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Sample records for synthetic lethality analysis

  1. Development of Synthetic Lethality Anticancer Therapeutics

    PubMed Central

    2015-01-01

    The concept of synthetic lethality (the creation of a lethal phenotype from the combined effects of mutations in two or more genes) has recently been exploited in various efforts to develop new genotype-selective anticancer therapeutics. These efforts include screening for novel anticancer agents, identifying novel therapeutic targets, characterizing mechanisms of resistance to targeted therapy, and improving efficacies through the rational design of combination therapy. This review discusses recent developments in synthetic lethality anticancer therapeutics, including poly ADP-ribose polymerase inhibitors for BRCA1- and BRCA2-mutant cancers, checkpoint inhibitors for p53 mutant cancers, and small molecule agents targeting RAS gene mutant cancers. Because cancers are caused by mutations in multiple genes and abnormalities in multiple signaling pathways, synthetic lethality for a specific tumor suppressor gene or oncogene is likely cell context-dependent. Delineation of the mechanisms underlying synthetic lethality and identification of treatment response biomarkers will be critical for the success of synthetic lethality anticancer therapy. PMID:24893124

  2. The population genetics of synthetic lethals.

    PubMed

    Phillips, P C; Johnson, N A

    1998-09-01

    Synthetic lethals are variants at different loci that have little or no effect on viability singly but cause lethality in combination. The importance of synthetic lethals and, more generally, of synthetic deleterious loci (SDL) has been controversial. Here, we derive the expected frequencies for SDL under a mutation-selection balance for the complete haploid model and selected cases of the diploid model. We have also obtained simple approximations that demonstrate good fit to exact solutions based on numerical iterations. In the haploid case, equilibrium frequencies of carrier haplotypes (individuals with only a single mutation) are comparable to analogous single-locus results, after allowing for the effects of linkage. Frequencies in the diploid case, however, are much higher and more comparable to the square root of the single-locus results. In particular, when selection operates only on the double-mutant homozygote and linkage is not too tight, the expected frequency of the carriers is approximately the quartic root of the ratio between the mutation rate and the selection coefficient of the synthetics. For a reasonably wide set of models, the frequencies of carriers can be on the order of a few percent. The equilibrium frequencies of these deleterious alleles can be relatively high because, with SDL, both dominance and epistasis act to shield carriers from exposure to selection. We also discuss the possible role of SDL in maintaining genetic variation and in hybrid breakdown. PMID:9725860

  3. Synthetic lethal approaches to breast cancer therapy.

    PubMed

    Rehman, Farah L; Lord, Christopher J; Ashworth, Alan

    2010-12-01

    The promise of personalized therapy for breast cancer is that therapeutic efficacy will be increased while toxic effects are reduced to a minimum. To achieve this goal, there is now an emphasis on the design of therapies that are based not only on the clinical manifestations of the disease, but also on the underlying molecular and cellular biology of cancer. However, identifying targets for personalized therapies in breast cancer is challenging. Here, we describe how biological concepts such as synthetic lethality and oncogene addiction can be used to identify new therapeutic targets and approaches. We discuss the current clinical developments in implementing synthetic lethality therapies, and highlight new ways in which this approach could be used to target specific subsets of breast cancer. PMID:20956981

  4. Synthetic lethal approaches for assessing combinatorial efficacy of chemotherapeutic drugs.

    PubMed

    Jackson, Rebecca A; Chen, Ee Sin

    2016-06-01

    The recent advances in pharmacogenomics have made personalized medicine no longer a pipedream but a precise and powerful way to tailor individualized cancer treatment strategies. Cancer is a devastating disease, and contemporary chemotherapeutic strategies now integrate several agents in the treatment of some types of cancer, with the intent to block more than one target simultaneously. This constitutes the premise of synthetic lethality, an attractive therapeutic strategy already demonstrating clinical success in patients with breast and ovarian cancers. Synthetic lethal combinations offer the potential to also target the hitherto "undruggable" mutations that have challenged the cancer field for decades. However, synthetic lethality in clinical cancer therapy is very much still in its infancy, and selecting the most appropriate combinations-or synthetic lethal pairs-is not always an intuitive process. Here, we review some of the recent progress in identifying synthetic lethal combinations and their potential for therapy and highlight some of the tools through which synthetic lethal pairs are identified. PMID:26803999

  5. Approaches to identifying synthetic lethal interactions in cancer.

    PubMed

    Thompson, Jordan M; Nguyen, Quy H; Singh, Manpreet; Razorenova, Olga V

    2015-06-01

    Targeting synthetic lethal interactions is a promising new therapeutic approach to exploit specific changes that occur within cancer cells. Multiple approaches to investigate these interactions have been developed and successfully implemented, including chemical, siRNA, shRNA, and CRISPR library screens. Genome-wide computational approaches, such as DAISY, also have been successful in predicting synthetic lethal interactions from both cancer cell lines and patient samples. Each approach has its advantages and disadvantages that need to be considered depending on the cancer type and its molecular alterations. This review discusses these approaches and examines case studies that highlight their use. PMID:26029013

  6. Approaches to Identifying Synthetic Lethal Interactions in Cancer

    PubMed Central

    Thompson, Jordan M.; Nguyen, Quy H.; Singh, Manpreet; Razorenova, Olga V.

    2015-01-01

    Targeting synthetic lethal interactions is a promising new therapeutic approach to exploit specific changes that occur within cancer cells. Multiple approaches to investigate these interactions have been developed and successfully implemented, including chemical, siRNA, shRNA, and CRISPR library screens. Genome-wide computational approaches, such as DAISY, also have been successful in predicting synthetic lethal interactions from both cancer cell lines and patient samples. Each approach has its advantages and disadvantages that need to be considered depending on the cancer type and its molecular alterations. This review discusses these approaches and examines case studies that highlight their use. PMID:26029013

  7. Moving ahead on harnessing synthetic lethality to fight cancer

    PubMed Central

    Jerby-Arnon, Livnat; Ruppin, Eytan

    2015-01-01

    We have recently developed a data-mining pipeline that comprehensively identifies cancer unique susceptibilities, following the concept of Synthetic Lethality (SL). The approach enables, for the first time, to identify and harness genome-scale SL-networks to accurately predict gene essentiality, drug response, and clinical prognosis in cancer. PMID:27308440

  8. Annotating novel genes by integrating synthetic lethals and genomic information

    PubMed Central

    Schöner, Daniel; Kalisch, Markus; Leisner, Christian; Meier, Lukas; Sohrmann, Marc; Faty, Mahamadou; Barral, Yves; Peter, Matthias; Gruissem, Wilhelm; Bühlmann, Peter

    2008-01-01

    Background Large scale screening for synthetic lethality serves as a common tool in yeast genetics to systematically search for genes that play a role in specific biological processes. Often the amounts of data resulting from a single large scale screen far exceed the capacities of experimental characterization of every identified target. Thus, there is need for computational tools that select promising candidate genes in order to reduce the number of follow-up experiments to a manageable size. Results We analyze synthetic lethality data for arp1 and jnm1, two spindle migration genes, in order to identify novel members in this process. To this end, we use an unsupervised statistical method that integrates additional information from biological data sources, such as gene expression, phenotypic profiling, RNA degradation and sequence similarity. Different from existing methods that require large amounts of synthetic lethal data, our method merely relies on synthetic lethality information from two single screens. Using a Multivariate Gaussian Mixture Model, we determine the best subset of features that assign the target genes to two groups. The approach identifies a small group of genes as candidates involved in spindle migration. Experimental testing confirms the majority of our candidates and we present she1 (YBL031W) as a novel gene involved in spindle migration. We applied the statistical methodology also to TOR2 signaling as another example. Conclusion We demonstrate the general use of Multivariate Gaussian Mixture Modeling for selecting candidate genes for experimental characterization from synthetic lethality data sets. For the given example, integration of different data sources contributes to the identification of genetic interaction partners of arp1 and jnm1 that play a role in the same biological process. PMID:18194531

  9. Gene essentiality and synthetic lethality in haploid human cells.

    PubMed

    Blomen, Vincent A; Májek, Peter; Jae, Lucas T; Bigenzahn, Johannes W; Nieuwenhuis, Joppe; Staring, Jacqueline; Sacco, Roberto; van Diemen, Ferdy R; Olk, Nadine; Stukalov, Alexey; Marceau, Caleb; Janssen, Hans; Carette, Jan E; Bennett, Keiryn L; Colinge, Jacques; Superti-Furga, Giulio; Brummelkamp, Thijn R

    2015-11-27

    Although the genes essential for life have been identified in less complex model organisms, their elucidation in human cells has been hindered by technical barriers. We used extensive mutagenesis in haploid human cells to identify approximately 2000 genes required for optimal fitness under culture conditions. To study the principles of genetic interactions in human cells, we created a synthetic lethality network focused on the secretory pathway based exclusively on mutations. This revealed a genetic cross-talk governing Golgi homeostasis, an additional subunit of the human oligosaccharyltransferase complex, and a phosphatidylinositol 4-kinase β adaptor hijacked by viruses. The synthetic lethality map parallels observations made in yeast and projects a route forward to reveal genetic networks in diverse aspects of human cell biology. PMID:26472760

  10. Synthetic lethality for linking the mycophenolate mofetil mode of action with molecular disease and drug profiles.

    PubMed

    Söllner, Johannes; Mayer, Paul; Heinzel, Andreas; Fechete, Raul; Siehs, Christian; Oberbauer, Rainer; Mayer, Bernd

    2012-10-30

    Systematic study of the effect of mycophenolate mofetil (MMF) on the molecular level in the context of other drugs and molecular disease profiles became possible due to the availability of large scale molecular profiles on both disease characterization and drug mode of action. Such analysis is of particular value in elucidating alternative drug use for addressing clinically unmet needs, and the concept of synthetic lethality provides an alternative tool for such repositioning strategies. Resting on consolidation of transcriptomics data and literature mining, a MMF molecular footprint became available including a set of 170 genes specifically affected by the drug. Analysis of this profile on a molecular pathway level reveals a set of 14 pathways as affected. Next to assignment of molecular pathways and associated diseases synergistic drug combinations are proposed by utilizing the synthetic lethal interaction network. Of particular interest is the combination of MMF with adenosine deaminase inhibitors, sulfasalazine, and other selected drugs interfering with calcium-based regulatory pathways and metabolism. Indeed analysis of drugs in clinical trials positively identifies combinations with MMF in the context of synthetic lethality and affected pathways, particularly in diseases such as multiple sclerosis, vasculitis, GVHD and lupus nephritis. Importantly, the synthetic lethal interaction of the drug mode of action is an interesting basis for rational repositioning strategies by suggesting combinations which exhibit a synergistic rather than a mere additive effect, as for example is evident for the combination of tacrolimus and MMF. Inherent is also the assessment of possible adverse effects of drug combinations. PMID:23014771

  11. Syn-Lethality: An Integrative Knowledge Base of Synthetic Lethality towards Discovery of Selective Anticancer Therapies

    PubMed Central

    Li, Xue-juan; Mishra, Shital K.; Wu, Min; Zhang, Fan

    2014-01-01

    Synthetic lethality (SL) is a novel strategy for anticancer therapies, whereby mutations of two genes will kill a cell but mutation of a single gene will not. Therefore, a cancer-specific mutation combined with a drug-induced mutation, if they have SL interactions, will selectively kill cancer cells. While numerous SL interactions have been identified in yeast, only a few have been known in human. There is a pressing need to systematically discover and understand SL interactions specific to human cancer. In this paper, we present Syn-Lethality, the first integrative knowledge base of SL that is dedicated to human cancer. It integrates experimentally discovered and verified human SL gene pairs into a network, associated with annotations of gene function, pathway, and molecular mechanisms. It also includes yeast SL genes from high-throughput screenings which are mapped to orthologous human genes. Such an integrative knowledge base, organized as a relational database with user interface for searching and network visualization, will greatly expedite the discovery of novel anticancer drug targets based on synthetic lethality interactions. The database can be downloaded as a stand-alone Java application. PMID:24864230

  12. Synthetic lethality-based targets for discovery of new cancer therapeutics.

    PubMed

    Weidle, Ulrich H; Maisel, Daniela; Eick, Dirk

    2011-01-01

    Synthetic lethality is based on the incompatibility of cell survival with the loss of function of two or more genes, not with loss of function of a single gene. If targets of synthetic lethality are deregulated or mutated in cancer cells, the strategy of synthetic lethality can result in significant increase of therapeutic efficacy and a favourable therapeutic window. In this review, we discuss synthetic lethality based on deficient DNA repair mechanisms, activating mutations of RAS, loss of function mutations of the tumor suppressor genes p53, Rb and von Hippel-Lindau, and disruption of interactive protein kinase networks in the context of development of new anticancer agents. PMID:21737609

  13. Synthetic lethal approaches exploiting DNA damage in aggressive myeloma

    PubMed Central

    Cottini, Francesca; Hideshima, Teru; Suzuki, Rikio; Tai, Yu-Tzu; Bianchini, Giampaolo; Richardson, Paul G.; Anderson, Kenneth C.; Tonon, Giovanni

    2015-01-01

    Ongoing DNA damage is a common feature of epithelial cancers. Here we show that tumor cells derived from multiple myeloma (MM), a disease of clonal plasma cells, demonstrate DNA replicative stress leading to DNA damage. We identified a poor prognosis subset of MM with extensive chromosomal instability and replicative stress which rely on ATR to compensate for DNA replicative stress; conversely, silencing of ATR or treatment with a specific ATR inhibitor triggers MM cell apoptosis. We show that oncogenes such as MYC induce DNA damage in MM cells not only by increased replicative stress, but also via increased oxidative stress, and that ROS-inducer piperlongumine triggers further DNA damage and apoptosis. Importantly, ATR inhibition combined with piperlongumine triggers synergistic MM cytotoxicity. This synthetic lethal approach, enhancing oxidative stress while concomitantly blocking replicative stress response, provides a novel combination targeted therapy to address an unmet medical need in this subset of MM. PMID:26080835

  14. RAS Synthetic Lethal Screens Revisited: Still Seeking the Elusive Prize?

    PubMed Central

    Downward, Julian

    2015-01-01

    The RAS genes are critical oncogenic drivers activated by point mutation in some 20% of human malignancies. However, no pharmacological approaches to targeting RAS proteins directly have yet succeeded, leading to suggestions that these proteins may be “undruggable.” This has led to two alternative indirect approaches to targeting RAS function in cancer. One has been to target RAS signaling pathways downstream at tractable enzymes such as kinases, particularly in combination. The other, which is the focus of this review, has been to seek targets that are essential in cells bearing an activated RAS oncogene, but not those without. This synthetic lethal approach, while rooted in ideas from invertebrate genetics, has been inspired most strongly by the successful use of PARP inhibitors, such as olaparib, in the clinic to treat BRCA defective cancers. Several large-scale screens have been carried out using RNA interference-mediated expression silencing to find genes that are uniquely essential to RAS mutant but not wild type cells. These screens have been notable for the low degree of overlap between their results, with the possible exception of proteasome components, and have yet to lead to successful new clinical approaches to the treatment of RAS mutant cancers. Possible reasons for these disappointing results are discussed here, along with a re-evaluation of the approaches taken. Based on experience to date, RAS synthetic lethality has so far fallen some way short of its original promise and remains unproven as an approach to finding effective new ways of tackling RAS mutant cancers. PMID:25878361

  15. Synthetic lethality in ATM-deficient RAD50-mutant tumors underlie outlier response to cancer therapy

    PubMed Central

    Al-Ahmadie, Hikmat; Iyer, Gopa; Hohl, Marcel; Asthana, Saurabh; Inagaki, Akiko; Schultz, Nikolaus; Hanrahan, Aphrothiti J.; Scott, Sasinya N.; Brannon, A. Rose; McDermott, Gregory C.; Pirun, Mono; Ostrovnaya, Irina; Kim, Philip; Socci, Nicholas D.; Viale, Agnes; Schwartz, Gary K.; Reuter, Victor; Bochner, Bernard H.; Rosenberg, Jonathan E.; Bajorin, Dean F.; Berger, Michael F.; Petrini, John H.J.; Solit, David B.; Taylor, Barry S.

    2014-01-01

    Metastatic solid tumors are almost invariably fatal. Patients with disseminated small-cell cancers have a particularly unfavorable prognosis with most succumbing to their disease within two years. Here, we report on the genetic and functional analysis of an outlier curative response of a patient with metastatic small cell cancer to combined checkpoint kinase 1 (Chk1) inhibition and DNA damaging chemotherapy. Whole-genome sequencing revealed a clonal hemizygous mutation in the Mre11 complex gene RAD50 that attenuated ATM signaling which in the context of Chk1 inhibition contributed, via synthetic lethality, to extreme sensitivity to irinotecan. As Mre11 mutations occur in a diversity of human tumors, the results suggest a tumor-specific combination therapy strategy whereby checkpoint inhibition in combination with DNA damaging chemotherapy is synthetically lethal in tumor but not normal cells with somatic mutations that impair Mre11 complex function. PMID:24934408

  16. Malignancy of Cancers and Synthetic Lethal Interactions Associated With Mutations of Cancer Driver Genes

    PubMed Central

    Wang, Xiaosheng; Zhang, Yue; Han, Ze-Guang; He, Kun-Yan

    2016-01-01

    Abstract The mutation status of cancer driver genes may correlate with different degrees of malignancy of cancers. The doubling time and multidrug resistance are 2 phenotypes that reflect the degree of malignancy of cancer cells. Because most of cancer driver genes are hard to target, identification of their synthetic lethal partners might be a viable approach to treatment of the cancers with the relevant mutations. The genome-wide screening for synthetic lethal partners is costly and labor intensive. Thus, a computational approach facilitating identification of candidate genes for a focus synthetic lethal RNAi screening will accelerate novel anticancer drug discovery. We used several publicly available cancer cell lines and tumor tissue genomic data in this study. We compared the doubling time and multidrug resistance between the NCI-60 cell lines with mutations in some cancer driver genes and those without the mutations. We identified some candidate synthetic lethal genes to the cancer driver genes APC, KRAS, BRAF, PIK3CA, and TP53 by comparison of their gene phenotype values in cancer cell lines with the relevant mutations and wild-type background. Further, we experimentally validated some of the synthetic lethal relationships we predicted. We reported that mutations in some cancer driver genes mutations in some cancer driver genes such as APC, KRAS, or PIK3CA might correlate with cancer proliferation or drug resistance. We identified 40, 21, 5, 43, and 18 potential synthetic lethal genes to APC, KRAS, BRAF, PIK3CA, and TP53, respectively. We found that some of the potential synthetic lethal genes show significantly higher expression in the cancers with mutations of their synthetic lethal partners and the wild-type counterparts. Further, our experiments confirmed several synthetic lethal relationships that are novel findings by our methods. We experimentally validated a part of the synthetic lethal relationships we predicted. We plan to perform further

  17. A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy.

    PubMed

    Srivas, Rohith; Shen, John Paul; Yang, Chih Cheng; Sun, Su Ming; Li, Jianfeng; Gross, Andrew M; Jensen, James; Licon, Katherine; Bojorquez-Gomez, Ana; Klepper, Kristin; Huang, Justin; Pekin, Daniel; Xu, Jia L; Yeerna, Huwate; Sivaganesh, Vignesh; Kollenstart, Leonie; van Attikum, Haico; Aza-Blanc, Pedro; Sobol, Robert W; Ideker, Trey

    2016-08-01

    An emerging therapeutic strategy for cancer is to induce selective lethality in a tumor by exploiting interactions between its driving mutations and specific drug targets. Here we use a multi-species approach to develop a resource of synthetic lethal interactions relevant to cancer therapy. First, we screen in yeast ∼169,000 potential interactions among orthologs of human tumor suppressor genes (TSG) and genes encoding drug targets across multiple genotoxic environments. Guided by the strongest signal, we evaluate thousands of TSG-drug combinations in HeLa cells, resulting in networks of conserved synthetic lethal interactions. Analysis of these networks reveals that interaction stability across environments and shared gene function increase the likelihood of observing an interaction in human cancer cells. Using these rules, we prioritize ∼10(5) human TSG-drug combinations for future follow-up. We validate interactions based on cell and/or patient survival, including topoisomerases with RAD17 and checkpoint kinases with BLM. PMID:27453043

  18. A Synthetic Lethal Screen Identifies DNA Repair Pathways that Sensitize Cancer Cells to Combined ATR Inhibition and Cisplatin Treatments

    PubMed Central

    Mohni, Kareem N.; Thompson, Petria S.; Luzwick, Jessica W.; Glick, Gloria G.; Pendleton, Christopher S.; Lehmann, Brian D.; Pietenpol, Jennifer A.; Cortez, David

    2015-01-01

    The DNA damage response kinase ATR may be a useful cancer therapeutic target. ATR inhibition synergizes with loss of ERCC1, ATM, XRCC1 and DNA damaging chemotherapy agents. Clinical trials have begun using ATR inhibitors in combination with cisplatin. Here we report the first synthetic lethality screen with a combination treatment of an ATR inhibitor (ATRi) and cisplatin. Combination treatment with ATRi/cisplatin is synthetically lethal with loss of the TLS polymerase ζ and 53BP1. Other DNA repair pathways including homologous recombination and mismatch repair do not exhibit synthetic lethal interactions with ATRi/cisplatin, even though loss of some of these repair pathways sensitizes cells to cisplatin as a single-agent. We also report that ATRi strongly synergizes with PARP inhibition, even in homologous recombination-proficient backgrounds. Lastly, ATR inhibitors were able to resensitize cisplatin-resistant cell lines to cisplatin. These data provide a comprehensive analysis of DNA repair pathways that exhibit synthetic lethality with ATR inhibitors when combined with cisplatin chemotherapy, and will help guide patient selection strategies as ATR inhibitors progress into the cancer clinic. PMID:25965342

  19. ATR pathway inhibition is synthetically lethal in cancer cells with ERCC1 deficiency

    PubMed Central

    Mohni, Kareem N.; Kavanaugh, Gina M.; Cortez, David

    2014-01-01

    The DNA damage response kinase ATR and its effector kinase CHEK1 are required for cancer cells to survive oncogene-induced replication stress. ATR inhibitors exhibit synthetic lethal interactions with deficiencies in the DNA damage response enzymes ATM and XRCC1 and with overexpression of the cell cycle kinase Cyclin E. Here we report a systematic screen to identify synthetic lethal interactions with ATR-pathway targeted drugs, rationalized by their predicted therapeutic utility in the oncology clinic. We found that reduced function in the ATR pathway itself provided the strongest synthetic lethal interaction. In addition, we found that loss of the structure specific-endonuclease ERCC1-XPF (ERCC4) is synthetic lethal with ATR pathway inhibitors. ERCC1-deficient cells exhibited elevated levels of DNA damage, which was increased further by ATR inhibition. When treated with ATR or CHEK1 inhibitors, ERCC1-deficient cells arrested in S phase and failed to complete cell cycle transit even after drug removal. Notably, triple-negative breast cancer cells and non-small cell lung cancer cells depleted of ERCC1 exhibited increased sensitivity to ATR-pathway targeted drugs. Overall, we concluded that ATR pathway-targeted drugs may offer particular utility in cancers with reduced ATR pathway function or reduced levels of ERCC4 activity. PMID:24662920

  20. Synthetic Lethality Reveals Mechanisms of Mycobacterium tuberculosis Resistance to β-Lactams

    PubMed Central

    Lun, Shichun; Miranda, David; Kubler, Andre; Guo, Haidan; Maiga, Mariama C.; Winglee, Kathryn; Pelly, Shaaretha

    2014-01-01

    ABSTRACT Most β-lactam antibiotics are ineffective against Mycobacterium tuberculosis due to the microbe’s innate resistance. The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains has prompted interest to repurpose this class of drugs. To identify the genetic determinants of innate β-lactam resistance, we carried out a synthetic lethality screen on a transposon mutant library for susceptibility to imipenem, a carbapenem β-lactam antibiotic. Mutations in 74 unique genes demonstrated synthetic lethality. The majority of mutations were in genes associated with cell wall biosynthesis. A second quantitative real-time PCR (qPCR)-based synthetic lethality screen of randomly selected mutants confirmed the role of cell wall biosynthesis in β-lactam resistance. The global transcriptional response of the bacterium to β-lactams was investigated, and changes in levels of expression of cell wall biosynthetic genes were identified. Finally, we validated these screens in vivo using the MT1616 transposon mutant, which lacks a functional acyl-transferase gene. Mice infected with the mutant responded to β-lactam treatment with a 100-fold decrease in bacillary lung burden over 4 weeks, while the numbers of organisms in the lungs of mice infected with wild-type bacilli proliferated. These findings reveal a road map of genes required for β-lactam resistance and validate synthetic lethality screening as a promising tool for repurposing existing classes of licensed, safe, well-characterized antimicrobials against tuberculosis. PMID:25227469

  1. ATR pathway inhibition is synthetically lethal in cancer cells with ERCC1 deficiency.

    PubMed

    Mohni, Kareem N; Kavanaugh, Gina M; Cortez, David

    2014-05-15

    The DNA damage response kinase ATR and its effector kinase CHEK1 are required for cancer cells to survive oncogene-induced replication stress. ATR inhibitors exhibit synthetic lethal interactions, with deficiencies in the DNA damage response enzymes ATM and XRCC1 and with overexpression of the cell cycle kinase cyclin E. Here, we report a systematic screen to identify synthetic lethal interactions with ATR pathway-targeted drugs, rationalized by their predicted therapeutic utility in the oncology clinic. We found that reduced function in the ATR pathway itself provided the strongest synthetic lethal interaction. In addition, we found that loss of the structure-specific endonuclease ERCC1-XPF (ERCC4) is synthetic lethal with ATR pathway inhibitors. ERCC1-deficient cells exhibited elevated levels of DNA damage, which was increased further by ATR inhibition. When treated with ATR or CHEK1 inhibitors, ERCC1-deficient cells were arrested in S-phase and failed to complete cell-cycle transit even after drug removal. Notably, triple-negative breast cancer cells and non-small cell lung cancer cells depleted of ERCC1 exhibited increased sensitivity to ATR pathway-targeted drugs. Overall, we concluded that ATR pathway-targeted drugs may offer particular utility in cancers with reduced ATR pathway function or reduced levels of ERCC4 activity. PMID:24662920

  2. Analysis of Synthetic Polymers.

    ERIC Educational Resources Information Center

    Smith, Charles G.; And Others

    1989-01-01

    Reviews techniques for the characterization and analysis of synthetic polymers, copolymers, and blends. Includes techniques for structure determination, separation, and quantitation of additives and residual monomers; determination of molecular weight; and the study of thermal properties including degradation mechanisms. (MVL)

  3. Composite synthetic lethal identification of membrane traffic inhibitors

    PubMed Central

    Duncan, Mara C.; Ho, David G.; Huang, Jing; Jung, Michael E.; Payne, Gregory S.

    2007-01-01

    Small molecule inhibitors provide powerful tools to characterize highly dynamic and complex eukaryotic cell pathways such as those mediating membrane traffic. However, a lack of easy and generalizable assays has constrained identification of novel inhibitors despite availability of diverse chemical libraries. Here, we report a facile growth-based strategy in yeast to screen for pathway-specific inhibitors. The approach uses well characterized synthetic genetic growth defects to guide design of cells genetically sensitized for inhibition of chosen pathways. With this strategy, we identified a family of piperazinyl phenylethanone compounds as inhibitors of traffic between the trans-Golgi network (TGN) and endosomes that depends on the clathrin adaptor complex AP-1. The compounds did not significantly alter other trafficking pathways involving the TGN or endosomes, indicating specificity. Compound treatment also altered localization of AP-1 in mammalian cells. These previously uncharacterized inhibitors will be useful for future studies of clathrin-mediated transport in yeast, and potentially in other organisms. Furthermore, the easily automated technology should be adaptable for identification of inhibitors of other cellular processes. PMID:17404221

  4. SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets.

    PubMed

    Guo, Jing; Liu, Hui; Zheng, Jie

    2016-01-01

    Synthetic lethality (SL) is a type of genetic interaction between two genes such that simultaneous perturbations of the two genes result in cell death or a dramatic decrease of cell viability, while a perturbation of either gene alone is not lethal. SL reflects the biologically endogenous difference between cancer cells and normal cells, and thus the inhibition of SL partners of genes with cancer-specific mutations could selectively kill cancer cells but spare normal cells. Therefore, SL is emerging as a promising anticancer strategy that could potentially overcome the drawbacks of traditional chemotherapies by reducing severe side effects. Researchers have developed experimental technologies and computational prediction methods to identify SL gene pairs on human and a few model species. However, there has not been a comprehensive database dedicated to collecting SL pairs and related knowledge. In this paper, we propose a comprehensive database, SynLethDB (http://histone.sce.ntu.edu.sg/SynLethDB/), which contains SL pairs collected from biochemical assays, other related databases, computational predictions and text mining results on human and four model species, i.e. mouse, fruit fly, worm and yeast. For each SL pair, a confidence score was calculated by integrating individual scores derived from different evidence sources. We also developed a statistical analysis module to estimate the druggability and sensitivity of cancer cells upon drug treatments targeting human SL partners, based on large-scale genomic data, gene expression profiles and drug sensitivity profiles on more than 1000 cancer cell lines. To help users access and mine the wealth of the data, we developed other practical functionalities, such as search and filtering, orthology search, gene set enrichment analysis. Furthermore, a user-friendly web interface has been implemented to facilitate data analysis and interpretation. With the integrated data sets and analytics functionalities, SynLethDB would

  5. Identification of essential genes and synthetic lethal gene combinations in Escherichia coli K-12.

    PubMed

    Mori, Hirotada; Baba, Tomoya; Yokoyama, Katsushi; Takeuchi, Rikiya; Nomura, Wataru; Makishi, Kazuichi; Otsuka, Yuta; Dose, Hitomi; Wanner, Barry L

    2015-01-01

    Here we describe the systematic identification of single genes and gene pairs, whose knockout causes lethality in Escherichia coli K-12. During construction of precise single-gene knockout library of E. coli K-12, we identified 328 essential gene candidates for growth in complex (LB) medium. Upon establishment of the Keio single-gene deletion library, we undertook the development of the ASKA single-gene deletion library carrying a different antibiotic resistance. In addition, we developed tools for identification of synthetic lethal gene combinations by systematic construction of double-gene knockout mutants. We introduce these methods herein. PMID:25636612

  6. High throughput synthetic lethality screen reveals a tumorigenic role of adenylate cyclase in fumarate hydratase-deficient cancer cells

    PubMed Central

    2014-01-01

    Background Synthetic lethality is an appealing technique for selectively targeting cancer cells which have acquired molecular changes that distinguish them from normal cells. High-throughput RNAi-based screens have been successfully used to identify synthetic lethal pathways with well-characterized tumor suppressors and oncogenes. The recent identification of metabolic tumor suppressors suggests that the concept of synthetic lethality can be applied to selectively target cancer metabolism as well. Results Here, we perform a high-throughput RNAi screen to identify synthetic lethal genes with fumarate hydratase (FH), a metabolic tumor suppressor whose loss-of-function has been associated with hereditary leiomyomatosis and renal cell carcinoma (HLRCC). Our unbiased screen identified synthetic lethality between FH and several genes in heme metabolism, in accordance with recent findings. Furthermore, we identified an enrichment of synthetic lethality with adenylate cyclases. The effects were validated in an embryonic kidney cell line (HEK293T) and in HLRCC-patient derived cells (UOK262) via both genetic and pharmacological inhibition. The reliance on adenylate cyclases in FH-deficient cells is consistent with increased cyclic-AMP levels, which may act to regulate cellular energy metabolism. Conclusions The identified synthetic lethality of FH with adenylate cyclases suggests a new potential target for treating HLRCC patients. PMID:24568598

  7. KRAS mutant NSCLC, a new opportunity for the synthetic lethality therapeutic approach.

    PubMed

    de Castro Carpeño, Javier; Belda-Iniesta, Cristóbal

    2013-04-01

    K-RAS accounts for 90% of RAS mutations in lung adenocarcinomas, the most commonly mutated oncogene in NSCLC, with mutations detected in about 25% of all tumors. Direct inhibition of KRAS has proven clinically challenging. So far, no successful targeted therapy has been developed and remains an elusive target for cancer therapy. Despite significant efforts, currently there are no drugs directly targeting mutated KRAS. Thus, new strategies have emerged for targeting RAS including the use of synthetic lethality. A specific knowledge of individual tumor molecular abnormalities that result in oncogene-specific "synthetic lethal" interactions will allow the rationale to combine promising targeted therapies for KRAS-mutated NSCLC. In this article, we review the new approach based on testing drugs or combinations of agents that work downstream of activated K-RAS. PMID:25806225

  8. MYC pathway activation in triple-negative breast cancer is synthetic lethal with CDK inhibition

    PubMed Central

    Horiuchi, Dai; Kusdra, Leonard; Huskey, Noelle E.; Chandriani, Sanjay; Lenburg, Marc E.; Gonzalez-Angulo, Ana Maria; Creasman, Katelyn J.; Bazarov, Alexey V.; Smyth, James W.; Davis, Sarah E.; Yaswen, Paul; Mills, Gordon B.; Esserman, Laura J.

    2012-01-01

    Estrogen, progesterone, and HER2 receptor-negative triple-negative breast cancers encompass the most clinically challenging subtype for which targeted therapeutics are lacking. We find that triple-negative tumors exhibit elevated MYC expression, as well as altered expression of MYC regulatory genes, resulting in increased activity of the MYC pathway. In primary breast tumors, MYC signaling did not predict response to neoadjuvant chemotherapy but was associated with poor prognosis. We exploit the increased MYC expression found in triple-negative breast cancers by using a synthetic-lethal approach dependent on cyclin-dependent kinase (CDK) inhibition. CDK inhibition effectively induced tumor regression in triple-negative tumor xenografts. The proapoptotic BCL-2 family member BIM is up-regulated after CDK inhibition and contributes to this synthetic-lethal mechanism. These results indicate that aggressive breast tumors with elevated MYC are uniquely sensitive to CDK inhibitors. PMID:22430491

  9. Epigenetic synthetic lethality in ovarian clear cell carcinoma: EZH2 and ARID1A mutations

    PubMed Central

    Bitler, Benjamin G; Aird, Katherine M; Zhang, Rugang

    2016-01-01

    The components of the Switch/Sucrose non-fermentable (SWI/SNF) complex are mutated in approximately 20% of human cancers. The A/T-rich interacting domain 1A (ARID1A) subunit has one of the highest mutation rates. Most notably, ARID1A is mutated in over 50% of ovarian clear cell carcinomas (OCCCs). We reported that inhibition of enhancer of zeste homology 2 (EZH2) is synthetically lethal in ARID1A-mutated OCCC. PMID:27308548

  10. Epigenetic synthetic lethality in ovarian clear cell carcinoma: EZH2 and ARID1A mutations.

    PubMed

    Bitler, Benjamin G; Aird, Katherine M; Zhang, Rugang

    2016-01-01

    The components of the Switch/Sucrose non-fermentable (SWI/SNF) complex are mutated in approximately 20% of human cancers. The A/T-rich interacting domain 1A (ARID1A) subunit has one of the highest mutation rates. Most notably, ARID1A is mutated in over 50% of ovarian clear cell carcinomas (OCCCs). We reported that inhibition of enhancer of zeste homology 2 (EZH2) is synthetically lethal in ARID1A-mutated OCCC. PMID:27308548

  11. Cancer-Specific Synthetic Lethality between ATR and CHK1 Kinase Activities.

    PubMed

    Sanjiv, Kumar; Hagenkort, Anna; Calderón-Montaño, José Manuel; Koolmeister, Tobias; Reaper, Philip M; Mortusewicz, Oliver; Jacques, Sylvain A; Kuiper, Raoul V; Schultz, Niklas; Scobie, Martin; Charlton, Peter A; Pollard, John R; Berglund, Ulrika Warpman; Altun, Mikael; Helleday, Thomas

    2016-01-12

    ATR and CHK1 maintain cancer cell survival under replication stress and inhibitors of both kinases are currently undergoing clinical trials. As ATR activity is increased after CHK1 inhibition, we hypothesized that this may indicate an increased reliance on ATR for survival. Indeed, we observe that replication stress induced by the CHK1 inhibitor AZD7762 results in replication catastrophe and apoptosis, when combined with the ATR inhibitor VE-821 specifically in cancer cells. Combined treatment with ATR and CHK1 inhibitors leads to replication fork arrest, ssDNA accumulation, replication collapse, and synergistic cell death in cancer cells in vitro and in vivo. Inhibition of CDK reversed replication stress and synthetic lethality, demonstrating that regulation of origin firing by ATR and CHK1 explains the synthetic lethality. In conclusion, this study exemplifies cancer-specific synthetic lethality between two proteins in the same pathway and raises the prospect of combining ATR and CHK1 inhibitors as promising cancer therapy. PMID:26748709

  12. Cancer-Specific Synthetic Lethality between ATR and CHK1 Kinase Activities

    PubMed Central

    Sanjiv, Kumar; Hagenkort, Anna; Calderón-Montaño, José Manuel; Koolmeister, Tobias; Reaper, Philip M.; Mortusewicz, Oliver; Jacques, Sylvain A.; Kuiper, Raoul V.; Schultz, Niklas; Scobie, Martin; Charlton, Peter A.; Pollard, John R.; Berglund, Ulrika Warpman; Altun, Mikael; Helleday, Thomas

    2015-01-01

    Summary ATR and CHK1 maintain cancer cell survival under replication stress and inhibitors of both kinases are currently undergoing clinical trials. As ATR activity is increased after CHK1 inhibition, we hypothesized that this may indicate an increased reliance on ATR for survival. Indeed, we observe that replication stress induced by the CHK1 inhibitor AZD7762 results in replication catastrophe and apoptosis, when combined with the ATR inhibitor VE-821 specifically in cancer cells. Combined treatment with ATR and CHK1 inhibitors leads to replication fork arrest, ssDNA accumulation, replication collapse, and synergistic cell death in cancer cells in vitro and in vivo. Inhibition of CDK reversed replication stress and synthetic lethality, demonstrating that regulation of origin firing by ATR and CHK1 explains the synthetic lethality. In conclusion, this study exemplifies cancer-specific synthetic lethality between two proteins in the same pathway and raises the prospect of combining ATR and CHK1 inhibitors as promising cancer therapy. PMID:26748709

  13. Targeting EZH2 methyltransferase activity in ARID1A mutated cancer cells is synthetic lethal

    PubMed Central

    Biter, Benjamin G.; Aird, Katherine M.; Garipov, Azat; Li, Hua; Amatangelo, Michael; Kossenkov, Andrew V.; Schultz, David C.; Liu, Qin; Shih, Ie-Ming; Conejo-Garcia, Jose R.; Speicher, David W.; Zhang, Rugang

    2015-01-01

    ARID1A, a chromatin remodeler, shows one of the highest mutation rates across many cancer types. Notably, ARID1A is mutated in over 50% of ovarian clear cell carcinomas, which currently has no effective therapy. To date, clinically applicable targeted cancer therapy based on ARID1A mutational status has not been described. Here we show that inhibition of the EZH2 methyltransferase acts in a synthetic lethal manner in ARID1A mutated ovarian cancer cells. ARID1A mutational status correlates with response to the EZH2 inhibitor. We identified PIK3IP1 as a direct ARID1A/EZH2 target, which is upregulated by EZH2 inhibition and contributes to the observed synthetic lethality by inhibiting PI3K/AKT signaling. Significantly, EZH2 inhibition causes regression of ARID1A mutated ovarian tumors in vivo. Together, these data demonstrate for the first time a synthetic lethality between ARID1A mutation and EZH2 inhibition. They indicate that pharmacological inhibition of EZH2 represents a novel treatment strategy for ARID1A mutated cancers. PMID:25686104

  14. Hyperactivated Wnt signaling induces synthetic lethal interaction with Rb inactivation by elevating TORC1 activities.

    PubMed

    Zhang, Tianyi; Liao, Yang; Hsu, Fu-Ning; Zhang, Robin; Searle, Jennifer S; Pei, Xun; Li, Xuan; Ryoo, Hyung Don; Ji, Jun-Yuan; Du, Wei

    2014-05-01

    Inactivation of the Rb tumor suppressor can lead to increased cell proliferation or cell death depending on specific cellular context. Therefore, identification of the interacting pathways that modulate the effect of Rb loss will provide novel insights into the roles of Rb in cancer development and promote new therapeutic strategies. Here, we identify a novel synthetic lethal interaction between Rb inactivation and deregulated Wg/Wnt signaling through unbiased genetic screens. We show that a weak allele of axin, which deregulates Wg signaling and increases cell proliferation without obvious effects on cell fate specification, significantly alters metabolic gene expression, causes hypersensitivity to metabolic stress induced by fasting, and induces synergistic apoptosis with mutation of fly Rb ortholog, rbf. Furthermore, hyperactivation of Wg signaling by other components of the Wg pathway also induces synergistic apoptosis with rbf. We show that hyperactivated Wg signaling significantly increases TORC1 activity and induces excessive energy stress with rbf mutation. Inhibition of TORC1 activity significantly suppressed synergistic cell death induced by hyperactivated Wg signaling and rbf inactivation, which is correlated with decreased energy stress and decreased induction of apoptotic regulator expression. Finally the synthetic lethality between Rb and deregulated Wnt signaling is conserved in mammalian cells and that inactivation of Rb and APC induces synergistic cell death through a similar mechanism. These results suggest that elevated TORC1 activity and metabolic stress underpin the evolutionarily conserved synthetic lethal interaction between hyperactivated Wnt signaling and inactivated Rb tumor suppressor. PMID:24809668

  15. CDK1 Is a Synthetic Lethal Target for KRAS Mutant Tumours

    PubMed Central

    Costa-Cabral, Sara; Brough, Rachel; Konde, Asha; Aarts, Marieke; Campbell, James; Marinari, Eliana; Riffell, Jenna; Bardelli, Alberto; Torrance, Christopher; Lord, Christopher J.; Ashworth, Alan

    2016-01-01

    Activating KRAS mutations are found in approximately 20% of human cancers but no RAS-directed therapies are currently available. Here we describe a novel, robust, KRAS synthetic lethal interaction with the cyclin dependent kinase, CDK1. This was discovered using parallel siRNA screens in KRAS mutant and wild type colorectal isogenic tumour cells and subsequently validated in a genetically diverse panel of 26 colorectal and pancreatic tumour cell models. This established that the KRAS/CDK1 synthetic lethality applies in tumour cells with either amino acid position 12 (p.G12V, pG12D, p.G12S) or amino acid position 13 (p.G13D) KRAS mutations and can also be replicated in vivo in a xenograft model using a small molecule CDK1 inhibitor. Mechanistically, CDK1 inhibition caused a reduction in the S-phase fraction of KRAS mutant cells, an effect also characterised by modulation of Rb, a master control of the G1/S checkpoint. Taken together, these observations suggest that the KRAS/CDK1 interaction is a robust synthetic lethal effect worthy of further investigation. PMID:26881434

  16. RADical response puts an exceptional responder in CHKmate: a synthetic lethal curative response to DNA-damaging chemotherapy?

    PubMed Central

    Peng, Guang; Woodman, Scott E.; Mills, Gordon B.

    2014-01-01

    Summary In this issue of Cancer Discovery, AI-Ahmadie and colleagues identify a somatic mutation in the Rad50 gene as a likely contributing factor to an unusual curative response to systemic combination therapy employing the DNA-damaging agent, irinotecan, and a checkpoint kinase 1(Chk1) inhibitor in a patient with recurrent, metastatic small-cell cancer. This study highlights the importance of in-depth analysis of exceptional responders to chemo and targeted therapy in early phase clinical trials and opens new avenues for developing cancer genome-based combination therapy to improve the efficacy of traditional chemotherapy through synthetically lethal interactions. PMID:25185187

  17. KRAS mutant NSCLC, a new opportunity for the synthetic lethality therapeutic approach

    PubMed Central

    Belda-Iniesta, Cristóbal

    2013-01-01

    K-RAS accounts for 90% of RAS mutations in lung adenocarcinomas, the most commonly mutated oncogene in NSCLC, with mutations detected in about 25% of all tumors. Direct inhibition of KRAS has proven clinically challenging. So far, no successful targeted therapy has been developed and remains an elusive target for cancer therapy. Despite significant efforts, currently there are no drugs directly targeting mutated KRAS. Thus, new strategies have emerged for targeting RAS including the use of synthetic lethality. A specific knowledge of individual tumor molecular abnormalities that result in oncogene-specific “synthetic lethal” interactions will allow the rationale to combine promising targeted therapies for KRAS-mutated NSCLC. In this article, we review the new approach based on testing drugs or combinations of agents that work downstream of activated K-RAS. PMID:25806225

  18. Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells.

    PubMed

    Scholl, Claudia; Fröhling, Stefan; Dunn, Ian F; Schinzel, Anna C; Barbie, David A; Kim, So Young; Silver, Serena J; Tamayo, Pablo; Wadlow, Raymond C; Ramaswamy, Sridhar; Döhner, Konstanze; Bullinger, Lars; Sandy, Peter; Boehm, Jesse S; Root, David E; Jacks, Tyler; Hahn, William C; Gilliland, D Gary

    2009-05-29

    An alternative to therapeutic targeting of oncogenes is to perform "synthetic lethality" screens for genes that are essential only in the context of specific cancer-causing mutations. We used high-throughput RNA interference (RNAi) to identify synthetic lethal interactions in cancer cells harboring mutant KRAS, the most commonly mutated human oncogene. We find that cells that are dependent on mutant KRAS exhibit sensitivity to suppression of the serine/threonine kinase STK33 irrespective of tissue origin, whereas STK33 is not required by KRAS-independent cells. STK33 promotes cancer cell viability in a kinase activity-dependent manner by regulating the suppression of mitochondrial apoptosis mediated through S6K1-induced inactivation of the death agonist BAD selectively in mutant KRAS-dependent cells. These observations identify STK33 as a target for treatment of mutant KRAS-driven cancers and demonstrate the potential of RNAi screens for discovering functional dependencies created by oncogenic mutations that may enable therapeutic intervention for cancers with "undruggable" genetic alterations. PMID:19490892

  19. A Synthetic Lethal Screen Identifies a Role for Lin-44/Wnt in C. elegans Embryogenesis

    PubMed Central

    Hartin, Samantha N.; Hudson, Martin L.; Yingling, Curtis; Ackley, Brian D.

    2015-01-01

    Background The C. elegans proteins PTP-3/LAR-RPTP and SDN-1/Syndecan are conserved cell adhesion molecules. Loss-of-function (LOF) mutations in either ptp-3 or sdn-1 result in low penetrance embryonic developmental defects. Work from other systems has shown that syndecans can function as ligands for LAR receptors in vivo. We used double mutant analysis to test whether ptp-3 and sdn-1 function in a linear genetic pathway during C. elegans embryogenesis. Results We found animals with LOF in both sdn-1 and ptp-3 exhibited a highly penetrant synthetic lethality (SynLet), with only a small percentage of animals surviving to adulthood. Analysis of the survivors demonstrated that these animals had a synergistic increase in the penetrance of embryonic developmental defects. Together, these data strongly suggested PTP-3 and SDN-1 function in parallel during embryogenesis. We subsequently used RNAi to knockdown ~3,600 genes predicted to encode secreted and/or transmembrane molecules to identify genes that interacted with ptp-3 or sdn-1. We found that the Wnt ligand, lin-44, was SynLet with sdn-1, but not ptp-3. We used 4-dimensional time-lapse analysis to characterize the interaction between lin-44 and sdn-1. We found evidence that loss of lin-44 caused defects in the polarization and migration of endodermal precursors during gastrulation, a previously undescribed role for lin-44 that is strongly enhanced by the loss of sdn-1. Conclusions PTP-3 and SDN-1 function in compensatory pathways during C. elegans embryonic and larval development, as simultaneous loss of both genes has dire consequences for organismal survival. The Wnt ligand lin-44 contributes to the early stages of gastrulation in parallel to sdn-1, but in a genetic pathway with ptp-3. Overall, the SynLet phenotype provides a robust platform to identify ptp-3 and sdn-1 interacting genes, as well as other genes that function in development, yet might be missed in traditional forward genetic screens. PMID:25938228

  20. Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models

    PubMed Central

    Chowdhury, Ratul; Chowdhury, Anupam; Maranas, Costas D.

    2015-01-01

    Essentiality (ES) and Synthetic Lethality (SL) information identify combination of genes whose deletion inhibits cell growth. This information is important for both identifying drug targets for tumor and pathogenic bacteria suppression and for flagging and avoiding gene deletions that are non-viable in biotechnology. In this study, we performed a comprehensive ES and SL analysis of two important eukaryotic models (S. cerevisiae and CHO cells) using a bilevel optimization approach introduced earlier. Information gleaned from this study is used to propose specific model changes to remedy inconsistent with data model predictions. Even for the highly curated Yeast 7.11 model we identified 50 changes (metabolic and GPR) leading to the correct prediction of an additional 28% of essential genes and 36% of synthetic lethals along with a 53% reduction in the erroneous identification of essential genes. Due to the paucity of mutant growth phenotype data only 12 changes were made for the CHO 1.2 model leading to an additional correctly predicted 11 essential and eight non-essential genes. Overall, we find that CHO 1.2 was 76% less accurate than the Yeast 7.11 metabolic model in predicting essential genes. Based on this analysis, 14 (single and double deletion) maximally informative experiments are suggested to improve the CHO cell model by using information from a mouse metabolic model. This analysis demonstrates the importance of single and multiple knockout phenotypes in assessing and improving model reconstructions. The advent of techniques such as CRISPR opens the door for the global assessment of eukaryotic models. PMID:26426067

  1. Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models.

    PubMed

    Chowdhury, Ratul; Chowdhury, Anupam; Maranas, Costas D

    2015-01-01

    Essentiality (ES) and Synthetic Lethality (SL) information identify combination of genes whose deletion inhibits cell growth. This information is important for both identifying drug targets for tumor and pathogenic bacteria suppression and for flagging and avoiding gene deletions that are non-viable in biotechnology. In this study, we performed a comprehensive ES and SL analysis of two important eukaryotic models (S. cerevisiae and CHO cells) using a bilevel optimization approach introduced earlier. Information gleaned from this study is used to propose specific model changes to remedy inconsistent with data model predictions. Even for the highly curated Yeast 7.11 model we identified 50 changes (metabolic and GPR) leading to the correct prediction of an additional 28% of essential genes and 36% of synthetic lethals along with a 53% reduction in the erroneous identification of essential genes. Due to the paucity of mutant growth phenotype data only 12 changes were made for the CHO 1.2 model leading to an additional correctly predicted 11 essential and eight non-essential genes. Overall, we find that CHO 1.2 was 76% less accurate than the Yeast 7.11 metabolic model in predicting essential genes. Based on this analysis, 14 (single and double deletion) maximally informative experiments are suggested to improve the CHO cell model by using information from a mouse metabolic model. This analysis demonstrates the importance of single and multiple knockout phenotypes in assessing and improving model reconstructions. The advent of techniques such as CRISPR opens the door for the global assessment of eukaryotic models. PMID:26426067

  2. Towards a compendium of essential genes – From model organisms to synthetic lethality in cancer cells

    PubMed Central

    Zhan, Tianzuo; Boutros, Michael

    2016-01-01

    Abstract Essential genes are defined by their requirement to sustain life in cells or whole organisms. The systematic identification of essential gene sets not only allows insights into the fundamental building blocks of life, but may also provide novel therapeutic targets in oncology. The discovery of essential genes has been tightly linked to the development and deployment of various screening technologies. Here, we describe how gene essentiality was addressed in different eukaryotic model organisms, covering a range of organisms from yeast to mouse. We describe how increasing knowledge of evolutionarily divergent genomes facilitate identification of gene essentiality across species. Finally, the impact of gene essentiality and synthetic lethality on cancer research and the clinical translation of screening results are highlighted. PMID:26627871

  3. Inhibition of the Polyamine Synthesis Pathway Is Synthetically Lethal with Loss of Argininosuccinate Synthase 1.

    PubMed

    Locke, Matthew; Ghazaly, Essam; Freitas, Marta O; Mitsinga, Mikaella; Lattanzio, Laura; Lo Nigro, Cristiana; Nagano, Ai; Wang, Jun; Chelala, Claude; Szlosarek, Peter; Martin, Sarah A

    2016-08-01

    Argininosuccinate synthase 1 (ASS1) is the rate-limiting enzyme for arginine biosynthesis. ASS1 expression is lost in a range of tumor types, including 50% of malignant pleural mesotheliomas. Starving ASS1-deficient cells of arginine with arginine blockers such as ADI-PEG20 can induce selective lethality and has shown great promise in the clinical setting. We have generated a model of ADI-PEG20 resistance in mesothelioma cells. This resistance is mediated through re-expression of ASS1 via demethylation of the ASS1 promoter. Through coordinated transcriptomic and metabolomic profiling, we have shown that ASS1-deficient cells have decreased levels of acetylated polyamine metabolites, together with a compensatory increase in the expression of polyamine biosynthetic enzymes. Upon arginine deprivation, polyamine metabolites are decreased in the ASS1-deficient cells and in plasma isolated from ASS1-deficient mesothelioma patients. We identify a synthetic lethal dependence between ASS1 deficiency and polyamine metabolism, which could potentially be exploited for the treatment of ASS1-negative cancers. PMID:27452468

  4. Synthetic antibodies with a human framework that protect mice from lethal Sudan ebolavirus challenge.

    PubMed

    Chen, Gang; Koellhoffer, Jayne F; Zak, Samantha E; Frei, Julia C; Liu, Nina; Long, Hua; Ye, Wei; Nagar, Kaajal; Pan, Guohua; Chandran, Kartik; Dye, John M; Sidhu, Sachdev S; Lai, Jonathan R

    2014-10-17

    The ebolaviruses cause severe and rapidly progressing hemorrhagic fever. There are five ebolavirus species; although much is known about Zaire ebolavirus (EBOV) and its neutralization by antibodies, little is known about Sudan ebolavirus (SUDV), which is emerging with increasing frequency. Here we describe monoclonal antibodies containing a human framework that potently inhibit infection by SUDV and protect mice from lethal challenge. The murine antibody 16F6, which binds the SUDV envelope glycoprotein (GP), served as the starting point for design. Sequence and structural alignment revealed similarities between 16F6 and YADS1, a synthetic antibody with a humanized scaffold. A focused phage library was constructed and screened to impart 16F6-like recognition properties onto the YADS1 scaffold. A panel of 17 antibodies were characterized and found to have a range of neutralization potentials against a pseudotype virus infection model. Neutralization correlated with GP binding as determined by ELISA. Two of these clones, E10 and F4, potently inhibited authentic SUDV and conferred protection and memory immunity in mice from lethal SUDV challenge. E10 and F4 were further shown to bind to the same epitope on GP as 16F6 with comparable affinities. These antibodies represent strong immunotherapeutic candidates for treatment of SUDV infection. PMID:25140871

  5. KEAP1-dependent synthetic lethality induced by AKT and TXNRD1 inhibitors in lung cancer

    PubMed Central

    Dai, Bingbing; Yoo, Suk-Yuong; Bartholomeusz, Geoffrey; Graham, Ryan A.; Majidi, Mourad; Yan, Shaoyu; Meng, Jieru; Ji, Lin; Coombes, Kevin; Minna, John D.; Fang, Bingliang; Roth, Jack A.

    2013-01-01

    Intrinsic resistance to agents targeting phosphatidylinositol-3-kinase (PI3K)/AKT pathway is one of the major challenges in cancer treatment with such agents. The objective of this study is to identify the genes or pathways that can be targeted to overcome the resistance of non-small cell lung cancer to the AKT inhibitor, MK2206, which is currently being evaluated in phase I and II clinical trials. Using a genome-wide small interfering RNA (siRNA) library screening and biological characterization we identified that inhibition of Thioredoxin Reductase-1 (TXNRD1), one of the key anti-oxidant enzymes, with siRNAs or its inhibitor, Auranofin, sensitized non-small cell lung cancer cells to MK2206 treatment in vitro and in vivo. We found that simultaneous inhibition of TXNRD1 and AKT pathways induced robust reactive oxygen species (ROS) production, which was involved in c-Jun N-terminal Kinase (JNK, MAPK8) activation and cell apoptosis. Furthermore we found that the synthetic lethality interaction between the TXNRD1 and AKT pathways occurred through the KEAP1/NRF2 cellular antioxidant pathway. Lastly, we found that synthetic lethality induced by TXNRD1 and AKT inhibitors relied on wild type KEAP1 function. Our study indicates that targeting the interaction between AKT and TXNRD1 antioxidant pathways with MK2206 and Auranofin, a FDA approved drug, is a rational strategy to treat lung cancer and that KEAP1 mutation status may offer a predicative biomarker for such combination approaches. PMID:23824739

  6. Identification of synthetic lethality of PLK1 inhibition and microtubule-destabilizing drugs.

    PubMed

    Hugle, M; Belz, K; Fulda, S

    2015-12-01

    Polo-like kinase 1 (PLK1) is frequently overexpressed in cancer, which correlates with poor prognosis. Therefore, we investigated PLK1 as therapeutic target using rhabdomyosarcoma (RMS) as a model. Here, we identify a novel synthetic lethal interaction of PLK1 inhibitors and microtubule-destabilizing drugs in preclinical RMS models and elucidate the underlying molecular mechanisms of this synergism. PLK1 inhibitors (i.e., BI 2536 and BI 6727) synergistically induce apoptosis together with microtubule-destabilizing drugs (i.e., vincristine (VCR), vinblastine (VBL) and vinorelbine (VNR)) in several RMS cell lines (combination index <0.9) including a patient-derived primary RMS culture. Importantly, PLK1 inhibitors and VCR cooperate to significantly suppress RMS growth in two in vivo models, including a mouse xenograft model, without causing additive toxicity. In addition, no toxicity was observed in non-malignant fibroblast or myoblast cultures. Mechanistically, BI 2536/VCR co-treatment triggers mitotic arrest, which initiates mitochondrial apoptosis by inactivation of antiapoptotic BCL-2 family proteins, followed by BAX/BAK activation, production of reactive oxygen species (ROS) and activation of caspase-dependent or caspase-independent effector pathways. This conclusion is supported by data showing that BI 2536/VCR-induced apoptosis is significantly inhibited by preventing cells to enter mitosis, by overexpression of BCL-2 or a non-degradable MCL-1 mutant, by BAK knockdown, ROS scavengers, caspase inhibition or endonuclease G silencing. This identification of a novel synthetic lethality of PLK1 inhibitors and microtubule-destabilizing drugs has important implications for developing PLK1 inhibitor-based combination treatments. PMID:26024389

  7. Cell line name recognition in support of the identification of synthetic lethality in cancer from text

    PubMed Central

    Kaewphan, Suwisa; Van Landeghem, Sofie; Ohta, Tomoko; Van de Peer, Yves; Ginter, Filip; Pyysalo, Sampo

    2016-01-01

    Motivation: The recognition and normalization of cell line names in text is an important task in biomedical text mining research, facilitating for instance the identification of synthetically lethal genes from the literature. While several tools have previously been developed to address cell line recognition, it is unclear whether available systems can perform sufficiently well in realistic and broad-coverage applications such as extracting synthetically lethal genes from the cancer literature. In this study, we revisit the cell line name recognition task, evaluating both available systems and newly introduced methods on various resources to obtain a reliable tagger not tied to any specific subdomain. In support of this task, we introduce two text collections manually annotated for cell line names: the broad-coverage corpus Gellus and CLL, a focused target domain corpus. Results: We find that the best performance is achieved using NERsuite, a machine learning system based on Conditional Random Fields, trained on the Gellus corpus and supported with a dictionary of cell line names. The system achieves an F-score of 88.46% on the test set of Gellus and 85.98% on the independently annotated CLL corpus. It was further applied at large scale to 24 302 102 unannotated articles, resulting in the identification of 5 181 342 cell line mentions, normalized to 11 755 unique cell line database identifiers. Availability and implementation: The manually annotated datasets, the cell line dictionary, derived corpora, NERsuite models and the results of the large-scale run on unannotated texts are available under open licenses at http://turkunlp.github.io/Cell-line-recognition/. Contact: sukaew@utu.fi PMID:26428294

  8. A screen for dynein synthetic lethals in Aspergillus nidulans identifies spindle assembly checkpoint genes and other genes involved in mitosis.

    PubMed Central

    Efimov, V P; Morris, N R

    1998-01-01

    Cytoplasmic dynein is a ubiquitously expressed microtubule motor involved in vesicle transport, mitosis, nuclear migration, and spindle orientation. In the filamentous fungus Aspergillus nidulans, inactivation of cytoplasmic dynein, although not lethal, severely impairs nuclear migration. The role of dynein in mitosis and vesicle transport in this organism is unclear. To investigate the complete range of dynein function in A. nidulans, we searched for synthetic lethal mutations that significantly reduced growth in the absence of dynein but had little effect on their own. We isolated 19 sld (synthetic lethality without dynein) mutations in nine different genes. Mutations in two genes exacerbate the nuclear migration defect seen in the absence of dynein. Mutations in six other genes, including sldA and sldB, show a strong synthetic lethal interaction with a mutation in the mitotic kinesin bimC and, thus, are likely to play a role in mitosis. Mutations in sldA and sldB also confer hypersensitivity to the microtubule-destabilizing drug benomyl. sldA and sldB were cloned by complementation of their mutant phenotypes using an A. nidulans autonomously replicating vector. Sequencing revealed homology to the spindle assembly checkpoint genes BUB1 and BUB3 from Saccharomyces cerevisiae. Genetic interaction between dynein and spindle assembly checkpoint genes, as well as other mitotic genes, indicates that A. nidulans dynein plays a role in mitosis. We suggest a model for dynein motor action in A. nidulans that can explain dynein involvement in both mitosis and nuclear distribution. PMID:9584089

  9. ATM and MET kinases are synthetic lethal with non-genotoxic activation of p53

    PubMed Central

    Sullivan, Kelly D.; Padilla-Just, Nuria; Henry, Ryan E.; Porter, Christopher C.; Kim, Jihye; Tentler, John J.; Eckhardt, S. Gail; Tan, Aik Choon; DeGregori, James; Espinosa, Joaquín M.

    2012-01-01

    The p53 tumor suppressor orchestrates alternative stress responses including cell cycle arrest and apoptosis, but the mechanisms defining cell fate upon p53 activation are poorly understood. Several small molecule activators of p53 have been developed, including Nutlin-3, but their therapeutic potential is limited by the fact that they induce reversible cell cycle arrest in most cancer cell types. We report here the results of a ‘Synthetic Lethal with Nutlin-3’ genome-wide shRNA screen, which revealed that the ATM and MET kinases govern cell fate choice upon p53 activation. Genetic or pharmacological interference with ATM or MET activity converts the cellular response from cell cycle arrest into apoptosis in diverse cancer cell types without affecting expression of key p53 target genes. ATM and MET inhibitors enable Nutlin-3 to kill tumor spheroids. These results identify novel pathways controlling the cellular response to p53 activation and aid in the design of p53-based therapies. PMID:22660439

  10. Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation.

    PubMed Central

    Costa, P J; Arndt, K M

    2000-01-01

    Strong evidence indicates that transcription elongation by RNA polymerase II (pol II) is a highly regulated process. Here we present genetic results that indicate a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. A screen for synthetic lethal mutations was carried out with an rtf1 deletion mutation to identify factors that interact with Rtf1 or regulate the same process as Rtf1. The screen uncovered mutations in SRB5, CTK1, FCP1, and POB3. These genes encode an Srb/mediator component, a CTD kinase, a CTD phosphatase, and a protein involved in the regulation of transcription by chromatin structure, respectively. All of these gene products have been directly or indirectly implicated in transcription elongation, indicating that Rtf1 may also regulate this process. In support of this view, we show that RTF1 functionally interacts with genes that encode known elongation factors, including SPT4, SPT5, SPT16, and PPR2. We also show that a deletion of RTF1 causes sensitivity to 6-azauracil and mycophenolic acid, phenotypes correlated with a transcription elongation defect. Collectively, our results suggest that Rtf1 may function as a novel transcription elongation factor in yeast. PMID:11014804

  11. In Silico Screening Identifies a Novel Potential PARP1 Inhibitor Targeting Synthetic Lethality in Cancer Treatment

    PubMed Central

    Li, Jian; Zhou, Nan; Cai, Peiling; Bao, Jinku

    2016-01-01

    Synthetic lethality describes situations in which defects in two different genes or pathways together result in cell death. This concept has been applied to drug development for cancer treatment, as represented by Poly (ADP-ribose) polymerase (PARPs) inhibitors. In the current study, we performed a computational screening to discover new PARP inhibitors. Among the 11,247 compounds analyzed, one natural product, ZINC67913374, stood out by its superior performance in the simulation analyses. Compared with the FDA approved PARP1 inhibitor, olaparib, our results demonstrated that the ZINC67913374 compound achieved a better grid score (−86.8) and amber score (−51.42). Molecular dynamics simulations suggested that the PARP1-ZINC67913374 complex was more stable than olaparib. The binding free energy for ZINC67913374 was −177.28 kJ/mol while that of olaparib was −159.16 kJ/mol. These results indicated ZINC67913374 bound to PARP1 with a higher affinity, which suggest ZINC67913374 has promising potential for cancer drug development. PMID:26907257

  12. Overcoming myelosuppression due to synthetic lethal toxicity for FLT3-targeted acute myeloid leukemia therapy

    PubMed Central

    Warkentin, Alexander A; Lopez, Michael S; Lasater, Elisabeth A; Lin, Kimberly; He, Bai-Liang; Leung, Anskar YH; Smith, Catherine C; Shah, Neil P; Shokat, Kevan M

    2014-01-01

    Activating mutations in FLT3 confer poor prognosis for individuals with acute myeloid leukemia (AML). Clinically active investigational FLT3 inhibitors can achieve complete remissions but their utility has been hampered by acquired resistance and myelosuppression attributed to a ‘synthetic lethal toxicity’ arising from simultaneous inhibition of FLT3 and KIT. We report a novel chemical strategy for selective FLT3 inhibition while avoiding KIT inhibition with the staurosporine analog, Star 27. Star 27 maintains potency against FLT3 in proliferation assays of FLT3-transformed cells compared with KIT-transformed cells, shows no toxicity towards normal human hematopoiesis at concentrations that inhibit primary FLT3-mutant AML blast growth, and is active against mutations that confer resistance to clinical inhibitors. As a more complete understanding of kinase networks emerges, it may be possible to define anti-targets such as KIT in the case of AML to allow improved kinase inhibitor design of clinical agents with enhanced efficacy and reduced toxicity. DOI: http://dx.doi.org/10.7554/eLife.03445.001 PMID:25531068

  13. Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase.

    PubMed

    Frezza, Christian; Zheng, Liang; Folger, Ori; Rajagopalan, Kartik N; MacKenzie, Elaine D; Jerby, Livnat; Micaroni, Massimo; Chaneton, Barbara; Adam, Julie; Hedley, Ann; Kalna, Gabriela; Tomlinson, Ian P M; Pollard, Patrick J; Watson, Dave G; Deberardinis, Ralph J; Shlomi, Tomer; Ruppin, Eytan; Gottlieb, Eyal

    2011-09-01

    Fumarate hydratase (FH) is an enzyme of the tricarboxylic acid cycle (TCA cycle) that catalyses the hydration of fumarate into malate. Germline mutations of FH are responsible for hereditary leiomyomatosis and renal-cell cancer (HLRCC). It has previously been demonstrated that the absence of FH leads to the accumulation of fumarate, which activates hypoxia-inducible factors (HIFs) at normal oxygen tensions. However, so far no mechanism that explains the ability of cells to survive without a functional TCA cycle has been provided. Here we use newly characterized genetically modified kidney mouse cells in which Fh1 has been deleted, and apply a newly developed computer model of the metabolism of these cells to predict and experimentally validate a linear metabolic pathway beginning with glutamine uptake and ending with bilirubin excretion from Fh1-deficient cells. This pathway, which involves the biosynthesis and degradation of haem, enables Fh1-deficient cells to use the accumulated TCA cycle metabolites and permits partial mitochondrial NADH production. We predicted and confirmed that targeting this pathway would render Fh1-deficient cells non-viable, while sparing wild-type Fh1-containing cells. This work goes beyond identifying a metabolic pathway that is induced in Fh1-deficient cells to demonstrate that inhibition of haem oxygenation is synthetically lethal when combined with Fh1 deficiency, providing a new potential target for treating HLRCC patients. PMID:21849978

  14. In Silico Screening Identifies a Novel Potential PARP1 Inhibitor Targeting Synthetic Lethality in Cancer Treatment.

    PubMed

    Li, Jian; Zhou, Nan; Cai, Peiling; Bao, Jinku

    2016-01-01

    Synthetic lethality describes situations in which defects in two different genes or pathways together result in cell death. This concept has been applied to drug development for cancer treatment, as represented by Poly (ADP-ribose) polymerase (PARPs) inhibitors. In the current study, we performed a computational screening to discover new PARP inhibitors. Among the 11,247 compounds analyzed, one natural product, ZINC67913374, stood out by its superior performance in the simulation analyses. Compared with the FDA approved PARP1 inhibitor, olaparib, our results demonstrated that the ZINC67913374 compound achieved a better grid score (-86.8) and amber score (-51.42). Molecular dynamics simulations suggested that the PARP1-ZINC67913374 complex was more stable than olaparib. The binding free energy for ZINC67913374 was -177.28 kJ/mol while that of olaparib was -159.16 kJ/mol. These results indicated ZINC67913374 bound to PARP1 with a higher affinity, which suggest ZINC67913374 has promising potential for cancer drug development. PMID:26907257

  15. Synthetic lethality between CCNE1 amplification and loss of BRCA1.

    PubMed

    Etemadmoghadam, Dariush; Weir, Barbara A; Au-Yeung, George; Alsop, Kathryn; Mitchell, Gillian; George, Joshy; Davis, Sally; D'Andrea, Alan D; Simpson, Kaylene; Hahn, William C; Bowtell, David D L

    2013-11-26

    High-grade serous ovarian cancers (HGSCs) are characterized by a high frequency of TP53 mutations, BRCA1/2 inactivation, homologous recombination dysfunction, and widespread copy number changes. Cyclin E1 (CCNE1) gene amplification has been reported to occur independently of BRCA1/2 mutation, and it is associated with primary treatment failure and reduced patient survival. Insensitivity of CCNE1-amplified tumors to platinum cross-linking agents may be partly because of an intact BRCA1/2 pathway. Both BRCA1/2 dysfunction and CCNE1 amplification are known to promote genomic instability and tumor progression. These events may be mutually exclusive, because either change provides a path to tumor development, with no selective advantage to having both mutations. Using data from a genome-wide shRNA synthetic lethal screen, we show that BRCA1 and members of the ubiquitin pathway are selectively required in cancers that harbor CCNE1 amplification. Furthermore, we show specific sensitivity of CCNE1-amplified tumor cells to the proteasome inhibitor bortezomib. These findings provide an explanation for the observed mutual exclusivity of CCNE1 amplification and BRCA1/2 loss in HGSC and suggest a unique therapeutic approach for treatment-resistant CCNE1-amplified tumors. PMID:24218601

  16. Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition.

    PubMed

    Shen, John Paul; Srivas, Rohith; Gross, Andrew; Li, Jianfeng; Jaehnig, Eric J; Sun, Su Ming; Bojorquez-Gomez, Ana; Licon, Katherine; Sivaganesh, Vignesh; Xu, Jia L; Klepper, Kristin; Yeerna, Huwate; Pekin, Daniel; Qiu, Chu Ping; van Attikum, Haico; Sobol, Robert W; Ideker, Trey

    2015-11-01

    Chemical inhibitors of the checkpoint kinases have shown promise in the treatment of cancer, yet their clinical utility may be limited by a lack of molecular biomarkers to identify specific patients most likely to respond to therapy. To this end, we screened 112 known tumor suppressor genes for synthetic lethal interactions with inhibitors of the CHEK1 and CHEK2 checkpoint kinases. We identified eight interactions, including the Replication Factor C (RFC)-related protein RAD17. Clonogenic assays in RAD17 knockdown cell lines identified a substantial shift in sensitivity to checkpoint kinase inhibition (3.5-fold) as compared to RAD17 wild-type. Additional evidence for this interaction was found in a large-scale functional shRNA screen of over 100 genotyped cancer cell lines, in which CHEK1/2 mutant cell lines were unexpectedly sensitive to RAD17 knockdown. This interaction was widely conserved, as we found that RAD17 interacts strongly with checkpoint kinases in the budding yeast Saccharomyces cerevisiae. In the setting of RAD17 knockdown, CHEK1/2 inhibition was found to be synergistic with inhibition of WEE1, another pharmacologically relevant checkpoint kinase. Accumulation of the DNA damage marker γH2AX following chemical inhibition or transient knockdown of CHEK1, CHEK2 or WEE1 was magnified by knockdown of RAD17. Taken together, our data suggest that CHEK1 or WEE1 inhibitors are likely to have greater clinical efficacy in tumors with RAD17 loss-of-function. PMID:26437225

  17. Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition

    PubMed Central

    Shen, John Paul; Srivas, Rohith; Gross, Andrew; Li, Jianfeng; Jaehnig, Eric J.; Sun, Su Ming; Bojorquez-Gomez, Ana; Licon, Katherine; Sivaganesh, Vignesh; Xu, Jia L.; Klepper, Kristin; Yeerna, Huwate; Pekin, Daniel; Qiu, Chu Ping; van Attikum, Haico; Sobol, Robert W.; Ideker, Trey

    2015-01-01

    Chemical inhibitors of the checkpoint kinases have shown promise in the treatment of cancer, yet their clinical utility may be limited by a lack of molecular biomarkers to identify specific patients most likely to respond to therapy. To this end, we screened 112 known tumor suppressor genes for synthetic lethal interactions with inhibitors of the CHEK1 and CHEK2 checkpoint kinases. We identified eight interactions, including the Replication Factor C (RFC)-related protein RAD17. Clonogenic assays in RAD17 knockdown cell lines identified a substantial shift in sensitivity to checkpoint kinase inhibition (3.5-fold) as compared to RAD17 wild-type. Additional evidence for this interaction was found in a large-scale functional shRNA screen of over 100 genotyped cancer cell lines, in which CHEK1/2 mutant cell lines were unexpectedly sensitive to RAD17 knockdown. This interaction was widely conserved, as we found that RAD17 interacts strongly with checkpoint kinases in the budding yeast Saccharomyces cerevisiae. In the setting of RAD17 knockdown, CHEK1/2 inhibition was found to be synergistic with inhibition of WEE1, another pharmacologically relevant checkpoint kinase. Accumulation of the DNA damage marker γH2AX following chemical inhibition or transient knockdown of CHEK1, CHEK2 or WEE1 was magnified by knockdown of RAD17. Taken together, our data suggest that CHEK1 or WEE1 inhibitors are likely to have greater clinical efficacy in tumors with RAD17 loss-of-function. PMID:26437225

  18. Differential regulation and synthetic lethality of exclusive RB1 and CDKN2A mutations in lung cancer.

    PubMed

    Kim, Nayoung; Song, Mee; Kim, Somin; Seo, Yujeong; Kim, Yonghwan; Yoon, Sukjoon

    2016-01-01

    Genetic alterations in lung cancer are distinctly represented in non-small cell lung carcinoma (NSCLC) and small cell lung carcinoma (SCLC). Mutation of the RB1 and CDKN2A genes, which are tightly associated with cell cycle regulation, is exclusive to SCLC and NSCLC cells, respectively. Through the systematic analysis of transcriptome and proteome datasets for 318 cancer cell lines, we characterized differential gene expression and protein regulation in RB1-mutant SCLC and CDKN2A-mutant NSCLC. Many of the genes and proteins associated with RB1-mutant SCLC cell lines belong to functional categories of gene expression and transcription, whereas those associated with CDKN2A-mutant NSCLC cell lines were enriched in gene sets of the extracellular matrix and focal adhesion. These results indicate that the loss of RB1 and CDKN2A function induces distinctively different signaling cascades in SCLC and NSCLC cells. In addition, knockdown of the RB1 gene in CKDN2A-mutant cell lines (and vice versa) synergistically inhibits cancer cell proliferation. The present study on the exclusive role of RB1 and CDKN2A mutations in lung cancer subtypes demonstrates a synthetic lethal strategy for cancer regulation. PMID:26647789

  19. Determination of synthetic lethal interactions in KRAS oncogene-dependent cancer cells reveals novel therapeutic targeting strategies

    PubMed Central

    Steckel, Michael; Molina-Arcas, Miriam; Weigelt, Britta; Marani, Michaela; Warne, Patricia H; Kuznetsov, Hanna; Kelly, Gavin; Saunders, Becky; Howell, Michael; Downward, Julian; Hancock, David C

    2012-01-01

    Oncogenic mutations in RAS genes are very common in human cancer, resulting in cells with well-characterized selective advantages, but also less well-understood vulnerabilities. We have carried out a large-scale loss-of-function screen to identify genes that are required by KRAS-transformed colon cancer cells, but not by derivatives lacking this oncogene. Top-scoring genes were then tested in a larger panel of KRAS mutant and wild-type cancer cells. Cancer cells expressing oncogenic KRAS were found to be highly dependent on the transcription factor GATA2 and the DNA replication initiation regulator CDC6. Extending this analysis using a collection of drugs with known targets, we found that cancer cells with mutant KRAS showed selective addiction to proteasome function, as well as synthetic lethality with topoisomerase inhibition. Combination targeting of these functions caused improved killing of KRAS mutant cells relative to wild-type cells. These observations suggest novel targets and new ways of combining existing therapies for optimal effect in RAS mutant cancers, which are traditionally seen as being highly refractory to therapy. PMID:22613949

  20. Synthetic lethal targeting of PTEN-deficient cancer cells using selective disruption of polynucleotide kinase/phosphatase.

    PubMed

    Mereniuk, Todd R; El Gendy, Mohamed A M; Mendes-Pereira, Ana M; Lord, Christopher J; Ghosh, Sunita; Foley, Edan; Ashworth, Alan; Weinfeld, Michael

    2013-10-01

    A recent screen of 6,961 siRNAs to discover possible synthetic lethal partners of the DNA repair protein polynucleotide kinase/phosphatase (PNKP) led to the identification of the potent tumor suppressor phosphatase and tensin homolog deleted on chromosome 10 (PTEN). Here, we have confirmed the PNKP/PTEN synthetic lethal partnership in a variety of different cell lines including the PC3 prostate cancer cell line, which is naturally deficient in PTEN. We provide evidence that codepletion of PTEN and PNKP induces apoptosis. In HCT116 colon cancer cells, the loss of PTEN is accompanied by an increased background level of DNA double-strand breaks, which accumulate in the presence of an inhibitor of PNKP DNA 3'-phosphatase activity. Complementation of PC3 cells with several well-characterized mutated PTEN cDNAs indicated that the critical function of PTEN required to prevent toxicity induced by an inhibitor of PNKP is most likely associated with its cytoplasmic lipid phosphatase activity. Finally, we show that modest inhibition of PNKP in a PTEN knockout background enhances cellular radiosensitivity, suggesting that such a "synthetic sickness" approach involving the combination of PNKP inhibition with radiotherapy may be applicable to PTEN-deficient tumors. PMID:23883586

  1. Natural and glucosyl flavonoids inhibit poly(ADP-ribose) polymerase activity and induce synthetic lethality in BRCA mutant cells

    PubMed Central

    MAEDA, JUNKO; ROYBAL, ERICA J.; BRENTS, COLLEEN A.; UESAKA, MITSURU; AIZAWA, YASUSHI; KATO, TAKAMITSU A.

    2014-01-01

    Poly(ADP-ribose) polymerase (PARP) inhibitors have been proven to represent superior clinical agents targeting DNA repair mechanisms in cancer therapy. We investigated PARP inhibitory effects of the natural and synthetic flavonoids (quercetin, rutin, monoglucosyl rutin and maltooligosyl rutin) and tested the synthetic lethality in BRCA2 mutated cells. In vitro ELISA assay suggested that the flavonoids have inhibitory effects on PARP activity, but glucosyl modifications reduced the inhibitory effect. Cytotoxicity tests of Chinese hamster cells defective in BRCA2 gene (V-C8) and its parental V79 cells showed BRCA2-dependent synthetic lethality when treated with the flavonoids. BRCA2 mutated cells were three times more sensitive to the flavonoids than the wild-type and gene complemented cells. Reduced toxicity was observed in a glucosyl modification-dependent manner. The present study provides support for the clinical use of new treatment drugs, and is the beginning of the potential application of flavonoids in cancer prevention and the periodic consumption of appropriate flavonoids to reduce cancer risk in individuals carrying a mutant allele of the BRCA2 gene. PMID:24317580

  2. Synthetic lethal screening reveals FGFR as one of the combinatorial targets to overcome resistance to Met-targeted therapy

    PubMed Central

    Kim, Bogyou; Wang, Shangzi; Lee, Ji Min; Jeong, Yunju; Ahn, TaeJin; Son, Dae-Soon; Park, Hye Won; Yoo, Hyeon-seok; Song, Yun-Jeong; Lee, Eunjin; Oh, Young Mi; Lee, Saet Byoul; Choi, Jaehyun; Murray, Joseph C; Zhou, Yan; Song, Paul H; Kim, Kyung-Ah; Weiner, Louis M

    2014-01-01

    Met is a receptor tyrosine kinase that promotes cancer progression. In addition, Met has been implicated in resistance of tumors to various targeted therapies such as EGFR inhibitors in lung cancers, and has been prioritized as a key molecular target for cancer therapy. However, the underlying mechanism of resistance to Met targeting drugs is poorly understood. Here, we describe screening of 1310 genes to search for key regulators related to drug resistance to an anti-Met therapeutic antibody (SAIT301) by employing a siRNA-based synthetic lethal screening method. We found that knockdown of 69 genes in Met-amplified MKN45 cells sensitized the anti-tumor activity of SAIT301. Pathway analysis of these 69 genes implicated FGFR as a key regulator for anti-proliferative effects of Met targeting drugs. Inhibition of FGFR3 increased target cell apoptosis through the suppression of Bcl-xL expression, followed by reduced cancer cell growth in the presence of Met targeting drugs. Treatment of cells with the FGFR inhibitors substantially restored the efficacy of SAIT301 in SAIT301-resistant cells and enhanced the efficacy in SAIT301-sensitive cells. In addition to FGFR3, integrin β3 is another potential target for combination treatment with SAIT301. Suppression of integrin β3 decreased AKT phosphorylation in SAIT301-resistant cells and restores SAIT301 responsiveness in HCC1954 cells, which are resistant to SAIT301. Gene expression analysis using CCLE database shows cancer cells with high levels of FGFR and integrin β3 are resistant to crizotinib treatment, suggesting FGFR and integrin β3 could be used as predictive markers for Met targeted therapy and provide a potential therapeutic option to overcome acquired and innate resistance for the Met targeting drugs. PMID:24662823

  3. A synthetic lethality-based strategy to treat cancers harboring a genetic deficiency in the chromatin remodeling factor BRG1.

    PubMed

    Oike, Takahiro; Ogiwara, Hideaki; Tominaga, Yuichi; Ito, Kentaro; Ando, Osamu; Tsuta, Koji; Mizukami, Tatsuji; Shimada, Yoko; Isomura, Hisanori; Komachi, Mayumi; Furuta, Koh; Watanabe, Shun-Ichi; Nakano, Takashi; Yokota, Jun; Kohno, Takashi

    2013-09-01

    The occurrence of inactivating mutations in SWI/SNF chromatin-remodeling genes in common cancers has attracted a great deal of interest. However, mechanistic strategies to target tumor cells carrying such mutations are yet to be developed. This study proposes a synthetic-lethality therapy for treating cancers deficient in the SWI/SNF catalytic (ATPase) subunit, BRG1/SMARCA4. The strategy relies upon inhibition of BRM/SMARCA2, another catalytic SWI/SNF subunit with a BRG1-related activity. Immunohistochemical analysis of a cohort of non-small-cell lung carcinomas (NSCLC) indicated that 15.5% (16 of 103) of the cohort, corresponding to preferentially undifferentiated tumors, was deficient in BRG1 expression. All BRG1-deficient cases were negative for alterations in known therapeutic target genes, for example, EGFR and DDR2 gene mutations, ALK gene fusions, or FGFR1 gene amplifications. RNA interference (RNAi)-mediated silencing of BRM suppressed the growth of BRG1-deficient cancer cells relative to BRG1-proficient cancer cells, inducing senescence via activation of p21/CDKN1A. This growth suppression was reversed by transduction of wild-type but not ATPase-deficient BRG1. In support of these in vitro results, a conditional RNAi study conducted in vivo revealed that BRM depletion suppressed the growth of BRG1-deficient tumor xenografts. Our results offer a rationale to develop BRM-ATPase inhibitors as a strategy to treat BRG1/SMARCA4-deficient cancers, including NSCLCs that lack mutations in presently known therapeutic target genes. PMID:23872584

  4. Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

    PubMed Central

    Aziz, Ramy K.; Monk, Jonathan M.; Lewis, Robert M.; In Loh, Suh; Mishra, Arti; Abhay Nagle, Amrita; Satyanarayana, Chitkala; Dhakshinamoorthy, Saravanakumar; Luche, Michele; Kitchen, Douglas B.; Andrews, Kathleen A.; Fong, Nicole L.; Li, Howard J.; Palsson, Bernhard O.; Charusanti, Pep

    2015-01-01

    Mathematical models of metabolism from bacterial systems biology have proven their utility across multiple fields, for example metabolic engineering, growth phenotype simulation, and biological discovery. The usefulness of the models stems from their ability to compute a link between genotype and phenotype, but their ability to accurately simulate gene-gene interactions has not been investigated extensively. Here we assess how accurately a metabolic model for Escherichia coli computes one particular type of gene-gene interaction, synthetic lethality, and find that the accuracy rate is between 25% and 43%. The most common failure modes were incorrect computation of single gene essentiality and biological information that was missing from the model. Moreover, we performed virtual and biological screening against several synthetic lethal pairs to explore whether two-compound formulations could be found that inhibit the growth of Gram-negative bacteria. One set of molecules was identified that, depending on the concentrations, inhibits E. coli and S. enterica serovar Typhimurium in an additive or antagonistic manner. These findings pinpoint specific ways in which to improve the predictive ability of metabolic models, and highlight one potential application of systems biology to drug discovery and translational medicine. PMID:26531810

  5. A synthetic lethal screen identifies ATR-inhibition as a novel therapeutic approach for POLD1-deficient cancers

    PubMed Central

    Hocke, Sandra; Guo, Yang; Job, Albert; Orth, Michael; Ziesch, Andreas; Lauber, Kirsten; De Toni, Enrico N; Gress, Thomas M.; Herbst, Andreas; Göke, Burkhard; Gallmeier, Eike

    2016-01-01

    The phosphoinositide 3-kinase-related kinase ATR represents a central checkpoint regulator and mediator of DNA-repair. Its inhibition selectively eliminates certain subsets of cancer cells in various tumor types, but the underlying genetic determinants remain enigmatic. Here, we applied a synthetic lethal screen directed against 288 DNA-repair genes using the well-defined ATR knock-in model of DLD1 colorectal cancer cells to identify potential DNA-repair defects mediating these effects. We identified a set of DNA-repair proteins, whose knockdown selectively killed ATR-deficient cancer cells. From this set, we further investigated the profound synthetic lethal interaction between ATR and POLD1. ATR-dependent POLD1 knockdown-induced cell killing was reproducible pharmacologically in POLD1-depleted DLD1 cells and a panel of other colorectal cancer cell lines by using chemical inhibitors of ATR or its major effector kinase CHK1. Mechanistically, POLD1 depletion in ATR-deficient cells caused caspase-dependent apoptosis without preceding cell cycle arrest and increased DNA-damage along with impaired DNA-repair. Our data could have clinical implications regarding tumor genotype-based cancer therapy, as inactivating POLD1 mutations have recently been identified in small subsets of colorectal and endometrial cancers. POLD1 deficiency might thus represent a predictive marker for treatment response towards ATR- or CHK1-inhibitors that are currently tested in clinical trials. PMID:26755646

  6. Synthetic predator cues impair immune function and make the biological pesticide Bti more lethal for vector mosquitoes.

    PubMed

    Op De Beeck, Lin; Janssens, Lizanne; Stoks, Robby

    2016-03-01

    The control of vector mosquitoes is one of the biggest challenges facing humankind with the use of chemical pesticides often leading to environmental impact and the evolution of resistance. Although to a lesser extent, this also holds for Bacillus thuringiensis israelensis (Bti), the most widely used biological pesticide to control mosquito populations. This raises the need for the development of integrated pest management strategies that allow the reduction of Bti concentrations without loss of the mosquito control efficiency. To this end, we tested in a laboratory experiment the combined effects of larval exposure to a sublethal Bti concentration and predation risk cues on life history and physiology of larval and adult Culex pipiens mosquitoes. Besides natural predator kairomones and prey alarm cues, we also tested synthetic kairomones of Notonecta predators. Neither Bti nor predation risk cues affected mortality, yet when both stressors were combined mortality increased on average by 133% compared to the treatment with only predation risk cues. This synergistic interaction was also present when Bti was combined with synthetic kairomones. This was further reflected in changes of the composite index of population performance, which suggested lowered per capita growth rates in mosquitoes exposed to Bti but only when Bti was combined with synthetic kairomones. Furthermore, predation risk cues shortened larval development time, reduced mass at metamorphosis in males, and had an immunosuppressive effect in larval and adult mosquitoes which may affect the mosquito vector competence. We provide the first demonstration that synthetic kairomones may generate similar effects on prey as natural kairomones. The identified immunosuppressive effect of synthetic kairomones and the novel lethal synergism type between a biological pesticide and synthetic predator kairomones provide an important proof of principle illustrating the potential of this combination for integrated

  7. Synthetic lethal compound combinations reveal a fundamental connection between wall teichoic acid and peptidoglycan biosyntheses in Staphylococcus aureus

    PubMed Central

    Campbell, Jennifer; Singh, Atul K.; Santa Maria, John P.; Kim, Younghoon; Brown, Stephanie; Swoboda, Jonathan G.; Mylonakis, Eleftherios; Wilkinson, Brian J.; Walker, Suzanne

    2010-01-01

    Methicillin resistance in Staphylococcus aureus depends on the production of mecA, which encodes penicillin-binding protein 2A (PBP2A), an acquired peptidoglycan transpeptidase (TP) with reduced susceptibility to beta-lactam antibiotics. PBP2A crosslinks nascent peptidoglycan when the native TPs are inhibited by beta-lactams. Although mecA expression is essential for beta-lactam resistance, it is not sufficient. Here we show that blocking the expression of wall teichoic acids (WTAs) by inhibiting the first enzyme in the pathway, TarO, sensitizes MRSA strains to beta-lactams even though the beta-lactam-resistant transpeptidase, PBP2A, is still expressed. The dramatic synergy between TarO inhibitors and beta-lactams is noteworthy not simply because strategies to overcome methicillin-resistant S. aureus (MRSA) are desperately needed, but because neither TarO nor the activities of the native TPs are essential in MRSA strains. The “synthetic lethality” of inhibiting TarO and the native TPs suggests a functional connection between ongoing WTA expression and peptidoglycan assembly in S. aureus. Indeed, transmission electron microscopy shows that S. aureus cells blocked in WTA synthesis have extensive defects in septation and cell separation, indicating dysregulated cell wall assembly and degradation. Our studies imply that WTAs play a fundamental role in S. aureus cell division and raise the possibility that synthetic lethal compound combinations may have therapeutic utility for overcoming antibiotic resistant bacterial infections. PMID:20961110

  8. Alisertib added to rituximab and vincristine is synthetic lethal and potentially curative in mice with aggressive DLBCL co-overexpressing MYC and BCL2.

    PubMed

    Mahadevan, Daruka; Morales, Carla; Cooke, Laurence S; Manziello, Ann; Mount, David W; Persky, Daniel O; Fisher, Richard I; Miller, Thomas P; Qi, Wenqing

    2014-01-01

    Pearson correlation coefficient for expression analysis of the Lymphoma/Leukemia Molecular Profiling Project (LLMPP) demonstrated Aurora A and B are highly correlated with MYC in DLBCL and mantle cell lymphoma (MCL), while both Auroras correlate with BCL2 only in DLBCL. Auroras are up-regulated by MYC dysregulation with associated aneuploidy and resistance to microtubule targeted agents such as vincristine. Myc and Bcl2 are differentially expressed in U-2932, TMD-8, OCI-Ly10 and Granta-519, but only U-2932 cells over-express mutated p53. Alisertib [MLN8237 or M], a highly selective small molecule inhibitor of Aurora A kinase, was synergistic with vincristine [VCR] and rituximab [R] for inhibition of cell proliferation, abrogation of cell cycle checkpoints and enhanced apoptosis versus single agent or doublet therapy. A DLBCL (U-2932) mouse model showed tumor growth inhibition (TGI) of ∼ 10-20% (p = 0.001) for M, VCR and M-VCR respectively, while R alone showed ∼ 50% TGI (p = 0.001). M-R and VCR-R led to tumor regression [TR], but relapsed 10 days after discontinuing therapy. In contrast, M-VCR-R demonstrated TR with no relapse >40 days after stopping therapy with a Kaplan-Meier survival of 100%. Genes that are modulated by M-VCR-R (CENP-C, Auroras) play a role in centromere-kinetochore function in an attempt to maintain mitosis in the presence of synthetic lethality. Together, our data suggest that the interaction between alisertib plus VCR plus rituximab is synergistic and synthetic lethal in Myc and Bcl-2 co-expressing DLBCL. Alisertib plus vincristine plus rituximab [M-VCR-R] may represent a new strategy for DLBCL therapy. PMID:24893165

  9. Alisertib Added to Rituximab and Vincristine Is Synthetic Lethal and Potentially Curative in Mice with Aggressive DLBCL Co-Overexpressing MYC and BCL2

    PubMed Central

    Mahadevan, Daruka; Morales, Carla; Cooke, Laurence S.; Manziello, Ann; Mount, David W.; Persky, Daniel O.; Fisher, Richard I.; Miller, Thomas P.; Qi, Wenqing

    2014-01-01

    Pearson correlation coefficient for expression analysis of the Lymphoma/Leukemia Molecular Profiling Project (LLMPP) demonstrated Aurora A and B are highly correlated with MYC in DLBCL and mantle cell lymphoma (MCL), while both Auroras correlate with BCL2 only in DLBCL. Auroras are up-regulated by MYC dysregulation with associated aneuploidy and resistance to microtubule targeted agents such as vincristine. Myc and Bcl2 are differentially expressed in U-2932, TMD-8, OCI-Ly10 and Granta-519, but only U-2932 cells over-express mutated p53. Alisertib [MLN8237 or M], a highly selective small molecule inhibitor of Aurora A kinase, was synergistic with vincristine [VCR] and rituximab [R] for inhibition of cell proliferation, abrogation of cell cycle checkpoints and enhanced apoptosis versus single agent or doublet therapy. A DLBCL (U-2932) mouse model showed tumor growth inhibition (TGI) of ∼10–20% (p = 0.001) for M, VCR and M-VCR respectively, while R alone showed ∼50% TGI (p = 0.001). M-R and VCR-R led to tumor regression [TR], but relapsed 10 days after discontinuing therapy. In contrast, M-VCR-R demonstrated TR with no relapse >40 days after stopping therapy with a Kaplan-Meier survival of 100%. Genes that are modulated by M-VCR-R (CENP-C, Auroras) play a role in centromere-kinetochore function in an attempt to maintain mitosis in the presence of synthetic lethality. Together, our data suggest that the interaction between alisertib plus VCR plus rituximab is synergistic and synthetic lethal in Myc and Bcl-2 co-expressing DLBCL. Alisertib plus vincristine plus rituximab [M-VCR-R] may represent a new strategy for DLBCL therapy. PMID:24893165

  10. Equation of state and fragmentation issues in computational lethality analysis

    SciTech Connect

    Trucano, T.G.

    1993-07-01

    The purpose of this report is to summarize the status of computational analysis of hypervelocity impact lethality in relatively nontechnical terms from the perspective of the author. It is not intended to be a review of the technical literature on the problems of concern. The discussion is focused by concentrating on two phenomenology areas which are of particular concern in computational impact studies. First, the material`s equation of state, specifically the treatment of expanded states of metals undergoing shock vaporization, is discussed. Second, the process of dynamic fragmentation is addressed. In both cases, the context of the discussion deals with inaccuracies and difficulties associated with numerical hypervelocity impact simulations. Laboratory experimental capabilities in hypervelocity impact for impact velocities greater than 10.0 km/s are becoming increasingly viable. This paper also gives recommendations for experimental thrusts which utilize these capabilities that will help to resolve the uncertainties in the numerical lethality studies that are pointed out in the present report.

  11. Synthetic substrates for enzyme analysis

    DOEpatents

    Bissell, E.R.; Mitchell, A.R.; Pearson, K.W.; Smith, R.E.

    1983-06-14

    Synthetic substrates are provided which may be represented as A-D. The A moiety includes an amino acid, polypeptide, or derivative. The D moiety includes 7-amino coumarin derivatives having an electron withdrawing substituent group at the 3 position carbon or fused between the 3 and 4 position carbons. No Drawings

  12. Synthetic substrates for enzyme analysis

    DOEpatents

    Bissell, Eugene R.; Mitchell, Alexander R.; Pearson, Karen W.; Smith, Robert E.

    1983-01-01

    Synthetic substrates are provided which may be represented as A-D. The A moiety thereof includes an amino acid, polypeptide, or derivative thereof. The D moiety thereof includes 7-amino coumarin derivatives having an electron withdrawing substituent group at the 3 position carbon or fused between the 3 and 4 position carbons.

  13. A synthetic lethal screen identifies the Vitamin D receptor as a novel gemcitabine sensitizer in pancreatic cancer cells

    PubMed Central

    Bhattacharjee, V; Zhou, Y; Yen, TJ

    2014-01-01

    Overcoming chemoresistance of pancreatic cancer (PCa) cells should significantly extend patient survival. The current treatment modalities rely on a variety of DNA damaging agents including gemcitabine, FOLFIRINOX, and Abraxane that activate cell cycle checkpoints, which allows cells to survive these drug treaments. Indeed, these treatment regimens have only extended patient survival by a few months. The complex microenvironment of PCa tumors has been shown to complicate drug delivery thus decreasing the sensitivity of PCa tumors to chemotherapy. In this study, a genome-wide siRNA library was used to conduct a synthetic lethal screen of Panc1 cells that was treated with gemcitabine. A sublethal dose (50 nM) of the drug was used to model situations of limiting drug availability to PCa tumors in vivo. Twenty-seven validated sensitizer genes were identified from the screen including the Vitamin D receptor (VDR). Gemcitabine sensitivity was shown to be VDR dependent in multiple PCa cell lines in clonogenic survival assays. Sensitization was not achieved through checkpoint override but rather through disrupting DNA repair. VDR knockdown disrupted the cells’ ability to form phospho-γH2AX and Rad51 foci in response to gemcitabine treatment. Disruption of Rad51 foci formation, which compromises homologous recombination, was consistent with increased sensitivity of PCa cells to the PARP inhibitor Rucaparib. Thus inhibition of VDR in PCa cells provides a new way to enhance the efficacy of genotoxic drugs. PMID:25558828

  14. MAX inactivation in small cell lung cancer disrupts MYC-SWI/SNF programs and is synthetic lethal with BRG1.

    PubMed

    Romero, Octavio A; Torres-Diz, Manuel; Pros, Eva; Savola, Suvi; Gomez, Antonio; Moran, Sebastian; Saez, Carmen; Iwakawa, Reika; Villanueva, Alberto; Montuenga, Luis M; Kohno, Takashi; Yokota, Jun; Sanchez-Cespedes, Montse

    2014-03-01

    Our knowledge of small cell lung cancer (SCLC) genetics is still very limited, amplification of L-MYC, N-MYC, and C-MYC being some of the well-established gene alterations. Here, we report our discovery of tumor-specific inactivation of the MYC-associated factor X gene, MAX, in SCLC. MAX inactivation is mutually exclusive with alterations of MYC and BRG1, the latter coding for an ATPase of the switch/sucrose nonfermentable (SWI/SNF) complex. We demonstrate that BRG1 regulates the expression of MAX through direct recruitment to the MAX promoter, and that depletion of BRG1 strongly hinders cell growth, specifically in MAX-deficient cells, heralding a synthetic lethal interaction. Furthermore, MAX requires BRG1 to activate neuroendocrine transcriptional programs and to upregulate MYC targets, such as glycolysis-related genes. Finally, inactivation of the MAX dimerization protein, MGA, was also observed in both non-small cell lung cancer and SCLC. Our results provide evidence that an aberrant SWI/SNF-MYC network is essential for lung cancer development. PMID:24362264

  15. Identification of cetrimonium bromide and irinotecan as compounds with synthetic lethality against NDRG1 deficient prostate cancer cells

    PubMed Central

    Wissing, Michel D.; Mendonca, Janet; Kim, Eunice; Kim, Eugene; Shim, Joong S.; Kaelber, Nadine S.; Kant, Huub; Hammers, Hans; Commes, Therese; Van Diest, Paul J.; Liu, Jun O.; Kachhap, Sushant K.

    2013-01-01

    The N-myc downstream regulated gene 1 (NDRG1) has been identified as a metastasis-suppressor gene in prostate cancer (PCa). Compounds targeting PCa cells deficient in NDRG1 could potentially decrease invasion/metastasis of PCa. A cell based screening strategy was employed to identify small molecules that selectively target NDRG1 deficient PCa cells. DU-145 PCa cells rendered deficient in NDRG1 expression by a lentiviral shRNA-mediated knockdown strategy were used in the primary screen. Compounds filtered from the primary screen were further validated through proliferation and clonogenic survival assays in parental and NDRG1 knockdown PCa cells. Screening of 3360 compounds revealed irinotecan and cetrimonium bromide (CTAB) as compounds that exhibited synthetic lethality against NDRG1 deficient PCa cells. A three-dimensional (3-D) invasion assay was utilized to test the ability of CTAB to inhibit invasion of DU-145 cells. CTAB was found to remarkably decrease invasion of DU-145 cells in collagen matrix. Our results suggest that CTAB and irinotecan could be further explored for their potential clinical benefit in patients with NDRG1 deficient PCa. PMID:23377825

  16. In vivo toxic and lethal cardiovascular effects of a synthetic polymeric 1,3-dodecylpyridinium salt in rodents

    SciTech Connect

    Grandic, Marjana; Sepcic, Kristina; Turk, Tom; Juntes, Polona; Frangez, Robert

    2011-08-15

    APS12-2 is one in a series of synthetic analogs of the polymeric alkylpyridinium salts isolated from the marine sponge Reniera sarai. As it is a potential candidate for treating non small cell lung cancer (NSCLC), we have studied its possible toxic and lethal effects in vivo. The median lethal dose (LD{sub 50}) of APS12-2 in mice was determined to be 11.5 mg/kg. Electrocardiograms, arterial blood pressure and respiratory activity were recorded under general anesthesia in untreated, pharmacologically vagotomized and artificially ventilated rats injected with APS12-2. In one group, the in vivo effects of APS12-2 were studied on nerve-evoked muscle contraction. Administration of APS12-2 at a dose of 8 mg/kg caused a progressive reduction of arterial blood pressure to a mid-circulatory value, accompanied by bradycardia, myocardial ischemia, ventricular extrasystoles, and second degree atrio-ventricular block. Similar electrocardiogram and arterial blood pressure changes caused by APS12-2 (8 mg/kg) were observed in animals pretreated with atropine and in artificially ventilated animals, indicating that hypoxia and cholinergic effects do not play a crucial role in the toxicity of APS12-2. Application of APS12-2 at sublethal doses (4 and 5.5 mg/kg) caused a decrease of arterial blood pressure, followed by an increase slightly above control values. We found that APS12-2 causes lysis of rat erythrocytes in vitro, therefore it is reasonable to expect the same effect in vivo. Indeed, hyperkalemia was observed in the blood of experimental animals. Hyperkalemia probably plays an important role in APS12-2 cardiotoxicity since no evident changes in histopathology of the heart were found. However, acute lesions were observed in the pulmonary vessels of rats after application of 8 mg/kg APS12-2. Predominant effects were dilation of interalveolar blood vessels and lysis of aggregated erythrocytes within their lumina. - Highlights: > LD{sub 50} estimated in mice (11.5 mg/kg) revealed

  17. Identification of novel synergistic targets for rational drug combinations with PI3 kinase inhibitors using siRNA synthetic lethality screening against GBM

    PubMed Central

    Kim, Yong-Wan; Liu, Ta Jen; Koul, Dimpy; Tiao, Ningyi; Feroze, Abdullah H.; Wang, Jing; Powis, Garth; Yung, W. K. Alfred

    2011-01-01

    Several small molecules that inhibit the PI3 kinase (PI3K)-Akt signaling pathway are in clinical development. Although many of these molecules have been effective in preclinical models, it remains unclear whether this strategy alone will be sufficient to interrupt the molecular events initiated and maintained by signaling along the pathways because of the activation of other pathways that compensate for the inhibition of the targeted kinase. In this study, we performed a synthetic lethality screen to identify genes or pathways whose inactivation, in combination with the PI3K inhibitors PX-866 and NVPBEZ-235, might result in a lethal phenotype in glioblastoma multiforme (GBM) cells. We screened GBM cells (U87, U251, and T98G) with a large-scale, short hairpin RNA library (GeneNet), which contains 43 800 small interfering RNA sequences targeting 8500 well-characterized human genes. To decrease off-target effects, we selected overlapping genes among the 3 cell lines that synergized with PX-866 to induce cell death. To facilitate the identification of potential targets, we used a GSE4290 dataset and The Cancer Genome Atlas GBM dataset, identifying 15 target genes overexpressed in GBM tissues. We further analyzed the selected genes using Ingenuity Pathway Analysis software and showed that the 15 genes were closely related to cancer-promoting pathways, and a highly interconnected network of aberrations along the MYC, P38MAPK, and ERK signaling pathways were identified. Our findings suggest that inhibition of these pathways might increase tumor sensitivity to PX-866 and therefore represent a potential clinical therapeutic strategy. PMID:21430111

  18. miR-342 overexpression results in a synthetic lethal phenotype in BRCA1-mutant HCC1937 breast cancer cells

    PubMed Central

    Crippa, Elisabetta; Folini, Marco; Pennati, Marzia; Zaffaroni, Nadia; Pierotti, Marco A.; Gariboldi, Manuela

    2016-01-01

    Expression of miR-342 has been strongly correlated with estrogen receptor (ER) status in breast cancer, where it is highest in ER-positive and lowest in triple-negative tumors. We investigated the effects of miR-342 transfection in the triple-negative breast cancer cell lines MDA-MB-231 and HCC1937, the latter carrying a germ-line BRCA1 mutation. Reconstitution of miR-342 led to caspase-dependent induction of apoptosis only in HCC1937 cells, while overexpression of wild-type BRCA1 in HCC1937 cells counteracted miR-342-mediated induction of apoptosis, suggesting that miR-342 overexpression and the lack of functional BRCA1 result in a synthetic lethal phenotype. Moreover, siRNA-mediated depletion of BRCA1 in MDA-MB-231 cells expressing the wild-type protein led to apoptosis upon transfection with miR-342. Using an in silico approach and a luciferase reporter system, we identified and functionally validated the Baculoviral IAP repeat-containing 6 gene (BIRC6), which encodes the anti-apoptotic factor Apollon/BRUCE, as a target of miR-342. In our model, BIRC6 likely acts as a determinant of the miRNA-dependent induction of apoptosis in BRCA1-mutant HCC1937 cells. Together, our findings suggest a tumor-suppressive function of miR-342 that could be exploited in the treatment of a subset of BRCA1-mutant hereditary breast cancers. PMID:26919240

  19. Targeting glutamine metabolism in multiple myeloma enhances BIM binding to BCL-2 eliciting synthetic lethality to venetoclax.

    PubMed

    Bajpai, R; Matulis, S M; Wei, C; Nooka, A K; Von Hollen, H E; Lonial, S; Boise, L H; Shanmugam, M

    2016-07-28

    Multiple myeloma (MM) is a plasma cell malignancy that is largely incurable due to development of resistance to therapy-elicited cell death. Nutrients are intricately connected to maintenance of cellular viability in part by inhibition of apoptosis. We were interested to determine if examination of metabolic regulation of BCL-2 proteins may provide insight on alternative routes to engage apoptosis. MM cells are reliant on glucose and glutamine and withdrawal of either nutrient is associated with varying levels of apoptosis. We and others have demonstrated that glucose maintains levels of key resistance-promoting BCL-2 family member, myeloid cell leukemic factor 1 (MCL-1). Cells continuing to survive in the absence of glucose or glutamine were found to maintain expression of MCL-1 but importantly induce pro-apoptotic BIM expression. One potential mechanism for continued survival despite induction of BIM could be due to binding and sequestration of BIM to alternate pro-survival BCL-2 members. Our investigation revealed that cells surviving glutamine withdrawal in particular, enhance expression and binding of BIM to BCL-2, consequently sensitizing these cells to the BH3 mimetic venetoclax. Glutamine deprivation-driven sensitization to venetoclax can be reversed by metabolic supplementation with TCA cycle intermediate α-ketoglutarate. Inhibition of glucose metabolism with the GLUT4 inhibitor ritonavir elicits variable cytotoxicity in MM that is marginally enhanced with venetoclax treatment, however, targeting glutamine metabolism with 6-diazo-5-oxo-l-norleucine uniformly sensitized MM cell lines and relapse/refractory patient samples to venetoclax. Our studies reveal a potent therapeutic strategy of metabolically driven synthetic lethality involving targeting glutamine metabolism for sensitization to venetoclax in MM. PMID:26640142

  20. Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers

    PubMed Central

    Hoffman, Gregory R.; Rahal, Rami; Buxton, Frank; Xiang, Kay; McAllister, Gregory; Frias, Elizabeth; Bagdasarian, Linda; Huber, Janina; Lindeman, Alicia; Chen, Dongshu; Romero, Rodrigo; Ramadan, Nadire; Phadke, Tanushree; Haas, Kristy; Jaskelioff, Mariela; Wilson, Boris G.; Meyer, Matthew J.; Saenz-Vash, Veronica; Zhai, Huili; Myer, Vic E.; Porter, Jeffery A.; Keen, Nicholas; McLaughlin, Margaret E.; Mickanin, Craig; Roberts, Charles W. M.; Stegmeier, Frank; Jagani, Zainab

    2014-01-01

    Defects in epigenetic regulation play a fundamental role in the development of cancer, and epigenetic regulators have recently emerged as promising therapeutic candidates. We therefore set out to systematically interrogate epigenetic cancer dependencies by screening an epigenome-focused deep-coverage design shRNA (DECODER) library across 58 cancer cell lines. This screen identified BRM/SMARCA2, a DNA-dependent ATPase of the mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complex, as being essential for the growth of tumor cells that harbor loss of function mutations in BRG1/SMARCA4. Depletion of BRM in BRG1-deficient cancer cells leads to a cell cycle arrest, induction of senescence, and increased levels of global H3K9me3. We further demonstrate the selective dependency of BRG1-mutant tumors on BRM in vivo. Genetic alterations of the mSWI/SNF chromatin remodeling complexes are the most frequent among chromatin regulators in cancers, with BRG1/SMARCA4 mutations occurring in ∼10–15% of lung adenocarcinomas. Our findings position BRM as an attractive therapeutic target for BRG1 mutated cancers. Because BRG1 and BRM function as mutually exclusive catalytic subunits of the mSWI/SNF complex, we propose that such synthetic lethality may be explained by paralog insufficiency, in which loss of one family member unveils critical dependence on paralogous subunits. This concept of “cancer-selective paralog dependency” may provide a more general strategy for targeting other tumor suppressor lesions/complexes with paralogous subunits. PMID:24520176

  1. C. elegans ten-1 is synthetic lethal with mutations in cytoskeleton regulators, and enhances many axon guidance defective mutants

    PubMed Central

    2010-01-01

    Background Teneurins are transmembrane proteins that assist morphogenetic processes in many organisms. ten-1 is the C. elegans teneurin homolog with two transcripts, ten-1a and ten-1b, that respectively encode a long (TEN-1L) and short (TEN-1S) form of the protein. We previously isolated a C. elegans mutant where one pharyngeal neuron was frequently misplaced, and now show that it corresponds to a novel allele of ten-1. Results The novel ten-1(et5) allele is a hypomorph since its post-embryonic phenotype is weaker than the null alleles ten-1(ok641) and ten-1(tm651). ten-1 mutants have defects in all pharyngeal neurons that we examined, and in vivo reporters show that only the long form of the ten-1 gene is expressed in the pharynx, specifically in six marginal cells and the M2 neurons. Defects in the pharyngeal M2 neurons were enhanced when the ten-1(ok641) mutation was combined with mutations in the following genes: mig-14, unc-5, unc-51, unc-52 and unc-129. None of the body neurons examined show any defects in the ten-1(ok641) mutant, but genetic interaction studies reveal that ten-1(ok641) is synthetic lethal with sax-3, unc-34 and unc-73, and examination of the hypodermal cells in embryos of the ten-1(ok641) mutant point to a role of ten-1 during hypodermal cell morphogenesis. Conclusions Our results are consistent with ten-1 normally providing a function complementary to the cytoskeletal remodeling processes that occur in migrating cells or cells undergoing morphogenesis. It is possible that ten-1 influences the composition/distribution of extracellular matrix. PMID:20497576

  2. ATR inhibition induces synthetic lethality and overcomes chemoresistance in TP53- or ATM-defective chronic lymphocytic leukemia cells.

    PubMed

    Kwok, Marwan; Davies, Nicholas; Agathanggelou, Angelo; Smith, Edward; Oldreive, Ceri; Petermann, Eva; Stewart, Grant; Brown, Jeff; Lau, Alan; Pratt, Guy; Parry, Helen; Taylor, Malcolm; Moss, Paul; Hillmen, Peter; Stankovic, Tatjana

    2016-02-01

    TP53 and ataxia telangiectasia mutated (ATM) defects are associated with genomic instability, clonal evolution, and chemoresistance in chronic lymphocytic leukemia (CLL). Currently, therapies capable of providing durable remissions in relapsed/refractory TP53- or ATM-defective CLL are lacking. Ataxia telangiectasia and Rad3-related (ATR) mediates response to replication stress, the absence of which leads to collapse of stalled replication forks into chromatid fragments that require resolution through the ATM/p53 pathway. Here, using AZD6738, a novel ATR kinase inhibitor, we investigated ATR inhibition as a synthetically lethal strategy to target CLL cells with TP53 or ATM defects. Irrespective of TP53 or ATM status, induction of CLL cell proliferation upregulated ATR protein, which then became activated in response to replication stress. In TP53- or ATM-defective CLL cells, inhibition of ATR signaling by AZD6738 led to an accumulation of unrepaired DNA damage, which was carried through into mitosis because of defective cell cycle checkpoints, resulting in cell death by mitotic catastrophe. Consequently, AZD6738 was selectively cytotoxic to both TP53- and ATM-defective CLL cell lines and primary cells. This was confirmed in vivo using primary xenograft models of TP53- or ATM-defective CLL, where treatment with AZD6738 resulted in decreased tumor load and reduction in the proportion of CLL cells with such defects. Moreover, AZD6738 sensitized TP53- or ATM-defective primary CLL cells to chemotherapy and ibrutinib. Our findings suggest that ATR is a promising therapeutic target for TP53- or ATM-defective CLL that warrants clinical investigation. PMID:26563132

  3. Synthetic Lethal Therapy for KRAS Mutant Non-small-cell Lung Carcinoma with Nanoparticle-mediated CDK4 siRNA Delivery

    PubMed Central

    Mao, Cheng-Qiong; Xiong, Meng-Hua; Liu, Yang; Shen, Song; Du, Xiao-Jiao; Yang, Xian-Zhu; Dou, Shuang; Zhang, Pei-Zhuo; Wang, Jun

    2014-01-01

    The KRAS mutation is present in ~20% of lung cancers and has not yet been effectively targeted for therapy. This mutation is associated with a poor prognosis in non-small-cell lung carcinomas (NSCLCs) and confers resistance to standard anticancer treatment drugs, including epidermal growth factor receptor tyrosine kinase inhibitors. In this study, we exploited a new therapeutic strategy based on the synthetic lethal interaction between cyclin-dependent kinase 4 (CDK4) downregulation and the KRAS mutation to deliver micellar nanoparticles (MNPs) containing small interfering RNA targeting CDK4 (MNPsiCDK4) for treatment in NSCLCs harboring the oncogenic KRAS mutation. Following MNPsiCDK4 administration, CDK4 expression was decreased, accompanied by inhibited cell proliferation, specifically in KRAS mutant NSCLCs. However, this intervention was harmless to normal KRAS wild-type cells, confirming the proposed mechanism of synthetic lethality. Moreover, systemic delivery of MNPsiCDK4 significantly inhibited tumor growth in an A549 NSCLC xenograft murine model, with depressed expression of CDK4 and mutational KRAS status, suggesting the therapeutic promise of MNPsiCDK4 delivery in KRAS mutant NSCLCs via a synthetic lethal interaction between KRAS and CDK4. PMID:24496383

  4. Synthetic aperture interferometry: error analysis

    SciTech Connect

    Biswas, Amiya; Coupland, Jeremy

    2010-07-10

    Synthetic aperture interferometry (SAI) is a novel way of testing aspherics and has a potential for in-process measurement of aspherics [Appl. Opt.42, 701 (2003)].APOPAI0003-693510.1364/AO.42.000701 A method to measure steep aspherics using the SAI technique has been previously reported [Appl. Opt.47, 1705 (2008)].APOPAI0003-693510.1364/AO.47.001705 Here we investigate the computation of surface form using the SAI technique in different configurations and discuss the computational errors. A two-pass measurement strategy is proposed to reduce the computational errors, and a detailed investigation is carried out to determine the effect of alignment errors on the measurement process.

  5. Chitin synthase III: Synthetic lethal mutants and “stress related” chitin synthesis that bypasses the CSD3/CHS6 localization pathway

    PubMed Central

    Osmond, Barbara C.; Specht, Charles A.; Robbins, Phillips W.

    1999-01-01

    We screened Saccharomyces strains for mutants that are synthetically lethal with deletion of the major chitin synthase gene CHS3. In addition to finding, not surprisingly, that mutations in major cell wall-related genes such as FKS1 (glucan synthase) and mutations in any of the Golgi glycosylation complex genes (MNN9 family) are lethal in combination with chs3Δ, we found that a mutation in Srv2p, a bifunctional regulatory gene, is notably lethal in the chs3 deletion. In extending studies of fks1-chitin synthase 3 interactions, we made the surprising discovery that deletion of CSD3/CHS6, a gene normally required for Chs3p delivery and activity in vivo, was not lethal with fks1 and, in fact, that lack of Csd3p/Chs6p did not decrease the high level of stress-related chitin made in the fks1 mutant. This finding suggests that “stress response” chitin synthesis proceeds through an alternate Chs3p targeting pathway. PMID:10500155

  6. An arf1Delta synthetic lethal screen identifies a new clathrin heavy chain conditional allele that perturbs vacuolar protein transport in Saccharomyces cerevisiae.

    PubMed Central

    Chen, C Y; Graham, T R

    1998-01-01

    ADP-ribosylation factor (ARF) is a small GTP-binding protein that is thought to regulate the assembly of coat proteins on transport vesicles. To identify factors that functionally interact with ARF, we have performed a genetic screen in Saccharomyces cerevisiae for mutations that exhibit synthetic lethality with an arf1Delta allele and defined seven genes by complementation tests (SWA1-7 for synthetically lethal with arf1Delta). Most of the swa mutants exhibit phenotypes comparable to arf1Delta mutants such as temperature-conditional growth, hypersensitivity to fluoride ions, and partial protein transport and glycosylation defects. Here, we report that swa5-1 is a new temperature-sensitive allele of the clathrin heavy chain gene (chc1-5), which carries a frameshift mutation near the 3' end of the CHC1 open reading frame. This genetic interaction between arf1 and chc1 provides in vivo evidence for a role for ARF in clathrin coat assembly. Surprisingly, strains harboring chc1-5 exhibited a significant defect in transport of carboxypeptidase Y or carboxypeptidase S to the vacuole that was not observed in other chc1 ts mutants. The kinetics of invertase secretion or transport of alkaline phosphatase to the vacuole were not significantly affected in the chc1-5 mutant, further implicating clathrin specifically in the Golgi to vacuole transport pathway for carboxypeptidase Y. PMID:9755191

  7. Hyper-active non-homologous end joining selects for synthetic lethality resistant and pathological Fanconi anemia hematopoietic stem and progenitor cells.

    PubMed

    Du, Wei; Amarachintha, Surya; Wilson, Andrew F; Pang, Qishen

    2016-01-01

    The prominent role of Fanconi anemia (FA) proteins involves homologous recombination (HR) repair. Poly[ADP-ribose] polymerase1 (PARP1) functions in multiple cellular processes including DNA repair and PARP inhibition is an emerging targeted therapy for cancer patients deficient in HR. Here we show that PARP1 activation in hematopoietic stem and progenitor cells (HSPCs) in response to genotoxic or oxidative stress attenuates HSPC exhaustion. Mechanistically, PARP1 controls the balance between HR and non-homologous end joining (NHEJ) in double strand break (DSB) repair by preventing excessive NHEJ. Disruption of the FA core complex skews PARP1 function in DSB repair and led to hyper-active NHEJ in Fanca(-/-) or Fancc(-/-) HSPCs. Re-expression of PARP1 rescues the hyper-active NHEJ phenotype in Brca1(-/-)Parp1(-/-) but less effective in Fanca(-/-)Parp1(-/-) cells. Inhibition of NHEJ prevents myeloid/erythroid pathologies associated with synthetic lethality. Our results suggest that hyper-active NHEJ may select for "synthetic lethality" resistant and pathological HSPCs. PMID:26916217

  8. Differences in Expression of Key DNA Damage Repair Genes after Epigenetic-Induced BRCAness Dictate Synthetic Lethality with PARP1 Inhibition.

    PubMed

    Wiegmans, Adrian P; Yap, Pei-Yi; Ward, Ambber; Lim, Yi Chieh; Khanna, Kum Kum

    2015-10-01

    The triple-negative breast cancer (TNBC) subtype represents a cancer that is highly aggressive with poor patient outcome. Current preclinical success has been gained through synthetic lethality, targeting genome instability with PARP inhibition in breast cancer cells that harbor silencing of the homologous recombination (HR) pathway. Histone deacetylase inhibitors (HDACi) are a class of drugs that mediate epigenetic changes in expression of HR pathway genes. Here, we compare the activity of the pan-HDAC inhibitor suberoylanilide hydroxamic acid (SAHA), the class I/IIa HDAC inhibitor valproic acid (VPA), and the HDAC1/2-specific inhibitor romidepsin (ROMI) for their capability to regulate DNA damage repair gene expression and in sensitizing TNBC to PARPi. We found that two of the HDACis tested, SAHA and ROMI, but not VPA, indeed inhibit HR repair and that RAD51, BARD1, and FANCD2 represent key proteins whose inhibition is required for HDACi-mediated therapy with PARP inhibition in TNBC. We also observed that restoration of BRCA1 function stabilizes the genome compared with mutant BRCA1 that results in enhanced polyploid population after combination treatment with HDACi and PARPi. Furthermore, we found that overexpression of the key HR protein RAD51 represents a mechanism for this resistance, promoting aberrant repair and the enhanced polyploidy observed. These findings highlight the key components of HR in guiding synthetic lethality with PARP inhibition and support the rationale for utilizing the novel combination of HDACi and PARPi against TNBC in the clinical setting. PMID:26294743

  9. Non-lethal sampling of walleye for stable isotope analysis: a comparison of three tissues

    USGS Publications Warehouse

    Chipps, Steven R.; VanDeHey, J.A.; Fincel, M.J.

    2012-01-01

    Stable isotope analysis of fishes is often performed using muscle or organ tissues that require sacrificing animals. Non-lethal sampling provides an alternative for evaluating isotopic composition for species of concern or individuals of exceptional value. Stable isotope values of white muscle (lethal) were compared with those from fins and scales (non-lethal) in walleye, Sander vitreus (Mitchill), from multiple systems, size classes and across a range of isotopic values. Isotopic variability was also compared among populations to determine the potential of non-lethal tissues for diet-variability analyses. Muscle-derived isotope values were enriched compared with fins and depleted relative to scales. A split-sample validation technique and linear regression found that isotopic composition of walleye fins and scales was significantly related to that in muscle tissue for both δ13C and δ15N (r2 = 0.79–0.93). However, isotopic variability was significantly different between tissue types in two of six populations for δ15N and three of six populations for δ13C. Although species and population specific, these findings indicate that isotopic measures obtained from non-lethal tissues are indicative of those obtained from muscle.

  10. Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC

    PubMed Central

    Aziz, Ramy K.; Khaw, Valerie L.; Monk, Jonathan M.; Brunk, Elizabeth; Lewis, Robert; Loh, Suh I.; Mishra, Arti; Nagle, Amrita A.; Satyanarayana, Chitkala; Dhakshinamoorthy, Saravanakumar; Luche, Michele; Kitchen, Douglas B.; Andrews, Kathleen A.; Palsson, Bernhard Ø.; Charusanti, Pep

    2015-01-01

    Mathematical models of biochemical networks form a cornerstone of bacterial systems biology. Inconsistencies between simulation output and experimental data point to gaps in knowledge about the fundamental biology of the organism. One such inconsistency centers on the gene aldA in Escherichia coli: it is essential in a computational model of E. coli metabolism, but experimentally it is not. Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA. Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100–200 μM individual concentrations. These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics. PMID:26441892

  11. Genome-wide profiling of genetic synthetic lethality identifies CDK12 as a novel determinant of PARP1/2 inhibitor sensitivity

    PubMed Central

    Bajrami, Ilirjana; Frankum, Jessica R.; Konde, Asha; Miller, Rowan E.; Rehman, Farah L.; Brough, Rachel; Campbell, James; Sims, David; Rafiq, Rumana; Hooper, Sean; Chen, Lina; Kozarewa, Iwanka; Assiotis, Ioannis; Fenwick, Kerry; Natrajan, Rachael; Lord, Christopher J.; Ashworth, Alan

    2016-01-01

    Small molecule inhibitors of PARP1/2 such as olaparib have been proposed to serve as a synthetic lethal therapy for cancers that harbor BRCA1 or BRCA2 mutations. Indeed, in clinical trials PARP1/2 inhibitors elicit sustained anti-tumor responses in patients with germ-line BRCA gene mutations. In hypothesizing that additional genetic determinants might direct use of these drugs, we conducted a genome-wide synthetic lethal screen for candidate olaparib sensitivity genes. In support of this hypothesis, the set of identified genes included known determinants of olaparib sensitivity, such as BRCA1, RAD51 and Fanconi’s anemia susceptibility genes. Additionally, the set included genes implicated in established networks of DNA repair, DNA cohesion and chromatin remodelling, none of which were known previously to confer sensitivity to PARP1/2 inhibition. Notably, integration of the list of candidate sensitivity genes with data from tumor DNA sequencing studies identified CDK12 deficiency as a clinically relevant biomarker of PARP1/2 inhibitor sensitivity. In models of high-grade serous ovarian cancer (HGS-OVCa), CDK12 attenuation was sufficient to confer sensitivity to PARP1/2 inhibition, suppression of DNA repair via homologous recombination and reduced expression of BRCA1. As one of only nine genes known to be mutated in HGS-OVCa, CDK12 has properties that should confirm interest in its utility as a biomarker, particularly in ongoing clinical trials of PARP1/2 inhibitors and other agents that trigger replication fork arrest. PMID:24240700

  12. Dual inhibition of EGFR and MET induces synthetic lethality in triple-negative breast cancer cells through downregulation of ribosomal protein S6

    PubMed Central

    YI, YONG WEON; YOU, KYUSIC; BAE, EDWARD JEONG; KWAK, SAHNG-JUNE; SEONG, YEON-SUN; BAE, INSOO

    2015-01-01

    Triple-negative breast cancer (TNBC) exhibits innate resistance to the EGFR inhibition despite high level expression of EGFR. Recently, we found that the proliferation of basal-like (BL) subtype TNBC cells is synergistically inhibited by combination of EGFR and PI3K/AKT inhibitors. On the contrary, TNBC cells of mesenchymal stem-like (MSL) subtype are resistant to these combinations. To identify potential synthetic lethal interaction of compounds for treatment of MSL subtype TNBC cells, we performed MTT screening of MDA-MB-231 cells with a small library of receptor tyrosine kinase inhibitors (RTKIs) in the presence of gefitinib, an EGFR inhibitor. We identified MET inhibitors as potent RTKIs that caused synthetic lethality in combination with gefitinib in MDA-MB-231 cells. We demonstrated that combination of a MET inhibitor SU11274 with various EGFR inhibitors resulted in synergistic suppression of cell viability (in MTT assay) and cell survival (in colony formation assay) of MSL subtype TNBC cells. We further demonstrated that SU11274 alone induced G2 arrest and gefitinib/SU11274 combination sustained the SU11274-induced G2 arrest in these cells. In addition, SU11274/gefitinib combination synergistically reduced the level of ribosomal protein S6 (RPS6) in MSL subtype TNBC cells. In addition, knockdown of RPS6 itself, in both HS578T and MDA-MB-231, markedly reduced the proliferation of these cells. Taken together, our data suggest that dual targeting of EGFR and MET inhibits the proliferation of MSL subtype TNBC cells through down-regulation of RPS6. PMID:25955731

  13. Dual inhibition of EGFR and MET induces synthetic lethality in triple-negative breast cancer cells through downregulation of ribosomal protein S6.

    PubMed

    Yi, Yong Weon; You, Kyusic; Bae, Edward Jeong; Kwak, Sahng-June; Seong, Yeon-Sun; Bae, Insoo

    2015-07-01

    Triple-negative breast cancer (TNBC) exhibits innate resistance to the EGFR inhibition despite high level expression of EGFR. Recently, we found that the proliferation of basal-like (BL) subtype TNBC cells is synergistically inhibited by combination of EGFR and PI3K/AKT inhibitors. On the contrary, TNBC cells of mesenchymal stem-like (MSL) subtype are resistant to these combinations. To identify potential synthetic lethal interaction of compounds for treatment of MSL subtype TNBC cells, we performed MTT screening of MDA-MB‑231 cells with a small library of receptor tyrosine kinase inhibitors (RTKIs) in the presence of gefitinib, an EGFR inhibitor. We identified MET inhibitors as potent RTKIs that caused synthetic lethality in combination with gefitinib in MDA-MB‑231 cells. We demonstrated that combination of a MET inhibitor SU11274 with various EGFR inhibitors resulted in synergistic suppression of cell viability (in MTT assay) and cell survival (in colony formation assay) of MSL subtype TNBC cells. We further demonstrated that SU11274 alone induced G2 arrest and gefitinib/SU11274 combination sustained the SU11274-induced G2 arrest in these cells. In addition, SU11274/gefitinib combination synergistically reduced the level of ribosomal protein S6 (RPS6) in MSL subtype TNBC cells. In addition, knockdown of RPS6 itself, in both HS578T and MDA-MB‑231, markedly reduced the proliferation of these cells. Taken together, our data suggest that dual targeting of EGFR and MET inhibits the proliferation of MSL subtype TNBC cells through downregulation of RPS6. PMID:25955731

  14. Synthetic Lethality Screen Identifies RPS6KA2 as Modifier of Epidermal Growth Factor Receptor Activity in Pancreatic Cancer12

    PubMed Central

    Milosevic, Nada; Kühnemuth, Benjamin; Mühlberg, Leonie; Ripka, Stefanie; Griesmann, Heidi; Lölkes, Carolin; Buchholz, Malte; Aust, Daniela; Pilarsky, Christian; Krug, Sebastian; Gress, Thomas; Michl, Patrick

    2013-01-01

    Pancreatic cancer is characterized by a high degree of resistance to chemotherapy. Epidermal growth factor receptor (EGFR) inhibition using the small-molecule inhibitor erlotinib was shown to provide a small survival benefit in a subgroup of patients. To identify kinases whose inhibition acts synergistically with erlotinib, we employed a kinome-wide small-interfering RNA (siRNA)-based loss-of-function screen in the presence of erlotinib. Of 779 tested kinases, we identified several targets whose inhibition acted synergistically lethal with EGFR inhibition by erlotinib, among them the S6 kinase ribosomal protein S6 kinase 2 (RPS6KA2)/ribosomal S6 kinase 3. Activated RPS6KA2 was expressed in approximately 40% of 123 human pancreatic cancer tissues. RPS6KA2 was shown to act downstream of EGFR/RAS/mitogen-activated protein kinase kinase (MEK)/extracellular-signal regulated kinase (ERK) signaling and was activated by EGF independently of the presence of KRAS mutations. Knockdown of RPS6KA2 by siRNA led to increased apoptosis only in the presence of erlotinib, whereas RPS6KA2 activation or overexpression rescued from erlotinib- and gemcitabine-induced apoptosis. This effect was at least in part mediated by downstream activation of ribosomal protein S6. Genetic as well as pharmacological inhibition of RPS6KA2 by the inhibitor BI-D1870 acted synergistically with erlotinib. By applying this synergistic lethality screen using a kinome-wide RNA interference-library approach, we identified RPS6KA2 as potential drug target whose inhibition synergistically enhanced the effect of erlotinib on tumor cell survival. This kinase therefore represents a promising drug candidate suitable for the development of novel inhibitors for pancreatic cancer therapy. PMID:24403857

  15. A Synthetic Vision Preliminary Integrated Safety Analysis

    NASA Technical Reports Server (NTRS)

    Hemm, Robert; Houser, Scott

    2001-01-01

    This report documents efforts to analyze a sample of aviation safety programs, using the LMI-developed integrated safety analysis tool to determine the change in system risk resulting from Aviation Safety Program (AvSP) technology implementation. Specifically, we have worked to modify existing system safety tools to address the safety impact of synthetic vision (SV) technology. Safety metrics include reliability, availability, and resultant hazard. This analysis of SV technology is intended to be part of a larger effort to develop a model that is capable of "providing further support to the product design and development team as additional information becomes available". The reliability analysis portion of the effort is complete and is fully documented in this report. The simulation analysis is still underway; it will be documented in a subsequent report. The specific goal of this effort is to apply the integrated safety analysis to SV technology. This report also contains a brief discussion of data necessary to expand the human performance capability of the model, as well as a discussion of human behavior and its implications for system risk assessment in this modeling environment.

  16. Hyper-active non-homologous end joining selects for synthetic lethality resistant and pathological Fanconi anemia hematopoietic stem and progenitor cells

    PubMed Central

    Du, Wei; Amarachintha, Surya; Wilson, Andrew F.; Pang, Qishen

    2016-01-01

    The prominent role of Fanconi anemia (FA) proteins involves homologous recombination (HR) repair. Poly[ADP-ribose] polymerase1 (PARP1) functions in multiple cellular processes including DNA repair and PARP inhibition is an emerging targeted therapy for cancer patients deficient in HR. Here we show that PARP1 activation in hematopoietic stem and progenitor cells (HSPCs) in response to genotoxic or oxidative stress attenuates HSPC exhaustion. Mechanistically, PARP1 controls the balance between HR and non-homologous end joining (NHEJ) in double strand break (DSB) repair by preventing excessive NHEJ. Disruption of the FA core complex skews PARP1 function in DSB repair and led to hyper-active NHEJ in Fanca−/− or Fancc−/− HSPCs. Re-expression of PARP1 rescues the hyper-active NHEJ phenotype in Brca1−/−Parp1−/− but less effective in Fanca−/−Parp1−/− cells. Inhibition of NHEJ prevents myeloid/erythroid pathologies associated with synthetic lethality. Our results suggest that hyper-active NHEJ may select for “synthetic lethality” resistant and pathological HSPCs. PMID:26916217

  17. Novel synthetic plasmid and Doggybone™ DNA vaccines induce neutralizing antibodies and provide protection from lethal influenza challenge in mice

    PubMed Central

    Scott, Veronica L; Patel, Ami; Villarreal, Daniel O; Hensley, Scott E; Ragwan, Edwin; Yan, Jian; Sardesai, Niranjan Y; Rothwell, Paul J; Extance, Jonathan P; Caproni, Lisa J; Weiner, David B

    2015-01-01

    Nucleic acid-based vaccines (NAVs) are a promising alternative to conventional influenza vaccines with the potential to increase influenza vaccine availability due to their simplicity in design and rapid speed of production. NAVs can also target multiple influenza antigens and control flu variants. Traditionally NAVs have been DNA plasmids however, we are continuing to explore new methods that may enhance vaccine efficacy. Recently new focus has been on RNA cassettes as NAVs. RNA vaccines combine conceptual advantages in that they focus on delivery of only the coding cassette. However, RNA vaccines have a short half-life and cause interferon-induced fevers. Here we describe a new NAV approach where we study delivery of a linear DNA cassette [Doggybone™ linear closed DNA [(dbDNA™)] produced by an enzymatic process that yields an antigen expression cassette comprising a promoter, DNA antigen, poly A tail, and telomeric ends. This focused approach has many of the advantages of plasmid DNA as well as a minimal cassette size similar to RNA strategies. For this study, we characterized the specific CD4+ and CD8+ T cell responses and determined the hemagglutination inhibition (HI) titers induced by dbDNA™ and compared the responses with those of an optimized plasmid DNA (pDNA) vaccine encoding the same H1N1 influenza A/PR/8/34 HA gene. Immunizations with the constructs resulted in similar humoral and cellular immune responses. Both constructs induced high-titer HI antibodies and fully protected animals from lethal viral challenge. The data obtained from this study provides important validation for further development of novel vector approaches. PMID:26091432

  18. Combined STAT3 and BCR-ABL1 Inhibition Induces Synthetic Lethality in Therapy-Resistant Chronic Myeloid Leukemia

    PubMed Central

    Mason, Clinton C.; Vellore, Nadeem A.; Resetca, Diana; Zabriskie, Matthew S.; Zhang, Tian Y.; Khorashad, Jamshid S.; Engar, Alexander J.; Reynolds, Kimberly R.; Anderson, David J.; Senina, Anna; Pomicter, Anthony D.; Arpin, Carolynn C.; Ahmad, Shazia; Heaton, William L.; Tantravahi, Srinivas K.; Todic, Aleksandra; Moriggl, Richard; Wilson, Derek J.; Baron, Riccardo

    2014-01-01

    Mutations in the BCR-ABL1 kinase domain are an established mechanism of tyrosine kinase inhibitor (TKI) resistance in Philadelphia chromosome-positive leukemia, but fail to explain many cases of clinical TKI failure. In contrast, it is largely unknown why some patients fail TKI therapy despite continued suppression of BCR-ABL1 kinase activity, a situation termed BCRABL1 kinase-independent TKI resistance. Here, we identified activation of signal transducer and activator of transcription 3 (STAT3) by extrinsic or intrinsic mechanisms as an essential feature of BCR-ABL1 kinase-independent TKI resistance. By combining synthetic chemistry, in vitro reporter assays, and molecular dynamics-guided rational inhibitor design and high-throughput screening, we discovered BP-5-087, a potent and selective STAT3 SH2 domain inhibitor that reduces STAT3 phosphorylation and nuclear transactivation. Computational simulations, fluorescence polarization assays, and hydrogen-deuterium exchange assays establish direct engagement of STAT3 by BP-5-087 and provide a high-resolution view of the STAT3 SH2 domain/BP-5-087 interface. In primary cells from CML patients with BCR-ABL1 kinase-independent TKI resistance, BP-5-087 (1.0 μM) restored TKI sensitivity to therapy-resistant CML progenitor cells, including leukemic stem cells (LSCs). Our findings implicate STAT3 as a critical signaling node in BCR-ABL1 kinase-independent TKI resistance, and suggest that BP-5-087 has clinical utility for treating malignancies characterized by STAT3 activation. PMID:25134459

  19. Combined STAT3 and BCR-ABL1 inhibition induces synthetic lethality in therapy-resistant chronic myeloid leukemia.

    PubMed

    Eiring, A M; Page, B D G; Kraft, I L; Mason, C C; Vellore, N A; Resetca, D; Zabriskie, M S; Zhang, T Y; Khorashad, J S; Engar, A J; Reynolds, K R; Anderson, D J; Senina, A; Pomicter, A D; Arpin, C C; Ahmad, S; Heaton, W L; Tantravahi, S K; Todic, A; Colaguori, R; Moriggl, R; Wilson, D J; Baron, R; O'Hare, T; Gunning, P T; Deininger, M W

    2015-03-01

    Mutations in the BCR-ABL1 kinase domain are an established mechanism of tyrosine kinase inhibitor (TKI) resistance in Philadelphia chromosome-positive leukemia, but fail to explain many cases of clinical TKI failure. In contrast, it is largely unknown why some patients fail TKI therapy despite continued suppression of BCR-ABL1 kinase activity, a situation termed BCR-ABL1 kinase-independent TKI resistance. Here, we identified activation of signal transducer and activator of transcription 3 (STAT3) by extrinsic or intrinsic mechanisms as an essential feature of BCR-ABL1 kinase-independent TKI resistance. By combining synthetic chemistry, in vitro reporter assays, and molecular dynamics-guided rational inhibitor design and high-throughput screening, we discovered BP-5-087, a potent and selective STAT3 SH2 domain inhibitor that reduces STAT3 phosphorylation and nuclear transactivation. Computational simulations, fluorescence polarization assays and hydrogen-deuterium exchange assays establish direct engagement of STAT3 by BP-5-087 and provide a high-resolution view of the STAT3 SH2 domain/BP-5-087 interface. In primary cells from chronic myeloid leukemia (CML) patients with BCR-ABL1 kinase-independent TKI resistance, BP-5-087 (1.0 μM) restored TKI sensitivity to therapy-resistant CML progenitor cells, including leukemic stem cells. Our findings implicate STAT3 as a critical signaling node in BCR-ABL1 kinase-independent TKI resistance, and suggest that BP-5-087 has clinical utility for treating malignancies characterized by STAT3 activation. PMID:25134459

  20. Loss of ypk1 function causes rapamycin sensitivity, inhibition of translation initiation and synthetic lethality in 14-3-3-deficient yeast.

    PubMed Central

    Gelperin, Daniel; Horton, Lynn; DeChant, Anne; Hensold, Jack; Lemmon, Sandra K

    2002-01-01

    14-3-3 proteins bind to phosphorylated proteins and regulate a variety of cellular activities as effectors of serine/threonine phosphorylation. To define processes requiring 14-3-3 function in yeast, mutants with increased sensitivity to reduced 14-3-3 protein levels were identified by synthetic lethal screening. One mutation was found to be allelic to YPK1, which encodes a Ser/Thr protein kinase. Loss of Ypk function causes hypersensitivity to rapamycin, similar to 14-3-3 mutations and other mutations affecting the TOR signaling pathway in yeast. Similar to treatment with rapamycin, loss of Ypk function disrupted translation, at least in part by causing depletion of eIF4G, a central adaptor protein required for cap-dependent mRNA translation initiation. In addition, Ypk1 as well as eIF4G protein levels were rapidly depleted upon nitrogen starvation, but not during glucose starvation, even though both conditions inhibit translation initiation. These results suggest that Ypk regulates translation initiation in response to nutrient signals, either through the TOR pathway or in a functionally related pathway parallel to TOR. PMID:12196392

  1. microRNA-206 impairs c-Myc-driven cancer in a synthetic lethal manner by directly inhibiting MAP3K13

    PubMed Central

    Han, Han; Chen, Yuxing; Cheng, Li; Prochownik, Edward V.; Li, Youjun

    2016-01-01

    c-Myc (Myc) is one of the most frequently dysregulated oncogenic transcription factors in human cancer. By functionally screening a microRNA (miR) library, we identified miR-206 as being a synthetic lethal in Myc over-expressing human cancer cells. miR-206 inhibited MAP3K13, which resulted in Myc protein de-stabilization, and an inhibition of anchorage-independent growth and in vivo tumorigenesis by Myc over-expressing human cancer cells. Eliminating MAP3K13 by shRNA recapitulated the effects caused by miR-206, thus supporting the idea that miR-206's effect on Myc was mediated through MAP3K13. Conversely, enforced expression of MAP3K13 stabilized Myc by promoting its N-terminal phosphorylation and enhancing its transcriptional activity. Gene expression analyses of breast cancers expressing high levels of Myc indicated that low miR-206 expression and high MAP3K13 expression correlated with poor patient survival. The critical link between miR-206 and MAP3K13 in the development of Myc over-expressing human cancers suggests potential points of therapeutic intervention for this molecular sub-category. PMID:26918941

  2. A Synthetic Lethal Interaction between Glutathione Synthesis and Mitochondrial Reactive Oxygen Species Provides a Tumor-Specific Vulnerability Dependent on STAT3

    PubMed Central

    Garama, Daniel J.; Harris, Tiffany J.; White, Christine L.; Rossello, Fernando J.; Abdul-Hay, Maher

    2015-01-01

    Increased production of mitochondrion-derived reactive oxygen species (ROS) is characteristic of a metabolic shift observed during malignant transformation. While the exact sources and roles of ROS in tumorigenesis remain to be defined, it has become clear that maintaining redox balance is critical for cancer cell proliferation and survival and, as such, may represent a vulnerability that can be exploited therapeutically. STAT3, a latent cytosolic transcription factor activated by diverse cytokines and growth factors, has been shown to exhibit an additional, nontranscriptional function in mitochondria, including modulation of electron transport chain activity. In particular, malignant transformation by Ras oncogenes exploits mitochondrial STAT3 functions. We used mass spectrometry-based metabolomics profiling to explore the biochemical basis for the STAT3 dependence of Ras transformation. We identified the gamma-glutamyl cycle, the production of glutathione, and the regulation of ROS as a mitochondrion-STAT3-dependent pathway in Ras-transformed cells. Experimental inhibition of key enzymes in the glutathione cycle resulted in the depletion of glutathione, accumulation of ROS, oxidative DNA damage, and cell death in an oncogenic Ras- and mitochondrial STAT3-dependent manner. These data uncover a synthetic lethal interaction involving glutathione production and mitochondrial ROS regulation in Ras-transformed cells that is governed by mitochondrial STAT3 and might be exploited therapeutically. PMID:26283727

  3. Identification of unique sensitizing targets for anti-inflammatory CDDO-Me in metastatic melanoma by a large-scale synthetic lethal RNAi screening

    PubMed Central

    Ekmekcioglu, Suhendan; Grimm, Elizabeth A.

    2013-01-01

    Summary CDDO-Me has been shown to exert potent anti-inflammatory activity for chronic kidney disease and antitumor activity for several tumors, including melanoma, in early clinical trials. To improve CDDO-Me response in melanoma, we utilized a large-scale synthetic lethal RNAi screen targeting 6,000 human druggable genes to identify targets that would sensitize melanoma cells to CDDO-Me. Based on screening results, five unique genes (GNPAT, SUMO1, SPINT2, FLI1, and SSX1) significantly potentiated the growth-inhibitory effects of CDDO-Me and induced apoptosis in A375, a BRAF mutated melanoma line (P<0.001). These five genes were then individually validated as targets to potentiate CDDO-Me activity, and related downstream signaling pathways of these genes were analyzed. In addition, the levels of phosphorylated Erk1/2, Akt, GSK-2, and PRAS40 were dramatically decreased by downregulating each of these five genes separately, suggesting a set of common mediators. Our findings indicate that GNPAT, SUMO1, SPINT2, FLI1, and SSX1 play critical roles in synergy with inflammation pathways in modulating melanoma cell survival, and could serve as sensitizing targets to enhance CDDO-Me efficacy in melanoma growth control. PMID:23020131

  4. A synthetic-lethality RNAi screen reveals an ERK-mTOR co-targeting pro-apoptotic switch in PIK3CA+ oral cancers

    PubMed Central

    Yamaguchi, Kosuke; Iglesias-Bartolomé, Ramiro; Wang, Zhiyong; Callejas-Valera, Juan Luis; Amornphimoltham, Panomwat; Molinolo, Alfredo A.; Cohen, Ezra E.; Califano, Joseph A.; Lippman, Scott M.; Luo, Ji; Gutkind, J. Silvio

    2016-01-01

    mTOR inhibition has emerged as a promising strategy for head and neck squamous cell carcinomas (HNSCC) treatment. However, most targeted therapies ultimately develop resistance due to the activation of adaptive survival signaling mechanisms limiting the activity of targeted agents. Thus, co-targeting key adaptive mechanisms may enable more effective cancer cell killing. Here, we performed a synthetic lethality screen using shRNA libraries to identify druggable candidates for combinatorial signal inhibition. We found that the ERK pathway was the most highly represented. Combination of rapamycin with trametinib, a MEK1/2 inhibitor, demonstrated strong synergism in HNSCC-derived cells in vitro and in vivo, including HNSCC cells expressing the HRAS and PIK3CA oncogenes. Interestingly, cleaved caspase-3 was potently induced by the combination therapy in PIK3CA+ cells in vitro and tumor xenografts. Moreover, ectopic expression of PIK3CA mutations into PIK3CA− HNSCC cells sensitized them to the pro-apoptotic activity of the combination therapy. These findings indicate that co-targeting the mTOR/ERK pathways may provide a suitable precision strategy for HNSCC treatment. Moreover, PIK3CA+ HNSCC are particularly prone to undergo apoptosis after mTOR and ERK inhibition, thereby providing a potential biomarker of predictive value for the selection of patients that may benefit from this combination therapy. PMID:26882569

  5. Computational Modeling And Analysis Of Synthetic Jets

    NASA Technical Reports Server (NTRS)

    Mittal, Rajat; Cattafesta, Lou

    2005-01-01

    In the last report we focused on the study of 3D synthetic jets of moderate jet aspect-ratio. Jets in quiescent and cross-flow cases were investigated. Since most of the synthetic jets in practical applications are found to be of large aspect ratio, the focus was shifted to studying synthetic jets of large aspect ratio. In the current year, further progress has been made by studying jets of aspect ratio 8 and infinity. Some other aspects of the jet, like the vorticity flux is looked into apart from analyzing the vortex dynamics, velocity profiles and the other dynamical characteristics of the jet which allows us to extract some insight into the effect of these modifications on the jet performance. Also, efforts were made to qualitatively validate the simulated results with the NASA Langley test cases at higher jet Reynolds number for the quiescent jet case.

  6. Evidence that synthetic lethality underlies the mutual exclusivity of oncogenic KRAS and EGFR mutations in lung adenocarcinoma

    PubMed Central

    Unni, Arun M; Lockwood, William W; Zejnullahu, Kreshnik; Lee-Lin, Shih-Queen; Varmus, Harold

    2015-01-01

    Human lung adenocarcinomas (LUAD) contain mutations in EGFR in ∼15% of cases and in KRAS in ∼30%, yet no individual adenocarcinoma appears to carry activating mutations in both genes, a finding we have confirmed by re-analysis of data from over 600 LUAD. Here we provide evidence that co-occurrence of mutations in these two genes is deleterious. In transgenic mice programmed to express both mutant oncogenes in the lung epithelium, the resulting tumors express only one oncogene. We also show that forced expression of a second oncogene in human cancer cell lines with an endogenous mutated oncogene is deleterious. The most prominent features accompanying loss of cell viability were vacuolization, other changes in cell morphology, and increased macropinocytosis. Activation of ERK, p38 and JNK in the dying cells suggests that an overly active MAPK signaling pathway may mediate the phenotype. Together, our findings indicate that mutual exclusivity of oncogenic mutations may reveal unexpected vulnerabilities and therapeutic possibilities. DOI: http://dx.doi.org/10.7554/eLife.06907.001 PMID:26047463

  7. Enhanced non-homologous end joining contributes toward synthetic lethality of pathological RAD51C mutants with poly (ADP-ribose) polymerase.

    PubMed

    Somyajit, Kumar; Mishra, Anup; Jameei, Aida; Nagaraju, Ganesh

    2015-01-01

    Poly (ADP-ribose) polymerase 1 (PARP1) inhibitors are actively under clinical trials for the treatment of breast and ovarian cancers that arise due to mutations in BRCA1 and BRCA2. The RAD51 paralog RAD51C has been identified as a breast and ovarian cancer susceptibility gene. The pathological RAD51C mutants that were identified in cancer patients are hypomorphic with partial repair function. However, targeting cancer cells that express hypomorphic mutants of RAD51C is highly challenging. Here, we report that RAD51C-deficient cells can be targeted by a 'synthetic lethal' approach using PARP inhibitor and this sensitivity was attributed to accumulation of cells in the G2/M and chromosomal aberrations. In addition, spontaneous hyperactivation of PARP1 was evident in RAD51C-deficient cells. Interestingly, RAD51C-negative cells exhibited enhanced recruitment of non-homologous end joining (NHEJ) proteins onto chromatin and this accumulation correlated with increased activity of error-prone NHEJ as well as genome instability leading to cell death. Notably, inhibition of DNA-PKcs or depletion of KU70 or Ligase IV rescued this phenotype. Strikingly, stimulation of NHEJ by low dose of ionizing radiation (IR) in the PARP inhibitor-treated RAD51C-deficient cells and cells expressing pathological RAD51C mutants induced enhanced toxicity 'synergistically'. These results demonstrate that cancer cells arising due to hypomorphic mutations in RAD51C can be specifically targeted by a 'synergistic approach' and imply that this strategy can be potentially applied to cancers with hypomorphic mutations in other homologous recombination pathway genes. PMID:25292178

  8. A Synthetic Lethality Screen Using a Focused siRNA Library to Identify Sensitizers to Dasatinib Therapy for the Treatment of Epithelial Ovarian Cancer

    PubMed Central

    Pathak, Harsh B.; Zhou, Yan; Sethi, Geetika; Hirst, Jeff; Schilder, Russell J.; Golemis, Erica A.; Godwin, Andrew K.

    2015-01-01

    Molecular targeted therapies have been the focus of recent clinical trials for the treatment of patients with recurrent epithelial ovarian cancer (EOC). The majority have not fared well as monotherapies for improving survival of these patients. Poor bioavailability, lack of predictive biomarkers, and the presence of multiple survival pathways can all diminish the success of a targeted agent. Dasatinib is a tyrosine kinase inhibitor of the Src-family kinases (SFK) and in preclinical studies shown to have substantial activity in EOC. However, when evaluated in a phase 2 clinical trial for patients with recurrent or persistent EOC, it was found to have minimal activity. We hypothesized that synthetic lethality screens performed using a cogently designed siRNA library would identify second-site molecular targets that could synergize with SFK inhibition and improve dasatinib efficacy. Using a systematic approach, we performed primary siRNA screening using a library focused on 638 genes corresponding to a network centered on EGFR, HER2, and the SFK-scaffolding proteins BCAR1, NEDD9, and EFS to screen EOC cells in combination with dasatinib. We followed up with validation studies including deconvolution screening, quantitative PCR to confirm effective gene silencing, correlation of gene expression with dasatinib sensitivity, and assessment of the clinical relevance of hits using TCGA ovarian cancer data. A refined list of five candidates (CSNK2A1, DAG1, GRB2, PRKCE, and VAV1) was identified as showing the greatest potential for improving sensitivity to dasatinib in EOC. Of these, CSNK2A1, which codes for the catalytic alpha subunit of protein kinase CK2, was selected for additional evaluation. Synergistic activity of the clinically relevant inhibitor of CK2, CX-4945, with dasatinib in reducing cell proliferation and increasing apoptosis was observed across multiple EOC cell lines. This overall approach to improving drug efficacy can be applied to other targeted agents

  9. A multifactorial analysis of factors related to lethality after treatment of perforated gastroduodenal ulcer. 1935-1985.

    PubMed Central

    Svanes, C; Salvesen, H; Espehaug, B; Søreide, O; Svanes, K

    1989-01-01

    One thousand one hundred and twenty-eight patients treated for perforated gastroduodenal ulcer during the years 1935-1985 were studied at the Haukeland University Hospital. The majority of patients (97.7%) were treated surgically. The data was analyzed by contingency tables and chi square testing, and a stepwise logistic regression analysis was performed in order to reveal interactions between variables and to elucidate time trends in lethality rates. The total postperforation lethality was 7.4%, the postsurgical death rate was 6.6%, and the death rate among conservatively treated patients was 42.3%. Lethality was significantly influenced by year of hospital admission and increased markedly with the age of the patients. For all age groups, the lethality decreased markedly with time. Treatment delay was associated with a moderate but significant increase in lethality. In patients with gastric ulcer the lethality was 3.6 times higher than in those with duodenal ulcer. The death rate was similar in the duodenal and pyloric ulcer groups. Death rate decreased with time in both stomach ulcer, duodenal, and pyloric ulcer patients. There was no sex difference and no difference between patients treated with simple suture or gastric resection. PMID:2930287

  10. Determinants of the lethality of climate-related disasters in the Caribbean Community (CARICOM): a cross-country analysis

    PubMed Central

    Andrewin, Aisha N.; Rodriguez-Llanes, Jose M.; Guha-Sapir, Debarati

    2015-01-01

    Floods and storms are climate-related hazards posing high mortality risk to Caribbean Community (CARICOM) nations. However risk factors for their lethality remain untested. We conducted an ecological study investigating risk factors for flood and storm lethality in CARICOM nations for the period 1980–2012. Lethality - deaths versus no deaths per disaster event- was the outcome. We examined biophysical and social vulnerability proxies and a decadal effect as predictors. We developed our regression model via multivariate analysis using a generalized logistic regression model with quasi-binomial distribution; removal of multi-collinear variables and backward elimination. Robustness was checked through subset analysis. We found significant positive associations between lethality, percentage of total land dedicated to agriculture (odds ratio [OR] 1.032; 95% CI: 1.013–1.053) and percentage urban population (OR 1.029, 95% CI 1.003–1.057). Deaths were more likely in the 2000–2012 period versus 1980–1989 (OR 3.708, 95% CI 1.615–8.737). Robustness checks revealed similar coefficients and directions of association. Population health in CARICOM nations is being increasingly impacted by climate-related disasters connected to increasing urbanization and land use patterns. Our findings support the evidence base for setting sustainable development goals (SDG). PMID:26153115

  11. Determinants of the lethality of climate-related disasters in the Caribbean Community (CARICOM): a cross-country analysis.

    PubMed

    Andrewin, Aisha N; Rodriguez-Llanes, Jose M; Guha-Sapir, Debarati

    2015-01-01

    Floods and storms are climate-related hazards posing high mortality risk to Caribbean Community (CARICOM) nations. However risk factors for their lethality remain untested. We conducted an ecological study investigating risk factors for flood and storm lethality in CARICOM nations for the period 1980-2012. Lethality--deaths versus no deaths per disaster event- was the outcome. We examined biophysical and social vulnerability proxies and a decadal effect as predictors. We developed our regression model via multivariate analysis using a generalized logistic regression model with quasi-binomial distribution; removal of multi-collinear variables and backward elimination. Robustness was checked through subset analysis. We found significant positive associations between lethality, percentage of total land dedicated to agriculture (odds ratio [OR] 1.032; 95% CI: 1.013-1.053) and percentage urban population (OR 1.029, 95% CI 1.003-1.057). Deaths were more likely in the 2000-2012 period versus 1980-1989 (OR 3.708, 95% CI 1.615-8.737). Robustness checks revealed similar coefficients and directions of association. Population health in CARICOM nations is being increasingly impacted by climate-related disasters connected to increasing urbanization and land use patterns. Our findings support the evidence base for setting sustainable development goals (SDG). PMID:26153115

  12. Determinants of the lethality of climate-related disasters in the Caribbean Community (CARICOM): a cross-country analysis

    NASA Astrophysics Data System (ADS)

    Andrewin, Aisha N.; Rodriguez-Llanes, Jose M.; Guha-Sapir, Debarati

    2015-07-01

    Floods and storms are climate-related hazards posing high mortality risk to Caribbean Community (CARICOM) nations. However risk factors for their lethality remain untested. We conducted an ecological study investigating risk factors for flood and storm lethality in CARICOM nations for the period 1980-2012. Lethality - deaths versus no deaths per disaster event- was the outcome. We examined biophysical and social vulnerability proxies and a decadal effect as predictors. We developed our regression model via multivariate analysis using a generalized logistic regression model with quasi-binomial distribution; removal of multi-collinear variables and backward elimination. Robustness was checked through subset analysis. We found significant positive associations between lethality, percentage of total land dedicated to agriculture (odds ratio [OR] 1.032; 95% CI: 1.013-1.053) and percentage urban population (OR 1.029, 95% CI 1.003-1.057). Deaths were more likely in the 2000-2012 period versus 1980-1989 (OR 3.708, 95% CI 1.615-8.737). Robustness checks revealed similar coefficients and directions of association. Population health in CARICOM nations is being increasingly impacted by climate-related disasters connected to increasing urbanization and land use patterns. Our findings support the evidence base for setting sustainable development goals (SDG).

  13. Analysis of the Liver Soluble Proteome from Bull Terriers Affected with Inherited Lethal Acrodermatitis

    PubMed Central

    Mouat, Michael F.; Mauldin, Elizabeth A.; Casal, Margret L.

    2012-01-01

    Lethal acrodermatitis (LAD) is a genetic disease affecting bull terrier dogs. The phenotype is similar to that for acrodermatitis enteropathica in humans, but is currently without treatment. The purpose of the research presented here is to determine the biochemical defects associated with LAD using proteomic methodologies. Two affected (male and female) and one unaffected (male) bull terrier pups were euthanized at 14 weeks of age, their livers dissected and prepared for two-dimensional gel electrophoresis (2DE) and densitometry. Approximately 200 protein spots were observed. The density of the spots within each gel was normalized to the total spot volume of the gel; only those soluble liver protein spots that were consistently different in both of the livers of the affected pups compared to the unaffected pup were excised manually and submitted for MALDI mass spectrometry. Thirteen proteins were identified as differentially expressed in the affected, compared to the unaffected, pups. The proteins were involved in numerous cellular physiological functions, including chaperones, calcium binding, and energy metabolism, as well as being associated with the inflammatory response. Of note were haptoglobin, glutamine synthetase, prohibitin and keratin 10 which exhibited at least a 4-fold level of differential expression. These data represent the first proteomic analysis of this mutation. The differentially expressed proteins that were identified may be key in understanding the etiology of LAD, and may lead to diagnostic tools for its identification within the bull terrier population. PMID:17693109

  14. Non-lethal weapons technologies--the case for independent scientific analysis.

    PubMed

    Altmann, J

    2001-01-01

    Various technologies have been proposed for non-lethal weapons (NLW), some of them credible, or at least plausible, but strong claims were made for others without evidence or references. Five such technologies are examined. For the chemical and biological examples, detailed information is lacking but the diminishing number of such claims over time and general scientific knowledge suggest that fulfilment of the promises is improbable. For acoustic weapons, a detailed study found that many of the claims are plainly untrue. In this case, even wrong values for physiological thresholds were presented. Civil and military NLW programmes in the USA put their main emphasis on simple, short-term technologies rather than exotic ones. In order to avoid dangers arising from unrealistic promises, the concept of preventive arms control should be applied to NLW. Its first step is a scientific analysis, investigating the new weapons, the propagation of their effects and the effect on the targets. Such detailed studies are needed for each proposed NLW technology. PMID:11578041

  15. Integrating ethical analysis "into the DNA" of synthetic biology.

    PubMed

    Heavey, Patrick

    2015-02-01

    Current ethical analysis tends to evaluate synthetic biology at an overview level. Synthetic biology, however, is an umbrella term that covers a variety of areas of research. These areas contain, in turn, a hierarchy of different research fields. This abstraction hierarchy-the term is borrowed from engineering-permits synthetic biologists to specialise to a very high degree. Though synthetic biology per se may create profound ethical challenges, much of the day-to-day research does not. Yet seemingly innocuous research could lead to ethically problematic results. For example, Dolly the sheep resulted from a long series of research steps, none of which presented any ethical problems. The atomic bomb was developed as a result of Einstein's uncontentions theoretical research that proved the equivalence of matter and energy. Therefore it would seem wise for ethicists to evaluate synbio research across its subfields and through its abstraction hierarchies, comparing and inter-relating the various areas of research. In addition, it would be useful if journals that publish synbio papers require an ethical statement from authors, as standard practice, so as to encourage scientists to constantly engage with ethical issues in their work. Also, this would allow an ethical snapshot of the state of the research at any given time to exist, allowing for accurate evaluation by scientists and ethicists, regulators and policymakers. PMID:25185871

  16. Preliminary Integrated Safety Analysis of Synthetic Vision Conducted

    NASA Technical Reports Server (NTRS)

    Reveley, Mary S.

    2002-01-01

    The goal of the NASA Aviation Safety Program is to develop and demonstrate technologies that could help reduce the aviation fatal accident rate by a factor of 5 by the year 2007 and by a factor of 10 by the year 2022. Integrated safety analysis of day-to-day operations and risks within those operations will provide an understanding of the Aviation Safety Program portfolio beyond what is now available. Synthetic vision is the first of the Aviation Safety Program technologies that has been analyzed by the Logistics Management Institute under a contract with the NASA Glenn Research Center. These synthetic vision analyses include both a reliability analysis and a computer simulation model.

  17. FTIR analysis and monitoring of synthetic aviation engine oils.

    PubMed

    Adams, Mike J; Romeo, Melissa J; Rawson, Paul

    2007-10-15

    Synthetic turbine oils from military aircraft engines were analysed for antioxidant content and total acid number using infrared (IR) spectroscopy. Two-dimensional IR correlation analysis was employed to investigate and interpret observed trends in the spectra, as acid was formed and antioxidant species were depleted in the oils, as a function of aging and engine wear. Principal components and partial least squares algorithms were used and compared for the development of calibration and prediction models. Transmission IR spectrometry is demonstrated to be effective for the analysis and monitoring of synthetic aviation turbine engine oils and shown to provide rapid and accurate information as compared with traditional analytical techniques and methods. PMID:19073081

  18. Analysis of new aphid lethal paralysis virus (ALPV) isolates suggests evolution of two ALPV species.

    PubMed

    Liu, Sijun; Vijayendran, Diveena; Carrillo-Tripp, Jimena; Miller, W Allen; Bonning, Bryony C

    2014-12-01

    Aphid lethal paralysis virus (ALPV; family Dicistroviridae) was first isolated from the bird cherry-oat aphid, Rhopalosiphum padi. ALPV-like virus sequences have been reported from many insects and insect predators. We identified a new isolate of ALPV (ALPV-AP) from the pea aphid, Acyrthosiphon pisum, and a new isolate (ALPV-DvV) from western corn rootworm, Diabrotica virgifera virgifera. ALPV-AP has an ssRNA genome of 9940 nt. Based on phylogenetic analysis, ALPV-AP was closely related to ALPV-AM, an ALPV isolate from honeybees, Apis mellifera, in Spain and Brookings, SD, USA. The distinct evolutionary branches suggested the existence of two lineages of the ALPV virus. One consisted of ALPV-AP and ALPV-AM, whilst all other isolates of ALPV grouped into the other lineage. The similarity of ALPV-AP and ALPV-AM was up to 88 % at the RNA level, compared with 78-79 % between ALPV-AP and other ALPV isolates. The sequence identity of proteins between ALPV-AP and ALPV-AM was 98-99 % for both ORF1 and ORF2, whilst only 85-87 % for ORF1 and 91-92 % for ORF2 between ALPV-AP and other ALPV isolates. Sequencing of RACE (rapid amplification of cDNA ends) products and cDNA clones of the virus genome revealed sequence variation in the 5' UTRs and in ORF1, indicating that ALPV may be under strong selection pressure, which could have important biological implications for ALPV host range and infectivity. Our results indicated that ALPV-like viruses infect insects in the order Coleoptera, in addition to the orders Hemiptera and Hymenoptera, and we propose that ALPV isolates be classified as two separate viral species. PMID:25170050

  19. Protection Against Lethal Sendai Virus Infection by in vivo Priming of Virus-Specific Cytotoxic T Lymphocytes with a Free Synthetic Peptide

    NASA Astrophysics Data System (ADS)

    Kast, W. Martin; Roux, Laurent; Curren, Joseph; Blom, Hendrika J. J.; Voordouw, Arie C.; Meloen, Rob H.; Kolakofsky, Daniel; Melief, Cornelis J. M.

    1991-03-01

    The only peptide of Sendai virus that is recognized by cytotoxic T lymphocytes (CTL) in B6 mice was found with (i) the use of recombinant vaccinia virus constructs containing separate genes of Sendai virus and (ii) a set of overlapping peptides completely spanning the identified nucleoprotein (NP) gene product. This immunodominant NP peptide is recognized by Sendai virus-specific CTL that are known to have therapeutic effects in vivo. By subcutaneous immunization, this peptide induced Sendai virus and NP peptide-specific CTL memory responses in vivo. Most importantly, mice that had been immunized with this peptide were protected against a lethal virus dose, indicating that viral peptides can be used as antiviral T-cell vaccines. The induction of T-cell memory by free peptide immunization potentially has wide applicability in biology and medicine, including protection against infectious disease.

  20. Synthetic aperture sonar imaging using joint time-frequency analysis

    NASA Astrophysics Data System (ADS)

    Wang, Genyuan; Xia, Xiang-Gen

    1999-03-01

    The non-ideal motion of the hydrophone usually induces the aperture error of the synthetic aperture sonar (SAS), which is one of the most important factors degrading the SAS imaging quality. In the SAS imaging, the return signals are usually nonstationary due to the non-ideal hydrophone motion. In this paper, joint time-frequency analysis (JTFA), as a good technique for analyzing nonstationary signals, is used in the SAS imaging. Based on the JTFA of the sonar return signals, a novel SAS imaging algorithm is proposed. The algorithm is verified by simulation examples.

  1. [ANALYSIS OF A LETHAL OUTCOME RISK AFTER TRAUMA IN HIV-INFECTED PATIENTS IN POLYSYSTEMIC INJURY].

    PubMed

    Guryev, S O; Solovyov, O S; Tanasiyenko, P V

    2016-02-01

    Abstract The data, concerning clinic--epidemiologic and clinic--nosological characteristic of a HIV-infected injured persons in polytrauma were adduced. There was established, that polysystemic injuries (PSI) in a HIV-infected persons occur in a younger injured patients, a trauma environment is quite a speciphic one (criminal trauma prevails), as well as mechanism of the injury occurrence (falling down is much more freqent), and the risk of a lethal outcome is determined by predominantly cranial, thoracic and abdominal components of injury. A lethal outcome occurrence risk in HIV-infected injured persons in PSI in accordance to the age signs and traumagenesis is lesser, than in a control body. It is necessary to prolong the investigations, concerning studying this phenomenon and other peculiarities of a traumatic disease in HIV-infected injured persons in polytrauma. PMID:27244924

  2. Synthetic Training Data Generation for Activity Monitoring and Behavior Analysis

    NASA Astrophysics Data System (ADS)

    Monekosso, Dorothy; Remagnino, Paolo

    This paper describes a data generator that produces synthetic data to simulate observations from an array of environment monitoring sensors. The overall goal of our work is to monitor the well-being of one occupant in a home. Sensors are embedded in a smart home to unobtrusively record environmental parameters. Based on the sensor observations, behavior analysis and modeling are performed. However behavior analysis and modeling require large data sets to be collected over long periods of time to achieve the level of accuracy expected. A data generator - was developed based on initial data i.e. data collected over periods lasting weeks to facilitate concurrent data collection and development of algorithms. The data generator is based on statistical inference techniques. Variation is introduced into the data using perturbation models.

  3. Dynamic flux balance analysis for synthetic microbial communities.

    PubMed

    Henson, Michael A; Hanly, Timothy J

    2014-10-01

    Dynamic flux balance analysis (DFBA) is an extension of classical flux balance analysis that allows the dynamic effects of the extracellular environment on microbial metabolism to be predicted and optimised. Recently this computational framework has been extended to microbial communities for which the individual species are known and genome-scale metabolic reconstructions are available. In this review, the authors provide an overview of the emerging DFBA approach with a focus on two case studies involving the conversion of mixed hexose/pentose sugar mixtures by synthetic microbial co-culture systems. These case studies illustrate the key requirements of the DFBA approach, including the incorporation of individual species metabolic reconstructions, formulation of extracellular mass balances, identification of substrate uptake kinetics, numerical solution of the coupled linear program/differential equations and model adaptation for common, suboptimal growth conditions and identified species interactions. The review concludes with a summary of progress to date and possible directions for future research. PMID:25257022

  4. Economic Deprivation as a Predictor of the Direction of Lethal Violence: An Analysis of Italian Provinces.

    PubMed

    Stack, Steven; Laubepin, Frederique; Vichi, Monica; Minelli, Giada; Lester, David; Ferracuti, Stefano; Girardi, Paolo; Pompili, Maurizio

    2016-07-01

    Research on suicide and homicide rates has neglected an integrated model seeking to explain social variation in the direction of lethal violence. The present investigation explores the association between measures of social deprivation on the relative incidence of suicide over homicide in Italian provinces. Data refer to official government sources on lethal violence rates and measures of social deprivation. The central dependent variable (SHR) is the tendency towards suicide measured as the suicide rate divided by the sum of the suicide and homicide rates. Data were available for 102 Italian provinces in the Census year 2001. The percentage of the population marked by two indicators of deprivation (low education, household population density) were negatively associated with the SHR. The results are largely consistent with a stream of previous research that connects deprivation with a relatively high probability for disadvantaged populations to direct aggression outwardly in the form of homicide rather than inwardly in the form of suicide. The present study specifies which elements of deprivation best predict the direction of violence and is the first study for the Italian context. PMID:26881819

  5. Histone acetylation and gene expression analysis of sex lethal mutants in Drosophila.

    PubMed Central

    Bhadra, U; Pal-Bhadra, M; Birchler, J A

    2000-01-01

    The evolution of sex determination mechanisms is often accompanied by reduction in dosage of genes on a whole chromosome. Under these circumstances, negatively acting regulatory genes would tend to double the expression of the genome, which produces compensation of the single-sex chromosome and increases autosomal gene expression. Previous work has suggested that to reduce the autosomal expression to the female level, these dosage effects are modified by a chromatin complex specific to males, which sequesters a histone acetylase to the X. The reduced autosomal histone 4 lysine 16 (H4Lys16) acetylation results in lowered autosomal expression, while the higher acetylation on the X is mitigated by the male-specific lethal complex, preventing overexpression. In this report, we examine how mutations in the principal sex determination gene, Sex lethal (Sxl), impact the H4 acetylation and gene expression on both the X and autosomes. When Sxl expression is missing in females, we find that the sequestration occurs concordantly with reductions in autosomal H4Lys16 acetylation and gene expression on the whole. When Sxl is ectopically expressed in Sxl(M) mutant males, the sequestration is disrupted, leading to an increase in autosomal H4Lys16 acetylation and overall gene expression. In both cases we find relatively little effect upon X chromosomal gene expression. PMID:10835396

  6. Time-frequency analysis of synthetic aperture radar signals

    SciTech Connect

    Johnston, B.

    1996-08-01

    Synthetic aperture radar (SAR) has become an important tool for remote sensing of the environment. SAR is a set of digital signal processing algorithms that are used to focus the signal returned to the radar because radar systems in themselves cannot produce the high resolution images required in remote sensing applications. To reconstruct an image, several parameters must be estimated and the quality of output image depends on the degree of accuracy of these parameters. In this thesis, we derive the fundamental SAR algorithms and concentrate on the estimation of one of its critical parameters. We show that the common technique for estimating this particular parameter can sometimes lead to erroneous results and reduced quality images. We also employ time-frequency analysis techniques to examine variations in the radar signals caused by platform motion and show how these results can be used to improve output image quality.

  7. Hypoxia Potentiates the Radiation-Sensitizing Effect of Olaparib in Human Non-Small Cell Lung Cancer Xenografts by Contextual Synthetic Lethality

    PubMed Central

    Jiang, Yanyan; Verbiest, Tom; Devery, Aoife M.; Bokobza, Sivan M.; Weber, Anika M.; Leszczynska, Katarzyna B.; Hammond, Ester M.; Ryan, Anderson J.

    2016-01-01

    synthetic killing, and that tumor hypoxia may be a potential biomarker for selecting patients who may get the greatest benefit from the addition of olaparib to radiation therapy. PMID:27020103

  8. Synthetic Lethal Screen Demonstrates That a JAK2 Inhibitor Suppresses a BCL6-dependent IL10RA/JAK2/STAT3 Pathway in High Grade B-cell Lymphoma.

    PubMed

    Beck, Daniel; Zobel, Jenny; Barber, Ruth; Evans, Sian; Lezina, Larissa; Allchin, Rebecca L; Blades, Matthew; Elliott, Richard; Lord, Christopher J; Ashworth, Alan; Porter, Andrew C G; Wagner, Simon D

    2016-08-01

    We demonstrate the usefulness of synthetic lethal screening of a conditionally BCL6-deficient Burkitt lymphoma cell line, DG75-AB7, with a library of small molecules to determine survival pathways suppressed by BCL6 and suggest mechanism-based treatments for lymphoma. Lestaurtinib, a JAK2 inhibitor and one of the hits from the screen, repressed survival of BCL6-deficient cells in vitro and reduced growth and proliferation of xenografts in vivo BCL6 deficiency in DG75-AB7 induced JAK2 mRNA and protein expression and STAT3 phosphorylation. Surface IL10RA was elevated by BCL6 deficiency, and blockade of IL10RA repressed STAT3 phosphorylation. Therefore, we define an IL10RA/JAK2/STAT3 pathway each component of which is repressed by BCL6. We also show for the first time that JAK2 is a direct BCL6 target gene; BCL6 bound to the JAK2 promoter in vitro and was enriched by ChIP-seq. The place of JAK2 inhibitors in the treatment of diffuse large B-cell lymphoma has not been defined; we suggest that JAK2 inhibitors might be most effective in poor prognosis ABC-DLBCL, which shows higher levels of IL10RA, JAK2, and STAT3 but lower levels of BCL6 than GC-DLBCL and might be usefully combined with novel approaches such as inhibition of IL10RA. PMID:27268052

  9. Loss of Apm1, the μ1 Subunit of the Clathrin-Associated Adaptor-Protein-1 Complex, Causes Distinct Phenotypes and Synthetic Lethality with Calcineurin Deletion in Fission Yeast

    PubMed Central

    Kita, Ayako; Sugiura, Reiko; Shoji, Hiromi; He, Yi; Deng, Lu; Lu, Yabin; Sio, Susie O.; Takegawa, Kaoru; Sakaue, Motoyoshi; Shuntoh, Hisato; Kuno, Takayoshi

    2004-01-01

    Calcineurin is a highly conserved regulator of Ca2+ signaling in eukaryotes. In fission yeast, calcineurin is not essential for viability but is required for cytokinesis and Cl- homeostasis. In a genetic screen for mutations that are synthetically lethal with calcineurin deletion, we isolated a mutant, cis1-1/apm1-1, an allele of the apm1+ gene that encodes a homolog of the mammalian μ1A subunit of the clathrin-associated adaptor protein-1 (AP-1) complex. The cis1-1/apm1-1 mutant as well as the apm1-deleted (Δapm1) cells showed distinct phenotypes: temperature sensitivity; tacrolimus (FK506) sensitivity; and pleiotropic defects in cytokinesis, cell integrity, and vacuole fusion. Electron micrographs revealed that Δapm1 cells showed large vesicular structures associated with Golgi stacks and accumulated post-Golgi secretory vesicles. Δapm1 cells also showed the massive accumulation of the exocytic v-SNARE Syb1 in the Golgi/endosomes and a reduced secretion of acid phosphatase. These phenotypes observed in apm1 mutations were accentuated upon temperature up-shift and FK506 treatment. Notably, Apm1-GFP localized to the Golgi/endosomes, the spindle pole bodies, and the medial region. These findings suggest a role for Apm1 associated with the Golgi/endosome function, thereby affecting various cellular processes, including secretion, cytokinesis, vacuole fusion, and cell integrity and also suggest that calcineurin is involved in these events. PMID:15047861

  10. Regulation of the Gene Sex-Lethal: A Comparative Analysis of Drosophila Melanogaster and Drosophila Subobscura

    PubMed Central

    Penalva, LOF.; Sakamoto, H.; Navarro-Sabate, A.; Sakashita, E.; Granadino, B.; Segarra, C.; Sanchez, L.

    1996-01-01

    The Drosophila gene Sex-lethal (Sxl) controls the processes of sex determination and dosage compensation. A Drosophila subobscura genomic fragment containing all the exons and the late and early promotors in the Sxl gene of D. melanogaster was isolated. Early Sxl expression in D. subobscura seems to be controlled at the transcriptional level, possibly by the X:A signal. In the region upstream of the early Sxl transcription initiation site are two conserved regions suggested to be involved in the early activation of Sxl. Late Sxl expression in D. subobscura produces four transcripts in adult females and males. In males, the transcripts have an additional exon which contains three translational stop codons so that a truncated, presumably nonfunctional Sxl protein is produced. The Sxl pre-mRNA of D. subobscura lacks the poly-U sequence presented at the polypirimidine tract of the 3' splice site of the male-specific exon present in D. melanogaster. Introns 2 and 3 contain the Sxl-binding poly-U stretches, whose localization in intron 2 varies but in intron 3 is conserved. The Sxl protein is fully conserved at the amino acid level in both species. PMID:8978052

  11. Biophysical analysis of a lethal laminin alpha-1 mutation reveals altered self-interaction.

    PubMed

    Patel, Trushar R; Nikodemus, Denise; Besong, Tabot M D; Reuten, Raphael; Meier, Markus; Harding, Stephen E; Winzor, Donald J; Koch, Manuel; Stetefeld, Jörg

    2016-01-01

    Laminins are key basement membrane molecules that influence several biological activities and are linked to a number of diseases. They are secreted as heterotrimeric proteins consisting of one α, one β, and one γ chain, followed by their assembly into a polymer-like sheet at the basement membrane. Using sedimentation velocity, dynamic light scattering, and surface plasmon resonance experiments, we studied self-association of three laminin (LM) N-terminal fragments α-1 (hLM α-1N), α-5 (hLM α-5N) and β-3 (hLM β-3N) originating from the short arms of the human laminin αβγ heterotrimer. Corresponding studies of the hLM α-1N C49S mutant, equivalent to the larval lethal C56S mutant in zebrafish, have shown that this mutation causes enhanced self-association behavior, an observation that provides a plausible explanation for the inability of laminin bearing this mutation to fulfill functional roles in vivo, and hence for the deleterious pathological consequences of the mutation on lens function. PMID:26215696

  12. Development of synthetic flood damage curve by explicit costs analysis

    NASA Astrophysics Data System (ADS)

    Martina, Mario; Molinari, Daniela; Dottori, Francesco; Scorzini, Annarita

    2015-04-01

    Damage modelling is a key component in flood risk assessments. A conventional approach for estimating direct flood damages is the use of depth-damage functions. However, at present, there are few studies that describe in detail the parameters involved in the models and the hypotheses used for the development of these functions based on synthetic approaches and/or actual flood damage data. In this work a synthetic approach was adopted for the development of a damage model for residential buildings. The approach follows the loss assessment procedure usually applied by the insurance loss adjusters. Required information consisted of all those variables that are necessary to define hazard characteristics at building location, compute the exposure value of the building and the replacement costs of its components. In detail, the model requires four input tables. The hazard module includes the variables describing the features of the flood event at building location (e.g. water depth outside the building, water depth inside the basement, maximum velocity of the flood, duration of the event, contaminant and sediment load). The exposure module includes both extensive variables (e.g. foot print area, number of floors) and "vulnerability" variables, where the latter affect damage estimation in two different ways: by changing the replacement value/unit prices of the building and its components (e.g. the finishing level, building type) or by modifying the function(s) describing damage mechanisms (e.g. building structure, plant distribution). The replacement values table and the unit-price table include respectively the replacement value of the building and the unitary replacement costs of the different building components (e.g. doors and pavement replacement per square meter). The final output of the model is represented by different sets of damage functions describing all the building components (e.g. plasters, plants), depending on hazard, exposure and vulnerability

  13. Impact of insecticides on the invasive Halyomorpha halys (Hemiptera: Pentatomidae): analysis of insecticide lethality.

    PubMed

    Leskey, Tracy C; Lee, Doo-Hyung; Short, Brent D; Wright, Starker E

    2012-10-01

    The efficacy of 37 insecticide treatments against adult Halyomorpha halys (Stål) was established based on exposure to 18-h old dry insecticide residue in laboratory bioassays. Individual adult H. halys were exposed to an insecticide residue for 4.5 h and then monitored daily for survivorship over a 7-d period. The proportion of dead and moribund insects was used as an estimate of overall insecticide efficacy against H. halys immediately after the exposure period and over the 7-d trial. Among all materials evaluated, 14 insecticides exhibited increasing efficacy, in which the percentage of dead and moribund insects (used as a measure of insecticide efficacy) increased by > 10% after 7 d. By contrast, insecticide efficacy values of eight insecticides declined by > 10% (based on recovery of adults from a moribund state) over the 7-d period with most belonging to the pyrethroid class. In this study, the efficacy value of neonicotinoid, acetamiprid, showed the greatest decline from 93 to 10% over 7 d. A lethality index (scale of 0-100) was developed to compare insecticides based on quantifying the immediate and longer-term effects of insecticide exposure on H. halys. Among all materials evaluated, dimethoate, malathion, bifenthrin, methidathion, endosulfan, methomyl, chlorpyrifos, acephate, fenpropathrin, and permethrin yielded the highest values (> 75) because of a high degree of immediate mortality with very little recovery. Our results provide baseline information regarding potential of candidate insecticides against adult H. halys and highlight the need to consider longer-term effects in establishing overall efficacy ratings against this invasive species. PMID:23156170

  14. Seamless Synthetic Aperture Radar Archive for Interferometry Analysis

    NASA Astrophysics Data System (ADS)

    Baker, S.; Meertens, C. M.; Phillips, D. A.; Crosby, C.; Fielding, E. J.; Nicoll, J.; Bryson, G.; Buechler, B.; Baru, C.

    2012-12-01

    The NASA Advancing Collaborative Connections for Earth System Science (ACCESS) Seamless Synthetic Aperture Radar (SAR) Archive (SSARA) project is a 2-year collaboration between UNAVCO/WInSAR, the Alaska Satellite Facility (ASF), the Jet Propulsion Laboratory (JPL), and the San Diego Supercomputer Center (SDSC) to design and implement a seamless distributed access system for SAR data and derived data products (i.e. terrain corrected interferograms). A seamless SAR archive increases the accessibility and the utility of SAR science data to solid Earth and cryospheric science researchers. Building on the established webs services and APIs at UNAVCO and ASF, the SSARA project will provide simple web services tools to seamlessly and effectively exchange and share space- and airborne SAR metadata, archived SAR data, and on-demand derived products between the distributed archives and individual users. Development of standard formats for data products and new QC/QA definitions will be implemented to streamline data usage and enable advanced query capabilities. The new ACCESS-developed tools will help overcome the obstacles of heterogeneous archive access protocols and data formats, data provider access policy constraints, and will also enable interoperability with key information technology development systems such as the NASA/JPL QuakeSim and ARIA projects, which provide higher level resources for geodetic data processing, data assimilation and modeling, and integrative analysis for scientific research and hazards applications. The SSARA project will significantly enhance mature IT capabilities at ASF's NASA-supported DAAC, the GEO Supersites archive, supported operationally by UNAVCO, and UNAVCO's WInSAR and EarthScope SAR archives that are supported by NASA, NSF, and the USGS in close collaboration with ESA/ESRIN.

  15. Data Analysis Methods for Synthetic Polymer Mass Spectrometry: Autocorrelation

    PubMed Central

    Wallace, William E.; Guttman, Charles M.

    2002-01-01

    Autocorrelation is shown to be useful in describing the periodic patterns found in high- resolution mass spectra of synthetic polymers. Examples of this usefulness are described for a simple linear homopolymer to demonstrate the method fundamentals, a condensation polymer to demonstrate its utility in understanding complex spectra with multiple repeating patterns on different mass scales, and a condensation copolymer to demonstrate how it can elegantly and efficiently reveal unexpected phenomena. It is shown that using autocorrelation to determine where the signal devolves into noise can be useful in determining molecular mass distributions of synthetic polymers, a primary focus of the NIST synthetic polymer mass spectrometry effort. The appendices describe some of the effects of transformation from time to mass space when time-of-flight mass separation is used, as well as the effects of non-trivial baselines on the autocorrelation function.

  16. MYC, Metabolic Synthetic Lethality, and Cancer.

    PubMed

    Hsieh, Annie L; Dang, Chi V

    2016-01-01

    The MYC oncogene plays a pivotal role in the development and progression of human cancers. It encodes a transcription factor that has broad reaching effects on many cellular functions, most importantly in driving cell growth through regulation of genes involved in ribosome biogenesis, metabolism, and cell cycle. Upon binding DNA with its partner MAX, MYC recruits factors that release paused RNA polymerases to drive transcription and amplify gene expression. At physiologic levels of MYC, occupancy of high-affinity DNA-binding sites drives 'house-keeping' metabolic genes and those involved in ribosome and mitochondrial biogenesis for biomass accumulation. At high oncogenic levels of MYC, invasion of low-affinity sites and enhancer sequences alter the transcriptome and cause metabolic imbalances, which activates stress response and checkpoints such as p53. Loss of checkpoints unleashes MYC's full oncogenic potential to couple metabolism with neoplastic cell growth and division. Cells that overexpress MYC, however, are vulnerable to metabolic perturbations that provide potential new avenues for cancer therapy. PMID:27557535

  17. Experimental Analysis of Impinging Single and Twin Circular Synthetic Jets

    NASA Astrophysics Data System (ADS)

    Cardone, Gennaro; Greco, Carlo Salvatore; Castrillo, Giusy; Astarita, Tommaso; Experimental Thermo-Fluid-Dynamics Research Team

    2015-11-01

    The behavior of impinging single synthetic jet and twin circular synthetic jets in phase opposition is experimentally investigated by using Particle Image Velocimetry (PIV) at Reynolds and Strouhal numbers equal to 5100 and 0.024, respectively. Different inter-axes distances for the twin configuration and several nozzle-to-plate distances have been investigated. The time-averaged behavior of the all velocity components are reported and discussed. Their distributions, near the impinging plate, are described for both the synthetic jet configurations and for all the nozzle-to-plate distances. At low nozzle-to-plate distance (H/D <4) the axial velocity profile near the impinging plate shows a double peak with a minimum on the jet axis. Instead, at high nozzle-to-plate distance (H/D >6), the axial velocity profile is bell-shaped. This is ascribed to the adverse pressure gradient strength and the potential core-like region extension. Indeed, the turbulence distribution shows a region characterized by low values, resembling the potential core region of continuous jets. Comparing the two synthetic jet configurations, a higher centerline velocity and a smaller jet width have been found for the twin case.

  18. SAMPLING AND ANALYSIS OF BUTADIENE AT A SYNTHETIC RUBBER PLANT

    EPA Science Inventory

    Butadiene emission samples were collected from the process vent stream of a plant manufacturing synthetic rubber from styrene and butadiene. Samples were collected by modification of the evacuated container sampling procedure, outlined in Section 7.1.1 of EPA Method 18. On-site a...

  19. What Are Reasons for the Large Gender Differences in the Lethality of Suicidal Acts? An Epidemiological Analysis in Four European Countries

    PubMed Central

    Heinrichs, Katherina; Székely, András; Tóth, Mónika Ditta; Coyne, James; Quintão, Sónia; Arensman, Ella; Coffey, Claire; Maxwell, Margaret; Värnik, Airi; van Audenhove, Chantal; McDaid, David; Sarchiapone, Marco; Schmidtke, Armin; Genz, Axel; Gusmão, Ricardo; Hegerl, Ulrich

    2015-01-01

    Background In Europe, men have lower rates of attempted suicide compared to women and at the same time a higher rate of completed suicides, indicating major gender differences in lethality of suicidal behaviour. The aim of this study was to analyse the extent to which these gender differences in lethality can be explained by factors such as choice of more lethal methods or lethality differences within the same suicide method or age. In addition, we explored gender differences in the intentionality of suicide attempts. Methods and Findings Methods. Design: Epidemiological study using a combination of self-report and official data. Setting: Mental health care services in four European countries: Germany, Hungary, Ireland, and Portugal. Data basis: Completed suicides derived from official statistics for each country (767 acts, 74.4% male) and assessed suicide attempts excluding habitual intentional self-harm (8,175 acts, 43.2% male). Main Outcome Measures and Data Analysis. We collected data on suicidal acts in eight regions of four European countries participating in the EU-funded “OSPI-Europe”-project (www.ospi-europe.com). We calculated method-specific lethality using the number of completed suicides per method * 100 / (number of completed suicides per method + number of attempted suicides per method). We tested gender differences in the distribution of suicidal acts for significance by using the χ2-test for two-by-two tables. We assessed the effect sizes with phi coefficients (φ). We identified predictors of lethality with a binary logistic regression analysis. Poisson regression analysis examined the contribution of choice of methods and method-specific lethality to gender differences in the lethality of suicidal acts. Findings Main Results Suicidal acts (fatal and non-fatal) were 3.4 times more lethal in men than in women (lethality 13.91% (regarding 4106 suicidal acts) versus 4.05% (regarding 4836 suicidal acts)), the difference being significant for the

  20. Analysis of Parent Synthetic Cannabinoids in Blood and Urinary Metabolites by Liquid Chromatography Tandem Mass Spectrometry.

    PubMed

    Knittel, Jessica L; Holler, Justin M; Chmiel, Jeffrey D; Vorce, Shawn P; Magluilo, Joseph; Levine, Barry; Ramos, Gerardo; Bosy, Thomas Z

    2016-04-01

    Synthetic cannabinoids emerged on the designer drug market in recent years due to their ability to produce cannabis-like effects without the risk of detection by traditional drug testing techniques such as immunoassay and gas chromatography-mass spectrometry. As government agencies work to schedule existing synthetic cannabinoids, new, unregulated and structurally diverse compounds continue to be developed and sold. Synthetic cannabinoids undergo extensive metabolic conversion. Consequently, both blood and urine specimens may play an important role in the forensic analysis of synthetic cannabinoids. It has been observed that structurally similar synthetic cannabinoids follow common metabolic pathways, which often produce metabolites with similar metabolic transformations. Presented are two validated quantitative methods for extracting and identifying 15 parent synthetic cannabinoids in blood, 17 synthetic cannabinoid metabolites in urine and the qualitative identification of 2 additional parent compounds. The linear range for most synthetic cannabinoid compounds monitored was 0.1-10 ng/mL with the limit of detection between 0.01 and 0.5 ng/mL. Selectivity, specificity, accuracy, precision, recovery and matrix effect were also examined and determined to be acceptable for each compound. The validated methods were used to analyze a compilation of synthetic cannabinoid investigative cases where both blood and urine specimens were submitted. The study suggests a strong correlation between the metabolites detected in urine and the parent compounds found in blood. PMID:26792810

  1. [Analysis of a synthetic onion aroma (author's transl)].

    PubMed

    Ledl, F

    1975-02-01

    A complex mixture of compounds possessing an intensive aroma of onions is obtained, when propionaldehyde, propionaldehyde and acetaldehyde are treated with hydrogen sulfide and ammonia. Dihydrodithiazines, diethyltrithiolane, diethyl-methyl-1,3-dithiine and in small quantities diethyltetrathiane, dimethylthiophene, dipropyldisulfide, dipropenylsulfide, alkylpyridines, and the condensation products of aldehydes can be proved by the GC-MS-technic. The compositions of the synthetic onion aroma corresponds slightly with the composition of the natural onion aroma. PMID:1224790

  2. Quantitative proteomics analysis of zebrafish exposed to sub-lethal dosages of β-methyl-amino-L-alanine (BMAA)

    PubMed Central

    Frøyset, Ann Kristin; Khan, Essa Ahsan; Fladmark, Kari Espolin

    2016-01-01

    The non-protein amino acid β-methylamino-L-alanine (BMAA) is a neurotoxin present in microalgae and shown to accumulate in the food web. BMAA has been linked to the complex neurodegenerative disorder of Guam and to increased incidents sporadic ALS. Two main neurotoxic routes are suggested; an excitotoxic by acting as an agonist towards glutamate receptors and a metabolic by misincorporating into cellular proteins. We have used zebrafish, an increasingly used model for neurodegenerative diseases, to further identify signaling components involved in BMAA-induced toxicity. Zebrafish embryos were exposed to sub-lethal dosages of BMAA and a label-free proteomics analysis was conducted on larvae 4 days post fertilization. The exposed larvae showed no developmental abnormalities, but a reduced heart rate and increased expression of GSK3 isoforms. Search towards a reviewed database containing 2968 entries identified 480 proteins. Only 17 of these were regulated 2-fold or more in the exposed larvae. Seven of these proteins could be associated to glutamate receptor signaling and recycling. The remaining nine have all been linked to disturbance in protein homeostasis, reactive oxygen species (ROS) development or neuronal cell death. We also found that BMAA influenced the endocannabinoid system by up-regulation of fatty acid amide hydrolase (FAAH) and that FAAH inhibitor URB597 reduced the BMAA effect on heart rate and GSK3 expression. PMID:27404450

  3. Quantitative proteomics analysis of zebrafish exposed to sub-lethal dosages of β-methyl-amino-L-alanine (BMAA).

    PubMed

    Frøyset, Ann Kristin; Khan, Essa Ahsan; Fladmark, Kari Espolin

    2016-01-01

    The non-protein amino acid β-methylamino-L-alanine (BMAA) is a neurotoxin present in microalgae and shown to accumulate in the food web. BMAA has been linked to the complex neurodegenerative disorder of Guam and to increased incidents sporadic ALS. Two main neurotoxic routes are suggested; an excitotoxic by acting as an agonist towards glutamate receptors and a metabolic by misincorporating into cellular proteins. We have used zebrafish, an increasingly used model for neurodegenerative diseases, to further identify signaling components involved in BMAA-induced toxicity. Zebrafish embryos were exposed to sub-lethal dosages of BMAA and a label-free proteomics analysis was conducted on larvae 4 days post fertilization. The exposed larvae showed no developmental abnormalities, but a reduced heart rate and increased expression of GSK3 isoforms. Search towards a reviewed database containing 2968 entries identified 480 proteins. Only 17 of these were regulated 2-fold or more in the exposed larvae. Seven of these proteins could be associated to glutamate receptor signaling and recycling. The remaining nine have all been linked to disturbance in protein homeostasis, reactive oxygen species (ROS) development or neuronal cell death. We also found that BMAA influenced the endocannabinoid system by up-regulation of fatty acid amide hydrolase (FAAH) and that FAAH inhibitor URB597 reduced the BMAA effect on heart rate and GSK3 expression. PMID:27404450

  4. Screening and analysis of genes expressed upon infection of broad bean with Clover yellow vein virus causing lethal necrosis.

    PubMed

    Nakahara, Kenji S; Kitazawa, Hiroaki; Atsumi, Go; Choi, Sun Hee; Suzuki, Yuji; Uyeda, Ichiro

    2011-01-01

    Clover yellow vein virus (ClYVV) causes lethal systemic necrosis in legumes, including broad bean (Vicia faba) and pea (Pisum sativum). To identify host genes involved in necrotic symptom expression after ClYVV infection, we screened cDNA fragments in which expression was changed in advance of necrotic symptom expression in broad bean (V. faba cv. Wase) using the differential display technique and secondarily with Northern blot analysis. Expression changes were confirmed in 20 genes, and the six that exhibited the most change were analyzed further. These six genes included a gene that encodes a putative nitrate-induced NOI protein (VfNOI), and another was homologous to an Arabidopsis gene that encodes a glycine- and proline-rich protein GPRP (VfGPRP). We recently reported that necrotic symptom development in ClYVV-infected pea is associated with expression of salicylic acid (SA)-dependent pathogenesis-related (PR) proteins and requires SA-dependent host responses. Interestingly, VfNOI and VfGPRP expression was correlated with that of the putative SA-dependent PR proteins in ClYVV-infected broad bean. However, broad bean infected with a recombinant ClYVV expressing the VfGPRP protein showed weaker symptoms and less viral multiplication than that infected with ClYVV expressing the GFP protein. These results imply that VfGPRP plays a role in defense against ClYVV rather than in necrotic symptom expression. PMID:21767375

  5. Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer

    PubMed Central

    Bova, G. Steven; Kallio, Heini M.L.; Annala, Matti; Kivinummi, Kati; Högnäs, Gunilla; Häyrynen, Sergei; Rantapero, Tommi; Kivinen, Virpi; Isaacs, William B.; Tolonen, Teemu; Nykter, Matti; Visakorpi, Tapio

    2016-01-01

    We report the first combined analysis of whole-genome sequence, detailed clinical history, and transcriptome sequence of multiple prostate cancer metastases in a single patient (A21). Whole-genome and transcriptome sequence was obtained from nine anatomically separate metastases, and targeted DNA sequencing was performed in cancerous and noncancerous foci within the primary tumor specimen removed 5 yr before death. Transcriptome analysis revealed increased expression of androgen receptor (AR)-regulated genes in liver metastases that harbored an AR p.L702H mutation, suggesting a dominant effect by the mutation despite being present in only one of an estimated 16 copies per cell. The metastases harbored several alterations to the PI3K/AKT pathway, including a clonal truncal mutation in PIK3CG and present in all metastatic sites studied. The list of truncal genomic alterations shared by all metastases included homozygous deletion of TP53, hemizygous deletion of RB1 and CHD1, and amplification of FGFR1. If the patient were treated today, given this knowledge, the use of second-generation androgen-directed therapies, cessation of glucocorticoid administration, and therapeutic inhibition of the PI3K/AKT pathway or FGFR1 receptor could provide personalized benefit. Three previously unreported truncal clonal missense mutations (ABCC4 p.R891L, ALDH9A1 p.W89R, and ASNA1 p.P75R) were expressed at the RNA level and assessed as druggable. The truncal status of mutations may be critical for effective actionability and merit further study. Our findings suggest that a large set of deeply analyzed cases could serve as a powerful guide to more effective prostate cancer basic science and personalized cancer medicine clinical trials. PMID:27148588

  6. A population-based analysis of clustering identifies a strong genetic contribution to lethal prostate cancer

    PubMed Central

    Nelson, Quentin; Agarwal, Neeraj; Stephenson, Robert; Cannon-Albright, Lisa A.

    2013-01-01

    Background: Prostate cancer is a common and often deadly cancer. Decades of study have yet to identify genes that explain much familial prostate cancer. Traditional linkage analysis of pedigrees has yielded results that are rarely validated. We hypothesize that there are rare segregating variants responsible for high-risk prostate cancer pedigrees, but recognize that within-pedigree heterogeneity is responsible for significant noise that overwhelms signal. Here we introduce a method to identify homogeneous subsets of prostate cancer, based on cancer characteristics, which show the best evidence for an inherited contribution. Methods: We have modified an existing method, the Genealogical Index of Familiality (GIF) used to show evidence for significant familial clustering. The modification allows a test for excess familial clustering of a subset of prostate cancer cases when compared to all prostate cancer cases. Results: Consideration of the familial clustering of eight clinical subsets of prostate cancer cases compared to the expected familial clustering of all prostate cancer cases identified three subsets of prostate cancer cases with evidence for familial clustering significantly in excess of expected. These subsets include prostate cancer cases diagnosed before age 50 years, prostate cancer cases with body mass index (BMI) greater than or equal to 30, and prostate cancer cases for whom prostate cancer contributed to death. Conclusions: This analysis identified several subsets of prostate cancer cases that cluster significantly more than expected when compared to all prostate cancer familial clustering. A focus on high-risk prostate cancer cases or pedigrees with these characteristics will reduce noise and could allow identification of the rare predisposition genes or variants responsible. PMID:23970893

  7. Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer.

    PubMed

    Bova, G Steven; Kallio, Heini M L; Annala, Matti; Kivinummi, Kati; Högnäs, Gunilla; Häyrynen, Sergei; Rantapero, Tommi; Kivinen, Virpi; Isaacs, William B; Tolonen, Teemu; Nykter, Matti; Visakorpi, Tapio

    2016-05-01

    We report the first combined analysis of whole-genome sequence, detailed clinical history, and transcriptome sequence of multiple prostate cancer metastases in a single patient (A21). Whole-genome and transcriptome sequence was obtained from nine anatomically separate metastases, and targeted DNA sequencing was performed in cancerous and noncancerous foci within the primary tumor specimen removed 5 yr before death. Transcriptome analysis revealed increased expression of androgen receptor (AR)-regulated genes in liver metastases that harbored an AR p.L702H mutation, suggesting a dominant effect by the mutation despite being present in only one of an estimated 16 copies per cell. The metastases harbored several alterations to the PI3K/AKT pathway, including a clonal truncal mutation in PIK3CG and present in all metastatic sites studied. The list of truncal genomic alterations shared by all metastases included homozygous deletion of TP53, hemizygous deletion of RB1 and CHD1, and amplification of FGFR1. If the patient were treated today, given this knowledge, the use of second-generation androgen-directed therapies, cessation of glucocorticoid administration, and therapeutic inhibition of the PI3K/AKT pathway or FGFR1 receptor could provide personalized benefit. Three previously unreported truncal clonal missense mutations (ABCC4 p.R891L, ALDH9A1 p.W89R, and ASNA1 p.P75R) were expressed at the RNA level and assessed as druggable. The truncal status of mutations may be critical for effective actionability and merit further study. Our findings suggest that a large set of deeply analyzed cases could serve as a powerful guide to more effective prostate cancer basic science and personalized cancer medicine clinical trials. PMID:27148588

  8. Fentanyl-Laced 'Norco' Is Lethal, Report Warns

    MedlinePlus

    ... fullstory_160158.html Fentanyl-Laced 'Norco' Is Lethal, Report Warns New street drug combines two synthetic opioids ... imprint and were beige instead of white. The report was published online July 27 in the journal ...

  9. Geomorphological analysis and prioritization of sub-watersheds using Snyder's synthetic unit hydrograph method

    NASA Astrophysics Data System (ADS)

    Singh, Nivedita; Singh, K. K.

    2014-11-01

    The present study makes an attempt to prioritize sub-watersheds based on Snyder's synthetic unit hydrograph method. Snyder's method of synthetic unit hydrograph calculates peak discharge and lag time of the unit hydrograph for each sub-watersheds. Compound values of ranking are calculated from assigned rankings to parameters, viz. peak discharge and lag time. Depending on the range of the compound values sub-watersheds are classified as high, medium and low soil-erosive sub-watersheds. The priorities obtained from Snyder's synthetic unit hydrograph method are compared with the methods of morphometric analysis and land use/land cover analysis. On comparison of priorities for Dangri River watershed, Panchkula District, Haryana (India), among the three methods it was found that the sub-watershed (SW1) has the same priority. Among all the three methods, Snyder's synthetic unit hydrograph is a better method, as it is easier to use and less data intensive.

  10. Seamless Synthetic Aperture Radar Archive for Interferometry Analysis

    NASA Astrophysics Data System (ADS)

    Baker, S.; Baru, C.; Bryson, G.; Buechler, B.; Crosby, C.; Fielding, E.; Meertens, C.; Nicoll, J.; Youn, C.

    2014-11-01

    The NASA Advancing Collaborative Connections for Earth System Science (ACCESS) seamless synthetic aperture radar (SAR) archive (SSARA) project is a collaboration between UNAVCO, the Alaska Satellite Facility (ASF), the Jet Propulsion Laboratory (JPL), and OpenTopography at the San Diego Supercomputer Center (SDSC) to design and implement a seamless distributed access system for SAR data and derived interferometric SAR (InSAR) data products. A unified application programming interface (API) has been created to search the SAR archives at ASF and UNAVCO, 30 and 90-m SRTM DEM data available through OpenTopography, and tropospheric data from the NASA OSCAR project at JPL. The federated query service provides users a single access point to search for SAR granules, InSAR pairs, and corresponding DEM and tropospheric data products from the four archives, as well as the ability to search and download pre-processed InSAR products from ASF and UNAVCO.

  11. Synthetic plant defense elicitors

    PubMed Central

    Bektas, Yasemin; Eulgem, Thomas

    2015-01-01

    To defend themselves against invading pathogens plants utilize a complex regulatory network that coordinates extensive transcriptional and metabolic reprogramming. Although many of the key players of this immunity-associated network are known, the details of its topology and dynamics are still poorly understood. As an alternative to forward and reverse genetic studies, chemical genetics-related approaches based on bioactive small molecules have gained substantial popularity in the analysis of biological pathways and networks. Use of such molecular probes can allow researchers to access biological space that was previously inaccessible to genetic analyses due to gene redundancy or lethality of mutations. Synthetic elicitors are small drug-like molecules that induce plant defense responses, but are distinct from known natural elicitors of plant immunity. While the discovery of some synthetic elicitors had already been reported in the 1970s, recent breakthroughs in combinatorial chemical synthesis now allow for inexpensive high-throughput screens for bioactive plant defense-inducing compounds. Along with powerful reverse genetics tools and resources available for model plants and crop systems, comprehensive collections of new synthetic elicitors will likely allow plant scientists to study the intricacies of plant defense signaling pathways and networks in an unparalleled fashion. As synthetic elicitors can protect crops from diseases, without the need to be directly toxic for pathogenic organisms, they may also serve as promising alternatives to conventional biocidal pesticides, which often are harmful for the environment, farmers and consumers. Here we are discussing various types of synthetic elicitors that have been used for studies on the plant immune system, their modes-of-action as well as their application in crop protection. PMID:25674095

  12. The VG/GA strain of Newcastle disease virus: Mucosal immunity, protection against lethal challenge and molecular analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The VG/GA strain of Newcastle disease virus (NDV) isolated from the intestine of healthy turkeys has been proposed to replicate in the respiratory and intestinal tract of chickens. In this study, the virus distribution, the mucosal and systemic immune response, the efficacy against lethal challenge...

  13. An analysis of foliage induced azimuthal synthetic pattern distortions

    NASA Astrophysics Data System (ADS)

    Toups, M. F.

    1992-05-01

    Phase and amplitude fluctuations induced by wave propagation through foliage limit the ability of a synthetic aperture radar (SAR) system to image a target under foliage. One-way measurements of these fluctuations were done using the NASA/JPL C-, L-, UHF band SAR during the Lincoln Laboratory July 1990 Foliage Penetration Experiment. In this experiment, single-frequency CW signal sources, 'tone generators', were placed in the open and under foliage in order to measure one-way propagation. Three tone generator sites located under trees and one tone generator site in the open were utilized. Tone generators at the open site were used as controls. At each site, six tone generators were deployed, one for each frequency and polarization utilized by the NASA/JPL SAR system. The statistical properties of the phase and amplitude fluctuations induced by the foliage are determined for each tone generator site, frequency, and polarization. The effect of these amplitude and phase fluctuations on the ability of a SAR system to image a target *bscured by foliage is shown. These results are compared with the measured ground truth for each tone generator site. The ground truth measured during the experiment includes foliage densities, moisture contents, and permittivities.

  14. Perspective - synthetic DEMs: A vital underpinning for the quantitative future of landform analysis?

    NASA Astrophysics Data System (ADS)

    Hillier, J. K.; Sofia, G.; Conway, S. J.

    2015-12-01

    Physical processes, including anthropogenic feedbacks, sculpt planetary surfaces (e.g. Earth's). A fundamental tenet of geomorphology is that the shapes created, when combined with other measurements, can be used to understand those processes. Artificial or synthetic digital elevation models (DEMs) might be vital in progressing further with this endeavour in two ways. First, synthetic DEMs can be built (e.g. by directly using governing equations) to encapsulate the processes, making predictions from theory. A second, arguably underutilised, role is to perform checks on accuracy and robustness that we dub "synthetic tests". Specifically, synthetic DEMs can contain a priori known, idealised morphologies that numerical landscape evolution models, DEM-analysis algorithms, and even manual mapping can be assessed against. Some such tests, for instance examining inaccuracies caused by noise, are moderately commonly employed, whilst others are much less so. Derived morphological properties, including metrics and mapping (manual and automated), are required to establish whether or not conceptual models represent reality well, but at present their quality is typically weakly constrained (e.g. by mapper inter-comparison). Relatively rare examples illustrate how synthetic tests can make strong "absolute" statements about landform detection and quantification; for example, 84 % of valley heads in the real landscape are identified correctly. From our perspective, it is vital to verify such statistics quantifying the properties of landscapes as ultimately this is the link between physics-driven models of processes and morphological observations that allows quantitative hypotheses to be tested. As such the additional rigour possible with this second usage of synthetic DEMs feeds directly into a problem central to the validity of much of geomorphology. Thus, this note introduces synthetic tests and DEMs and then outlines a typology of synthetic DEMs along with their benefits

  15. Analysis of Eisenia fetida earthworm responses to sub-lethal C60 nanoparticle exposure using (1)H-NMR based metabolomics.

    PubMed

    Lankadurai, Brian P; Nagato, Edward G; Simpson, André J; Simpson, Myrna J

    2015-10-01

    The enhanced production and environmental release of Buckminsterfullerene (C60) nanoparticles will likely increase the exposure and risk to soil dwelling organisms. We used (1)H NMR-based metabolomics to investigate the response of Eisenia fetida earthworms to sub-lethal C60 nanoparticle exposure in both contact and soil tests. Principal component analysis of (1)H NMR data showed clear separation between controls and exposed earthworms after just 2 days of exposure, however as exposure time increased the separation decreased in soil but increased in contact tests suggesting potential adaptation during soil exposure. The amino acids leucine, valine, isoleucine and phenylalanine, the nucleoside inosine, and the sugars glucose and maltose emerged as potential bioindicators of exposure to C60 nanoparticles. The significant responses observed in earthworms using NMR-based metabolomics after exposure to very low concentrations of C60 nanoparticles suggests the need for further investigations to better understand and predict their sub-lethal toxicity. PMID:26024814

  16. End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

    DOE PAGESBeta

    Linshiz, Gregory; Jensen, Erik; Stawski, Nina; Bi, Changhao; Elsbree, Nick; Jiao, Hong; Kim, Jungkyu; Mathies, Richard; Keasling, Jay D.; Hillson, Nathan J.

    2016-02-02

    Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. Here, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, andmore » proteogenic and metabolic output analysis. Finally, taken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis.« less

  17. Application of non-lethal stable isotope analysis to assess feeding patterns of juvenile pallid sturgeon Scaphirhynchus albus: A comparison of tissue types and sample preservation methods

    USGS Publications Warehouse

    Andvik, R.T.; VanDeHey, J.A.; Fincel, M.J.; French, William E.; Bertrand, K.N.; Chipps, S.R.; Klumb, R.A.; Graeb, B.D.S.

    2010-01-01

    Traditional techniques for stable isotope analysis (SIA) generally require sacrificing animals to collect tissue samples; this can be problematic when studying diets of endangered species such as the pallid sturgeon Scaphirhynchus albus. Our objectives were to (i) determine if pectoral fin tissue (non-lethal) could be a substitute for muscle tissue (lethal) in SIA of juvenile pallid sturgeon, and (ii) evaluate the influence of preservation techniques on stable isotope values. In the laboratory, individual juvenile pallid sturgeon were held for up to 186 day and fed chironomids, fish, or a commercially available pellet diet. Significant, positive relationships (r2 ??? 0.8) were observed between fin and muscle tissues for both ??15N and ??13C; in all samples isotopes were enriched in fins compared to muscle tissue. Chironomid and fish based diets of juvenile pallid sturgeon were distinguishable for fast growing fish (0.3 mm day-1) using stable ??15N and ??13C isotopes. Frozen and preserved fin tissue ??15N isotopes were strongly related (r2 = 0.89) but ??13C isotopes were weakly related (r2 = 0.16). Therefore, freezing is recommended for preservation of fin clips to avoid the confounding effect of enrichment by ethanol. This study demonstrates the utility of a non-lethal technique to assess time integrated food habits of juvenile pallid sturgeon and should be applicable to other threatened or endangered species. ?? 2010 Blackwell Verlag, Berlin.

  18. Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy

    PubMed Central

    Noor, Elad; van der Oost, John; de Vos, Willem M.; Kengen, Servé W. M.; Martins dos Santos, Vitor A. P.

    2016-01-01

    The strong advances in synthetic biology enable the engineering of novel functions and complex biological features in unprecedented ways, such as implementing synthetic autotrophic metabolism into heterotrophic hosts. A key challenge for the sustainable production of fuels and chemicals entails the engineering of synthetic autotrophic organisms that can effectively and efficiently fix carbon dioxide by using sustainable energy sources. This challenge involves the integration of carbon fixation and energy uptake systems. A variety of carbon fixation pathways and several types of photosystems and other energy uptake systems can be chosen and, potentially, modularly combined to design synthetic autotrophic metabolism. Prior to implementation, these designs can be evaluated by the combination of several computational pathway analysis techniques. Here we present a systematic, integrated in silico analysis of photo-electro-autotrophic pathway designs, consisting of natural and synthetic carbon fixation pathways, a proton-pumping rhodopsin photosystem for ATP regeneration and an electron uptake pathway. We integrated Flux Balance Analysis of the heterotrophic chassis Escherichia coli with kinetic pathway analysis and thermodynamic pathway analysis (Max-min Driving Force). The photo-electro-autotrophic designs are predicted to have a limited potential for anaerobic, autotrophic growth of E. coli, given the relatively low ATP regenerating capacity of the proton pumping rhodopsin photosystems and the high ATP maintenance of E. coli. If these factors can be tackled, our analysis indicates the highest growth potential for the natural reductive tricarboxylic acid cycle and the synthetic pyruvate synthase–pyruvate carboxylate -glyoxylate bicycle. Both carbon fixation cycles are very ATP efficient, while maintaining fast kinetics, which also results in relatively low estimated protein costs for these pathways. Furthermore, the synthetic bicycles are highly thermodynamic

  19. ROUND ROBIN ANALYSIS OF ALCOHOL AND CARBONYL SYNTHETIC EXHAUST SAMPLES

    EPA Science Inventory

    Recent changes in regulatory practices have brought about a need for speciated analysis of the volatile organic components of vehicle exhaust. he purpose of this study was to allow interested laboratories to participate in a Round Robin so that each could assess their speciation ...

  20. Synthetical Reliability Analysis Model of CNC Software System

    NASA Astrophysics Data System (ADS)

    Xu, Yue; Xia, Yinjie; Wan, Yi

    CNC technology is the core of advanced manufacturing technology, and CNC software system is the very important part of numerical control system. The entire CNC system will not work normally, once the potential failure makes the software invalid. As to the current study of CNC sysytem, in use of the FAULT glitch tree, established a glitch tree for the CNC system; find the minimum cut sets with Fussed method and then according to the probability of several common glitches, make quantitative analysis in the reliability of the CNC system so that scientific ways can be provided for the reliability design, maintenance and management of the CNC system.

  1. Unsteady flow and heat transfer analysis of an impinging synthetic jet

    NASA Astrophysics Data System (ADS)

    Bazdidi-Tehrani, Farzad; Karami, Mahdi; Jahromi, Mehdi

    2011-11-01

    The present paper focuses on the analysis of unsteady flow and heat transfer regarding an axisymmetric impinging synthetic jet on a constant heat flux disc. Synthetic jet is a zero net mass flux jet that provides an unsteady flow without any external source of fluid. Present results are validated against the available experimental data showing that the SST/ k - ω turbulence model is more accurate and reliable than the standard and low- Re k - ɛ models for predicting heat transfer from an impinging synthetic jet. It is found that the time-averaged Nusselt number enhances as the nozzle-to-plate distance is increased. As the oscillation frequency in the range of 16-400 Hz is increased, the heat transfer is enhanced. It is shown that the instantaneous Nu distribution along the wall is influenced mainly by the interaction of produced vortex ring and wall boundary layer. Also, the fluctuation level of Nu decreases as the frequency is raised.

  2. 1H NMR-Based Metabolomic Analysis of Sub-Lethal Perfluorooctane Sulfonate Exposure to the Earthworm, Eisenia fetida, in Soil

    PubMed Central

    Lankadurai, Brian P.; Furdui, Vasile I.; Reiner, Eric J.; Simpson, André J.; Simpson, Myrna J.

    2013-01-01

    1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS) in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg) for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that were comprised of two separate modes of action: a non-polar narcosis type mechanism after two days of exposure and increased fatty acid oxidation after seven and fourteen days of exposure. Univariate statistical analysis revealed that 2-hexyl-5-ethyl-3-furansulfonate (HEFS), betaine, leucine, arginine, glutamate, maltose and ATP are potential indicators of PFOS exposure, as the concentrations of these metabolites fluctuated significantly. Overall, NMR-based metabolomic analysis suggests elevated fatty acid oxidation, disruption in energy metabolism and biological membrane structure and a possible interruption of ATP synthesis. These conclusions obtained from analysis of the metabolic profile in response to sub-lethal PFOS exposure indicates that NMR-based metabolomics is an excellent discovery tool when the mode of action (MOA) of contaminants is not clearly defined. PMID:24958147

  3. 1H NMR-Based Metabolomic Analysis of Sub-Lethal Perfluorooctane Sulfonate Exposure to the Earthworm, Eisenia fetida, in Soil.

    PubMed

    Lankadurai, Brian P; Furdui, Vasile I; Reiner, Eric J; Simpson, André J; Simpson, Myrna J

    2013-01-01

    1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS) in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg) for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that were comprised of two separate modes of action: a non-polar narcosis type mechanism after two days of exposure and increased fatty acid oxidation after seven and fourteen days of exposure. Univariate statistical analysis revealed that 2-hexyl-5-ethyl-3-furansulfonate (HEFS), betaine, leucine, arginine, glutamate, maltose and ATP are potential indicators of PFOS exposure, as the concentrations of these metabolites fluctuated significantly. Overall, NMR-based metabolomic analysis suggests elevated fatty acid oxidation, disruption in energy metabolism and biological membrane structure and a possible interruption of ATP synthesis. These conclusions obtained from analysis of the metabolic profile in response to sub-lethal PFOS exposure indicates that NMR-based metabolomics is an excellent discovery tool when the mode of action (MOA) of contaminants is not clearly defined. PMID:24958147

  4. Performance analysis of improved methodology for incorporation of spatial/spectral variability in synthetic hyperspectral imagery

    NASA Astrophysics Data System (ADS)

    Scanlan, Neil W.; Schott, John R.; Brown, Scott D.

    2003-12-01

    Synthetic imagery has traditionally been used to support sensor design by enabling design engineers to pre-evaluate image products during the design and development stages. Increasingly exploitation analysts are looking to synthetic imagery as a way to develop and test exploitation algorithms before image data are available from new sensors. Even when sensors are available, synthetic imagery can significantly aid in algorithm development by providing a wide range of "ground truthed" images with varying illumination, atmospheric, viewing and scene conditions. One limitation of synthetic data is that the background variability is often too bland. It does not exhibit the spatial and spectral variability present in real data. In this work, four fundamentally different texture modeling algorithms will first be implemented as necessary into the Digital Imaging and Remote Sensing Image Generation (DIRSIG) model environment. Two of the models to be tested are variants of a statistical Z-Score selection model, while the remaining two involve a texture synthesis and a spectral end-member fractional abundance map approach, respectively. A detailed comparative performance analysis of each model will then be carried out on several texturally significant regions of the resultant synthetic hyperspectral imagery. The quantitative assessment of each model will utilize a set of three peformance metrics that have been derived from spatial Gray Level Co-Occurrence Matrix (GLCM) analysis, hyperspectral Signal-to-Clutter Ratio (SCR) measures, and a new concept termed the Spectral Co-Occurrence Matrix (SCM) metric which permits the simultaneous measurement of spatial and spectral texture. Previous research efforts on the validation and performance analysis of texture characterization models have been largely qualitative in nature based on conducting visual inspections of synthetic textures in order to judge the degree of similarity to the original sample texture imagery. The quantitative

  5. Performance analysis of improved methodology for incorporation of spatial/spectral variability in synthetic hyperspectral imagery

    NASA Astrophysics Data System (ADS)

    Scanlan, Neil W.; Schott, John R.; Brown, Scott D.

    2004-01-01

    Synthetic imagery has traditionally been used to support sensor design by enabling design engineers to pre-evaluate image products during the design and development stages. Increasingly exploitation analysts are looking to synthetic imagery as a way to develop and test exploitation algorithms before image data are available from new sensors. Even when sensors are available, synthetic imagery can significantly aid in algorithm development by providing a wide range of "ground truthed" images with varying illumination, atmospheric, viewing and scene conditions. One limitation of synthetic data is that the background variability is often too bland. It does not exhibit the spatial and spectral variability present in real data. In this work, four fundamentally different texture modeling algorithms will first be implemented as necessary into the Digital Imaging and Remote Sensing Image Generation (DIRSIG) model environment. Two of the models to be tested are variants of a statistical Z-Score selection model, while the remaining two involve a texture synthesis and a spectral end-member fractional abundance map approach, respectively. A detailed comparative performance analysis of each model will then be carried out on several texturally significant regions of the resultant synthetic hyperspectral imagery. The quantitative assessment of each model will utilize a set of three peformance metrics that have been derived from spatial Gray Level Co-Occurrence Matrix (GLCM) analysis, hyperspectral Signal-to-Clutter Ratio (SCR) measures, and a new concept termed the Spectral Co-Occurrence Matrix (SCM) metric which permits the simultaneous measurement of spatial and spectral texture. Previous research efforts on the validation and performance analysis of texture characterization models have been largely qualitative in nature based on conducting visual inspections of synthetic textures in order to judge the degree of similarity to the original sample texture imagery. The quantitative

  6. Analysis of the full-length genome sequence of papaya lethal yellowing virus (PLYV), determined by deep sequencing, confirms its classification in the genus Sobemovirus.

    PubMed

    Pereira, Alvaro J; Alfenas-Zerbini, Poliane; Cascardo, Renan S; Andrade, Eduardo C; Murilo Zerbini, F

    2012-10-01

    Papaya lethal yellowing virus (PLYV) causes an economically important disease in papayas in northeastern Brazil. Based on biological and molecular properties, PLYV has been tentatively assigned to the genus Sobemovirus. We report the sequence of the full-length genome of a PLYV isolate from Brazil, determined by deep sequencing. The PLYV genome is 4,145 nt long and contains four ORFs, with an arrangement identical to that of sobemoviruses. The polyprotein and CP display significant sequence identity with the corresponding proteins of other sobemoviruses. Pairwise comparisons and phylogenetic analysis based on complete nucleotide sequences confirm the classification of PLYV in the genus Sobemovirus. PMID:22743825

  7. Structure-Based Systematic Isolation of Conditional-Lethal Mutations in the Single Yeast Calmodulin Gene

    PubMed Central

    Ohya, Y.; Botstein, D.

    1994-01-01

    Conditional-lethal mutations of the single calmodulin gene in Saccharomyces cerevisiae have been very difficult to isolate by random and systematic methods, despite the fact that deletions cause recessive lethality. We report here the isolation of numerous conditional-lethal mutants that were recovered by systematically altering phenylalanine residues. The phenylalanine residues of calmodulin were implicated in function both by structural studies of calmodulin bound to target peptides and by their extraordinary conservation in evolution. Seven single and 26 multiple Phe -> Ala mutations were constructed. Mutant phenotypes were examined in a haploid cmd1 disrupted strain under three conditions: single copy, low copy, and overexpressed. Whereas all but one of the single mutations caused no obvious phenotype, most of the multiple mutations caused obvious growth phenotypes. Five were lethal, 6 were lethal only in synthetic medium, 13 were temperature-sensitive lethal and 2 had no discernible phenotypic consequences. Overexpression of some of the mutant genes restored the phenotype to nearly wild type. Several temperature-sensitive calmodulin mutations were suppressed by elevated concentration of CaCl(2) in the medium. Mutant calmodulin protein was detected at normal levels in extracts of most of the lethal mutant cells, suggesting that the deleterious phenotypes were due to loss of the calmodulin function and not protein instability. Analysis of diploid strains heterozygous for all combinations of cmd1-ts alleles revealed four intragenic complementation groups. The contributions of individual phe->ala changes to mutant phenotypes support the idea of internal functional redundancy in the symmetrical calmodulin protein molecule. These results suggest that the several phenylalanine residues in calmodulin are required to different extents in different combinations in order to carry out each of the several essential tasks. PMID:7896089

  8. Clinical parameters, postmortem analysis and estimation of lethal dose in victims of a massive intoxication with diethylene glycol.

    PubMed

    Ferrari, Luis A; Giannuzzi, Leda

    2005-10-01

    could be observed. The lethal dose for human beings estimated in this work ranged from 0.014 to 0.170 mg DEG/kg body weight. This is a lower lethal dose than reported in a separate incident in Haiti. These results may contribute to the understanding of DEG's metabolic pathway and provides data from lethal doses in humans. PMID:15979833

  9. Application of non-lethal stable isotope analysis to assess feeding patterns of juvenile pallid sturgeon Scaphirhynchus albus: a comparison of tissue types and sample preservation methods

    USGS Publications Warehouse

    Andvik, R.T.; VanDeHey, J.A.; Fincel, M.J.; French, William E.; Bertrand, K.N.; Chipps, Steven R.; Klumb, R.A.; Graeb, B.D.S.

    2010-01-01

    Traditional techniques for stable isotope analysis (SIA) generally require sacrificing animals to collect tissue samples; this can be problematic when studying diets of endangered species such as the pallid sturgeon Scaphirhynchus albus. Our objectives were to (i) determine if pectoral fin tissue (non-lethal) could be a substitute for muscle tissue (lethal) in SIA of juvenile pallid sturgeon, and (ii) evaluate the influence of preservation techniques on stable isotope values. In the laboratory, individual juvenile pallid sturgeon were held for up to 186 day and fed chironomids, fish, or a commercially available pellet diet. Significant, positive relationships (r² ≥ 0.8) were observed between fin and muscle tissues for both δ15N and δ13C; in all samples isotopes were enriched in fins compared to muscle tissue. Chironomid and fish based diets of juvenile pallid sturgeon were distinguishable for fast growing fish (0.3 mm day−1) using stable δ15N and δ13C isotopes. Frozen and preserved fin tissue δ15N isotopes were strongly related (r2 = 0.89) but δ13C isotopes were weakly related (r2 = 0.16). Therefore, freezing is recommended for preservation of fin clips to avoid the confounding effect of enrichment by ethanol. This study demonstrates the utility of a non-lethal technique to assess time integrated food habits of juvenile pallid sturgeon and should be applicable to other threatened or endangered species.

  10. [Evaluation of the diagnostic usefulness for ultrasonographic and echocardiographic lethal markers in fetal pulmonary hypoplasia. Analysis of 11 cases].

    PubMed

    Kieszek, S; Kaczmarek, P; Czichos, E; Respondek, M

    1996-07-01

    Results of ultrasonographic and echocardiographic studies of 11 fetuses were analysed retrospectively in relation to their pulmonary hypoplasia. Congenital malformations, quality of hydramnios and echocardiographical measurements of fetal chest were estimated. The best symptoms of pulmonary hypoplasia were: oligo/ahydramnios, absence of fetal breathing movements and malformations in fetal chest cavity (diaphragmatic hernia, cardiomegaly, hydrothorax). Systemic malformations were present in each case. The measurements such as CC, CA, HA, (CA-HA) x 100/CA were not accurate enough and we did not find any statistical differences between the control and the studied group. Finding several factors predisposing to lung hypoplasia means that its lethal form may be present in fetus. PMID:9138996

  11. Perspective - Synthetic DEMs: A vital underpinning for the quantitative future of landform analysis?

    NASA Astrophysics Data System (ADS)

    Hillier, John K.; Sofia, Giulia; Conway, Susan

    2015-04-01

    Physical processes, including anthropogenic feedbacks, sculpt planetary surfaces (e.g., Earth's). A fundamental tenet of Geomorphology is that the shapes created, when combined with other measurements, can be used to understand those processes. Morphological data, including metrics and mapping (manual and automated), are a key resource in this endeavour. However, how good are these data that analyses rely on? Artificial or synthetic DEMs are widely used to examine the distortions of 'noise' (e.g., on topographic parameters), but only rarely to make strong 'absolute' statements about landform detection and quantification; e.g., 84% of the river channels in the real landscape are found, or 47% of all actual drumlins H > 3 m are mapped. In theory synthetic DEMs a priori containing known, idealised components can give such absolute conclusions regarding effectiveness if they can be constructed so as to represent well the actual landscapes. So, do we need good realistic synthetic DEMs, how can we best construct them, and what for? From our perspective, they are vital to verify the statistics that will link physics-driven models of processes to morphological observations, allowing quantitative hypotheses to be formulated and tested. We will outline current approaches, and some speculations about the future, but we are seeking a discussion on how best to construct realistic synthetic DEMs and proceed with uncertainty-aware landscape analysis to examine physical processes.

  12. Fractal image analysis - Application to the topography of Oregon and synthetic images.

    NASA Technical Reports Server (NTRS)

    Huang, Jie; Turcotte, Donald L.

    1990-01-01

    Digitized topography for the state of Oregon has been used to obtain maps of fractal dimension and roughness amplitude. The roughness amplitude correlates well with variations in relief and is a promising parameter for the quantitative classification of landforms. The spatial variations in fractal dimension are low and show no clear correlation with different tectonic settings. For Oregon the mean fractal dimension from a two-dimensional spectral analysis is D = 2.586, and for a one-dimensional spectral analysis the mean fractal dimension is D = 1.487, which is close to the Brown noise value D = 1.5. Synthetic two-dimensional images have also been generated for a range of D values. For D = 2.6, the synthetic image has a mean one-dimensional spectral fractal dimension D = 1.58, which is consistent with the results for Oregon. This approach can be easily applied to any digitzed image that obeys fractal statistics.

  13. Coal liquefaction processes and development requirements analysis for synthetic fuels production

    NASA Technical Reports Server (NTRS)

    1980-01-01

    Focus of the study is on: (1) developing a technical and programmatic data base on direct and indirect liquefaction processes which have potential for commercialization during the 1980's and beyond, and (2) performing analyses to assess technology readiness and development trends, development requirements, commercial plant costs, and projected synthetic fuel costs. Numerous data sources and references were used as the basis for the analysis results and information presented.

  14. Synthetic fuels and the environment: an environmental and regulatory impacts analysis

    SciTech Connect

    1980-06-01

    Since July 1979 when DOE/EV-0044 report Environmental Analysis of Synthetic Liquid fuels was published the synthetic fuels program proposals of the Administration have undergone significant modifications. The program year for which the development goal of 1.5 million barrels per day is to be reached has been changed from 1990 to 1995. The program plan is now proposed to have two stages to ensure, among other things, better environmental protection: an initial stage emphasizing applied research and development (R and D), including environmental research, followed by a second stage that would accelerate deployment of those synthetic fuel technologies then judged most ready for rapid deployment and economic operation within the environmental protection requirements. These program changes have significantly expanded the scope of technologies to be considered in this environmental analysis and have increased the likelihood that accelerated environmental R and D efforts will be successful in solving principal environmental and worker safety concerns for most technologies prior to the initiation of the second stage of the accelerated deployment plan. Information is presented under the following section headings: summary; study description; the technologies and their environmental concerns (including, coal liquefaction and gasification, oil shale production, biomass and urban waste conversion); regulatory and institutional analyses; and environmental impacts analysis (including air and water quaility analyses, impacts of carbon dioxide and acid rain, water availability, solid and hazardous wastes, coal mining environmental impacts, transportation issues, community growth and change, and regional impacts). Additional information is presented in seventeen appendixes. (JGB)

  15. Rapid in vivo analysis of synthetic promoters for plant pathogen phytosensing

    PubMed Central

    2011-01-01

    Background We aimed to engineer transgenic plants for the purpose of early detection of plant pathogen infection, which was accomplished by employing synthetic pathogen inducible promoters fused to reporter genes for altered phenotypes in response to the pathogen infection. Toward this end, a number of synthetic promoters consisting of inducible regulatory elements fused to a red fluorescent protein (RFP) reporter were constructed for use in phytosensing. Results For rapid analysis, an Agrobacterium-mediated transient expression assay was evaluated, then utilized to assess the inducibility of each synthetic promoter construct in vivo. Tobacco (Nicotiana tabacum cv. Xanthi) leaves were infiltrated with Agrobacterium harboring the individual synthetic promoter-reporter constructs. The infiltrated tobacco leaves were re-infiltrated with biotic (bacterial pathogens) or abiotic (plant defense signal molecules salicylic acid, ethylene and methyl jasmonate) agents 24 and 48 hours after initial agroinfiltration, followed by RFP measurements at relevant time points after treatment. These analyses indicated that the synthetic promoter constructs were capable of conferring the inducibility of the RFP reporter in response to appropriate phytohormones and bacterial pathogens, accordingly. Conclusions These observations demonstrate that the Agrobacterium-mediated transient expression is an efficient method for in vivo assays of promoter constructs in less than one week. Our results provide the opportunity to gain further insights into the versatility of the expression system as a potential tool for high-throughput in planta expression screening prior to generating stably transgenic plants for pathogen phytosensing. This system could also be utilized for temporary phytosensing; e.g., not requiring stably transgenic plants. PMID:22093754

  16. Quantitative Analysis of Cis-Regulatory Element Activity Using Synthetic Promoters in Transgenic Plants.

    PubMed

    Benn, Geoffrey; Dehesh, Katayoon

    2016-01-01

    Synthetic promoters, introduced stably or transiently into plants, are an invaluable tool for the identification of functional regulatory elements and the corresponding transcription factor(s) that regulate the amplitude, spatial distribution, and temporal patterns of gene expression. Here, we present a protocol describing the steps required to identify and characterize putative cis-regulatory elements. These steps include application of computational tools to identify putative elements, construction of a synthetic promoter upstream of luciferase, identification of transcription factors that regulate the element, testing the functionality of the element introduced transiently and/or stably into the species of interest followed by high-throughput luciferase screening assays, and subsequent data processing and statistical analysis. PMID:27557758

  17. Analysis and optimization of a synthetic milkweed floral attractant for mosquitoes.

    PubMed

    Otienoburu, Philip E; Ebrahimi, Babak; Phelan, P Larry; Foster, Woodbridge A

    2012-07-01

    A pentane extract of flowers of common milkweed, Asclepias syriaca (Asclepiadaceae), elicited significant orientation from both male and female Culex pipiens in a dual-port flight olfactometer. Analysis of the extract by gas chromatography-mass spectrometry revealed six major constituents in order of relative abundance: benzaldehyde, (E)-β-ocimene, phenylacetaldehyde, benzyl alcohol, nonanal, and (E)-2-nonenal. Although not all were collected from the headspace profile of live flowers, a synthetic blend of these six compounds, when presented to mosquitoes in the same levels and proportions that occur in the extract, elicited a response comparable to the extract. Subtractive behavioral bioassays demonstrated that a three-component blend consisting of benzaldehyde, phenylacetaldehyde, and (E)-2-nonenal was as attractive as the full blend. These findings suggest the potential use of synthetic floral-odor blends for monitoring or control of both male and female disease-vectoring mosquitoes. PMID:22711028

  18. Functional analysis of endoplasmic reticulum glucosyltransferase (UGGT): Synthetic chemistry's initiative in glycobiology.

    PubMed

    Ito, Yukishige; Takeda, Yoichi; Seko, Akira; Izumi, Masayuki; Kajihara, Yasuhiro

    2015-05-01

    UGGT1 is called as a folding sensor protein that recognizes misfolded glycoproteins and selectively glucosylates high-mannose-type glycans on the proteins. However, conventional approaches using naturally occurring glycoproteins is not optimum in performing precise analysis of the unique properties of UGGT1. We have demonstrated that high-mannose-type glycans, in which various hydrophobic aglycons were introduced, act as good substrates for UGGT1 and are useful analytical tools for its characterization. Moreover, we found that UGGT2, an isoform UGGT1, is also capable of glucosylating these synthetic substrates. Our strategy stemmed on synthetic chemistry has been further strengthened by total synthesis of homogeneous glycoproteins in correctly folded as well as in intentionally misfolded forms. PMID:25481681

  19. Metabolomics Analysis Identifies D-Alanine-D-alanine Ligase as the Primary Lethal Target of D-cycloserine in Mycobacteria

    PubMed Central

    Halouska, Steven; Fenton, Robert J.; Zinniel, Denise K.; Marshall, Darrell D.; Barletta, Raúl G.; Powers, Robert

    2014-01-01

    D-cycloserine is an effective second line antibiotic used as a last resort to treat multi (MDR)- and extensively (XDR)- drug resistant strains of Mycobacterium tuberculosis. D-cycloserine interferes with the formation of peptidoglycan biosynthesis by competitive inhibition of Alanine racemase (Alr) and D-Alanine-D-alanine ligase (Ddl). Although, the two enzymes are known to be inhibited, the in vivo lethal target is still unknown. Our NMR metabolomics work has revealed that Ddl is the primary target of DCS, as cell growth is inhibited when the production of D-alanyl-D-alanine is halted. It is shown that inhibition of Alr may contribute indirectly by lowering the levels of D-alanine thus allowing DCS to outcompete D-alanine for Ddl binding. The NMR data also supports the possibility of a transamination reaction to produce D-alanine from pyruvate and glutamate, thereby bypassing Alr inhibition. Furthermore, the inhibition of peptidoglycan synthesis results in a cascading effect on cellular metabolism as there is a shift toward the catabolic routes to compensate for accumulation of peptidoglycan precursors. PMID:24303782

  20. Fiber optic evaporation analysis of environmental parameters and of synthetic urine samples

    NASA Astrophysics Data System (ADS)

    Preter, Eyal; Katzman, Moshe; Oren, Ziv; Ronen, Maria; Gerber, Doron; Zadok, Avi

    2015-09-01

    The evaporation rate of water droplets is evaluated as a function of temperature and relative humidity using a fiber-optic sensor. Either parameter may be monitored when the other is known, with uncertainties of 0.5 deg. C or 1.5% relative humidity. Further, the sensor is used in the analysis of negative control synthetic solutions, made to mimic human urine. Samples of binary mixtures of the solution with water at different volume ratios are categorized using correlation analysis of the recorded evaporation dynamics, with 87% success. The results represent an important first step towards potential use of the sensor in point-of-care diagnostics.

  1. Report of five novel and one recurrent COL2A1 mutations with analysis of genotype-phenotype correlation in patients with a lethal type II collagen disorder.

    PubMed

    Mortier, G R; Weis, M; Nuytinck, L; King, L M; Wilkin, D J; De Paepe, A; Lachman, R S; Rimoin, D L; Eyre, D R; Cohn, D H

    2000-04-01

    Achondrogenesis II-hypochondrogenesis and severe spondyloepiphyseal dysplasia congenita (SEDC) are lethal forms of dwarfism caused by dominant mutations in the type II collagen gene (COL2A1). To identify the underlying defect in seven cases with this group of conditions, we used the combined strategy of cartilage protein analysis and COL2A1 mutation analysis. Overmodified type II collagen and the presence of type I collagen was found in the cartilage matrix of all seven cases. Five patients were heterozygous for a nucleotide change that predicted a glycine substitution in the triple helical domain (G313S, G517V, G571A, G910C, G943S). In all five cases, analysis of cartilage type II collagen suggested incorporation of the abnormal alpha1(II) chain in the extracellular collagen trimers. The G943S mutation has been reported previously in another unrelated patient with a strikingly similar phenotype, illustrating the possible specific effect of the mutation. The radiographically less severely affected patient was heterozygous for a 4 bp deletion in the splice donor site of intron 35, likely to result in aberrant splicing. One case was shown to be heterozygous for a single nucleotide change predicted to result in a T1191N substitution in the carboxy-propeptide of the proalpha1(II) collagen chain. Study of the clinical, radiographic, and morphological features of the seven cases supports evidence for a phenotypic continuum between achondrogenesis II-hypochondrogenesis and lethal SEDC and suggests a relationship between the amount of type I collagen in the cartilage and the severity of the phenotype. PMID:10745044

  2. A high-throughput pipeline for the production of synthetic antibodies for analysis of ribonucleoprotein complexes.

    PubMed

    Na, Hong; Laver, John D; Jeon, Jouhyun; Singh, Fateh; Ancevicius, Kristin; Fan, Yujie; Cao, Wen Xi; Nie, Kun; Yang, Zhenglin; Luo, Hua; Wang, Miranda; Rissland, Olivia; Westwood, J Timothy; Kim, Philip M; Smibert, Craig A; Lipshitz, Howard D; Sidhu, Sachdev S

    2016-04-01

    Post-transcriptional regulation of mRNAs plays an essential role in the control of gene expression. mRNAs are regulated in ribonucleoprotein (RNP) complexes by RNA-binding proteins (RBPs) along with associated protein and noncoding RNA (ncRNA) cofactors. A global understanding of post-transcriptional control in any cell type requires identification of the components of all of its RNP complexes. We have previously shown that these complexes can be purified by immunoprecipitation using anti-RBP synthetic antibodies produced by phage display. To develop the large number of synthetic antibodies required for a global analysis of RNP complex composition, we have established a pipeline that combines (i) a computationally aided strategy for design of antigens located outside of annotated domains, (ii) high-throughput antigen expression and purification in Escherichia coli, and (iii) high-throughput antibody selection and screening. Using this pipeline, we have produced 279 antibodies against 61 different protein components of Drosophila melanogaster RNPs. Together with those produced in our low-throughput efforts, we have a panel of 311 antibodies for 67 RNP complex proteins. Tests of a subset of our antibodies demonstrated that 89% immunoprecipitate their endogenous target from embryo lysate. This panel of antibodies will serve as a resource for global studies of RNP complexes in Drosophila. Furthermore, our high-throughput pipeline permits efficient production of synthetic antibodies against any large set of proteins. PMID:26847261

  3. Amphetamine binding to synthetic melanin and scatchard analysis of binding data.

    PubMed

    Gautam, Lata; Scott, Karen S; Cole, Michael D

    2005-01-01

    Previous research into drug-hair binding shows that hair color affects drug-hair binding. There are no structural disparities in hair of different colors other than the type and content of melanin present. For this reason, this investigation focuses on synthetic eumelanin as a site for drug interaction using amphetamine as the candidate drug. The binding study was carried out at room temperature. The interaction between synthetic eumelanin and amphetamine was monitored using UV-Vis spectrophotometry at 257.2 nm. As the molecular weight of melanin is unknown, the number of binding sites could not be calculated directly. Hence the ratio of the number of mumoles of drug bound and the dry weight of melanin in mug was considered. Equilibrium was reached when approximately 32% of the drug was bound to melanin. Hence this study proves that amphetamine binds to synthetic eumelanin in vitro. Data interpretation using Scatchard analysis yielded a curvilinear plot with upward concavity indicating multiple binding sites on melanin and negative cooperativity. PMID:16105258

  4. Synthetic environments

    NASA Astrophysics Data System (ADS)

    Lukes, George E.; Cain, Joel M.

    1996-02-01

    The Advanced Distributed Simulation (ADS) Synthetic Environments Program seeks to create robust virtual worlds from operational terrain and environmental data sources of sufficient fidelity and currency to interact with the real world. While some applications can be met by direct exploitation of standard digital terrain data, more demanding applications -- particularly those support operations 'close to the ground' -- are well-served by emerging capabilities for 'value-adding' by the user working with controlled imagery. For users to rigorously refine and exploit controlled imagery within functionally different workstations they must have a shared framework to allow interoperability within and between these environments in terms of passing image and object coordinates and other information using a variety of validated sensor models. The Synthetic Environments Program is now being expanded to address rapid construction of virtual worlds with research initiatives in digital mapping, softcopy workstations, and cartographic image understanding. The Synthetic Environments Program is also participating in a joint initiative for a sensor model applications programer's interface (API) to ensure that a common controlled imagery exploitation framework is available to all researchers, developers and users. This presentation provides an introduction to ADS and the associated requirements for synthetic environments to support synthetic theaters of war. It provides a technical rationale for exploring applications of image understanding technology to automated cartography in support of ADS and related programs benefitting from automated analysis of mapping, earth resources and reconnaissance imagery. And it provides an overview and status of the joint initiative for a sensor model API.

  5. Estimation of the synthetic routes of seized methamphetamines using GC-MS and multivariate analysis.

    PubMed

    Choe, Sanggil; Lee, Jaesin; Choi, Hyeyoung; Park, Yujin; Lee, Heesang; Jo, Jiyeong; Park, Yonghoon; Kim, Eunmi; Pyo, Jaesung; Lee, Hun Joo; Kim, Suncheun

    2016-02-01

    One hundred and twenty six seized methamphetamine (MA) samples were analyzed using GC-MS. All the peaks that appeared in the chromatograms were investigated and 61 impurities including n-octacosane (internal standard) were identified. Among them, 37 impurities were already known or newly identified by comparing with commercial library entries and 18 impurities were detected for the first time. To estimate the synthetic routes of MA samples, route specific impurities had to be selected for each method. Two naphthalenes, 1,3-dimethyl-2-phenylnaphthalene and 1-benzyl-3-methylnaphthalene were selected as Nagai route specific impurities and three diasteromers, UK-19.62(58_165_178) I, UK-19.95(58_165_178) II, UK-20.49(58_165_178) III were also selected not only for their high frequency detection only in Nagai samples but also for the high principal component analysis (PCA) correlation values. For the Emde route, N,N-dimethyl-3,4-diphenylhexane-2,5-diamine and N-methyl-1-{4-[2-(methylamino)propyl]phenyl}-1-phenylpropan-2-amine were selected as route specific impurities, and N,N-di(β-phenylisopropyl)amine I (DPIA I), N,N-di(β-phenylisopropyl)amine II (DPIA II), N,N-di(β-phenylisopropyl)methylamine I (DPIMA I) and N,N-di(β-phenylisopropyl)methylamine II (DPIMA II) were selected for the Leuckart route. With these route specific impurities, synthetic routes could be identified for 78 of the 126 samples. The 61 impurities were registered in AMDIS target component library and the GC-MS data were deconvoluted. After AMDIS deconvolution, a matrix file was composed and then multivariate analyses were performed to estimate the synthetic route for unknown samples. The unsupervised methods, hierarchical clustering analysis (HCA) and PCA clustered the samples according to the closeness between samples. Two classification functions were obtained from discriminant analysis (DA) and the synthetic routes of the unknown samples were predicted using these two functions. PMID:26765094

  6. Analysis of mechanical strength to fixing the femoral neck fracture in synthetic bone type Asnis

    PubMed Central

    Freitas, Anderson; Lula, Welder Fernandes; de Oliveira, Jonathan Sampaio; Maciel, Rafael Almeida; Souto, Diogo Ranier de Macedo; Godinho, Patrick Fernandes

    2014-01-01

    OBJECTIVE: To analyze the results of biomechanical assays of fixation of Pauwels type III femoral neck fracture in synthetic bone, using 7.5mm cannulated screws in inverted triangle formation, in relation to the control group. METHODS: Ten synthetic bones were used, from a domestic brand, divided into two groups: test and control. In the test group, a 70° tilt osteotomy of the femoral neck was fixated using three cannulated screws in inverted triangle formation. The resistance of this fixation and its rotational deviation were analyzed at 5mm displacement (phase 1) and 10mm displacement (phase 2). The control group was tested in its integrity until the fracture of the femoral neck occurred. The Mann-Whitney test was used for group analysis and comparison. RESULTS: The values in the test group in phase 1, in samples 1-5, showed a mean of 579N and SD =77N. Rotational deviations showed a mean of 3.33°, SD = 2.63°. In phase 2, the mean was 696N and SD =106N. The values of the maximum load in the control group had a mean of 1329N and SD=177N. CONCLUSION: The analysis of mechanical strength between the groups determined a statistically significant lower value in the test group. Level of Evidence III, Control Case. PMID:25246851

  7. Analysis coherent signal processing methods in synthetic aperture radar on small-scale viewing angles under voluntary movement aircraft

    NASA Astrophysics Data System (ADS)

    Anikin, Sergey N.; Vishentsev, Mihail V.; Stukalova, Anna S.

    2007-02-01

    In the article realize analysis the coherent processing method which uses to form synthetic aperture antenna on a board of aircraft. The factors, which send for distortion radar image on small-scale viewing angle during high-intensity maneuvering velocity shown for considering method of synthesizing aperture antenna. A synthetic aperture antenna software model was designing and analyzing. Some results of research of the coherent processing methods for receiving earth's imagery are shown.

  8. Quantitative wake analysis of a freely swimming fish using 3D synthetic aperture PIV

    NASA Astrophysics Data System (ADS)

    Mendelson, Leah; Techet, Alexandra H.

    2015-07-01

    Synthetic aperture PIV (SAPIV) is used to quantitatively analyze the wake behind a giant danio ( Danio aequipinnatus) swimming freely in a seeded quiescent tank. The experiment is designed with minimal constraints on animal behavior to ensure that natural swimming occurs. The fish exhibits forward swimming and turning behaviors at speeds between 0.9 and 1.5 body lengths/second. Results show clearly isolated and linked vortex rings in the wake structure, as well as the thrust jet coming off of a visual hull reconstruction of the fish body. As a benchmark for quantitative analysis of volumetric PIV data, the vortex circulation and impulse are computed using methods consistent with those applied to planar PIV data. Volumetric momentum analysis frameworks are discussed for linked and asymmetric vortex structures, laying a foundation for further volumetric studies of swimming hydrodynamics with SAPIV. Additionally, a novel weighted refocusing method is presented as an improvement to SAPIV reconstruction.

  9. Proteomic analysis of differentiating neuroblastoma cells treated with sub-lethal neurite inhibitory concentrations of diazinon: Identification of novel biomarkers of effect

    SciTech Connect

    Harris, W.; Sachana, M.; Flaskos, J.; Hargreaves, A.J.

    2009-10-15

    In previous work we showed that sub-lethal levels of diazinon inhibited neurite outgrowth in differentiating N2a neuroblastoma cells. Western blotting analysis targeted at proteins involved in axon growth and stress responses, revealed that such exposure led to a reduction in the levels of neurofilament heavy chain, microtubule associated protein 1 B (MAP 1B) and HSP-70. The aim of this study was to apply the approach of 2 dimensional polyacrylamide gel electrophoresis and mass spectrometry to identify novel biomarkers of effect. A number of proteins were found to be up-regulated compared to the control on silver-stained gels. These were classified in to 3 main groups of proteins: cytosolic factors, chaperones and the actin-binding protein cofilin, all of which are involved in cell differentiation, survival or metabolism. The changes observed for cofilin were further confirmed by quantitative Western blotting analysis with anti-actin and anti-cofilin antibodies. Indirect immunofluorescence staining with the same antibodies indicated that the microfilament network was disrupted in diazinon-treated cells. Our data suggest that microfilament organisation is disrupted by diazinon exposure, which may be related to increased cofilin expression.

  10. [Analysis of 5S rDNA changes in synthetic allopolyploids Triticum x Aegilops].

    PubMed

    Shcherban', A B; Sergeeva, E M; Badaeva, E D; Salina, E A

    2008-01-01

    By the example of three synthetic allopolyploids: Aegilops sharonensis x Ae. umbellulata (2n =28), Triticum urartu x Ae. tauschii (2n =28), T. dicoccoides x Ae. tauschii (2n =42) the 5S rDNA changes at the early stage of allopolyploidization were investigated. Using fluorescent in situ hybridization (FISH), the quantitative changes affecting the separate loci of one of the parental genomes were revealed in plants of S3 generation of each hybrid combination. Souther hybridization with genomic DNA of allopolyploid T. urartu x Ae. tauschii (TMU38 x TQ27) revealed lower intensity of the fragments from Ae. tauschii compared with the T. urartu fragments. It may be confirmation of the reduction of signal on 1D chromosome that was revealed in this hybrid using FISH. Both appearance of a new 5S rDNA fragments and full disappearance of fragments from parental species were not showed by Southern hybridization, as well as PCR-analysis of 5-15 plants of S2-S3 generations. The changes were not found under comparison of primary structure of nine 5S rDNA sequences of allopolyploid TMU38 x TQ27 with analogous sequences from parental species genomes. The observable similarity by FISH results of one of the studied synthetic allopolyploids with natural allopolyploid of similar genome composition indicates the early formation of unique for each allopolyploid 5S rDNA organization. PMID:18856060

  11. Nuclear Test Depth Determination with Synthetic Modelling: Global Analysis from PNEs to DPRK-2016

    NASA Astrophysics Data System (ADS)

    Rozhkov, Mikhail; Stachnik, Joshua; Baker, Ben; Epiphansky, Alexey; Bobrov, Dmitry

    2016-04-01

    Seismic event depth determination is critical for the event screening process at the International Data Center, CTBTO. A thorough determination of the event depth can be conducted mostly through additional special analysis because the IDC's Event Definition Criteria is based, in particular, on depth estimation uncertainties. This causes a large number of events in the Reviewed Event Bulletin to have depth constrained to the surface making the depth screening criterion not applicable. Further it may result in a heavier workload to manually distinguish between subsurface and deeper crustal events. Since the shape of the first few seconds of signal of very shallow events is very sensitive to the depth phases, cross correlation between observed and theoretic seismograms can provide a basis for the event depth estimation, and so an expansion to the screening process. We applied this approach mostly to events at teleseismic and partially regional distances. The approach was found efficient for the seismic event screening process, with certain caveats related mostly to poorly defined source and receiver crustal models which can shift the depth estimate. An adjustable teleseismic attenuation model (t*) for synthetics was used since this characteristic is not known for most of the rays we studied. We studied a wide set of historical records of nuclear explosions, including so called Peaceful Nuclear Explosions (PNE) with presumably known depths, and recent DPRK nuclear tests. The teleseismic synthetic approach is based on the stationary phase approximation with hudson96 program, and the regional modelling was done with the generalized ray technique by Vlastislav Cerveny modified to account for the complex source topography. The software prototype is designed to be used for the Expert Technical Analysis at the IDC. With this, the design effectively reuses the NDC-in-a-Box code and can be comfortably utilized by the NDC users. The package uses Geotool as a front-end for data

  12. Fourier analysis of parallel inexact Block-Jacobi splitting with transport synthetic acceleration in slab geometry

    SciTech Connect

    Rosa, M.; Warsa, J. S.; Chang, J. H.

    2006-07-01

    A Fourier analysis is conducted for the discrete-ordinates (SN) approximation of the neutron transport problem solved with Richardson iteration (Source Iteration) and Richardson iteration preconditioned with Transport Synthetic Acceleration (TSA), using the Parallel Block-Jacobi (PBJ) algorithm. Both 'traditional' TSA (TTSA) and a 'modified' TSA (MTSA), in which only the scattering in the low order equations is reduced by some non-negative factor {beta} and < 1, are considered. The results for the un-accelerated algorithm show that convergence of the PBJ algorithm can degrade. The PBJ algorithm with TTSA can be effective provided the {beta} parameter is properly tuned for a given scattering ratio c, but is potentially unstable. Compared to TTSA, MTSA is less sensitive to the choice of {beta}, more effective for the same computational effort (c'), and it is unconditionally stable. (authors)

  13. Critical analysis on nanostructured CoFeB synthetic orthogonal ferrimagnet

    SciTech Connect

    Chen, Y. S.; Lin, J. G.; Cheng, Chih-Wei; Chern, G.

    2014-09-21

    Critical analysis on the magnetic properties of synthetic ferrimagnet (SyF), Ta/MgO/CoFeB/Ru/CoFeB/MgO/Ta, is demonstrated via both static and dynamic techniques. With the Ru thickness being 2.3 nm, the coupling between two CoFeB layers becomes orthogonal, which can be used for spin-transfer-torque nano-oscillator (STNO). The fitting of angular dependent ferromagnetic resonance (FMR) allows the precise determination of magnetic anisotropy of each CoFeB layer, the relative magnetizations and the exchange field near the frequency of STNO applications. In addition, the mechanism of resonance broadening at out-of-plane direction is identified to be magnetic inhomogeneity by fitting the angular dependent linewidth of FMR spectra, which provides indispensable information for the future design of STNO devices.

  14. Synthetic Aperture Radar Interferometry for Digital Elevation Model of Kuwait Desert - Analysis of Errors

    NASA Astrophysics Data System (ADS)

    Jassar, H. K. Al; Rao, K. S.

    2012-07-01

    Using different combinations of 29 Advanced Synthetic Aperture Radar (ASAR) images, 43 Digital Elevations Models (DEM) were generated adopting SAR Interferometry (InSAR) technique. Due to sand movement in desert terrain, there is a poor phase correlation between different SAR images. Therefore, suitable methodology for generating DEMs of Kuwait desert terrain using InSAR technique were worked out. Time series analysis was adopted to derive the best DEM out of 43 DEMs. The problems related to phase de-correlation over desert terrain are discussed. Various errors associated with the DEM generation are discussed which include atmospheric effects, penetration into soil medium, sand movement. The DEM of Shuttle Radar Topography Mission (SRTM) is used as a reference. The noise levels of DEM of SRTM are presented.

  15. Synthetic graph generation for data-intensive HPC benchmarking: Scalability, analysis and real-world application

    SciTech Connect

    Powers, Sarah S.; Lothian, Joshua

    2014-12-01

    The benchmarking effort within the Extreme Scale Systems Center at Oak Ridge National Laboratory seeks to provide High Performance Computing benchmarks and test suites of interest to the DoD sponsor. The work described in this report is a part of the effort focusing on graph generation. A previously developed benchmark, SystemBurn, allows the emulation of a broad spectrum of application behavior profiles within a single framework. To complement this effort, similar capabilities are desired for graph-centric problems. This report described the in-depth analysis of the generated synthetic graphs' properties at a variety of scales using different generator implementations and examines their applicability to replicating real world datasets.

  16. Analysis of wideband forward looking synthetic aperture radar for sensing land mines

    NASA Astrophysics Data System (ADS)

    Kovvali, Narayan; Carin, Lawrence

    2004-08-01

    Signal processing algorithms are considered for the analysis of wideband, forward looking synthetic aperture radar data and for sensing metal and plastic land mines, with principal application to unpaved roads. Simple prescreening algorithms are considered for reduction of the search space required for a subsequent classifier. The classifier employs features based on viewing the target at multiple ranges, with classification implemented via a support vector machine and a relevance vector machine (RVM). Concerning classifier training, we consider cases for which training is performed on both mine and nonmine (clutter) data. In addition, motivated by the fact that the clutter statistics may vary significantly between the training and testing data, we also consider RVM implementation when we only train on mine data.

  17. Genomewide Clonal Analysis of Lethal Mutations in the Drosophila melanogaster Eye: Comparison of the X Chromosome and Autosomes

    PubMed Central

    Call, Gerald B.; Olson, John M.; Chen, Jiong; Villarasa, Nikki; Ngo, Kathy T.; Yabroff, Allison M.; Cokus, Shawn; Pellegrini, Matteo; Bibikova, Elena; Bui, Chris; Cespedes, Albert; Chan, Cheryl; Chan, Stacy; Cheema, Amrita K.; Chhabra, Akanksha; Chitsazzadeh, Vida; Do, Minh-Tu; Fang, Q. Angela; Folick, Andrew; Goodstein, Gelsey L.; Huang, Cheng R.; Hung, Tony; Kim, Eunha; Kim, William; Kim, Yulee; Kohan, Emil; Kuoy, Edward; Kwak, Robert; Lee, Eric; Lee, JiEun; Lin, Henry; Liu, H-C. Angela; Moroz, Tatiana; Prasad, Tharani; Prashad, Sacha L.; Patananan, Alexander N.; Rangel, Alma; Rosselli, Desiree; Sidhu, Sohrab; Sitz, Daniel; Taber, Chelsea E.; Tan, Jingwen; Topp, Kasey; Tran, PhuongThao; Tran, Quynh-Minh; Unkovic, Mary; Wells, Maggie; Wickland, Jessica; Yackle, Kevin; Yavari, Amir; Zaretsky, Jesse M.; Allen, Christopher M.; Alli, Latifat; An, Ju; Anwar, Abbas; Arevalo, Sonia; Ayoub, Danny; Badal, Shawn S.; Baghdanian, Armonde; Baghdanian, Arthur H.; Baumann, Sara A.; Becerra, Vivian N.; Chan, Hei J.; Chang, Aileen E.; Cheng, Xibin A.; Chin, Mabel; Chong, Fleurette; Crisostomo, Carlyn; Datta, Sanjit; Delosreyes, Angela; Diep, Francie; Ekanayake, Preethika; Engeln, Mark; Evers, Elizabeth; Farshidi, Farzin; Fischer, Katrina; Formanes, Arlene J.; Gong, Jun; Gupta, Riju; Haas, Blake E.; Hahm, Vicky; Hsieh, Michael; Hui, James Z.; Iao, Mei L.; Jin, Sophia D.; Kim, Angela Y.; Kim, Lydia S-H.; King, Megan; Knudsen-Robbins, Chloe; Kohanchi, David; Kovshilovskaya, Bogdana; Ku, Amy; Kung, Raymond W.; Landig, Mark E. L.; Latterman, Stephanie S.; Lauw, Stephanie S.; Lee, Daniel S.; Lee, Joann S.; Lei, Kai C.; Leung, Lesley L.; Lerner, Renata; Lin, Jian-ya; Lin, Kathleen; Lim, Bryon C.; Lui, Crystal P. Y.; Liu, Tiffany Q.; Luong, Vincent; Makshanoff, Jacob; Mei, An-Chi; Meza, Miguel; Mikhaeil, Yara A.; Moarefi, Majid; Nguyen, Long H.; Pai, Shekhar S.; Pandya, Manish; Patel, Aadit R.; Picard, Paul D.; Safaee, Michael M.; Salame, Carol; Sanchez, Christian; Sanchez, Nina; Seifert, Christina C.; Shah, Abhishek; Shilgevorkyan, Oganes H.; Singh, Inderroop; Soma, Vanessa; Song, Junia J.; Srivastava, Neetika; Sta.Ana, Jennifer L.; Sun, Christie; Tan, Diane; Teruya, Alison S.; Tikia, Robyn; Tran, Trinh; Travis, Emily G.; Trinh, Jennifer D.; Vo, Diane; Walsh, Thomas; Wong, Regan S.; Wu, Katherine; Wu, Ya-Whey; Yang, Nkau X. V.; Yeranosian, Michael; Yu, James S.; Zhou, Jennifer J.; Zhu, Ran X.; Abrams, Anna; Abramson, Amanda; Amado, Latiffe; Anderson, Jenny; Bashour, Keenan; Beyer, Elsa; Bookatz, Allen; Brewer, Sarah; Buu, Natalie; Calvillo, Stephanie; Cao, Joseph; Chan, Amy; Chan, Jenny; Chang, Aileen; Chang, Daniel; Chang, Yuli; Chen, YiBing; Choi, Joo; Chou, Jeyling; Dang, Peter; Datta, Sumit; Davarifar, Ardy; Deravanesian, Artemis; Desai, Poonam; Fabrikant, Jordan; Farnad, Shahbaz; Fu, Katherine; Garcia, Eddie; Garrone, Nick; Gasparyan, Srpouhi; Gayda, Phyllis; Go, Sherrylene; Goffstein, Chad; Gonzalez, Courtney; Guirguis, Mariam; Hassid, Ryan; Hermogeno, Brenda; Hong, Julie; Hong, Aria; Hovestreydt, Lindsay; Hu, Charles; Huff, Devon; Jamshidian, Farid; Jen, James; Kahen, Katrin; Kao, Linda; Kelley, Melissa; Kho, Thomas; Kim, Yein; Kim, Sarah; Kirkpatrick, Brian; Langenbacher, Adam; Laxamana, Santino; Lee, Janet; Lee, Chris; Lee, So-Youn; Lee, ToHang S.; Lee, Toni; Lewis, Gemma; Lezcano, Sheila; Lin, Peter; Luu, Thanh; Luu, Julie; Marrs, Will; Marsh, Erin; Marshall, Jamie; Min, Sarah; Minasian, Tanya; Minye, Helena; Misra, Amit; Morimoto, Miles; Moshfegh, Yasaman; Murray, Jessica; Nguyen, Kha; Nguyen, Cynthia; Nodado, Ernesto; O'Donahue, Amanda; Onugha, Ndidi; Orjiakor, Nneka; Padhiar, Bhavin; Paul, Eric; Pavel-Dinu, Mara; Pavlenko, Alex; Paz, Edwin; Phaklides, Sarah; Pham, Lephong; Poulose, Preethi; Powell, Russell; Pusic, Aya; Ramola, Divi; Regalia, Kirsten; Ribbens, Meghann; Rifai, Bassel; Saakyan, Manyak; Saarikoski, Pamela; Segura, Miriam; Shadpour, Farnaz; Shemmassian, Aram; Singh, Ramnik; Singh, Vivek; Skinner, Emily; Solomin, Daniel; Soneji, Kosha; Spivey, Kristin; Stageberg, Erika; Stavchanskiy, Marina; Tekchandani, Leena; Thai, Leo; Thiyanaratnam, Jayantha; Tong, Maurine; Toor, Aneet; Tovar, Steve; Trangsrud, Kelly; Tsang, Wah-Yung; Uemura, Marc; Vollmer, Emily; Weiss, Emily; Wood, Damien; Wu, Joy; Wu, Sophia; Wu, Winston; Xu, Qing; Yamauchi, Yuki; Yarosh, Will; Yee, Laura; Yen, George; Banerjee, Utpal

    2007-01-01

    Using a large consortium of undergraduate students in an organized program at the University of California, Los Angeles (UCLA), we have undertaken a functional genomic screen in the Drosophila eye. In addition to the educational value of discovery-based learning, this article presents the first comprehensive genomewide analysis of essential genes involved in eye development. The data reveal the surprising result that the X chromosome has almost twice the frequency of essential genes involved in eye development as that found on the autosomes. PMID:17720911

  18. Gene expression analysis of host innate immune responses in the central nervous system following lethal CVS-11 infection in mice.

    PubMed

    Sugiura, Naoko; Uda, Akihiko; Inoue, Satoshi; Kojima, Daisuke; Hamamoto, Noriko; Kaku, Yoshihiro; Okutani, Akiko; Noguchi, Akira; Park, Chun-Ho; Yamada, Akio

    2011-01-01

    The central nervous system (CNS) tissue of mice infected with the CVS-11 strain of rabies virus (RABV) was subjected to gene expression analysis using microarray and canonical pathway analyses. Genes associated with innate immunity as well as inflammatory responses were significantly up-regulated, corroborating with the previous findings obtained using attenuated viruses that did not induce a fatal outcome in infected mice. Histopathological examination showed that neurons in the cerebellum had undergone apoptosis. Although the extent of Fas ligand up-regulation was not so prominent, perforin and granzyme genes were highly expressed in the CNS of mice infected with CVS-11. The presence of perforin and granzymes both in the Purkinje cells and CD3 T lymphocytes strongly suggested that apoptosis of the former cells was induced by the latter cells. PMID:22116324

  19. Genetic analysis of Enterobius vermicularis isolated from a chimpanzee with lethal hemorrhagic colitis and pathology of the associated lesions.

    PubMed

    Yaguchi, Yuji; Okabayashi, Sachi; Abe, Niichiro; Masatou, Haruhisa; Iida, Shinya; Teramoto, Isao; Matsubayashi, Makoto; Shibahara, Tomoyuki

    2014-11-01

    Human pinworms, Enterobius vermicularis, are normally recognized as minor pathogens. However, a fatal case of human pinworm infection has been reported in a nonhuman primate, a zoo reared chimpanzee. Here, we histopathologically examined the lesions in tissues from the deceased chimpanzee and genetically characterized the isolated worms to investigate the pathogenicity and determine the phylogeny. We identified ulcers deep in the submucosa where many parasites were found to have invaded the lamina propria mucosa or submucous tissue. An inflammatory reaction consisting mainly of neutrophils and lymphocytes but not eosinophils was observed around the parasites, and intense hemorrhage in the lamina propria was confirmed. The parasites were morphologically similar to E. vermicularis based on the shape of the copulatory spicules. Mitochondrial cytochrome c oxidase subunit 1 gene products were amplified from worm DNA by PCR and were genetically identified as E. vermicularis based on >98.7% similarity of partial sequences. Phylogenetic analysis revealed that the sequences clustered together with other chimpanzee E. vermicularis isolates in a group which has been referred to as type C and which differs from human isolates (type A). The samples were negative for bacterial pathogens and Entamoeba histolytica indicating that E. vermicularis could be pathogenic in chimpanzees. Phylogenetic clustering of the isolates indicated that the parasite may be host specific. PMID:25138069

  20. Lethality test system

    SciTech Connect

    Parsons, W.M.; Sims, J.R.; Parker, J.V.

    1986-01-01

    The Lethality Test System (LTS), presently under construction at Los Alamos, is an electromagnetic launcher facility designed to perform impact experiments at velocities up to 15 km/s. The launcher is a 25 mm round bore, plasma armature railgun extending 22 m in length. Preinjection is accomplished with a two-stage gas gun capable of 7 km/s. The railgun power supply utilizes traction motors, vacuum interrupters, and pulse transformers. An assembly of 28 traction motors, equipped with flywheels, stores approximately 80 MJ at 92% of full speed and energizes the primary windings of three pulse transformers at a current of 50 kA. At peak current an array of vacuum interrupters disconnects the transformer primary windings and forces the current to flow in the secondary windings. The secondary windings are connected to the railgun, and by staging the vacuum interrupter openings, a 1 MA to 1.3 MA ramped current waveform will be delivered to the railgun.

  1. The Lethality Test System

    NASA Astrophysics Data System (ADS)

    Parsons, W. M.; Sims, J. R.; Parker, J. V.

    1986-11-01

    The Lethality Test System (LTS) under construction at Los Alamos is an electromagnetic launcher facility designed to perform impact experiments at velocities up to 15 km/sec. The launcher is a 25 mm round bore, plasma armature railgun 22 m in length. Preinjection is accomplished with a two-stage light gas gun capable of 7 km/sec. The railgun power supply utilizes traction motors, vacuum interrupters, and pulse transformers. An assembly of 28 traction motors, equipped with flywheels, stores approximately 80 MJ at 92 percent of full speed and energizes the primary windings of three pulse transformers at a current of 50 kA. At peak current an array of vacuum interrupters disconnects the transformer primary windings and forces the current to flow in the secondary windings. The secondary windings are connected to the railgun, and by staging the vacuum interrupter openings, a 1-1.3 MA ramped current waveform will be delivered to the railgun.

  2. Co-lethality studied as an asset against viral drug escape: the HIV protease case

    PubMed Central

    2010-01-01

    Background Co-lethality, or synthetic lethality is the documented genetic situation where two, separately non-lethal mutations, become lethal when combined in one genome. Each mutation is called a "synthetic lethal" (SL) or a co-lethal. Like invariant positions, SL sets (SL linked couples) are choice targets for drug design against fast-escaping RNA viruses: mutational viral escape by loss of affinity to the drug may induce (synthetic) lethality. Results From an amino acid sequence alignment of the HIV protease, we detected the potential SL couples, potential SL sets, and invariant positions. From the 3D structure of the same protein we focused on the ones that were close to each other and accessible on the protein surface, to possibly bind putative drugs. We aligned 24,155 HIV protease amino acid sequences and identified 290 potential SL couples and 25 invariant positions. After applying the distance and accessibility filter, three candidate drug design targets of respectively 7 (under the flap), 4 (in the cantilever) and 5 (in the fulcrum) amino acid positions were found. Conclusions These three replication-critical targets, located outside of the active site, are key to our anti-escape strategy. Indeed, biological evidence shows that 2/3 of those target positions perform essential biological functions. Their mutational variations to escape antiviral medication could be lethal, thus limiting the apparition of drug-resistant strains. Reviewers This article was reviewed by Arcady Mushegian, Shamil Sunyaev and Claus Wilke. PMID:20565756

  3. Molecular analysis of genetic fidelity in Cannabis sativa L. plants grown from synthetic (encapsulated) seeds following in vitro storage.

    PubMed

    Lata, Hemant; Chandra, Suman; Techen, Natascha; Khan, Ikhlas A; ElSohly, Mahmoud A

    2011-12-01

    The increasing utilization of synthetic (encapsulated) seeds for germplasm conservation and propagation necessitates the assessment of genetic stability of conserved propagules following their plantlet conversion. We have assessed the genetic stability of synthetic seeds of Cannabis sativa L. during in vitro multiplication and storage for 6 months at different growth conditions using inter simple sequence repeat (ISSR) DNA fingerprinting. Molecular analysis of randomly selected plants from each batch was conducted using 14 ISSR markers. Of the 14 primers tested, nine produced 40 distinct and reproducible bands. All the ISSR profiles from in vitro stored plants were monomorphic and comparable to the mother plant which confirms the genetic stability among the clones. GC analysis of six major cannabinoids [Δ(9)-tetrahydrocannabinol, tetrahydrocannabivarin, cannabidiol, cannabichromene, cannabigerol and cannabinol] showed homogeneity in the re-grown clones and the mother plant with insignificant differences in cannabinoids content, thereby confirming the stability of plants derived from synthetic seeds following 6 months storage. PMID:21805186

  4. Analysis of Past and Present Synthetic Methodologies on Medicinal Chemistry: Where Have All the New Reactions Gone?

    PubMed

    Brown, Dean G; Boström, Jonas

    2016-05-26

    An analysis of chemical reactions used in current medicinal chemistry (2014), three decades ago (1984), and in natural product total synthesis has been conducted. The analysis revealed that of the current most frequently used synthetic reactions, none were discovered within the past 20 years and only two in the 1980s and 1990s (Suzuki-Miyaura and Buchwald-Hartwig). This suggests an inherent high bar of impact for new synthetic reactions in drug discovery. The most frequently used reactions were amide bond formation, Suzuki-Miyaura coupling, and SNAr reactions, most likely due to commercial availability of reagents, high chemoselectivity, and a pressure on delivery. We show that these practices result in overpopulation of certain types of molecular shapes to the exclusion of others using simple PMI plots. We hope that these results will help catalyze improvements in integration of new synthetic methodologies as well as new library design. PMID:26571338

  5. The 2008 Super Tuesday Tornado Outbreak: Synthetic Dual Doppler Analysis of Contrasting Tornadic Storm Types

    NASA Technical Reports Server (NTRS)

    Knupp, Kevin R.; Coleman, Timothy; Carey, Larry; Peterson, Walt; Elkins, Calvin

    2008-01-01

    During the Super Tuesday Tornado Outbreak on 5-6 February, a significant number of storms passed within about 40 km of WSR-88D radars. This distance, combined with the significant motion vector (from the southwest at 20-25 m per second) of relatively steady storms, is amenable to a synthetic dual Doppler analysis during the times when the storms passed the WSR-88D locations. Nine storms will be analyzed using the SDD technique. The following table provides their general characteristics and nearest approach to the 88D radars. For this data set, storm structure ranges from isolated supercell to QLCS. Each storm will be analyzed for a 40-60 min period during passage by the WSR-88D radar to determine general storm properties. Analysis of high-resolution single Doppler data around the time of passage (plus or minus 30 min), combined with 1-2 SDD analyses, will be used to examine the kinematic structure of low-level circulations (e.g., mesocyclone, downdraft) and the relation to the parent storm. This analysis may provide insights on the fundamental differences between cyclonic circulations in supercell storms and those within QCLS's.

  6. Synthetic Aperture Radar (sar) and Optical Imagery Data Fusion: Crop Yield Analysis in Southeast Asia

    NASA Astrophysics Data System (ADS)

    Parks, S. M.

    2012-08-01

    With the expanding energy crisis and rising food prices, crop yield analysis in Southeast Asia is an increasingly important topic in this region. Rice is the most important food crop in Southeast Asia and the ability to accurately predict crop yields during a growing season is useful for decision-makers, aid providers, and commercial trade organizations. The use of optical satellite image data by itself is difficult due to the almost constant cloud in many parts of Southeast Asia. However, Synthetic Aperture Radar (SAR), or SAR data, which can image the Earth's surface through cloud cover, is suitable for many agricultural purposes, such as the detection of rice fields, and the identification of different crop species. Crop yield analysis is difficult in this region due to many factors. Rice cropping systems are often characterized by the type of rice planted, the size of rice field, the sowing dates for different fields, different types of rice cropping systems from one area to another, as well as cultural practices such as sowing and transplanting. This paper will discuss the use of SAR data fused with optical imagery to improve the ability to perform crop yield analysis on rice crops in Southeast Asia.

  7. Passive Synthetic Aperture Hitchhiker Imaging of Ground Moving Targets - Part 2: Performance Analysis.

    PubMed

    Wacks, Steven; Yazici, Birsen

    2014-07-01

    In Part 1 of this work, we present a passive synthetic aperture imaging and velocity estimation method for ground moving targets using a network of passive receivers. The method involves inversion of a Radon transform type forward model via a novel filtered backprojection approach combined with entropy optimization. The method is applicable to noncooperative transmitters of opportunity where the transmitter locations and transmitted waveforms are unknown. Furthermore, it can image multiple targets moving at different velocities in arbitrary imaging geometries. In this paper, we present a detailed analysis of the performance of our method. First the resolution analysis in position and velocity spaces is presented. The analysis identifies several factors that contribute positively or negativity towards position and velocity resolution. Next, we present a novel theory to analyze and predict smearing artifacts in position images due to error in velocity estimation of moving targets. Specifically, we show that small errors in the velocity estimation result in small positioning errors. We present extensive numerical simulations to demonstrate the theoretical results. While our primary interest lies in radar, the theory, methods and algorithms introduced in our work are also applicable to passive acoustic, seismic, and microwave imaging. PMID:25020091

  8. Cell-to-Cell Communication Circuits: Quantitative Analysis of Synthetic Logic Gates

    PubMed Central

    Hoffman-Sommer, Marta; Supady, Adriana; Klipp, Edda

    2012-01-01

    One of the goals in the field of synthetic biology is the construction of cellular computation devices that could function in a manner similar to electronic circuits. To this end, attempts are made to create biological systems that function as logic gates. In this work we present a theoretical quantitative analysis of a synthetic cellular logic-gates system, which has been implemented in cells of the yeast Saccharomyces cerevisiae (Regot et al., 2011). It exploits endogenous MAP kinase signaling pathways. The novelty of the system lies in the compartmentalization of the circuit where all basic logic gates are implemented in independent single cells that can then be cultured together to perform complex logic functions. We have constructed kinetic models of the multicellular IDENTITY, NOT, OR, and IMPLIES logic gates, using both deterministic and stochastic frameworks. All necessary model parameters are taken from literature or estimated based on published kinetic data, in such a way that the resulting models correctly capture important dynamic features of the included mitogen-activated protein kinase pathways. We analyze the models in terms of parameter sensitivity and we discuss possible ways of optimizing the system, e.g., by tuning the culture density. We apply a stochastic modeling approach, which simulates the behavior of whole populations of cells and allows us to investigate the noise generated in the system; we find that the gene expression units are the major sources of noise. Finally, the model is used for the design of system modifications: we show how the current system could be transformed to operate on three discrete values. PMID:22934039

  9. Synthetic vascular hemodialysis access vs native arteriovenous fistula: A cost-utility analysis

    PubMed Central

    Rosas, Sylvia E; Feldman, Harold I

    2011-01-01

    Objective To determine the cost-effectiveness of two different vascular access strategies among incident dialysis patients. Summary Background Data Vascular access is a principal cause of morbidity and cost in hemodialysis patients. Recent guidelines and initiatives are intended to increase the proportion of patients with a fistula. However, there is growing awareness of the high prevalence of fistula failures and attendant complications. Methods A decision analysis using a Markov model was implemented to compare two different vascular access strategies among incident dialysis patients: a) placing an arteriovenous fistula (AVF1st) as the initial access followed by a synthetic vascular access if the AVF did not mature compared to b) placing a synthetic vascular access (SVA1st) as the initial access device. The cost-utility was evaluated across a range of the risk of complications from temporary catheters and SVA. Results Under base case assumptions, the AVF1st strategy yielded 2.19 QALYs compared to 2.06 QALYs from the SVA1st strategy. The incremental cost-effectiveness was $9389/QALY for AVF1st compared to SVA1st and was less than $50,000 per QALY as long as the probability of maturation is 36% or greater. AVF1st was the dominant strategy when the AVF maturation rate was 69% or greater. Conclusion The high risk of complications of temporary catheters and the overall low AVF maturation rate explain why a universal policy of AVF 1st for all incident dialysis patients may not optimize clinical outcomes. Strong consideration should be given to a more patient-centered approach taking into account the likelihood of AVF maturation. PMID:21918428

  10. Constraining shallow seismic event depth via synthetic modeling for Expert Technical Analysis at the IDC

    NASA Astrophysics Data System (ADS)

    Stachnik, J.; Rozhkov, M.; Baker, B.; Bobrov, D.; Friberg, P. A.

    2015-12-01

    Depth of event is an important criterion of seismic event screening at the International Data Center, CTBTO. However, a thorough determination of the event depth can be conducted mostly through special analysis because the IDC's Event Definition Criteria is based, in particular, on depth estimation uncertainties. This causes a large number of events in the Reviewed Event Bulletin to have depth constrained to the surface. When the true origin depth is greater than that reasonable for a nuclear test (3 km based on existing observations), this may result in a heavier workload to manually distinguish between shallow and deep events. Also, IDC depth criterion is not applicable to the events with the small t(pP-P) travel time difference, which is the case of the nuclear test. Since the shape of the first few seconds of signal of very shallow events is very sensitive to the presence of the depth phase, cross correlation between observed and theoretic seismogram can provide an estimate for the depth of the event, and so provide an expansion to the screening process. We exercised this approach mostly with events at teleseismic and partially regional distances. We found that such approach can be very efficient for the seismic event screening process, with certain caveats related mostly to the poorly defined crustal models at source and receiver which can shift the depth estimate. We used adjustable t* teleseismic attenuation model for synthetics since this characteristic is not determined for most of the rays we studied. We studied a wide set of historical records of nuclear explosions, including so called Peaceful Nuclear Explosions (PNE) with presumably known depths, and recent DPRK nuclear tests. The teleseismic synthetic approach is based on the stationary phase approximation with Robert Herrmann's hudson96 program, and the regional modelling was done with the generalized ray technique by Vlastislav Cerveny modified to the complex source topography.

  11. Method of reliable determination of minimal lethal antibiotic concentrations.

    PubMed Central

    Pearson, R D; Steigbigel, R T; Davis, H T; Chapman, S W

    1980-01-01

    The lack of a standardized, statistically reliable method for in vitro determinations of the minimal lethal or bactericidal concentrations of antibiotics has complicated analyses of isolates of Staphylococcus aureus which appear to be inhibited but not killed by the usual concentrations of cell wall-active antibiotics. We describe a method which identifies some of the covariants involved in determinations of minimal lethal concentrations. Lethality was defined as a 99.9% reduction in the initial inoculum of bacteria after 24 h of incubation. We limited the sample volume to 0.01 ml to minimize the inhibitory effect of antibiotic and corresponding rejection values, which detected lethality with a high degree of sensitivity and specificity. When the number of colonies on subculture was equal to or less than the rejection value, the antibiotic was considered lethal for the test organism. Rejection values encompassed initial inocula from 10(5) to 10(7) colony-forming units per ml for single and duplicate samples and allowed for 1 or 5% variability in pipette volumes and errors in initial inoculum determinations. This method was used to determine the minimal lethal concentrations of semi-synthetic penicillins for S. aureau isolates, one of which was tolerant to the killing action of penicillin. Images PMID:7447427

  12. Multi-Resolution Clustering Analysis and Visualization of Around One Million Synthetic Earthquake Events

    NASA Astrophysics Data System (ADS)

    Kaneko, J. Y.; Yuen, D. A.; Dzwinel, W.; Boryszko, K.; Ben-Zion, Y.; Sevre, E. O.

    2002-12-01

    The study of seismic patterns with synthetic data is important for analyzing the seismic hazard of faults because one can precisely control the spatial and temporal domains. Using modern clustering analysis from statistics and a recently introduced visualization software, AMIRA, we have examined the multi-resolution nature of a total assemblage involving 922,672 earthquake events in 4 numerically simulated models, which have different constitutive parameters, with 2 disparately different time intervals in a 3D spatial domain. The evolution of stress and slip on the fault plane was simulated with the 3D elastic dislocation theory for a configuration representing the central San Andreas Fault (Ben-Zion, J. Geophys. Res., 101, 5677-5706, 1996). The 4 different models represent various levels of fault zone disorder and have the following brittle properties and names: uniform properties (model U), a Parkfield type Asperity (A), fractal properties (F), and multi-size-heterogeneities (model M). We employed the MNN (mutual nearest neighbor) clustering method and developed a C-program that calculates simultaneously a number of parameters related to the location of the earthquakes and their magnitude values .Visualization was then used to look at the geometrical locations of the hypocenters and the evolution of seismic patterns. We wrote an AmiraScript that allows us to pass the parameters in an interactive format. With data sets consisting of 150 year time intervals, we have unveiled the distinctly multi-resolutional nature in the spatial-temporal pattern of small and large earthquake correlations shown previously by Eneva and Ben-Zion (J. Geophys. Res., 102, 24513-24528, 1997). In order to search for clearer possible stationary patterns and substructures within the clusters, we have also carried out the same analysis for corresponding data sets with time extending to several thousand years. The larger data sets were studied with finer and finer time intervals and multi

  13. Analysis of new synthetic drugs by ion mobility time-of-flight mass spectrometry.

    PubMed

    Sysoev, Alexey A; Poteshin, Sergey S; Chernyshev, Denis M; Karpov, Alexander V; Tuzkov, Yuriy B; Kyzmin, Vyacheslav V; Sysoev, Alexander A

    2014-01-01

    Characteristic ion mobility mass spectrometry data, reduced mobility, and limits of detection (signal-to-noise ratio = 3) were determined for six synthetic drugs and cocaine by ion mobility time-of-flight mass spectrometry (IM-TOF-MS) with electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI). The studied synthetic illicit drugs recently appeared on the recreational drug market as designer drugs and were methylone, 4-MEC (4'-methylethcathinone), 3,4-MDPV (3,4-methylenedioxypyrovalerone), JWH-210 [4-ethylnaphthalen-1-yl-(1-pentylindol-3-yl)methanone], JWH-250 [2-(2-methoxyphenyl)-1-(1-pentyl-1H-indol-3-yl)ethanone], and JWH-203 [1-pentyl-3-(2'-chlorophenylacetyl) indole]. Absolute reduced mobilities in nitrogen were 1.35, 1.28, 1.41, 1.30, 1.18, 0.98, 1.09, and 1.07 cm2V(-1)s(-1), for methylone [M-H]+, methylone [M+H]+, 4-MEC [M-H]+, 4-MEC [M+H]+, 3,4-MDPV [M+H]+, JWH-210 [M+H]+, JWH-250 [M+H]+, and JWH-203 [M+H]+, respectively. Selected illicit drugs are easily identified by IM-TOF-MS during a 100s analysis. Relative Limits of detection ranged from 4 to 400 nM are demonstrated for these compounds. Such relative limits of detection correspond to 14 pg to 2 ng absolute limits of detection. Better detection limits are obtained in APCI mode for all the illicit drugs except cocaine. ESI mode was found to be preferable for the IM-TOF-MS detection of cocaine at trace levels. A single sample analysis is completed in an order of magnitude less time than that for conventional liquid chromatography/mass spectrometry approach. The application allows one to consider IM-TOF-MS as a good candidate for a method to determine quickly the recently surfaced designer drugs marketed on the internet as "bath salts," "spice," and "herbal blends". PMID:24895779

  14. [From synthetic biology to synthetic humankind].

    PubMed

    Nouvel, Pascal

    2015-01-01

    In this paper, we propose an historical survey of the expression "synthetic biology" in order to identify its main philosophical components. The result of the analysis is then used to investigate the meaning of the notion of "synthetic man". It is shown that both notions share a common philosophical background that can be summed up by the short but meaningful assertion: "biology is technology". The analysis allows us to distinguish two notions that are often confused in transhumanist literature: the notion of synthetic man and the notion of renewed man. The consequences of this crucial distinction are discussed. PMID:26238764

  15. Rare earth element concentrations in geological and synthetic samples using synchrotron X-ray fluorescence analysis

    USGS Publications Warehouse

    Chen, J.R.; Chao, E.C.T.; Back, J.M.; Minkin, J.A.; Rivers, M.L.; Sutton, S.R.; Cygan, G.L.; Grossman, J.N.; Reed, M.J.

    1993-01-01

    The concentrations of rare earth elements (REEs) in specific mineral grains from the Bayan Obo ore deposit and synthetic high-silica glass samples have been measured by synchrotron X-ray fluorescence (SXRF) analysis using excitation of the REE K lines between 33 and 63 keV. Because SXRF, a nondestructive analytical technique, has much lower minimum detection limits (MDLs) for REEs, it is an important device that extends the in situ analytical capability of electron probe microanalysis (EPMA). The distribution of trace amounts of REEs in common rock-forming minerals, as well as in REE minerals and minerals having minor quantities of REEs, can be analyzed with SXRF. Synchrotron radiation from a bending magnet and a wiggler source at the National Synchrotron Light Source, Brookhaven National Laboratory, was used to excite the REEs. MDLs of 6 ppm (La) to 26 ppm (Lu) for 3600 s in 60-??m-thick standard samples were obtained with a 25-??m diameter wiggler beam. The MDLs for the light REEs were a factor of 10-20 lower than the MDLs obtained with a bending magnet beam. The SXRF REE concentrations in mineral grains greater than 25 ??m compared favorably with measurements using EPMA. Because EPMA offered REE MDLs as low as several hundred ppm, the comparison was limited to the abundant light REEs (La, Ce, Pr, Nd). For trace values of medium and heavy REEs, the SXRF concentrations were in good agreement with measurements using instrumental neutron activation analysis (INAA), a bulk analysis technique. ?? 1993.

  16. A new mixed micellar electrokinetic chromatography method for analysis of natural and synthetic anabolic steroids.

    PubMed

    Zhang, Lan; Chen, Jinfeng; He, Yu; Chi, Yuwu; Chen, Guonan

    2009-01-15

    A simple, rapid and low-costing new mixed surfactant MEKC method has been developed for the analysis of five neutral anabolic steroids in this paper. It was found that the bile salt coupling with Triton X-100 was a suitable bi-micellar surfactant for the separation of these anabolic steroids with similar structure. The separation conditions were optimized in detail. The five natural and synthetic anabolic steroids, such as androstenedione (AD), 19-norandrostenedione (NAD), 1,4-androstadiene-3,17-dione (ADD), methandrostenolone (MA) and methyltestosterone (MT) were separated and detected in an alkaline buffer system (pH 9.0) containing 15 mM Britton-Robinson (BR) buffer, 50mM sodium cholate (SC) and 0.1% (v/v) Triton X-100 with detection wavelength at 241 nm and 18 kV of separation voltage. Under the optimal conditions, five coexistence neutral steroids were completely separated within 12 min with the detection limits ranged from 0.20 to 0.51 microg/mL. This method was successfully used for detection and confirmation of the anabolic steroid methandrostenolone in methandrostenolone tablets and in the real human urine, GC-MS method was applied to confirm the free methandrostenolone existence in the urine sample in order to validate the reliability of MEKC method. PMID:19064082

  17. Synthetic spectral analysis of a kinetic model for slow-magnetosonic waves in solar corona

    NASA Astrophysics Data System (ADS)

    Ruan, Wenzhi; He, Jiansen; Zhang, Lei; Vocks, Christian; Marsch, Eckart; Tu, Chuanyi; Peter, Hardi; Wang, Linghua

    2016-03-01

    We propose a kinetic model of slow-magnetosonic waves to explain various observational features associated with the propagating intensity disturbances (PIDs) occurring in the solar corona. The characteristics of slow mode waves, e.g, inphase oscillations of density, velocity, and thermal speed, are reproduced in this kinetic model. Moreover, the red-blue (R-B) asymmetry of the velocity distribution as self-consistently generated in the model is found to be contributed from the beam component, as a result of the competition between Landau resonance and Coulomb collisions. Furthermore, we synthesize the spectral lines and make the spectral analysis, based on the kinetic simulation data of the flux tube plasmas and the hypothesis of the surrounding background plasmas. It is found that the fluctuations of parameters of the synthetic spectral lines are basically consistent with the observations: (1) the line intensity, Doppler shift, and line width are fluctuating in phase; (2) the R-B asymmetry usually oscillate out of phase with the former three parameters; (3) the blueward asymmetry is more evident than the redward asymmetry in the R-B fluctuations. The oscillations of line parameters become weakened for the case with denser surrounding background plasmas. Similar to the observations, there is no doubled-frequency oscillation of the line width for the case with flux-tube plasmas flowing bulkly upward among the static background plasmas. Therefore, we suggest that the "wave + beam flow" kinetic model may be a viable interpretation for the PIDs observed in the solar corona.

  18. ATLAS Versus NextGen Model Atmospheres: A Combined Analysis of Synthetic Spectral Energy Distributions

    NASA Astrophysics Data System (ADS)

    Bertone, E.; Buzzoni, A.; Chávez, M.; Rodríguez-Merino, L. H.

    2004-08-01

    We carried out a critical appraisal of the two theoretical models, Kurucz' ATLAS9 and PHOENIX/NextGen, for stellar atmosphere synthesis. Our tests relied on the theoretical fit of spectral energy distributions (SEDs) for a sample of 334 target stars along the whole spectral-type sequence, from the classical optical catalogs of Gunn & Stryker and Jacoby et al. The best-fitting physical parameters (Teff, logg) of stars allowed an independent calibration of the temperature and bolometric scale versus empirical classification parameters (i.e., spectral type and MK luminosity class); in addition, the comparison of the synthetic templates from the ATLAS and NextGen grids allowed us to probe the capability of the models to match spectrophotometric properties of real stars and assess the impact of the different input physics. We can sketch the following main conclusions of our analysis: (1) Fitting accuracy of both theoretical libraries drastically degrades at low Teff at which both ATLAS and NextGen models still fail to properly account for the contribution of molecular features in the observed SED of K-M stars. (2) Compared with empirical calibrations, both ATLAS and NextGen fits tend, on average, to predict slightly warmer (by 4%-8%) Teff for both giant and dwarf stars of fixed spectral type, but ATLAS provides, in general, a sensibly better fit (a factor of 2 lower σ of flux residuals) than NextGen. (3) There is a striking tendency of NextGen to label target stars with an effective temperature and surface gravity higher than that of ATLAS. The effect is especially evident for MK I-III objects for which about one in four stars is clearly misclassified by NextGen in logg. This is a consequence of some ``degeneracy'' in the solution space, partly induced by the different input physics and geometry constraints in the computation of the integrated emerging flux (ATLAS model atmospheres assume standard plane-parallel layers, while NextGen adopts, for low-gravity stars, a

  19. A kinematic analysis of the spine during rugby scrummaging on natural and synthetic turfs

    PubMed Central

    Swaminathan, Ramesh; Williams, Jonathan M.; Jones, Michael D.; Theobald, Peter S.

    2016-01-01

    ABSTRACT Artificial surfaces are now an established alternative to grass (natural) surfaces in rugby union. Little is known, however, about their potential to reduce injury. This study characterises the spinal kinematics of rugby union hookers during scrummaging on third-generation synthetic (3G) and natural pitches. The spine was sectioned into five segments, with inertial sensors providing three-dimensional kinematic data sampled at 40 Hz/sensor. Twenty-two adult, male community club and university-level hookers were recruited. An equal number were analysed whilst scrummaging on natural or synthetic turf. Players scrummaging on synthetic turf demonstrated less angular velocity in the lower thoracic spine for right and left lateral bending and right rotation. The general reduction in the range of motion and velocities, extrapolated over a prolonged playing career, may mean that the synthetic turf could result in fewer degenerative injuries. It should be noted, however, that this conclusion considers only the scrummaging scenario. PMID:26375051

  20. A kinematic analysis of the spine during rugby scrummaging on natural and synthetic turfs.

    PubMed

    Swaminathan, Ramesh; Williams, Jonathan M; Jones, Michael D; Theobald, Peter S

    2016-01-01

    Artificial surfaces are now an established alternative to grass (natural) surfaces in rugby union. Little is known, however, about their potential to reduce injury. This study characterises the spinal kinematics of rugby union hookers during scrummaging on third-generation synthetic (3G) and natural pitches. The spine was sectioned into five segments, with inertial sensors providing three-dimensional kinematic data sampled at 40 Hz/sensor. Twenty-two adult, male community club and university-level hookers were recruited. An equal number were analysed whilst scrummaging on natural or synthetic turf. Players scrummaging on synthetic turf demonstrated less angular velocity in the lower thoracic spine for right and left lateral bending and right rotation. The general reduction in the range of motion and velocities, extrapolated over a prolonged playing career, may mean that the synthetic turf could result in fewer degenerative injuries. It should be noted, however, that this conclusion considers only the scrummaging scenario. PMID:26375051

  1. Coal conversion processes and analysis methodologies for synthetic fuels production. [technology assessment and economic analysis of reactor design for coal gasification

    NASA Technical Reports Server (NTRS)

    1979-01-01

    Information to identify viable coal gasification and utilization technologies is presented. Analysis capabilities required to support design and implementation of coal based synthetic fuels complexes are identified. The potential market in the Southeast United States for coal based synthetic fuels is investigated. A requirements analysis to identify the types of modeling and analysis capabilities required to conduct and monitor coal gasification project designs is discussed. Models and methodologies to satisfy these requirements are identified and evaluated, and recommendations are developed. Requirements for development of technology and data needed to improve gasification feasibility and economies are examined.

  2. Gonadosomatic mosaicism for lethal mutations in Drosophila lethal mutations disturbing larval development

    SciTech Connect

    Ivanov, A.I.; Sakharova, N.Yu.

    1988-11-01

    Phenogenetic analysis of autonomous lethal mutations obtained by the method of gonadosomatic mosaicism which manifested during larval stages, established that the nuclei of hypodermal cells, salivary glands suprapharyngeal ganglion, pharynx, esophagus, gizzard, and hindgut are the derivatives of the same nucleus (from the first two nuclei of cleavage) as the nuclei of the cells of the imaginal-somatic tissues.

  3. Nucleus anomaly test and chromosomal analysis of bone marrow cells of the Chinese hamster and dominant lethal test in male mice after treatment with fluorescent whitening agents.

    PubMed

    Müller, D; Fritz, H; Langauer, M; Strasser, F F

    1975-01-01

    Four fluorescent whitening agents (FWAs) were tested for mutagenic activity after oral administration in the following three different mammalian test systems: (1) Dominant lethal test in the male mouse; (2) Cytogenetic studies on metaphase chromosomes from the bone marrow of the Chinese hamster; (3) Nucleus anomaly test in somatic interphase cells (bone marrow) of the Chinese hamster. These investigations yielded no evidence of dominant lethal effects of any of the four compounds on the progeny of male mice. Furthermore, the data obtained from chromosome analyses and the nucleus anomaly test revealed no effects at all. Thus, the results obtained in all these tests gave no indication of mutagenic activity after the administration of these compounds in dosages up to approximately 1/3 or the LD50. PMID:1064545

  4. Synthetic Aperture Radar Interferometry Analysis of Ground Deformation within the Coso Geothermal Site, California

    NASA Astrophysics Data System (ADS)

    Brawner, Erik

    Earth's surface movement may cause as a potential hazard to infrastructure and people. Associated earthquake hazards pose a potential side effect of geothermal activity. Modern remote sensing techniques known as Interferometric Synthetic Aperture Radar (InSAR) can measure surface change with a high degree of precision to mm scale movements. Previous work has identified a deformation anomaly within the Coso Geothermal site in eastern California. Surface changes have not been analyzed since the 1990s, allowing a decade of geothermal production impact to occur since previously assessed. In this study, InSAR data was acquired and analyzed between the years 2005 and 2010. Acquired by the ENVISAT satellite from both ascending and descending modes. This provides an independent dataset from previous work. Incorporating data generated from a new sensor covering a more modern temporal study period. Analysis of this time period revealed a subsidence anomaly in correlation with the extents of the geothermal production area under current operation. Maximum subsidence rates in the region reached approximately 3.8 cm/yr. A similar rate assessed from previous work throughout the 1990s. The correlation of subsidence patterns suggests a linear source of deformation from measurements spanning multiple decades. Regions of subsidence branch out from the main anomaly to the North-Northeast and to the South where additional significant peaks of subsidence occurring. The extents of the deformation anomaly directly correlate with the dispersal of geothermal production well site locations. Depressurization within the geothermal system provides a leading cause to surface subsidence from excessive extraction of hydrothermal fluids. As a result of minimal reinjection of production fluids.

  5. Retrospective analysis of synthetic cannabinoids in serum samples--epidemiology and consumption patterns.

    PubMed

    Jaenicke, Nathalie J; Pogoda, Werner; Paulke, Alexander; Wunder, Cora; Toennes, Stefan W

    2014-09-01

    Herbal mixtures contain synthetic cannabinoids, which can cause severe intoxications. Due to the great variety and the changing spectrum of substances on the drug market, prevalence data are limited, and data on prevalence rates of synthetic cannabinoids in forensic cases are not available. The present study was performed to survey the prevalence of synthetic cannabinoids in cases of traffic and criminal offences in the German state Hesse in 2010. The applied analytical method covered all synthetic cannabinoids on the drug market at that time, and with 20% of the blood samples (422 out of 2201) a representative number was reanalyzed. In twelve samples synthetic cannabinoids were identified and a prevalence of 2.8% was estimated. Consumption patterns showed predominantly cases of multi-drug consumption (10 cases); the combination with cannabis or alcohol was frequent (four cases each). The observed deficits were moderate with the exception of aggravation of paranoia in one case. The symptoms were either compatible with the effects of cannabinoid agonists or attributable to alcohol or other drugs found in the blood samples. Our current analytical strategy is to perform such analyses only in cases where use is suspected or where symptoms are not explained by routine toxicological analyses. Hence, the positive rate is rather low highlighting the need to keep up with the developments on the drug market and to establish sensitive screening methods covering a broad range of substances that can be updated fast, e.g., relying on collections of mass spectrometric reference data. PMID:25050839

  6. Analysis of synthetic motor oils for additive elements by ICP-AES

    SciTech Connect

    Williams, M.C.; Salmon, S.G.

    1995-12-31

    Standard motor oils are made by blending paraffinic or naphthenic mineral oil base stocks with additive packages containing anti-wear agents, dispersants, corrosion inhibitors, and viscosity index improvers. The blender can monitor the correct addition of the additives by determining the additive elements in samples dissolved in a solvent by ICP-AES. Internal standardization is required to control sample transport interferences due to differences in viscosity between samples and standards. Synthetic motor oils, made with poly-alpha-olefins and trimethylol propane esters, instead of mineral oils, pose an additional challenge since these compounds affect the plasma as well as having sample transport interference considerations. The synthetic lubricant base stocks add significant oxygen to the sample matrix, which makes the samples behave differently than standards prepared in mineral oil. Determination of additive elements in synthetic motor oils will be discussed.

  7. Analysis of the structure of synthetic and natural melanins by solid-phase

    SciTech Connect

    Duff, G.A.; Roberts, J.E.; Foster, N.

    1988-09-06

    The structures of one synthetic and two natural melanins are examined by solid-state NMR using cross polarization, magic angle sample spinning, and high-power proton decoupling. The structural features of synthetic dopa malanin are compared to those of melanin from malignant melanoma cells grown in culture and sepia melanin from squid ink. Natural abundance /sup 13/C and /sup 15/N spectra show resonances consistent with known pyrrolic and indolic structures within the heterogeneous biopolymer; /sup 13/C spectra indicate the presence of aliphatic residues in all three materials. These solid-phase experiments illustrate the promise of solid-phase NMR for elucidating structural from insoluble biomaterials.

  8. Synthetic profile analysis of the observed (0,0) Swan band of Comet Halley

    SciTech Connect

    Krishna swamy, K.S. )

    1991-05-01

    The time-dependent rotational population distribution for the (0,0) band of the Swan system was carried out. These population distributions are used to calculate the synthetic spectra over the wavelength region 5165-5132 A for comparing with the excellent spectra of Lambert et al. (1990) for Comet Halley. The synthetic spectra for the rotational population distribution corresponding to a time interval of about 8000 sec gives a good fit to the observed spectra over the whole special region. This seems to indicate that the level population does not appear to have reached the steady state values. 16 refs.

  9. Hair analysis as a tool to evaluate the prevalence of synthetic cannabinoids in different populations of drug consumers.

    PubMed

    Salomone, A; Luciano, C; Di Corcia, D; Gerace, E; Vincenti, M

    2014-01-01

    Among the new psychoactive products, herbal mixtures containing synthetic cannabimimetics are likely the most abused worldwide. In this study, a specific ultra high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method for the detection of 23 synthetic cannabinoids in hair samples was developed in order to (1) expand the number of screened compounds, coherent with new substances emerging in the European territory, (2) evaluate their consumption on a large period of examination, and (3) evaluate the diffusion of cannabimimetics among different populations of drug consumers. The method employs digestion of hair sample with NaOH followed by extraction with n-hexane/ethylacetate, and injection into the UHPLC-MS/MS system. After validation, the method was applied to the analysis of 344 hair samples previously tested in our laboratory for the most common drugs. Overall, 15 samples were found positive for at least one synthetic cannabinoid. Coherent with previously published results, the present data show that young males, former or still active Cannabis consumers, represent the population most often involved in synthetic cannabimimetics consumption. Several cases of poly-abuse were also determined. The drug most frequently detected was JWH-073 (11 samples) generally at low concentration (mean 7.69 ± 14.4 pg/mg, median 1.9 pg/mg, range 1.6-50.5 pg/mg), followed by JWH-122 (8 samples, mean concentration: 544 ± 968 pg/mg, median 28.4 pg/mg, range 7.4-2800 pg/mg). Other detected drugs included JWH-250, JWH-081, JWH-018, JWH-210, JWH-019, and AM-1220. For several positive samples, the synthetic cannabinoid concentration was lower than 50 pg/mg, underlining the need for established cut-off values for discrimination between chronic consumption and occasional use (or external contamination). PMID:24115381

  10. Definition of lethality thresholds for KE less-lethal projectiles

    NASA Astrophysics Data System (ADS)

    Cuadros, Jaime H.

    1997-01-01

    The interest in the definition and application of the lethality threshold for KE less-lethal projectiles has increased in the last few years, as the demand for proper use of these weapons has increased from the public at large and the law enforcement community. Experiments have been performed and reported utilizing commercially available projectiles in 12 ga., 37 mm against an anthropomorphic dummy and damage criteria developed by the automobile industry. The utility of the method is discussed and future trends are presented.

  11. An Assessment of Social Welfare in Spain: Territorial Analysis Using a Synthetic Welfare Indicator

    ERIC Educational Resources Information Center

    Espina, Pilar Zarzosa; Arechavala, Noelia Somarriba

    2013-01-01

    The aim of this paper is measure social welfare in Spanish provinces. To achieve this, we use the distance method P[subscript 2] to compose a synthetic indicator of welfare for 2007, the last year for which data are available. The index comprises information on different social indicators from various life domains and enables a classification of…

  12. Analysis of synthetic and biological microparticles on several flow cytometric platforms

    EPA Science Inventory

    Microparticles (MPs) are membrane vesicles (0.1 to 1 urn) released from cells upon activation. The limit of detection ofmost standard flow cytometers is just below 1 urn. Recent advances enable detection of particles lower than 0.5 urn, Synthetic. beads are used to define size ra...

  13. Analysis of risk factors associated with vaginal erosion after synthetic sling procedures for stress urinary incontinence.

    PubMed

    Chen, Huey-Yi; Ho, Ming; Hung, Yao-Ching; Huang, Li-Chia

    2008-01-01

    The goal of this study was to analyze the risk factors associated with vaginal erosion after synthetic sling procedure for stress urinary incontinence. Follow-up evaluations were at 1 week, 1 to 3 months, 6 months, and annually after the operation. The evaluations included detailed history taking, vaginal examinations, and perineal ultrasonographic urethrocystography. The vaginal erosion rate (6/239) after the synthetic sling procedure was 2.5%. We assessed the relationship between clinical features and vaginal erosion. Of these, only diabetes mellitus (DM) was a significant risk factor for vaginal erosion. Women with DM were 8.3 times more at risk than women without DM for developing vaginal erosion after synthetic sling procedure (p < 0.05). The vaginal erosion-free rate during the 24-month follow-up decreased significantly in women with DM. The rate of vaginal erosion associated with type III multifilamentous polypropylene sling (intravaginal slingplasty) is 10.7% more than that with type I monofilament polypropylene sling (such as tension-free vaginal tape and inside out transobturator vaginal tape) (p = 0.054). Women with DM should be informed that vaginal erosion is a possible complication after synthetic sling procedure. PMID:17594046

  14. Evaluation and haplotype analysis of elite synthetic hexaploid wheat lines for resistance to Hessian fly

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Synthetic hexaploid wheat (SHW), derived from tetraploid wheat ' Aegilops tauschii hybrid, is an excellent source of resistance genes for various diseases and insects in wheat. The objectives of this study were to evaluate the elite SHW lines developed at the International Maize and Wheat Improvemen...

  15. Molecular genetic analysis of the Influenza A(H1N1)pdm09 virus from lethal and recovered cases in Russia from 2009 to 2014: Deletions in the nucleoprotein.

    PubMed

    Yatsyshina, Svetlana; Renteeva, Anna; Deviatkin, Andrei; Vorobyeva, Nadezhda; Minenko, Angrey; Valdokhina, Anna; Elkina, Mariya; Kuleshov, Konstantin; Shipulin, German

    2015-08-01

    Influenza A(H1N1)pdm09 virus caused about 2000 laboratory confirmed lethal cases in Russia during 2009-2010 and 1302, 135 and 29 cases in the 2010-2011, 2012-2013 and 2013-2014 seasons respectively. The on average short duration (7.8±5 days) of lethal cases of Influenza A(H1N1)pdm09 infections in Russia suggests primary viral rather than secondary bacterial pneumonia. Hemorrhagic syndrome was recorded in 36.6% of patients. An examination of 221 lung samples from lethal influenza cases for the presence of bacterial DNA that could cause pneumonia did not reveal bacterial superinfections in 86% of cases. Molecular-genetic analyses of Influenza A(H1N1)pdm09 viruses from lethal and recovered cases were performed. Amino acids G and N at position 222 of the influenza virus hemagglutinin, which increase the affinity for the lower respiratory tract receptors, were detected more often in the lungs of patients who died than in respiratory swabs collected from recovered patients (p<0.0001 and p=0.007). Viruses harboring various mutations (222D/G/N/S) was significantly associated with lung samples compared with respiratory swabs from recovered patients (p<0.0001). Amino acid 222E, which increases the affinity for upper respiratory tract receptors, was found more frequently in recovered patients than in patients with lethal disease (27% versus 3%, p=0.005). Phylogenetic analysis identified an isolated cluster of viruses in the 2009-2010 season that harbored amino acid 222E, which could explain the high transmissibility of the virus at the beginning of the pandemic. Bayesian skyline plot implied a decline in the effective population size of Influenza A(H1N1)pdm09 viruses in Russia from 2010-2011 to 2011-2012, followed by an increase in 2012-2013; this trend was accompanied by the increased genetic diversity of the hemagglutinin antigenic sites. Mutations of viral RNA leading to oseltamivir resistance were found in 2.8% of tested patients during only 2010-2011 season. Deletions

  16. Genome-wide association for grain morphology in synthetic hexaploid wheats using digital imaging analysis

    PubMed Central

    2014-01-01

    Background Grain size and shape greatly influence grain weight which ultimately enhances grain yield in wheat. Digital imaging (DI) based phenomic characterization can capture the three dimensional variation in grain size and shape than has hitherto been possible. In this study, we report the results from using digital imaging of grain size and shape to understand the relationship among different components of this trait, their contribution to enhance grain weight, and to identify genomic regions (QTLs) controlling grain morphology using genome wide association mapping with high density diversity array technology (DArT) and allele-specific markers. Results Significant positive correlations were observed between grain weight and grain size measurements such as grain length (r = 0.43), width, thickness (r = 0.64) and factor from density (FFD) (r = 0.69). A total of 231 synthetic hexaploid wheats (SHWs) were grouped into five different sub-clusters by Bayesian structure analysis using unlinked DArT markers. Linkage disequilibrium (LD) decay was observed among DArT loci > 10 cM distance and approximately 28% marker pairs were in significant LD. In total, 197 loci over 60 chromosomal regions and 79 loci over 31 chromosomal regions were associated with grain morphology by genome wide analysis using general linear model (GLM) and mixed linear model (MLM) approaches, respectively. They were mainly distributed on homoeologous group 2, 3, 6 and 7 chromosomes. Twenty eight marker-trait associations (MTAs) on the D genome chromosomes 2D, 3D and 6D may carry novel alleles with potential to enhance grain weight due to the use of untapped wild accessions of Aegilops tauschii. Statistical simulations showed that favorable alleles for thousand kernel weight (TKW), grain length, width and thickness have additive genetic effects. Allelic variations for known genes controlling grain size and weight, viz. TaCwi-2A, TaSus-2B, TaCKX6-3D and TaGw2-6A, were also associated

  17. Analysis of the Greenland Ice Sheet's surface hydrology using Synthetic Aperture Radar imagery

    NASA Astrophysics Data System (ADS)

    Miles, Katie; Benedek, Corinne; Tedesco, Marco; Willis, Ian

    2016-04-01

    The behaviour of surface water on the Greenland Ice Sheet (GrIS) has recently received much attention due to its ponding to form supraglacial lakes. These can drain and impact ice sheet dynamics by facilitating increased basal sliding, thus leading to a more rapid transfer of ice to the oceans and contributing to rising sea levels. Research into supraglacial lakes has primarily used the optical and infrared wavelength bands of MODIS due to their high temporal resolution. However, this comes with an associated low spatial resolution, potentially resulting in smaller lakes being overlooked, and an inability to image through clouds or in darkness. Conversely, Synthetic Aperture Radar (SAR), a satellite-borne active imaging method uses microwave wavelength bands which are unaffected by cloud or lack of illumination from the sun. SAR imagery often has a much higher spatial resolution than optical imagery without compromising temporal resolution, and radar systems have even detected lakes covered by ice/snow or buried at shallow depths [Koenig et al., 2015]. This gives SAR imagery the potential to significantly increase the size of the database of supraglacial lakes. The current Sentinel-1A mission comprises two polar-orbiting satellites performing C-band SAR imaging, and provides a novel method for investigating the surface hydrology of the GrIS. Here, we explore a year's worth of images since the launch of Sentinel-1A in April 2014. These images have a higher spatial (5 m x 20 m) and temporal (up to daily) resolution than any previously available imagery, so will revolutionise the amount of information that can be yielded about GrIS hydrology. We use these images in combination with other remotely sensed data, including Landsat-8 imagery, to elicit spatial and temporal variations in the water content of the GrIS's surface ice layers. Our primary focus is on the area upstream of Jakobshavn Isbræ, where preliminary analysis has indicated that liquid water may persist

  18. Synthetic fuels

    SciTech Connect

    Sammons, V.O.

    1980-01-01

    This guide is designed for those who wish to learn more about the science and technology of synthetic fuels by reviewing materials in the collections of the Library of Congress. This is not a comprehensive bibliography, it is designed to put the reader on target. Subject headings used by the Library of Congress under which books on synthetic fuels can be located are: oil-shale industry; oil-shales; shale oils; synthetic fuels; synthetic fuels industry; coal gasification; coal liquefaction; fossil fuels; hydrogen as fuel; oil sands; petroleum, synthesis gas; biomass energy; pyrolysis; and thermal oil recovery. Basic texts, handbooks, government publications, journals, etc. were included. (DP)

  19. Analysis of ligand binding to the synthetic dodecapeptide 185-196 of the acetylcholine receptor alpha subunit.

    PubMed

    Neumann, D; Barchan, D; Fridkin, M; Fuchs, S

    1986-12-01

    A synthetic dodecapeptide corresponding to residues 185-196 of the Torpedo acetylcholine receptor alpha subunit, which contains the adjacent cysteine residues at positions 192 and 193, was recently shown by us to contain the essential elements for alpha-bungarotoxin binding. In the present study, we have used Sepharose-linked peptides for quantitative analysis of the cholinergic binding properties of this and other synthetic peptides. Sepharose-linked peptides corresponding to residues 1-20, 126-143, 143-158, 169-181, 185-196, 193-210, and 394-409 of the alpha subunit of Torpedo acetylcholine receptor, as well as a peptide corresponding to residues 185-196 of the alpha subunit of human acetylcholine receptor, were tested for their toxin-binding capacity. Of these immobilized peptides, only peptide 185-196 of the Torpedo acetylcholine receptor bound toxin significantly, thus verifying that this synthetic peptide contains essential components of the receptor toxin-binding site. Analysis of toxin binding to the peptide yielded a dissociation constant of 3.5 X 10(-5) M. This binding was inhibited by various cholinergic ligands. The inhibition potency obtained was alpha-bungarotoxin greater than Naja naja siamensis toxin greater than d-tubocurarine greater than decamethonium greater than acetylcholine greater than carbamoylcholine. This pharmacological profile resembles that of the nicotinic acetylcholine receptor and therefore suggests that the synthetic dodecapeptide also includes the neurotransmitter binding site. Reduction and carboxymethylation of the cysteine residues on peptide 185-196 inhibit its capacity to bind toxin, demonstrating that an intact disulfide is required for toxin binding. A decrease in toxin binding was also obtained following chemical modification of the tryptophan residue at position 187, thus implying its possible involvement in toxin binding. The failure to detect binding of toxin to the corresponding human sequence 185-196, in which the

  20. Analysis of ligand binding to the synthetic dodecapeptide 185-196 of the acetylcholine receptor alpha subunit.

    PubMed Central

    Neumann, D; Barchan, D; Fridkin, M; Fuchs, S

    1986-01-01

    A synthetic dodecapeptide corresponding to residues 185-196 of the Torpedo acetylcholine receptor alpha subunit, which contains the adjacent cysteine residues at positions 192 and 193, was recently shown by us to contain the essential elements for alpha-bungarotoxin binding. In the present study, we have used Sepharose-linked peptides for quantitative analysis of the cholinergic binding properties of this and other synthetic peptides. Sepharose-linked peptides corresponding to residues 1-20, 126-143, 143-158, 169-181, 185-196, 193-210, and 394-409 of the alpha subunit of Torpedo acetylcholine receptor, as well as a peptide corresponding to residues 185-196 of the alpha subunit of human acetylcholine receptor, were tested for their toxin-binding capacity. Of these immobilized peptides, only peptide 185-196 of the Torpedo acetylcholine receptor bound toxin significantly, thus verifying that this synthetic peptide contains essential components of the receptor toxin-binding site. Analysis of toxin binding to the peptide yielded a dissociation constant of 3.5 X 10(-5) M. This binding was inhibited by various cholinergic ligands. The inhibition potency obtained was alpha-bungarotoxin greater than Naja naja siamensis toxin greater than d-tubocurarine greater than decamethonium greater than acetylcholine greater than carbamoylcholine. This pharmacological profile resembles that of the nicotinic acetylcholine receptor and therefore suggests that the synthetic dodecapeptide also includes the neurotransmitter binding site. Reduction and carboxymethylation of the cysteine residues on peptide 185-196 inhibit its capacity to bind toxin, demonstrating that an intact disulfide is required for toxin binding. A decrease in toxin binding was also obtained following chemical modification of the tryptophan residue at position 187, thus implying its possible involvement in toxin binding. The failure to detect binding of toxin to the corresponding human sequence 185-196, in which the

  1. 77 FR 6548 - Notice of Availability of Ballistic Survivability, Lethality and Vulnerability Analyses

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-08

    ... Laboratory's (ARL's), Survivability, Lethality Analysis Directorate (SLAD) is a leader in ballistic..., telephone (410) 278- 5028. For further technical information, please contact Denise Jordan, (410)...

  2. Generation of synthetic image sequences for the verification of matching and tracking algorithms for deformation analysis

    NASA Astrophysics Data System (ADS)

    Bethmann, F.; Jepping, C.; Luhmann, T.

    2013-04-01

    This paper reports on a method for the generation of synthetic image data for almost arbitrary static or dynamic 3D scenarios. Image data generation is based on pre-defined 3D objects, object textures, camera orientation data and their imaging properties. The procedure does not focus on the creation of photo-realistic images under consideration of complex imaging and reflection models as they are used by common computer graphics programs. In contrast, the method is designed with main emphasis on geometrically correct synthetic images without radiometric impact. The calculation process includes photogrammetric distortion models, hence cameras with arbitrary geometric imaging characteristics can be applied. Consequently, image sets can be created that are consistent to mathematical photogrammetric models to be used as sup-pixel accurate data for the assessment of high-precision photogrammetric processing methods. In the first instance the paper describes the process of image simulation under consideration of colour value interpolation, MTF/PSF and so on. Subsequently the geometric quality of the synthetic images is evaluated with ellipse operators. Finally, simulated image sets are used to investigate matching and tracking algorithms as they have been developed at IAPG for deformation measurement in car safety testing.

  3. Analysis of Microbe-Associated Molecular Pattern-Responsive Synthetic Promoters with the Parsley Protoplast System.

    PubMed

    Kanofsky, Konstantin; Lehmeyer, Mona; Schulze, Jutta; Hehl, Reinhard

    2016-01-01

    Plants recognize pathogens by microbe-associated molecular patterns (MAMPs) and subsequently induce an immune response. The regulation of gene expression during the immune response depends largely on cis-sequences conserved in promoters of MAMP-responsive genes. These cis-sequences can be analyzed by constructing synthetic promoters linked to a reporter gene and by testing these constructs in transient expression systems. Here, the use of the parsley (Petroselinum crispum) protoplast system for analyzing MAMP-responsive synthetic promoters is described. The synthetic promoter consists of four copies of a potential MAMP-responsive cis-sequence cloned upstream of a minimal promoter and the uidA reporter gene. The reporter plasmid contains a second reporter gene, which is constitutively expressed and hence eliminates the requirement of a second plasmid used as a transformation control. The reporter plasmid is transformed into parsley protoplasts that are elicited by the MAMP Pep25. The MAMP responsiveness is validated by comparing the reporter gene activity from MAMP-treated and untreated cells and by normalizing reporter gene activity using the constitutively expressed reporter gene. PMID:27557767

  4. Atomic force microscopy analysis of synthetic membranes applied in release studies

    NASA Astrophysics Data System (ADS)

    Olejnik, Anna; Nowak, Izabela

    2015-11-01

    Synthetic membranes are commonly used in drug release studies and are applied mostly in quality control. They contain pores through which the drug can be diffused directly into the receptor fluid. Investigation of synthetic membranes permits determination of their structure and characterization of their properties. We suggest that the preliminary characterization of the membranes can be relevant to the interpretation of the release results. The aim of this study was to compare eight synthetic membranes by using atomic force microscopy in order to predict and understand their behavior in the release experiments. The results proved that polytetrafluoroethylene membrane was not suitable for the release study of tetrapeptide due to its hydrophobic nature, thickness and the specific structure with high trapezoid shaped blocks. The additional substructures in pores of mixed cellulose esters and nylon membranes detected by AFM influenced the diffusion rate of the active compound. These findings indicate that the selection of the membrane for the release studies should be performed cautiously by taking into consideration the membrane properties and by analyzing them prior the experiment.

  5. [Lethal intoxication with baclofen].

    PubMed

    Dukova, O A; Pokrovsky, A A; Melent'ev, A V; Krasnov, E A; Suvorova, E V; Efremov, A A

    2015-01-01

    The objective of the present study was to select and develop simpler methods for the quantitative determination of baclofen in blood with the use of HPLC and tandem MS (MS-MS) techniques and its qualitative determination in cadaveric organs by the GC/MS technique. These mathods were shown to be suitable for the purpose of forensic medical analysis, clinical, toxicological, and therapeutic monitoring. The special emphasis is laid on the methods used to investigate the biological materials obtained from the subjects who died from baclofen intoxication. PMID:25874317

  6. Numerical analysis of thermally assisted spin-transfer torque magnetization reversal in synthetic ferrimagnetic free layers

    SciTech Connect

    Shen, J.; Shi, M.; Tanaka, T. Matsuyama, K.

    2015-05-07

    The spin transfer torque magnetization reversal of synthetic ferrimagnetic free layers under pulsed temperature rise was numerically studied by solving the Landau–Lifshitz–Gilbert equation, taking into account the stochastic random fields, the temperature dependence of magnetic parameters, and the spin torque terms. The anti-parallel magnetization configuration was retained at the elevated temperature, due to interlayer dipole coupling. A significant thermal assistance effect, resulting in a 40% reduction in the switching current, was demonstrated during a nanosecond pulsed temperature rise up to 77% of the Curie temperature.

  7. Direct spectrophotometric method for analysis of food supplements containing synthetic polyhydroquinones

    NASA Astrophysics Data System (ADS)

    Vasilevsky, A. M.; Konoplev, G. A.; Stepanova, O. S.; Toropov, D. K.; Zagorsky, A. L.

    2016-04-01

    A novel direct spectrophotometric method for quantitative determination of Oxiphore® drug substance (synthetic polyhydroquinone complex) in food supplements is developed. Absorption spectra of Oxiphore® water solutions in the ultraviolet region are presented. Samples preparation procedures and mathematical methods of spectra post-analytical procession are discussed. Basic characteristics of the automatic CCD-based UV spectrophotometer and special software implementing the developed method are described. The results of the trials of the developed method and software are analyzed: the error of determination for Oxiphore® concentration in water solutions of the isolated substance and singlecomponent food supplements did not exceed 15% (average error was 7…10%).

  8. Numerical analysis of thermally assisted spin-transfer torque magnetization reversal in synthetic ferrimagnetic free layers

    NASA Astrophysics Data System (ADS)

    Shen, J.; Shi, M.; Tanaka, T.; Matsuyama, K.

    2015-05-01

    The spin transfer torque magnetization reversal of synthetic ferrimagnetic free layers under pulsed temperature rise was numerically studied by solving the Landau-Lifshitz-Gilbert equation, taking into account the stochastic random fields, the temperature dependence of magnetic parameters, and the spin torque terms. The anti-parallel magnetization configuration was retained at the elevated temperature, due to interlayer dipole coupling. A significant thermal assistance effect, resulting in a 40% reduction in the switching current, was demonstrated during a nanosecond pulsed temperature rise up to 77% of the Curie temperature.

  9. Cotton crop spectral imaging analysis: a web-based hyperspectral synthetic imagery simulation system

    NASA Astrophysics Data System (ADS)

    Alarcon, Vladimir J.; Sassenrath, Gretchen F.

    2004-11-01

    The development of spectral libraries for specific vegetation species and soils is useful for identifying different physiological or physical-chemical characteristics. Usually, spectral libraries are provided as a data-base add-in of current commercial software used for analyzing hyperspectral imagery. The use of those databases requires installation of the software in the user"s machine for either visualizing or using the spectral libraries. There are also spectral libraries available on the web but the data is static and partitioned by spectrum of vegetation or soil because the size of the files of actual hyperspectral images precludes it"s publication on the web. In this paper, a web-based simulation environment for generating hyperspectral synthetic imagery of cotton plots is presented. The system was developed using Java and is based on a previous synthetic imagery program1. The mathematical and numerical formulation of the model is briefly sketched. The core computing components of the simulation environment were written in C for their computational efficiency. The emerging Java Native Interface (JNI) technique and standard Java techniques were used to design a user-friendly simulator. The simulation system provides interactive user control and real time visualization of the resulting hyperspectral image through standard web browsers. It shows potential for providing web-based hyperspectral libraries, in the form of images, for public use.

  10. Robustness Analysis of Regional Water Supply Portfolios using Synthetic Inflow Scenarios with Variable Drought Frequency

    NASA Astrophysics Data System (ADS)

    Herman, J. D.; Zeff, H. B.; Lamontagne, J. R.; Reed, P. M.; Characklis, G. W.

    2015-12-01

    Robustness analyses of water supply systems have moved toward exploratory simulation to discover scenarios in which existing or planned policies may fail to meet stakeholder objectives. Such assessments rely heavily on the choice of plausible future scenarios, which, in the case of drought management, requires sampling or generating a broad ensemble of reservoir inflows which do not necessarily reflect the historical record. Here we adapt a widely used synthetic streamflow generation method to adjust the frequency of low-flow periods, which can be related to impactful historical events from the perspective of decision makers. Specifically, the modified generation procedure allows the user to specify parameters n, p such that events with observed weekly non-exceedance frequency p appear in the synthetic scenario with approximate frequency np (i.e., the pth percentile flow occurs n times more frequently). Additionally, the generator preserves the historical autocorrelation of streamflow and its seasonality, as well as approximate multi-site correlation. Using model simulations from recent work in multi-objective urban drought portfolio planning in North Carolina, a region whose water supply faces both climate and population pressures, we illustrate the decision-relevant consequences caused by raising the frequency of low flows associated with the 2007-2008 drought. This method explores system performance under extreme events of increasing frequency prior to reconciling these findings with climate model projections, and thus can be used to support bottom-up robustness methods in water systems planning.