. We identified the promoter regions bound by three neurogenic E2f factors in neural precursor cells in a genome-wide manner. Through bioinformatic analyses and integration of published genomic data sets we uncovered hundreds of transcriptionally active E2f-bound promoters corresponding to genes that control cell fate processes, including key transcriptional regulators and members of the Notch, fibroblast growth factor, Wnt and Tgf-β signaling pathways. We also demonstrate a striking enrichment of the CCCTC binding factor transcription factor (Ctcf) at E2f3-bound nervous system-related genes, suggesting a potential regulatory co-factor for E2f3 in controlling differentiation. Finally, we provide the first demonstration of extensive tissue specificity among E2f target genes in mammalian cells, whereby E2f3 promoter binding is well conserved between neural and muscle precursors at genes associated with cell cycle processes, but is tissue-specific at differentiation-associated genes. Our findings implicate the cell cycle pathway as a widespread regulator of cell fate genes, and suggest that E2f3 proteins control cell type-specific differentiation programs by regulating unique sets of target genes. This work significantly enhances our understanding of how the cell cycle machinery impacts cell fate and differentiation, and will

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

    NASA Astrophysics Data System (ADS)

    Mongin, Emmanuel; Dewar, Ken; Blanchette, Mathieu

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

  16. Selective inhibition of regulatory T cells by targeting the PI3K-Akt pathway.

    PubMed

    Abu-Eid, Rasha; Samara, Raed N; Ozbun, Laurent; Abdalla, Maher Y; Berzofsky, Jay A; Friedman, Kevin M; Mkrtichyan, Mikayel; Khleif, Samir N

    2014-11-01

    Despite the strides that immunotherapy has made in mediating tumor regression, the clinical effects are often transient, and therefore more durable responses are still needed. The temporary nature of the therapy-induced immune response can be attributed to tumor immune evasion mechanisms, mainly the effect of suppressive immune cells and, in particular, regulatory T cells (Treg). Although the depletion of Tregs has been shown to be effective in enhancing immune responses, selective depletion of these suppressive cells without affecting other immune cells has not been very successful, and new agents are sought. We found that PI3K-Akt pathway inhibitors selectively inhibit Tregs with minimal effect on conventional T cells (Tconv). Our results clearly show selective in vitro inhibition of activation (as represented by a decrease in downstream signaling) and proliferation of Tregs in comparison with Tconvs when treated with different Akt and PI3K inhibitors. This effect has been observed in both human and murine CD4 T cells. In vivo treatment with these inhibitors resulted in a significant and selective reduction in Tregs in both naïve and tumor-bearing mice. Furthermore, these PI3K-Akt inhibitors led to a significant therapeutic antitumor effect, which was shown to be Treg dependent. Here, we report the use of PI3K-Akt pathway inhibitors as potent agents for the selective depletion of suppressive Tregs. We show that these inhibitors are able to enhance the antitumor immune response and are therefore promising clinical reagents for Treg depletion. PMID:25080445

  17. Selective inhibition of regulatory T cells by targeting PI3K-Akt pathway

    PubMed Central

    Abu-Eid, R; Samara, RN; Ozbun, L; Abdalla, MY; Berzofsky, JA; Friedman, KM; Mkrtichyan, M; Khleif, SN

    2014-01-01

    Despite the strides that immunotherapy has made in mediating tumor regression, the clinical effects are often transient, and therefore more durable responses still are needed. The temporary nature of the therapy-induced immune response can be attributed to tumor immune evasion mechanisms, mainly the effect of suppressive immune cells and, in particular, T regulatory cells (Treg). Although the depletion of Treg has been shown to be effective in enhancing immune responses, selective depletion of these suppressive cells without affecting other immune cells has not been very successful, and new agents are sought. We found that PI3K-Akt pathway inhibitors selectively inhibit Treg with minimal effect on conventional T cells (Tconv). Our results clearly show selective in vitro inhibition of activation (as represented by a decrease in downstream signaling) and proliferation of Treg in comparison to Tconv when treated with different Akt and PI3K inhibitors. This effect has been observed in both human and murine CD4 T cells. In vivo treatment with these inhibitors resulted in a significant and selective reduction in Treg both in naïve and tumor-bearing mice. Furthermore, these PI3K-Akt inhibitors led to a significant therapeutic antitumor effect, which was shown to be Treg-dependent. Here, we report the use of PI3K-Akt pathway inhibitors as potent agents for the selective depletion of suppressive Treg. We show that these inhibitors are able to enhance the antitumor immune response and are therefore promising clinical reagents for Treg-depletion. PMID:25080445

  18. Quantitative comparison of cis-regulatory element (CRE) activities in transgenic Drosophila melanogaster.

    PubMed

    Rogers, William A; Williams, Thomas M

    2011-01-01

    Gene expression patterns are specified by cis-regulatory element (CRE) sequences, which are also called enhancers or cis-regulatory modules. A typical CRE possesses an arrangement of binding sites for several transcription factor proteins that confer a regulatory logic specifying when, where, and at what level the regulated gene(s) is expressed. The full set of CREs within an animal genome encodes the organism's program for development, and empirical as well as theoretical studies indicate that mutations in CREs played a prominent role in morphological evolution. Moreover, human genome wide association studies indicate that genetic variation in CREs contribute substantially to phenotypic variation. Thus, understanding regulatory logic and how mutations affect such logic is a central goal of genetics. Reporter transgenes provide a powerful method to study the in vivo function of CREs. Here a known or suspected CRE sequence is coupled to heterologous promoter and coding sequences for a reporter gene encoding an easily observable protein product. When a reporter transgene is inserted into a host organism, the CRE's activity becomes visible in the form of the encoded reporter protein. P-element mediated transgenesis in the fruit fly species Drosophila (D.) melanogaster has been used for decades to introduce reporter transgenes into this model organism, though the genomic placement of transgenes is random. Hence, reporter gene activity is strongly influenced by the local chromatin and gene environment, limiting CRE comparisons to being qualitative. In recent years, the phiC31 based integration system was adapted for use in D. melanogaster to insert transgenes into specific genome landing sites. This capability has made the quantitative measurement of gene and, relevant here, CRE activity feasible. The production of transgenic fruit flies can be outsourced, including phiC31-based integration, eliminating the need to purchase expensive equipment and/or have proficiency at

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

    PubMed

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

    2015-01-01

    The intracellular level of bilirubin (BR), an endogenous antioxidant that is cytotoxic at high concentrations, is tightly controlled within the optimal therapeutic range. We have recently described a concerted intracellular BR regulation by two microsomal enzymes: heme oxygenase 1 (HMOX1), essential for BR production and cytochrome P450 2A5 (CYP2A5), a BR oxidase. Herein, we describe targeting of these enzymes to hepatic mitochondria during oxidative stress. The kinetics of microsomal and mitochondrial BR oxidation were compared. Treatment of DBA/2J mice with 200mgpyrazole/kg/day for 3days increased hepatic intracellular protein carbonyl content and induced nucleo-translocation of Nrf2. HMOX1 and CYP2A5 proteins and activities were elevated in microsomes and mitoplasts but not the UGT1A1, a catalyst of BR glucuronidation. A CYP2A5 antibody inhibited 75% of microsomal BR oxidation. The inhibition was absent in control mitoplasts but elevated to 50% after treatment. An adrenodoxin reductase antibody did not inhibit microsomal BR oxidation but inhibited 50% of mitochondrial BR oxidation. Ascorbic acid inhibited 5% and 22% of the reaction in control and treated microsomes, respectively. In control mitoplasts the inhibition was 100%, which was reduced to 50% after treatment. Bilirubin affinity to mitochondrial and microsomal CYP2A5 enzyme is equally high. Lastly, the treatment neither released cytochrome c into cytoplasm nor dissipated membrane potential, indicating the absence of mitochondrial membrane damage. Collectively, the observations suggest that BR regulatory enzymes are recruited to mitochondria during oxidative stress and BR oxidation by mitochondrial CYP2A5 is supported by mitochondrial mono-oxygenase system. The induced recruitment potentially confers membrane protection. PMID:25478736

  20. VEGFA/VEGFR2-targeted therapies prevent the VEGFA-induced proliferation of regulatory T cells in cancer

    PubMed Central

    Terme, Magali; Tartour, Eric; Taieb, Julien

    2013-01-01

    Some of the anti-angiogenic agents currently used to treat solid malignancies have effects on tumor endothelial cells as well as on immune cells. We have recently demonstrated that targeting the vascular endothelial growth factor A (VEGFA)/VEGF receptor 2 (VEGFR2) signaling pathway reduces the proportion of regulatory T cells (Treg) in a mouse model of colorectal cancer (CRC) and in metastatic CRC patients as it inhibits tumor-induced Treg proliferation. PMID:24083078

  1. 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

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

    PubMed Central

    Lu, Yulan; Zhou, Yuanpeng; Tian, Weidong

    2013-01-01

    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. PMID:24003029

  3. 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

  4. 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.

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

    PubMed Central

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

    2015-01-01

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

  6. 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. PMID:25324314

  7. Distinctive Expression of Bcl-2 Factors in Regulatory T Cells Determines a Pharmacological Target to Induce Immunological Tolerance

    PubMed Central

    Gabriel, Sarah Sharon; Bon, Nina; Chen, Jin; Wekerle, Thomas; Bushell, Andrew; Fehr, Thomas; Cippà, Pietro Ernesto

    2016-01-01

    Distinctive molecular characteristics of functionally diverse lymphocyte populations may represent novel pharmacological targets for immunotherapy. The intrinsic apoptosis pathway is differently regulated among conventional and regulatory T cells (Tregs). Targeted pharmacological modulation of this pathway with a small molecule Bcl-2/Bcl-xL inhibitor (ABT-737) caused a selective depletion of effector T cells and a relative enrichment of Tregs in vivo. Treatment with ABT-737 resulted in a tolerogenic milieu, which was exploited to alleviate graft-versus-host disease, to prevent allograft rejection in a stringent fully MHC-mismatched skin transplantation model and to induce immunological tolerance in combination with bone marrow transplantation. This concept has the potential to find various applications for immunotherapy, since it allows pharmacologic exploitation of the immunomodulatory properties of Tregs without the need for cell manipulation ex vivo. PMID:26973650

  8. 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

  9. Comparison of measured and modeled BRDF of natural targets

    NASA Astrophysics Data System (ADS)

    Boucher, Yannick; Cosnefroy, Helene; Petit, Alain D.; Serrot, Gerard; Briottet, Xavier

    1999-07-01

    The Bidirectional Reflectance Distribution Function (BRDF) plays a major role to evaluate or simulate the signatures of natural and artificial targets in the solar spectrum. A goniometer covering a large spectral and directional domain has been recently developed by the ONERA/DOTA. It was designed to allow both laboratory and outside measurements. The spectral domain ranges from 0.40 to 0.95 micrometer, with a resolution of 3 nm. The geometrical domain ranges 0 - 60 degrees for the zenith angle of the source and the sensor, and 0 - 180 degrees for the relative azimuth between the source and the sensor. The maximum target size for nadir measurements is 22 cm. The spatial target irradiance non-uniformity has been evaluated and then used to correct the raw measurements. BRDF measurements are calibrated thanks to a spectralon reference panel. Some BRDF measurements performed on sand and short grass and are presented here. Eight bidirectional models among the most popular models found in the literature have been tested on these measured data set. A code fitting the model parameters to the measured BRDF data has been developed. The comparative evaluation of the model performances is carried out, versus different criteria (root mean square error, root mean square relative error, correlation diagram . . .). The robustness of the models is evaluated with respect to the number of BRDF measurements, noise and interpolation.

  10. MicroRNA-17 Modulates Regulatory T Cell Function by Targeting Co-regulators of the Foxp3 Transcription Factor.

    PubMed

    Yang, Huang-Yu; Barbi, Joseph; Wu, Chao-Yi; Zheng, Ying; Vignali, Paolo D A; Wu, Xingmei; Tao, Jin-Hui; Park, Benjamin V; Bandara, Shashika; Novack, Lewis; Ni, Xuhao; Yang, Xiaoping; Chang, Kwang-Yu; Wu, Ren-Chin; Zhang, Junran; Yang, Chih-Wei; Pardoll, Drew M; Li, Huabin; Pan, Fan

    2016-07-19

    Regulatory T (Treg) cells are important in maintaining self-tolerance and immune homeostasis. The Treg cell transcription factor Foxp3 works in concert with other co-regulatory molecules, including Eos, to determine the transcriptional signature and characteristic suppressive phenotype of Treg cells. Here, we report that the inflammatory cytokine interleukin-6 (IL-6) actively repressed Eos expression through microRNA-17 (miR-17). miR-17 expression increased in Treg cells in the presence of IL-6, and its expression negatively correlated with that of Eos. Treg cell suppressive activity was diminished upon overexpression of miR-17 in vitro and in vivo, which was mitigated upon co-expression of an Eos mutant lacking miR-17 target sites. Also, RNAi of miR-17 resulted in enhanced suppressive activity. Ectopic expression of miR-17 imparted effector-T-cell-like characteristics to Treg cells via the de-repression of genes encoding effector cytokines. Thus, miR-17 provides a potent layer of Treg cell control through targeting Eos and additional Foxp3 co-regulators. PMID:27438767

  11. Genome-wide characterization of cis-acting DNA targets reveals the transcriptional regulatory framework of opaque2 in maize.

    PubMed

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

    2015-03-01

    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

  12. Mapping the DNA-binding domain and target sequences of the Streptomyces peucetius daunorubicin biosynthesis regulatory protein, DnrI.

    PubMed

    Sheldon, Paul J; Busarow, Sara B; Hutchinson, C Richard

    2002-04-01

    Streptomyces antibiotic regulatory proteins (SARPs) constitute a novel family of transcriptional activators that control the expression of several diverse anti-biotic biosynthetic gene clusters. The Streptomyces peucetius DnrI protein, one of only a handful of these proteins yet discovered, controls the biosynthesis of the polyketide antitumour antibiotics daunorubicin and doxorubicin. Recently, comparative analyses have revealed significant similarities among the predicted DNA-binding domains of the SARPs and the C-terminal DNA-binding domain of the OmpR family of regulatory proteins. Using the crystal structure of the OmpR-binding domain as a template, DnrI was mapped by truncation and site-directed mutagenesis. Several highly conserved residues within the N-terminus are crucial for DNA binding and protein function. Tandemly arranged heptameric imperfect repeat sequences are found within the -35 promoter regions of target genes. Substitutions for each nucleotide within the repeats of the dnrG-dpsABCD promoter were performed by site-directed mutagenesis. The mutant promoter fragments were found to have modified binding characteristics in gel mobility shift assays. The spacing between the repeat target sequences is also critical for successful occupation by DnrI and, therefore, competent transcriptional activation of the dnrG-dpsABCD operon. PMID:11972782

  13. DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

    PubMed Central

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

    2014-01-01

    In vivo methods such as ChIP-chip are well-established techniques used to determine global gene targets for transcription factors. However, they are of limited use in exploring bacterial two component regulatory systems with uncharacterized activation conditions. Such systems regulate transcription only when activated in the presence of unique signals. Since these signals are often unknown, the in vitro microarray based method described in this video article can be used to determine gene targets and binding sites for response regulators. This DNA-affinity-purified-chip method may be used for any purified regulator in any organism with a sequenced genome. The protocol involves allowing the purified tagged protein to bind to sheared genomic DNA and then affinity purifying the protein-bound DNA, followed by fluorescent labeling of the DNA and hybridization to a custom tiling array. Preceding steps that may be used to optimize the assay for specific regulators are also described. The peaks generated by the array data analysis are used to predict binding site motifs, which are then experimentally validated. The motif predictions can be further used to determine gene targets of orthologous response regulators in closely related species. We demonstrate the applicability of this method by determining the gene targets and binding site motifs and thus predicting the function for a sigma54-dependent response regulator DVU3023 in the environmental bacterium Desulfovibrio vulgaris Hildenborough. PMID:25079303

  14. Global Identification of SMAD2 Target Genes Reveals a Role for Multiple Co-regulatory Factors in Zebrafish Early Gastrulas*

    PubMed Central

    Liu, Zhaoting; Lin, Xiwen; Cai, Zhaoping; Zhang, Zhuqiang; Han, Chunsheng; Jia, Shunji; Meng, Anming; Wang, Qiang

    2011-01-01

    Nodal and Smad2/3 signals play pivotal roles in mesendoderm induction and axis determination during late blastulation and early gastrulation in vertebrate embryos. However, Smad2/3 direct target genes during those critical developmental stages have not been systematically identified. Here, through ChIP-chip assay, we show that the promoter/enhancer regions of 679 genes are bound by Smad2 in the zebrafish early gastrulas. Expression analyses confirm that a significant proportion of Smad2 targets are indeed subjected to Nodal/Smad2 regulation at the onset of gastrulation. The co-existence of DNA-binding sites of other transcription factors in the Smad2-bound regions allows the identification of well known Smad2-binding partners, such as FoxH1 and Lef1/β-catenin, as well as many previously unknown Smad2 partners, including Oct1 and Gata6, during embryogenesis. We demonstrate that Oct1 physically associates with and enhances the transcription and mesendodermal induction activity of Smad2, whereas Gata6 exerts an inhibitory role in Smad2 signaling and mesendodermal induction. Thus, our study systemically uncovers a large number of Smad2 targets in early gastrulas and suggests cooperative roles of Smad2 and other transcription factors in controlling target gene transcription, which will be valuable for studying regulatory cascades during germ layer formation and patterning of vertebrate embryos. PMID:21669877

  15. 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.

  16. 78 FR 60240 - Non-Application of Previously Withdrawn Regulatory Provisions Governing Targeted Dumping in...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-01

    ... Targeted Dumping in Antidumping Duty Investigations, 73 FR 74930 (Dec. 10, 2008) (``Withdrawal Notice... Determination of Sales at Less than Fair Value, 75 FR 59217 (Sept. 27, 2010), and Issues and Decision Memorandum... Fair Value and Antidumping Duty Order, 75 FR 70203 (Nov. 17, 2010) (``Final Determination'')....

  17. Comparison of effects of sonar bandwidth for underwater target classification

    NASA Astrophysics Data System (ADS)

    Azimi-Sadjadi, Mahmood R.; Yao, De; Li, Donghui; Jamshidi, Arta A.; Dobeck, Gerald J.

    2000-08-01

    In this paper, two different data sets which use linear FM incident signals with different bandwidths, namely 40 KHz and 80 KHz, are used for benchmarking. The goal is to study the effects of using larger bandwidth for underwater target classification. The classification system is formed of several subsystems including preprocessing, a subband decomposition suing wavelet packets, linear predictive coding in subbands, feature selection and neural network classifier. The classification performance is demonstrated on ten noisy realizations of the data sets formed by adding synthesized reverberation effects with 12 dB signal-to- reverberation ratio. The ROC and the error location plots for these dat sets are generated. To compare the generalization and robustness of the system on these data sets, the error and classification rate statistics are generated using Monte Carlo simulations on a large set of noisy data. The results point to the fact that the wideband sonar provides better robustness property. Three-aspect fusion is also adopted which yields almost perfect classification performance. These issues will be thoroughly studied and analyzed in this paper.

  18. Antigen targeting to dendritic cells combined with transient regulatory T cell inhibition results in long-term tumor regression

    PubMed Central

    Unger, Wendy WJ; Mayer, Christian T; Engels, Steef; Hesse, Christina; Perdicchio, Maurizio; Puttur, Franz; Streng-Ouwehand, Ingeborg; Litjens, Manja; Kalay, Hakan; Berod, Luciana; Sparwasser, Tim; van Kooyk, Yvette

    2014-01-01

    Therapeutic vaccinations against cancer are still largely ineffective. Major caveats are inefficient delivery of tumor antigens to dendritic cells (DCs) and excessive immune suppression by Foxp3+ regulatory T cells (Tregs), resulting in defective T cell priming and failure to induce tumor regression. To circumvent these problems we evaluated a novel combinatorial therapeutic strategy. We show that tumor antigen targeting to DC-SIGN in humanized hSIGN mice via glycans or specific antibodies induces superior T cell priming. Next, this targeted therapy was combined with transient Foxp3+ Treg depletion employing hSIGNxDEREG mice. While Treg depletion alone slightly delayed B16-OVA melanoma growth, only the combination therapy instigated long-term tumor regression in a substantial fraction of mice. This novel strategy resulted in optimal generation of antigen-specific activated CD8+ T cells which accumulated in regressing tumors. Notably, Treg depletion also allowed the local appearance of effector T cells specific for endogenous B16 antigens. This indicates that antitumor immune responses can be broadened by therapies aimed at controlling Tregs in tumor environments. Thus, transient inhibition of Treg-mediated immune suppression potentiates DC targeted antigen vaccination and tumor-specific immunity. PMID:26405564

  19. CRISPR-Cas9 Genome Editing of a Single Regulatory Element Nearly Abolishes Target Gene Expression in Mice

    PubMed Central

    Han, Yu; Slivano, Orazio J.; Christie, Christine K.; Cheng, Albert W.; Miano, Joseph M.

    2014-01-01

    Objective To ascertain the importance of a single regulatory element in the control of Cnn1 expression using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) genome editing. Approach and Results The CRISPR/Cas9 system was used to produce 3/18 founder mice carrying point mutations in an intronic CArG box of the smooth muscle cell (SMC)-restricted Cnn1 gene. Each founder was bred for germ line transmission of the mutant CArG box and littermate interbreeding to generate homozygous mutant (Cnn1ΔCArG/ΔCArG) mice. Quantitative RT-PCR, Western blotting, and confocal immunofluorescence microscopy showed dramatic reductions in Cnn1 mRNA and CNN1 protein expression in Cnn1ΔCArG/ΔCArG mice with no change in other SMC-restricted genes and little evidence of off-target edits elsewhere in the genome. In vivo chromatin immunoprecipitation assay revealed a sharp decrease in binding of SRF to the mutant CArG box. Loss of CNN1 expression was coincident with an increase in Ki-67 positive cells in the normal vessel wall. Conclusion CRISPR/Cas9 genome editing of a single CArG box nearly abolishes Cnn1 expression in vivo and evokes increases in SMC DNA synthesis. This facile genome editing system paves the way for a new generation of studies designed to test the importance of individual regulatory elements in living animals, including regulatory variants in conserved sequence blocks linked to human disease. PMID:25538209

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

    PubMed Central

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

    2009-01-01

    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. PMID:19901328

  1. IκB Kinase ε Targets Interferon Regulatory Factor 1 in Activated T Lymphocytes

    PubMed Central

    Sgarbanti, Marco; Marsili, Giulia; Remoli, Anna Lisa; Stellacci, Emilia; Mai, Antonello; Rotili, Dante; Perrotti, Edvige; Acchioni, Chiara; Orsatti, Roberto; Iraci, Nunzio; Ferrari, Mathieu; Borsetti, Alessandra

    2014-01-01

    IκB kinase ε (IKK-ε) has an essential role as a regulator of innate immunity, functioning downstream of pattern recognition receptors to modulate NF-κB and interferon (IFN) signaling. In the present study, we investigated IKK-ε activation following T cell receptor (TCR)/CD28 stimulation of primary CD4+ T cells and its role in the stimulation of a type I IFN response. IKK-ε was activated following TCR/CD28 stimulation of primary CD4+ T cells; however, in T cells treated with poly(I·C), TCR/CD28 costimulation blocked induction of IFN-β transcription. We demonstrated that IKK-ε phosphorylated the transcription factor IFN regulatory factor 1 (IRF-1) at amino acid (aa) 215/219/221 in primary CD4+ T cells and blocked its transcriptional activity. At the mechanistic level, IRF-1 phosphorylation impaired the physical interaction between IRF-1 and the NF-κB RelA subunit and interfered with PCAF-mediated acetylation of NF-κB RelA. These results demonstrate that TCR/CD28 stimulation of primary T cells stimulates IKK-ε activation, which in turn contributes to suppression of IFN-β production. PMID:24396068

  2. 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.

  3. 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.

    2010-08-19

    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.

  4. Epigenetic Enzymes Are the Therapeutic Targets for CD4+CD25+/highFoxp3+ Regulatory T Cells

    PubMed Central

    Pastrana, Jahaira Lopez; Shao, Ying; Chernaya, Valeria; Wang, Hong; Yang, Xiao-feng

    2014-01-01

    CD4+CD25+/highFoxp3+ regulatory T cells (Tregs) are a subset of CD4+ T cells that play an essential role in maintaining peripheral immune tolerance. Several transcriptional co-factors have been recently identified, which form complexes with Tregs transcription factor Foxp3 and contribute in the suppressive function of Tregs. However, Foxp3 is still defined as a “master” (multiple pathway) regulator gene that controls the development and stability of Tregs. Due to its importance, the regulatory mechanisms underlying Foxp3 expression have been a focus of intensive investigation. Recent progress suggests that the epigenetics mechanisms responsible for regulating the Foxp3 gene expression are key components of Tregs suppressive activity. This review not only discusses the basic concepts of Tregs biology and epigenetic modifications. We also analyze the translational clinical aspect of Tregs epigenetic modifications, focusing on several ongoing clinical trials as well as FDA approved epigenetic based drugs. The new progress in identifying epigenetic enzymes functional in Treg cells is a new target for the development of novel therapeutic approaches for autoimmune and inflammatory diseases, graft-versus-host disease and cancers. PMID:25193380

  5. The Nude Mutant Gene Foxn1 is a HOXC13 Regulatory Target during Hair Follicle and Nail Differentiation

    PubMed Central

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

    2011-01-01

    Among the Hox genes, Hoxc13 has been shown to be essential for proper hair shaft differentiation as Hoxc13 gene-targeted (Hoxc13tm1Mrc) mice completely lack external hair. Because of the remarkable overt phenotypic parallels to the Foxn1nu (nude) mutant mice, we sought to determine whether Hoxc13 and Foxn1 might act in a common pathway of hair follicle (HF) differentiation. We show that the alopecia exhibited by both the Hoxc13tm1Mrc and Foxn1nu mice is due to strikingly similar defects in hair shaft differentiation and that both mutants suffer from a severe nail dystrophy. These phenotypic similarities are consistent with the extensive overlap between Hoxc13 and Foxn1 expression patterns in the HF and the nail matrix. Furthermore, DNA microarray analysis of skin from Hoxc13tm1Mrc mice identified Foxn1 as significantly down-regulated along with numerous hair keratin genes. This Foxn1 down-regulation apparently reflects the loss of direct transcriptional control by HOXC13 as indicated by our results obtained through co-transfection and chromatin immunoprecipitation (ChIP) assays. As presented in the discussion, these data support a regulatory model of keratinocyte differentiation in which HOXC13-dependent activation of Foxn1 is part of a regulatory cascade controlling the expression of terminal differentiation markers. PMID:21191399

  6. Degeneration of a CRISPR/Cas system and its regulatory target during the evolution of a pathogen

    PubMed Central

    Sampson, Timothy R; Weiss, David S

    2013-01-01

    CRISPR/Cas systems are bacterial RNA-guided endonuclease machineries that target foreign nucleic acids. Recently, we demonstrated that the Cas protein Cas9 controls gene expression and virulence in Francisella novicida by altering the stability of the mRNA for an immunostimulatory bacterial lipoprotein (BLP). Genomic analyses, however, revealed that Francisella species with increased virulence harbor degenerated CRISPR/Cas systems. We hypothesize that CRISPR/Cas degeneration removed a barrier against genome alterations, which resulted in enhanced virulence. Importantly, the BLP locus was also lost; likely a necessary adaptation in the absence of Cas9-mediated repression. CRISPR/Cas systems likely play regulatory roles in numerous bacteria, and these data suggest additional genomic changes may be required to maintain fitness after CRISPR/Cas loss in such bacteria, having important evolutionary implications. PMID:24100224

  7. Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals

    PubMed Central

    Henriques, Telmo; Gilchrist, Daniel A.; Nechaev, Sergei; Bern, Michael; Muse, Ginger W.; Burkholder, Adam; Fargo, David C.; Adelman, Karen

    2013-01-01

    SUMMARY Metazoan gene expression is often regulated after the recruitment of RNA polymerase II (Pol II) to promoters, through the controlled release of promoter-proximally paused Pol II into productive RNA synthesis. Despite the prevalence of paused Pol II, very little is known about the dynamics of these early elongation complexes or the fate of short transcription start site-associated (tss) RNAs they produce. Here, we demonstrate that paused elongation complexes can be remarkably stable, with half-lives exceeding 15 minutes at genes with inefficient pause release. Promoter-proximal termination by Pol II is infrequent and released tssRNAs are targeted for rapid degradation. Further, we provide evidence that the predominant tssRNA species observed are nascent RNAs held within early elongation complexes. We propose that stable pausing of polymerase provides a temporal window of opportunity for recruitment of factors to modulate gene expression and that the nascent tssRNA represents an appealing target for these interactions. PMID:24184211

  8. The histone methyltransferase DOT1L: regulatory functions and a cancer therapy target

    PubMed Central

    Wong, Matthew; Polly, Patsie; Liu, Tao

    2015-01-01

    DOT1L is a unique histone methyltransferase that targets the histone H3 lysine 79 (H3K79) residue for mono-, di- and tri- methylation. Histone H3K79 mono- and di-methylation results in active gene transcription, while H3K79 tri-methylation is associated with gene repression. DOT1L has a critical role in regulating gene transcription, development, cell cycle progression, somatic reprogramming and DNA damage repair. DOT1L interacts with Mixed Lineage Leukemia (MLL) fusion proteins, leading to enhanced H3K79 methylation, maintenance of open chromatin, overexpression of downstream oncogenes and leukemogenesis. Importantly, small molecule DOT1L inhibitors have been recently developed, and one of the DOT1L inhibitors is already under investigation in a Phase I clinical trial in patients with MLL fusion gene-driven leukemia. PMID:26609488

  9. 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.

  10. Top-Down Targeted Proteomics Reveals Decrease in Myosin Regulatory Light-Chain Phosphorylation That Contributes to Sarcopenic Muscle Dysfunction.

    PubMed

    Gregorich, Zachery R; Peng, Ying; Cai, Wenxuan; Jin, Yutong; Wei, Liming; Chen, Albert J; McKiernan, Susan H; Aiken, Judd M; Moss, Richard L; Diffee, Gary M; Ge, Ying

    2016-08-01

    Sarcopenia, the loss of skeletal muscle mass and function with advancing age, is a significant cause of disability and loss of independence in the elderly and thus, represents a formidable challenge for the aging population. Nevertheless, the molecular mechanism(s) underlying sarcopenia-associated muscle dysfunction remain poorly understood. In this study, we employed an integrated approach combining top-down targeted proteomics with mechanical measurements to dissect the molecular mechanism(s) in age-related muscle dysfunction. Top-down targeted proteomic analysis uncovered a progressive age-related decline in the phosphorylation of myosin regulatory light chain (RLC), a critical protein involved in the modulation of muscle contractility, in the skeletal muscle of aging rats. Top-down tandem mass spectrometry analysis identified a previously unreported bis-phosphorylated proteoform of fast skeletal RLC and localized the sites of decreasing phosphorylation to Ser14/15. Of these sites, Ser14 phosphorylation represents a previously unidentified site of phosphorylation in RLC from fast-twitch skeletal muscle. Subsequent mechanical analysis of single fast-twitch fibers isolated from the muscles of rats of different ages revealed that the observed decline in RLC phosphorylation can account for age-related decreases in the contractile properties of sarcopenic fast-twitch muscles. These results strongly support a role for decreasing RLC phosphorylation in sarcopenia-associated muscle dysfunction and suggest that therapeutic modulation of RLC phosphorylation may represent a new avenue for the treatment of sarcopenia. PMID:27362462

  11. Genome-wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I

    PubMed Central

    Peña-Hernández, Rodrigo; Marques, Maud; Hilmi, Khalid; Zhao, Teijun; Saad, Amine; Alaoui-Jamali, Moulay A.; del Rincon, Sonia V.; Ashworth, Todd; Roy, Ananda L.; Emerson, Beverly M.; Witcher, Michael

    2015-01-01

    CCCTC-binding factor (CTCF) is a key regulator of nuclear chromatin structure and gene regulation. The impact of CTCF on transcriptional output is highly varied, ranging from repression to transcriptional pausing and transactivation. The multifunctional nature of CTCF may be directed solely through remodeling chromatin architecture. However, another hypothesis is that the multifunctional nature of CTCF is mediated, in part, through differential association with protein partners having unique functions. Consistent with this hypothesis, our mass spectrometry analyses of CTCF interacting partners reveal a previously undefined association with the transcription factor general transcription factor II-I (TFII-I). Biochemical fractionation of CTCF indicates that a distinct CTCF complex incorporating TFII-I is assembled on DNA. Unexpectedly, we found that the interaction between CTCF and TFII-I is essential for directing CTCF to the promoter proximal regulatory regions of target genes across the genome, particularly at genes involved in metabolism. At genes coregulated by CTCF and TFII-I, we find knockdown of TFII-I results in diminished CTCF binding, lack of cyclin-dependent kinase 8 (CDK8) recruitment, and an attenuation of RNA polymerase II phosphorylation at serine 5. Phenotypically, knockdown of TFII-I alters the cellular response to metabolic stress. Our data indicate that TFII-I directs CTCF binding to target genes, and in turn the two proteins cooperate to recruit CDK8 and enhance transcription initiation. PMID:25646466

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

    PubMed Central

    2013-01-01

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

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

    PubMed

    Kuhlmann-Gottke, Johanna; Duchow, Karin

    2015-11-01

    At present, there is no separate regulatory framework for cell-based medicinal products (CBMP) for veterinary use at the European or German level. Current European and national regulations exclusively apply to the corresponding medicinal products for human use. An increasing number of requests for the regulatory classification of CBMP for veterinary use, such as allogeneic stem cell preparations and dendritic cell-based autologous tumour vaccines, and a rise in scientific advice for companies developing these products, illustrate the need for adequate legislation. Currently, advice is given and decisions are made on a case-by-case basis regarding the regulatory classification and authorisation requirements.Since some of the CBMP - in particular in the area of stem-cell products - are developed in parallel for human and veterinary use, there is an urgent need to create specific legal definitions, regulations, and guidelines for these complex innovative products in the veterinary sector as well. Otherwise, there is a risk that that the current legal grey area regarding veterinary medicinal products will impede therapeutic innovations in the long run. A harmonised EU-wide approach is desirable. Currently the European legislation on veterinary medicinal products is under revision. In this context, veterinary therapeutics based on allogeneic cells and tissues will be defined and regulated. Certainly, the legal framework does not have to be as comprehensive as for human CBMP; a leaner solution is conceivable, similar to the special provisions for advanced-therapy medicinal products laid down in the German Medicines Act. PMID:26369765

  14. Quantitative comparison of tumor delivery for multiple targeted nanoparticles simultaneously by multiplex ICP-MS.

    PubMed

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

    2014-01-01

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

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

    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. CCR6 regulates EAE pathogenesis by controlling regulatory CD4+ T-cell recruitment to target tissues.

    PubMed

    Villares, Ricardo; Cadenas, Vanessa; Lozano, María; Almonacid, Luis; Zaballos, Angel; Martínez-A, Carlos; Varona, Rosa

    2009-06-01

    The T-cell subsets, characterized by their cytokine production profiles and immune regulatory functions, depend on correct in vivo location to interact with accessory or target cells for effective immune responses. Differentiation of naive CD4(+) T cells into effectors is accompanied by sequentially regulated expression of the chemokine receptors responsible for cell recruitment to specific tissues. We studied CCR6 function in EAE, a CD4(+) T-cell-mediated CNS disease characterized by mononuclear infiltration and demyelination. CCR6(-/-) mice showed an altered time course of EAE development, with delayed onset, a higher clinical score, and more persistent symptoms than in controls. An imbalanced cytokine profile and reduced Foxp3(+) cell frequency characterized CNS tissues from CCR6(-/-) compared with CCR6(+/+) mice during the disease effector phase. Transfer of CCR6(+/+) Treg to CCR6(-/-) mice the day before EAE induction reduced the clinical score associated with an increased in infiltrating Foxp3(+) cells and recovery of the cytokine balance in CCR6(-/-) mouse CNS. Competitive assays between CCR6(+/+) and CCR6(-/-) Treg adoptively transferred to CCR6(-/-) mice showed impaired ability of CCR6(-/-) Treg to infiltrate CNS tissues in EAE-affected mice. Our data indicate a CCR6 requirement by CD4(+) Treg to downregulate the CNS inflammatory process and neurological signs associated with EAE. PMID:19499521

  18. The ubiquitin-dependent targeting pathway in Saccharomyces cerevisiae plays a critical role in multiple chromatin assembly regulatory steps.

    PubMed Central

    Harkness, Troy A A; Davies, Gerald F; Ramaswamy, Vijay; Arnason, Terra G

    2002-01-01

    In a screen designed to isolate Saccharomyces cerevisiae strains defective for in vitro chromatin assembly, two temperature-sensitive (ts) mutants were obtained: rmc1 and rmc3 (remodeling of chromatin). Cloning of RMC1 and RMC3 revealed a broad role for the ubiquitin-dependent targeting cascade as the ubiquitin-protein ligases (E3s), the anaphase promoting complex (APC; RMC1 encodes APC5) and Rsp5p, respectively, were identified. Genetic studies linked the rmc1/apc5 chromatin assembly defect to APC function: rmc1/apc5 genetically interacted with apc9Delta, apc10Delta, and cdc26Delta mutants. Furthermore, phenotypes associated with the rmc1/apc5 allele were consistent with defects in chromatin metabolism and in APC function: (i) UV sensitivity, (ii) plasmid loss, (iii) accumulation of G2/M cells, and (iv) suppression of the ts defect by growth on glucose-free media and by expression of ubiquitin. On the other hand, the multifunctional E3, Rsp5p, was shown to be required for both in vitro and in vivo chromatin assembly, as well as for the proper transcriptional and translational control of at least histone H3. The finding that the distinctly different E3 enzymes, APC and Rsp5p, both play roles in regulating chromatin assembly highlight the depth of the regulatory networks at play. The significance of these findings will be discussed. PMID:12399376

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

    PubMed Central

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

    2005-01-01

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

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

    PubMed

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

    2015-09-01

    Gonococci secrete chromosomal DNA into the extracellular environment using a type IV secretion system (T4SS). The secreted DNA acts in natural transformation and initiates biofilm development. Although the DNA and its effects are detectable, structural components of the T4SS are present at very low levels, suggestive of uncharacterized regulatory control. We sought to better characterize the expression and regulation of T4SS genes and found that the four operons containing T4SS genes are transcribed at very different levels. Increasing transcription of two of the operons through targeted promoter mutagenesis did not increase DNA secretion. The stability and steady-state levels of two T4SS structural proteins were affected by a homolog of tail-specific protease. An RNA switch was also identified that regulates translation of a third T4SS operon. The switch mechanism relies on two putative stem-loop structures contained within the 5' untranslated region of the transcript, one of which occludes the ribosome binding site and start codon. Mutational analysis of these stem loops supports a model in which induction of an alternative structure relieves repression. Taken together, these results identify multiple layers of regulation, including transcriptional, translational and post-translational mechanisms controlling T4SS gene expression and DNA secretion. PMID:26076069

  1. Structure and regulatory targets of SCO3201, a highly promiscuous TetR-like regulator of Streptomyces coelicolor M145.

    PubMed

    Xu, Delin; Waack, Paul; Zhang, Qizhong; Werten, Sebastiaan; Hinrichs, Winfried; Virolle, Marie-Joelle

    2014-07-18

    SCO3201, a regulator of the TetR family, is a strong repressor of both morphological differentiation and antibiotic production when overexpressed in Streptomyces coelicolor. Here, we report the identification of 14 novel putative regulatory targets of this regulator using in vitro formaldehyde cross-linking. Direct binding of purified His6-SCO3201 was demonstrated for the promoter regions of 5 regulators (SCO1716, SCO1950, SCO3367, SCO4009 and SCO5046), a putative histidine phosphatase (SCO1809), an acetyltransferase (SCO0988) and the polyketide synthase RedX (SCO5878), using EMSA. Reverse transcriptional analysis demonstrated that the expression of the transcriptional regulators SCO1950, SCO4009, SCO5046, as well as of SCO0988 and RedX was down regulated, upon SCO3201 overexpression, whereas the expression of SCO1809 and SCO3367 was up regulated. A consensus binding motif was derived via alignment of the promoter regions of the genes negatively regulated. The positions of the predicted operator sites were consistent with a direct repressive effect of SCO3201 on 5 out of 7 of these promoters. Furthermore, the 2.1Å crystal structure of SCO3201 was solved, which provides a possible explanation for the high promiscuity of this regulator that might account for its dramatic effect on the differentiation process of S. coelicolor. PMID:24928397

  2. Daam2-PIP5K is a regulatory pathway for Wnt signaling and therapeutic target for remyelination in the CNS.

    PubMed

    Lee, Hyun Kyoung; Chaboub, Lesley S; Zhu, Wenyi; Zollinger, Daniel; Rasband, Matthew N; Fancy, Stephen P J; Deneen, Benjamin

    2015-03-18

    Wnt signaling plays an essential role in developmental and regenerative myelination of the CNS; however, contributions of proximal regulators of the Wnt receptor complex to these processes remain undefined. To identify components of the Wnt pathway that regulate these processes, we applied a multifaceted discovery platform and found that Daam2-PIP5K comprise a novel pathway regulating Wnt signaling and myelination. Using dorsal patterning of the chick spinal cord we found that Daam2 promotes Wnt signaling and receptor complex formation through PIP5K-PIP2. Analysis of Daam2 function in oligodendrocytes (OLs) revealed that it suppresses OL differentiation during development, after white matter injury (WMI), and is expressed in human white matter lesions. These findings suggest a pharmacological strategy to inhibit Daam2-PIP5K function, application of which stimulates remyelination after WMI. Put together, our studies integrate information from multiple systems to identify a novel regulatory pathway for Wnt signaling and potential therapeutic target for WMI. PMID:25754822

  3. Daam2-PIP5K Is a Regulatory Pathway for Wnt Signaling and Therapeutic Target for Remyelination in the CNS

    PubMed Central

    Lee, Hyun Kyoung; Chaboub, Lesley S.; Zhu, Wenyi; Zollinger, Daniel; Rasband, Matthew N.; Fancy, Stephen P.J.; Deneen, Benjamin

    2015-01-01

    SUMMARY Wnt signaling plays an essential role in developmental and regenerative myelination of the CNS; however, contributions of proximal regulators of the Wnt receptor complex to these processes remain undefined. To identify components of the Wnt pathway that regulate these processes, we applied a multifaceted discovery platform and found that Daam2-PIP5K comprise a novel pathway regulating Wnt signaling and myelination. Using dorsal patterning of the chick spinal cord we found that Daam2 promotes Wnt signaling and receptor complex formation through PIP5K-PIP2. Analysis of Daam2 function in oligodendrocytes (OLs) revealed that it suppresses OL differentiation during development, after white matter injury (WMI), and is expressed in human white matter lesions. These findings suggest a pharmacological strategy to inhibit Daam2-PIP5K function, application of which stimulates remyelination after WMI. Put together, our studies integrate information from multiple systems to identify a novel regulatory pathway for Wnt signaling and potential therapeutic target for WMI. PMID:25754822

  4. 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

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

    PubMed

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

    2014-02-01

    Modern radiotherapy requires accurate region of interest (ROI) inputs for plan optimization and delivery. Target delineation, however, remains operator-dependent and potentially serves as a major source of treatment delivery error. In order to optimize this critical, yet observer-driven process, a flexible web-based platform for individual and cooperative target delineation analysis and instruction was developed in order to meet the following unmet needs: (1) an open-source/open-access platform for automated/semiautomated quantitative interobserver and intraobserver ROI analysis and comparison, (2) a real-time interface for radiation oncology trainee online self-education in ROI definition, and (3) a source for pilot data to develop and validate quality metrics for institutional and cooperative group quality assurance efforts. The resultant software, Target Contour Testing/Instructional Computer Software (TaCTICS), developed using Ruby on Rails, has since been implemented and proven flexible, feasible, and useful in several distinct analytical and research applications. PMID:24043593

  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. Targeting Tuberculosis and HIV Infection-Specific Regulatory T Cells with MEK/ERK Signaling Pathway Inhibitors

    PubMed Central

    Lieske, Nora V.; Tonby, Kristian; Kvale, Dag; Dyrhol-Riise, Anne M.; Tasken, Kjetil

    2015-01-01

    Human regulatory T cells (Tregs) are essential in maintaining immunological tolerance and suppress effector T cells. Tregs are commonly up-regulated in chronic infectious diseases such as tuberculosis (TB) and human immunodeficiency virus (HIV) infection and thereby hamper disease-specific immune responses and eradication of pathogens. The MEK/ERK signaling pathway is involved in regulation of the FoxP3 transcription factor, which directs a lineage-specific transcriptional program to define Tregs and control their suppressive function. Here, we aimed to target activation of disease-specific Tregs by inhibition of the MEK/ERK signaling pathway based on the hypothesis that this would improve anti-HIV and anti-TB immunity. Stimulation of T cells from untreated TB (n = 12) and HIV (n = 8) patients with disease-specific antigens in vitro in the presence of the MEK inhibitor (MEKI) trametinib (GSK1120212) resulted in significant down-regulation of both FoxP3 levels (MFI) and fractions of resting (CD45RA+FoxP3+) and activated (CD45RA−FoxP3++) Tregs. MEKI also reduced the levels of specific T effector cells expressing the pro-inflammatory cytokines (IFN-γ, TNF-α and IL-2) in both HIV and TB patients. In conclusion, MEKIs modulate disease antigen-specific Treg activation and may have potential application in new treatment strategies in chronic infectious diseases where reduction of Treg activity would be favorable. Whether MEKIs can be used in current HIV or TB therapy regimens needs to be further investigated. PMID:26544592

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

    PubMed Central

    Caron, Kathleen M.; Soo, Shiu-Ching; Wetsel, William C.; Stocco, Douglas M.; Clark, Barbara J.; Parker, Keith L.

    1997-01-01

    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. PMID:9326645

  9. Comparison of strategies for identification of regulatory quantitative trait loci of transcript expression traits.

    PubMed

    Franceschini, Nora; Wojczynski, Mary K; Göring, Harald H H; Peralta, Juan Manuel; Dyer, Thomas D; Li, Xia; Li, Hao; North, Kari E

    2007-01-01

    In order to identify regulatory genes, we determined the heritability of gene transcripts, performed linkage analysis to identify quantitative trait loci (QTLs), and evaluated the evidence for shared genetic effects among transcripts with co-localized QTLs in non-diseased participants from 14 CEPH (Centre d'Etude du Polymorphisme Humain) Utah families. Seventy-six percent of transcripts had a significant heritability and 54% of them had LOD score >or= 1.8. Bivariate genetic analysis of 15 transcripts that had co-localized QTLs on 4q28.2-q31.1 identified significant genetic correlation among some transcripts although no improvement in the magnitude of LOD scores in this region was noted. Similar results were found in analysis of 12 transcripts, that had co-localized QTLs in the 13q34 region. Principal-component analyses did not improve the ability to identify chromosomal regions of co-localized gene expressions. PMID:18466588

  10. Comparison of strategies for identification of regulatory quantitative trait loci of transcript expression traits

    PubMed Central

    Franceschini, Nora; Wojczynski, Mary K; Göring, Harald HH; Peralta, Juan Manuel; Dyer, Thomas D; Li, Xia; Li, Hao; North, Kari E

    2007-01-01

    In order to identify regulatory genes, we determined the heritability of gene transcripts, performed linkage analysis to identify quantitative trait loci (QTLs), and evaluated the evidence for shared genetic effects among transcripts with co-localized QTLs in non-diseased participants from 14 CEPH (Centre d'Etude du Polymorphisme Humain) Utah families. Seventy-six percent of transcripts had a significant heritability and 54% of them had LOD score ≥ 1.8. Bivariate genetic analysis of 15 transcripts that had co-localized QTLs on 4q28.2-q31.1 identified significant genetic correlation among some transcripts although no improvement in the magnitude of LOD scores in this region was noted. Similar results were found in analysis of 12 transcripts, that had co-localized QTLs in the 13q34 region. Principal-component analyses did not improve the ability to identify chromosomal regions of co-localized gene expressions. PMID:18466588

  11. 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.

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

    PubMed

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

    2012-04-01

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

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

    PubMed

    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

    2016-04-01

    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 inSOX2are 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 ofPTCH1in 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 ofptch1in 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 thePTCH1locus to regulatePTCH1expression, findings that were validated both in vitro and in vivo. Together, these results demonstrate thatPTCH1mutations 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 eitherPTCH1orSOX2. PMID:26893459

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

    PubMed Central

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

    2015-01-01

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

  15. 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

    2015-01-01

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

  16. 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. PMID:20688192

  17. 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. PMID:25563193

  18. Comparison of human observer and algorithmic target detection in nonurban forward-looking infrared imagery

    NASA Astrophysics Data System (ADS)

    Weber, Bruce A.

    2005-07-01

    We have performed an experiment that compares the performance of human observers with that of a robust algorithm for the detection of targets in difficult, nonurban forward-looking infrared imagery. Our purpose was to benchmark the comparison and document performance differences for future algorithm improvement. The scale-insensitive detection algorithm, used as a benchmark by the Night Vision Electronic Sensors Directorate for algorithm evaluation, employed a combination of contrastlike features to locate targets. Detection receiver operating characteristic curves and observer-confidence analyses were used to compare human and algorithmic responses and to gain insight into differences. The test database contained ground targets, in natural clutter, whose detectability, as judged by human observers, ranged from easy to very difficult. In general, as compared with human observers, the algorithm detected most of the same targets, but correlated confidence with correct detections poorly and produced many more false alarms at any useful level of performance. Though characterizing human performance was not the intent of this study, results suggest that previous observational experience was not a strong predictor of human performance, and that combining individual human observations by majority vote significantly reduced false-alarm rates.

  19. In vivo inhibition of human CD19 targeted effector T cells by natural T regulatory cells in a xenotransplant murine model of B cell malignancy

    PubMed Central

    Lee, James; Hayman, Erik; Pegram, Hollie; Santos, Elmer; Heller, Glen; Sadelain, Michel; Brentjens, Renier J.

    2011-01-01

    Human T cells genetically modified to express chimeric antigen receptors (CARs) specific to the B cell tumor antigen CD19 can successfully eradicate systemic human CD19+ tumors in immunocompromised SCID-Beige mice. However, in the clinical setting, CD4+ CD25hi T regulatory cells (Tregs) present within the tumor microenvironment are potent suppressors of tumor-targeted effector T cells. In order to assess the impact of Tregs on CAR-modified T cells in the SCID-Beige xenotransplant model, we isolated, genetically targeted and expanded natural T regulatory cells (nTregs). In vitro, nTregs, modified to express CD19 targeted CARs efficiently inhibited the proliferation of activated human T cells, as well as the capacity of CD19-targeted 19-28z+ effector T cells to lyse CD19+ Raji tumor cells. Intravenous infusion of CD19-targeted nTregs into SCID-Beige mice with systemic Raji tumors traffic to sites of tumor and recapitulate a clinically relevant hostile tumor microenvironment. Anti-tumor efficacy of subsequently infused 19-28z+ effector T cells was fully abrogated as assessed by long-term survival of treated mice. Optimal suppression by genetically targeted nTregs was dependent on nTreg to effector T cell ratios and in vivo nTreg activation. Prior infusion of cyclophosphamide in the setting of this nTreg-mediated hostile microenvironment was able to restore the anti-tumor activity of subsequently infused 19-28z+ effector T cells through the eradication of tumor targeted nTregs. These findings have significant implications on the design of future clinical trials utilizing CAR-based adoptive T cell therapies of cancer. PMID:21487038

  20. Complement regulatory protein expression by a human oligodendrocyte cell line: cytokine regulation and comparison with astrocytes.

    PubMed Central

    Gasque, P; Morgan, B P

    1996-01-01

    Rat oligodendrocytes spontaneously activate complement (C) and lack the C inhibitor CD59. As a consequence, rat oligodendrocytes are susceptible to lysis by autologous C in vitro. Expression of C inhibitors on human oligodendrocytes in vitro and other human glia has yet to be well characterized. We have previously shown expression at the mRNA level of the membrane inhibitors CD59, decay-accelerating factor (DAF; CD55) and membrane cofactor protein (MCP; CD46) in human astrocytes. We here examine the expression of membrane and secreted C inhibitors by the oligodendrocyte cell line, HOG. HOG cells abundantly expressed CD59, assessed at protein and mRNA level, and expressed DAF and MCP, albeit at a lower level. Expression of all three inhibitors was enhanced by incubation with interferon-gamma or with phorbol ester (PMA). Complement receptor type 1 (CR1; CD35) was neither expressed constitutively nor induced by cytokines. HOG also constitutively secreted C1-inhibitor, S-protein and clusterin. Factor H was secreted only after stimulation with cytokines. C4b binding protein was expressed at a very low level and was detected only at the mRNA level by reverse transcriptase-polymerase chain reaction (RT-PCR). For comparison, astrocyte expression of CD59, DAF, MCP and CR1 was confirmed at the mRNA and protein levels. HOG did not activate C spontaneously, as judged by the lack of deposition of C fragments, and were not lysed by C even after inhibition of CD59 and DAF using specific monoclonal antibodies. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:8958045

  1. Army Research Laboratory ultrawide-band testbed radar and comparisons of target data with models

    NASA Astrophysics Data System (ADS)

    Happ, Lynn; Ressler, Marc A.; Sturgess, Keith; Bennett, Matthew; Carin, Lawrence; Vitebskiey, S.

    1995-06-01

    Over the years, many different sensor types have been evaluated in an attempt to satisfy the need to detect and discriminate tactical and strategic targets concealed in foliage or underground. In large measure these early efforts were disappointing because of the lack of appropriate technologies. Today, by taking advantage of commercial off-the-shelf processors, an advanced analog-to-digital (A/D) converter, and lessons learned, a highly capable impulse radar has been designed and assembled to investigate an ultra-wideband (UWB) radar approach for ground penetration (GPEN) radar studies. The testbed consists of several major subsystems that are modular to allow for the evaluation of alternate approaches. The testbed radar subsystem consist of the antenna, the transmitter, the A/D converter, the processor/data storage system, the timing and control assembly, the positioning subsystem, and the operator interface computer. Many of the subassemblies exist as standard 19 inch rackmount units or as VME-compatible printed circuit assemblies. Much of the system operation is controlled by software, allowing easy modifications or other future upgrades. Data collected with this upgraded system will be used for measuring and analyzing the basic phenomenology of radar propagation through the ground and the response of targets, clutter, and targets embedded in clutter. One important aspect of basic phenomenology studies is validation of models with data. Range profiles of synthetic aperature radar (SAR) processed data from the Army Research Laboratory UWB radar is compared to 3D method of moments models for similar targets. In this paper, a mix of canonical and mine-like targets are examined and compared. Comparison between data and models shows some correlation, thus validating the need for further investigation.

  2. 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

  3. 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.

  4. 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.

  5. Comparisons of target detection in clutter using data from the 1993 FOPEN experiments

    NASA Astrophysics Data System (ADS)

    Winter, Edwin M.; Schlangen, Michael J.; Hendrickson, Clark R.

    1994-06-01

    During 1993, a series of experiments were performed under the Advanced Research Projects Agency (ARPA) sponsorship using the SRI ultra-wide band UHF synthetic aperture radar (SAR). These experiments were performed over a variety of clutter backgrounds to assess the foliage penetration capability of the technology and to investigate target detection in clutter. Experiments were conducted observing tropical rain forest backgrounds in Panama, several different desert backgrounds in the Yuma vicinity, and the mid-latitude temperate forest of Maine. SAR images were formed from the raw data using Differential GPS to aid in the focusing. The three locations represent different levels of foliage cover, ranging from the sparsely vegetated desert sites to the triple canopied rain forest. The characteristics of each site are discussed first through a presentation of photography and SAR imagery. The clutter characteristics are studied through a comparison of the cumulative distributions, which are plotted using a variety of conventions. For each case, at least one reference target is included in the test scene. The signal of that target as processed by a common algorithm will be compared to the processed clutter distribution.

  6. Comparisons of target detection clutter using data from the 1993 FOPEN experiments

    NASA Astrophysics Data System (ADS)

    Winter, E. M.; Schlangen, M. J.; Hendrickson, C. R.

    1994-10-01

    During 1993, a series of experiments were performed under the Advanced Research Projects Agency (ARPA) sponsorship using the SRI Ultra-Wide Band UHF Synthetic Aperture Radar (SAR). These experiments were performed over a variety of clutter backgrounds to assess the foliage penetration capability of the technology and to investigate target detection in clutter. Experiments were conducted observing tropical rain forest backgrounds in Panama, several different desert backgrounds in the Yuma vicinity, and the mid-latitude temperate forest of Maine. SAR images were formed from the raw data using Differential GPS to aid in the focusing. The three locations represent different levels of foliage cover, ranging from the sparsely vegetated desert sites to the triple canopied rain forest. The characteristics of each site are discussed first through a presentation of photography and SAR imagery. The clutter characteristics are studied through a comparison of the cumulative distributions, which are plotted using a variety of conventions (e.g., log-normal, normal, Weibull). For each case, at least one reference target is included in the test scene. The signal of that target as processed by a common algorithm will be compared to the processed clutter distribution.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2015-07-01

    i-cisTarget is a web tool to predict regulators of a set of genomic regions, such as ChIP-seq peaks or co-regulated/similar enhancers. i-cisTarget can also be used to identify upstream regulators and their target enhancers starting from a set of co-expressed genes. Whereas the original version of i-cisTarget was focused on Drosophila data, the 2015 update also provides support for human and mouse data. i-cisTarget detects transcription factor motifs (position weight matrices) and experimental data tracks (e.g. from ENCODE, Roadmap Epigenomics) that are enriched in the input set of regions. As experimental data tracks we include transcription factor ChIP-seq data, histone modification ChIP-seq data and open chromatin data. The underlying processing method is based on a ranking-and-recovery procedure, allowing accurate determination of enrichment across heterogeneous datasets, while also discriminating direct from indirect target regions through a 'leading edge' analysis. We illustrate i-cisTarget on various Ewing sarcoma datasets to identify EWS-FLI1 targets starting from ChIP-seq, differential ATAC-seq, differential H3K27ac and differential gene expression data. Use of i-cisTarget is free and open to all, and there is no login requirement. Address: http://gbiomed.kuleuven.be/apps/lcb/i-cisTarget. PMID:25925574

  9. Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks

    PubMed Central

    Fischer, Martin; Grossmann, Patrick; Padi, Megha; DeCaprio, James A.

    2016-01-01

    Cell cycle (CC) and TP53 regulatory networks are frequently deregulated in cancer. While numerous genome-wide studies of TP53 and CC-regulated genes have been performed, significant variation between studies has made it difficult to assess regulation of any given gene of interest. To overcome the limitation of individual studies, we developed a meta-analysis approach to identify high confidence target genes that reflect their frequency of identification in independent datasets. Gene regulatory networks were generated by comparing differential expression of TP53 and CC-regulated genes with chromatin immunoprecipitation studies for TP53, RB1, E2F, DREAM, B-MYB, FOXM1 and MuvB. RNA-seq data from p21-null cells revealed that gene downregulation by TP53 generally requires p21 (CDKN1A). Genes downregulated by TP53 were also identified as CC genes bound by the DREAM complex. The transcription factors RB, E2F1 and E2F7 bind to a subset of DREAM target genes that function in G1/S of the CC while B-MYB, FOXM1 and MuvB control G2/M gene expression. Our approach yields high confidence ranked target gene maps for TP53, DREAM, MMB-FOXM1 and RB-E2F and enables prediction and distinction of CC regulation. A web-based atlas at www.targetgenereg.org enables assessing the regulation of any human gene of interest. PMID:27280975

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

    PubMed

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

    2013-09-01

    The broadly conserved Class III homeodomain leucine zipper (HD-ZIPIII) and KANADI transcription factors have opposing and transformational effects on polarity and growth in all tissues and stages of the plant's life. To obtain a comprehensive understanding of how these factors work, we have identified transcripts that change in response to induced HD-ZIPIII or KANADI function. Additional criteria used to identify high-confidence targets among this set were presence of an adjacent HD-ZIPIII binding site, expression enriched within a subdomain of the shoot apical meristem, mutant phenotype showing defect in polar leaf and/or meristem development, physical interaction between target gene product and HD-ZIPIII protein, opposite regulation by HD-ZIPIII and KANADI, and evolutionary conservation of the regulator-target relationship. We find that HD-ZIPIII and KANADI regulate tissue-specific transcription factors involved in subsidiary developmental decisions, nearly all major hormone pathways, and new actors (such as indeterminate domain4) in the ad/abaxial regulatory network. Multiple feedback loops regulating HD-ZIPIII and KANADI are identified, as are mechanisms through which HD-ZIPIII and KANADI oppose each other. This work lays the foundation needed to understand the components, structure, and workings of the ad/abaxial regulatory network directing basic plant growth and development. PMID:24076978

  11. Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks.

    PubMed

    Fischer, Martin; Grossmann, Patrick; Padi, Megha; DeCaprio, James A

    2016-07-27

    Cell cycle (CC) and TP53 regulatory networks are frequently deregulated in cancer. While numerous genome-wide studies of TP53 and CC-regulated genes have been performed, significant variation between studies has made it difficult to assess regulation of any given gene of interest. To overcome the limitation of individual studies, we developed a meta-analysis approach to identify high confidence target genes that reflect their frequency of identification in independent datasets. Gene regulatory networks were generated by comparing differential expression of TP53 and CC-regulated genes with chromatin immunoprecipitation studies for TP53, RB1, E2F, DREAM, B-MYB, FOXM1 and MuvB. RNA-seq data from p21-null cells revealed that gene downregulation by TP53 generally requires p21 (CDKN1A). Genes downregulated by TP53 were also identified as CC genes bound by the DREAM complex. The transcription factors RB, E2F1 and E2F7 bind to a subset of DREAM target genes that function in G1/S of the CC while B-MYB, FOXM1 and MuvB control G2/M gene expression. Our approach yields high confidence ranked target gene maps for TP53, DREAM, MMB-FOXM1 and RB-E2F and enables prediction and distinction of CC regulation. A web-based atlas at www.targetgenereg.org enables assessing the regulation of any human gene of interest. PMID:27280975

  12. 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

  13. Comparison of Regulatory T Cells in Hemodialysis Patients and Healthy Controls: Implications for Cell Therapy in Transplantation

    PubMed Central

    Afzali, Behdad; Edozie, Francis C.; Fazekasova, Henrieta; Scottà, Cristiano; Mitchell, Peter J.; Canavan, James B.; Kordasti, Shahram Y.; Chana, Prabhjoat S.; Ellis, Richard; Lord, Graham M.; John, Susan; Hilton, Rachel; Lechler, Robert I.

    2013-01-01

    Summary Background and objectives Cell-based therapy with natural (CD4+CD25hiCD127lo) regulatory T cells to induce transplant tolerance is now technically feasible. However, regulatory T cells from hemodialysis patients awaiting transplantation may be functionally/numerically defective. Human regulatory T cells are also heterogeneous, and some are able to convert to proinflammatory Th17 cells. This study addresses the suitability of regulatory T cells from hemodialysis patients for cell-based therapy in preparation for the first clinical trials in renal transplant recipients (the ONE Study). Design, setting, participants, & measurements Healthy controls and age- and sex-matched hemodialysis patients without recent illness/autoimmune disease on established, complication-free hemodialysis for a minimum of 6 months were recruited. Circulating regulatory T cells were studied by flow cytometry to compare the regulatory T cell subpopulations. Regulatory T cells from members of each group were compared for suppressive function and plasticity (IL-17–producing capacity) before and after in vitro expansion with and without Rapamycin, using standard assays. Results Both groups had similar total regulatory T cells and subpopulations I and III. In each subpopulation, regulatory T cells expressed similar levels of the function-associated markers CD27, CD39, HLA-DR, and FOXP3. Hemodialysis regulatory T cells were less suppressive, expanded poorly compared with healthy control regulatory T cells, and produced IL-17 in the absence of Rapamycin. However, Rapamycin efficiently expanded hemodialysis regulatory T cells to a functional and stable cell product. Conclusions Rapamycin-based expansion protocols should enable clinical trials of cell-based immunotherapy for the induction of tolerance to renal allografts using hemodialysis regulatory T cells. PMID:23580782

  14. Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System

    PubMed Central

    Galgano, Alessia; Forrer, Michael; Jaskiewicz, Lukasz; Kanitz, Alexander; Zavolan, Mihaela; Gerber, André P.

    2008-01-01

    Genome-wide identification of mRNAs regulated by RNA-binding proteins is crucial to uncover post-transcriptional gene regulatory systems. The conserved PUF family RNA-binding proteins repress gene expression post-transcriptionally by binding to sequence elements in 3′-UTRs of mRNAs. Despite their well-studied implications for development and neurogenesis in metazoa, the mammalian PUF family members are only poorly characterized and mRNA targets are largely unknown. We have systematically identified the mRNAs associated with the two human PUF proteins, PUM1 and PUM2, by the recovery of endogenously formed ribonucleoprotein complexes and the analysis of associated RNAs with DNA microarrays. A largely overlapping set comprised of hundreds of mRNAs were reproducibly associated with the paralogous PUM proteins, many of them encoding functionally related proteins. A characteristic PUF-binding motif was highly enriched among PUM bound messages and validated with RNA pull-down experiments. Moreover, PUF motifs as well as surrounding sequences exhibit higher conservation in PUM bound messages as opposed to transcripts that were not found to be associated, suggesting that PUM function may be modulated by other factors that bind conserved elements. Strikingly, we found that PUF motifs are enriched around predicted miRNA binding sites and that high-confidence miRNA binding sites are significantly enriched in the 3′-UTRs of experimentally determined PUM1 and PUM2 targets, strongly suggesting an interaction of human PUM proteins with the miRNA regulatory system. Our work suggests extensive connections between the RBP and miRNA post-transcriptional regulatory systems and provides a framework for deciphering the molecular mechanism by which PUF proteins regulate their target mRNAs. PMID:18776931

  15. 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

    2006-10-01

    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. PMID:16985282

  16. Structure-function analysis of the beta regulatory subunit of protein kinase CK2 by targeting embryonic stem cell.

    PubMed

    Ziercher, Léa; Filhol, Odile; Laudet, Béatrice; Prudent, Renaud; Cochet, Claude; Buchou, Thierry

    2011-10-01

    Programs that govern stem cell maintenance and pluripotency are dependent on extracellular factors and of intrinsic cell modulators. Embryonic stem (ES) cells with a specific depletion of the gene encoding the regulatory subunit of protein kinase CK2 (CK2β) revealed a viability defect. However, analysis of CK2β functions along the neural lineage established CK2β as a positive regulator for neural stem/progenitor cell (NSC) proliferation and multipotency. By using an in vitro genetic conditional approach, we demonstrate in this work that specific domains of CK2β involved in the regulatory function towards CK2 catalytic subunits are crucial structural determinants for ES cell homeostasis. PMID:21861102

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

    PubMed

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

    2016-07-01

    There is mounting evidence that regulatory variation plays an important role in genetic risk for schizophrenia. Here, we specifically search for regulatory variants at risk by sequencing promoter regions of twenty-three genes implied in schizophrenia by copy number variant or genome-wide association studies. After strict quality control, a total of 55,206bp per sample were analyzed in 526 schizophrenia cases and 516 controls from Galicia, NW Spain, using the Applied Biosystems SOLiD System. Variants were filtered based on frequency from public databases, chromatin states from the RoadMap Epigenomics Consortium at tissues relevant for schizophrenia, such as fetal brain, mid-frontal lobe, and angular gyrus, and prediction of functionality from RegulomeDB. The proportion of rare variants at polycomb repressive chromatin state at relevant tissues was higher in cases than in controls. The proportion of rare variants with predicted regulatory role was significantly higher in cases than in controls (P=0.0028, OR=1.93, 95% C.I.=1.23-3.04). Combination of information from both sources led to the identification of an excess of carriers of rare variants with predicted regulatory role located at polycomb repressive chromatin state at relevant tissues in cases versus controls (P=0.0016, OR=19.34, 95% C.I.=2.45-2495.26). The variants are located at two genes affected by the 17q12 copy number variant, LHX1 and HNF1B. These data strongly suggest that a specific epigenetic mechanism, chromatin remodeling by histone modification during early development, may be impaired in a subset of schizophrenia patients, in agreement with previous data. PMID:27066855

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

    PubMed

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

    2015-01-01

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

  19. Identification and Comparison of Aberrant Key Regulatory Networks in Breast, Colon, Liver, Lung, and Stomach Cancers through Methylome Database Analysis

    PubMed Central

    Kim, Byungtak; Kang, Seongeun; Jeong, Gookjoo; Park, Sung-Bin; Kim, Sun Jung

    2014-01-01

    Aberrant methylation of specific CpG sites at the promoter is widely responsible for genesis and development of various cancer types. Even though the microarray-based methylome analyzing techniques have contributed to the elucidation of the methylation change at the genome-wide level, the identification of key methylation markers or top regulatory networks appearing common in highly incident cancers through comparison analysis is still limited. In this study, we in silico performed the genome-wide methylation analysis on each 10 sets of normal and cancer pairs of five tissues: breast, colon, liver, lung, and stomach. The methylation array covers 27,578 CpG sites, corresponding to 14,495 genes, and significantly hypermethylated or hypomethylated genes in the cancer were collected (FDR adjusted p-value <0.05; methylation difference >0.3). Analysis of the dataset confirmed the methylation of previously known methylation markers and further identified novel methylation markers, such as GPX2, CLDN15, and KL. Cluster analysis using the methylome dataset resulted in a diagram with a bipartite mode distinguishing cancer cells from normal cells regardless of tissue types. The analysis further revealed that breast cancer was closest with lung cancer, whereas it was farthest from colon cancer. Pathway analysis identified that either the “cancer” related network or the “cancer” related bio-function appeared as the highest confidence in all the five cancers, whereas each cancer type represents its tissue-specific gene sets. Our results contribute toward understanding the essential abnormal epigenetic pathways involved in carcinogenesis. Further, the novel methylation markers could be applied to establish markers for cancer prognosis. PMID:24842468

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

    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.

  1. A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: application to Arabidopsis.

    PubMed

    Shamloo-Dashtpagerdi, Roohollah; Razi, Hooman; Aliakbari, Massumeh; Lindlöf, Angelica; Ebrahimi, Mahdi; Ebrahimie, Esmaeil

    2015-01-01

    Cis regulatory elements (CREs), located within promoter regions, play a significant role in the blueprint for transcriptional regulation of genes. There is a growing interest to study the combinatorial nature of CREs including presence or absence of CREs, the number of occurrences of each CRE, as well as of their order and location relative to their target genes. Comparative promoter analysis has been shown to be a reliable strategy to test the significance of each component of promoter architecture. However, it remains unclear what level of difference in the number of occurrences of each CRE is of statistical significance in order to explain different expression patterns of two genes. In this study, we present a novel statistical approach for pairwise comparison of promoters of Arabidopsis genes in the context of number of occurrences of each CRE within the promoters. First, using the sample of 1000 Arabidopsis promoters, the results of the goodness of fit test and non-parametric analysis revealed that the number of occurrences of CREs in a promoter sequence is Poisson distributed. As a promoter sequence contained functional and non-functional CREs, we addressed the issue of the statistical distribution of functional CREs by analyzing the ChIP-seq datasets. The results showed that the number of occurrences of functional CREs over the genomic regions was determined as being Poisson distributed. In accordance with the obtained distribution of CREs occurrences, we suggested the Audic and Claverie (AC) test to compare two promoters based on the number of occurrences for the CREs. Superiority of the AC test over Chi-square (2×2) and Fisher's exact tests was also shown, as the AC test was able to detect a higher number of significant CREs. The two case studies on the Arabidopsis genes were performed in order to biologically verify the pairwise test for promoter comparison. Consequently, a number of CREs with significantly different occurrences was identified between

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

    PubMed Central

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

    2016-01-01

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

  3. Genome-wide identification of miR-200 targets reveals a regulatory network controlling cell invasion.

    PubMed

    Bracken, Cameron P; Li, Xiaochun; Wright, Josephine A; Lawrence, David M; Pillman, Katherine A; Salmanidis, Marika; Anderson, Matthew A; Dredge, B Kate; Gregory, Philip A; Tsykin, Anna; Neilsen, Corine; Thomson, Daniel W; Bert, Andrew G; Leerberg, Joanne M; Yap, Alpha S; Jensen, Kirk B; Khew-Goodall, Yeesim; Goodall, Gregory J

    2014-09-17

    The microRNAs of the miR-200 family maintain the central characteristics of epithelia and inhibit tumor cell motility and invasiveness. Using the Ago-HITS-CLIP technology for transcriptome-wide identification of direct microRNA targets in living cells, along with extensive validation to verify the reliability of the approach, we have identified hundreds of miR-200a and miR-200b targets, providing insights into general features of miRNA target site selection. Gene ontology analysis revealed a predominant effect of miR-200 targets in widespread coordinate control of actin cytoskeleton dynamics. Functional characterization of the miR-200 targets indicates that they constitute subnetworks that underlie the ability of cancer cells to migrate and invade, including coordinate effects on Rho-ROCK signaling, invadopodia formation, MMP activity, and focal adhesions. Thus, the miR-200 family maintains the central characteristics of the epithelial phenotype by acting on numerous targets at multiple levels, encompassing both cytoskeletal effectors that control actin filament organization and dynamics, and upstream signals that locally regulate the cytoskeleton to maintain cell morphology and prevent cell migration. PMID:25069772

  4. Genome-wide identification of miR-200 targets reveals a regulatory network controlling cell invasion

    PubMed Central

    Bracken, Cameron P; Li, Xiaochun; Wright, Josephine A; Lawrence, David M; Pillman, Katherine A; Salmanidis, Marika; Anderson, Matthew A; Dredge, B Kate; Gregory, Philip A; Tsykin, Anna; Neilsen, Corine; Thomson, Daniel W; Bert, Andrew G; Leerberg, Joanne M; Yap, Alpha S; Jensen, Kirk B; Khew-Goodall, Yeesim; Goodall, Gregory J

    2014-01-01

    The microRNAs of the miR-200 family maintain the central characteristics of epithelia and inhibit tumor cell motility and invasiveness. Using the Ago-HITS-CLIP technology for transcriptome-wide identification of direct microRNA targets in living cells, along with extensive validation to verify the reliability of the approach, we have identified hundreds of miR-200a and miR-200b targets, providing insights into general features of miRNA target site selection. Gene ontology analysis revealed a predominant effect of miR-200 targets in widespread coordinate control of actin cytoskeleton dynamics. Functional characterization of the miR-200 targets indicates that they constitute subnetworks that underlie the ability of cancer cells to migrate and invade, including coordinate effects on Rho-ROCK signaling, invadopodia formation, MMP activity, and focal adhesions. Thus, the miR-200 family maintains the central characteristics of the epithelial phenotype by acting on numerous targets at multiple levels, encompassing both cytoskeletal effectors that control actin filament organization and dynamics, and upstream signals that locally regulate the cytoskeleton to maintain cell morphology and prevent cell migration. PMID:25069772

  5. 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.

  6. Comparison and Analysis of Regulatory and Derived Requirements for Certain DOE Spent Nuclear Fuel Shipments; Lessons Learned for Future Spent Fuel Transportation Campaigns

    SciTech Connect

    Kramer, George L., Ph.D.; Fawcett, Rick L.; Rieke, Philip C.

    2003-02-27

    Radioactive materials transportation is stringently regulated by the Department of Transportation and the Nuclear Regulatory Commission to protect the public and the environment. As a Federal agency, however, the U.S. Department of Energy (DOE) must seek State, Tribal and local input on safety issues for certain transportation activities. This interaction has invariably resulted in the imposition of extra-regulatory requirements, greatly increasing transportation costs and delaying schedules while not significantly enhancing the level of safety. This paper discusses the results an analysis of the regulatory and negotiated requirements established for a July 1998 shipment of spent nuclear fuel from foreign countries through the west coast to the Idaho National Engineering and Environmental Laboratory (INEEL). Staff from the INEEL Nuclear Materials Engineering and Disposition Department undertook the analysis in partnership with HMTC, to discover if there were instances where requirements derived from stakeholder interactions duplicate, contradict, or otherwise overlap with regulatory requirements. The study exhaustively lists and classifies applicable Department of Transportation (DOT) and Nuclear Regulatory Commission (NRC) regulations. These are then compared with a similarly classified list of requirements from the Environmental Impact Statements (EIS) and those developed during stakeholder negotiations. Comparison and analysis reveals numerous attempts to reduce transportation risk by imposing more stringent safety measures than those required by DOT and NRC. These usually took the form of additional inspection, notification and planning requirements. There are also many instances of overlap with, and duplication of regulations. Participants will gain a greater appreciation for the need to understand the risk-oriented basis of the radioactive materials regulations and their effectiveness in ensuring safety when negotiating extra-regulatory requirements.

  7. Screening of Target Genes and Regulatory Function of miRNAs as Prognostic Indicators for Prostate Cancer.

    PubMed

    Xiaoli, Zhang; Yawei, Wei; Lianna, Liu; Haifeng, Li; Hui, Zhang

    2015-01-01

    BACKGROUND MicroRNAs expression profiling of prostate cancer is becoming increasingly used due to its usefulness in diagnosis, staging, prognosis, and response to treatment. The aim of this study was to screen differentially expressed miRNAs in prostate cancer and analyze the functions and signal pathways of their target genes. MATERIAL AND METHODS High-throughput data of miRNAs were downloaded from The Cancer Genome Atlas (TCGA) database. A total of 551 samples (52 normal and 499 prostate cancer cases) and 1046 miRNAs expression values were selected for further analysis. Differentially expressed miRNAs between normal and prostate cancer tissues were identified using SAMR. StarBase and TargetScan software were used to predict the miRNAs' target group and target genes, respectively. GO functional and KEGG pathway analysis was conducted on up/down-regulated expressed miRNA with DAVID. Finally, survival analysis was performed to evaluate the association of differently expressed miRNAs signature and overall survival of prostate cancer patients. RESULTS A total of 162 miRNAs were differentially expressed between normal and prostate cancer samples, including 128 up-regulated and 38 down-regulated ones; hsa-mir-153-2, hsa-mir-92a-1, and hsa-mir-182 (up-regulated); and hsa-mir-29a, hsa-mir-10a, and hsa-mir-221 (down-regulated) were identified as good biomarkers. In GO and KEGG analysis, target genes of down-regulated miRNAs were significantly enriched in positive ion combination and JAK-STAT pathway annotation, respectively; the ones with up-regulated miRNAs were significantly enriched in the function of plasma membrane and MARK signaling pathway annotation, respectively. Patients were categorized into low- or high-score groups according to their risk scores from each miRNA. The patients in the low-score group had better overall survival compared with those in high-score group. CONCLUSIONS The 6 differentially expressed miRNAs and their target genes were used to define

  8. Screening of Target Genes and Regulatory Function of miRNAs as Prognostic Indicators for Prostate Cancer

    PubMed Central

    Xiaoli, Zhang; Yawei, Wei; Lianna, Liu; Haifeng, Li; Hui, Zhang

    2015-01-01

    Background MicroRNAs expression profiling of prostate cancer is becoming increasingly used due to its usefulness in diagnosis, staging, prognosis, and response to treatment. The aim of this study was to screen differentially expressed miRNAs in prostate cancer and analyze the functions and signal pathways of their target genes. Material/Methods High-throughput data of miRNAs were downloaded from The Cancer Genome Atlas (TCGA) database. A total of 551 samples (52 normal and 499 prostate cancer cases) and 1046 miRNAs expression values were selected for further analysis. Differentially expressed miRNAs between normal and prostate cancer tissues were identified using SAMR. StarBase and TargetScan software were used to predict the miRNAs’ target group and target genes, respectively. GO functional and KEGG pathway analysis was conducted on up/down-regulated expressed miRNA with DAVID. Finally, survival analysis was performed to evaluate the association of differently expressed miRNAs signature and overall survival of prostate cancer patients. Results A total of 162 miRNAs were differentially expressed between normal and prostate cancer samples, including 128 up-regulated and 38 down-regulated ones; hsa-mir-153-2, hsa-mir-92a-1, and hsa-mir-182 (up-regulated); and hsa-mir-29a, hsa-mir-10a, and hsa-mir-221 (down-regulated) were identified as good biomarkers. In GO and KEGG analysis, target genes of down-regulated miRNAs were significantly enriched in positive ion combination and JAK-STAT pathway annotation, respectively; the ones with up-regulated miRNAs were significantly enriched in the function of plasma membrane and MARK signaling pathway annotation, respectively. Patients were categorized into low- or high-score groups according to their risk scores from each miRNA. The patients in the low-score group had better overall survival compared with those in high-score group. Conclusions The 6 differentially expressed miRNAs and their target genes were used to define

  9. 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.

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

    PubMed Central

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

    2016-01-01

    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. PMID:27161996

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

    PubMed

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

    2016-01-01

    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. PMID:27161996

  12. 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.

  13. Comparison of Ti-Zr-V nonevaporable getter films deposited using alloy or twisted wire sputter-targets

    SciTech Connect

    Valizadeh, R.; Malyshev, O. B.; Colligon, J. S.; Hannah, A.; Vishnyakov, V. M.

    2010-11-15

    A comparison of the performance of nonevaporable getter (NEG) films deposited using two different types of targets has been made to find the one that has the best pumping properties. For the first time, the NEG coating was deposited using a preformed Ti-Zr-V alloy target. The NEG film characterization and pumping properties have been studied in comparison with a film deposited using the commonly used three-wire twisted target. It was demonstrated that the alloy target produces a NEG coating with uniform composition both laterally and in depth. The composition of the film was found to be the same as the target. Film topography and microstructure with 5 nm grain sizes were found to be the same for both targets. The main result is that the activation temperature of the NEG coating deposited using the Ti-Zr-V alloy target is 160 deg. C, which is 20 deg. C lower than for NEG coatings deposited using three twisted wires.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

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

  16. p53-dependent inhibition of mammalian cell survival by a genetically selected peptide aptamer that targets the regulatory subunit of protein kinase CK2.

    PubMed

    Martel, V; Filhol, O; Colas, P; Cochet, C

    2006-11-30

    Based on the perturbation of its expression in human cancers and on its involvement in transformation and tumorigenesis, protein kinase CK2 has recently attracted attention as a potential therapeutic target. To assess the value of CK2 as a target for antiproliferative strategies, we have initiated a program aiming to develop inhibitors targeting specifically the regulatory CK2beta subunit. Here, we use a two-hybrid approach to isolate from combinatorial libraries, peptide aptamers that specifically interact with CK2beta. One of these (P1), which has significant sequence homology to the cytomegalovirus IE2 protein, binds with high affinity to the N-terminal domain of CK2beta without disrupting the formation of the CK2 holoenzyme. Expression of green fluorescent protein (GFP)-P1 in different mammalian cell lines activates p53 phosphorylation on serine 15, induces an upregulation of p21 and the release of the Cyt-C and apoptosis-inducing factor proapoptotic proteins triggering caspase-dependent and caspase-independent apoptosis. GFP-P1-induced apoptosis is associated with a p53-dependent pathway as cell death was abrogated in p53 knocked out cells. In summary, our data show that genetically selected peptide aptamers that specifically target CK2beta can induce apoptosis in mammalian cells through the recruitment of a p53-dependent apoptosis pathway. They also emphasize the critical role of CK2beta for cell survival and might allow the design of novel proapoptotic agents targeting this protein. PMID:16751801

  17. Nonlinear acoustic landmine detection: Comparison of ``off target'' soil background and ``on target'' soil-mine nonlinear effects

    NASA Astrophysics Data System (ADS)

    Korman, Murray S.

    2005-09-01

    When airborne sound at two primary tones, f1, f2 (closely spaced near a resonance) excites the soil surface over a buried landmine, soil wave motion interacts with the landmine generating a scattered surface profile which can be measured over the ``target.'' Profiles at f1, f2, and f1-(f2-f1), f2+(f2-f1), 2f1-(f2-f1), f1+f2 and 2f2+(f2-f1) (among others) are measured for a VS 1.6 plastic, inert, anti-tank landmine, buried at 3.6 cm in sifted loess soil. It is observed that the ``on target'' to ``off target'' contrast ratio for the sum frequency component can be ~20 dB higher than for either primary. The vibration interaction between the top-plate interface of a buried plastic landmine and the soil above it appears to exhibit many characteristics of the mesoscopic/nanoscale nonlinear effects that are observed in geomaterials like sandstone. Near resonance, the bending (softening) of a family of increasing amplitude tuning curves, involving the vibration over the landmine, exhibits a linear relationship between the peak particle velocity and corresponding frequency. Tuning curve experiments along with two-tone tests are performed both on and off the mine in an effort to understand the nonlinearities in each case. [Work supported by U.S. Army RDECOM CERDEC, NVESD.

  18. 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.

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

    PubMed Central

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

    2015-01-01

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

  20. Nonlinear acoustic landmine detection: comparison of off-target soil background and on-target soil-mine nonlinear effects

    NASA Astrophysics Data System (ADS)

    Korman, Murray S.; Sabatier, James M.; Pauls, Kathleen E.; Genis, Sean A.

    2006-05-01

    When airborne sound at two primary tones, f I, f II (closely spaced near a resonance) excites the soil surface over a buried landmine, soil wave motion interacts with the landmine generating a scattered surface profile which can be measured over the "target." Profiles at the primaries f I, f II, and nonlinearly generated combination frequencies f I-(f II-f I) and f II+(f II-f I) , 2f I-(f II-f I), f I+f II and 2f II+(f II-f I) (among others) have been measured for a VS 2.2 plastic, inert, anti-tank landmine, buried at 3.6 cm in sifted loess soil and in a gravel road bed. [M.S. Korman and J.M. Sabatier, J. Acoust. Soc. Am. 116, 3354-3369 (2004)]. It is observed that the "on target" to "off target" contrast ratio for the sum frequency component can be ~20 dB higher than for either primary. The vibration interaction between the top-plate interface of a buried plastic landmine and the soil above it appears to exhibit many characteristics of the mesoscopic/nanoscale nonlinear effects that are observed in geomaterials like sandstone. Near resonance, the bending (softening) of a family of increasing amplitude tuning curves, involving the vibration over the landmine, exhibits a linear relationship between the peak particle velocity and corresponding frequency. Tuning curve experiments are performed both on and off the mine in an effort to understand the nonlinearities in each case.

  1. Genomic analysis of xCT-mediated regulatory network: identification of novel targets against AIDS-associated lymphoma

    PubMed Central

    Dai, Lu; Cao, Yueyu; Chen, Yihan; Kaleeba, Johnan A.R.; Zabaleta, Jovanny; Qin, Zhiqiang

    2015-01-01

    Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of primary effusion lymphoma (PEL), a rapidly progressing malignancy mostly arising in HIV-infected patients. Even under conventional chemotherapy, PEL continues to portend nearly 100% mortality within several months, which urgently requires novel therapeutic strategies. We have previously demonstrated that targeting xCT, an amino acid transporter for cystine/glutamate exchange, induces significant PEL cell apoptosis through regulation of multiple host and viral factors. More importantly, one of xCT selective inhibitors, Sulfasalazine (SASP), effectively prevents PEL tumor progression in an immune-deficient xenograft model. In the current study, we use Illumina microarray to explore the profile of genes altered by SASP treatment within 3 KSHV+ PEL cell-lines, and discover that many genes involved in oxidative stress/antioxidant defense system, apoptosis/anti-apoptosis/cell death, and cellular response to unfolded proteins/topologically incorrect proteins are potentially regulated by xCT. We further validate 2 downstream candidates, OSGIN1 (oxidative stress-induced growth inhibitor 1) and XRCC5 (X-ray repair cross-complementing protein 5), and evaluate their functional relationship with PEL cell survival/proliferation and chemoresistance, respectively. Together, our data indicate that targeting these novel xCT-regulated downstream genes may represent a promising new therapeutic strategy against PEL and/or other AIDS-related lymphoma. PMID:25860939

  2. Implant assisted-magnetic drug targeting: Comparison of in vitro experiments with theory

    NASA Astrophysics Data System (ADS)

    Avilés, Misael O.; Ebner, Armin D.; Ritter, James A.

    Implant assisted-magnetic drug targeting (IA-MDT) was studied both in vitro and theoretically, with extensive comparisons made between model and experiment. Magnetic drug carrier particles (MDCPs) comprised of magnetite encased in a polymer were collected magnetically using a ferromagnetic, coiled, wire stent as the implant and a NdFeB permanent magnet for the applied magnetic field. A 2-D mathematical model with no adjustable parameters was developed and compared to the 3-D experimental results. The effects of the fluid velocity, stent and MDCP properties, and magnetic field strength on the performance of the system were evaluated in terms of the capture efficiency (CE) of the MDCPs. In nearly all cases, the parametric trends predicted by the model were in good agreement with the experimental results: the CE always increased with decreasing velocity, increasing magnetic field strength, increasing MDCP size or magnetite content, or increasing wire size. The only exception was when experiments showed an increase in the CE with an increase in the number of loops in the wire, while the model showed no dependence. The discrepancies between experiment and theory were attributed to phenomena not accounted for by the model, such as 3-D to 2-D geometric and magnetic field orientation differences, and interparticle interactions between the MDCPs that lead to magnetic agglomeration and shearing force effects. Overall, this work showed the effectiveness of a stent-based IA-MDT system through both in vitro experimentation and corroborated theory, with the designs of the ferromagnetic wire and the MDCPs both being paramount to the CE.

  3. E3 Ubiquitin Ligase Cbl-b Regulates Thymic-Derived CD4+CD25+ Regulatory T Cell Development by Targeting Foxp3 for Ubiquitination.

    PubMed

    Zhao, Yixia; Guo, Hui; Qiao, Guilin; Zucker, Mark; Langdon, Wallace Y; Zhang, Jian

    2015-02-15

    CD28 costimulation is essential for the development of thymic-derived CD4(+)CD25(+)Foxp3(+) regulatory T cells ("tTregs"). E3 ubiquitin ligase Cbl-b has been shown to regulate CD28 dependence of T cell activation. In this paper, we report that the loss of Cbl-b partially but significantly rescues the defective development of tTregs in Cd28(-/-) mice. This partial rescue is independent of IL-2. Mechanistically, Cbl-b binds to Foxp3 upon TCR stimulation and, together with Stub1, targets Foxp3 for ubiquitination and subsequently degradation in the proteasome. As Cbl-b self-ubiquitination and proteasomal degradation is impaired in Cd28(-/-) T cells, the defective development of tTregs in Cd28(-/-) mice may in part be due to increased Foxp3 ubiquitination and degradation targeted by Stub1 and Cbl-b. Treating Cd28(-/-) mice with a proteasome inhibitor completely rescues defective tTreg development in these mice. Therefore, Cbl-b, together with Stub1, ubiquitinate Foxp3, and regulate tTreg development. PMID:25560411

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

    PubMed

    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

    2014-10-01

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

  5. Paracrine co-delivery of TGF-β and IL-2 using CD4-targeted nanoparticles for induction and maintenance of regulatory T cells.

    PubMed

    McHugh, Michael D; Park, Jason; Uhrich, Ross; Gao, Wenda; Horwitz, David A; Fahmy, Tarek M

    2015-08-01

    The cytokine milieu is critical for orchestration of lineage development towards effector T cell (Teff) or regulatory T cell (Treg) subsets implicated in the progression of cancer and autoimmune disease. Importantly, the fitness and survival of the Treg subset is dependent on the cytokines Interleukin-2 (IL-2) and transforming growth factor beta (TGF-β). The production of these cytokines is impaired in autoimmunity increasing the probability of Treg conversion to aggressive effector cells in a proinflammatory microenvironment. Therapy using soluble TGF-β and IL-2 administration is hindered by the cytokines' toxic pleiotropic effects and hence bioavailability to CD4(+) T cell targets. Thus, there is a clear need for a strategy that rectifies the cytokine milieu in autoimmunity and inflammation leading to enhanced Treg stability, frequency and number. Here we show that inert biodegradable nanoparticles (NP) loaded with TGF-β and IL-2 and targeted to CD4(+) cells can induce CD4(+) Tregs in-vitro and expand their number in-vivo. The stability of induced Tregs with cytokine-loaded NP was enhanced leading to retention of their suppressive phenotype even in the presence of proinflammatory cytokines. Our results highlight the importance of a nanocarrier-based approach for stabilizing and expanding Tregs essential for cell-immunotherapy of inflammation and autoimmune disease. PMID:25974747

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

    PubMed Central

    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. PMID:25826566

  7. p53 Tumor Suppressor Protein Stability and Transcriptional Activity Are Targeted by Kaposi's Sarcoma-Associated Herpesvirus-Encoded Viral Interferon Regulatory Factor 3

    PubMed Central

    Baresova, Petra; Musilova, Jana; Pitha, Paula M.

    2014-01-01

    Viruses have developed numerous strategies to counteract the host cell defense. Kaposi's sarcoma-associated herpesvirus (KSHV) is a DNA tumor virus linked to the development of Kaposi's sarcoma, Castleman's disease, and primary effusion lymphoma (PEL). The virus-encoded viral interferon regulatory factor 3 (vIRF-3) gene is a latent gene which is involved in the regulation of apoptosis, cell cycle, antiviral immunity, and tumorigenesis. vIRF-3 was shown to interact with p53 and inhibit p53-mediated apoptosis. However, the molecular mechanism underlying this phenomenon has not been established. Here, we show that vIRF-3 associates with the DNA-binding domain of p53, inhibits p53 phosphorylation on serine residues S15 and S20, and antagonizes p53 oligomerization and the DNA-binding affinity. Furthermore, vIRF-3 destabilizes p53 protein by increasing the levels of p53 polyubiquitination and targeting p53 for proteasome-mediated degradation. Consequently, vIRF-3 attenuates p53-mediated transcription of the growth-regulatory p21 gene. These effects of vIRF-3 are of biological relevance since the knockdown of vIRF-3 expression in KSHV-positive BC-3 cells, derived from PEL, leads to an increase in p53 phosphorylation, enhancement of p53 stability, and activation of p21 gene transcription. Collectively, these data suggest that KSHV evolved an efficient mechanism to downregulate p53 function and thus facilitate uncontrolled cell proliferation and tumor growth. PMID:24248600

  8. 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

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

    PubMed

    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

  10. 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

  11. 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

  12. 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...

  13. 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. PMID:27117425

  14. 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

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

    PubMed

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

    2016-06-01

    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. 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

  17. 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. PMID:25940475

  18. Unfolding-resistant translocase targeting: a novel mechanism for outer mitochondrial membrane localization exemplified by the Bbeta2 regulatory subunit of protein phosphatase 2A.

    PubMed

    Dagda, Ruben K; Barwacz, Chris A; Cribbs, J Thomas; Strack, Stefan

    2005-07-22

    Heterotrimeric serine/threonine protein phosphatase 2A (PP2A) consists of scaffolding (A), catalytic (C), and variable (B, B', and B'') subunits. Variable subunits dictate subcellular localization and substrate specificity of the PP2A holoenzyme. The Bbeta regulatory subunit gene is mutated in spinocerebellar ataxia type 12, and one of its splice variants, Bbeta2, targets PP2A to mitochondria to promote apoptosis in PC12 cells (Dagda, R. K., Zaucha, J. A., Wadzinski, B. E., and Strack, S. (2003) J. Biol. Chem. 278, 24976-24985). Here, we report that Bbeta2 is localized to the outer mitochondrial membrane by a novel mechanism, combining a cryptic mitochondrial import signal with a structural arrest domain. Scanning mutagenesis demonstrates that basic and hydrophobic residues mediate mitochondrial association and the proapoptotic activity of Bbeta2. When fused to green fluorescent protein, the N terminus of Bbeta2 acts as a cleavable mitochondrial import signal. Surprisingly, full-length Bbeta2 is not detectably cleaved and is retained at the outer mitochondrial membrane, even though it interacts with the TOM22 import receptor, as shown by luciferase complementation in intact cells. Mutations that open the C-terminal beta-propeller of Bbeta2 facilitate mitochondrial import, indicating that this rigid fold acts as a stop-transfer domain by resisting the partial unfolding step prerequisite for matrix translocation. Because hybrids of prototypical import and beta-propeller domains recapitulate this behavior, we predict the existence of other similarly localized proteins and a selection against highly stable protein folds in the mitochondrial matrix. This unfolding-resistant targeting to the mitochondrial translocase is necessary but not sufficient for the proapoptotic activity of Bbeta2, which also requires association with the rest of the PP2A holoenzyme. PMID:15923182

  19. Regulatory effects of a Mnk2-eIF4E feedback loop during mTORC1 targeting of human medulloblastoma cells.

    PubMed

    Eckerdt, Frank; Beauchamp, Elspeth; Bell, Jonathan; Iqbal, Asneha; Su, Bing; Fukunaga, Rikiro; Lulla, Rishi R; Goldman, Stewart; Platanias, Leonidas C

    2014-09-30

    The mTOR pathway controls mRNA translation of mitogenic proteins and is a central regulator of metabolism in malignant cells. Development of malignant cell resistance is a limiting factor to the effects of mTOR inhibitors, but the mechanisms accounting for such resistance are not well understood. We provide evidence that mTORC1 inhibition by rapamycin results in engagement of a negative feedback regulatory loop in malignant medulloblastoma cells, involving phosphorylation of the eukaryotic translation-initiation factor eIF4E. This eIF4E phosphorylation is Mnk2- mediated, but Mnk1-independent, and acts as a survival mechanism for medulloblastoma cells. Pharmacological targeting of Mnk1/2 or siRNA-mediated knockdown of Mnk2 sensitizes medulloblastoma cells to mTOR inhibition and promotes suppression of malignant cell proliferation and anchorage-independent growth. Altogether, these findings provide evidence for the existence of a Mnk2-controlled feedback loop in medulloblastoma cells that accounts for resistance to mTOR inhibitors, and raise the potential for combination treatments of mTOR and Mnk inhibitors for the treatment of medulloblastoma. PMID:25193863

  20. Targeting the oncogene B lymphoma deregulator IgH 3' regulatory region does not impede the in vivo inflammatory response in mice.

    PubMed

    Saad, Faten; Saintamand, Alexis; Rouaud, Pauline; Denizot, Yves

    2014-01-01

    The IgH 3' regulatory region (3'RR), encompassing the four transcriptional enhancers hs3a-hs1,2-hs3b-hs4, is a potent lymphoma oncogene deregulator but its role in B cell-mediated inflammatory responses is unknown. We investigated the 3'RR involvement in the in vivo pristane-induced inflammatory response in BALB/c mice. The lack of the 3'RR in BALB/c mice had no wide effect on the incidence, the kinetic of development and the cellular composition of peritoneal ascites. Ascite pro-inflammatory cytokines levels (IL-6, IL-21, IL-12/23, TNF-α) were unchanged while anti-inflammatory cytokines levels (IL-10, interferon-γ) were slightly increased in 3'RR-deficient BALB/c mice as compared to wt BALB/c mice. In conclusion, the 3'RR is dispensable for the efficient recruitment of immune cells and the normal development of an inflammatory response in the in vivo pristane-induced inflammatory model. The 3'RR might be considered as a potential suitable target for anti-lymphoma pharmacological therapy without potent adverse effect on normal immune and inflammatory responses. PMID:25594069

  1. 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

  2. Targeting the oncogene B lymphoma deregulator IgH 3′ regulatory region does not impede the in vivo inflammatory response in mice

    PubMed Central

    Saad, Faten; Saintamand, Alexis; Rouaud, Pauline; Denizot, Yves

    2014-01-01

    The IgH 3′ regulatory region (3′RR), encompassing the four transcriptional enhancers hs3a-hs1,2-hs3b-hs4, is a potent lymphoma oncogene deregulator but its role in B cell-mediated inflammatory responses is unknown. We investigated the 3′RR involvement in the in vivo pristane-induced inflammatory response in BALB/c mice. The lack of the 3′RR in BALB/c mice had no wide effect on the incidence, the kinetic of development and the cellular composition of peritoneal ascites. Ascite pro-inflammatory cytokines levels (IL-6, IL-21, IL-12/23, TNF-α) were unchanged while anti-inflammatory cytokines levels (IL-10, interferon-γ) were slightly increased in 3′RR-deficient BALB/c mice as compared to wt BALB/c mice. In conclusion, the 3′RR is dispensable for the efficient recruitment of immune cells and the normal development of an inflammatory response in the in vivo pristane-induced inflammatory model. The 3′RR might be considered as a potential suitable target for anti-lymphoma pharmacological therapy without potent adverse effect on normal immune and inflammatory responses. PMID:25594069

  3. 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.

  4. Quantitative comparison of the expression of myogenic regulatory factors in flounder ( Paralichthys olivaceus) embryos and adult tissues

    NASA Astrophysics Data System (ADS)

    Zhang, Yuqing; Tan, Xungang; Xu, Peng; Sun, Wei; Xu, Yongli; Zhang, Peijun

    2010-03-01

    MyoD, Myf5, and myogenin are myogenic regulatory factors that play important roles during myogenesis. It is thought that MyoD and Myf5 are required for myogenic determination, while myogenin is important for terminal differentiation and lineage maintenance. To better understand the function of myogenic regulatory factors in muscle development of flounder, an important economic fish in Asia, real-time quantitative RT-PCR was used to characterize the expression patterns of MyoD, Myf5, and myogenin at early stages of embryo development, and in different tissues of the adult flounder. The results show that, Myf5 is the first gene to be expressed during the early stages of flounder development, followed by MyoD and myogenin. The expressions of Myf5, yoD, and myogenin at the early stages have a common characteristic: expression gradually increased to a peak level, and then gradually decreased to an extremely low level. In the adult flounder, the expression of the three genes in muscle is much higher than that in other tissues, indicating that they are important for muscle growth and maintenance of grown fish. During embryonic stages, the expression level of MyoD might serve an important role in the balance between muscle cell differentiation and proliferation. When the MyoD expression is over 30% of its highest level, the muscle cells enter the differentiation stage.

  5. Comparison of different sample and target preparation procedures for PIXE analysis of biological materials

    NASA Astrophysics Data System (ADS)

    Maenhaut, W.; De Reu, L.; Vandenhaute, J.

    1984-04-01

    Four different methods for preparing PIXE targets from biological samples were compared. All methods involved doping with an internal standard and preparing target deposits of 1-4 mg/cm 2 on a thin substrate. In method A targets were prepared using powdered freeze-dried material. Methods B and C both included a low temperature ashing preconcentration step and method D involved an acid digestion in a teflon bomb. The procedures were applied to reference materials (e.g. NBS standards) and to "real" samples such as human kidneys and a liver, which had been analyzed by neutron activation analysis (NAA). For most elements good agreement was observed between the results of the four target preparation methods and the reference values or the NAA results. Exceptions, however, were Br, Se and Cd, which were lost in some methods. The detection limits in the different methods are compared.

  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 monostatic and bistatic bearing estimation performance for low RCS targets

    NASA Astrophysics Data System (ADS)

    Boyle, Robert J.; Wasylkiwskyj, Wasyl

    1994-07-01

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

  8. Comparison of CRISPR/Cas9 expression constructs for efficient targeted mutagenesis in rice.

    PubMed

    Mikami, Masafumi; Toki, Seiichi; Endo, Masaki

    2015-08-01

    The CRISPR/Cas9 system is an efficient tool used for genome editing in a variety of organisms. Despite several recent reports of successful targeted mutagenesis using the CRISPR/Cas9 system in plants, in each case the target gene of interest, the Cas9 expression system and guide-RNA (gRNA) used, and the tissues used for transformation and subsequent mutagenesis differed, hence the reported frequencies of targeted mutagenesis cannot be compared directly. Here, we evaluated mutation frequency in rice using different Cas9 and/or gRNA expression cassettes under standardized experimental conditions. We introduced Cas9 and gRNA expression cassettes separately or sequentially into rice calli, and assessed the frequency of mutagenesis at the same endogenous targeted sequences. Mutation frequencies differed significantly depending on the Cas9 expression cassette used. In addition, a gRNA driven by the OsU6 promoter was superior to one driven by the OsU3 promoter. Using an all-in-one expression vector harboring the best combined Cas9/gRNA expression cassette resulted in a much improved frequency of targeted mutagenesis in rice calli, and bi-allelic mutant plants were produced in the T0 generation. The approach presented here could be adapted to optimize the construction of Cas9/gRNA cassettes for genome editing in a variety of plants. PMID:26188471

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

    PubMed

    Yang, Lixue; Chen, Kean

    2015-11-01

    To improve the design of underwater target recognition systems based on auditory perception, this study compared human listeners with automatic classifiers. Performances measures and strategies in three discrimination experiments, including discriminations between man-made and natural targets, between ships and submarines, and among three types of ships, were used. In the experiments, the subjects were asked to assign a score to each sound based on how confident they were about the category to which it belonged, and logistic regression, which represents linear discriminative models, also completed three similar tasks by utilizing many auditory features. The results indicated that the performances of logistic regression improved as the ratio between inter- and intra-class differences became larger, whereas the performances of the human subjects were limited by their unfamiliarity with the targets. Logistic regression performed better than the human subjects in all tasks but the discrimination between man-made and natural targets, and the strategies employed by excellent human subjects were similar to that of logistic regression. Logistic regression and several human subjects demonstrated similar performances when discriminating man-made and natural targets, but in this case, their strategies were not similar. An appropriate fusion of their strategies led to further improvement in recognition accuracy. PMID:26627787

  10. 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

  11. Dosimetric comparison of four target alignment methods for prostate cancer radiotherapy

    SciTech Connect

    O'Daniel, Jennifer C.; Dong Lei . E-mail: ldong@mdanderson.org; Zhang Lifei; Crevoisier, Renaud de; Wang He; Lee, Andrew K.; Cheung, Rex; Tucker, Susan L.; Kudchadker, Rajat J.; Bonnen, Mark D.; Cox, James D.; Mohan, Radhe; Kuban, Deborah A.

    2006-11-01

    Purpose: The aim of this study was to compare the dosimetric consequences of 4 treatment delivery techniques for prostate cancer patients treated with intensity-modulated radiotherapy (IMRT). Methods and Materials: During an 8-week course of radiotherapy, 10 patients underwent computed tomography (CT) scans 3 times per week (243 total) before daily treatment with a CT-linear accelerator. Treatment delivery was simulated by realigning a fixed-margin treatment plan on each CT scan and calculating doses. The alignment methods were those based on the following: skin marks, bony registration, ultrasonography (United States), and in-room CT. For the last two methods, prostate was the alignment target. The dosimetric effects of these alignment methods on the prostate, seminal vesicles, rectum, and bladder were compared. The average daily minimum dose to 0.1 cm{sup 3} was used as the metric for target coverage. Results: Skin and bone alignments provided acceptable prostate coverage for only 70% of patients, US alignment for 90%, and CT alignment for 100%. CT-based alignment of the prostate provided seminal vesicle (SV) coverage of {>=}69 Gy for all patients; US and bone alignments provided SV coverage of {>=}60 Gy. This SV coverage may be acceptable for early-stage cancer (equivalent SV dose = 55.8 Gy at 1.8 Gy per fraction), but unacceptable for late-stage cancer (SV dose = 75.6 Gy). At 75.6 Gy, the acceptable rate for SV coverage was 40% for skin and bone alignments, 70% for US, and 80% for CT. Conclusions: Direct target alignment methods (US and CT) provided better target coverage. CT-guided alignment provided the best and most consistent dosimetric coverage. A larger planning target volume margin is needed for SV coverage when the alignment target is the prostate.

  12. Comparison of Custom Capture for Targeted Next-Generation DNA Sequencing

    PubMed Central

    Samorodnitsky, Eric; Datta, Jharna; Jewell, Benjamin M.; Hagopian, Raffi; Miya, Jharna; Wing, Michele R.; Damodaran, Senthilkumar; Lippus, Juliana M.; Reeser, Julie W.; Bhatt, Darshna; Timmers, Cynthia D.; Roychowdhury, Sameek

    2016-01-01

    Targeted, capture-based DNA sequencing is a cost-effective method to focus sequencing on a coding region or other customized region of the genome. There are multiple targeted sequencing methods available, but none has been systematically investigated and compared. We evaluated four commercially available custom-targeted DNA technologies for next-generation sequencing with respect to on-target sequencing, uniformity, and ability to detect single-nucleotide variations (SNVs) and copy number variations. The technologies that used sonication for DNA fragmentation displayed impressive uniformity of capture, whereas the others had shorter preparation times, but sacrificed uniformity. One of those technologies, which uses transposase for DNA fragmentation, has a drawback requiring sample pooling, and the last one, which uses restriction enzymes, has a limitation depending on restriction enzyme digest sites. Although all technologies displayed some level of concordance for calling SNVs, the technologies that require restriction enzymes or transposase missed several SNVs largely because of the lack of coverage. All technologies performed well for copy number variation calling when compared to single-nucleotide polymorphism arrays. These results enable laboratories to compare these methods to make informed decisions for their intended applications. PMID:25528188

  13. Comparison of custom capture for targeted next-generation DNA sequencing.

    PubMed

    Samorodnitsky, Eric; Datta, Jharna; Jewell, Benjamin M; Hagopian, Raffi; Miya, Jharna; Wing, Michele R; Damodaran, Senthilkumar; Lippus, Juliana M; Reeser, Julie W; Bhatt, Darshna; Timmers, Cynthia D; Roychowdhury, Sameek

    2015-01-01

    Targeted, capture-based DNA sequencing is a cost-effective method to focus sequencing on a coding region or other customized region of the genome. There are multiple targeted sequencing methods available, but none has been systematically investigated and compared. We evaluated four commercially available custom-targeted DNA technologies for next-generation sequencing with respect to on-target sequencing, uniformity, and ability to detect single-nucleotide variations (SNVs) and copy number variations. The technologies that used sonication for DNA fragmentation displayed impressive uniformity of capture, whereas the others had shorter preparation times, but sacrificed uniformity. One of those technologies, which uses transposase for DNA fragmentation, has a drawback requiring sample pooling, and the last one, which uses restriction enzymes, has a limitation depending on restriction enzyme digest sites. Although all technologies displayed some level of concordance for calling SNVs, the technologies that require restriction enzymes or transposase missed several SNVs largely because of the lack of coverage. All technologies performed well for copy number variation calling when compared to single-nucleotide polymorphism arrays. These results enable laboratories to compare these methods to make informed decisions for their intended applications. PMID:25528188

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

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  15. COMPARISON OF R- AND Q-MODES IN TARGET TRANSFORMATION FACTOR ANALYSIS FOR RESOLVING ENVIRONMENTAL DATA

    EPA Science Inventory

    A target transformation factor analysis has been used for the quantitative resolution of environmental data. The initial studies have utilized the correlation between samples as the matrix defining the relationships within the data. The analysis of this matrix is a Q-mode analysi...

  16. Differential Phosphorylation of a Regulatory Subunit of Protein Kinase CK2 by Target of Rapamycin Complex 1 Signaling and the Cdc-like Kinase Kns1*

    PubMed Central

    Sanchez-Casalongue, Manuel E.; Lee, Jaehoon; Diamond, Aviva; Shuldiner, Scott; Moir, Robyn D.; Willis, Ian M.

    2015-01-01

    Transcriptional regulation of ribosome and tRNA synthesis plays a central role in determining protein synthetic capacity and is tightly controlled in response to nutrient availability and cellular stress. In Saccharomyces cerevisiae, the regulation of ribosome and tRNA synthesis was recently shown to involve the Cdc-like kinase Kns1 and the GSK-3 kinase Mck1. In this study, we explored additional roles for these conserved kinases in processes connected to the target of rapamycin complex 1 (TORC1). We conducted a synthetic chemical-genetic screen in a kns1Δ mck1Δ strain and identified many novel rapamycin-hypersensitive genes. Gene ontology analysis showed enrichment for TORC1-regulated processes (vesicle-mediated transport, autophagy, and regulation of cell size) and identified new connections to protein complexes including the protein kinase CK2. CK2 is considered to be a constitutively active kinase and in budding yeast, the holoenzyme comprises two regulatory subunits, Ckb1 and Ckb2, and two catalytic subunits, Cka1 and Cka2. We show that Ckb1 is differentially phosphorylated in vivo and that Kns1 mediates this phosphorylation when nutrients are limiting and under all tested stress conditions. We determined that the phosphorylation of Ckb1 does not detectably affect the stability of the CK2 holoenzyme but correlates with the reduced occupancy of Ckb1 on tRNA genes after rapamycin treatment. Thus, the differential occupancy of tRNA genes by CK2 is likely to modulate its activation of RNA polymerase III transcription. Our data suggest that TORC1, via its effector kinase Kns1, may regulate the association of CK2 with some of its substrates by phosphorylating Ckb1. PMID:25631054

  17. Differential phosphorylation of a regulatory subunit of protein kinase CK2 by target of rapamycin complex 1 signaling and the Cdc-like kinase Kns1.

    PubMed

    Sanchez-Casalongue, Manuel E; Lee, Jaehoon; Diamond, Aviva; Shuldiner, Scott; Moir, Robyn D; Willis, Ian M

    2015-03-13

    Transcriptional regulation of ribosome and tRNA synthesis plays a central role in determining protein synthetic capacity and is tightly controlled in response to nutrient availability and cellular stress. In Saccharomyces cerevisiae, the regulation of ribosome and tRNA synthesis was recently shown to involve the Cdc-like kinase Kns1 and the GSK-3 kinase Mck1. In this study, we explored additional roles for these conserved kinases in processes connected to the target of rapamycin complex 1 (TORC1). We conducted a synthetic chemical-genetic screen in a kns1Δ mck1Δ strain and identified many novel rapamycin-hypersensitive genes. Gene ontology analysis showed enrichment for TORC1-regulated processes (vesicle-mediated transport, autophagy, and regulation of cell size) and identified new connections to protein complexes including the protein kinase CK2. CK2 is considered to be a constitutively active kinase and in budding yeast, the holoenzyme comprises two regulatory subunits, Ckb1 and Ckb2, and two catalytic subunits, Cka1 and Cka2. We show that Ckb1 is differentially phosphorylated in vivo and that Kns1 mediates this phosphorylation when nutrients are limiting and under all tested stress conditions. We determined that the phosphorylation of Ckb1 does not detectably affect the stability of the CK2 holoenzyme but correlates with the reduced occupancy of Ckb1 on tRNA genes after rapamycin treatment. Thus, the differential occupancy of tRNA genes by CK2 is likely to modulate its activation of RNA polymerase III transcription. Our data suggest that TORC1, via its effector kinase Kns1, may regulate the association of CK2 with some of its substrates by phosphorylating Ckb1. PMID:25631054

  18. A comparison study of optimal and suboptimal intervention policies for gene regulatory networks in the presence of uncertainty

    PubMed Central

    2014-01-01

    Perfect knowledge of the underlying state transition probabilities is necessary for designing an optimal intervention strategy for a given Markovian genetic regulatory network. However, in many practical situations, the complex nature of the network and/or identification costs limit the availability of such perfect knowledge. To address this difficulty, we propose to take a Bayesian approach and represent the system of interest as an uncertainty class of several models, each assigned some probability, which reflects our prior knowledge about the system. We define the objective function to be the expected cost relative to the probability distribution over the uncertainty class and formulate an optimal Bayesian robust intervention policy minimizing this cost function. The resulting policy may not be optimal for a fixed element within the uncertainty class, but it is optimal when averaged across the uncertainly class. Furthermore, starting from a prior probability distribution over the uncertainty class and collecting samples from the process over time, one can update the prior distribution to a posterior and find the corresponding optimal Bayesian robust policy relative to the posterior distribution. Therefore, the optimal intervention policy is essentially nonstationary and adaptive. PMID:24708650

  19. Effects of target size on the comparison of photon and charged particle dose distributions

    SciTech Connect

    Phillips, M.H.; Frankel, K.A.; Tjoa, T.; Lyman, J.T.; Fabrikant, J.I.; Levy, R.P.

    1989-12-01

    The work presented here is part of an ongoing project to quantify and evaluate the differences in the use of different radiation types and irradiation geometries in radiosurgery. We are examining dose distributions for photons using the Gamma Knife'' and the linear accelerator arc methods, as well as different species of charged particles from protons to neon ions. A number of different factors need to be studied to accurately compare the different modalities such as target size, shape and location, the irradiation geometry, and biological response. This presentation focuses on target size, which has a large effect on the dose distributions in normal tissue surrounding the lesion. This work concentrates on dose distributions found in radiosurgery, as opposed to those usually found in radiotherapy. 5 refs., 2 figs.

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

    PubMed Central

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

    2014-01-01

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

  1. 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.

  2. Targeting Neuropilin-1 to Inhibit VEGF Signaling in Cancer: Comparison of Therapeutic Approaches

    PubMed Central

    Gabhann, Feilim Mac; Popel, Aleksander S

    2006-01-01

    Angiogenesis (neovascularization) plays a crucial role in a variety of physiological and pathological conditions including cancer, cardiovascular disease, and wound healing. Vascular endothelial growth factor (VEGF) is a critical regulator of angiogenesis. Multiple VEGF receptors are expressed on endothelial cells, including signaling receptor tyrosine kinases (VEGFR1 and VEGFR2) and the nonsignaling co-receptor Neuropilin-1. Neuropilin-1 binds only the isoform of VEGF responsible for pathological angiogenesis (VEGF165), and is thus a potential target for inhibiting VEGF signaling. Using the first molecularly detailed computational model of VEGF and its receptors, we have shown previously that the VEGFR–Neuropilin interactions explain the observed differential effects of VEGF isoforms on VEGF signaling in vitro, and demonstrated potent VEGF inhibition by an antibody to Neuropilin-1 that does not block ligand binding but blocks subsequent receptor coupling. In the present study, we extend that computational model to simulation of in vivo VEGF transport and binding, and predict the in vivo efficacy of several Neuropilin-targeted therapies in inhibiting VEGF signaling: (a) blocking Neuropilin-1 expression; (b) blocking VEGF binding to Neuropilin-1; (c) blocking Neuropilin–VEGFR coupling. The model predicts that blockade of Neuropilin–VEGFR coupling is significantly more effective than other approaches in decreasing VEGF–VEGFR2 signaling. In addition, tumor types with different receptor expression levels respond differently to each of these treatments. In designing human therapeutics, the mechanism of attacking the target plays a significant role in the outcome: of the strategies tested here, drugs with similar properties to the Neuropilin-1 antibody are predicted to be most effective. The tumor type and the microenvironment of the target tissue are also significant in determining therapeutic efficacy of each of the treatments studied. PMID:17196035

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

    PubMed

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

    1992-12-01

    The purpose of this study was to examine the relationship between heart rate (HR) and oxygen consumption (VO2) for aerobic dance exercise. Therefore, eleven females completed 20 minutes of aerobic dance with continuous monitoring of HR and VO2. These physiological responses were analyzed with correlation/regression techniques. The results showed that for aerobic dance to produce a response in excess of 50% of VO2 max, the target HR must be approximately 80% of the age-predicted HR max or greater. In contrast, previously reported data for treadmill running shows that 50% of VO2 max is achieved at approximately 65% of age-predicted HR max in females. The maximum heart rate reserve (Karvonen) method was also found to underestimate the actual VO2 of AD. With the Karvonen method, the target heart rate must approximate 65% of maximum HR reserve in order to elicit a VO2 response which is representative of 50% of VO2 max. These data support recent research which illustrates that target heart rate prescriptions derived from treadmill testing may fail to accurately place AD participants in the recommended training zone. PMID:1293420

  4. 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

  5. Comparison of mammography sensitivity after reduction mammoplasty targeting the glandular and fat tissue

    PubMed Central

    Çakır, Murat; Küçükkartallar, Tevfik; Tekin, Ahmet; Selimoğlu, Nebil; Poyraz, Necdet; Belviranlı, Mehmet Metin; Kartal, Adil

    2015-01-01

    Objective: Mammography may have some limitations in the diagnosis and screening of breast cancer for women who have previously undergone breast reduction surgery. This study aimed to investigate how the structural defects in the breast tissue formed by postoperative changes are reflected on mammography. Material and Methods: The records of patients who had previously undergone breast reduction surgery and who were requested to undergo mammography for breast cancer screening by the general surgery clinic were retrospectively studied. The patients’ ages, surgical procedures, postoperative follow-up periods, amount of removed material, and histopathological and mammographic results were studied. The patients were classified into 3 groups: those older than 40 years who underwent reduction mammoplasty targeting predominantly the glandular tissue (group 1), those younger than 40 years who underwent reduction mammoplasty targeting predominantly the fat tissue (group 2), and those older than 40 years who were diagnosed with breast hypertrophy and were not operated (group 3). Results: The mean follow-up period of the patients was 6 (2–10) years. The mean value of resected tissue was 1120 g (680–2070) in group 1 and 1220 g (720–1980) in group 2. The mean age at the time of surgery was 45 (40–70) years for group 1 and 35 (24–40) years for group 2. All patients in group 1 were classified in Breast Imaging-Reporting and Data System (BI-RADS) category 1–2; 28 patients in group 2 were classified in BI-RADS 1–2, 4 were classified in BI-RADS 3, and 8 were classified in BI-RADS 0. In group 3, 35 patients were classified in BI-RADS 1–2, 4 were classified in BI-RADS 3, and 1 was classified in BI-RADS 0. Conclusion: We believe that breast reduction surgery targeting predominantly the glandular tissue in patients older than 40 years increases mammographic sensitivity. PMID:26170752

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

    PubMed Central

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

    2009-01-01

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

  7. 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.

  8. 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.

  9. Electron Beam Distruption due to Ion Release from Targets - Comparison Between Computer Calculations and Observations

    NASA Astrophysics Data System (ADS)

    Hughes, Thomas P.; Davis, Harold A.; Vermare, Christophe; Moir, David C.; Olson, Russell T.; Monty Wood, W.

    2001-10-01

    Experiments have been performed on the first axis of the DARHT electron beam accelerator to study the effects on the beam of ion emission from surfaces struck by electrons (see preceding abstract). Calculations using the two- and three-dimensional Lsp particle-in-cell code were performed to compare with experimental results. Two-dimensional calculations, which allow the release of ions when the impacted surface temperature increases by 300 deg C, accurately replicate the experimental results showing beam blow-up downstream of the surface just after ion emission. Three-dimensional calculations show the onset of a hose instability after beam blow up in agreement with observations. A comparison of calculations to identify the dominant ion species with direct ion measurements will be presented.

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

    SciTech Connect

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

    2011-04-01

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

  11. The regulatory roles of microRNA-146b-5p and its target platelet-derived growth factor receptor α (PDGFRA) in erythropoiesis and megakaryocytopoiesis.

    PubMed

    Zhai, Peng-Fei; Wang, Fang; Su, Rui; Lin, Hai-Shuang; Jiang, Chong-Liang; Yang, Gui-Hua; Yu, Jia; Zhang, Jun-Wu

    2014-08-15

    Emerging evidence has shown that microRNAs have key roles in regulating various normal physiological processes, whereas their deregulated expression is correlated with various diseases. The miR-146 family includes miR-146a and miR-146b, with a distinct expression spectrum in different hematopoietic cells. Recent work indicated that miR-146a has a close relationship with inflammation and autoimmune diseases. miR-146-deficient mice have developed some abnormal hematopoietic phenotypes, suggesting the potential functions of miR-146 in hematopoietic development. In this study, we found that miR-146b was consistently up-regulated in both K562 and CD34(+) hematopoietic stem/progenitor cells (HSPCs) undergoing either erythroid or megakaryocytic differentiation. Remarkably, erythroid and megakaryocytic maturation of K562 cells was induced by excess miR-146b but inhibited by decreased miR-146b levels. More importantly, an mRNA encoding receptor tyrosine kinase, namely platelet-derived growth factor receptor α (PDGFRA), was identified and validated as a direct target of miR-146b in hematopoietic cells. Gain-of-function and loss-of-function assays showed that PDGFRA functioned as a negative regulator in erythroid and megakaryocytic differentiation. miR-146b could ultimately affect the expression of the GATA-1 gene, which is regulated by HEY1 (Hairy/enhancer-of-split related with YRPW motif protein 1), a transcriptional repressor, via inhibition of the PDGFRA/JNK/JUN/HEY1 pathway. Lentivirus-mediated gene transfer also demonstrated that the overexpression of miR-146b promoted erythropoiesis and megakaryocytopoiesis of HSPCs via its regulation on the PDGFRA gene and effects on GATA-1 expression. Moreover, we confirmed that the binding of GATA-1 to the miR-146b promoter and induction of miR-146b during hematopoietic maturation were dependent on GATA-1. Therefore, miR-146b, PDGFRA, and GATA-1 formed a regulatory circuit to promote erythroid and megakaryocytic differentiation

  12. 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

  13. Comparison of horizontal head movements evoked by auditory and visual targets.

    PubMed

    Fuller, J H

    1996-01-01

    Head movement propensity-the pattern of head saccades dependent on methods of target presentation-varies among individuals. The present group of 9 young adults was previously ranked in a visual saccadic task according to this propensity. The present report examines how and why this propensity changes if the saccades are made to auditory targets. 1) Spatially identical, interleaved, auditorily and visually elicited horizontal saccadic gaze shifts (jumps) differed in amplitude and in starting and/or ending position. The jumps were executed in two head movement modes: first, the non-aligned mode was a standard reaction-time single gaze step between two points. Second, the head-aligned mode required alignment of the head with the fixation (starting) point; thereafter both modes were identical. All results in the auditory task are expressed relative to the visual results. 2) In the non-aligned mode, head movement amplitudes were increased on average by 15% (for example, an 80 degrees jump elicited a 12 degrees larger head movement), and velocity decreased by 12%, reflecting the increased demands of the auditory task. More importantly, the differences between subjects was narrowed; that is, head movement propensity was homogenized in the auditory task. In the visual task, head-movers willingly move their heads off and across the midline, whereas non-movers are unwilling to leave the midline from eccentric starting points or to eccentric ending points. This is called the midline attraction effect and was previously linked to spatial reference frames. The homogenization in the auditory task was characterized by head-movers increasing, and non-movers decreasing, their midline attraction, suggesting altered spatial reference frames. 3) For heuristic purposes, the ideal head-mover is defined by a gain of 1.0 in the visual task, and by external earth-fixed reference frames. Similarly, the ideal non-mover has a gain of 0.0 and has a bias toward body (or some par of the body

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

    NASA Astrophysics Data System (ADS)

    Kulesza, Joel A.; Arzu Alpan, F.

    2016-02-01

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

  15. Quantitative-Proteomic Comparison of Alpha and Beta Cells to Uncover Novel Targets for Lineage Reprogramming

    PubMed Central

    Mertins, Philipp; Udeshi, Namrata D.; Dančík, Vlado; Fomina-Yadlin, Dina; Kubicek, Stefan; Clemons, Paul A.; Schreiber, Stuart L.; Carr, Steven A.; Wagner, Bridget K.

    2014-01-01

    Type-1 diabetes (T1D) is an autoimmune disease in which insulin-secreting pancreatic beta cells are destroyed by the immune system. An emerging strategy to regenerate beta-cell mass is through transdifferentiation of pancreatic alpha cells to beta cells. We previously reported two small molecules, BRD7389 and GW8510, that induce insulin expression in a mouse alpha cell line and provide a glimpse into potential intermediate cell states in beta-cell reprogramming from alpha cells. These small-molecule studies suggested that inhibition of kinases in particular may induce the expression of several beta-cell markers in alpha cells. To identify potential lineage reprogramming protein targets, we compared the transcriptome, proteome, and phosphoproteome of alpha cells, beta cells, and compound-treated alpha cells. Our phosphoproteomic analysis indicated that two kinases, BRSK1 and CAMKK2, exhibit decreased phosphorylation in beta cells compared to alpha cells, and in compound-treated alpha cells compared to DMSO-treated alpha cells. Knock-down of these kinases in alpha cells resulted in expression of key beta-cell markers. These results provide evidence that perturbation of the kinome may be important for lineage reprogramming of alpha cells to beta cells. PMID:24759943

  16. 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

  17. 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

  18. 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

  19. a Band Selection Method for Sub-Pixel Target Detection in Hyperspectral Images Based on Laboratory and Field Reflectance Spectral Comparison

    NASA Astrophysics Data System (ADS)

    Sharifi hashjin, S.; Darvishi, A.; Khazai, S.; Hatami, F.; Jafari houtki, M.

    2016-06-01

    In recent years, developing target detection algorithms has received growing interest in hyperspectral images. In comparison to the classification field, few studies have been done on dimension reduction or band selection for target detection in hyperspectral images. This study presents a simple method to remove bad bands from the images in a supervised manner for sub-pixel target detection. The proposed method is based on comparing field and laboratory spectra of the target of interest for detecting bad bands. For evaluation, the target detection blind test dataset is used in this study. Experimental results show that the proposed method can improve efficiency of the two well-known target detection methods, ACE and CEM.

  20. 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

  1. 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. PMID:27499756

  2. 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

  3. 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

  4. A dimensionless dynamic contrast enhanced MRI parameter for intra-prostatic tumour target volume delineation: initial comparison with histology

    NASA Astrophysics Data System (ADS)

    Hrinivich, W. Thomas; Gibson, Eli; Gaed, Mena; Gomez, Jose A.; Moussa, Madeleine; McKenzie, Charles A.; Bauman, Glenn S.; Ward, Aaron D.; Fenster, Aaron; Wong, Eugene

    2014-03-01

    Purpose: T2 weighted and diffusion weighted magnetic resonance imaging (MRI) show promise in isolating prostate tumours. Dynamic contrast enhanced (DCE)-MRI has also been employed as a component in multi-parametric tumour detection schemes. Model-based parameters such as Ktrans are conventionally used to characterize DCE images and require arterial contrast agent (CR) concentration. A robust parameter map that does not depend on arterial input may be more useful for target volume delineation. We present a dimensionless parameter (Wio) that characterizes CR wash-in and washout rates without requiring arterial CR concentration. Wio is compared to Ktrans in terms of ability to discriminate cancer in the prostate, as demonstrated via comparison with histology. Methods: Three subjects underwent DCE-MRI using gadolinium contrast and 7 s imaging temporal resolution. A pathologist identified cancer on whole-mount histology specimens, and slides were deformably registered to MR images. The ability of Wio maps to discriminate cancer was determined through receiver operating characteristic curve (ROC) analysis. Results: There is a trend that Wio shows greater area under the ROC curve (AUC) than Ktrans with median AUC values of 0.74 and 0.69 respectively, but the difference was not statistically significant based on a Wilcoxon signed-rank test (p = 0.13). Conclusions: Preliminary results indicate that Wio shows potential as a tool for Ktrans QA, showing similar ability to discriminate cancer in the prostate as Ktrans without requiring arterial CR concentration.

  5. An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets

    PubMed Central

    Zeller, Karen I; Jegga, Anil G; Aronow, Bruce J; O'Donnell, Kathryn A; Dang, Chi V

    2003-01-01

    We report a database of genes responsive to the Myc oncogenic transcription factor. The database Myc Target Gene prioritizes candidate target genes according to experimental evidence and clusters responsive genes into functional groups. We coupled the prioritization of target genes with phylogenetic sequence comparisons to predict c-Myc target binding sites, which are in turn validated by chromatin immunoprecipitation assays. This database is essential for the understanding of the genetic regulatory networks underlying the genesis of cancers. PMID:14519204

  6. 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.

  7. 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

  8. Identification of orthologous target pairs with shared active compounds and comparison of organism-specific activity patterns.

    PubMed

    Dimova, Dilyana; Stumpfe, Dagmar; Bajorath, Jürgen

    2015-11-01

    A systematic search for active small molecules shared by orthologous targets was carried out, leading to the identification of 803 compound-based orthologous target pairs covering a total of 938 orthologues, 358 unique targets and 98 organisms. Many orthologous target pairs were found to have substantial compound coverage, enabling the introduction of an orthologous target pairs classification including 'organism cliffs' and 'potency-retaining' pairs. A total of 158 orthologous target pairs involving human orthologues were identified, which were typically associated with drug discovery-relevant targets, organism combinations and compound data. Orthologous target pairs with human orthologues included 83 potency-retaining orthologous target pairs covering a variety of targets and organisms. On the basis of these orthologous target pairs, the compound search was further extended and 1149 potent compounds were identified that only had reported activities for non-human orthologues of 48 therapeutic targets, but not their human counterparts, hence providing a large pool of candidate compounds for further evaluation. The complete set of orthologous target pairs identified in our analysis, the orthologous target pairs classification including associated data and all candidate compounds are made freely available. PMID:25931211

  9. Functional Comparison of Human Adenomatous Polyposis Coli (APC) and APC-Like in Targeting Beta-Catenin for Degradation

    PubMed Central

    Schneikert, Jean; Vijaya Chandra, Shree Harsha; Ruppert, Jan Gustav; Ray, Suparna; Wenzel, Eva Maria; Behrens, Jürgen

    2013-01-01

    Truncating mutations affect the adenomatous polyposis coli (APC) gene in most cases of colon cancer, resulting in the stabilization of β-catenin and uncontrolled cell proliferation. We show here that colon cancer cell lines express also the paralog APC-like (APCL or APC2). RNA interference revealed that it controls the level and/or the activity of β-catenin, but it is less efficient and binds less well to β-catenin than APC, thereby providing one explanation as to why the gene is not mutated in colon cancer. A further comparison indicates that APCL down-regulates the β-catenin level despite the lack of the 15R region known to be important in APC. To understand this discrepancy, we performed immunoprecipitation experiments that revealed that phosphorylated β-catenin displays a preference for binding to the 15 amino acid repeats (15R) rather than the first 20 amino acid repeat of APC. This suggests that the 15R region constitutes a gate connecting the steps of β-catenin phosphorylation and subsequent ubiquitination/degradation. Using RNA interference and domain swapping experiments, we show that APCL benefits from the 15R of truncated APC to target β-catenin for degradation, in a process likely involving heterodimerization of the two partners. Our data suggest that the functional complementation of APCL by APC constitutes a substantial facet of tumour development, because the truncating mutations of APC in colorectal tumours from familial adenomatous polyposis (FAP) patients are almost always selected for the retention of at least one 15R. PMID:23840886

  10. Bioinformatic Description of Immunotherapy Targets for Pediatric T-Cell Leukemia and the Impact of Normal Gene Sets Used for Comparison

    PubMed Central

    Orentas, Rimas J.; Nordlund, Jessica; He, Jianbin; Sindiri, Sivasish; Mackall, Crystal; Fry, Terry J.; Khan, Javed

    2014-01-01

    Pediatric lymphoid leukemia has the highest cure rate of all pediatric malignancies, yet due to its prevalence, still accounts for the majority of childhood cancer deaths and requires long-term highly toxic therapy. The ability to target B-cell ALL with immunoglobulin-like binders, whether anti-CD22 antibody or anti-CD19 CAR-Ts, has impacted treatment options for some patients. The development of new ways to target B-cell antigens continues at rapid pace. T-cell ALL accounts for up to 20% of childhood leukemia but has yet to see a set of high-value immunotherapeutic targets identified. To find new targets for T-ALL immunotherapy, we employed a bioinformatic comparison to broad normal tissue arrays, hematopoietic stem cells (HSC), and mature lymphocytes, then filtered the results for transcripts encoding plasma membrane proteins. T-ALL bears a core T-cell signature and transcripts encoding TCR/CD3 components and canonical markers of T-cell development predominate, especially when comparison was made to normal tissue or HSC. However, when comparison to mature lymphocytes was also undertaken, we identified two antigens that may drive, or be associated with leukemogenesis; TALLA-1 and hedgehog interacting protein. In addition, TCR subfamilies, CD1, activation and adhesion markers, membrane-organizing molecules, and receptors linked to metabolism and inflammation were also identified. Of these, only CD52, CD37, and CD98 are currently being targeted clinically. This work provides a set of targets to be considered for future development of immunotherapies for T-ALL. PMID:24959420

  11. Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA

    PubMed Central

    Göpel, Yvonne; Papenfort, Kai; Reichenbach, Birte; Vogel, Jörg; Görke, Boris

    2013-01-01

    Bacterial small RNAs (sRNAs) are well established to regulate diverse cellular processes, but how they themselves are regulated is less understood. Recently, we identified a regulatory circuit wherein the GlmY and GlmZ sRNAs of Escherichia coli act hierarchically to activate mRNA glmS, which encodes glucosamine-6-phosphate (GlcN6P) synthase. Although the two sRNAs are highly similar, only GlmZ is a direct activator that base-pairs with the glmS mRNA, aided by protein Hfq. GlmY, however, does not bind Hfq and activates glmS indirectly by protecting GlmZ from RNA cleavage. This complex regulation feedback controls the levels of GlmS protein in response to its product, GlcN6P, a key metabolite in cell wall biosynthesis. Here, we reveal the molecular basis for the regulated turnover of GlmZ, identifying RapZ (RNase adaptor protein for sRNA GlmZ; formerly YhbJ) as a novel type of RNA-binding protein that recruits the major endoribonuclease RNase E to GlmZ. This involves direct interaction of RapZ with the catalytic domain of RNase E. GlmY binds RapZ through a secondary structure shared by both sRNAs and therefore acts by molecular mimicry as a specific decoy for RapZ. Thus, in analogy to regulated proteolysis, RapZ is an adaptor, and GlmY is an anti-adaptor in regulated turnover of a regulatory small RNA. PMID:23475961

  12. 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

  13. 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

  14. 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

  15. Genome-Wide Mapping of Targets of Maize Histone Deacetylase HDA101 Reveals Its Function and Regulatory Mechanism during Seed Development.

    PubMed

    Yang, Hua; Liu, Xinye; Xin, Mingming; Du, Jinkun; Hu, Zhaorong; Peng, HuiRu; Rossi, Vincenzo; Sun, Qixin; Ni, Zhongfu; Yao, Yingyin

    2016-03-01

    Histone deacetylases (HDACs) regulate histone acetylation levels by removing the acetyl group from lysine residues. The maize (Zea mays)HDACHDA101 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 inhda101mutants. To investigate HDA101 function during the early stages of seed development, we performed genome-wide mapping of HDA101 binding sites. We observed that, like mammalianHDACs, 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

  16. The Diabetes Drug Target MitoNEET Governs a Novel Trafficking Pathway to Rebuild an Fe-S Cluster into Cytosolic Aconitase/Iron Regulatory Protein 1*

    PubMed Central

    Ferecatu, Ioana; Gonçalves, Sergio; Golinelli-Cohen, Marie-Pierre; Clémancey, Martin; Martelli, Alain; Riquier, Sylvie; Guittet, Eric; Latour, Jean-Marc; Puccio, Hélène; Drapier, Jean-Claude; Lescop, Ewen; Bouton, Cécile

    2014-01-01

    In eukaryotes, mitochondrial iron-sulfur cluster (ISC), export and cytosolic iron-sulfur cluster assembly (CIA) machineries carry out biogenesis of iron-sulfur (Fe-S) clusters, which are critical for multiple essential cellular pathways. However, little is known about their export out of mitochondria. Here we show that Fe-S assembly of mitoNEET, the first identified Fe-S protein anchored in the mitochondrial outer membrane, strictly depends on ISC machineries and not on the CIA or CIAPIN1. We identify a dedicated ISC/export pathway in which augmenter of liver regeneration, a mitochondrial Mia40-dependent protein, is specific to mitoNEET maturation. When inserted, the Fe-S cluster confers mitoNEET folding and stability in vitro and in vivo. The holo-form of mitoNEET is resistant to NO and H2O2 and is capable of repairing oxidatively damaged Fe-S of iron regulatory protein 1 (IRP1), a master regulator of cellular iron that has recently been involved in the mitochondrial iron supply. Therefore, our findings point to IRP1 as the missing link to explain the function of mitoNEET in the control of mitochondrial iron homeostasis. PMID:25012650

  17. Recruiting Injection Drug Users: A Three-Site Comparison of Results and Experiences with Respondent-Driven and Targeted Sampling Procedures

    PubMed Central

    Risser, Jan M. H.; McGoy, Shanell; Becker, Adam B.; Rehman, Hafeez; Jefferson, Mary; Griffin, Vivian; Wolverton, Marcia; Tortu, Stephanie

    2006-01-01

    Several recent studies have utilized respondent-driven sampling (RDS) methods to survey hidden populations such as commercial sex-workers, men who have sex with men (MSM) and injection drug users (IDU). Few studies, however, have provided a direct comparison between RDS and other more traditional sampling methods such as venue-based, targeted or time/space sampling. The current study sampled injection drug users in three U.S. cities using RDS and targeted sampling (TS) methods and compared their effectiveness in terms of recruitment efficiency, logistics, and sample demographics. Both methods performed satisfactorily. The targeted method required more staff time per-recruited respondent and had a lower proportion of screened respondents who were eligible than RDS, while RDS respondents were offered higher incentives for participation. PMID:16933101

  18. Comparison of ganglion cell signals and psychophysical localization of moving targets can help define central motion mechanisms.

    PubMed

    Lee, Barry B; Rüttiger, Lukas; Sun, Hao

    2005-01-01

    Vernier acuity thresholds can be related to visibility of targets. This is considered in relation to retinal signals. Spatial precision of macaque ganglion cell responses to moving targets was assessed by neurometric analysis and compared with psychophysical performance. Under some conditions the amplitude of ganglion cell signals per se may relate target visibility to spatial precision of psychophysical performance. Other conditions are more complex; we suggest central mechanisms may adapt their properties, eg their dimensions, depending on the stochastic properties of ganglion cell signals. Thus, the relation of Vernier acuity to the visibility of targets is a rule of thumb which has a complex relation to physiological substrates. PMID:16178152

  19. Regulatory effects of intermittent noxious stimulation on spinal cord injury-sensitive microRNAs and their presumptive targets following spinal cord contusion

    PubMed Central

    Strickland, Eric R.; Woller, Sarah A.; Garraway, Sandra M.; Hook, Michelle A.; Grau, James W.; Miranda, Rajesh C.

    2014-01-01

    Uncontrollable nociceptive stimulation adversely affects recovery in spinally contused rats. Spinal cord injury (SCI) results in altered microRNA (miRNA) expression both at, and distal to the lesion site. We hypothesized that uncontrollable nociception further influences SCI-sensitive miRNAs and associated gene targets, potentially explaining the progression of maladaptive plasticity. Our data validated previously described sensitivity of miRNAs to SCI alone. Moreover, following SCI, intermittent noxious stimulation decreased expression of miR124 in dorsal spinal cord 24 h after stimulation and increased expression of miR129-2 in dorsal, and miR1 in ventral spinal cord at 7 days. We also found that brain-derived neurotrophic factor (BDNF) mRNA expression was significantly down-regulated 1 day after SCI alone, and significantly more so, after SCI followed by tailshock. Insulin-like growth factor-1 (IGF-1) mRNA expression was significantly increased at both 1 and 7 days post-SCI, and significantly more so, 7 days post-SCI with shock. MiR1 expression was positively and significantly correlated with IGF-1, but not BDNF mRNA expression. Further, stepwise linear regression analysis indicated that a significant proportion of the changes in BDNF and IGF-1 mRNA expression were explained by variance in two groups of miRNAs, implying co-regulation. Collectively, these data show that uncontrollable nociception which activates sensorimotor circuits distal to the injury site, influences SCI-miRNAs and target mRNAs within the lesion site. SCI-sensitive miRNAs may well mediate adverse consequences of uncontrolled sensorimotor activation on functional recovery. However, their sensitivity to distal sensory input also implicates these miRNAs as candidate targets for the management of SCI and neuropathic pain. PMID:25278846

  20. Identification and Comparison of Academic Self Regulatory Learning Strategy Use of Students Enrolled in Traditional and Accelerated Baccalaureate Degree Nursing Programs

    ERIC Educational Resources Information Center

    Mullen, Patricia A.

    2009-01-01

    Objective: To explore and compare the use of metacognitive, cognitive, and environmental resource management self regulatory learning (SRL) strategies used by a national sample of students enrolled in traditional and accelerated baccalaureate nursing programs. Background: Learner focused reforms in nursing education require students to assume more…

  1. 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.

  2. 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

  3. Selecting molecular therapeutic drug targets based on the expression profiles of intrahepatic cholangiocarcinomas and miRNA-mRNA regulatory networks.

    PubMed

    Sun, Boshi; Xie, Changming; Zheng, Tongsen; Yin, Dalong; Wang, Jiabei; Liang, Yingjian; Li, Yuejin; Yang, Guangchao; Shi, Huawen; Pei, Tiemin; Han, Jihua; Liu, Lianxin

    2016-01-01

    The incidence of intrahepatic cholangiocarcinoma (ICC) is increasing yearly, making it the second most common carcinoma after hepatocellular carcinoma among primary malignant liver tumors. Integrated miRNA and mRNA analysis is becoming more frequently used in antitumor ICC treatment. However, this approach generates vast amounts of data, which leads to difficulties performing comprehensive analyses to identify specific therapeutic drug targets. In this study, we provide an in-depth analysis of ICC function, identifying potential highly potent antitumor drugs for antitumor therapy. Two sets of whole genome expression profiles were obtained from the Gene Expression Omnibus (GEO) database. Using modular bioinformatic analysis, six core functional modules were identified for ICC. Based on a Fisher's test of the Cmap small molecule drug database, 65 drug components were identified that regulated the genes of these six core modules. Literature mining was then used to identify 15 new potential antitumor drugs. PMID:26498995

  4. Measurement of plasma momentum exerted on target by a small helicon plasma thruster and comparison with direct thrust measurement

    NASA Astrophysics Data System (ADS)

    Takahashi, Kazunori; Komuro, Atsushi; Ando, Akira

    2015-02-01

    Momentum, i.e., force, exerted from a small helicon plasma thruster to a target plate is measured simultaneously with a direct thrust measurement using a thrust balance. The calibration coefficient relating a target displacement to a steady-state force is obtained by supplying a dc to a calibration coil mounted on the target, where a force acting to a small permanent magnet located near the coil is directly measured by using a load cell. As the force exerted by the plasma flow to the target plate is in good agreement with the directly measured thrust, the validity of the target technique is demonstrated under the present operating conditions, where the thruster is operated in steady-state. Furthermore, a calibration coefficient relating a swing amplitude of the target to an impulse bit is also obtained by pulsing the calibration coil current. The force exerted by the pulsed plasma, which is estimated from the measured impulse bit and the pulse width, is also in good agreement with that obtained for the steady-state operation; hence, the thrust assessment of the helicon plasma thruster by the target is validated for both the steady-state and pulsed operations.

  5. Quantitative morphological comparison of axon-targeting strategies for gene therapies directed to the nigro-striatal projection.

    PubMed

    Padmanabhan, S; Kareva, T; Kholodilov, N; Burke, R E

    2014-02-01

    Cellular targeting of mRNAs and proteins to axons is essential for axon growth during development and is likely to be important for adult maintenance as well. Given the importance and potency of these axon-targeting motifs to the biology of axons, it seems possible that they can be used in the design of transgenes that are intended to enhance axon growth or maintenance, so as to improve potency and minimize off-target effects. To investigate this possibility, it is first essential to assess known motifs for their efficacy. We have therefore evaluated four axon-targeting motifs, using adeno-associated viral vector-mediated gene delivery in the nigro-striatal dopaminergic system, a projection that is predominantly affected in Parkinson's disease. We have tested two mRNA axonal zipcodes, the 3' untranslated region (UTR) of β-actin and 3' UTR of tau, and two axonal-targeting protein motifs, the palmitoylation signal sequence in GAP-43 and the last 15 amino acids in the amyloid precursor protein, to direct the expression of the fluorescent protein Tomato in axons. These sequences, fused to Tomato, were able to target its expression to dopaminergic axons. Based on quantification of Tomato-positive axons, and the density of striatal innervation, we conclude that the C-terminal of the amyloid precursor protein is the most effective axon-targeting motif. PMID:24305419

  6. Measurement of plasma momentum exerted on target by a small helicon plasma thruster and comparison with direct thrust measurement.

    PubMed

    Takahashi, Kazunori; Komuro, Atsushi; Ando, Akira

    2015-02-01

    Momentum, i.e., force, exerted from a small helicon plasma thruster to a target plate is measured simultaneously with a direct thrust measurement using a thrust balance. The calibration coefficient relating a target displacement to a steady-state force is obtained by supplying a dc to a calibration coil mounted on the target, where a force acting to a small permanent magnet located near the coil is directly measured by using a load cell. As the force exerted by the plasma flow to the target plate is in good agreement with the directly measured thrust, the validity of the target technique is demonstrated under the present operating conditions, where the thruster is operated in steady-state. Furthermore, a calibration coefficient relating a swing amplitude of the target to an impulse bit is also obtained by pulsing the calibration coil current. The force exerted by the pulsed plasma, which is estimated from the measured impulse bit and the pulse width, is also in good agreement with that obtained for the steady-state operation; hence, the thrust assessment of the helicon plasma thruster by the target is validated for both the steady-state and pulsed operations. PMID:25725840

  7. 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

  8. 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. PMID:26668381

  9. EBNA2 Drives Formation of New Chromosome Binding Sites and Target Genes for B-Cell Master Regulatory Transcription Factors RBP-jκ and EBF1

    PubMed Central

    Lu, Fang; Chen, Horng-Shen; Kossenkov, Andrew V.; DeWispeleare, Karen; Won, Kyoung-Jae; Lieberman, Paul M.

    2016-01-01

    Epstein-Barr Virus (EBV) transforms resting B-lymphocytes into proliferating lymphoblasts to establish latent infections that can give rise to malignancies. We show here that EBV-encoded transcriptional regulator EBNA2 drives the cooperative and combinatorial genome-wide binding of two master regulators of B-cell fate, namely EBF1 and RBP-jκ. Previous studies suggest that these B-cell factors are statically bound to target gene promoters. In contrast, we found that EBNA2 induces the formation of new binding for both RBP-jκ and EBF1, many of which are in close physical proximity in the cellular and viral genome. These newly induced binding sites co-occupied by EBNA2-EBF1-RBP-jκ correlate strongly with transcriptional activation of linked genes that are important for B-lymphoblast function. Conditional expression or repression of EBNA2 leads to a rapid alteration in RBP-jκ and EBF1 binding. Biochemical and shRNA depletion studies provide evidence for cooperative assembly at co-occupied sites. These findings reveal that EBNA2 facilitate combinatorial interactions to induce new patterns of transcription factor occupancy and gene programming necessary to drive B-lymphoblast growth and survival. PMID:26752713

  10. EBNA2 Drives Formation of New Chromosome Binding Sites and Target Genes for B-Cell Master Regulatory Transcription Factors RBP-jκ and EBF1.

    PubMed

    Lu, Fang; Chen, Horng-Shen; Kossenkov, Andrew V; DeWispeleare, Karen; Won, Kyoung-Jae; Lieberman, Paul M

    2016-01-01

    Epstein-Barr Virus (EBV) transforms resting B-lymphocytes into proliferating lymphoblasts to establish latent infections that can give rise to malignancies. We show here that EBV-encoded transcriptional regulator EBNA2 drives the cooperative and combinatorial genome-wide binding of two master regulators of B-cell fate, namely EBF1 and RBP-jκ. Previous studies suggest that these B-cell factors are statically bound to target gene promoters. In contrast, we found that EBNA2 induces the formation of new binding for both RBP-jκ and EBF1, many of which are in close physical proximity in the cellular and viral genome. These newly induced binding sites co-occupied by EBNA2-EBF1-RBP-jκ correlate strongly with transcriptional activation of linked genes that are important for B-lymphoblast function. Conditional expression or repression of EBNA2 leads to a rapid alteration in RBP-jκ and EBF1 binding. Biochemical and shRNA depletion studies provide evidence for cooperative assembly at co-occupied sites. These findings reveal that EBNA2 facilitate combinatorial interactions to induce new patterns of transcription factor occupancy and gene programming necessary to drive B-lymphoblast growth and survival. PMID:26752713

  11. 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

  12. 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.

  13. 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.

  14. 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

    2016-08-01

    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. PMID:27378648

  15. 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.

  16. 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…

  17. COMPARISON OF THE RELATIVE INHIBITION OF ACETYLCHOLINESTERASE AND NEUROPATHY TARGET ESTERASE IN RATS AND HENS GIVEN CHOLINESTERASE INHIBITORS

    EPA Science Inventory

    Inhibition of neuropathy target esterase (NTE, neurotoxic esterase) and acetylcholinesterase (AME) activities was compared in brain and spinal cords of adult. hile Leghorn hens and adult male Long Evans rats 4-48 hr after administration of tri-ortho-tolyl phosphate (TOTP po, 50-5...

  18. Comparison of the pharmacological profiles of murine antisense oligonucleotides targeting apolipoprotein B and microsomal triglyceride transfer protein.

    PubMed

    Lee, Richard G; Fu, Wuxia; Graham, Mark J; Mullick, Adam E; Sipe, Donna; Gattis, Danielle; Bell, Thomas A; Booten, Sheri; Crooke, Rosanne M

    2013-03-01

    Therapeutic agents that suppress apolipoprotein B (apoB) and microsomal triglyceride transfer protein (MTP) levels/activity are being developed in the clinic to benefit patients who are unable to reach target LDL-C levels with maximally tolerated lipid-lowering drugs. To compare and contrast the metabolic consequences of reducing these targets, murine-specific apoB or MTP antisense oligonucleotides (ASOs) were administered to chow-fed and high fat-fed C57BL/6 or to chow-fed and Western diet-fed LDLr⁻/⁻ mice for periods ranging from 2 to 12 weeks, and detailed analyses of various factors affecting fatty acid metabolism were performed. Administration of these drugs significantly reduced target hepatic mRNA and protein, leading to similar reductions in hepatic VLDL/triglyceride secretion. MTP ASO treatment consistently led to increases in hepatic triglyceride accumulation and biomarkers of hepatotoxicity relative to apoB ASO due in part to enhanced expression of peroxisome proliferator activated receptor γ target genes and the inability to reduce hepatic fatty acid synthesis. Thus, although both drugs effectively lowered LDL-C levels in mice, the apoB ASO produced a more positive liver safety profile. PMID:23220583

  19. Regulatory Snapshots: integrative mining of regulatory modules from expression time series and regulatory networks.

    PubMed

    Gonçalves, Joana P; Aires, Ricardo S; Francisco, Alexandre P; Madeira, Sara C

    2012-01-01

    Explaining regulatory mechanisms is crucial to understand complex cellular responses leading to system perturbations. Some strategies reverse engineer regulatory interactions from experimental data, while others identify functional regulatory units (modules) under the assumption that biological systems yield a modular organization. Most modular studies focus on network structure and static properties, ignoring that gene regulation is largely driven by stimulus-response behavior. Expression time series are key to gain insight into dynamics, but have been insufficiently explored by current methods, which often (1) apply generic algorithms unsuited for expression analysis over time, due to inability to maintain the chronology of events or incorporate time dependency; (2) ignore local patterns, abundant in most interesting cases of transcriptional activity; (3) neglect physical binding or lack automatic association of regulators, focusing mainly on expression patterns; or (4) limit the discovery to a predefined number of modules. We propose Regulatory Snapshots, an integrative mining approach to identify regulatory modules over time by combining transcriptional control with response, while overcoming the above challenges. Temporal biclustering is first used to reveal transcriptional modules composed of genes showing coherent expression profiles over time. Personalized ranking is then applied to prioritize prominent regulators targeting the modules at each time point using a network of documented regulatory associations and the expression data. Custom graphics are finally depicted to expose the regulatory activity in a module at consecutive time points (snapshots). Regulatory Snapshots successfully unraveled modules underlying yeast response to heat shock and human epithelial-to-mesenchymal transition, based on regulations documented in the YEASTRACT and JASPAR databases, respectively, and available expression data. Regulatory players involved in functionally enriched

  20. Comparison between experiments and molecular dynamic simulations of spallation induced by ultra-short laser shock on micrometric Tantalum targets

    NASA Astrophysics Data System (ADS)

    Cuq-Lelandais, Jean-Paul; Boustie, Michel; Soulard, Laurent; Berthe, Laurent; Sollier, Arnaud; Bontaz-Carion, Joelle; Combis, Patrick; de Resseguier, Thibaut; Lescoute, Emilien

    2009-06-01

    Shock wave propagation and the spallation within materials induced by laser shock have been investigated for roughly two decades. With the latest laser technologies evolution, one can access to shorter regimes in durations, going below the picosecond range. Shots performed with the LULI 100TW facility evidence the possibility to obtain spallation in a few microns thick metallic target. Such conditions provide an experimental data layout directly comparable with molecular dynamic simulations accessible to these scales. Molecular dynamic simulations on a single crystal of Tantalum have been performed with the CEA TERA 10 computer. First, the Hugoniot calculated by the equilibrium molecular dynamics has been compared with experimental data to check the potential (EAM) relevance to reproduce the shock wave propagation. Then, a large scale simulation on a micrometric target has been performed. We have observed the microscopic ductile damage process, the pore apparition and their time and space evolution. The results are compared with experimental results and classical one- dimensional hydrodynamic simulations.

  1. 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

  2. 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). PMID:25283368

  3. International Comparisons to Assess Effects of Payment and Regulatory Changes in the United States on Anemia Practice in Patients on Hemodialysis: The Dialysis Outcomes and Practice Patterns Study.

    PubMed

    Fuller, Douglas S; Bieber, Brian A; Pisoni, Ronald L; Li, Yun; Morgenstern, Hal; Akizawa, Tadao; Jacobson, Stefan H; Locatelli, Francesco; Port, Friedrich K; Robinson, Bruce M

    2016-07-01

    For years, erythropoiesis-stimulating agent (ESA) use among patients on dialysis was much higher in the United States than in Europe or Japan. Sweeping changes to dialysis reimbursement and regulatory policies for ESA in the United States in 2011 were expected to reduce ESA use and hemoglobin levels. We used the Dialysis Outcomes and Practice Patterns Study (DOPPS) data from 7129 patients in 223 in-center hemodialysis facilities (average per month) to estimate and compare time trends in ESA dose and hemoglobin levels among patients on hemodialysis in the United States, Germany, Italy, Spain, the United Kingdom, and Japan. From 2010 to 2013, substantial declines in ESA use and hemoglobin levels occurred in the United States but not in other DOPPS countries. Between August of 2010 and April of 2013, mean weekly ESA dose in the United States decreased 40.4% for black patients and 38.0% for nonblack patients; mean hemoglobin decreased from 11.5 g/dl in black patients and 11.4 g/dl in nonblack patients to 10.6 g/dl in both groups. In 2010 and 2013, adjusted weekly ESA doses per kilogram were 41% and 11% lower, respectively, in patients in Europe and 60% and 18% lower, respectively, in patients in Japan than in nonblack patients in the United States. Adjusted hemoglobin levels in 2010 and 2013 were 0.07 g/dl lower and 0.56 g/dl higher, respectively, in patients in Europe and 0.93 and 0.01 g/dl lower, respectively, in patients in Japan than in nonblack patients in the United States. In conclusion, ESA dosing reductions in the United States likely reflect efforts in response to changes in reimbursement policy and regulatory guidance. PMID:26582402

  4. Regulatory RNAs

    PubMed Central

    Vazquez-Anderson, Jorge; Contreras, Lydia M

    2013-01-01

    RNAs have many important functional properties, including that they are independently controllable and highly tunable. As a result of these advantageous properties, their use in a myriad of sophisticated devices has been widely explored. Yet, the exploitation of RNAs for synthetic applications is highly dependent on the ability to characterize the many new molecules that continue to be discovered by large-scale sequencing and high-throughput screening techniques. In this review, we present an exhaustive survey of the most recent synthetic bacterial riboswitches and small RNAs while emphasizing their virtues in gene expression management. We also explore the use of these RNA components as building blocks in the RNA synthetic biology toolbox and discuss examples of synthetic RNA components used to rewire bacterial regulatory circuitry. We anticipate that this field will expand its catalog of smart devices by mimicking and manipulating natural RNA mechanisms and functions. PMID:24356572

  5. 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.

  6. 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

  7. Comparison of dissociation mechanism between collisionally activated dissociation and charge inversion using alkali metal targets for chlorophenol isomers

    NASA Astrophysics Data System (ADS)

    Hayakawa, Shigeo; Kawamura, Yoshiaki; Takahashi, Yutaka

    2005-11-01

    Chlorinated aromatic compounds are well-known environmental pollutants whose toxicities depend dramatically on the chlorine substitution pattern, making differentiation of chlorophenol isomers important for environmental analysis. Collisionally activated dissociation (CAD) spectra and charge inversion spectra of ortho-, meta-, and para-chlorophenols (ClC6H4OH) and their partially deuterated forms (ClC6H4OD) were measured using alkali metal targets. The peaks associated with C6H4O+ and C5H5Cl+ ions observed in the CAD spectra result from the loss of HCl and CO fragments, respectively, after the re-arrangement of the hydroxyl hydrogen atom. The peaks associated with C6H4OH- and ClC6H4O- ions observed in the charge inversion spectra result from Cl loss and from hydroxyl bond dissociation, respectively. Isomeric differentiation is possible based on the clear differences observed in the relative intensities of these pairs of peaks. Although the intensities of the peaks associated with C6H4O+ relative to those of C5H5Cl+ in the CAD spectra are independent of the target species, the intensities of the peaks associated with C6H4OH- relative to those of ClC6H4O- in the charge inversion spectra are target dependent. The isomeric dependence of the positive ion distribution patterns in the CAD spectra is proposed to be due to the differences in the rate of the hydrogen atom re-arrangement process. In contrast, the isomeric dependence of the negative ion distribution patterns in the charge inversion spectra is attributed to differences in the bond strength involved in the direct dissociation process in the neutral intermediate species.

  8. Comparison of the nutritional content of products, with and without nutrient claims, targeted at children in Brazil.

    PubMed

    Rodrigues, Vanessa Mello; Rayner, Mike; Fernandes, Ana Carolina; Oliveira, Renata Carvalho de; Proença, Rossana Pacheco da Costa; Fiates, Giovanna Medeiros Rataichesck

    2016-06-01

    Many children's food products highlight positive attributes on their front-of-package labels in the form of nutrient claims. This cross-sectional study investigated all retailed packaged foods (n 5620) in a major Brazilian supermarket, in order to identify the availability of products targeted at children, and to compare the nutritional content of products with and without nutrient claims on labels. Data on energy, carbohydrate, protein, fibre, Na and total and SFA content, along with the presence and type of nutrient claims, were obtained in-store from labels of all products. Products targeted at children were identified, divided into eight food groups and compared for their nutritional content per 100 g/ml and the presence of nutrient claims using the Mann-Whitney U test (P<0·05). Of the 535 food products targeted at children (9·5 % of all products), 270 (50·5 %) displayed nutrient claims on their labels. Children's products with nutrient claims had either a similar or worse nutritional content than their counterparts without nutrient claims. The major differences among groups were found in Group 8 (e.g. sauces and ready meals), in which children's products bearing nutrient claims had higher energy, carbohydrate, Na and total and SFA content per 100 g/ml than products without nutrient claims (P<0·05). This suggests that, to prevent misleading parents who are seeking healthier products for their children, the regulation on the use of nutrient claims should be revised, so that only products with appropriate nutrient profiles are allowed to display them. PMID:27040439

  9. Targeted Gene Delivery to the Enteric Nervous System Using AAV: A Comparison Across Serotypes and Capsid Mutants

    PubMed Central

    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

    2015-01-01

    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 mm2. 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. PMID:25592336

  10. Comparison Between Experiments and Molecular Dynamic Simulations of Spallation Induced by Ultra-Short Laser Shock on Micrometric Tantalum Targets

    NASA Astrophysics Data System (ADS)

    Cuq-Lelandais, J.-P.; Boustie, M.; Soulard, L.; Berthe, L.; Sollier, A.; Bontaz-Carion, J.; Combis, P.; de Rességuier, T.; Lescoute, E.

    2009-12-01

    Shock wave propagation and the spallation within materials induced by laser shock have been investigated for roughly two decades. With the latest laser technologies evolution, one can access to shorter regimes in durations, going below the picosecond range. Shots performed with the LULI 100 TW facility evidence the possibility to obtain spallation in a few microns thick metallic target. Such conditions provide an experimental data layout which may be directly comparable with molecular dynamic simulations reachable to these scales. Molecular dynamic simulations on a single crystal of Tantalum have been performed with the CEA TERA 10 computer. First, the Hugoniot calculated by the equilibrium molecular dynamics has been compared with experimental data to check the potential (EAM) relevance to reproduce the shock wave propagation. Then, large scale simulations on a micrometric target have been performed. We have observed the microscopic ductile damage process, the pore apparition and their time and space evolution. The results are compared with experimental results and classical one-dimensional hydrodynamic simulations.

  11. 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.

  12. Comparison of induced versus natural regulatory T cells of the same TCR specificity for induction of tolerance to an environmental antigen.

    PubMed

    Huang, Hui; Ma, Yanna; Dawicki, Wojciech; Zhang, Xiaobei; Gordon, John R

    2013-08-01

    Recent evidence shows that natural CD25(+)Foxp3(+) regulatory T cells (nTreg) and induced CD25(+)Foxp3(+) regulatory T cells (iTreg) both contribute to tolerance in mouse models of colitis and asthma, but there is little evidence regarding their relative contributions to this tolerance. We compared the abilities of nTreg and iTreg, both from OVA-TCR-transgenic OTII mice, to mediate tolerance in OVA-asthmatic C57BL/6 mice. The iTreg were differentiated from Th2 effector T cells by exposure to IL-10-differentiated dendritic cells (DC10) in vitro or in vivo, whereas we purified nTreg from allergen-naive mice and exposed them to DC10 before use. Each Treg population was subsequently repurified and tested for its therapeutic efficacy in vitro and in vivo. DC10 engaged the nTreg in a cognate fashion in Forster (or fluorescence) resonance energy transfer assays, and these nTreg reduced in vitro OVA-asthmatic Th2 effector T cell responses by 41-56%, whereas the comparator iTreg reduced these responses by 72-86%. Neutralization of IL-10, but not TGF-β, eliminated the suppressive activities of iTreg but not nTreg. Delivery of 5 × 10(5) purified nTreg reduced allergen challenge-induced airway IL-4 (p ≤ 0.03) and IL-5 (p ≤ 0.001) responses of asthmatic recipients by ≤ 23% but did not affect airway hyperresponsiveness or IgE levels, whereas equal numbers of iTreg of identical TCR specificity reduced all airway responses to allergen challenge by 82-96% (p ≤ 0.001) and fully normalized airway hyperresponsiveness. These data confirm that allergen-specific iTreg and nTreg have active roles in asthma tolerance and that iTreg are substantially more tolerogenic in this setting. PMID:23817420

  13. Comparison of Diagnostic Accuracy of PCR Targeting the 47-Kilodalton Protein Membrane Gene of Treponema pallidum and PCR Targeting the DNA Polymerase I Gene: Systematic Review and Meta-analysis.

    PubMed

    Gayet-Ageron, Angèle; Combescure, Christophe; Lautenschlager, Stephan; Ninet, Béatrice; Perneger, Thomas V

    2015-11-01

    Treponema pallidum PCR (Tp-PCR) testing now is recommended as a valid tool for the diagnosis of primary or secondary syphilis. The objectives were to systematically review and determine the optimal specific target gene to be used for Tp-PCR. Comparisons of the performance of the two main targets are tpp47 and polA genes were done using meta-analysis. Three electronic bibliographic databases, representing abstract books from five conferences specialized in infectious diseases from January 1990 to March 2015, were searched. Search keywords included ("syphilis" OR "Treponema pallidum" OR "neurosyphilis") AND ("PCR" OR "PCR" OR "molecular amplification"). We included diagnostic studies assessing the performance of Tp-PCR targeting tpp47 (tpp47-Tp-PCR) or the polA gene (polA-Tp-PCR) in ulcers from early syphilis. All studies were assessed against quality criteria using the QUADAS-2 tool. Of 37 studies identified, 62.2% were judged at low risk of bias or applicability. Most used the U.S. Centers for Disease Control and Prevention (CDC) case definitions for primary or secondary (early) syphilis (89.2%; n = 33); 15 (40.5%) used darkfield microscopy (DFM). We did not find differences in sensitivity and specificity between the two Tp-PCR methods in the subgroup of studies using adequate reference tests. Among studies using DFM as the reference test, sensitivities were 79.8% (95% confidence intervals [CI], 72.7 to 85.4%) and 71.4% (46.0 to 88.0%) for tpp47-Tp-PCR and polA-Tp-PCR (P = 0.217), respectively; respective specificities were 95.3% (93.5 to 96.6%) and 93.7% (91.8 to 95.2%) (P = 0.304). Our findings suggest that the two Tp-PCR methods have similar accuracy and could be used interchangeably. PMID:26311859

  14. Comparison of planning target volumes based on three-dimensional and four-dimensional CT imaging of thoracic esophageal cancer

    PubMed Central

    Wang, Wei; Li, Jianbin; Zhang, Yingjie; Shao, Qian; Xu, Min; Fan, Tingyong; Wang, Jinzhi

    2016-01-01

    Background and purpose To investigate the definition of planning target volumes (PTVs) based on four-dimensional computed tomography (4DCT) compared with conventional PTV definition and PTV definition using asymmetrical margins for thoracic primary esophageal cancer. Materials and methods Forty-three patients with esophageal cancer underwent 3DCT and 4DCT simulation scans during free breathing. The motions of primary tumors located in the proximal (group A), middle (group B), and distal (group C) thoracic esophagus were obtained from the 4DCT scans. PTV3D was defined on 3DCT using the tumor motion measured based on 4DCT, PTV conventional (PTVconv) was defined on 3DCT by adding a 1.0 cm margin to the clinical target volume, and PTV4D was defined as the union of the target volumes contoured on the ten phases of the 4DCT images. The centroid positions, volumetric differences, and dice similarity coefficients were evaluated for all PTVs. Results The median centroid shifts between PTV3D and PTV4D and between PTVconv and PTV4D in all three dimensions were <0.3 cm for the three groups. The median size ratios of PTV4D to PTV3D were 0.80, 0.88, and 0.71, and PTV4D to PTVconv were 0.67, 0.73, and 0.76 (χ2=−3.18, −2.98, and −3.06; P=0.001, 0.003, and 0.002) for groups A, B, and C, respectively. The dice similarity coefficients were 0.87, 0.90, and 0.81 between PTV4D and PTV3D and 0.80, 0.84, and 0.83 between PTV4D and PTVconv (χ2 =−3.18, −2.98, and −3.06; P=0.001, 0.003, and 0.002) for groups A, B, and C, respectively. The difference between the degree of inclusion of PTV4D in PTV3D and that of PTV4D in PTVconv was <2% for all groups. Compared with PTVconv, the amount of irradiated normal tissue for PTV3D was decreased by 11.81% and 11.86% in groups A and B, respectively, but was increased by 2.93% in group C. Conclusion For proximal and middle esophageal cancer, 3DCT-based PTV using asymmetrical margins provides good coverage of PTV4D; however, for distal

  15. SRD: a Staphylococcus regulatory RNA database.

    PubMed

    Sassi, Mohamed; Augagneur, Yoann; Mauro, Tony; Ivain, Lorraine; Chabelskaya, Svetlana; Hallier, Marc; Sallou, Olivier; Felden, Brice

    2015-05-01

    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

  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. Comparison of Control Approaches in Genetic Regulatory Networks by Using Stochastic Master Equation Models, Probabilistic Boolean Network Models and Differential Equation Models and Estimated Error Analyzes

    NASA Astrophysics Data System (ADS)

    Caglar, Mehmet Umut; Pal, Ranadip

    2011-03-01

    Central dogma of molecular biology states that ``information cannot be transferred back from protein to either protein or nucleic acid''. However, this assumption is not exactly correct in most of the cases. There are a lot of feedback loops and interactions between different levels of systems. These types of interactions are hard to analyze due to the lack of cell level data and probabilistic - nonlinear nature of interactions. Several models widely used to analyze and simulate these types of nonlinear interactions. Stochastic Master Equation (SME) models give probabilistic nature of the interactions in a detailed manner, with a high calculation cost. On the other hand Probabilistic Boolean Network (PBN) models give a coarse scale picture of the stochastic processes, with a less calculation cost. Differential Equation (DE) models give the time evolution of mean values of processes in a highly cost effective way. The understanding of the relations between the predictions of these models is important to understand the reliability of the simulations of genetic regulatory networks. In this work the success of the mapping between SME, PBN and DE models is analyzed and the accuracy and affectivity of the control policies generated by using PBN and DE models is compared.

  18. 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

  19. Comparison of nanoparticle penetration into solid tumors and sites of inflammation: studies using targeted and nontargeted liposomes

    PubMed Central

    Poh, Scott; Chelvam, Venkatesh; Low, Philip S

    2015-01-01

    Aim: The vast majority of nanomedicine research is focused on the use of nanoparticles for the diagnosis and treatment of cancer. However, the dense extracellular matrix of solid tumors restricts nanoparticle penetration, raising the question of whether the best applications of nanomedicines lie in oncology. Materials & methods: In this study, the uptake of folate-conjugated liposomes was compared between folate receptor-expressing tumors and folate receptor+ inflammatory lesions within the same mouse. Results: We demonstrate here that both folate-targeted and nontargeted liposomes accumulate more readily at sites of inflammation than in solid tumors. Conclusion: These data suggest that nanosized imaging and therapeutic agents may be better suited for the treatment and diagnosis of inflammatory/autoimmune diseases than cancer. PMID:25996118

  20. Comparison of radiohaloanalogues of meta-iodobenzylguanidine (MIBG) for a combined gene- and targeted radiotherapy approach to bladder carcinoma.

    PubMed

    Fullerton, Natasha E; Boyd, Marie; Ross, Susan C; Pimlott, Sally L; Babich, John; Kirk, David; Zalutsky, Michael R; Mairs, Robert J

    2005-11-01

    Targeted radiotherapy using radiolabelled meta-iodobenzylguanidine (MIBG) is a promising treatment option for bladder cancer, restricting the effects of radiotherapy to malignant cells thereby increasing efficacy and decreasing morbidity of radiotherapy. We investigated the efficacy of a combined gene therapy and targeted radiotherapy approach for bladder cancer using radiolabelled MIBG. The effectiveness of alternative radiohalogens and alternative preparations of radiolabelled MIBG for this therapeutic strategy were compared. Bladder cancer cells, EJ138, were transfected with a gene encoding the noradrenaline transporter (NAT) under the control of a tumour specific telomerase promoter, enabling them to actively take up radiolabelled MIBG. This resulted in tumour-specific cell kill. Uptake and retention of radioactivity in cells transfected with the NAT gene were compared with that obtained in cells transfected with the sodium iodide symporter (NIS) gene. Substantially greater uptake and longer retention of radioactivity in NAT-transfected cells was observed. Carrier-added (c.a.) [131I]MIBG, no-carrier added (n.c.a.) [131I]MIBG, and [211At]-labelled benzylguanidine (i.e. [211At] meta-astatobenzylguanidine (MABG)) were compared with respect to efficiency of induction of cell kill. N.c.a[(131)I]MIBG was more cytotoxic than c.a.[131I]MIBG. However, the alpha-emitter [211At]MABG was, by three orders of magnitude, more effective in causing tumour cell kill than the beta-emitter [131I]MIBG. We conclude that NAT gene transfer combined with the administration of n.c.a.[131I]MIBG or [211At]MABG, is a promising novel treatment approach for bladder cancer therapy. PMID:16787344

  1. Comprehensive comparison of the interaction of the E2 master regulator with its cognate target DNA sites in 73 human papillomavirus types by sequence statistics

    PubMed Central

    Sánchez, Ignacio E.; Dellarole, Mariano; Gaston, Kevin; de Prat Gay, Gonzalo

    2008-01-01

    Mucosal human papillomaviruses (HPVs) are etiological agents of oral, anal and genital cancer. Properties of high- and low-risk HPV types cannot be reduced to discrete molecular traits. The E2 protein regulates viral replication and transcription through a finely tuned interaction with four sites at the upstream regulatory region of the genome. A computational study of the E2–DNA interaction in all 73 types within the alpha papillomavirus genus, including all known mucosal types, indicates that E2 proteins have similar DNA discrimination properties. Differences in E2–DNA interaction among HPV types lie mostly in the target DNA sequence, as opposed to the amino acid sequence of the conserved DNA-binding alpha helix of E2. Sequence logos of natural and in vitro selected sites show an asymmetric pattern of conservation arising from indirect readout, and reveal evolutionary pressure for a putative methylation site. Based on DNA sequences only, we could predict differences in binding energies with a standard deviation of 0.64 kcal/mol. These energies cluster into six discrete affinity hierarchies and uncovered a fifth E2-binding site in the genome of six HPV types. Finally, certain distances between sites, affinity hierarchies and their eventual changes upon methylation, are statistically associated with high-risk types. PMID:18084026

  2. Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes.

    PubMed

    Abelin, Jennifer G; Patel, Jinal; Lu, Xiaodong; Feeney, Caitlin M; Fagbami, Lola; Creech, Amanda L; Hu, Roger; Lam, Daniel; Davison, Desiree; Pino, Lindsay; Qiao, Jana W; Kuhn, Eric; Officer, Adam; Li, Jianxue; Abbatiello, Susan; Subramanian, Aravind; Sidman, Richard; Snyder, Evan; Carr, Steven A; Jaffe, Jacob D

    2016-05-01

    Profiling post-translational modifications represents an alternative dimension to gene expression data in characterizing cellular processes. Many cellular responses to drugs are mediated by changes in cellular phosphosignaling. We sought to develop a common platform on which phosphosignaling responses could be profiled across thousands of samples, and created a targeted MS assay that profiles a reduced-representation set of phosphopeptides that we show to be strong indicators of responses to chemical perturbagens.To develop the assay, we investigated the coordinate regulation of phosphosites in samples derived from three cell lines treated with 26 different bioactive small molecules. Phosphopeptide analytes were selected from these discovery studies by clustering and picking 1 to 2 proxy members from each cluster. A quantitative, targeted parallel reaction monitoring assay was developed to directly measure 96 reduced-representation probes. Sample processing for proteolytic digestion, protein quantification, peptide desalting, and phosphopeptide enrichment have been fully automated, making possible the simultaneous processing of 96 samples in only 3 days, with a plate phosphopeptide enrichment variance of 12%. This highly reproducible process allowed ∼95% of the reduced-representation phosphopeptide probes to be detected in ∼200 samples.The performance of the assay was evaluated by measuring the probes in new samples generated under treatment conditions from discovery experiments, recapitulating the observations of deeper experiments using a fraction of the analytical effort. We measured these probes in new experiments varying the treatments, cell types, and timepoints to demonstrate generalizability. We demonstrated that the assay is sensitive to disruptions in common signaling pathways (e.g. MAPK, PI3K/mTOR, and CDK). The high-throughput, reduced-representation phosphoproteomics assay provides a platform for the comparison of perturbations across a range of

  3. 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

  4. Evaluation and comparison of two commercially available targeted next-generation sequencing platforms to assist oncology decision making

    PubMed Central

    Weiss, Glen J; Hoff, Brandi R; Whitehead, Robert P; Sangal, Ashish; Gingrich, Susan A; Penny, Robert J; Mallery, David W; Morris, Scott M; Thompson, Eric J; Loesch, David M; Khemka, Vivek

    2015-01-01

    Background It is widely acknowledged that there is value in examining cancers for genomic aberrations via next-generation sequencing (NGS). How commercially available NGS platforms compare with each other, and the clinical utility of the reported actionable results, are not well known. During the course of the current study, the Foundation One (F1) test generated data on a combination of somatic mutations, insertion and deletion polymorphisms, chromosomal abnormalities, and deoxyribonucleic acid (DNA) copy number changes at ~250× coverage, while the Paradigm Cancer Diagnostic (PCDx) test generated the same type of data at >5,000× coverage, plus provided messenger RNA (mRNA) expression levels. We sought to compare and evaluate paired formalin-fixed paraffin-embedded tumor tissue using these two platforms. Methods Samples from patients with advanced solid tumors were submitted to both the F1 and PCDx vendors for NGS analysis. Turnaround time (TAT) was calculated. Biomarkers were considered clinically actionable if they had a published association with treatment response in humans and were assigned to the following categories: commercially available drug (CA), clinical trial drug (CT), or neither option (hereafter referred to as “None”). Results The demographics of the 21 unique patient tumor samples included ten men and eleven women, with a median age of 56 years. Due to insufficient archival tissue from the same collection period, in one case, we used samples from different collections. PCDx reported first results faster than F1 in 20 cases. When received at both vendors on the same day, PCDx reported first results for 14 of 15 cases, with a median TAT of 9 days earlier than F1 (P<0.0001). Categorization of CA compared to CT and none significantly favored PCDx (P=0.012). Conclusion In the current analysis, commercially available NGS platforms provided clinically relevant actionable targets (CA or CT) in 47%–67% of diverse cancer types. In the samples

  5. Tumor Progression Locus 2 (Tpl2) Activates the Mammalian Target of Rapamycin (mTOR) Pathway, Inhibits Forkhead Box P3 (FoxP3) Expression, and Limits Regulatory T Cell (Treg) Immunosuppressive Functions.

    PubMed

    Li, Xin; Acuff, Nicole V; Peeks, Angela R; Kirkland, Rebecca; Wyatt, Kara D; Nagy, Tamas; Watford, Wendy T

    2016-08-01

    The serine/threonine kinase tumor progression locus 2 (Tpl2, also known as Map3k8/Cot) is a potent inflammatory mediator that drives the production of TNFα, IL-1β, and IFNγ. We previously demonstrated that Tpl2 regulates T cell receptor (TCR) signaling and modulates T helper cell differentiation. However, very little is known about how Tpl2 modulates the development of regulatory T cells (Tregs). Tregs are a specialized subset of T cells that express FoxP3 and possess immunosuppressive properties to limit excess inflammation. Because of the documented role of Tpl2 in promoting inflammation, we hypothesized that Tpl2 antagonizes Treg development and immunosuppressive function. Here we demonstrate that Tpl2 constrains the development of inducible Tregs. Tpl2(-/-) naïve CD4(+) T cells preferentially develop into FoxP3(+) inducible Tregs in vitro as well as in vivo in a murine model of ovalbumin (OVA)-induced systemic tolerance. Treg biasing of Tpl2(-/-) T cells depended on TCR signal strength and corresponded with reduced activation of the mammalian target of rapamycin (mTOR) pathway. Importantly, Tpl2(-/-) Tregs have basally increased expression of FoxP3 and immunosuppressive molecules, IL-10 and cytotoxic T lymphocyte-associated protein 4 (CTLA-4). Furthermore, they were more immunosuppressive in vivo in a T cell transfer model of colitis, as evidenced by reduced effector T cell accumulation, systemic production of inflammatory cytokines, and colonic inflammation. These results demonstrate that Tpl2 promotes inflammation in part by constraining FoxP3 expression and Treg immunosuppressive functions. Overall, these findings suggest that Tpl2 inhibition could be used to preferentially drive Treg induction and thereby limit inflammation in a variety of autoimmune diseases. PMID:27261457

  6. 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.

  7. 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

  8. 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

  9. Global and regional validation of the Collection 6 MODIS dark target aerosol products, and comparison to Collection 5

    NASA Astrophysics Data System (ADS)

    Munchak, L. A.; Levy, R. C.; Mattoo, S.

    2014-12-01

    The MODIS Collection 6 (C6) dark targets aerosol algorithms include several updates, including multiple wind speed look up tables over ocean and improved sensor calibration. We analyze the entirety of the MODIS-Aqua aerosol record against AERONET to characterize uncertainty in the products, and relate the new collection to the well-characterized Collection 5 (C5) products to understand specific improvements. Over land, ~70% of high quality AOD retrievals at 0.55 μm are within the C5 expected error bounds, which is comparable to C5; however, a slight overestimation of AOD at low optical depths and a slight underestimation at high optical depths that was observed in C5 has been eliminated in C6. The highest agreement with AERONET occurs in the Eastern U.S. and Europe. Regions with large surface reflectance, such as the Western U.S., or higher aerosol loading, including much of Africa and South America, remain a challenge. Over ocean, the inclusion of wind speed in the surface characterization has removed a wind speed dependant bias, and globally, ~63% of high quality AOD retrievals at 0.55 μm are within the C5 expected error bounds. The dust outflow regions off the coast of Africa show the poorest agreement with AERONET. The aerosol products validate acceptably for science, though users should be aware of some regional biases we present in this work.

  10. 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.

  11. 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. PMID:24607320

  12. 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

  13. Comparison of two poultry litter qPCR assays targeting the 16S rRNA gene of Brevibacterium sp.

    PubMed

    Ryu, Hodon; Elk, Michael; Khan, Izhar U H; Harwood, Valerie J; Molina, Marirosa; Edge, Thomas A; Domingo, Jorge Santo

    2014-01-01

    Chicken feces commonly contain human pathogens and are also important sources of fecal pollution in environmental waters. Consequently, methods that can detect chicken fecal pollution are needed in public health and environmental monitoring studies. In this study, we compared a previously developed SYBR green qPCR assay (LA35) to a novel TaqMan qPCR assay (CL) for the environmental detection of poultry-associated fecal pollution. We tested both assays against chicken litter (n = 40), chicken fecal samples (n = 186), non-chicken fecal sources (n = 484), and environmental water samples (n = 323). Most chicken litter samples (i.e., ≥ 98%) were positive for both assays with relatively high signal intensities, whereas only 23% and 12% of poultry fecal samples (n = 186) were positive with the LA35 and the CL assays, respectively. Data using fecal samples from non-target animal species showed that the assays are highly host-associated (≥ 95%). Bayesian statistical models showed that the two assays are associated with relatively low probability of false-positive and false-negative signals in water samples. The CL marker had a lower prevalence than the LA35 assay when tested against environmental water samples (i.e., 21% vs. 31% positive signals). However, by combining the results from the two assays the detection levels increased to 41%, suggesting that using multiple assays can improve the detection of chicken-fecal pollution in environmental waters. PMID:24169514

  14. 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

  15. Comparison of Diagnostic Accuracy of PCR Targeting the 47-Kilodalton Protein Membrane Gene of Treponema pallidum and PCR Targeting the DNA Polymerase I Gene: Systematic Review and Meta-analysis

    PubMed Central

    Combescure, Christophe; Lautenschlager, Stephan; Ninet, Béatrice; Perneger, Thomas V.

    2015-01-01

    Treponema pallidum PCR (Tp-PCR) testing now is recommended as a valid tool for the diagnosis of primary or secondary syphilis. The objectives were to systematically review and determine the optimal specific target gene to be used for Tp-PCR. Comparisons of the performance of the two main targets are tpp47 and polA genes were done using meta-analysis. Three electronic bibliographic databases, representing abstract books from five conferences specialized in infectious diseases from January 1990 to March 2015, were searched. Search keywords included (“syphilis” OR “Treponema pallidum” OR “neurosyphilis”) AND (“PCR” OR “PCR” OR “molecular amplification”). We included diagnostic studies assessing the performance of Tp-PCR targeting tpp47 (tpp47-Tp-PCR) or the polA gene (polA-Tp-PCR) in ulcers from early syphilis. All studies were assessed against quality criteria using the QUADAS-2 tool. Of 37 studies identified, 62.2% were judged at low risk of bias or applicability. Most used the U.S. Centers for Disease Control and Prevention (CDC) case definitions for primary or secondary (early) syphilis (89.2%; n = 33); 15 (40.5%) used darkfield microscopy (DFM). We did not find differences in sensitivity and specificity between the two Tp-PCR methods in the subgroup of studies using adequate reference tests. Among studies using DFM as the reference test, sensitivities were 79.8% (95% confidence intervals [CI], 72.7 to 85.4%) and 71.4% (46.0 to 88.0%) for tpp47-Tp-PCR and polA-Tp-PCR (P = 0.217), respectively; respective specificities were 95.3% (93.5 to 96.6%) and 93.7% (91.8 to 95.2%) (P = 0.304). Our findings suggest that the two Tp-PCR methods have similar accuracy and could be used interchangeably. PMID:26311859

  16. Variation in adverse drug reactions listed in product information for antidepressants and anticonvulsants, between the USA and Europe: a comparison review of paired regulatory documents

    PubMed Central

    Cornelius, Victoria R; Liu, Kun; Peacock, Janet; Sauzet, Odile

    2016-01-01

    Objective To compare consistency of adverse drug reaction (ADR) data in publicly available product information documents for brand drugs, between the USA and Europe. To assess the usefulness of information for prescribers and patients. Design A comparison review of product information documents for antidepressants and anticonvulsants concurrently marketed by the same pharmaceutical company in the USA and Europe. Setting For each drug, data were extracted from the US Product Inserts and the European Summary of Product Characteristics documents between 09/2013 and 01/2015. Participants Individuals contributing ADR information to product information documents. Main outcomes measures All ADRs reported in product information sections 5 and 6 (USA), and 4·4 and 4·8 (Europe). Results Twelve brand drugs—24 paired documents—were included. On average, there were 77 more ADRs reported in the USA compared with in the European product information document, with a median number of 201 ADRs (range: 65–425) and 114 (range: 56–265), respectively. More product information documents in the USA reported information on the source of evidence (10 vs 5) and risk (9 vs 5) for greater than 80% of ADRs included in the document. There was negligible information included regarding duration, severity, reversibility or recurrence of ADRs. On average, only 29% of ADR terms were reported in both paired documents. Conclusions Product information documents contained a large number of ADRs, but lacked contextual data and information important to patients and prescribers, such as duration, severity and reversibility. The ADR profile was found to be inconsistently reported between the USA and Europe, for the same drug. Identifying, selecting, summarising and presenting multidimensional harm data should be underpinned by practical evidence-based guidelines. In order for prescribers to provide considered risk-benefit advice across competing drug therapies to patients, they need access to

  17. Computational analysis and ratiometric comparison approaches aimed to assist column selection in hydrophilic interaction liquid chromatography-tandem mass spectrometry targeted metabolomics.

    PubMed

    Sampsonidis, Ioannis; Witting, Michael; Koch, Wendelin; Virgiliou, Christina; Gika, Helen G; Schmitt-Kopplin, Philippe; Theodoridis, Georgios A

    2015-08-01

    In the present work two different approaches, a semi-quantitative and a Derringer function approach, were developed to assist column selection for method development in targeted metabolomics. These approaches were applied in the performance assessment of three HILIC columns with different chemistries (an amide, a diol and a zwitterionic phase). This was the first step for the development of a HILIC UPLC-MS/MS method that should be capable to analyze a large number of polar metabolites. Two gradient elution profiles and two mobile phase pH values were tested for the analysis of multi-analyte mixtures. Acquired chromatographic data were firstly treated by a ratiometric, "semi-quantitative" approach which quantifies various overall analysis parameters (e.g. the percent of detected compounds, retentivity and resolved critical pairs). These parameters were used to assess chromatographic performance in a rather conventional/traditional and cumbersome/labor-intensive way. Secondly, a comprehensive and automated comparison of the three columns was performed by monitoring several well-known chromatographic parameters (peak width, resolution, tailing factor, etc.) using a lab-built programming script which calculates overall desirability utilizing Derringer functions. Derringer functions exhibit the advantage that column performance is ultimately expressed in an objective single and quantitative value which can be easily interpreted. In summary, results show that each column exhibits unique strengths in metabolic profiling of polar compounds. The applied methodology proved useful for the selection of the most effective chromatographic system during method development for LC-MS/MS targeted metabolomics, while it could further assist in the selection of chromatographic conditions for the development of multi-analyte methods. PMID:26122858

  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

    2016-01-01

    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 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. PMID:27167254

  19. Genome-wide map of regulatory interactions in the human genome.

    PubMed

    Heidari, Nastaran; Phanstiel, Douglas H; He, Chao; Grubert, Fabian; Jahanbani, Fereshteh; Kasowski, Maya; Zhang, Michael Q; Snyder, Michael P

    2014-12-01

    Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer-promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus. PMID:25228660

  20. 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

  1. A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo

    NASA Technical Reports Server (NTRS)

    Davidson, Eric H.; Rast, Jonathan P.; Oliveri, Paola; Ransick, Andrew; Calestani, Cristina; Yuh, Chiou-Hwa; Minokawa, Takuya; Amore, Gabriele; Hinman, Veronica; Arenas-Mena, Cesar; Otim, Ochan; Brown, C. Titus; Livi, Carolina B.; Lee, Pei Yun; Revilla, Roger; Schilstra, Maria J.; Clarke, Peter J C.; Rust, Alistair G.; Pan, Zhengjun; Arnone, Maria I.; Rowen, Lee; Cameron, R. Andrew; McClay, David R.; Hood, Leroy; Bolouri, Hamid

    2002-01-01

    We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.caltech.edu/mirsky/endomeso.htm (End-mes Gene Network Update) for the latest version. The network contains over 40 genes at present, many newly uncovered in the course of this work, and most encoding DNA-binding transcriptional regulatory factors. The architecture of the network was approached initially by construction of a logic model that integrated the extensive experimental evidence now available on endomesoderm specification. The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network. Five kinds of perturbation have been applied: (1) use of morpholino antisense oligonucleotides targeted to many of the key regulatory genes in the network; (2) transformation of other regulatory factors into dominant repressors by construction of Engrailed repressor domain fusions; (3) ectopic expression of given regulatory factors, from genetic expression constructs and from injected mRNAs; (4) blockade of the beta-catenin/Tcf pathway by introduction of mRNA encoding the intracellular domain of cadherin; and (5) blockade of the Notch signaling pathway by introduction of mRNA encoding the extracellular domain of the Notch receptor. The network model predicts the cis-regulatory inputs that link each gene into the network. Therefore, its architecture is testable by cis-regulatory analysis. Strongylocentrotus purpuratus and Lytechinus variegatus genomic BAC recombinants that include a large number of the genes in the network have been sequenced and annotated. Tests of the cis-regulatory predictions of

  2. Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice

    PubMed Central

    Smita, Shuchi; Katiyar, Amit; Chinnusamy, Viswanathan; Pandey, Dev M.; Bansal, Kailash C.

    2015-01-01

    MYB transcription factor (TF) is one of the largest TF families and regulates defense responses to various stresses, hormone signaling as well as many metabolic and developmental processes in plants. Understanding these regulatory hierarchies of gene expression networks in response to developmental and environmental cues is a major challenge due to the complex interactions between the genetic elements. Correlation analyses are useful to unravel co-regulated gene pairs governing biological process as well as identification of new candidate hub genes in response to these complex processes. High throughput expression profiling data are highly useful for construction of co-expression networks. In the present study, we utilized transcriptome data for comprehensive regulatory network studies of MYB TFs by “top-down” and “guide-gene” approaches. More than 50% of OsMYBs were strongly correlated under 50 experimental conditions with 51 hub genes via “top-down” approach. Further, clusters were identified using Markov Clustering (MCL). To maximize the clustering performance, parameter evaluation of the MCL inflation score (I) was performed in terms of enriched GO categories by measuring F-score. Comparison of co-expressed cluster and clads analyzed from phylogenetic analysis signifies their evolutionarily conserved co-regulatory role. We utilized compendium of known interaction and biological role with Gene Ontology enrichment analysis to hypothesize function of coexpressed OsMYBs. In the other part, the transcriptional regulatory network analysis by “guide-gene” approach revealed 40 putative targets of 26 OsMYB TF hubs with high correlation value utilizing 815 microarray data. The putative targets with MYB-binding cis-elements enrichment in their promoter region, functional co-occurrence as well as nuclear localization supports our finding. Specially, enrichment of MYB binding regions involved in drought-inducibility implying their regulatory role in drought

  3. Computational architecture of the yeast regulatory network

    NASA Astrophysics Data System (ADS)

    Maslov, Sergei; Sneppen, Kim

    2005-12-01

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

  4. 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

  5. Integrated-boost IMRT or 3-D-CRT using FET-PET based auto-contoured target volume delineation for glioblastoma multiforme - a dosimetric comparison

    PubMed Central

    2009-01-01

    Background Biological brain tumor imaging using O-(2-[18F]fluoroethyl)-L-tyrosine (FET)-PET combined with inverse treatment planning for locally restricted dose escalation in patients with glioblastoma multiforme seems to be a promising approach. The aim of this study was to compare inverse with forward treatment planning for an integrated boost dose application in patients suffering from a glioblastoma multiforme, while biological target volumes are based on FET-PET and MRI data sets. Methods In 16 glioblastoma patients an intensity-modulated radiotherapy technique comprising an integrated boost (IB-IMRT) and a 3-dimensional conventional radiotherapy (3D-CRT) technique were generated for dosimetric comparison. FET-PET, MRI and treatment planning CT (P-CT) were co-registrated. The integrated boost volume (PTV1) was auto-contoured using a cut-off tumor-to-brain ratio (TBR) of ≥ 1.6 from FET-PET. PTV2 delineation was MRI-based. The total dose was prescribed to 72 and 60 Gy for PTV1 and PTV2, using daily fractions of 2.4 and 2 Gy. Results After auto-contouring of PTV1 a marked target shape complexity had an impact on the dosimetric outcome. Patients with 3-4 PTV1 subvolumes vs. a single volume revealed a significant decrease in mean dose (67.7 vs. 70.6 Gy). From convex to complex shaped PTV1 mean doses decreased from 71.3 Gy to 67.7 Gy. The homogeneity and conformity for PTV1 and PTV2 was significantly improved with IB-IMRT. With the use of IB-IMRT the minimum dose within PTV1 (61.1 vs. 57.4 Gy) and PTV2 (51.4 vs. 40.9 Gy) increased significantly, and the mean EUD for PTV2 was improved (59.9 vs. 55.3 Gy, p < 0.01). The EUD for PTV1 was only slightly improved (68.3 vs. 67.3 Gy). The EUD for the brain was equal with both planning techniques. Conclusion In the presented planning study the integrated boost concept based on inversely planned IB-IMRT is feasible. The FET-PET-based automatically contoured PTV1 can lead to very complex geometric configurations, limiting the

  6. Validation of targeted next-generation sequencing for RAS mutation detection in FFPE colorectal cancer tissues: comparison with Sanger sequencing and ARMS-Scorpion real-time PCR

    PubMed Central

    Gao, Jie; Wu, Huanwen; Wang, Li; Zhang, Hui; Duan, Huanli; Lu, Junliang; Liang, Zhiyong

    2016-01-01

    Objective To validate the targeted next-generation sequencing (NGS) platform-Ion Torrent PGM for KRAS exon 2 and expanded RAS mutations detection in formalin-fixed paraffin-embedded (FFPE) colorectal cancer (CRC) specimens, with comparison of Sanger sequencing and ARMS-Scorpion real-time PCR. Setting Beijing, China. Participants 51 archived FFPE CRC samples (36 men, 15 women) were retrospectively randomly selected and then checked by an experienced pathologist for sequencing based on histological confirmation of CRC and availability of sufficient tissue. Methods RAS mutations were detected in the 51 FFPE CRC samples by PGM analysis, Sanger sequencing and the Therascreen KRAS assay, respectively. Agreement among the 3 methods was assessed. Assay sensitivity was further determined by sequencing serially diluted DNA from FFPE cell lines with known mutation statuses. Results 13 of 51 (25.5%) cases had a mutation in KRAS exon 2, as determined by PGM analysis. PGM analysis showed 100% (51/51) concordance with Sanger sequencing (κ=1.000, 95% CI 1 to 1) and 98.04% (50/51) agreement with the Therascreen assay (κ=0.947, 95% CI 0.844 to 1) for detecting KRAS exon 2 mutations, respectively. The only discrepant case harboured a KRAS exon 2 mutation (c.37G>T) that was not covered by the Therascreen kit. The dilution series experiment results showed that PGM was able to detect KRAS mutations at a frequency of as low as 1%. Importantly, RAS mutations other than KRAS exon 2 mutations were also detected in 10 samples by PGM. Furthermore, mutations in other CRC-related genes could be simultaneously detected in a single test by PGM. Conclusions The targeted NGS platform is specific and sensitive for KRAS exon 2 mutation detection and is appropriate for use in routine clinical testing. Moreover, it is sample saving and cost-efficient and time-efficient, and has great potential for clinical application to expand testing to include mutations in RAS and other CRC-related genes. PMID

  7. 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)

  8. 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. PMID:20439753

  9. Interrogating Transcriptional Regulatory Sequences in Tol2-Mediated Xenopus Transgenics

    PubMed Central

    Loots, Gabriela G.; Bergmann, Anne; Hum, Nicholas R.; Oldenburg, Catherine E.; Wills, Andrea E.; Hu, Na; Ovcharenko, Ivan; Harland, Richard M.

    2013-01-01

    Identifying gene regulatory elements and their target genes in vertebrates remains a significant challenge. It is now recognized that transcriptional regulatory sequences are critical in orchestrating dynamic controls of tissue-specific gene expression during vertebrate development and in adult tissues, and that these elements can be positioned at great distances in relation to the promoters of the genes they control. While significant progress has been made in mapping DNA binding regions by combining chromatin immunoprecipitation and next generation sequencing, functional validation remains a limiting step in improving our ability to correlate in silico predictions with biological function. We recently developed a computational method that synergistically combines genome-wide gene-expression profiling, vertebrate genome comparisons, and transcription factor binding-site analysis to predict tissue-specific enhancers in the human genome. We applied this method to 270 genes highly expressed in skeletal muscle and predicted 190 putative cis-regulatory modules. Furthermore, we optimized Tol2 transgenic constructs in Xenopus laevis to interrogate 20 of these elements for their ability to function as skeletal muscle-specific transcriptional enhancers during embryonic development. We found 45% of these elements expressed only in the fast muscle fibers that are oriented in highly organized chevrons in the Xenopus laevis tadpole. Transcription factor binding site analysis identified >2 Mef2/MyoD sites within ∼200 bp regions in 6 of the validated enhancers, and systematic mutagenesis of these sites revealed that they are critical for the enhancer function. The data described herein introduces a new reporter system suitable for interrogating tissue-specific cis-regulatory elements which allows monitoring of enhancer activity in real time, throughout early stages of embryonic development, in Xenopus. PMID:23874664

  10. 3 CFR - Regulatory Review

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 3 The President 1 2010-01-01 2010-01-01 false Regulatory Review Presidential Documents Other Presidential Documents Memorandum of January 30, 2009 Regulatory Review Memorandum for the Heads of Executive Departments and Agencies For well over two decades, the Office of Information and Regulatory Affairs (OIRA) at the Office of Management...

  11. Asymmetric Regulation of Peripheral Genes by Two Transcriptional Regulatory Networks

    PubMed Central

    Li, Jing-Ru; Suzuki, Takahiro; Nishimura, Hajime; Kishima, Mami; Maeda, Shiori; Suzuki, Harukazu

    2016-01-01

    Transcriptional regulatory network (TRN) reconstitution and deconstruction occur simultaneously during reprogramming; however, it remains unclear how the starting and targeting TRNs regulate the induction and suppression of peripheral genes. Here we analyzed the regulation using direct cell reprogramming from human dermal fibroblasts to monocytes as the platform. We simultaneously deconstructed fibroblastic TRN and reconstituted monocytic TRN; monocytic and fibroblastic gene expression were analyzed in comparison with that of fibroblastic TRN deconstruction only or monocytic TRN reconstitution only. Global gene expression analysis showed cross-regulation of TRNs. Detailed analysis revealed that knocking down fibroblastic TRN positively affected half of the upregulated monocytic genes, indicating that intrinsic fibroblastic TRN interfered with the expression of induced genes. In contrast, reconstitution of monocytic TRN showed neutral effects on the majority of fibroblastic gene downregulation. This study provides an explicit example that demonstrates how two networks together regulate gene expression during cell reprogramming processes and contributes to the elaborate exploration of TRNs. PMID:27483142

  12. Regulatory affairs administration as regulatory policy determinant

    SciTech Connect

    Forcier, J.R.

    1984-05-10

    It is the thesis of this article that the processing of a utility company's regulation-related work, the supporting tasks and the manner in which they are completed, can and does have a significant impact on the final results or work product of the regulatory affairs function, including even, potentially, the action of the regulatory agency. The article is therefore full of practical pointers on how the interface with the regulatory authority can best be organized, managed, and carried through to the attainment of optimum results for the utility. 2 references.

  13. ENFORCEMENT TARGETING 2001

    EPA Science Inventory

    A GIS based targeting methodology which uses multi-media state and federal regulatory data to identify watersheds in Texas, Louisiana, Arkansas, Oklahoma, and New Mexico that are vulnerable to environmental damage and/or have high chemical emissions to the environment. The assess...

  14. 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...

  15. 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. PMID:22588784

  16. T follicular regulatory cells.

    PubMed

    Sage, Peter T; Sharpe, Arlene H

    2016-05-01

    Pathogen exposure elicits production of high-affinity antibodies stimulated by T follicular helper (Tfh) cells in the germinal center reaction. Tfh cells provide both costimulation and stimulatory cytokines to B cells to facilitate affinity maturation, class switch recombination, and plasma cell differentiation within the germinal center. Under normal circumstances, the germinal center reaction results in antibodies that precisely target foreign pathogens while limiting autoimmunity and excessive inflammation. In order to have this degree of control, the immune system ensures Tfh-mediated B-cell help is regulated locally in the germinal center. The recently identified T follicular regulatory (Tfr) cell subset can migrate to the germinal center and inhibit Tfh-mediated B-cell activation and antibody production. Although many aspects of Tfr cell biology are still unclear, recent data have begun to delineate the specialized roles of Tfr cells in controlling the germinal center reaction. Here we discuss the current understanding of Tfr-cell differentiation and function and how this knowledge is providing new insights into the dynamic regulation of germinal centers, and suggesting more efficacious vaccine strategies and ways to treat antibody-mediated diseases. PMID:27088919

  17. 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

  18. A Pan-Cancer Modular Regulatory Network Analysis to Identify Common and Cancer-Specific Network Components

    PubMed Central

    Knaack, Sara A; Siahpirani, Alireza Fotuhi; Roy, Sushmita

    2014-01-01

    Many human diseases including cancer are the result of perturbations to transcriptional regulatory networks that control context-specific expression of genes. A comparative approach across multiple cancer types is a powerful approach to illuminate the common and specific network features of this family of diseases. Recent efforts from The Cancer Genome Atlas (TCGA) have generated large collections of functional genomic data sets for multiple types of cancers. An emerging challenge is to devise computational approaches that systematically compare these genomic data sets across different cancer types that identify common and cancer-specific network components. We present a module- and network-based characterization of transcriptional patterns in six different cancers being studied in TCGA: breast, colon, rectal, kidney, ovarian, and endometrial. Our approach uses a recently developed regulatory network reconstruction algorithm, modular regulatory network learning with per gene information (MERLIN), within a stability selection framework to predict regulators for individual genes and gene modules. Our module-based analysis identifies a common theme of immune system processes in each cancer study, with modules statistically enriched for immune response processes as well as targets of key immune response regulators from the interferon regulatory factor (IRF) and signal transducer and activator of transcription (STAT) families. Comparison of the inferred regulatory networks from each cancer type identified a core regulatory network that included genes involved in chromatin remodeling, cell cycle, and immune response. Regulatory network hubs included genes with known roles in specific cancer types as well as genes with potentially novel roles in different cancer types. Overall, our integrated module and network analysis recapitulated known themes in cancer biology and additionally revealed novel regulatory hubs that suggest a complex interplay of immune response, cell

  19. 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

  20. 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. PMID:21487236

  1. 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 ...

  2. 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.

  3. Comparison of 3-D Multi-Lag Cross-Correlation and Speckle Brightness Aberration Correction Algorithms on Static and Moving Targets

    PubMed Central

    Ivancevich, Nikolas M.; Dahl, Jeremy J.; Smith, Stephen W.

    2010-01-01

    Phase correction has the potential to increase the image quality of 3-D ultrasound, especially transcranial ultrasound. We implemented and compared 2 algorithms for aberration correction, multi-lag cross-correlation and speckle brightness, using static and moving targets. We corrected three 75-ns rms electronic aberrators with full-width at half-maximum (FWHM) auto-correlation lengths of 1.35, 2.7, and 5.4 mm. Cross-correlation proved the better algorithm at 2.7 and 5.4 mm correlation lengths (P < 0.05). Static cross-correlation performed better than moving-target cross-correlation at the 2.7 mm correlation length (P < 0.05). Finally, we compared the static and moving-target cross-correlation on a flow phantom with a skull casting aberrator. Using signal from static targets, the correction resulted in an average contrast increase of 22.2%, compared with 13.2% using signal from moving targets. The contrast-to-noise ratio (CNR) increased by 20.5% and 12.8% using static and moving targets, respectively. Doppler signal strength increased by 5.6% and 4.9% for the static and moving-targets methods, respectively. PMID:19942503

  4. Nuclear Regulatory Commission Semiannual Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-20

    ...) 2010, less the amounts appropriated from the Nuclear Waste Fund, amounts appropriated for Waste... agenda on April 26, 2010 (75 FR 21960). For this edition of the NRC's regulatory agenda, the most... publication of the last NRC semiannual agenda on April 26, 2010 (75 FR 21960). Within each group, the...

  5. NRC regulatory agenda

    SciTech Connect

    Not Available

    1991-04-01

    The NRC Regulatory Agenda is a compilation of all rules on which the NRC has recently completed action or has proposed, or is considering action and all petitions for rulemaking which have been received by the Commission and are pending disposition by the Commission. The Regulatory Agenda is updated and issued each quarter.

  6. NRC regulatory agenda

    SciTech Connect

    Not Available

    1992-05-01

    The NRC Regulatory Agenda is a compilation of all rules on which the NRC has recently completed action, or has proposed action, or is considering action, and all petitions for rulemaking which have been received by the Commission and are pending disposition by the Commission. The Regulatory Agenda is updated and issued each quarter.

  7. NRC Regulatory Agenda

    SciTech Connect

    Not Available

    1991-10-01

    The NRC Regulatory Agenda is a compilation of all rules on which the NRC has recently completed action, or has proposed action, or is considering action, and all petitions for rulemaking which have been received by the Commission and are pending disposition by the Commission. The Regulatory Agenda is updated and issued each quarter.

  8. NRC Regulatory Agenda

    SciTech Connect

    Not Available

    1991-08-01

    The NRC Regulatory Agenda is a compilation of all rules on which the NRC has recently completed action or has proposed, or is considering action and all petitions for rulemaking which have been received by the commission and are pending disposition by the Commission. The Regulatory Agenda is updated and issued each quarter.

  9. NRC regulatory agenda

    SciTech Connect

    Not Available

    1993-04-01

    The NRC Regulatory Agenda is a compilation of all rules on which the NRC has recently completed action, or has proposed action, or is considering action, and all petitions for rulemaking which have been received by the Commission and are pending disposition by the Commission. The Regulatory Agenda is updated and issued each quarter.

  10. NRC regulatory agenda

    SciTech Connect

    Not Available

    1990-07-01

    The NRC Regulatory Agenda is a compilation of all rules on which the NRC has proposed or is considering action and all petitions for rulemaking which have been received by the Commission and are pending disposition by the Commission. The Regulatory Agenda is updated and issued each quarter.

  11. Plant Regulatory Organizations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The chapter on Plant Regulatory Organizations is part of a book titled Pest Management and Phytosanitary Trade Barriers authored by Neil Heather (Australia) and Guy Hallman. It covers the role of plant regulatory organizations from the international to state level in protecting plant health. At on...

  12. CT angiography of neonates and infants: comparison of radiation dose and image quality of target mode prospectively ECG-gated 320-MDCT and ungated helical 64-MDCT.

    PubMed

    Jadhav, Siddharth P; Golriz, Farahnaz; Atweh, Lamya A; Zhang, Wei; Krishnamurthy, Rajesh

    2015-02-01

    OBJECTIVE. The purpose of this study was to evaluate the radiation dose and image quality of target mode prospectively ECG-gated volumetric CT angiography (CTA) performed with a 320-MDCT scanner compared with the radiation dose and image quality of ungated helical CTA performed with a 64-MDCT scanner. MATERIALS AND METHODS. An experience with CTA for cardiovascular indications in neonates and infants 0-6 months old was retrospectively assessed. Radiation doses and quantitative and qualitative image quality scores of 28 CTA examinations performed with a 320-MDCT scanner and volumetric target mode prospective ECG gating plus iterative reconstruction (target mode) were compared with the doses and scores of 28 CTA examinations performed with a 64-MDCT scanner and ungated helical scanning plus filtered back projection reconstruction (ungated mode). All target mode studies were performed during free breathing. Seven ungated CTA examinations (25%) were performed with general endotracheal anesthesia. The findings of 17 preoperative CTA examinations performed in target mode were also compared with surgical reports for evaluation of diagnostic accuracy. RESULTS. All studies performed with target mode technique were diagnostic for the main clinical indication. Effective doses were significantly lower in the target mode group (0.51 ± 0.19 mSv) compared with the ungated mode group (4.8 ± 1.4 mSv) (p < 0.0001). Quantitative analysis revealed no statistically significant difference between the two groups with respect to signal-to-noise ratio (of pulmonary artery and aorta) and contrast-to-noise ratio. Subjective image quality was significantly better with target mode than with ungated mode (p < 0.0001). CONCLUSION. Target mode prospectively ECG-gated volumetric scanning with iterative reconstruction performed with a 320-MDCT scanner has several benefits in cardiovascular imaging of neonates and infants, including low radiation dose, improved image quality, high diagnostic

  13. 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.

  14. Diversification of oral and aboral mesodermal regulatory states in pregastrular sea urchin embryos.

    PubMed

    Materna, Stefan C; Ransick, Andrew; Li, Enhu; Davidson, Eric H

    2013-03-01

    Specification of the non-skeletogenic mesoderm (NSM) in sea urchin embryos depends on Delta signaling. Signal reception leads to expression of regulatory genes that later contribute to the aboral NSM regulatory state. In oral NSM, this is replaced by a distinct oral regulatory state in consequence of Nodal signaling. Through regulome wide analysis we identify the homeobox gene not as an immediate Nodal target. not expression in NSM causes extinction of the aboral regulatory state in the oral NSM, and expression of a new suite of regulatory genes. All NSM specific regulatory genes are henceforth expressed exclusively, in oral or aboral domains, presaging the mesodermal cell types that will emerge. We have analyzed the regulatory linkages within the aboral NSM gene regulatory network. A linchpin of this network is gataE which as we show is a direct Gcm target and part of a feedback loop locking down the aboral regulatory state. PMID:23261933

  15. 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.

  16. 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

  17. 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.

  18. 78 FR 44279 - Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-23

    ...The Department of Justice is publishing its spring 2013 regulatory agenda pursuant to Executive Order 12866, ``Regulatory Planning and Review,'' 58 FR 51735, and the Regulatory Flexibility Act, 5 U.S.C. sections 601 to 612...

  19. The ensembl regulatory build.

    PubMed

    Zerbino, Daniel R; Wilder, Steven P; Johnson, Nathan; Juettemann, Thomas; Flicek, Paul R

    2015-01-01

    Most genomic variants associated with phenotypic traits or disease do not fall within gene coding regions, but in regulatory regions, rendering their interpretation difficult. We collected public data on epigenetic marks and transcription factor binding in human cell types and used it to construct an intuitive summary of regulatory regions in the human genome. We verified it against independent assays for sensitivity. The Ensembl Regulatory Build will be progressively enriched when more data is made available. It is freely available on the Ensembl browser, from the Ensembl Regulation MySQL database server and in a dedicated track hub. PMID:25887522

  20. 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

  1. 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.

  2. 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

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

    PubMed

    Kim, Jung Han

    2016-03-22

    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

  4. 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.

  5. NRC regulatory agenda

    SciTech Connect

    Not Available

    1990-10-01

    The Regulatory Agenda is a quarterly compilation of all rules on which the NRC has recently completed action or has proposed, or is considering action and of all petitions for rulemaking that the NRC has received that are pending disposition.

  6. NRC Regulatory Agenda

    SciTech Connect

    Not Available

    1989-10-01

    The Regulatory Agenda is a quarterly compilation of all rules on which the NRC has recently completed action or has proposed, or is considering action and of all petitions for rulemaking that the NRC has received that are pending disposition.

  7. NRC regulatory agenda

    SciTech Connect

    Not Available

    1990-04-01

    The Regulatory Agenda is a quarterly compilation of all rules on which the NRC has recently completed action or has proposed, or is considering action and of all petitions for rulemaking that the NRC has received that are pending disposition.

  8. Targeting the Wnt-Regulatory Protein CTNNBIP1 by microRNA-214 Enhances the Stemness and Self-Renewal of Cancer Stem-Like Cells in Lung Adenocarcinomas.

    PubMed

    Qi, Wei; Chen, Junying; Cheng, Xiaoming; Huang, Jiani; Xiang, Tong; Li, Qijing; Long, Haixia; Zhu, Bo

    2015-12-01

    A novel hypothesis in cancer biology proposes that cancer growth is driven by cancer stem-like cells (CSLCs), also called tumor-initiating cells, which can self-renew and differentiate into multilineage progeny in a fashion similar to stem cells. However, the impact and underlying mechanisms of this process in lung adenocarcinoma (LAC) remain to be elucidated. Here, we report that microRNA-214 (miR-214) contributes to cell self-renewal by directly targeting catenin beta interacting protein 1 (CTNNBIP1), a member of the Wnt signaling pathway. We demonstrate that miR-214 overexpression enhances stem-like properties in LAC cells and that miR-214 shows increased expression in CSLCs derived from primary tumor tissue and from two LAC cell lines (A549 and NCI-H1650). Strikingly, downregulation of miR-214 expression in CSLCs resulted in a significant decrease in spheroid formation and the expression of the stem-cell markers Nanog, Oct-4, and Sox-2. Finally, CTNNBIP1 was identified as a target of miR-214. miR-214 expression in LAC was negatively correlated with CTNNBIP1 expression and positively correlated with differentiated cellular states. Moreover, CTNNBIP1 expression correlated with longer overall survival in LAC patients. This study reveals that miR-214 plays a critical role in CSLC self-renewal and stemness by targeting CTNNBIP1. The identification of this functional miR-214-CTNNBIP1 interaction that regulates self-renewal in CSLCs has the potential to direct the development of novel therapeutic strategies for LAC. PMID:26299367

  9. Canadian drug regulatory framework.

    PubMed

    Kelly, L; Lazzaro, M; Petersen, C

    2007-03-01

    The role of regulatory drug submission evaluators in Canada is to critically assess both the data submitted and the sponsor's interpretation of the data in order to reach an evidence-, and context-based recommendation as to the potential benefits and potential harms (i.e., risks) associated with taking the drug under the proposed conditions of use. The purpose of this document is to outline the regulatory framework in which this assessment occurs, including: defining what "authorization to market a drug in Canada" means, in terms of the role of the sponsor, the responsibility of Health Canada in applying the Food and Drugs Act prior to and after marketing authorization, and the distinction between regulatory authorization versus physician authorization; highlighting organizational, process and legal factors within Health Canada related to authorization of clinical trials and authorization to market a drug; considerations during the review process, such as regulatory and scientific issues related to the drug, patient populations and trial designs; application of international guidelines, and decisions from other jurisdictions; regulatory realities regarding drug authorization, including the requirement for wording in the Product Monograph to accurately reflect the information currently available on the safe and effective use of a drug, and that hypothesis-confirming studies are essential to regulatory endorsement; current issues related to the review of therapies for dementia, such as assessing preventative treatments, and therapies that have symptomatic versus disease-modifying effects, statistical issues regarding missing data, and trial design issues. PMID:17469674

  10. Comparison of Laboratory and Ecological Host Range of the Saltcedar Leaf Beetle with Respect to Native Non-Target Frankenia species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Laboratory and field host specificity tests were conducted with the saltcedar biocontrol agent, Diorhabda elongata (Coleoptera: Chrysomelidae) from Crete, to assess the potential risk of impact to non-target North American Frankenia species. Larval survival was not significantly different between T...

  11. Small regulatory RNAs in Archaea

    PubMed Central

    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. PMID:24755959

  12. Modeling DNA sequence-based cis-regulatory gene networks.

    PubMed

    Bolouri, Hamid; Davidson, Eric H

    2002-06-01

    Gene network analysis requires computationally based models which represent the functional architecture of regulatory interactions, and which provide directly testable predictions. The type of model that is useful is constrained by the particular features of developmentally active cis-regulatory systems. These systems function by processing diverse regulatory inputs, generating novel regulatory outputs. A computational model which explicitly accommodates this basic concept was developed earlier for the cis-regulatory system of the endo16 gene of the sea urchin. This model represents the genetically mandated logic functions that the system executes, but also shows how time-varying kinetic inputs are processed in different circumstances into particular kinetic outputs. The same basic design features can be utilized to construct models that connect the large number of cis-regulatory elements constituting developmental gene networks. The ultimate aim of the network models discussed here is to represent the regulatory relationships among the genomic control systems of the genes in the network, and to state their functional meaning. The target site sequences of the cis-regulatory elements of these genes constitute the physical basis of the network architecture. Useful models for developmental regulatory networks must represent the genetic logic by which the system operates, but must also be capable of explaining the real time dynamics of cis-regulatory response as kinetic input and output data become available. Most importantly, however, such models must display in a direct and transparent manner fundamental network design features such as intra- and intercellular feedback circuitry; the sources of parallel inputs into each cis-regulatory element; gene battery organization; and use of repressive spatial inputs in specification and boundary formation. Successful network models lead to direct tests of key architectural features by targeted cis-regulatory analysis. PMID

  13. IMPaCT Back study protocol. Implementation of subgrouping for targeted treatment systems for low back pain patients in primary care: a prospective population-based sequential comparison

    PubMed Central

    2010-01-01

    Background Prognostic assessment tools to identify subgroups of patients at risk of persistent low back pain who may benefit from targeted treatments have been developed and validated in primary care. The IMPaCT Back study is investigating the effects of introducing and supporting a subgrouping for targeted treatment system in primary care. Methods/Design A prospective, population-based, quality improvement study in one Primary Care Trust in England with a before and after design. Phases 1 and 3 collect data on current practice, attitudes and behaviour of health care practitioners, patients' outcomes and health care costs. Phase 2 introduces and supports the subgrouping for targeted treatment system, via a multi-component, quality improvement intervention that includes educational courses and outreach visits led by opinion leaders, audit/feedback, mentoring and organisational support to embed the subgrouping tools within IT and clinical management systems. We aim to recruit 1000 low back pain patients aged 18 years and over consulting 7 GP practices within one Primary Care Trust in England, UK. The study includes GPs in participating practices and physiotherapists in associated services. The primary objective is to determine the effect of the subgrouping for targeted treatment system on back pain related disability and catastrophising at 2 and 6 months, comparing data from phase 1 with phase 3. Key secondary objectives are to determine the impact on: a) GPs' and physiotherapists' attitudes and behaviour regarding low back pain; b) The process of care that patients receive; c) The cost-effectiveness and sustainability of the new clinical system. Discussion This paper details the rationale, design, methods, planned analysis and operational aspects of the IMPaCT Back study. We aim to determine whether the new subgrouping for targeted treatment system is implemented and sustained in primary care, and evaluate its impact on clinical decision-making, patient outcomes and

  14. Measurement and comparison of one- and two-dimensional modulation transfer function of optical imaging systems based on the random target method

    NASA Astrophysics Data System (ADS)

    Kang, Jiqiang; Hao, Qun; Cheng, Xuemin

    2014-10-01

    One-dimensional modulation transfer function (1-D MTF) has been generally calculated to evaluate the image quality of optical imaging systems, such as the horizontal MTF and vertical MTF. These MTFs can be measured by the use of some mature ways. However, the information of 1-D MTF for performance evaluation may not enough for the systems handling two-dimensional (2-D) targets of high resolution, thus discussing 2-D MTF will be necessary. We investigate the measurement method for the 1-D and 2-D MTF of optical imaging systems based on the random target method, and the characteristics of 2-D MTF and 1-D MTF in terms of MTF values and cutoff frequency are also noted.

  15. Integrating structure- and ligand-based virtual screening: comparison of individual, parallel, and fused molecular docking and similarity search calculations on multiple targets.

    PubMed

    Tan, Lu; Geppert, Hanna; Sisay, Mihiret T; Gütschow, Michael; Bajorath, Jürgen

    2008-10-01

    Similarity searching is often used to preselect compounds for docking, thereby decreasing the size of screening databases. However, integrated structure- and ligand-based screening schemes are rare at present. Docking and similarity search calculations using 2D fingerprints were carried out in a comparative manner on nine target enzymes, for which significant numbers of diverse inhibitors could be obtained. In the absence of knowledge-based docking constraints and target-directed parameter optimisation, fingerprint searching displayed a clear preference over docking calculations. Alternative combinations of docking and similarity search results were investigated and found to further increase compound recall of individual methods in a number of instances. When the results of similarity searching and docking were combined, parallel selection of candidate compounds from individual rankings was generally superior to rank fusion. We suggest that complementary results from docking and similarity searching can be captured by integrated compound selection schemes. PMID:18651695

  16. A Randomized Comparison of Remifentanil Target-Controlled Infusion Versus Dexmedetomidine Single-Dose Administration: A Better Method for Smooth Recovery From General Sevoflurane Anesthesia.

    PubMed

    Park, Jeong-Soo; Kim, Ki-Joon; Lee, Jae Hoon; Jeong, Woong-Yoon; Lee, Jeong-Rim

    2016-01-01

    Remifentanil target-controlled infusion and dexmedetomidine single-dose administration are known to reduce airway response and hemodynamic stimulation during anesthetic recovery. We compared the effects of 2 drugs on the prevention of cough during emergence. We enrolled 70 female patients aged 20-60 years with American Society of Anesthesiologists (ASA) I-II who underwent general anesthesia for elective thyroidectomy. The patients were randomly assigned to remifentanil (group R) or dexmedetomidine (group D). Anesthesia was maintained with sevoflurane and effect-site target-controlled infusion of remifentanil. In group D, remifentanil was discontinued, and dexmedetomidine 0.5 μg/kg was given 10 minutes before the end of surgery. In group R, remifentanil target-controlled infusion at an effective-site concentration of 2.0 ng/mL was maintained during emergence until extubation. The cough grade, hemodynamic values, respiration, and other recovery profiles were evaluated during the periextubation period. The proportion of patients with no cough or just a single cough during extubation was significantly higher in group R than in group D (96.8% vs. 55.9%). The change of mean arterial pressure and heart rate were not significantly different during extubation in both groups. Respiratory rate and the incidence of residual sedation after extubation were lower in group R. There were no desaturation events and no differences in time to extubation or duration of postanesthesia care unit stay in both groups. Remifentanil target-controlled infusion reduces emergence cough from general anesthesia more effectively than single-dose dexmedetomidine. However, a single-dose of dexmedetomidine has the effect with respect to respiratory and hemodynamic stability during emergence. PMID:24100256

  17. Comparison of miRNAs and Their Targets in Seed Development between Two Maize Inbred Lines by High-Throughput Sequencing and Degradome Analysis

    PubMed Central

    Guo, Yu-Min; Yang, Min-Kai; Yang, Rong-Wu; Lu, Gui-Hua; Yang, Yong-Hua

    2016-01-01

    MicroRNAs (miRNAs) play an important role in plant growth, development, and response to environment. For identifying and comparing miRNAs and their targets in seed development between two maize inbred lines (i.e. PH6WC and PH4CV), two sRNAs and two degradome libraries were constructed. Through high-throughput sequencing and miRNA identification, 55 conserved and 24 novel unique miRNA sequences were identified in two sRNA libraries; moreover, through degradome sequencing and analysis, 137 target transcripts corresponding to 38 unique miRNA sequences were identified in two degradome libraries. Subsequently, 16 significantly differentially expressed miRNA sequences were verified by qRT-PCR, in which 9 verified sequences obviously target 30 transcripts mainly involved with regulation in flowering and development in embryo. Therefore, the results suggested that some miRNAs (e.g. miR156, miR171, miR396 and miR444) related reproductive development might differentially express in seed development between the PH6WC and PH4CV maize inbred lines in this present study. PMID:27463682

  18. PROGRESSION OF REGULATORY GENE EXPRESSION STATES IN FETAL AND ADULT PRO-T CELL DEVELOPMENT

    PubMed Central

    David-Fung, Elizabeth-Sharon; Yui, Mary A.; Morales, Marissa; Wang, Hua; Taghon, Tom; Diamond, Rochelle A.; Rothenberg, Ellen V.

    2014-01-01

    Precursors entering the T-cell developmental pathway traverse a progression of states characterized by distinctive patterns of gene expression. Of particular interest are regulatory genes, which ultimately control the dwell time of cells in each state and establish the mechanisms that propel them forward to subsequent states. Under particular genetic and developmental circumstances, the transitions between these states occur with different timing, and environmental feedbacks may shift the steady-state accumulations of cells in each state. The fetal transit through pro-T cell stages is faster than in the adult, and subject to somewhat different genetic requirements. To explore causes of such variation, this review presents previously unpublished data on differentiation gene activation in pro-T cells of pre-TCR deficient mutant mice, and a quantitative comparison of the profiles of transcription factor gene expression in pro-T cell subsets of fetal and adult wildtype mice. Against a background of consistent gene expression, several regulatory genes show marked differences between fetal and adult expression profiles, including those encoding two bHLH antagonist Id factors, the Ets family factor SpiB, and the Notch target gene Deltex1. The results also reveal global differences in regulatory alterations triggered by the first TCR-dependent selection events in fetal and adult thymopoiesis. PMID:16448545

  19. 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

  20. Comparison of hepatic transcription profiles of locked ribonucleic acid antisense oligonucleotides: evidence of distinct pathways contributing to non-target mediated toxicity in mice.

    PubMed

    Kakiuchi-Kiyota, Satoko; Koza-Taylor, Petra H; Mantena, Srinivasa R; Nelms, Linda F; Enayetallah, Ahmed E; Hollingshead, Brett D; Burdick, Andrew D; Reed, Lori A; Warneke, James A; Whiteley, Lawrence O; Ryan, Anne M; Mathialagan, Nagappan

    2014-03-01

    Development of LNA gapmers, antisense oligonucleotides used for efficient inhibition of target RNA expression, is limited by non-target mediated hepatotoxicity issues. In the present study, we investigated hepatic transcription profiles of mice administered non-toxic and toxic LNA gapmers. After repeated administration, a toxic LNA gapmer (TS-2), but not a non-toxic LNA gapmer (NTS-1), caused hepatocyte necrosis and increased serum alanine aminotransferase levels. Microarray data revealed that, in addition to gene expression patterns consistent with hepatotoxicity, 17 genes in the clathrin-mediated endocytosis (CME) pathway were altered in the TS-2 group. TS-2 significantly down-regulated myosin 1E (Myo1E), which is involved in release of clathrin-coated pits from plasma membranes. To map the earliest transcription changes associated with LNA gapmer-induced hepatotoxicity, a second microarray analysis was performed using NTS-1, TS-2, and a severely toxic LNA gapmer (HTS-3) at 8, 16, and 72 h following a single administration in mice. The only histopathological change observed was minor hepatic hypertrophy in all LNA groups across time points. NTS-1, but not 2 toxic LNA gapmers, increased immune response genes at 8 and 16 h but not at 72 h. TS-2 significantly perturbed the CME pathway only at 72 h, while Myo1E levels were decreased at all time points. In contrast, HTS-3 modulated DNA damage pathway genes at 8 and 16 h and also modulated the CME pathway genes (but not Myo1E) at 16 h. Our results may suggest that different LNAs modulate distinct transcriptional genes and pathways contributing to non-target mediated hepatotoxicity in mice. PMID:24336348

  1. Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus: Piranga).

    PubMed

    Manthey, Joseph D; Campillo, Luke C; Burns, Kevin J; Moyle, Robert G

    2016-07-01

    Restriction-site associated DNA sequencing (RAD-seq) and target capture of specific genomic regions, such as ultraconserved elements (UCEs), are emerging as two of the most popular methods for phylogenomics using reduced-representation genomic data sets. These two methods were designed to target different evolutionary timescales: RAD-seq was designed for population-genomic level questions and UCEs for deeper phylogenetics. The utility of both data sets to infer phylogenies across a variety of taxonomic levels has not been adequately compared within the same taxonomic system. Additionally, the effects of uninformative gene trees on species tree analyses (for target capture data) have not been explored. Here, we utilize RAD-seq and UCE data to infer a phylogeny of the bird genus Piranga The group has a range of divergence dates (0.5-6 myr), contains 11 recognized species, and lacks a resolved phylogeny. We compared two species tree methods for the RAD-seq data and six species tree methods for the UCE data. Additionally, in the UCE data, we analyzed a complete matrix as well as data sets with only highly informative loci. A complete matrix of 189 UCE loci with 10 or more parsimony informative (PI) sites, and an approximately 80% complete matrix of 1128 PI single-nucleotide polymorphisms (SNPs) (from RAD-seq) yield the same fully resolved phylogeny of Piranga We inferred non-monophyletic relationships of Piranga lutea individuals, with all other a priori species identified as monophyletic. Finally, we found that species tree analyses that included predominantly uninformative gene trees provided strong support for different topologies, with consistent phylogenetic results when limiting species tree analyses to highly informative loci or only using less informative loci with concatenation or methods meant for SNPs alone. PMID:26821912

  2. Cross-species comparison of in vivo PK/PD relationships for second-generation antisense oligonucleotides targeting apolipoprotein B-100.

    PubMed

    Yu, Rosie Z; Lemonidis, Kristina M; Graham, Mark J; Matson, John E; Crooke, Rosanne M; Tribble, Diane L; Wedel, Mark K; Levin, Arthur A; Geary, Richard S

    2009-03-01

    The in vivo pharmacokinetics/pharmacodynamics of 2'-O-(2-methoxyethyl) (2'-MOE) modified antisense oligonucleotides (ASOs), targeting apolipoprotein B-100 (apoB-100), were characterized in multiple species. The species-specific apoB antisense inhibitors demonstrated target apoB mRNA reduction in a drug concentration and time-dependent fashion in mice, monkeys, and humans. Consistent with the concentration-dependent decreases in liver apoB mRNA, reductions in serum apoB, and LDL-C, and total cholesterol were concurrently observed in animal models and humans. Additionally, the long duration of effect after cessation of dosing correlated well with the elimination half-life of 2'-MOE modified apoB ASOs studied in mice (t(1/2) congruent with 20 days) and humans (t(1/2) congruent with 30 days) following parental administrations. The plasma concentrations of ISIS 301012, observed in the terminal elimination phase of both mice and monkeys were in equilibrium with liver. The partition ratios between liver and plasma were similar, approximately 6000:1, across species, and thus provide a surrogate for tissue exposure in humans. Using an inhibitory E(max) model, the ASO liver EC(50s) were 101+/-32, 119+/-15, and 300+/-191 microg/g of ASO in high-fat-fed (HF) mice, transgenic mice containing the human apoB transgene, and monkeys, respectively. The estimated liver EC(50) in man, extrapolated from trough plasma exposure, was 81+/-122 microg/g. Therefore, extraordinary consistency of the exposure-response relationship for the apoB antisense inhibitor was observed across species, including human. The cross-species PK/PD relationships provide confidence in the use of pharmacology animal models to predict human dosing for second-generation ASOs targeting the liver. PMID:19056355

  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. 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.

  5. 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. PMID:25714030

  6. The Impact of Target Frequency on Intra-Individual Variability in Euthymic Bipolar Disorder: A Comparison of Two Sustained Attention Tasks

    PubMed Central

    Moss, Rachel Ann; Finkelmeyer, Andreas; Robinson, Lucy J.; Thompson, Jill M.; Watson, Stuart; Ferrier, I. Nicol; Gallagher, Peter

    2016-01-01

    Greater intra-individual variability (IIV) in reaction time (RT) on a sustained attention task has been reported in patients with bipolar disorder (BD) compared with healthy controls. However, it is unclear whether IIV is task specific, or whether it represents general cross-task impairment in BD. This study aimed to investigate whether IIV occurs in sustained attention tasks with different parameters. Twenty-two patients with BD (currently euthymic) and 17 controls completed two sustained attention tasks on different occasions: a low target frequency (~20%) Vigil continuous performance test (CPT) and a high target frequency (~70%) CPT version A-X (CPT-AX). Variability measures (individual standard deviation and coefficient of variation) were calculated per participant, and ex-Gaussian modeling was also applied. This was supplemented by Vincentile analysis to characterize RT distributions. Results indicated that participants (patients and controls) were generally slower and more variable when completing the Vigil CPT compared with CPT-AX. Significant group differences were also observed in the Vigil CPT, with euthymic BD patients being more variable than controls. This result suggests that IIV in BD demonstrates some degree of task specificity. Further research should incorporate analysis of additional RT distributional models (drift diffusion and fast Fourier transform) to fully characterize the pattern of IIV in BD, as well as its relationship to cognitive processes. PMID:27378954

  7. Cross-national invariance of dimensions of parental rearing behaviour: comparison of psychometric data of Swedish depressives and healthy subjects with Dutch target ratings on the EMBU.

    PubMed

    Arrindell, W A; Perris, C; Perris, H; Eisemann, M; van der Ende, J; von Knorring, L

    1986-03-01

    A psychometric study on Swedish and Dutch samples used the EMBU, a self-report instrument designed to assess memories of parents' rearing behaviour. Of the four primary factors identified previously with Dutch individuals (Rejection, Emotional Warmth, Over-protection, and Favouring Subject), the first three were retrieved in a similar form in the two Swedish groups (depressives and healthy, non-patients). Examination of the metric equivalence of the scales and the strength of the factors for each group indicated that comparisons of patterns and levels between groups from the respective countries on the three factors showing cross-national constancy would be warranted. Scale-level factor analyses of these dimensions produced identical two-factor compositions (CARE and PROTECTION) across national groups which further supported this conclusion. PMID:3719223

  8. In vitro and in silico evaluation of NF-κB targeted costunolide action on estrogen receptor-negative breast cancer cells--a comparison with normal breast cells.

    PubMed

    Pitchai, Daisy; Roy, Anita; Banu, Sakhila

    2014-10-01

    Costunolide, a sesquiterpene lactone is a plant-derived secondary metabolite found to be present in most of the pharmacologically active herbs, being the cause for their medicinal values. The present study aims to evaluate the cytotoxic effect of costunolide isolated from Costus speciosus rhizome extract on MDA-MB-231 cells and explore its targeted action in comparison with its action on the normal breast cells (MCF 10A). The effect of costunolide on cell viability of the cells was assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide viability assay. The targeted action of the compound was analyzed comparing the effectiveness of the compound to alter the protein expression levels of NF-κB subunits in the normal and the cancer cells using western blotting analysis. In silico studies were performed to predict the targeted interaction of costunolide with the NF-κB subunit proteins. Costunolide inhibited the cell viability of MDA-MB-231 cells in a dose-dependent manner leaving no significant change in the viability of the normal breast cells. The over expressed NF-κB subunits - p65, 52 and 100 in the cancer cells were found to be downregulated when treated with costunolide at an effective dose of 20 and 40 μM costunolide. In silico results provided stable interactions between costunolide and the target proteins, supporting the in vitro results in addition. Thus, costunolide derived from C. speciosus plant source elevates a fresh conviction for its use in breast cancer therapy for its cytotoxic efficacy and non-toxic nature. PMID:24733523

  9. 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...

  10. 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.

  11. EPAct Transportation Regulatory Activities

    SciTech Connect

    2011-11-21

    The U.S. Department of Energy's (DOE) Vehicle Technologies Program manages several transportation regulatory activities established by the Energy Policy Act of 1992 (EPAct), as amended by the Energy Conservation Reauthorization Act of 1998, EPAct 2005, and the Energy Independence and Security Act of 2007 (EISA).

  12. REFINE WETLAND REGULATORY PROGRAM

    EPA Science Inventory

    The Tribes will work toward refining a regulatory program by taking a draft wetland conservation code with permitting incorporated to TEB for review. Progress will then proceed in developing a permit tracking system that will track both Tribal and fee land sites within reservati...

  13. REGULATORY AIR QUALITY MODELS

    EPA Science Inventory

    Appendix W to 40CFR Part 51 (Guideline on Air Quality Models) specifies the models to be used for purposes of permitting, PSD, and SIPs. Through a formal regulatory process this modeling guidance is periodically updated to reflect current science. In the most recent action, thr...

  14. NRC regulatory agenda

    SciTech Connect

    Not Available

    1993-02-01

    This document is a compilation of all rules on which the NRC has recently completed action, or has proposed action, or is considered action, and all petitions for rulemaking which have been received by the Commission and are pending disposition by the Commission. The Regulatory Agenda is updated and issued each quarter.

  15. NRC regulatory agenda

    SciTech Connect

    Not Available

    1992-11-01

    This document provides a compilation of all rules on which the NRC has recently completed action, or has proposed action, or is considering action, and all petitions for rulemaking which have been received by the Commission and are pending disposition by the Commission. The Regulatory Agenda is updated and issued each quarter.

  16. NRC Regulatory Agenda

    SciTech Connect

    Not Available

    1992-07-01

    This document compilation of all rules on which the NRC has recently completed action, or has proposed action, or is considering action, and all petitions for rule making which have been received by the Commission and are pending disposition by the Commission. The Regulatory Agenda is updated and issued each quarter.

  17. 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.

  18. A comparison of the thick-target model with stereo data on the height structure of solar hard X-ray bursts

    NASA Technical Reports Server (NTRS)

    Brown, J. C.; Carlaw, V. A.; Cromwell, D.; Kane, S. R.

    1983-01-01

    The thick target, hard solar X-ray source height structure is predicted for the case of a beam that is injected vertically downward, having a power law spectrum, being dominated by Coulomb collisional energy losses, and being structurally characterized by the ratio of hard X-ray flux from an upper part of the source to that from the entire source. These predictions are compared with the flux ratios at 150 and 350 keV which were observed by two spacecraft for five events in which the solar limb occults part of the source for one spacecraft. The energy dependence of the occultation ratio is found to be inconsistent with that predicted by the model, and it is concluded that noncollisional losses must be significant in beam dynamics.

  19. Treatment of lung tumor colonies with 90Y targeted to blood vessels: comparison with the alpha-particle emitter 213Bi.

    PubMed

    Kennel, S J; Stabin, M; Yoriyaz, H; Brechbiel, M; Mirzadeh, S

    1999-01-01

    An in vivo lung tumor model system for radioimmunotherapy of lung metastases was used to test the relative effectiveness of the vascular- targeted beta-particle emitter 90Y, and alpha-particle emitter, 213Bi. Yttrium-90 was shown to be stably bound by CHXa" DTPA-MAb 201B conjugates and delivered efficiently to lung tumor blood vessels. Dosimetry calculations indicated that the lung received 16.2 Gy/MBq from treatment with 90Y MAb 201B, which was a sevenfold greater absorbed dose than any other organ examined. Therapy was optimal for 90Y with 3 MBq injected. Bismuth-213 MAb 201B also delivered a similar absorbed dose (15Gy/MBq) to the lung. Yttrium-90 was found to be slightly more effective against larger tumors than 213Bi, consistent with the larger range of 2 MeV beta particles from 90Y than the 8 MeV alpha particles from 213Bi. Treatment of EMT-6 tumors growing in immunodeficient SCID mice with 90Y or 213Bi MAb 201 resulted in significant destruction of tumor colonies; however, 90Y MAb 201B was toxic for the SCID mice, inflicting acute lung damage. In another tumor model, IC-12 rat tracheal carcinoma growing in SCID mouse lungs, 90Y therapy was more effective than 213Bi at destroying lung tumors. However, 90Y MAb 201B toxicity for the lung limited any therapeutic effect. We conclude that, although vascular-targeted 90Y MAb can be an effective therapeutic agent, particularly for larger tumors, in this model system, acute damage to the lung may limit its application. PMID:10096515

  20. Comparison of common platelet receptors between the chacma baboon (Papio ursinus) and human for use in pre-clinical human-targeted anti-platelet studies.

    PubMed

    Janse van Rensburg, Walter J

    2016-06-01

    Anti-platelet agents play a central part in the treatment and prevention of acute thrombotic events. Discriminating animal models are needed for the development of novel agents. The chacma baboon has been extensively used as a model to evaluate anti-platelet agents. However, limited data exist to prove the translatability of this species to humans. We aimed to determine the suitability of the chacma baboon in preclinical human targeted GPIIb/IIIa, GPIbα and P2Y12 studies. Light-transmission platelet aggregometry (LTA), whole blood impedance aggregometry, receptor number quantification and genomic DNA sequencing were performed. Baboon ADP and arachidonic acid-induced LTA aggregation results differed significantly from human values, even at increased concentrations. LTA ristocetin-induced agglutination was comparable between species, but baboon platelets needed twice the concentration of ristocetin to elicit a similar response. Citrated baboon blood had significantly less aggregation than humans when evaluated with impedance aggregometry. However, hirudinised baboon whole blood gave similar aggregation as humans at the same agonist concentrations. GPIIb, GPIIIa and GPIbα numbers were significantly more on the baboon platelets. None of the amino acids deemed vital for receptor function, ligand binding or receptor inhibition, were radically different between the species. However, a conservative change in a calcium-binding region of GPIIb may render the baboon platelets more sensitive to calcium-binding agents. The chacma baboon may be used for the evaluation of human-targeted GPIIb/IIIa-, GPIbα- and P2Y12-inhibiting agents. However, the best anticoagulant, optimal agonist concentrations, increase in receptor number and sequence differences must be considered for any future studies. PMID:26559117

  1. 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.

  2. 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

  3. Comparison of RF body coils for MRI at 3  T: a simulation study using parallel transmission on various anatomical targets.

    PubMed

    Wu, Xiaoping; Zhang, Xiaotong; Tian, Jinfeng; Schmitter, Sebastian; Hanna, Brian; Strupp, John; Pfeuffer, Josef; Hamm, Michael; Wang, Dingxin; Nistler, Juergen; He, Bin; Vaughan, Thomas J; Ugurbil, Kamil; Van de Moortele, Pierre-Francois

    2015-10-01

    The performance of multichannel transmit coil layouts and parallel transmission (pTx) RF pulse design was evaluated with respect to transmit B1 (B1 (+)) homogeneity and specific absorption rate (SAR) at 3 T 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 two or three 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 about eightfold 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 three-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

  4. Comparison of gull feces-specific assays targeting the 16S rRNA genes of Catellicoccus marimammalium and Streptococcus spp.

    PubMed

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

    2012-03-01

    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

  5. 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.

  6. 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/. PMID:25904632

  7. 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

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

    PubMed

    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

  9. 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

  10. Public opinion: Country comparisons

    NASA Astrophysics Data System (ADS)

    Hopkins, Debbie

    2015-11-01

    Climate change awareness, risk perception and policy support vary between and within countries. National-scale comparisons can help to explain this variability and be used to develop targeted interventions.

  11. The Prokineticins: A Novel Pair of Regulatory Peptides

    PubMed Central

    Zhou, Qun-Yong

    2009-01-01

    Secreted peptides play broad regulatory roles in brain function and elsewhere in the body. Prokineticins are a pair of newly identified regulatory peptides that signal through two highly homologous G protein–coupled receptors. Prokineticins possess a unique structural motif of five disulfide bonds and a completely conserved N-terminal hexapeptide sequence that is essential to biological activity. Diverse biological functions, including roles in development and cell differentiation, have been assigned to the prokineticins. A network of genes, subject to various transcriptional factors, may functionally converge on the prokineticins as regulatory targets. PMID:17200460

  12. 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.

  13. A direct sensitivity comparison between flow-modulated comprehensive 2D and 1D GC in untargeted and targeted MS-based experiments.

    PubMed

    Tranchida, Peter Q; Franchina, Flavio A; Zoccali, Mariosimone; Bonaccorsi, Ivana; Cacciola, Francesco; Mondello, Luigi

    2013-09-01

    The present contribution is focused on the measurement of the analytical sensitivity attained in untargeted/targeted MS/MS experiments, performed using flow-modulator comprehensive 2D and 1D GC. The comprehensive 2D experiment was performed by diverting part of the high flow (circa 80%) to flush the accumulation loop (about 28 mL/min) to waste, to reduce the gas flow entering the ion source. 1D analyses were performed through: (i) unmodulated and (ii) single column applications. An equivalent temperature program was applied in the modulated and unmodulated analyses, while a faster one was employed in the single column one. In all application types, the (same) triple quadrupole instrument was operated in the full-scan and multiple reaction monitoring modes. A genuine sweet orange oil and the same sample spiked with 20 phytosanitary compounds were employed to reach the research objective. The results highlight the problems related to the flow modulation-MS combination. Specifically, it was found that sensitivity was on average three to four times higher in unmodulated and optimized single-column applications. PMID:23868497

  14. 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$.

  15. Comparison of Recruitment Efforts Targeted at Primary Care Physicians versus the Community At Large for Participation in Alzheimer's Disease Clinical Trials

    PubMed Central

    Carr, Sarah A.; Davis, Roberta; Spencer, Diane; Smart, Marie; Hudson, Joanna; Freeman, Stephanie; Cooper, Greg E.; Schmitt, Fred A.; Markesbery, William R.; Danner, Deborah; Jicha, Greg A.

    2009-01-01

    Inefficient and delayed recruitment into clinical trials in Alzheimer's disease are major obstacles impeding progress in the discovery of more effective therapeutic strategies to combat this disease. Despite widespread recognition of this problem, limited empirical data demonstrating the effectiveness of specific recruitment strategies are available to guide recruitment endeavors. The present study was designed to evaluate the effectiveness of recruitment efforts targeting either the primary care health professionals (PCP) or patients and families with a community grass-roots outreach event (COE). The primary outcome measure was actual study recruitment and participation in the four months post-intervention. No research subjects were recruited from the PCP intervention, while 69 subjects were recruited into clinical studies from the COE activity (0% vs. 28%, P<0.0001, Fisher exact test). Barriers to recruitment success in the PCP arm included a perception of perceived harm to subjects from research participation and fear of losing patients through clinical research participation. Our results suggest that outreach efforts directed at the potential study subject/caregiver are not only cost-effective but are able to easily accomplish the desired result of direct recruitment into clinical research studies. PMID:19571728

  16. 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

  17. 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

  18. 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...

  19. Spanish regulatory approach for Biobanking

    PubMed Central

    Arias-Diaz, Javier; Martín-Arribas, María C; García del Pozo, Javier; Alonso, Carlos

    2013-01-01

    The Spanish regulatory framework for storage of samples for research responds to most issues raised by both researchers and society regarding biobanking. The Spanish regulation currently foresees three possible ways in which these samples are to be handled: (a) gathering for use in a specific project, (b) storage in a collection, and (c) storage in a Biobank. Samples incorporated into a ‘collection' can only be used by the investigator who requested them and cannot be transferred to third parties or used in research projects outside the particular research line foreseen in the original consent. On the other hand, the legal entity ‘Biobank' refers not only to a set of physical facilities but to the management of the samples stored under that label, and particularly to the requirements for their cession. An approach based on putting most of the regulatory weight on the biobank side has been chosen in order to guaranty the rights of the donors as well as to ease the task of the researchers. A Biobank requires both to be authorized and to be registered in a public Registry. The requirements are quite stringent, allowing for the consent to be given as ‘broad' in scope without implying being ‘blank.' In this regard, for Biobanks to justify the taking on of some of the donors' rights, a key requirement is to have an external ethics committee supervising the adequacy of samples cession and use, notwithstanding the need for a previous bioethical supervision of the target protocol. PMID:23188043

  20. The target tissue in autoimmunity--an influential niche.

    PubMed

    Hill, Natasha J; Hultcrantz, Monica; Sarvetnick, Nora; Flodström-Tullberg, Malin

    2007-03-01

    Central and peripheral tolerance mechanisms were for a long time the only regulatory circuits known in autoimmunity. It is now becoming clear that the target tissue itself may have the capacity to control its own destiny. Here we review mechanisms by which the target tissue regulates local inflammation, and the way this could influence progression to overt autoimmunity. Moreover, we discuss recent data showing that physiological properties of the target tissue can determine the organ specificity of autoimmune disease. These recent discoveries and ideas concerning the regulatory potential of the target tissue may, in the future, add a new dimension to our concept of regulatory circuits in autoimmunity. PMID:17301949

  1. 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.

  2. Told through the wine: A liquid chromatography-mass spectrometry interplatform comparison reveals the influence of the global approach on the final annotated metabolites in non-targeted metabolomics.

    PubMed

    Díaz, Ramon; Gallart-Ayala, Hector; Sancho, Juan V; Nuñez, Oscar; Zamora, Tatiana; Martins, Claudia P B; Hernández, Félix; Hernández-Cassou, Santiago; Saurina, Javier; Checa, Antonio

    2016-02-12

    This work focuses on the influence of the selected LC-HRMS platform on the final annotated compounds in non-targeted metabolomics. Two platforms that differed in columns, mobile phases, gradients, chromatographs, mass spectrometers (Orbitrap [Platform#1] and Q-TOF [Platform#2]), data processing and marker selection protocols were compared. A total of 42 wines samples from three different protected denomination of origin (PDO) were analyzed. At the feature level, good (O)PLS-DA models were obtained for both platforms (Q(2)[Platform#1]=0.89, 0.83 and 0.72; Q(2)[Platform#2]=0.86, 0.86 and 0.77 for Penedes, Ribera del Duero and Rioja wines respectively) with 100% correctly classified samples in all cases. At the annotated metabolite level, platforms proposed 9 and 8 annotated metabolites respectively which were identified by matching standards or the MS/MS spectra of the compounds. At this stage, there was no coincidence among platforms regarding the suggested metabolites. When screened on the raw data, 6 and 5 of these compounds were detected on the other platform with a similar trend. Some of the detected metabolites showed complimentary information when integrated on biological pathways. Through the use of some examples at the annotated metabolite level, possible explanations of this initial divergence on the results are presented. This work shows the complications that may arise on the comparison of non-targeted metabolomics platforms even when metabolite focused approaches are used in the identification. PMID:26795279

  3. 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.

  4. Mutational Robustness of Gene Regulatory Networks

    PubMed Central

    van Dijk, Aalt D. J.; van Mourik, Simon; van Ham, Roeland C. H. J.

    2012-01-01

    Mutational robustness of gene regulatory networks refers to their ability to generate constant biological output upon mutations that change network structure. Such networks contain regulatory interactions (transcription factor – target gene interactions) but often also protein-protein interactions between transcription factors. Using computational modeling, we study factors that influence robustness and we infer several network properties governing it. These include the type of mutation, i.e. whether a regulatory interaction or a protein-protein interaction is mutated, and in the case of mutation of a regulatory interaction, the sign of the interaction (activating vs. repressive). In addition, we analyze the effect of combinations of mutations and we compare networks containing monomeric with those containing dimeric transcription factors. Our results are consistent with available data on biological networks, for example based on evolutionary conservation of network features. As a novel and remarkable property, we predict that networks are more robust against mutations in monomer than in dimer transcription factors, a prediction for which analysis of conservation of DNA binding residues in monomeric vs. dimeric transcription factors provides indirect evidence. PMID:22295094

  5. Gene regulatory mechanisms underpinning prostate cancer susceptibility.

    PubMed

    Whitington, Thomas; Gao, Ping; Song, Wei; Ross-Adams, Helen; Lamb, Alastair D; Yang, Yuehong; Svezia, Ilaria; Klevebring, Daniel; Mills, Ian G; Karlsson, Robert; Halim, Silvia; Dunning, Mark J; Egevad, Lars; Warren, Anne Y; Neal, David E; Grönberg, Henrik; Lindberg, Johan; Wei, Gong-Hong; Wiklund, Fredrik

    2016-04-01

    Molecular characterization of genome-wide association study (GWAS) loci can uncover key genes and biological mechanisms underpinning complex traits and diseases. Here we present deep, high-throughput characterization of gene regulatory mechanisms underlying prostate cancer risk loci. Our methodology integrates data from 295 prostate cancer chromatin immunoprecipitation and sequencing experiments with genotype and gene expression data from 602 prostate tumor samples. The analysis identifies new gene regulatory mechanisms affected by risk locus SNPs, including widespread disruption of ternary androgen receptor (AR)-FOXA1 and AR-HOXB13 complexes and competitive binding mechanisms. We identify 57 expression quantitative trait loci at 35 risk loci, which we validate through analysis of allele-specific expression. We further validate predicted regulatory SNPs and target genes in prostate cancer cell line models. Finally, our integrated analysis can be accessed through an interactive visualization tool. This analysis elucidates how genome sequence variation affects disease predisposition via gene regulatory mechanisms and identifies relevant genes for downstream biomarker and drug development. PMID:26950096

  6. 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

  7. 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

  8. 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.

  9. 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

    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

  10. Comparison of injection drug users accessing syringes from pharmacies, syringe exchange programs, and other syringe sources to inform targeted HIV prevention and intervention strategies

    PubMed Central

    Rudolph, Abby E.; Crawford, Natalie D.; Ompad, Danielle C.; Benjamin, Ebele O.; Stern, Rachel J.; Fuller, Crystal M.

    2011-01-01

    Objective In New York, syringe exchange programs (SEPs) and pharmacies provide syringe access for IDUs but may be unable to meet the needs of all IDUs. This analysis aims to describe IDUs who access syringes through different outlets to help inform the prevention needs of IDUs who under-utilize safe syringe sources in a city where syringe availability is high relative to other U.S. cities. Design Cross-sectional study Setting New York City (2005–2007) Participants 285 IDUs recruited using street-intercept sampling Intervention(s) Not Applicable Main outcome measure(s) IDUs using SEPs, pharmacies, or other outlets as a primary syringe source were compared by sociodemographic characteristics, injection practices and medical service utilization. Results Chi-square tests and polytomous logistic regression were used to compare IDUs with different self-reported primary syringe sources used 6 months prior to study entry. Compared with IDUs using other syringe sources, those using primarily SEPs were less likely to be Black (AOR:0.26 95%CI:0.11–0.57), more likely to inject daily (AOR:3.32; 95%CI:1.58–6.98), and more likely to inject with a new syringe (AOR:2.68; 95%CI:1.30–5.54). Compared with IDUs using other syringe sources, those using primarily pharmacies were less likely to be Black (AOR:0.39; 95%CI0.17–0.90). Conclusion These data suggest that pharmacies and SEPs may be reaching different populations of IDUs and highlight a sub-population of highly marginalized IDUs (Black and infrequent injectors) who are under-utilizing safe syringe sources in New York City. Targeted interventions are needed to reduce racial disparities and increase utilization of safe syringe outlets. PMID:20199954

  11. Targets for Antibiotic and Health Care Resource Stewardship in Inpatient Community-Acquired Pneumonia: A Comparison of Management Practices with National Guideline Recommendations

    PubMed Central

    Jenkins, Timothy C.; Stella, Sarah A.; Cervantes, Lilia; Knepper, Bryan C.; Sabel, Allison L.; Price, Connie S.; Shockley, Lee; Hanley, Michael E.; Mehler, Philip S.; Burman, William J.

    2012-01-01

    Purpose Community-acquired pneumonia (CAP) is the most common infection leading to hospitalization in the U.S. The objective of this study was to evaluate management practices for inpatient CAP in relation to IDSA/ATS guidelines to identify opportunities for antibiotic and health care resource stewardship. Methods This was a retrospective cohort study of adults hospitalized for CAP at a single institution from April 15, 2008 – May 31, 2009. Results Of 209 cases, 166 (79%) were admitted to a medical ward and 43 (21%) to the intensive care unit (ICU). 61 (29%) cases were candidates for outpatient therapy per IDSA/ATS guidance with a CURB-65 score of 0 or 1 and absence of hypoxemia. 110 sputum cultures were ordered; however, an evaluable sample was obtained in 49 (45%) cases, median time from antibiotic initiation to specimen collection was 11 (IQR 6–19) hours, and a potential pathogen was identified in only 18 (16%). Blood cultures were routinely obtained for both non-ICU (81%) and ICU (95%) cases, but 15 of 36 (42%) positive cultures were false-positive results. The most common antibiotic regimen was ceftriaxone plus azithromycin (182, 87% cases). Discordant with IDSA/ATS recommendations, oral step-down therapy consisted of a new antibiotic class in 120 (66%), most commonly levofloxacin (101, 55%). Treatment durations were typically longer than suggested with a median of 10 (IQR 8 – 12) days. Conclusions In this cohort of patients hospitalized for CAP, management was frequently inconsistent with IDSA/ATS guideline recommendations revealing potential targets to reduce unnecessary antibiotic and health care resource utilization. PMID:23160837

  12. A 10-Year Retrospective Comparison of Two Target Sequences, REP-529 and B1, for Toxoplasma gondii Detection by Quantitative PCR

    PubMed Central

    Belaz, Sorya; Gangneux, Jean-Pierre; Dupretz, Peggy; Guiguen, Claude

    2015-01-01

    This study aimed to evaluate the repeated sequence REP-529 compared to that of the B1 gene in the molecular diagnosis of toxoplasmosis by quantitative PCR (qPCR) in routine diagnosis. Over a 10-year period (2003 to 2013), all patients prospectively diagnosed with a positive REP-529 qPCR result for toxoplasmosis were included. All DNA samples (76 samples from 56 patients) were simultaneously tested using the two qPCR methods (REP-529 and B1). The mean cycle threshold (CT) obtained with the B1 qPCR was significantly higher (+4.71 cycles) than that obtained with REP-529 qPCR (P < 0.0001). Thirty-one out of 69 extracts (45.6%) positive with REP-529 qPCR were not amplified with the B1 qPCR (relative sensitivity of 54.4% compared to that with REP-529), yielding false-negative results with 15/28 placenta, 5 cord blood, 2 amniotic fluid, 4 cerebrospinal fluid, 1 aqueous humor, 2 lymph node puncture, and 1 abortion product sample. This defect in sensitivity would have left 20/56 patients undiagnosed, distributed as follows: 12/40 congenital toxoplasmosis, 4/5 cerebral toxoplasmosis, 2/8 patients with retinochoroiditis, and 2 patients with chronic lymphadenopathy. This poor performance of B1 qPCR might be related to low parasite loads, since the mean Toxoplasma quantification in extracts with B1 false-negative results was 0.4 parasite/reaction. These results clearly show the superiority of the REP-529 sequence in the diagnosis of toxoplasmosis by PCR and suggest that this target should be adopted as part of the standardization of the PCR assay. PMID:25653416

  13. 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

  14. Regulatory aspects on nanomedicines.

    PubMed

    Sainz, Vanessa; Conniot, João; Matos, Ana I; Peres, Carina; Zupancic, Eva; Moura, Liane; Silva, Liana C; Florindo, Helena F; Gaspar, Rogério S

    2015-12-18

    Nanomedicines have been in the forefront of pharmaceutical research in the last decades, creating new challenges for research community, industry, and regulators. There is a strong demand for the fast development of scientific and technological tools to address unmet medical needs, thus improving human health care and life quality. Tremendous advances in the biomaterials and nanotechnology fields have prompted their use as promising tools to overcome important drawbacks, mostly associated to the non-specific effects of conventional therapeutic approaches. However, the wide range of application of nanomedicines demands a profound knowledge and characterization of these complex products. Their properties need to be extensively understood to avoid unpredicted effects on patients, such as potential immune reactivity. Research policy and alliances have been bringing together scientists, regulators, industry, and, more frequently in recent years, patient representatives and patient advocacy institutions. In order to successfully enhance the development of new technologies, improved strategies for research-based corporate organizations, more integrated research tools dealing with appropriate translational requirements aiming at clinical development, and proactive regulatory policies are essential in the near future. This review focuses on the most important aspects currently recognized as key factors for the regulation of nanomedicines, discussing the efforts under development by industry and regulatory agencies to promote their translation into the market. Regulatory Science aspects driving a faster and safer development of nanomedicines will be a central issue for the next years. PMID:26260323

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

    PubMed Central

    Harper, Sam; Ruder, Eric; Roman, Henry A.; Geggel, Amelia; Nweke, Onyemaechi; Payne-Sturges, Devon; Levy, Jonathan I.

    2013-01-01

    Formally evaluating how specific policy measures influence environmental justice is challenging, especially in the context of regulatory analyses in which quantitative comparisons are the norm. However, there is a large literature on developing and applying quantitative measures of health inequality in other settings, and these measures may be applicable to environmental regulatory analyses. In this paper, we provide information to assist policy decision makers in determining the viability of using measures of health inequality in the context of environmental regulatory analyses. We conclude that quantification of the distribution of inequalities in health outcomes across social groups of concern, considering both within-group and between-group comparisons, would be consistent with both the structure of regulatory analysis and the core definition of environmental justice. Appropriate application of inequality indicators requires thorough characterization of the baseline distribution of exposures and risks, leveraging data generally available within regulatory analyses. Multiple inequality indicators may be applicable to regulatory analyses, and the choice among indicators should be based on explicit value judgments regarding the dimensions of environmental justice of greatest interest. PMID:23999551

  16. 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

  17. 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

  18. 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

  19. Regulatory T cells in allergy and asthma.

    PubMed

    Larché, Mark

    2007-09-01

    Allergic diseases including asthma have risen considerably in prevalence in the last 50 years. A concomitant rise in autoimmune disease suggests a defect in immunoregulation, rather than a reduction in T-helper type 1 immunity. Immune responses to innocuous environmental antigens in health are characterized by dominant regulation through the production of interleukin-10 and transforming growth factor-beta. Recent studies suggest that diverse populations of regulatory T cells (Treg) play an important role in regulating T-helper type 2 (Th2) responses to allergens, maintaining functional tolerance. Regulatory responses appear to be compromised in allergic individuals but may be reconstituted to some extent with specific allergen immunotherapy. In experimental models, Treg can suppress Th2 responses to allergen, airway eosinophilia, mucous hypersecretion, and airway hyperresponsiveness. Further studies are required to precisely define the mechanisms of development and action of these cells, and to identify and evaluate novel targets for the treatment of allergic diseases. PMID:17873195

  20. Target capture and target ghosts

    NASA Astrophysics Data System (ADS)

    Auerbach, Steven P.

    1996-05-01

    Optimal detection methods for small targets rely on whitened matched filters, which convolve the measured data with the signal model, and whiten the result with the noise covariance. In real-world implementations of such filters, the noise covariance must be estimated from the data, and the resulting covariance estimate may be corrupted by presence of the target. The resulting loss in SNR is called 'target capture'. Target capture is often thought to be a problem only for bright targets. This presentation shows that target capture also arises for dim targets, leading to an SNR loss which is independent of target strength and depends on the averaging method used to estimate the noise covariance. This loss is due to a 'coherent beat' between the true noise and that portion of the estimated noise covariance due to the target. This beat leads to 'ghost targets', which diminish the target SNR by producing a negative target ghost at the target's position. A quantitative estimate of this effect will be given, and shown to agree with numerical results. The effect of averaging on SNR is also discussed for data scenes with synthetic injected targets, in cases where the noise covariance is estimated using 'no target' data. For these cases, it is shown that the so-called 'optimal' filter, which uses the true noise covariance, is actually worse than a 'sub-optimal' filter which estimates the noise from scene. This apparent contradiction is resolved by showing that the optimal filter is best if the same filter is used for many scenes, but is outperformed by a filter adapted to a specific scene.

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

    PubMed Central

    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. PMID:24265219

  2. Securities and Exchange Commission Semiannual Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-26

    ... [Securities and Exchange Commission Semiannual Regulatory Agenda ] Part XXIII Securities and Exchange Commission Semiannual Regulatory Agenda ] SECURITIES AND EXCHANGE COMMISSION (SEC) SECURITIES AND EXCHANGE COMMISSION 17 CFR Ch. II Regulatory Flexibility Agenda AGENCY: Securities and Exchange Commission. ACTION: Semiannual regulatory...

  3. Effects of species combination on comparative analyses of conserved regulatory elements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cross-species DNA sequence comparison is the primary approach to discover regulatory elements by identifying highly conserved sequences due to evolutionary constraints. Previously, we reported that a systematic approach, combining position-specific weight matrixes (JASPAR) and phylogenetic footprint...

  4. Systematic identification of conserved regulatory elements in upstream promoter regions of the cattle genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cross-species DNA sequence comparison is the primary approach to discover regulatory elements by identifying highly conserved sequences due to evolutionary constraints. Previously, we reported that a systematic approach, combining position-specific weight matrixes (JASPAR) and phylogenetic footprint...

  5. Prediction of conserved regulatory elements in promoter regions of the cattle genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cross-species DNA sequence comparison is the primary approach to discover regulatory elements by identifying highly conserved sequences due to evolutionary constraints. Previously, we reported that a systematic approach, combining position-specific weight matrixes (JASPAR) and phylogenetic footprint...

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

    PubMed

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

    2014-01-01

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

  7. T regulatory cells in allergy.

    PubMed

    Braga, M; Quecchia, C; Cavallucci, E; Di Giampaolo, L; Schiavone, C; Petrarca, C; Di Gioacchino, M

    2011-01-01

    The progressive understanding of the nature and mechanisms of T regulatory (Treg) cells in the last decade has changed the concept of immune tolerance, that is no longer considered as a mere lack of immune reactivity but as a finely regulated process that requires specific activity of cells, adhesion and secreted molecules. Tregs play a key role in maintenance of self-tolerance and induction of tolerance against ubiquitous innocuous non-self antigens, so preventing the onset of autoimmune diseases and allergies. This review will focus on the Treg response in allergy that is characterized by a down-regulation of allergen specific T cell proliferation and inhibition of both Th1 and Th2 cytokines production. Hence, Treg cells suppress allergen-specific Th1 and Th2 cell responses playing an important role in the physiological immune response to allergens. Further, Treg cells are able to suppress IgE production by B lymphocytes and directly or indirectly inhibit the activity of allergic inflammation effector cells, namely eosinophils, basophils and mastcells. Finally, increasing evidence suggests that Treg cells are also implicated in chronicity development of inflammatory diseases. This appears to happen through a fine interaction they entertain with resident tissue cells and has been particularly highlighted in the study of airways remodeling in asthma. The understanding of the mechanisms underlying allergen tolerance has brought new interest in the development of new allergy treatment, able to target Treg cells, both in allergy prevention and in the therapy of established allergy. PMID:21329567

  8. The core to regulatory reform

    SciTech Connect

    Partridge, J.W. Jr.

    1993-06-15

    Federal Energy Regulatory Commission (FERC) Orders 436, 500, and 636, the Clean Air Act Amendments of 1990, Public Utility Holding Company Act reform, and the 1992 Energy Policy Act all can have significant effects on an LDC's operations. Such changes in an LDC's environments must be balanced by changes within the utility, its marketplace, and its state regulatory environment. The question is where to start. For Columbia Gas Distribution Cos., based in Columbus, OH, the new operating foundation begins with each employee. Internal strength is critical in designing initiatives that meet the needs of the marketplace and are well-received by regulators. Employees must understand not only the regulatory environment in which the LDC operates, but also how their work contributes to a positive regulatory relationship. To achieve this, Columbia initiated the COntinuing Regulatory Education program, or CORE, in 1991. CORE is a regulatory-focused, information-initiative program coordinated by Columbia's Regulatory Policy, Planning, and Government Affairs Department. The CORE programs can take many forms, such as emerging issue discussions, dialogues with regulators and key parties, updates on regulatory fillings, regulatory policy meetings, and formal training classes. The speakers and discussion facilitators can range from human resource department trainers to senior officers, from regulatory department staff members to external experts, or from state commissioners to executives from other LDCs. The goals of CORE initiatives are to: Support a professional level of regulatory expertise through employee participation in well-developed regulatory programs presented by credible experts. Encourage a constructive state regulatory environment founded on communication and cooperation. CORE achieves these goals via five program levels: introductory basics, advanced learning, professional expertise, crossfunctional dialogues, and external idea exchanges.

  9. 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). VIEWPOINT © 2006 american chemical Society july 1, 2006 / EnvironmEntal SciEncE & tEchnology n 4055 The purpose of this feature article is to consider the roles of toxicogenomics in the field of regulatory ecotoxicology, explore current limitations in the science and practice of genomics, and propose possible avenues to approach and resolve some of the major challenges. A significant amount of input to our analysis came from a workshop sponsored by the Society of Environmental Toxicology and Chemistry (SETAC) in Pellston, Mich., in September 2005. A complete list of names and affiliations of the experts participating in that workshop is provided online in Table 1 of the Supporting Information for this paper.

  10. A compendium of Caenhorabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks

    PubMed Central

    Reece-Hoyes, John S; Deplancke, Bart; Shingles, Jane; Grove, Christian A; Hope, Ian A; Walhout, Albertha JM

    2005-01-01

    Background Transcription regulatory networks are composed of interactions between transcription factors and their target genes. Whereas unicellular networks have been studied extensively, metazoan transcription regulatory networks remain largely unexplored. Caenorhabditis elegans provides a powerful model to study such metazoan networks because its genome is completely sequenced and many functional genomic tools are available. While C. elegans gene predictions have undergone continuous refinement, this is not true for the annotation of functional transcription factors. The comprehensive identification of transcription factors is essential for the systematic mapping of transcription regulatory networks because it enables the creation of physical transcription factor resources that can be used in assays to map interactions between transcription factors and their target genes. Results By computational searches and extensive manual curation, we have identified a compendium of 934 transcription factor genes (referred to as wTF2.0). We find that manual curation drastically reduces the number of both false positive and false negative transcription factor predictions. We discuss how transcription factor splice variants and dimer formation may affect the total number of functional transcription factors. In contrast to mouse transcription factor genes, we find that C. elegans transcription factor genes do not undergo significantly more splicing than other genes. This difference may contribute to differences in organism complexity. We identify candidate redundant worm transcription factor genes and orthologous worm and human transcription factor pairs. Finally, we discuss how wTF2.0 can be used together with physical transcription factor clone resources to facilitate the systematic mapping of C. elegans transcription regulatory networks. Conclusion wTF2.0 provides a starting point to decipher the transcription regulatory networks that control metazoan development and function

  11. T regulatory cells in childhood asthma.

    PubMed

    Strickland, Deborah H; Holt, Patrick G

    2011-09-01

    Asthma is a chronic disease of the airways, most commonly driven by immuno-inflammatory responses to ubiquitous airborne antigens. Epidemiological studies have shown that disease is initiated early in life when the immune and respiratory systems are functionally immature and less able to maintain homeostasis in the face of continuous antigen challenge. Here, we examine the cellular and molecular mechanisms that underlie initial aeroallergen sensitization and the ensuing regulation of secondary responses to inhaled allergens in the airway mucosa. In particular, we focus on how T-regulatory (Treg) cells influence early asthma initiation and the potential of Treg cells as therapeutic targets for drug development in asthma. PMID:21798806

  12. 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.

  13. B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity

    PubMed Central

    Qian, Jason; Wang, Qiao; Dose, Marei; Pruett, Nathanael; Kieffer-Kwon, Kyong-Rim; Resch, Wolfgang; Liang, Genqing; Tang, Zhonghui; Mathé, Ewy; Benner, Christopher; Dubois, Wendy; Nelson, Steevenson; Vian, Laura; Oliveira, Thiago Y.; Jankovic, Mila; Hakim, Ofir; Gazumyan, Anna; Pavri, Rushad; Awasthi, Parirokh; Song, Bin; Liu, Geng; Chen, Longyun; Zhu, Shida; Feigenbaum, Lionel; Staudt, Louis; Murre, Cornelis; Ruan, Yijun; Robbiani, Davide F.; Pan-Hammarström, Qiang; Nussenzweig, Michel C.; Casellas, Rafael

    2014-01-01

    SUMMARY The antibody gene mutator activation-induced cytidine deaminase (AID) promiscuously damages oncogenes, leading to chromosomal translocations and tumorigenesis. Why nonimmunoglobulin loci are susceptible to AID activity is unknown. Here, we study AID-mediated lesions in the context of nuclear architecture and the B cell regulome. We show that AID targets are not randomly distributed across the genome but are predominantly grouped within super-enhancers and regulatory clusters. Unexpectedly, in these domains, AID deaminates active promoters and eRNA+ enhancers interconnected in some instances over megabases of linear chromatin. Using genome editing, we demonstrate that 3D-linked targets cooperate to recruit AID-mediated breaks. Furthermore, a comparison of hypermutation in mouse B cells, AID-induced kataegis in human lymphomas, and translocations in MEFs reveals that AID damages different genes in different cell types. Yet, in all cases, the targets are predominantly associated with topological complex, highly transcribed super-enhancers, demonstrating that these compartments are key mediators of AID recruitment. PMID:25483777

  14. Japanese pharmaceutical and regulatory environment.

    PubMed

    Nagata, Ryoichi; Rafizadeh-Kabe, Jean-David

    2002-12-01

    Drastic regulatory changes in Japan since 1997 have had a considerable impact on the way new medicines are developed. The regulatory authority itself has been transformed. Clinical trials are now performed according to international guidelines. Clinical data generated in one area are acceptable in the rest of the world in some cases through a bridging process that is viewed as only temporary. The future of drug development lies in multinational clinical trials and simultaneous submission to the major regulatory authorities. PMID:22034129

  15. 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…

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

    PubMed

    Schrider, Daniel R; Kern, Andrew D

    2015-12-01

    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

  17. 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

  18. Bovine viral diarrhea virus structural protein E2 as a complement regulatory protein.

    PubMed

    Ostachuk, Agustín

    2016-07-01

    Bovine viral diarrhea virus (BVDV) is a member of the genus Pestivirus, family Flaviviridae, and is one of the most widely distributed viruses in cattle worldwide. Approximately 60 % of cattle in endemic areas without control measures are infected with BVDV during their lifetime. This wide prevalence of BVDV in cattle populations results in significant economic losses. BVDV is capable of establishing persistent infections in its host due to its ability to infect fetuses, causing immune tolerance. However, this cannot explain how the virus evades the innate immune system. The objective of the present work was to test the potential activity of E2 as a complement regulatory protein. E2 glycoprotein, produced both in soluble and transmembrane forms in stable CHO-K1 cell lines, was able to reduce complement-mediated cell lysis up to 40 % and complement-mediated DNA fragmentation by 50 %, in comparison with cell lines not expressing the glycoprotein. This work provides the first evidence of E2 as a complement regulatory protein and, thus, the finding of a mechanism of immune evasion by BVDV. Furthermore, it is postulated that E2 acts as a self-associated molecular pattern (SAMP), enabling the virus to avoid being targeted by the immune system and to be recognized as self. PMID:27038454

  19. 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

  20. Targeting autophagy in neurodegenerative diseases.

    PubMed

    Vidal, René L; Matus, Soledad; Bargsted, Leslie; Hetz, Claudio

    2014-11-01

    The most prevalent neurodegenerative disorders involve protein misfolding and the aggregation of specific proteins. Autophagy is becoming an attractive target to treat neurodegenerative disorders through the selective degradation of abnormally folded proteins by the lysosomal pathway. However, accumulating evidence indicates that autophagy impairment at different regulatory steps may contribute to the neurodegenerative process. Thus, a complex scenario is emerging where autophagy may play a dual role in neurodegenerative diseases by causing the downstream effect of promoting the degradation of misfolded proteins and an upstream effect where its deregulation perturbs global proteostasis, contributing to disease progression. Challenges in the future development of therapeutic strategies to target the autophagy pathway are discussed. PMID:25270767

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

    PubMed Central

    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. PMID:26393364

  2. Building Developmental Gene Regulatory Networks

    PubMed Central

    Li, Enhu; Davidson, Eric H.

    2009-01-01

    Animal development is an elaborate process programmed by genomic regulatory instructions. Regulatory genes encode transcription factors and signal molecules, and their expression is under the control of cis-regulatory modules that define the logic of transcriptional responses to the inputs of other regulatory genes. The functional linkages amongst regulatory genes constitute the gene regulatory networks (GRNs) that govern cell specification and patterning in development. Constructing such networks requires identification of the regulatory genes involved and characterization of their temporal and spatial expression patterns. Interactions (activation/repression) among transcription factors or signals can be investigated by large-scale perturbation analysis, in which the function of each gene is specifically blocked. Resultant expression changes are then integrated to identify direct linkages, and to reveal the structure of the GRN. Predicted GRN linkages can be tested and verified by cis-regulatory analysis. The explanatory power of the GRN was shown in the lineage specification of sea urchin endomesoderm. Acquiring such networks is essential for a systematic and mechanistic understanding of the developmental process. PMID:19530131

  3. 75 FR 79759 - Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-20

    ... use throughout the rulemaking process. Timetable: Action Date FR Cite Notice: Public Meeting Framework... heating equipment. This is the second review for water heaters. Completed: Reason Date FR Cite Final... ``Regulatory Planning and Review,'' 58 FR 51735, and the Regulatory Flexibility Act, 5 U.S.C. 601 et...

  4. 76 FR 3825 - Regulatory Compliance

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-21

    ..., Washington, January 18, 2011 [FR Doc. 2011-1386 Filed 1-20-11; 8:45 am] Billing code 3110-01-P ... Documents#0;#0; ] Memorandum of January 18, 2011 Regulatory Compliance Memorandum for the Heads of Executive... accessible to the public, information concerning their regulatory compliance and enforcement activities,...

  5. Citizen participation on regulatory boards.

    PubMed

    Chesney, J D

    1984-01-01

    This article examines the relationship between regulatory board function and citizen participation. The research indicates that public members generally prefer advisory boards, while provider members prefer quasi-judicial bodies. Implications of these findings for structuring citizen participation in the regulatory process are examined. PMID:6736596

  6. 78 FR 1574 - Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-08

    ... and stability to receive opioid addiction treatment medication. Timetable: Action Date FR Cite NPRM 06/19/09 74 FR 29153 NPRM Comment Period End 08/18/09 Final Action 12/06/12 77 FR 72752 Regulatory... FR Cite NPRM 03/00/13 Regulatory Flexibility Analysis Required: Yes. Agency Contact: Charles...

  7. 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…

  8. 77 FR 7972 - Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-13

    ... agenda pursuant to Executive Order 12866, ``Regulatory Planning and Review,'' 58 FR 51735, and the... 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...

  9. Cancer-Associated Myeloid Regulatory Cells.

    PubMed

    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

  10. 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

  11. 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

  12. 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

  13. 78 FR 1636 - Semiannual Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-08

    ...This Regulatory Agenda is a semiannual summary of all current and projected rulemakings, existing regulations, and completed actions of the Small Business Administration (SBA). For this fall edition of the SBA's Regulatory Agenda, a Regulatory Plan that contains a list of the Agency's most important and significant regulatory actions and a Statement of Regulatory Priorities is also included.......

  14. Department of Justice Semiannual Regulatory Agenda

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-20

    ... [The Regulatory Plan and Unified Agenda of Federal Regulatory and Deregulatory Actions] Part XI Department of Justice Semiannual Regulatory Agenda ] DEPARTMENT OF JUSTICE (DOJ) DEPARTMENT OF JUSTICE 8 CFR Ch. V 21 CFR Ch. I 27 CFR Ch. II 28 CFR Ch. I, V Regulatory Agenda AGENCY: Department of Justice. ACTION: Semiannual regulatory agenda....

  15. A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(®) for methylome profiling.

    PubMed

    Clark, Christine; Palta, Priit; Joyce, Christopher J; Scott, Carol; Grundberg, Elin; Deloukas, Panos; Palotie, Aarno; Coffey, Alison J

    2012-01-01

    DNA methylation is one of the most studied epigenetic marks in the human genome, with the result that the desire to map the human methylome has driven the development of several methods to map DNA methylation on a genomic scale. Our study presents the first comparison of two of these techniques - the targeted approach of the Infinium HumanMethylation450 BeadChip® with the immunoprecipitation and sequencing-based method, MeDIP-seq. Both methods were initially validated with respect to bisulfite sequencing as the gold standard and then assessed in terms of coverage, resolution and accuracy. The regions of the methylome that can be assayed by both methods and those that can only be assayed by one method were determined and the discovery of differentially methylated regions (DMRs) by both techniques was examined. Our results show that the Infinium HumanMethylation450 BeadChip® and MeDIP-seq show a good positive correlation (Spearman correlation of 0.68) on a genome-wide scale and can both be used successfully to determine differentially methylated loci in RefSeq genes, CpG islands, shores and shelves. MeDIP-seq however, allows a wider interrogation of methylated regions of the human genome, including thousands of non-RefSeq genes and repetitive elements, all of which may be of importance in disease. In our study MeDIP-seq allowed the detection of 15,709 differentially methylated regions, nearly twice as many as the array-based method (8070), which may result in a more comprehensive study of the methylome. PMID:23209683

  16. 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. PMID:26945003

  17. 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

  18. [The regulatory role of autophagy in tumor process].

    PubMed

    Liu, Hong; Shao, Rong-guang

    2016-01-01

    Autophagy is a classical regulatory mechanism of energy metabolism and self-update system in the maintenance of the intracellular homeostasis and cell development. Autophagy has been recently found to play a role in tumor development. Autophagy regulates tumor formation, proliferation, metastasis, and metabolism. At the same time, the anticancer drugs formed with autophagic mediators have been used in the treatment, which suggested that improving autophagy activity to inhibit tumor has become a new way for cancer treatment of cancer patients. This article gives an overview of the regulatory mechanism of autophagy, the relationship between autophagy and tumor, and tumor therapy by targeting autophagy. PMID:27405157

  19. Bayesian Nonlinear Model Selection for Gene Regulatory Networks

    PubMed Central

    Ni, Yang; Stingo, Francesco C.; Baladandayuthapani, Veerabhadran

    2015-01-01

    Summary Gene regulatory networks represent the regulatory relationships between genes and their products and are important for exploring and defining the underlying biological processes of cellular systems. We develop a novel framework to recover the structure of nonlinear gene regulatory networks using semiparametric spline-based directed acyclic graphical models. Our use of splines allows the model to have both flexibility in capturing nonlinear dependencies as well as control of overfitting via shrinkage, using mixed model representations of penalized splines. We propose a novel discrete mixture prior on the smoothing parameter of the splines that allows for simultaneous selection of both linear and nonlinear functional relationships as well as inducing sparsity in the edge selection. Using simulation studies, we demonstrate the superior performance of our methods in comparison with several existing approaches in terms of network reconstruction and functional selection. We apply our methods to a gene expression dataset in glioblastoma multiforme, which reveals several interesting and biologically relevant nonlinear relationships. PMID:25854759

  20. 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…

  1. Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi

    PubMed Central

    2004-01-01

    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. PMID:15534694

  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. 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

  4. Homotypic Regulatory Clusters in Drosophila

    PubMed Central

    Lifanov, Alexander P.; Makeev, Vsevolod J.; Nazina, Anna G.; Papatsenko, Dmitri A.

    2003-01-01

    Cis-regulatory modules (CRMs) are transcription regulatory DNA segments (∼1 Kb range) that control the expression of developmental genes in higher eukaryotes. We analyzed clustering of known binding motifs for transcription factors (TFs) in over 60 known CRMs from 20 Drosophila developmental genes, and we present evidence that each type of recognition motif forms significant clusters within the regulatory regions regulated by the corresponding TF. We demonstrate how a search with a single binding motif can be applied to explore gene regulatory networks and to discover coregulated genes in the genome. We also discuss the potential of the clustering method in interpreting the differential response of genes to various levels of transcriptional regulators. PMID:12670999

  5. 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.

  6. Target assembly

    DOEpatents

    Lewis, Richard A.

    1980-01-01

    A target for a proton beam which is capable of generating neutrons for absorption in a breeding blanket includes a plurality of solid pins formed of a neutron emissive target material disposed parallel to the path of the beam and which are arranged axially in a plurality of layers so that pins in each layer are offset with respect to pins in all other layers, enough layers being used so that each proton in the beam will strike at least one pin with means being provided to cool the pins. For a 300 mA, 1 GeV beam (300 MW), stainless steel pins, 12 inches long and 0.23 inches in diameter are arranged in triangular array in six layers with one sixth of the pins in each layer, the number of pins being such that the entire cross sectional area of the beam is covered by the pins with minimum overlap of pins.

  7. 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.

  8. 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.

  9. NF-Y Binding Site Architecture Defines a C-Fos Targeted Promoter Class

    PubMed Central

    Haubrock, Martin; Hartmann, Fabian; Wingender, Edgar

    2016-01-01

    ChIP-seq experiments detect the chromatin occupancy of known transcription factors in a genome-wide fashion. The comparisons of several species-specific ChIP-seq libraries done for different transcription factors have revealed a complex combinatorial and context-specific co-localization behavior for the identified binding regions. In this study we have investigated human derived ChIP-seq data to identify common cis-regulatory principles for the human transcription factor c-Fos. We found that in four different cell lines, c-Fos targeted proximal and distal genomic intervals show prevalences for either AP-1 motifs or CCAAT boxes as known binding motifs for the transcription factor NF-Y, and thereby act in a mutually exclusive manner. For proximal regions of co-localized c-Fos and NF-YB binding, we gathered evidence that a characteristic configuration of repeating CCAAT motifs may be responsible for attracting c-Fos, probably provided by a nearby AP-1 bound enhancer. Our results suggest a novel regulatory function of NF-Y in gene-proximal regions. Specific CCAAT dimer repeats bound by the transcription factor NF-Y define this novel cis-regulatory module. Based on this behavior we propose a new enhancer promoter interaction model based on AP-1 motif defined enhancers which interact with CCAAT-box characterized promoter regions. PMID:27517874

  10. 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. PMID:25634733

  11. 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.

  12. 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.

  13. A method for comparing impacts with real targets to impacts onto the IAEA unyielding target

    SciTech Connect

    Ammerman, D. J.

    1991-01-01

    The severity of the IAEA accident conditions test requirement (IAEA 1990) of an impact onto an essentially unyielding target from a drop height of 9 meters encompasses a large fraction of all real world impacts. This is true, in part, because of the unyielding nature of the impact target. Impacts onto the unyielding target have severities equivalent to higher velocity impacts onto real targets which are not unyielding. The severity of impacts with yielding targets is decreased by the amount of the impact energy absorbed in damaging the target. In demonstrating the severity of the regulatory impact event it is advantageous to be able to relate this impact onto an essentially unyielding target to impacts with yielding targets.

  14. Genomic analysis of the hierarchical structure of regulatory networks

    PubMed Central

    Yu, Haiyuan; Gerstein, Mark

    2006-01-01

    A fundamental question in biology is how the cell uses transcription factors (TFs) to coordinate the expression of thousands of genes in response to various stimuli. The relationships between TFs and their target genes can be modeled in terms of directed regulatory networks. These relationships, in turn, can be readily compared with commonplace “chain-of-command” structures in social networks, which have characteristic hierarchical layouts. Here, we develop algorithms for identifying generalized hierarchies (allowing for various loop structures) and use these approaches to illuminate extensive pyramid-shaped hierarchical structures existing in the regulatory networks of representative prokaryotes (Escherichia coli) and eukaryotes (Saccharomyces cerevisiae), with most TFs at the bottom levels and only a few master TFs on top. These masters are situated near the center of the protein–protein interaction network, a different type of network from the regulatory one, and they receive most of the input for the whole regulatory hierarchy through protein interactions. Moreover, they have maximal influence over other genes, in terms of affecting expression-level changes. Surprisingly, however, TFs at the bottom of the regulatory hierarchy are more essential to the viability of the cell. Finally, one might think master TFs achieve their wide influence through directly regulating many targets, but TFs with most direct targets are in the middle of the hierarchy. We find, in fact, that these midlevel TFs are “control bottlenecks” in the hierarchy, and this great degree of control for “middle managers” has parallels in efficient social structures in various corporate and governmental settings. PMID:17003135

  15. Regulatory RNAs in Bacteria

    PubMed Central

    Waters, Lauren S.; Storz, Gisela

    2011-01-01

    RNA regulators in bacteria are a heterogenous group of molecules that act by various mechanisms to modulate a wide range of physiological responses. One class comprises riboswitches, which are parts of the mRNAs they regulate. These leader sequences fold into structures amenable to conformational changes upon the binding of small molecules. Riboswitches thus sense and respond to the availability of various nutrients in the cell. Other small transcripts bind to proteins, among them global regulators, and antagonize their functions. The largest and most extensively studied set of small RNA regulators act through base pairing with RNAs, usually modulating the translation and stability of mRNAs. The majority of these small RNAs regulate responses to changes in environmental conditions. Finally, a recently discovered group of RNA regulators, known as the CRISPR RNAs, contain short regions of homology to bacteriophage and plasmid sequences. CRISPR RNAs interfere with bacteriophage infection and plasmid conjugation by targeting the homologous foreign DNA through an unknown mechanism. Here we discuss what is known about these RNA regulators, as well as the many intriguing questions that remain to be addressed. PMID:19239884

  16. Accelerator target

    SciTech Connect

    Schlyer, D.J.; Ferrieri, R.A.; Koehler, C.

    1999-06-29

    A target includes a body having a depression in a front side for holding a sample for irradiation by a particle beam to produce a radioisotope. Cooling fins are disposed on a backside of the body opposite the depression. A foil is joined to the body front side to cover the depression and sample therein. A perforate grid is joined to the body atop the foil for supporting the foil and for transmitting the particle beam therethrough. A coolant is circulated over the fins to cool the body during the particle beam irradiation of the sample in the depression. 5 figs.

  17. Accelerator target

    DOEpatents

    Schlyer, David J.; Ferrieri, Richard A.; Koehler, Conrad

    1999-01-01

    A target includes a body having a depression in a front side for holding a sample for irradiation by a particle beam to produce a radioisotope. Cooling fins are disposed on a backside of the body opposite the depression. A foil is joined to the body front side to cover the depression and sample therein. A perforate grid is joined to the body atop the foil for supporting the foil and for transmitting the particle beam therethrough. A coolant is circulated over the fins to cool the bo