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Sample records for modular dna signal

  1. Construction of a modular dihydrofolate reductase cDNA gene: Analysis of signals utilized for efficient expression

    SciTech Connect

    Kaufman, J.; Sharp, P.A.

    1982-11-01

    Dihydrofolate reductase (DHFR) modular genes have been constructed with segments containing the adenovirus major late promoter, a 3' splice site from a variable region immunoglobulin gene, a DHFR cDNA, and portions of the simian virus 40 (SV40) genome, DNA-mediated transfer of these genes transformed Chinese hamster ovary DHFR/sup -/ cells to the DHFR/sup +/ phenotype. Transformants contained one to several copies of the transfected DNA integrated into the host genome. Clones subjected to growth in increasing concentrations of methotrexate eventually gave rise to lines containing several hundred copies of the transforming DNA. Analysis of the DHFr mRNA produced in amplified lines indicated the following: (i) All clones utilize the adenovirus major late promoter for transcription initiation. (ii) A hybrid intron formed by the 5' splice site of the adenovirus major late leader and a 3' splice site from a variable-region immunoglobulin gene is properly excised. (iii) The mRNA is not efficiently polyadenylated at sequences in the 3' end of the DHFR cDNA but rather uses polyadenylation signals downstream from the DHFR cDNA. Three independent clones produce a DHFR mRNA containing SV40 or pBR322 and SV40 sequences, and the RNA is polyadenylated at the SV40 late polyadenylation site. Another clone has recombined into cellular DNA and apparently uses a cellular sequence for polyadenylation. Introduction of a segment containing the SV40 early polyadenylation signal into the 3' end of the DHFR cDNA generated a recombinant capable of transforming cells to the DHFR/sup +/ phenotype with at least a 10-fold increase in efficiency, demonstrating the necessity for an efficient polyadenylation signal. Attachment of a DNA segment containing the transcription enhancer 72-base pair repeat) of SV40 further increased the biological activity of the modular DHFR gene 50- to 100-fold.

  2. Modularized TGFbeta-Smad Signaling Pathway

    NASA Technical Reports Server (NTRS)

    Li, Yongfeng; Wang, M.; Carra, C.; Cucinotta, F. A.

    2011-01-01

    The Transforming Growth Factor beta (TGFbeta) signaling pathway is a prominent regulatory signaling pathway controlling various important cellular processes. It can be induced by several factors, including ionizing radiation. It is regulated by Smads in a negative feedback loop through promoting increases in the regulatory Smads in the cell nucleus, and subsequent expression of inhibitory Smad, Smad7 to form a ubiquitin ligase with Smurf targeting active TGF receptors for degradation. In this work, we proposed a mathematical model to study the radiation-induced Smad-regulated TGF signaling pathway. By modularization, we are able to analyze each module (subsystem) and recover the nonlinear dynamics of the entire network system. Meanwhile the excitability, a common feature observed in the biological systems, along the TGF signaling pathway is discussed by mathematical analysis and numerical simulation.

  3. Defining a Modular Signalling Network from the Fly Interactome

    PubMed Central

    Baudot, Anaïs; Angelelli, Jean-Baptiste; Guénoche, Alain; Jacq, Bernard; Brun, Christine

    2008-01-01

    Background Signalling pathways relay information by transmitting signals from cell surface receptors to intracellular effectors that eventually activate the transcription of target genes. Since signalling pathways involve several types of molecular interactions including protein-protein interactions, we postulated that investigating their organization in the context of the global protein-protein interaction network could provide a new integrated view of signalling mechanisms. Results Using a graph-theory based method to analyse the fly protein-protein interaction network, we found that each signalling pathway is organized in two to three different signalling modules. These modules contain canonical proteins of the signalling pathways, known regulators as well as other proteins thereby predicted to participate to the signalling mechanisms. Connections between the signalling modules are prominent as compared to the other network's modules and interactions within and between signalling modules are among the more central routes of the interaction network. Conclusion Altogether, these modules form an interactome sub-network devoted to signalling with particular topological properties: modularity, density and centrality. This finding reflects the integration of the signalling system into cell functioning and its important role connecting and coordinating different biological processes at the level of the interactome. PMID:18489752

  4. Phylogenetic evidence for the modular evolution of metazoan signalling pathways.

    PubMed

    Babonis, Leslie S; Martindale, Mark Q

    2017-02-05

    Communication among cells was paramount to the evolutionary increase in cell type diversity and, ultimately, the origin of large body size. Across the diversity of Metazoa, there are only few conserved cell signalling pathways known to orchestrate the complex cell and tissue interactions regulating development; thus, modification to these few pathways has been responsible for generating diversity during the evolution of animals. Here, we summarize evidence for the origin and putative function of the intracellular, membrane-bound and secreted components of seven metazoan cell signalling pathways with a special focus on early branching metazoans (ctenophores, poriferans, placozoans and cnidarians) and basal unikonts (amoebozoans, fungi, filastereans and choanoflagellates). We highlight the modular incorporation of intra- and extracellular components in each signalling pathway and suggest that increases in the complexity of the extracellular matrix may have further promoted the modulation of cell signalling during metazoan evolution. Most importantly, this updated view of metazoan signalling pathways highlights the need for explicit study of canonical signalling pathway components in taxa that do not operate a complete signalling pathway. Studies like these are critical for developing a deeper understanding of the evolution of cell signalling.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.

  5. The discovery of modular binding domains: building blocks of cell signalling.

    PubMed

    Mayer, Bruce J

    2015-11-01

    Cell signalling - the ability of a cell to process information from the environment and change its behaviour in response - is a central property of life. Signalling depends on proteins that are assembled from a toolkit of modular domains, each of which confers a specific activity or function. The discovery of modular protein- and lipid-binding domains was a crucial turning point in understanding the logic and evolution of signalling mechanisms.

  6. DNA signals at isoform promoters

    PubMed Central

    Dai, Zhiming; Xiong, Yuanyan; Dai, Xianhua

    2016-01-01

    Transcriptional heterogeneity is extensive in the genome, and most genes express variable transcript isoforms. However, whether variable transcript isoforms of one gene are regulated by common promoter elements remain to be elucidated. Here, we investigated whether isoform promoters of one gene have separated DNA signals for transcription and translation initiation. We found that TATA box and nucleosome-disfavored DNA sequences are prevalent in distinct transcript isoform promoters of one gene. These DNA signals are conserved among species. Transcript isoform has a RNA-determined unstructured region around its start site. We found that these DNA/RNA features facilitate isoform transcription and translation. These results suggest a DNA-encoded mechanism by which transcript isoform is generated. PMID:27353836

  7. pH-programmable DNA logic arrays powered by modular DNAzyme libraries.

    PubMed

    Elbaz, Johann; Wang, Fuan; Remacle, Francoise; Willner, Itamar

    2012-12-12

    Nature performs complex information processing circuits, such the programmed transformations of versatile stem cells into targeted functional cells. Man-made molecular circuits are, however, unable to mimic such sophisticated biomachineries. To reach these goals, it is essential to construct programmable modular components that can be triggered by environmental stimuli to perform different logic circuits. We report on the unprecedented design of artificial pH-programmable DNA logic arrays, constructed by modular libraries of Mg(2+)- and UO(2)(2+)-dependent DNAzyme subunits and their substrates. By the appropriate modular design of the DNA computation units, pH-programmable logic arrays of various complexities are realized, and the arrays can be erased, reused, and/or reprogrammed. Such systems may be implemented in the near future for nanomedical applications by pH-controlled regulation of cellular functions or may be used to control biotransformations stimulated by bacteria.

  8. Tunable signal processing through modular control of transcription factor translocation.

    PubMed

    Hao, Nan; Budnik, Bogdan A; Gunawardena, Jeremy; O'Shea, Erin K

    2013-01-25

    Signaling pathways can induce different dynamics of transcription factor (TF) activation. We explored how TFs process signaling inputs to generate diverse dynamic responses. The budding yeast general stress-responsive TF Msn2 acted as a tunable signal processor that could track, filter, or integrate signals in an input-dependent manner. This tunable signal processing appears to originate from dual regulation of both nuclear import and export by phosphorylation, as mutants with one form of regulation sustained only one signal-processing function. Versatile signal processing by Msn2 is crucial for generating distinct dynamic responses to different natural stresses. Our findings reveal how complex signal-processing functions are integrated into a single molecule and provide a guide for the design of TFs with "programmable" signal-processing functions.

  9. Modular continuous wavelet processing of biosignals: extracting heart rate and oxygen saturation from a video signal

    PubMed Central

    2016-01-01

    A novel method of extracting heart rate and oxygen saturation from a video-based biosignal is described. The method comprises a novel modular continuous wavelet transform approach which includes: performing the transform, undertaking running wavelet archetyping to enhance the pulse information, extraction of the pulse ridge time–frequency information [and thus a heart rate (HRvid) signal], creation of a wavelet ratio surface, projection of the pulse ridge onto the ratio surface to determine the ratio of ratios from which a saturation trending signal is derived, and calibrating this signal to provide an absolute saturation signal (SvidO2). The method is illustrated through its application to a video photoplethysmogram acquired during a porcine model of acute desaturation. The modular continuous wavelet transform-based approach is advocated by the author as a powerful methodology to deal with noisy, non-stationary biosignals in general. PMID:27382479

  10. Modular continuous wavelet processing of biosignals: extracting heart rate and oxygen saturation from a video signal.

    PubMed

    Addison, Paul S

    2016-06-01

    A novel method of extracting heart rate and oxygen saturation from a video-based biosignal is described. The method comprises a novel modular continuous wavelet transform approach which includes: performing the transform, undertaking running wavelet archetyping to enhance the pulse information, extraction of the pulse ridge time-frequency information [and thus a heart rate (HRvid) signal], creation of a wavelet ratio surface, projection of the pulse ridge onto the ratio surface to determine the ratio of ratios from which a saturation trending signal is derived, and calibrating this signal to provide an absolute saturation signal (SvidO2). The method is illustrated through its application to a video photoplethysmogram acquired during a porcine model of acute desaturation. The modular continuous wavelet transform-based approach is advocated by the author as a powerful methodology to deal with noisy, non-stationary biosignals in general.

  11. BurrH: a new modular DNA binding protein for genome engineering

    PubMed Central

    Juillerat, Alexandre; Bertonati, Claudia; Dubois, Gwendoline; Guyot, Valérie; Thomas, Séverine; Valton, Julien; Beurdeley, Marine; Silva, George H.; Daboussi, Fayza; Duchateau, Philippe

    2014-01-01

    The last few years have seen the increasing development of new DNA targeting molecular tools and strategies for precise genome editing. However, opportunities subsist to either improve or expand the current toolbox and further broaden the scope of possible biotechnological applications. Here we report the discovery and the characterization of BurrH, a new modular DNA binding protein from Burkholderia rhizoxinica that is composed of highly polymorphic DNA targeting modules. We also engineered this scaffold to create a new class of designer nucleases that can be used to efficiently induce in vivo targeted mutagenesis and targeted gene insertion at a desired locus. PMID:24452192

  12. Modular Nuclease-Responsive DNA Three-Way Junction-Based Dynamic Assembly of a DNA Device and Its Sensing Application.

    PubMed

    Zhu, Jing; Wang, Lei; Xu, Xiaowen; Wei, Haiping; Jiang, Wei

    2016-04-05

    Here, we explored a modular strategy for rational design of nuclease-responsive three-way junctions (TWJs) and fabricated a dynamic DNA device in a "plug-and-play" fashion. First, inactivated TWJs were designed, which contained three functional domains: the inaccessible toehold and branch migration domains, the specific sites of nucleases, and the auxiliary complementary sequence. The actions of different nucleases on their specific sites in TWJs caused the close proximity of the same toehold and branch migration domains, resulting in the activation of the TWJs and the formation of a universal trigger for the subsequent dynamic assembly. Second, two hairpins (H1 and H2) were introduced, which could coexist in a metastable state, initially to act as the components for the dynamic assembly. Once the trigger initiated the opening of H1 via TWJs-driven strand displacement, the cascade hybridization of hairpins immediately switched on, resulting in the formation of the concatemers of H1/H2 complex appending numerous integrated G-quadruplexes, which were used to obtain label-free signal readout. The inherent modularity of this design allowed us to fabricate a flexible DNA dynamic device and detect multiple nucleases through altering the recognition pattern slightly. Taking uracil-DNA glycosylase and CpG methyltransferase M.SssI as models, we successfully realized the butt joint between the uracil-DNA glycosylase and M.SssI recognition events and the dynamic assembly process. Furthermore, we achieved ultrasensitive assay of nuclease activity and the inhibitor screening. The DNA device proposed here will offer an adaptive and flexible tool for clinical diagnosis and anticancer drug discovery.

  13. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits.

    PubMed

    Bhattacharyya, Roby P; Reményi, Attila; Yeh, Brian J; Lim, Wendell A

    2006-01-01

    Living cells display complex signal processing behaviors, many of which are mediated by networks of proteins specialized for signal transduction. Here we focus on the question of how the remarkably diverse array of eukaryotic signaling circuits may have evolved. Many of the mechanisms that connect signaling proteins into networks are highly modular: The core catalytic activity of a signaling protein is physically and functionally separable from molecular domains or motifs that determine its linkage to both inputs and outputs. This high degree of modularity may make these systems more evolvable-in principle, novel circuits, and therefore highly innovative regulatory behaviors, can arise from relatively simple genetic events such as recombination, deletion, or insertion. In support of this hypothesis, recent studies show that such modular systems can be exploited to engineer nonnatural signaling proteins and pathways with novel behavior.

  14. Regulated unfolding: a basic principle of intraprotein signaling in modular proteins.

    PubMed

    Schultz, Joachim E; Natarajan, Janani

    2013-11-01

    Modular proteins possess N-terminal sensor domains connected with different C-terminal output domains. Different output domains, for example, phosphodiesterases adenylyl cyclases, are regulated by identical N-terminal domains. Therefore, the mechanisms of intraprotein signaling share properties suitable to regulation of disparate output enzymes, which see the same signal but react differently. The common denominator is a reversible switch of folding/unfolding that connects sensor and output domains. In the inhibited state, output domains are restrained, whereas in the activated state domains are released to assemble according to intrinsic domain properties. We review recent work investigating the mechanism of intraprotein signaling and discuss how this signaling mechanism may have contributed to the evolutionary diversity of specific small molecule-binding domains without loss of regulatory properties.

  15. One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy

    PubMed Central

    Casini, Arturo; MacDonald, James T.; Jonghe, Joachim De; Christodoulou, Georgia; Freemont, Paul S.; Baldwin, Geoff S.; Ellis, Tom

    2014-01-01

    Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer this, we present MODAL: a Modular Overlap-Directed Assembly with Linkers strategy that brings modularity to overlap-directed methods, allowing assembly of an initial set of DNA parts into a variety of arrangements in one-pot reactions. MODAL is accompanied by a custom software tool that designs overlap linkers to guide assembly, allowing parts to be assembled in any specified order and orientation. The in silico design of synthetic orthogonal overlapping junctions allows for much greater efficiency in DNA assembly for a variety of different methods compared with using non-designed sequence. In tests with three different assembly technologies, the MODAL strategy gives assembly of both yeast and bacterial plasmids, composed of up to five DNA parts in the kilobase range with efficiencies of between 75 and 100%. It also seamlessly allows mutagenesis to be performed on any specified DNA parts during the process, allowing the one-step creation of construct libraries valuable for synthetic biology applications. PMID:24153110

  16. A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals

    PubMed Central

    Wang, Baojun; Barahona, Mauricio; Buck, Martin

    2013-01-01

    Cells perceive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate particular phenotypic responses. Here, we employ both single and mixed cell type populations, pre-programmed with engineered modular cell signalling and sensing circuits, as processing units to detect and integrate multiple environmental signals. Based on an engineered modular genetic AND logic gate, we report the construction of a set of scalable synthetic microbe-based biosensors comprising exchangeable sensory, signal processing and actuation modules. These cellular biosensors were engineered using distinct signalling sensory modules to precisely identify various chemical signals, and combinations thereof, with a quantitative fluorescent output. The genetic logic gate used can function as a biological filter and an amplifier to enhance the sensing selectivity and sensitivity of cell-based biosensors. In particular, an Escherichia coli consortium-based biosensor has been constructed that can detect and integrate three environmental signals (arsenic, mercury and copper ion levels) via either its native two-component signal transduction pathways or synthetic signalling sensors derived from other bacteria in combination with a cell-cell communication module. We demonstrate how a modular cell-based biosensor can be engineered predictably using exchangeable synthetic gene circuit modules to sense and integrate multiple-input signals. This study illustrates some of the key practical design principles required for the future application of these biosensors in broad environmental and healthcare areas. PMID:22981411

  17. A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals.

    PubMed

    Wang, Baojun; Barahona, Mauricio; Buck, Martin

    2013-02-15

    Cells perceive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate particular phenotypic responses. Here, we employ both single and mixed cell type populations, pre-programmed with engineered modular cell signalling and sensing circuits, as processing units to detect and integrate multiple environmental signals. Based on an engineered modular genetic AND logic gate, we report the construction of a set of scalable synthetic microbe-based biosensors comprising exchangeable sensory, signal processing and actuation modules. These cellular biosensors were engineered using distinct signalling sensory modules to precisely identify various chemical signals, and combinations thereof, with a quantitative fluorescent output. The genetic logic gate used can function as a biological filter and an amplifier to enhance the sensing selectivity and sensitivity of cell-based biosensors. In particular, an Escherichia coli consortium-based biosensor has been constructed that can detect and integrate three environmental signals (arsenic, mercury and copper ion levels) via either its native two-component signal transduction pathways or synthetic signalling sensors derived from other bacteria in combination with a cell-cell communication module. We demonstrate how a modular cell-based biosensor can be engineered predictably using exchangeable synthetic gene circuit modules to sense and integrate multiple-input signals. This study illustrates some of the key practical design principles required for the future application of these biosensors in broad environmental and healthcare areas.

  18. The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing

    PubMed Central

    Iranzo, Jaime

    2016-01-01

    ABSTRACT Virus genomes are prone to extensive gene loss, gain, and exchange and share no universal genes. Therefore, in a broad-scale study of virus evolution, gene and genome network analyses can complement traditional phylogenetics. We performed an exhaustive comparative analysis of the genomes of double-stranded DNA (dsDNA) viruses by using the bipartite network approach and found a robust hierarchical modularity in the dsDNA virosphere. Bipartite networks consist of two classes of nodes, with nodes in one class, in this case genomes, being connected via nodes of the second class, in this case genes. Such a network can be partitioned into modules that combine nodes from both classes. The bipartite network of dsDNA viruses includes 19 modules that form 5 major and 3 minor supermodules. Of these modules, 11 include tailed bacteriophages, reflecting the diversity of this largest group of viruses. The module analysis quantitatively validates and refines previously proposed nontrivial evolutionary relationships. An expansive supermodule combines the large and giant viruses of the putative order “Megavirales” with diverse moderate-sized viruses and related mobile elements. All viruses in this supermodule share a distinct morphogenetic tool kit with a double jelly roll major capsid protein. Herpesviruses and tailed bacteriophages comprise another supermodule, held together by a distinct set of morphogenetic proteins centered on the HK97-like major capsid protein. Together, these two supermodules cover the great majority of currently known dsDNA viruses. We formally identify a set of 14 viral hallmark genes that comprise the hubs of the network and account for most of the intermodule connections. PMID:27486193

  19. Engineering modular and tunable genetic amplifiers for scaling transcriptional signals in cascaded gene networks.

    PubMed

    Wang, Baojun; Barahona, Mauricio; Buck, Martin

    2014-08-01

    Synthetic biology aims to control and reprogram signal processing pathways within living cells so as to realize repurposed, beneficial applications. Here we report the design and construction of a set of modular and gain-tunable genetic amplifiers in Escherichia coli capable of amplifying a transcriptional signal with wide tunable-gain control in cascaded gene networks. The devices are engineered using orthogonal genetic components (hrpRS, hrpV and PhrpL) from the hrp (hypersensitive response and pathogenicity) gene regulatory network in Pseudomonas syringae. The amplifiers can linearly scale up to 21-fold the transcriptional input with a large output dynamic range, yet not introducing significant time delay or significant noise during signal amplification. The set of genetic amplifiers achieves different gains and input dynamic ranges by varying the expression levels of the underlying ligand-free activator proteins in the device. As their electronic counterparts, these engineered transcriptional amplifiers can act as fundamental building blocks in the design of biological systems by predictably and dynamically modulating transcriptional signal flows to implement advanced intra- and extra-cellular control functions.

  20. Design of a modular signal processing board (MSPB) for gamma-ray imaging applications

    NASA Astrophysics Data System (ADS)

    Bieberle, A.; Berger, R.; Yadav, R.; Schleicher, E.; Hampel, U.

    2012-01-01

    In this paper a new modular signal processing board (MSPB) for high-resolution gamma-ray computed tomography (GCT) is presented. The MSPB is optimised for parallel signal processing of eight detector channels operating in pulse counting mode. Signal processing stages comprise of variable gain amplifiers, pulse height discrimination stages, 13-bit counters with corresponding latches as well as logic circuitry for coordinated data transfer with a multitude of MSPBs. The digital signal processing units are realised in commercially available complex programmable logic devices (CPLD). Each MSPB is addressable by an 8-bit DIP-switch, which allows the use of up to 256 modules or 2048 detector pixels within one detector system. The geometry of the MSPB allows a multiple and seamless detector module arrangement, which eases the adaptation of a given gamma-ray detector system to specific industrial and laboratory applications. The choice of the electronic devices and the thermal design was optimised for low power consumption in order to minimise internal heat production, which would affect the characteristics of the detector's intrinsic gain strongly. Thermal measurements have been executed to prove the functionality of the thermal design.

  1. A modular library of small molecule signals regulates social behaviors in Caenorhabditis elegans.

    PubMed

    Srinivasan, Jagan; von Reuss, Stephan H; Bose, Neelanjan; Zaslaver, Alon; Mahanti, Parag; Ho, Margaret C; O'Doherty, Oran G; Edison, Arthur S; Sternberg, Paul W; Schroeder, Frank C

    2012-01-01

    The nematode C. elegans is an important model for the study of social behaviors. Recent investigations have shown that a family of small molecule signals, the ascarosides, controls population density sensing and mating behavior. However, despite extensive studies of C. elegans aggregation behaviors, no intraspecific signals promoting attraction or aggregation of wild-type hermaphrodites have been identified. Using comparative metabolomics, we show that the known ascarosides are accompanied by a series of derivatives featuring a tryptophan-derived indole moiety. Behavioral assays demonstrate that these indole ascarosides serve as potent intraspecific attraction and aggregation signals for hermaphrodites, in contrast to ascarosides lacking the indole group, which are repulsive. Hermaphrodite attraction to indole ascarosides depends on the ASK amphid sensory neurons. Downstream of the ASK sensory neuron, the interneuron AIA is required for mediating attraction to indole ascarosides instead of the RMG interneurons, which previous studies have shown to integrate attraction and aggregation signals from ASK and other sensory neurons. The role of the RMG interneuron in mediating aggregation and attraction is thought to depend on the neuropeptide Y-like receptor NPR-1, because solitary and social C. elegans strains are distinguished by different npr-1 variants. We show that indole ascarosides promote attraction and aggregation in both solitary and social C. elegans strains. The identification of indole ascarosides as aggregation signals reveals unexpected complexity of social signaling in C. elegans, which appears to be based on a modular library of ascarosides integrating building blocks derived from lipid β-oxidation and amino-acid metabolism. Variation of modules results in strongly altered signaling content, as addition of a tryptophan-derived indole unit to repellent ascarosides produces strongly attractive indole ascarosides. Our findings show that the library of

  2. DNA Charge Transport for Sensing and Signaling

    PubMed Central

    Sontz, Pamela A.; Muren, Natalie B.; Barton, Jacqueline K.

    2012-01-01

    Conspectus The DNA duplex is an exquisite macromolecular array that stores genetic information to encode proteins and regulate pathways, but its unique structure imparts chemical function that allows it also to mediate charge transport (CT). We have utilized diverse platforms to probe DNA CT, using spectroscopic, electrochemical, and even genetic methods. These studies have established powerful features of DNA CT chemistry. DNA CT can occur over long molecular distances as long as the bases are well stacked; perturbations in base stacking as arise with single base mismatches, DNA lesions, and the binding of some proteins that kink the DNA, all serve to inhibit DNA CT. Significantly, single molecule studies of DNA CT show that ground state CT can occur over 34 nm as long as the duplex is well stacked; one single base mismatch inhibits CT. The DNA duplex is an effective sensor for the integrity of the base pair stack. Moreover the efficiency of DNA CT is what one would expect for a stack of graphite sheets, equivalent to the stack of DNA base pairs, and independent of the sugar-phosphate backbone. Since DNA CT offers a means to carry out redox chemistry from a distance, we have considered how this chemistry might be used for long range signaling in a biological context. We have taken advantage of our chemical probes and platforms to characterize DNA CT also in the context of the cell. CT can occur over long distances, perhaps funneling damage to particular sites and insulating others from oxidative stress. Significantly, transcription factors that activate the genome to respond to oxidative stress can also be activated from a distance through DNA CT. Numerous proteins work to maintain the integrity of the genome and increasingly they have been found to contain [4Fe-4S] clusters that do not appear to carry out either structural or enzymatic roles. Using electrochemical methods, we find that DNA binding shifts the redox potentials of the clusters, activating them

  3. Modular and Stochastic Approaches to Molecular Pathway Models of ATM, TGF beta, and WNT Signaling

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; O'Neill, Peter; Ponomarev, Artem; Carra, Claudio; Whalen, Mary; Pluth, Janice M.

    2009-01-01

    Deterministic pathway models that describe the biochemical interactions of a group of related proteins, their complexes, activation through kinase, etc. are often the basis for many systems biology models. Low dose radiation effects present a unique set of challenges to these models including the importance of stochastic effects due to the nature of radiation tracks and small number of molecules activated, and the search for infrequent events that contribute to cancer risks. We have been studying models of the ATM, TGF -Smad and WNT signaling pathways with the goal of applying pathway models to the investigation of low dose radiation cancer risks. Modeling challenges include introduction of stochastic models of radiation tracks, their relationships to more than one substrate species that perturb pathways, and the identification of a representative set of enzymes that act on the dominant substrates. Because several pathways are activated concurrently by radiation the development of modular pathway approach is of interest.

  4. Modularity and functional plasticity of scaffold proteins as p(l)acemakers in cell signaling.

    PubMed

    Pan, Catherine Qiurong; Sudol, Marius; Sheetz, Michael; Low, Boon Chuan

    2012-11-01

    Cells coordinate and integrate various functional modules that control their dynamics, intracellular trafficking, metabolism and gene expression. Such capacity is mediated by specific scaffold proteins that tether multiple components of signaling pathways at plasma membrane, Golgi apparatus, mitochondria, endoplasmic reticulum, nucleus and in more specialized subcellular structures such as focal adhesions, cell-cell junctions, endosomes, vesicles and synapses. Scaffold proteins act as "pacemakers" as well as "placemakers" that regulate the temporal, spatial and kinetic aspects of protein complex assembly by modulating the local concentrations, proximity, subcellular dispositions and biochemical properties of the target proteins through the intricate use of their modular protein domains. These regulatory mechanisms allow them to gate the specificity, integration and crosstalk of different signaling modules. In addition to acting as physical platforms for protein assembly, many professional scaffold proteins can also directly modify the properties of their targets while they themselves can be regulated by post-translational modifications and/or mechanical forces. Furthermore, multiple scaffold proteins can form alliances of higher-order regulatory networks. Here, we highlight the emerging themes of scaffold proteins by analyzing their common and distinctive mechanisms of action and regulation, which underlie their functional plasticity in cell signaling. Understanding these mechanisms in the context of space, time and force should have ramifications for human physiology and for developing new therapeutic approaches to control pathological states and diseases.

  5. Neuronal apoptotic signaling pathways probed and intervened by synthetically and modularly modified (SMM) chemokines.

    PubMed

    Choi, Won-Tak; Kaul, Marcus; Kumar, Santosh; Wang, Jun; Kumar, I M Krishna; Dong, Chang-Zhi; An, Jing; Lipton, Stuart A; Huang, Ziwei

    2007-03-09

    As the main coreceptors for human immunodeficiency virus type 1 (HIV-1) entry, CXCR4 and CCR5 play important roles in HIV-associated dementia (HAD). HIV-1 glycoprotein gp120 contributes to HAD by causing neuronal damage and death, either directly by triggering apoptotic pathways or indirectly by stimulating glial cells to release neurotoxins. Here, to understand the mechanism of CXCR4 or CCR5 signaling in neuronal apoptosis associated with HAD, we have applied synthetically and modularly modified (SMM)-chemokine analogs derived from natural stromal cell-derived factor-1alpha or viral macrophage inflammatory protein-II as chemical probes of the mechanism(s) whereby these SMM-chemokines prevent or promote neuronal apoptosis. We show that inherently neurotoxic natural ligands of CXCR4, such as stromal cell-derived factor-1alpha or viral macrophage inflammatory protein-II, can be modified to protect neurons from apoptosis induced by CXCR4-preferring gp120(IIIB), and that the inhibition of CCR5 by antagonist SMM-chemokines, unlike neuroprotective CCR5 natural ligands, leads to neurotoxicity by activating a p38 mitogen-activated protein kinase (MAPK)-dependent pathway. Furthermore, we discover distinct signaling pathways activated by different chemokine ligands that are either natural agonists or synthetic antagonists, thus demonstrating a chemical biology strategy of using chemically engineered inhibitors of chemokine receptors to study the signaling mechanism of neuronal apoptosis and survival.

  6. Signal complexity and modular organization of the courtship behaviours of two sibling species of wolf spiders (Araneae: Lycosidae).

    PubMed

    Chiarle, Alberto; Isaia, Marco

    2013-07-01

    In this study, we compare the courtship behaviours of Pardosa proxima and P. vlijmi, two species of wolf spiders up to now regarded as "ethospecies", by means of motion analysis methodologies. In particular, we investigate the features of the signals, aiming at understanding the evolution of the courtship and its role in species delimitation and speciation processes. In our model, we highlight a modular structure of the behaviours and the presence of recurring units and phases. According to other similar cases concerning animal communication, we observed one highly variable and one stereotyped phase for both species. The stereotyped phase is here regarded as a signal related to species identity or an honest signal linked directly to the quality of the signaler. On the contrary, the variable phase aims to facilitate signal detection and assessment by the female reducing choice costs or errors. Variable phases include cues arisen from Fisherian runaway selection, female sensory exploitation and remaining of past selections.

  7. Atomically precise arrays of fluorescent silver clusters: a modular approach for metal cluster photonics on DNA nanostructures.

    PubMed

    Copp, Stacy M; Schultz, Danielle E; Swasey, Steven; Gwinn, Elisabeth G

    2015-03-24

    The remarkable precision that DNA scaffolds provide for arraying nanoscale optical elements enables optical phenomena that arise from interactions of metal nanoparticles, dye molecules, and quantum dots placed at nanoscale separations. However, control of ensemble optical properties has been limited by the difficulty of achieving uniform particle sizes and shapes. Ligand-stabilized metal clusters offer a route to atomically precise arrays that combine desirable attributes of both metals and molecules. Exploiting the unique advantages of the cluster regime requires techniques to realize controlled nanoscale placement of select cluster structures. Here we show that atomically monodisperse arrays of fluorescent, DNA-stabilized silver clusters can be realized on a prototypical scaffold, a DNA nanotube, with attachment sites separated by <10 nm. Cluster attachment is mediated by designed DNA linkers that enable isolation of specific clusters prior to assembly on nanotubes and preserve cluster structure and spectral purity after assembly. The modularity of this approach generalizes to silver clusters of diverse sizes and DNA scaffolds of many types. Thus, these silver cluster nano-optical elements, which themselves have colors selected by their particular DNA templating oligomer, bring unique dimensions of control and flexibility to the rapidly expanding field of nano-optics.

  8. Massively parallel classification of single-trial EEG signals using a min-max modular neural network.

    PubMed

    Lu, Bao-Liang; Shin, Jonghan; Ichikawa, Michinori

    2004-03-01

    This paper presents a method for classifying single-trial electroencephalogram (EEG) signals using min-max modular neural networks implemented in a massively parallel way. The method has three main steps. First, a large-scale, complex EEG classification problem is simply divided into a reasonable number of two-class subproblems, as small as needed. Second, the two-class subproblems are simply learned by individual smaller network modules in parallel. Finally, all the individual trained network modules are integrated into a hierarchical, parallel, and modular classifier according to two module combination laws. To demonstrate the effectiveness of the method, we perform simulations on fifteen different four-class EEG classification tasks, each of which consists of 1491 training and 636 test data. These EEG classification tasks were created using a set of non-averaged, single-trial hippocampal EEG signals recorded from rats; the features of the EEG signals are extracted using wavelet transform techniques. The experimental results indicate that the proposed method has several attractive features. 1) The method is appreciably faster than the existing approach that is based on conventional multilayer perceptrons. 2) Complete learning of complex EEG classification problems can be easily realized, and better generalization performance can be achieved. 3) The method scales up to large-scale, complex EEG classification problems.

  9. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types.

    PubMed

    Lever, Mark A; Torti, Andrea; Eickenbusch, Philip; Michaud, Alexander B; Šantl-Temkiv, Tina; Jørgensen, Bo Barker

    2015-01-01

    A method for the extraction of nucleic acids from a wide range of environmental samples was developed. This method consists of several modules, which can be individually modified to maximize yields in extractions of DNA and RNA or separations of DNA pools. Modules were designed based on elaborate tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world's oceans and the deepest borehole ever studied by scientific ocean drilling. Extraction yields of DNA and RNA are higher than with widely used commercial kits, indicating an advantage to optimizing extraction procedures to match specific sample characteristics. The ability to separate soluble extracellular DNA pools without cell lysis from intracellular and particle-complexed DNA pools may enable new insights into the cycling and preservation of DNA in environmental samples in the future. A general protocol is outlined, along with recommendations for optimizing this general protocol for specific sample types and research goals.

  10. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types

    PubMed Central

    Lever, Mark A.; Torti, Andrea; Eickenbusch, Philip; Michaud, Alexander B.; Šantl-Temkiv, Tina; Jørgensen, Bo Barker

    2015-01-01

    A method for the extraction of nucleic acids from a wide range of environmental samples was developed. This method consists of several modules, which can be individually modified to maximize yields in extractions of DNA and RNA or separations of DNA pools. Modules were designed based on elaborate tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world's oceans and the deepest borehole ever studied by scientific ocean drilling. Extraction yields of DNA and RNA are higher than with widely used commercial kits, indicating an advantage to optimizing extraction procedures to match specific sample characteristics. The ability to separate soluble extracellular DNA pools without cell lysis from intracellular and particle-complexed DNA pools may enable new insights into the cycling and preservation of DNA in environmental samples in the future. A general protocol is outlined, along with recommendations for optimizing this general protocol for specific sample types and research goals. PMID:26042110

  11. Nuclear DNA damage signalling to mitochondria in ageing

    PubMed Central

    Fang, Evandro Fei; Scheibye-Knudsen, Morten; Chua, Katrin F.; Mattson, Mark P.; Croteau, Deborah L.; Bohr, Vilhelm A.

    2016-01-01

    Mitochondrial dysfunction is a hallmark of ageing, and mitochondrial maintenance may lead to increased healthspan. Emerging evidence suggests a crucial role for signalling from the nucleus to mitochondria (NM signalling) in regulating mitochondrial function and ageing. An important initiator of NM signalling is nuclear DNA damage, which accumulates with age and may contribute to the development of age-associated diseases. DNA damage-dependent NM signalling constitutes a network that includes nuclear sirtuins and controls genomic stability and mitochondrial integrity. Pharmacological modulation of NM signalling is a promising novel approach for the prevention and treatment of age-associated diseases. PMID:26956196

  12. The evolution of the GPCR signaling system in eukaryotes: modularity, conservation, and the transition to metazoan multicellularity.

    PubMed

    de Mendoza, Alex; Sebé-Pedrós, Arnau; Ruiz-Trillo, Iñaki

    2014-03-01

    The G-protein-coupled receptor (GPCR) signaling system is one of the main signaling pathways in eukaryotes. Here, we analyze the evolutionary history of all its components, from receptors to regulators, to gain a broad picture of its system-level evolution. Using eukaryotic genomes covering most lineages sampled to date, we find that the various components of the GPCR signaling pathway evolved independently, highlighting the modular nature of this system. Our data show that some GPCR families, G proteins, and regulators of G proteins diversified through lineage-specific diversifications and recurrent domain shuffling. Moreover, most of the gene families involved in the GPCR signaling system were already present in the last common ancestor of eukaryotes. Furthermore, we show that the unicellular ancestor of Metazoa already had most of the cytoplasmic components of the GPCR signaling system, including, remarkably, all the G protein alpha subunits, which are typical of metazoans. Thus, we show how the transition to multicellularity involved conservation of the signaling transduction machinery, as well as a burst of receptor diversification to cope with the new multicellular necessities.

  13. Activation of DNA damage response signaling by condensed chromatin.

    PubMed

    Burgess, Rebecca C; Burman, Bharat; Kruhlak, Michael J; Misteli, Tom

    2014-12-11

    The DNA damage response (DDR) occurs in the context of chromatin, and architectural features of chromatin have been implicated in DNA damage signaling and repair. Whereas a role of chromatin decondensation in the DDR is well established, we show here that chromatin condensation is integral to DDR signaling. We find that, in response to DNA damage chromatin regions transiently expand before undergoing extensive compaction. Using a protein-chromatin-tethering system to create defined chromatin domains, we show that interference with chromatin condensation results in failure to fully activate DDR. Conversely, forced induction of local chromatin condensation promotes ataxia telangiectasia mutated (ATM)- and ATR-dependent activation of upstream DDR signaling in a break-independent manner. Whereas persistent chromatin compaction enhanced upstream DDR signaling from irradiation-induced breaks, it reduced recovery and survival after damage. Our results demonstrate that chromatin condensation is sufficient for activation of DDR signaling and is an integral part of physiological DDR signaling.

  14. DNA Damage Signals and Space Radiation Risk

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.

    2011-01-01

    Space radiation is comprised of high-energy and charge (HZE) nuclei and protons. The initial DNA damage from HZE nuclei is qualitatively different from X-rays or gamma rays due to the clustering of damage sites which increases their complexity. Clustering of DNA damage occurs on several scales. First there is clustering of single strand breaks (SSB), double strand breaks (DSB), and base damage within a few to several hundred base pairs (bp). A second form of damage clustering occurs on the scale of a few kbp where several DSB?s may be induced by single HZE nuclei. These forms of damage clusters do not occur at low to moderate doses of X-rays or gamma rays thus presenting new challenges to DNA repair systems. We review current knowledge of differences that occur in DNA repair pathways for different types of radiation and possible relationships to mutations, chromosomal aberrations and cancer risks.

  15. Design of a Modular DNA Triangular-Prism Sensor Enabling Ratiometric and Multiplexed Biomolecule Detection on a Single Microbead.

    PubMed

    Liu, Yu; Chen, Qiaoshu; Liu, Jianbo; Yang, Xiaohai; Guo, Qiuping; Li, Li; Liu, Wei; Wang, Kemin

    2017-03-21

    DNA nanostructures have emerged as powerful and versatile building blocks for the construction of programmable nanoscale structures and functional sensors for biomarker detection, disease diagnostics, and therapy. Here we integrated multiple sensing modules into a single DNA three-dimensional (3D) nanoarchitecture with a triangular-prism (TP) structure for ratiometric and multiplexed biomolecule detection on a single microbead. In our design, the complementary hybridization of three clip sequences formed TP nanoassemblies in which the six single-strand regions in the top and bottom faces act as binding sites for different sensing modules, including an anchor module, reference sequence module, and capture sequence module. The multifunctional modular TP nanostructures were thus exploited for ratiometric and multiplexed biomolecule detection on microbeads. Microbead imaging demonstrated that, after ratiometric self-calibration analysis, the imaging deviations resulting from uneven fluorescence intensity distribution and differing probe concentrations were greatly reduced. The rigid nanostructure also conferred the TP as a framework for geometric positioning of different capture sequences. The inclusion of multiple targets led to the formation of sandwich hybridization structures that gave a readily detectable optical response at different fluorescence channels and distinct fingerprint-like pattern arrays. This approach allowed us to discriminate multiplexed biomolecule targets in a simple and efficient fashion. In this module-designed strategy, the diversity of the controlled DNA assembly coupled with the geometrically well-defined rigid nanostructures of the TP assembly provides a flexible and reliable biosensing approach that shows great promise for biomedical applications.

  16. Noise-enhanced nonlinear response and the role of modular structure for signal detection in neuronal networks.

    PubMed

    Lopes, M A; Lee, K-E; Goltsev, A V; Mendes, J F F

    2014-11-01

    We show that sensory noise can enhance the nonlinear response of neuronal networks, and when delivered together with a weak signal, it improves the signal detection by the network. We reveal this phenomenon in neuronal networks that are in a dynamical state preceding a saddle-node bifurcation corresponding to the appearance of sustained network oscillations. In this state, even a weak subthreshold pulse can evoke a large-amplitude oscillation of neuronal activity. The signal-to-noise ratio reaches a maximum at an optimum level of sensory noise, manifesting stochastic resonance (SR) at the population level. We demonstrate SR by use of simulations and numerical integration of rate equations in a cortical model. Using this model, we mimic the experiments of Gluckman et al. [Phys. Rev. Lett. 77, 4098 (1996)PRLTAO0031-900710.1103/PhysRevLett.77.4098] that have given evidence of SR in mammalian brain. We also study neuronal networks in which neurons are grouped in modules and every module works in the regime of SR. We find that even a few modules can strongly enhance the reliability of signal detection in comparison with the case when a modular organization is absent.

  17. Robustness and modularity properties of a non-covalent DNA catalytic reaction

    PubMed Central

    Zhang, David Yu

    2010-01-01

    The biophysics of nucleic acid hybridization and strand displacement have been used for the rational design of a number of nanoscale structures and functions. Recently, molecular amplification methods have been developed in the form of non-covalent DNA catalytic reactions, in which single-stranded DNA (ssDNA) molecules catalyze the release of ssDNA product molecules from multi-stranded complexes. Here, we characterize the robustness and specificity of one such strand displacement-based catalytic reaction. We show that the designed reaction is simultaneously sensitive to sequence mutations in the catalyst and robust to a variety of impurities and molecular noise. These properties facilitate the incorporation of strand displacement-based DNA components in synthetic chemical and biological reaction networks. PMID:20194118

  18. Theory of force-extension curves for modular proteins and DNA hairpins

    NASA Astrophysics Data System (ADS)

    Bonilla, L. L.; Carpio, A.; Prados, A.

    2015-05-01

    We study a model describing the force-extension curves of modular proteins, nucleic acids, and other biomolecules made out of several single units or modules. At a mesoscopic level of description, the configuration of the system is given by the elongations of each of the units. The system free energy includes a double-well potential for each unit and an elastic nearest-neighbor interaction between them. Minimizing the free energy yields the system equilibrium properties whereas its dynamics is given by (overdamped) Langevin equations for the elongations, in which friction and noise amplitude are related by the fluctuation-dissipation theorem. Our results, both for the equilibrium and the dynamical situations, include analytical and numerical descriptions of the system force-extension curves under force or length control and agree very well with actual experiments in biomolecules. Our conclusions also apply to other physical systems comprising a number of metastable units, such as storage systems or semiconductor superlattices.

  19. An inducible long noncoding RNA amplifies DNA damage signaling

    PubMed Central

    Schmitt, Adam M.; Garcia, Julia T.; Hung, Tiffany; Flynn, Ryan A.; Shen, Ying; Qu, Kun; Payumo, Alexander Y.; Peres-da-Silva, Ashwin; Broz, Daniela Kenzelmann; Baum, Rachel; Guo, Shuling; Chen, James K.; Attardi, Laura D.; Chang, Howard Y.

    2016-01-01

    Long noncoding RNAs (lncRNAs) are prevalent genes with frequently exquisite regulation but mostly unknown functions. Here we demonstrate a role of lncRNAs in guiding organismal DNA damage response. DNA damage activates transcription of DINO (Damage Induced NOncoding) via p53. DINO is required for p53-dependent gene expression, cell cycle arrest, and apoptosis in response to DNA damage, and DINO expression suffice to activate damage signaling and cell cycle arrest in the absence of DNA damage. DINO binds to and promotes p53 protein stabilization, mediating a p53 auto-amplification loop. Dino knockout or promoter inactivation in mice dampens p53 signaling and ameliorates acute radiation syndrome in vivo. Thus, inducible lncRNA can create a feedback loop with its cognate transcription factor to amplify cellular signaling networks. PMID:27668660

  20. Comparative metabolomics reveals biogenesis of ascarosides, a modular library of small-molecule signals in C. elegans.

    PubMed

    von Reuss, Stephan H; Bose, Neelanjan; Srinivasan, Jagan; Yim, Joshua J; Judkins, Joshua C; Sternberg, Paul W; Schroeder, Frank C

    2012-01-25

    In the model organism Caenorhabditis elegans, a family of endogenous small molecules, the ascarosides function as key regulators of developmental timing and behavior that act upstream of conserved signaling pathways. The ascarosides are based on the dideoxysugar ascarylose, which is linked to fatty-acid-like side chains of varying lengths derived from peroxisomal β-oxidation. Despite the importance of ascarosides for many aspects of C. elegans biology, knowledge of their structures, biosynthesis, and homeostasis remains incomplete. We used an MS/MS-based screen to profile ascarosides in C. elegans wild-type and mutant metabolomes, which revealed a much greater structural diversity of ascaroside derivatives than previously reported. Comparison of the metabolomes from wild-type and a series of peroxisomal β-oxidation mutants showed that the enoyl CoA-hydratase MAOC-1 serves an important role in ascaroside biosynthesis and clarified the functions of two other enzymes, ACOX-1 and DHS-28. We show that, following peroxisomal β-oxidation, the ascarosides are selectively derivatized with moieties of varied biogenetic origin and that such modifications can dramatically affect biological activity, producing signaling molecules active at low femtomolar concentrations. Based on these results, the ascarosides appear as a modular library of small-molecule signals, integrating building blocks from three major metabolic pathways: carbohydrate metabolism, peroxisomal β-oxidation of fatty acids, and amino acid catabolism. Our screen further demonstrates that ascaroside biosynthesis is directly affected by nutritional status and that excretion of the final products is highly selective.

  1. Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1.

    PubMed

    Hauri, Simon; Wepf, Alexander; van Drogen, Audrey; Varjosalo, Markku; Tapon, Nic; Aebersold, Ruedi; Gstaiger, Matthias

    2013-01-01

    Tissue homeostasis is controlled by signaling systems that coordinate cell proliferation, cell growth and cell shape upon changes in the cellular environment. Deregulation of these processes is associated with human cancer and can occur at multiple levels of the underlying signaling systems. To gain an integrated view on signaling modules controlling tissue growth, we analyzed the interaction proteome of the human Hippo pathway, an established growth regulatory signaling system. The resulting high-resolution network model of 480 protein-protein interactions among 270 network components suggests participation of Hippo pathway components in three distinct modules that all converge on the transcriptional co-activator YAP1. One of the modules corresponds to the canonical Hippo kinase cassette whereas the other two both contain Hippo components in complexes with cell polarity proteins. Quantitative proteomic data suggests that complex formation with cell polarity proteins is dynamic and depends on the integrity of cell-cell contacts. Collectively, our systematic analysis greatly enhances our insights into the biochemical landscape underlying human Hippo signaling and emphasizes multifaceted roles of cell polarity complexes in Hippo-mediated tissue growth control.

  2. Enhanced photoacoustic signal from DNA assembled gold nanoparticle networks

    NASA Astrophysics Data System (ADS)

    Buchkremer, A.; Beckmann, M. F.; Linn, M.; Ruff, J.; Rosencrantz, R. R.; von Plessen, G.; Schmitz, G.; Simon, U.

    2014-12-01

    We report an experimental finding of photoacoustic signal enhancement from finite sized DNA-gold nanoparticle networks. We synthesized DNA-functionalized hollow and solid gold nanospheres (AuNS) to form finite sized networks, which were characterized by means of optical extinction spectroscopy, dynamic light scattering, and scanning electron microscopy in transmission mode. It is shown that the signal amplification scales with network size for networks comprising either hollow or solid AuNS as well as networks consisting of both types of nanoparticles. The laser intensities applied in our multispectral setup (λ = 650 nm, 850 nm, 905 nm) were low enough to maintain the structural integrity of the networks. This reflects that the binding and recognition properties of the temperature-sensitive cross-linking DNA-molecules are retained.

  3. Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling

    PubMed Central

    Fusco, Ludovico; Lefort, Riwal; Smith, Kevin; Benmansour, Fethallah; Gonzalez, German; Barillari, Caterina; Rinn, Bernd; Fleuret, Francois; Fua, Pascal

    2016-01-01

    Rho guanosine triphosphatases (GTPases) control the cytoskeletal dynamics that power neurite outgrowth. This process consists of dynamic neurite initiation, elongation, retraction, and branching cycles that are likely to be regulated by specific spatiotemporal signaling networks, which cannot be resolved with static, steady-state assays. We present NeuriteTracker, a computer-vision approach to automatically segment and track neuronal morphodynamics in time-lapse datasets. Feature extraction then quantifies dynamic neurite outgrowth phenotypes. We identify a set of stereotypic neurite outgrowth morphodynamic behaviors in a cultured neuronal cell system. Systematic RNA interference perturbation of a Rho GTPase interactome consisting of 219 proteins reveals a limited set of morphodynamic phenotypes. As proof of concept, we show that loss of function of two distinct RhoA-specific GTPase-activating proteins (GAPs) leads to opposite neurite outgrowth phenotypes. Imaging of RhoA activation dynamics indicates that both GAPs regulate different spatiotemporal Rho GTPase pools, with distinct functions. Our results provide a starting point to dissect spatiotemporal Rho GTPase signaling networks that regulate neurite outgrowth. PMID:26728857

  4. Assembly of Slx4 signaling complexes behind DNA replication forks.

    PubMed

    Balint, Attila; Kim, TaeHyung; Gallo, David; Cussiol, Jose Renato; Bastos de Oliveira, Francisco M; Yimit, Askar; Ou, Jiongwen; Nakato, Ryuichiro; Gurevich, Alexey; Shirahige, Katsuhiko; Smolka, Marcus B; Zhang, Zhaolei; Brown, Grant W

    2015-08-13

    Obstructions to replication fork progression, referred to collectively as DNA replication stress, challenge genome stability. In Saccharomyces cerevisiae, cells lacking RTT107 or SLX4 show genome instability and sensitivity to DNA replication stress and are defective in the completion of DNA replication during recovery from replication stress. We demonstrate that Slx4 is recruited to chromatin behind stressed replication forks, in a region that is spatially distinct from that occupied by the replication machinery. Slx4 complex formation is nucleated by Mec1 phosphorylation of histone H2A, which is recognized by the constitutive Slx4 binding partner Rtt107. Slx4 is essential for recruiting the Mec1 activator Dpb11 behind stressed replication forks, and Slx4 complexes are important for full activity of Mec1. We propose that Slx4 complexes promote robust checkpoint signaling by Mec1 by stably recruiting Dpb11 within a discrete domain behind the replication fork, during DNA replication stress.

  5. Ease fabrication of PCR modular chip for portable DNA detection kit

    NASA Astrophysics Data System (ADS)

    Whulanza, Yudan; Aditya, Rifky; Arvialido, Reyhan; Utomo, Muhammad S.; Bachtiar, Boy M.

    2017-02-01

    Engineering a lab-on-a-chip (LoC) to perform the DNA polymerase chain reaction (PCR) for malaria detection is the ultimate goal of this study. This paper investigates the ability to fabricate an LoC kit using conventional method to achieve the lowest production cost by using existing fabrication process. It has been known that majority of LoC was made of polydimethylsiloxane (PDMS) which in this study was realized through a contact mold process. CNC milling process was utilized to create channel features in the range of 150-250 µm on the mold. Characterization on the milling process was done to understand the shrinkage/contraction between mold to product, roughness and also angle of contact of PDMS surface. Ultimately, this paper also includes analysis on flow measurement and heat distribution of an assembled LoC PCR kit. The results show that the achieved dimension of microchannel is 227 µm wide with a roughness of 0.01 µm. The flow measurement indicates a deviation with simulation in the range of 10%. A heat distribution through the kit is achieved following the three temperature zones as desired.

  6. Modular multiantigen T cell epitope-enriched DNA vaccine against human leishmaniasis.

    PubMed

    Das, Shantanabha; Freier, Anja; Boussoffara, Thouraya; Das, Sushmita; Oswald, Detlef; Losch, Florian O; Selka, Melanie; Sacerdoti-Sierra, Nina; Schönian, Gabriele; Wiesmüller, Karl-Heinz; Seifert, Karin; Schroff, Matthias; Juhls, Christiane; Jaffe, Charles L; Roy, Syamal; Das, Pradeep; Louzir, Hechmi; Croft, Simon L; Modabber, Farrokh; Walden, Peter

    2014-04-30

    The leishmaniases are protozoal diseases that severely affect large populations in tropical and subtropical regions. There are only limited treatment options and preventative measures. Vaccines will be important for prevention, control and elimination of leishmaniasis, and could reduce the transmission and burden of disease in endemic populations. We report the development of a DNA vaccine against leishmaniasis that induced T cell-based immunity and is a candidate for clinical trials. The vaccine antigens were selected as conserved in various Leishmania species, different endemic regions, and over time. They were tested with T cells from individuals cured of leishmaniasis, and shown to be immunogenic and to induce CD4(+) and CD8(+) T cell responses in genetically diverse human populations of different endemic regions. The vaccine proved protective in a rodent model of infection. Thus, the immunogenicity of candidate vaccine antigens in human populations of endemic regions, as well as proof of principle for induction of specific immune responses and protection against Leishmania infection in mice, provides a viable strategy for T cell vaccine development.

  7. Signal-exon trap: a novel method for the identification of signal sequences from genomic DNA

    PubMed Central

    Péterfy, Miklós; Gyuris, Tibor; Takács, László

    2000-01-01

    We describe a genomic DNA-based signal sequence trap method, signal-exon trap (SET), for the identification of genes encoding secreted and membrane-bound proteins. SET is based on the coupling of an exon trap to the translation of captured exons, which allows screening of the exon-encoded polypeptides for signal peptide function. Since most signal sequences are expected to be located in the 5′-terminal exons of genes, we first demonstrate that trapping of these exons is feasible. To test the applicability of SET for the screening of complex genomic DNA, we evaluated two critical features of the method. Specificity was assessed by the analysis of random genomic DNA and efficiency was demonstrated by screening a 425 kb YAC known to contain the genes of four secretory or membrane-bound proteins. All trapped clones contained a translation initiation signal followed by a hydrophobic stretch of amino acids representing either a known signal peptide, transmembrane domain or novel sequence. Our results suggest that SET is a potentially useful method for the isolation of signal sequence-containing genes and may find application in the discovery of novel members of known secretory gene clusters, as well as in other positional cloning approaches. PMID:10710443

  8. The nucleosome: orchestrating DNA damage signaling and repair within chromatin.

    PubMed

    Agarwal, Poonam; Miller, Kyle M

    2016-10-01

    DNA damage occurs within the chromatin environment, which ultimately participates in regulating DNA damage response (DDR) pathways and repair of the lesion. DNA damage activates a cascade of signaling events that extensively modulates chromatin structure and organization to coordinate DDR factor recruitment to the break and repair, whilst also promoting the maintenance of normal chromatin functions within the damaged region. For example, DDR pathways must avoid conflicts between other DNA-based processes that function within the context of chromatin, including transcription and replication. The molecular mechanisms governing the recognition, target specificity, and recruitment of DDR factors and enzymes to the fundamental repeating unit of chromatin, i.e., the nucleosome, are poorly understood. Here we present our current view of how chromatin recognition by DDR factors is achieved at the level of the nucleosome. Emerging evidence suggests that the nucleosome surface, including the nucleosome acidic patch, promotes the binding and activity of several DNA damage factors on chromatin. Thus, in addition to interactions with damaged DNA and histone modifications, nucleosome recognition by DDR factors plays a key role in orchestrating the requisite chromatin response to maintain both genome and epigenome integrity.

  9. Activation of cellular signaling by 8-oxoguanine DNA glycosylase-1-initiated DNA base excision repair.

    PubMed

    German, Peter; Szaniszlo, Peter; Hajas, Gyorgy; Radak, Zsolt; Bacsi, Attila; Hazra, Tapas K; Hegde, Muralidhar L; Ba, Xueqing; Boldogh, Istvan

    2013-10-01

    Accumulation of 8-oxo-7,8-dihydroguanine (8-oxoG) in the DNA results in genetic instability and mutagenesis, and is believed to contribute to carcinogenesis, aging processes and various aging-related diseases. 8-OxoG is removed from the DNA via DNA base excision repair (BER), initiated by 8-oxoguanine DNA glycosylase-1 (OGG1). Our recent studies have shown that OGG1 binds its repair product 8-oxoG base with high affinity at a site independent from its DNA lesion-recognizing catalytic site and the OGG1•8-oxoG complex physically interacts with canonical Ras family members. Furthermore, exogenously added 8-oxoG base enters the cells and activates Ras GTPases; however, a link has not yet been established between cell signaling and DNA BER, which is the endogenous source of the 8-oxoG base. In this study, we utilized KG-1 cells expressing a temperature-sensitive mutant OGG1, siRNA ablation of gene expression, and a variety of molecular biological assays to define a link between OGG1-BER and cellular signaling. The results show that due to activation of OGG1-BER, 8-oxoG base is released from the genome in sufficient quantities for activation of Ras GTPase and resulting in phosphorylation of the downstream Ras targets Raf1, MEK1,2 and ERK1,2. These results demonstrate a previously unrecognized mechanism for cellular responses to OGG1-initiated DNA BER.

  10. Functionalization of DNA Nanostructures for Cell Signaling Applications

    NASA Astrophysics Data System (ADS)

    Pedersen, Ronnie O.

    Transforming growth factor beta (TGF-beta) is an important cytokine responsible for a wide range of different cellular functions including extracellular matrix formation, angiogenesis and epithelial-mesenchymal transition. We have sought to use self-assembling DNA nanostructures to influence TGF-beta signaling. The predictable Watson Crick base pairing allows for designing self-assembling nanoscale structures using oligonucleotides. We have used the method of DNA origami to assemble structures functionalized with multiple peptides that bind TGF-beta receptors outside the ligand binding domain. This allows the nanostructures to cluster TGF-beta receptors and lower the energy barrier of ligand binding thus sensitizing the cells to TGF-beta stimulation. To prove efficacy of our nanostructures we have utilized immunofluorescent staining of Smad2/4 in order to monitor TGF-beta mediated translocation of Smad2/4 to the cell nucleus. We have also utilized Smad2/4 responsive luminescence constructs that allows us to quantify TGF-beta stimulation with and without nanostructures. To functionalize our nanostructures we relied on biotin-streptavidin linkages. This introduces a multivalency that is not necessarily desirable in all designs. Therefore we have investigated alternative means of functionalization. The first approach is based on targeting DNA nanostructure by using zinc finger binding proteins. Efficacy of zinc finger binding proteins was assayed by the use of enzyme-linked immunosorbent (ELISA) assay and atomic force microscopy (AFM). While ELISA indicated a relative specificity of zinc finger proteins for target DNA sequences AFM showed a high degree of non-specific binding and insufficient affinity. The second approach is based on using peptide nucleic acid (PNA) incorporated in the nanostructure through base pairing. PNA is a synthetic DNA analog consisting of a backbone of repeating N-(2-aminoethyl)-glycine units to which purine and pyrimidine bases are linked by

  11. DNA damage response and sphingolipid signaling in liver diseases

    PubMed Central

    Matsuda, Yasunobu; Moro, Kazuki; Tsuchida, Junko; Soma, Daiki; Hirose, Yuki; Kobayashi, Takashi; Kosugi, Shin-ichi; Takabe, Kazuaki; Komatsu, Masaaki; Wakai, Toshifumi

    2016-01-01

    Patients with unresectable hepatocellular carcinoma (HCC) cannot generally be cured by systemic chemotherapy or radiotherapy due to their poor response to conventional therapeutic agents. The development of novel and efficient targeted therapies to increase their treatment options depends on the elucidation of the molecular mechanisms that underlie the pathogenesis of HCC. The DNA damage response (DDR) is a network of cell-signaling events that are triggered by DNA damage. Its dysregulation is thought to be one of the key mechanisms underlying the generation of HCC. Sphingosine-1-phosphate (S1P), a lipid mediator, has emerged as an important signaling molecule that has been found to be involved in many cellular functions. In the liver, the alteration of S1P signaling potentially affects the DDR pathways. In this review, we explore the role of the DDR in hepatocarcinogenesis of various etiologies, including hepatitis B and C infection and non-alcoholic steatohepatitis. Furthermore, we discuss the metabolism and functions of S1P that may affect the hepatic DDR. The elucidation of the pathogenic role of S1P may create new avenues of research into therapeutic strategies for patients with HCC. PMID:26514817

  12. Modular analysis of biological networks.

    PubMed

    Kaltenbach, Hans-Michael; Stelling, Jörg

    2012-01-01

    The analysis of complex biological networks has traditionally relied on decomposition into smaller, semi-autonomous units such as individual signaling pathways. With the increased scope of systems biology (models), rational approaches to modularization have become an important topic. With increasing acceptance of de facto modularity in biology, widely different definitions of what constitutes a module have sparked controversies. Here, we therefore review prominent classes of modular approaches based on formal network representations. Despite some promising research directions, several important theoretical challenges remain open on the way to formal, function-centered modular decompositions for dynamic biological networks.

  13. Entropy in DNA Double-Strand Break, Detection and Signaling

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Schindler, Christina; Heermann, Dieter

    2014-03-01

    In biology, the term entropy is often understood as a measure of disorder - a restrictive interpretation that can even be misleading. Recently it has become clearer and clearer that entropy, contrary to conventional wisdom, can help to order and guide biological processes in living cells. DNA double-strand breaks (DSBs) are among the most dangerous lesions and efficient damage detection and repair is essential for organism viability. However, what remains unknown is the precise mechanism of targeting the site of damage within billions of intact nucleotides and a crowded nuclear environment, a process which is often referred to as recruitment or signaling. Here we show that the change in entropy associated with inflicting a DSB facilitates the recruitment of damage sensor proteins. By means of computational modeling we found that higher mobility and local chromatin structure accelerate protein association at DSB ends. We compared the effect of different chromatin architectures on protein dynamics and concentrations in the vicinity of DSBs, and related these results to experiments on repair in heterochromatin. Our results demonstrate how entropy contributes to a more efficient damage detection. We identify entropy as the physical basis for DNA double-strand break signaling.

  14. Modular entanglement.

    PubMed

    Gualdi, Giulia; Giampaolo, Salvatore M; Illuminati, Fabrizio

    2011-02-04

    We introduce and discuss the concept of modular entanglement. This is the entanglement that is established between the end points of modular systems composed by sets of interacting moduli of arbitrarily fixed size. We show that end-to-end modular entanglement scales in the thermodynamic limit and rapidly saturates with the number of constituent moduli. We clarify the mechanisms underlying the onset of entanglement between distant and noninteracting quantum systems and its optimization for applications to quantum repeaters and entanglement distribution and sharing.

  15. Nanomaterial-Assisted Signal Enhancement of Hybridization for DNA Biosensors: A Review

    PubMed Central

    Liu, Jinhuai; Liu, Jinyun; Yang, Liangbao; Chen, Xing; Zhang, Meiyun; Meng, Fanli; Luo, Tao; Li, Minqiang

    2009-01-01

    Detection of DNA sequences has received broad attention due to its potential applications in a variety of fields. As sensitivity of DNA biosensors is determined by signal variation of hybridization events, the signal enhancement is of great significance for improving the sensitivity in DNA detection, which still remains a great challenge. Nanomaterials, which possess some unique chemical and physical properties caused by nanoscale effects, provide a new opportunity for developing novel nanomaterial-based signal-enhancers for DNA biosensors. In this review, recent progress concerning this field, including some newly-developed signal enhancement approaches using quantum-dots, carbon nanotubes and their composites reported by our group and other researchers are comprehensively summarized. Reports on signal enhancement of DNA biosensors by non-nanomaterials, such as enzymes and polymer reagents, are also reviewed for comparison. Furthermore, the prospects for developing DNA biosensors using nanomaterials as signal-enhancers in future are also indicated. PMID:22399999

  16. Ultrasensitive flow injection chemiluminescence detection of DNA hybridization using signal DNA probe modified with Au and CuS nanoparticles.

    PubMed

    Zhang, Shusheng; Zhong, Hua; Ding, Caifeng

    2008-10-01

    A novel and sensitive flow injection chemiluminescence assay for sequence-specific DNA detection based on signal amplification with nanoparticles (NPs) is reported in the present work. The "sandwich-type" DNA biosensor was fabricated with the thiol-functionalized capture DNA first immobilized on an Au electrode and hybridized with one end of target DNA, the other end of which was recognized with a signal DNA probe labeled with CuS NPs and Au NPs on the 3'- and 5'-terminus, respectively. The hybridization events were monitored by the CL intensity of luminol-H2O2-Cu(2+) after the cupric ions were dissolved from the hybrids. We demonstrated that the incorporation of Au NPs in this sensor design significantly enhanced the sensitivity and the selectivity because a single Au NP can be loaded with hundreds of signal DNA probe strands, which were modified with CuS NPs. The ratios of Au NPs, signal DNA probes, and CuS NPs modified on the gold electrode were approximately 1/101/103. A preconcentration process of cupric ions performed by anodic stripping voltammetry technology further increased the sensor performance. As a result of these two combined effects, this DNA sensor could detect as low as femtomolar target DNA and exhibited excellent selectivity against two-base mismatched DNA. Under the optimum conditions, the CL intensity was increased with the increase of the concentration of target DNA in the range of 2.0 x 10(-14)-2.0 x 10(-12) M. A detection limit of 4.8 x 10(-15) M target DNA was achieved.

  17. A modular system of DNA enhancer elements mediates tissue-specific activation of transcription by high dietary zinc in C. elegans

    PubMed Central

    Roh, Hyun Cheol; Dimitrov, Ivan; Deshmukh, Krupa; Zhao, Guoyan; Warnhoff, Kurt; Cabrera, Daniel; Tsai, Wendy; Kornfeld, Kerry

    2015-01-01

    Zinc is essential for biological systems, and aberrant zinc metabolism is implicated in a broad range of human diseases. To maintain homeostasis in response to fluctuating levels of dietary zinc, animals regulate gene expression; however, mechanisms that mediate the transcriptional response to fluctuating levels of zinc have not been fully defined. Here, we identified DNA enhancer elements that mediate intestine-specific transcriptional activation in response to high levels of dietary zinc in C. elegans. Using bioinformatics, we characterized an evolutionarily conserved enhancer element present in multiple zinc-inducible genes, the high zinc activation (HZA) element. The HZA was consistently adjacent to a GATA element that mediates expression in intestinal cells. Functional studies using transgenic animals demonstrated that this modular system of DNA enhancers mediates tissue-specific transcriptional activation in response to high levels of dietary zinc. We used this information to search the genome and successfully identified novel zinc-inducible genes. To characterize the mechanism of enhancer function, we demonstrated that the GATA transcription factor ELT-2 and the mediator subunit MDT-15 are necessary for zinc-responsive transcriptional activation. These findings define new mechanisms of zinc homeostasis and tissue-specific regulation of transcription. PMID:25552416

  18. DNA photonic nanowires with tunable FRET signals on the basis of toehold-mediated DNA strand displacement reactions.

    PubMed

    Wang, Bei; Wang, Xiaojing; Wei, Bing; Huang, Fujian; Yao, Dongbao; Liang, Haojun

    2017-03-02

    A DNA photonic nanowire with tunable FRET signals was fabricated on the basis of cascaded toehold-mediated DNA strand displacement reactions. Different DNA inputs were added to trigger the reaction network, and the corresponding FRET signals were obtained. Compared to the direct hybridization, this design is sensitive for 2 nM targets within 20 min and also causes color changes of the solution with blue-light excitation. It could also be applied in live cells to monitor MicroRNA with a simple modification which might become a low-cost method for further application in the future.

  19. Detection of DNA hybridization by field-effect DNA-based biosensors: mechanisms of signal generation and open questions.

    PubMed

    Cherstvy, A G

    2013-08-15

    We model theoretically the electrostatic effects taking place upon DNA hybridization in dense DNA arrays immobilized on a layer of Au nano-particles deposited on the surface of a field-effect-based DNA capacitive biosensor. We consider the influence of separation of a charged analyte from the sensor surface and the salinity of electrolyte solution, in the framework of both linear and nonlinear Poisson-Boltzmann theories. The latter predicts a substantially weaker sensor signals due to electrostatic saturation effects that is the main conclusion of this paper. We analyze how different physical parameters of dense DNA brushes affect the magnitude of hybridization signals. The list includes the fraction of DNA charge neutralization, the length and spatial conformations of adsorbed DNA molecules, as well as the discreteness of DNA charges. We also examine the effect of Donnan ionic equilibrium in DNA lattices on the sensor response. The validity of theoretical models is contrasted against recent experimental observations on detection of DNA hybridization via its intrinsic electric charge. The sensitivity of such biochemical sensing devices, their detection limit, and DNA hybridization efficiency are briefly discussed in the end.

  20. Hairpin DNA Switch for Ultrasensitive Spectrophotometric Detection of DNA Hybridization Based on Gold Nanoparticles and Enzyme Signal Amplification

    SciTech Connect

    Zhang, Youyu; Tang, Zhiwen; Wang, Jun; Wu, Hong; Maham, Aihui; Lin, Yuehe

    2010-08-01

    A novel DNA detection platform based on a hairpin-DNA switch, nanoparticles, and enzyme signal amplification for ultrasensitive detection of DNA hybridization has been developed in this work. In this DNA assay, a “stem-loop” DNA probe dually labeled with a thiol at its 5’ end and a biotin at its 3’ end, respectively, was used. This probe was immobilized on the gold nanoparticles (AuNPs) anchored by a protein, globulin, on a 96-well microplate. In the absence of target DNA, the immobilized probe with the stem-loop structure shields the biotin from being approached by a bulky horseradish peroxidase linked-avidin (avidin-HRP) conjugate due to the steric hindrance. However, in the presence of target DNA, the hybridization between the hairpin DNA probe and the target DNA causes significant conformational change of the probe, which forces biotin away from the surface of AuNPs. As a result, the biotin becomes accessible by the avidin-HRP, and the target hybridization event can be sensitively detected via the HRP catalyzed substrate 3, 3', 5, 5'-tetramethylbenzidine using spectrophometric method. Some experimental parameters governing the performance of the assay have been optimized. At optimal conditions, this DNA assay can detect DNA at the concentration of femtomolar level by means of a signal amplification strategy based on the combination of enzymes and nanoparticles. This approach also has shown excellent specificity to distinguish single-base mismatches of DNA targets because of the intrinsic high selectivity of the hairpin DNA probe.

  1. Electrochemical DNA probe for Hg(2+) detection based on a triple-helix DNA and Multistage Signal Amplification Strategy.

    PubMed

    Wang, Huan; Zhang, Yihe; Ma, Hongmin; Ren, Xiang; Wang, Yaoguang; Zhang, Yong; Wei, Qin

    2016-12-15

    In this work, an ultrasensitive electrochemical sensor was developed for detection of Hg(2+). Gold nanoparticles decorated bovine serum albumin reduction of graphene oxide (AuNP-BSA-rGO) were used as subsurface material for the immobilization of triple-helix DNA. The triple-helix DNA containing a thiol labelled single-stranded DNA (sDNA) and a thymine-rich DNA (T-rich DNA), which could be unwinded in the present of Hg(2+) to form more stable thymine-Hg(2+)-thymine (T-Hg(2+)-T) complex. T-Hg(2+)-T complex was then removed and the sDNA was left on the electrode. At this time, gold nanoparticle carrying thiol labelled cytosine-rich complementary DNA (cDNA-AuNP) could bind with the free sDNA. Meanwhile, the other free cDNA on AuNP could bind with each other in the present of Ag(+) to form the stable cytosine-Ag(+)-cytosine (C-Ag(+)-C) complex and circle amplification. Plenty of C-Ag(+)-C could form silver nanoclusters by electrochemical reduction and the striping signal of Ag could be measured for purpose of the final electrochemical detection of Hg(2+). This sensor could detect Hg(2+) over a wide concentration range from 0.1 to 130nM with a detection limit of 0.03nM.

  2. DNA supercoiling: A regulatory signal for the λ repressor

    PubMed Central

    Ding, Yue; Manzo, Carlo; Fulcrand, Geraldine; Leng, Fenfei; Dunlap, David; Finzi, Laura

    2014-01-01

    Topoisomerases, polymerases, and the chirality introduced by the binding of histones or nucleoid-associated proteins affect DNA supercoiling in vivo. However, supercoiling is not just a by-product of DNA metabolism. Supercoiling is an indicator of cell health, it modifies the accessibility of chromatin, and coordinates the transcription of genes. This suggests that regulatory, protein-mediated loops in DNA may sense supercoiling of the genome in which they are embedded. The λ repressor (CI) maintains the quiescent (lysogenic) transcriptome of bacteriophage λ in infected Escherichia coli. CI-mediated looping prevents overexpression of the repressor protein to preserve sensitivity to conditions that trigger virulence (lysis). Experiments were performed to assess how well the CI-mediated DNA loop traps superhelicity and determine whether supercoiling enhances CI-mediated DNA looping. CI oligomers partitioned plasmids into topological domains and prevented the passage of supercoiling between them. Furthermore, in single DNA molecules stretched and twisted with magnetic tweezers, levels of superhelical density confined in CI-mediated DNA loops ranged from −15% or +11%. Finally, in DNA under tensions that may occur in vivo, supercoiling lowered the free energy of loop formation and was essential for DNA looping. Supercoiling-enhanced looping can influence the maintenance of lysogeny in the λ repressor system; it can encode sensitivity to the energy level of the cell and creates independent topological domains of distinct superhelical density. PMID:25319264

  3. Novel signal amplification approach for HRP-based colorimetric genosensors using DNA binding protein tags.

    PubMed

    Aktas, Gülsen Betül; Skouridou, Vasso; Masip, Lluis

    2015-12-15

    The need for sensitive detection of DNA is growing as more specific DNA sequences are being correlated to gene markers for disease diagnosis, food safety and other security related applications. Detection in hybridization-based assays is usually achieved with target-specific ssDNA probes conjugated directly to enzyme labels like HRP that provide signal amplification or with nanoparticles functionalized with DNA and multiple HRP molecules. In order to overcome some of the drawbacks presented by these approaches, we developed a unique DNA sensing platform based on an HRP-DNA binding protein tag conjugate and a hybrid ssDNA-dsDNA detection probe. Specifically, in this work we describe the preparation and characterization of an HRP conjugate with scCro DNA binding protein tag and its application for the detection of a model ssDNA target sequence. By using the HRP-scCro conjugate together with a hybrid detection probe containing three scCro-specific dsDNA binding sites, we demonstrate an improvement by over 3-fold in both sensitivity and limit of detection of high-risk human papillomavirus (HPV16), compared to the standard ssDNA-HRP conjugate. These results show that the HRP-DNA binding protein tag conjugate can be used as an alternative and universal tool for signal enhancement in enzyme-linked assays suitable for integration in point-of-care systems.

  4. Genomic signal processing methods for computation of alignment-free distances from DNA sequences.

    PubMed

    Borrayo, Ernesto; Mendizabal-Ruiz, E Gerardo; Vélez-Pérez, Hugo; Romo-Vázquez, Rebeca; Mendizabal, Adriana P; Morales, J Alejandro

    2014-01-01

    Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments.

  5. Genomic Signal Processing Methods for Computation of Alignment-Free Distances from DNA Sequences

    PubMed Central

    Borrayo, Ernesto; Mendizabal-Ruiz, E. Gerardo; Vélez-Pérez, Hugo; Romo-Vázquez, Rebeca; Mendizabal, Adriana P.; Morales, J. Alejandro

    2014-01-01

    Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments. PMID:25393409

  6. Effect of structure on sensing performance of a target induced signaling probe shifting DNA-based (TISPS-DNA) sensor.

    PubMed

    Yu, Xiang; Yu, Zhigang; Li, Fengqin; Xu, Yanmei; He, Xunjun; Xu, Lan; Shi, Wenbing; Zhang, Guiling; Yan, Hong

    2017-05-15

    A type of "signal on" displacement-based sensors named target induced signaling probe shifting DNA-based (TISPS-DNA) sensor were developed for a designated DNA detection. The signaling mechanism of the signaling probe (SP) shifting different from the classical conformation/flexibility change mode endows the sensor with high sensitivity. Through using thiolated or no thiolated capturing probe (CP), two 3-probe sensing structures, sensor-1 and sensor-2, were designed and constructed. The systematical comparing research results show that both sensors exhibit some similarities or big differences in sensing performance. On the one hand, the similarity in structures determines the similarity in some aspects of signaling mechanism, background signal, signal changing form, anti-fouling ability and versatility; on the other hand, the slight difference in structures also results in two opposite hybridization modes of gradual increasing resistance and gradual decreasing resistance which can affect the hybridization efficiency between the assistant probe (AP) and the SP, further producing some big differences in sensing performance, for example, apparently different signal enhancement (SE) change, point mutation discrimination ability and response speed. Under the optimized fabrication and detection conditions, both sensors feature high sensitivity for target DNAs with the detection limits of ∼10 fM for sensor-1 and ∼7 fM for sensor-2, respectively. Among many acquired sensing virtues, the sensor-1 shows a peculiar specificity adjustability which is also a highlight in this work.

  7. Transcription factor modularity in a gene-centered C. elegans core neuronal protein–DNA interaction network

    PubMed Central

    Vermeirssen, Vanessa; Barrasa, M. Inmaculada; Hidalgo, César A.; Babon, Jenny Aurielle B.; Sequerra, Reynaldo; Doucette-Stamm, Lynn; Barabási, Albert-László; Walhout, Albertha J.M.

    2007-01-01

    Transcription regulatory networks play a pivotal role in the development, function, and pathology of metazoan organisms. Such networks are comprised of protein–DNA interactions between transcription factors (TFs) and their target genes. An important question pertains to how the architecture of such networks relates to network functionality. Here, we show that a Caenorhabditis elegans core neuronal protein–DNA interaction network is organized into two TF modules. These modules contain TFs that bind to a relatively small number of target genes and are more systems specific than the TF hubs that connect the modules. Each module relates to different functional aspects of the network. One module contains TFs involved in reproduction and target genes that are expressed in neurons as well as in other tissues. The second module is enriched for paired homeodomain TFs and connects to target genes that are often exclusively neuronal. We find that paired homeodomain TFs are specifically expressed in C. elegans and mouse neurons, indicating that the neuronal function of paired homeodomains is evolutionarily conserved. Taken together, we show that a core neuronal C. elegans protein–DNA interaction network possesses TF modules that relate to different functional aspects of the complete network. PMID:17513831

  8. Modular shield

    DOEpatents

    Snyder, Keith W.

    2002-01-01

    A modular system for containing projectiles has a sheet of material including at least a polycarbonate layer held by a metal frame having a straight frame member corresponding to each straight edge of the sheet. Each frame member has a U-shaped shield channel covering and holding a straight edge of the sheet and an adjacent U-shaped clamp channel rigidly held against the shield channel. A flexible gasket separates each sheet edge from its respective shield channel; and each frame member is fastened to each adjacent frame member only by clamps extending between adjacent clamp channels.

  9. Modular Certification

    NASA Technical Reports Server (NTRS)

    Rushby, John; Miner, Paul S. (Technical Monitor)

    2002-01-01

    Airplanes are certified as a whole: there is no established basis for separately certifying some components, particularly software-intensive ones, independently of their specific application in a given airplane. The absence of separate certification inhibits the development of modular components that could be largely "precertified" and used in several different contexts within a single airplane, or across many different airplanes. In this report, we examine the issues in modular certification of software components and propose an approach based on assume-guarantee reasoning. We extend the method from verification to certification by considering behavior in the presence of failures. This exposes the need for partitioning, and separation of assumptions and guarantees into normal and abnormal cases. We then identify three classes of property that must be verified within this framework: safe function, true guarantees, and controlled failure. We identify a particular assume-guarantee proof rule (due to McMillan) that is appropriate to the applications considered, and formally verify its soundness in PVS.

  10. A superstructure-based electrochemical assay for signal-amplified detection of DNA methyltransferase activity.

    PubMed

    Zhang, Hui; Yang, Yin; Dong, Huilei; Cai, Chenxin

    2016-12-15

    DNA methyltransferase (MTase) activity is highly correlated with the occurrence and development of cancer. This work reports a superstructure-based electrochemical assay for signal-amplified detection of DNA MTase activity using M.SssI as an example. First, low-density coverage of DNA duplexes on the surface of the gold electrode was achieved by immobilized mercaptohexanol, followed by immobilization of DNA duplexes. The duplex can be cleaved by BstUI endonuclease in the absence of DNA superstructures. However, the cleavage is blocked after the DNA is methylated by M.SssI. The DNA superstructures are formed with the addition of helper DNA. By using an electroactive complex, RuHex, which can bind to DNA double strands, the activity of M.SssI can be quantitatively detected by differential pulse voltammetry. Due to the high site-specific cleavage by BstUI and signal amplification by the DNA superstructure, the biosensor can achieve ultrasensitive detection of DNA MTase activity down to 0.025U/mL. The method can be used for evaluation and screening of the inhibitors of MTase, and thus has potential in the discovery of methylation-related anticancer drugs.

  11. Deficient DNA damage signaling leads to chemoresistance to cisplatin in oral cancer

    PubMed Central

    Wang, Ling; Mosel, Adam J.; Oakley, Gregory G.; Peng, Aimin

    2012-01-01

    Activation of the cellular DNA damage response (DDR) is an important determinant of cell sensitivity to cisplatin and other chemotherapeutic drugs that eliminate tumor cells through induction of DNA damage. It is therefore important to investigate whether alterations of the DNA damage signaling pathway confer chemoresistance in cancer cells, and whether pharmacological manipulation of the DDR pathway can re-sensitize these cells to cancer therapy. In a panel of oral/laryngeal squamous cell carcinoma (SCC) cell lines, we observed deficiencies in DNA damage signaling in correlation with cisplatin-resistance, but not with DNA repair. These deficiencies are consistent with reduced expression of components of the ATM-dependent signaling pathway and, in particular, strong up-regulation of Wip1, a negative regulator of the ATM pathway. Wip1 knockdown or inhibition enhanced DNA damage signaling and re-sensitized oral SCC cells to cisplatin. In contrast to the previously reported involvement of Wip1 in cancer, Wip1 up-regulation and function in these SCC cells is independent of p53. Finally, using xenograft tumor models, we demonstrated that Wip1 up-regulation promotes tumorigenesis and its inhibition improves the tumor response to cisplatin. Thus, this study reveals that chemoresistance in oral SCCs is partially attributed to deficiencies in DNA damage signaling, and Wip1 is an effective drug target for enhanced cancer therapy. PMID:22973056

  12. The Mre11 complex: at the crossroads of dna repair and checkpoint signalling.

    PubMed

    D'Amours, Damien; Jackson, Stephen P

    2002-05-01

    The Mre11 complex is a multisubunit nuclease that is composed of Mre11, Rad50 and Nbs1/Xrs2. Mutations in the genes that encode components of this complex result in DNA- damage sensitivity, genomic instability, telomere shortening and aberrant meiosis. The molecular defect that underlies these phenotypes has long been thought to be related to a DNA repair deficiency. However, recent studies have uncovered functions for the Mre11 complex in checkpoint signalling and DNA replication.

  13. Ultrasensitive fluorescence polarization DNA detection by target assisted exonuclease III-catalyzed signal amplification.

    PubMed

    Zhang, Min; Guan, Yi-Meng; Ye, Bang-Ce

    2011-03-28

    Single stranded DNA sequences can be detected by target assisted exonuclease III-catalyzed signal amplification fluorescence polarization (TAECA-FP). The method offers an impressive detection limit of 83 aM within one hour for DNA detection and exhibits high discrimination ability even against a single base mismatch.

  14. DNA sequence and structure requirements for cleavage of V(D)J recombination signal sequences.

    PubMed Central

    Cuomo, C A; Mundy, C L; Oettinger, M A

    1996-01-01

    Purified RAG1 and RAG2 proteins can cleave DNA at V(D)J recombination signals. In dissecting the DNA sequence and structural requirements for cleavage, we find that the heptamer and nonamer motifs of the recombination signal sequence can independently direct both steps of the cleavage reaction. Proper helical spacing between these two elements greatly enhances the efficiency of cleavage, whereas improper spacing can lead to interference between the two elements. The signal sequences are surprisingly tolerant of structural variation and function efficiently when nicks, gaps, and mismatched bases are introduced or even when the signal sequence is completely single stranded. Sequence alterations that facilitate unpairing of the bases at the signal/coding border activate the cleavage reaction, suggesting that DNA distortion is critical for V(D)J recombination. PMID:8816481

  15. The basic chemistry of exercise-induced DNA oxidation: oxidative damage, redox signaling, and their interplay.

    PubMed

    Cobley, James N; Margaritelis, Nikos V; Morton, James P; Close, Graeme L; Nikolaidis, Michalis G; Malone, John K

    2015-01-01

    Acute exercise increases reactive oxygen and nitrogen species generation. This phenomenon is associated with two major outcomes: (1) redox signaling and (2) macromolecule damage. Mechanistic knowledge of how exercise-induced redox signaling and macromolecule damage are interlinked is limited. This review focuses on the interplay between exercise-induced redox signaling and DNA damage, using hydroxyl radical ((·)OH) and hydrogen peroxide (H2O2) as exemplars. It is postulated that the biological fate of H2O2 links the two processes and thus represents a bifurcation point between redox signaling and damage. Indeed, H2O2 can participate in two electron signaling reactions but its diffusion and chemical properties permit DNA oxidation following reaction with transition metals and (·)OH generation. It is also considered that the sensing of DNA oxidation by repair proteins constitutes a non-canonical redox signaling mechanism. Further layers of interaction are provided by the redox regulation of DNA repair proteins and their capacity to modulate intracellular H2O2 levels. Overall, exercise-induced redox signaling and DNA damage may be interlinked to a greater extent than was previously thought but this requires further investigation.

  16. Modular and coordinated expression of immune system regulatory and signaling components in the developing and adult nervous system.

    PubMed

    Monzón-Sandoval, Jimena; Castillo-Morales, Atahualpa; Crampton, Sean; McKelvey, Laura; Nolan, Aoife; O'Keeffe, Gerard; Gutierrez, Humberto

    2015-01-01

    During development, the nervous system (NS) is assembled and sculpted through a concerted series of neurodevelopmental events orchestrated by a complex genetic programme. While neural-specific gene expression plays a critical part in this process, in recent years, a number of immune-related signaling and regulatory components have also been shown to play key physiological roles in the developing and adult NS. While the involvement of individual immune-related signaling components in neural functions may reflect their ubiquitous character, it may also reflect a much wider, as yet undescribed, genetic network of immune-related molecules acting as an intrinsic component of the neural-specific regulatory machinery that ultimately shapes the NS. In order to gain insights into the scale and wider functional organization of immune-related genetic networks in the NS, we examined the large scale pattern of expression of these genes in the brain. Our results show a highly significant correlated expression and transcriptional clustering among immune-related genes in the developing and adult brain, and this correlation was the highest in the brain when compared to muscle, liver, kidney and endothelial cells. We experimentally tested the regulatory clustering of immune system (IS) genes by using microarray expression profiling in cultures of dissociated neurons stimulated with the pro-inflammatory cytokine TNF-alpha, and found a highly significant enrichment of immune system-related genes among the resulting differentially expressed genes. Our findings strongly suggest a coherent recruitment of entire immune-related genetic regulatory modules by the neural-specific genetic programme that shapes the NS.

  17. DNA Damage Signalling and Repair Inhibitors: The Long-Sought-After Achilles’ Heel of Cancer

    PubMed Central

    Velic, Denis; Couturier, Anthony M.; Ferreira, Maria Tedim; Rodrigue, Amélie; Poirier, Guy G.; Fleury, Fabrice; Masson, Jean-Yves

    2015-01-01

    For decades, radiotherapy and chemotherapy were the two only approaches exploiting DNA repair processes to fight against cancer. Nowadays, cancer therapeutics can be a major challenge when it comes to seeking personalized targeted medicine that is both effective and selective to the malignancy. Over the last decade, the discovery of new targeted therapies against DNA damage signalling and repair has offered the possibility of therapeutic improvements in oncology. In this review, we summarize the current knowledge of DNA damage signalling and repair inhibitors, their molecular and cellular effects, and future therapeutic use. PMID:26610585

  18. Incorporating Motif Analysis into Gene Co-expression Networks Reveals Novel Modular Expression Pattern and New Signaling Pathways

    PubMed Central

    Ma, Shisong; Shah, Smit; Bohnert, Hans J.; Snyder, Michael; Dinesh-Kumar, Savithramma P.

    2013-01-01

    Understanding of gene regulatory networks requires discovery of expression modules within gene co-expression networks and identification of promoter motifs and corresponding transcription factors that regulate their expression. A commonly used method for this purpose is a top-down approach based on clustering the network into a range of densely connected segments, treating these segments as expression modules, and extracting promoter motifs from these modules. Here, we describe a novel bottom-up approach to identify gene expression modules driven by known cis-regulatory motifs in the gene promoters. For a specific motif, genes in the co-expression network are ranked according to their probability of belonging to an expression module regulated by that motif. The ranking is conducted via motif enrichment or motif position bias analysis. Our results indicate that motif position bias analysis is an effective tool for genome-wide motif analysis. Sub-networks containing the top ranked genes are extracted and analyzed for inherent gene expression modules. This approach identified novel expression modules for the G-box, W-box, site II, and MYB motifs from an Arabidopsis thaliana gene co-expression network based on the graphical Gaussian model. The novel expression modules include those involved in house-keeping functions, primary and secondary metabolism, and abiotic and biotic stress responses. In addition to confirmation of previously described modules, we identified modules that include new signaling pathways. To associate transcription factors that regulate genes in these co-expression modules, we developed a novel reporter system. Using this approach, we evaluated MYB transcription factor-promoter interactions within MYB motif modules. PMID:24098147

  19. Bidirectional coupling of splicing and ATM signaling in response to transcription-blocking DNA damage

    PubMed Central

    Tresini, Maria; Marteijn, Jurgen A.; Vermeulen, Wim

    2016-01-01

    ABSTRACT In response to DNA damage cells activate intricate protein networks to ensure genomic fidelity and tissue homeostasis. DNA damage response signaling pathways coordinate these networks and determine cellular fates, in part, by modulating RNA metabolism. Here we discuss a replication-independent pathway activated by transcription-blocking DNA lesions, which utilizes the ATM signaling kinase to regulate spliceosome function in a reciprocal manner. We present a model according to which, displacement of co-transcriptional spliceosomes from lesion-arrested RNA polymerases, culminates in R-loop formation and non-canonical ATM activation. ATM signals in a feed-forward fashion to further impede spliceosome organization and regulates UV-induced gene expression and alternative splicing genome-wide. This reciprocal coupling between ATM and the spliceosome highlights the importance of ATM signaling in the cellular response to transcription-blocking lesions and supports a key role of the splicing machinery in this process. PMID:26913497

  20. A multiscale products technique for denoising of DNA capillary electrophoresis signals

    NASA Astrophysics Data System (ADS)

    Gao, Qingwei; Lu, Yixiang; Sun, Dong; Zhang, Dexiang

    2013-06-01

    Since noise degrades the accuracy and precision of DNA capillary electrophoresis (CE) analysis, signal denoising is thus important to facilitate the postprocessing of CE data. In this paper, a new denoising algorithm based on dyadic wavelet transform using multiscale products is applied for the removal of the noise in the DNA CE signal. The adjacent scale wavelet coefficients are first multiplied to amplify the significant features of the CE signal while diluting noise. Then, noise is suppressed by applying a multiscale threshold to the multiscale products instead of directly to the wavelet coefficients. Finally, the noise-free CE signal is recovered from the thresholded coefficients by using inverse dyadic wavelet transform. We compare the performance of the proposed algorithm with other denoising methods applied to the synthetic CE and real CE signals. Experimental results show that the new scheme achieves better removal of noise while preserving the shape of peaks corresponding to the analytes in the sample.

  1. Modular robot

    DOEpatents

    Ferrante, T.A.

    1997-11-11

    A modular robot may comprise a main body having a structure defined by a plurality of stackable modules. The stackable modules may comprise a manifold, a valve module, and a control module. The manifold may comprise a top surface and a bottom surface having a plurality of fluid passages contained therein, at least one of the plurality of fluid passages terminating in a valve port located on the bottom surface of the manifold. The valve module is removably connected to the manifold and selectively fluidically connects the plurality of fluid passages contained in the manifold to a supply of pressurized fluid and to a vent. The control module is removably connected to the valve module and actuates the valve module to selectively control a flow of pressurized fluid through different ones of the plurality of fluid passages in the manifold. The manifold, valve module, and control module are mounted together in a sandwich-like manner and comprise a main body. A plurality of leg assemblies are removably connected to the main body and are removably fluidically connected to the fluid passages in the manifold so that each of the leg assemblies can be selectively actuated by the flow of pressurized fluid in different ones of the plurality of fluid passages in the manifold. 12 figs.

  2. Modular robot

    DOEpatents

    Ferrante, Todd A.

    1997-01-01

    A modular robot may comprise a main body having a structure defined by a plurality of stackable modules. The stackable modules may comprise a manifold, a valve module, and a control module. The manifold may comprise a top surface and a bottom surface having a plurality of fluid passages contained therein, at least one of the plurality of fluid passages terminating in a valve port located on the bottom surface of the manifold. The valve module is removably connected to the manifold and selectively fluidically connects the plurality of fluid passages contained in the manifold to a supply of pressurized fluid and to a vent. The control module is removably connected to the valve module and actuates the valve module to selectively control a flow of pressurized fluid through different ones of the plurality of fluid passages in the manifold. The manifold, valve module, and control module are mounted together in a sandwich-like manner and comprise a main body. A plurality of leg assemblies are removably connected to the main body and are removably fluidically connected to the fluid passages in the manifold so that each of the leg assemblies can be selectively actuated by the flow of pressurized fluid in different ones of the plurality of fluid passages in the manifold.

  3. The role of poly(ADP-ribose) in the DNA damage signaling network.

    PubMed

    Malanga, Maria; Althaus, Felix R

    2005-06-01

    DNA damage signaling is crucial for the maintenance of genome integrity. In higher eukaryotes a NAD+-dependent signal transduction mechanism has evolved to protect cells against the genome destabilizing effects of DNA strand breaks. The mechanism involves 2 nuclear enzymes that sense DNA strand breaks, poly(ADP-ribose) polymerase-1 and -2 (PARP-1 and PARP-2). When activated by DNA breaks, these PARPs use NAD+ to catalyze their automodification with negatively charged, long and branched ADP-ribose polymers. Through recruitment of specific proteins at the site of damage and regulation of their activities, these polymers may either directly participate in the repair process or coordinate repair through chromatin unfolding, cell cycle progression, and cell survival-cell death pathways. A number of proteins, including histones, DNA topoisomerases, DNA methyltransferase-1 as well as DNA damage repair and checkpoint proteins (p23, p21, DNA-PK, NF-kB, XRCC1, and others) can be targeted in this manner; the interaction involves a specific poly(ADP-ribose)-binding sequence motif of 20-26 amino acids in the target domains.

  4. A coarse-grained DNA model for the prediction of current signals in DNA translocation experiments

    NASA Astrophysics Data System (ADS)

    Weik, Florian; Kesselheim, Stefan; Holm, Christian

    2016-11-01

    We present an implicit solvent coarse-grained double-stranded DNA (dsDNA) model confined to an infinite cylindrical pore that reproduces the experimentally observed current modulations of a KaCl solution at various concentrations. Our model extends previous coarse-grained and mean-field approaches by incorporating a position dependent friction term on the ions, which Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] identified as an essential ingredient to correctly reproduce the experimental data of Smeets et al. [Nano Lett. 6, 89 (2006)]. Our approach reduces the computational effort by orders of magnitude compared with all-atom simulations and serves as a promising starting point for modeling the entire translocation process of dsDNA. We achieve a consistent description of the system's electrokinetics by using explicitly parameterized ions, a friction term between the DNA beads and the ions, and a lattice-Boltzmann model for the solvent.

  5. The multifaceted influence of histone deacetylases on DNA damage signalling and DNA repair

    PubMed Central

    Roos, Wynand Paul; Krumm, Andrea

    2016-01-01

    Histone/protein deacetylases play multiple roles in regulating gene expression and protein activation and stability. Their deregulation during cancer initiation and progression cause resistance to therapy. Here, we review the role of histone deacetylases (HDACs) and the NAD+ dependent sirtuins (SIRTs) in the DNA damage response (DDR). These lysine deacetylases contribute to DNA repair by base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), non-homologous end joining (NHEJ), homologous recombination (HR) and interstrand crosslink (ICL) repair. Furthermore, we discuss possible mechanisms whereby these histone/protein deacetylases facilitate the switch between DNA double-strand break (DSB) repair pathways, how SIRTs play a central role in the crosstalk between DNA repair and cell death pathways due to their dependence on NAD+, and the influence of small molecule HDAC inhibitors (HDACi) on cancer cell resistance to genotoxin based therapies. Throughout the review, we endeavor to identify the specific HDAC targeted by HDACi leading to therapy sensitization. PMID:27738139

  6. Distinct immune responses of recombinant plasmid DNA replicon vaccines expressing two types of antigens with or without signal sequences.

    PubMed

    Yu, Yun-Zhou; Li, Na; Wang, Wen-Bin; Wang, Shuang; Ma, Yao; Yu, Wei-Yuan; Sun, Zhi-Wei

    2010-11-03

    Here, DNA replicon vaccines encoding the Hc domain of botulinum neurotoxin serotype A (AHc) or the receptor binding domain of anthrax protective antigen (PA4) with or without signal sequences were evaluated in mice. Strong antibody and protective responses were elicited only from AHc DNA vaccines with an Ig κ signal sequence or tissue plasminogen activator signal sequence. Meanwhile, there were no differences in total antibody responses or isotypes, lymphocyte proliferative responses, cytokine profiles and protective immune responses with the PA4 DNA vaccines with or without a signal sequence. Therefore, use of targeting sequences in designing DNA replicon vaccines depends on the specific antigen.

  7. Expression Profile of DNA Damage Signaling Genes in Proton Exposed Mouse Brain

    NASA Astrophysics Data System (ADS)

    Ramesh, Govindarajan; Wu, Honglu

    Exposure of living systems to radiation results in a wide assortment of lesions, the most signif-icant of is damage to genomic DNA which induce several cellular functions such as cell cycle arrest, repair, apoptosis etc. The radiation induced DNA damage investigation is one of the im-portant area in biology, but still the information available regarding the effects of proton is very limited. In this report, we investigated the differential gene expression pattern of DNA damage signaling genes particularly, damaged DNA binding, repair, cell cycle arrest, checkpoints and apoptosis using quantitative real-time RT-PCR array in proton exposed mouse brain tissues. The expression profiles showed significant changes in DNA damage related genes in 2Gy proton exposed mouse brain tissues as compared with control brain tissues. Furthermore, we also show that significantly increased levels of apoptotic related genes, caspase-3 and 8 activities in these cells, suggesting that in addition to differential expression of DNA damage genes, the alteration of apoptosis related genes may also contribute to the radiation induced DNA damage followed by programmed cell death. In summary, our findings suggest that proton exposed brain tissue undergo severe DNA damage which in turn destabilize the chromatin stability.

  8. Extracellular Self-DNA (esDNA), but Not Heterologous Plant or Insect DNA (etDNA), Induces Plasma Membrane Depolarization and Calcium Signaling in Lima Bean (Phaseolus lunatus) and Maize (Zea mays)

    PubMed Central

    Barbero, Francesca; Guglielmotto, Michela; Capuzzo, Andrea; Maffei, Massimo E.

    2016-01-01

    Extracellular self-DNA (esDNA) is produced during cell and tissue damage or degradation and has been shown to induce significant responses in several organisms, including plants. While the inhibitory effects of esDNA have been shown in conspecific individuals, little is known on the early events involved upon plant esDNA perception. We used electrophysiology and confocal laser scanning microscopy calcium localization to evaluate the plasma membrane potential (Vm) variations and the intracellular calcium fluxes, respectively, in Lima bean (Phaseolus lunatus) and maize (Zea mays) plants exposed to esDNA and extracellular heterologous DNA (etDNA) and to etDNA from Spodoptera littoralis larvae and oral secretions. In both species, esDNA induced a significant Vm depolarization and an increased flux of calcium, whereas etDNA was unable to exert any of these early signaling events. These findings confirm the specificity of esDNA to induce plant cell responses and to trigger early signaling events that eventually lead to plant response to damage. PMID:27690017

  9. Extracellular Self-DNA (esDNA), but Not Heterologous Plant or Insect DNA (etDNA), Induces Plasma Membrane Depolarization and Calcium Signaling in Lima Bean (Phaseolus lunatus) and Maize (Zea mays).

    PubMed

    Barbero, Francesca; Guglielmotto, Michela; Capuzzo, Andrea; Maffei, Massimo E

    2016-09-29

    Extracellular self-DNA (esDNA) is produced during cell and tissue damage or degradation and has been shown to induce significant responses in several organisms, including plants. While the inhibitory effects of esDNA have been shown in conspecific individuals, little is known on the early events involved upon plant esDNA perception. We used electrophysiology and confocal laser scanning microscopy calcium localization to evaluate the plasma membrane potential (Vm) variations and the intracellular calcium fluxes, respectively, in Lima bean (Phaseolus lunatus) and maize (Zea mays) plants exposed to esDNA and extracellular heterologous DNA (etDNA) and to etDNA from Spodoptera littoralis larvae and oral secretions. In both species, esDNA induced a significant Vm depolarization and an increased flux of calcium, whereas etDNA was unable to exert any of these early signaling events. These findings confirm the specificity of esDNA to induce plant cell responses and to trigger early signaling events that eventually lead to plant response to damage.

  10. Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks.

    PubMed

    Zhou, Chunshui; Elia, Andrew E H; Naylor, Maria L; Dephoure, Noah; Ballif, Bryan A; Goel, Gautam; Xu, Qikai; Ng, Aylwin; Chou, Danny M; Xavier, Ramnik J; Gygi, Steven P; Elledge, Stephen J

    2016-06-28

    The DNA damage response (DDR) is regulated by a protein kinase signaling cascade that orchestrates DNA repair and other processes. Identifying the substrate effectors of these kinases is critical for understanding the underlying physiology and mechanism of the response. We have used quantitative mass spectrometry to profile DDR-dependent phosphorylation in budding yeast and genetically explored the dependency of these phosphorylation events on the DDR kinases MEC1, RAD53, CHK1, and DUN1. Based on these screens, a database containing many novel DDR-regulated phosphorylation events has been established. Phosphorylation of many of these proteins has been validated by quantitative peptide phospho-immunoprecipitation and examined for functional relevance to the DDR through large-scale analysis of sensitivity to DNA damage in yeast deletion strains. We reveal a link between DDR signaling and the metabolic pathways of inositol phosphate and phosphatidyl inositol synthesis, which are required for resistance to DNA damage. We also uncover links between the DDR and TOR signaling as well as translation regulation. Taken together, these data shed new light on the organization of DDR signaling in budding yeast.

  11. Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks

    PubMed Central

    Zhou, Chunshui; Elia, Andrew E. H.; Naylor, Maria L.; Ballif, Bryan A.; Goel, Gautam; Xu, Qikai; Ng, Aylwin; Chou, Danny M.; Xavier, Ramnik J.; Gygi, Steven P.; Elledge, Stephen J.

    2016-01-01

    The DNA damage response (DDR) is regulated by a protein kinase signaling cascade that orchestrates DNA repair and other processes. Identifying the substrate effectors of these kinases is critical for understanding the underlying physiology and mechanism of the response. We have used quantitative mass spectrometry to profile DDR-dependent phosphorylation in budding yeast and genetically explored the dependency of these phosphorylation events on the DDR kinases MEC1, RAD53, CHK1, and DUN1. Based on these screens, a database containing many novel DDR-regulated phosphorylation events has been established. Phosphorylation of many of these proteins has been validated by quantitative peptide phospho-immunoprecipitation and examined for functional relevance to the DDR through large-scale analysis of sensitivity to DNA damage in yeast deletion strains. We reveal a link between DDR signaling and the metabolic pathways of inositol phosphate and phosphatidyl inositol synthesis, which are required for resistance to DNA damage. We also uncover links between the DDR and TOR signaling as well as translation regulation. Taken together, these data shed new light on the organization of DDR signaling in budding yeast. PMID:27298372

  12. Signal amplification for DNA detection based on the HRP-functionalized Fe3O4 nanoparticles.

    PubMed

    Dong, Xiao-Ya; Mi, Xiao-Na; Wang, Bo; Xu, Jing-Juan; Chen, Hong-Yuan

    2011-04-15

    An electrochemical approach for the sensitive detection of sequence-specific DNA has been developed. Horseradish peroxidase (HRP) assembled on the Fe(3)O(4) nanoparticles (NPs) were utilized as signal amplification sources. High-content HRP was adsorbed on the Fe(3)O(4) NPs via layer-by-layer (LbL) technique to prepare HRP-functionalized Fe(3)O(4) NPs. Signal probe and diluting probe were then immobilized on the HRP-functionalized Fe(3)O(4) NPs through the bridge of Au NPs. Thereafter, the resulting DNA-Au-HRP-Fe(3)O(4) (DAHF) bioconjugates were successfully anchored to the gold nanofilm (GNF) modified electrode surface for the construction of sandwich-type electrochemical DNA biosensor. The electrochemical behaviors of the prepared biosensor had been investigated by the cyclic voltammetry (CV), chronoamperometry (i-t), and electrochemical impedance spectroscopy (EIS). Under optimal conditions, the proposed strategy could detect the target DNA down to the level of 0.7 fmol with a dynamic range spanning 4 orders of magnitude and exhibited excellent discrimination to two-base mismatched DNA and non-complementary DNA sequences.

  13. The Impact of Hedgehog Signaling Pathway on DNA Repair Mechanisms in Human Cancer

    PubMed Central

    Meng, Erhong; Hanna, Ann; Samant, Rajeev S.; Shevde, Lalita A.

    2015-01-01

    Defined cellular mechanisms have evolved that recognize and repair DNA to protect the integrity of its structure and sequence when encountering assaults from endogenous and exogenous sources. There are five major DNA repair pathways: mismatch repair, nucleotide excision repair, direct repair, base excision repair and DNA double strand break repair (including non-homologous end joining and homologous recombination repair). Aberrant activation of the Hedgehog (Hh) signaling pathway is a feature of many cancer types. The Hh pathway has been documented to be indispensable for epithelial-mesenchymal transition, invasion and metastasis, cancer stemness, and chemoresistance. The functional transcription activators of the Hh pathway include the GLI proteins. Inhibition of the activity of GLI can interfere with almost all DNA repair types in human cancer, indicating that Hh/GLI functions may play an important role in enabling tumor cells to survive lethal types of DNA damage induced by chemotherapy and radiotherapy. Thus, Hh signaling presents an important therapeutic target to overcome DNA repair-enabled multi-drug resistance and consequently increase chemotherapeutic response in the treatment of cancer. PMID:26197339

  14. Opposing roles of RNF8/RNF168 and deubiquitinating enzymes in ubiquitination-dependent DNA double-strand break response signaling and DNA-repair pathway choice

    PubMed Central

    Nakada, Shinichiro

    2016-01-01

    The E3 ubiquitin ligases ring finger protein (RNF) 8 and RNF168 transduce the DNA double-strand break (DSB) response (DDR) signal by ubiquitinating DSB sites. The depletion of RNF8 or RNF168 suppresses the accumulation of DNA-repair regulating factors such as 53BP1 and RAP80 at DSB sites, suggesting roles for RNF8- and RNF168-mediated ubiquitination in DSB repair. This mini-review provides a brief overview of the RNF8- and RNF168-dependent DDR-signaling and DNA-repair pathways. The choice of DNA-repair pathway when RNF8- and RNF168-mediated ubiquitination-dependent DDR signaling is negatively regulated by deubiquitinating enzymes (DUBs) is reviewed to clarify how the opposing roles of RNF8/RNF168 and DUBs regulate ubiquitination-dependent DDR signaling and the choice of DNA-repair pathway. PMID:26983989

  15. Portable modular detection system

    DOEpatents

    Brennan, James S.; Singh, Anup; Throckmorton, Daniel J.; Stamps, James F.

    2009-10-13

    Disclosed herein are portable and modular detection devices and systems for detecting electromagnetic radiation, such as fluorescence, from an analyte which comprises at least one optical element removably attached to at least one alignment rail. Also disclosed are modular detection devices and systems having an integrated lock-in amplifier and spatial filter and assay methods using the portable and modular detection devices.

  16. Effects of DNA probe and target flexibility on the performance of a "signal-on" electrochemical DNA sensor.

    PubMed

    Wu, Yao; Lai, Rebecca Y

    2014-09-02

    We report the effect of the length and identity of a nontarget binding spacer in both the probe and target sequences on the overall performance of a folding-based electrochemical DNA sensor. Six near-identical DNA probes were used in this study; the main differences between these probes are the length (6, 10, or 14 bases) and identity (thymine (T) or adenine (A)) of the spacer connecting the two target binding domains. Despite the differences, the signaling mechanism of these sensors remains essentially the same. The methylene blue (MB)-modified probe assumes a linear unstructured conformation in the absence of the target; upon hybridization to the target, the probe adopts a "close" conformation, resulting in an increase in the MB current. Among the six sensors, the T14 and A14 sensors showed the largest signal increase upon target hybridization, highlighting the significance of probe flexibility on sensor performance. In addition to the target without a midsequence spacer, 12 other targets, each with a different oligo-T or oligo-A spacer, were used to elucidate the effect of target flexibility on the sensors' signaling capacity. For all six sensors, hybridization to targets with a 2- or 3-base spacer resulted in the largest signal increase. Higher signal enhancement was also observed with targets with an oligo-A spacer. For this sensor design, addition of a long nontarget binding spacer to the probe sequence is advantageous, as it provides flexibility for optimal target capture. The length of the spacer in the target sequence, however, should be adequately long to enable efficient hybridization yet does not introduce undesirable electrostatic and crowding effects.

  17. Signalling of DNA damage and cytokines across cell barriers exposed to nanoparticles depends on barrier thickness

    NASA Astrophysics Data System (ADS)

    Sood, A.; Salih, S.; Roh, D.; Lacharme-Lora, L.; Parry, M.; Hardiman, B.; Keehan, R.; Grummer, R.; Winterhager, E.; Gokhale, P. J.; Andrews, P. W.; Abbott, C.; Forbes, K.; Westwood, M.; Aplin, J. D.; Ingham, E.; Papageorgiou, I.; Berry, M.; Liu, J.; Dick, A. D.; Garland, R. J.; Williams, N.; Singh, R.; Simon, A. K.; Lewis, M.; Ham, J.; Roger, L.; Baird, D. M.; Crompton, L. A.; Caldwell, M. A.; Swalwell, H.; Birch-Machin, M.; Lopez-Castejon, G.; Randall, A.; Lin, H.; Suleiman, M.-S.; Evans, W. H.; Newson, R.; Case, C. P.

    2011-12-01

    The use of nanoparticles in medicine is ever increasing, and it is important to understand their targeted and non-targeted effects. We have previously shown that nanoparticles can cause DNA damage to cells cultured below a cellular barrier without crossing this barrier. Here, we show that this indirect DNA damage depends on the thickness of the cellular barrier, and it is mediated by signalling through gap junction proteins following the generation of mitochondrial free radicals. Indirect damage was seen across both trophoblast and corneal barriers. Signalling, including cytokine release, occurred only across bilayer and multilayer barriers, but not across monolayer barriers. Indirect toxicity was also observed in mice and using ex vivo explants of the human placenta. If the importance of barrier thickness in signalling is a general feature for all types of barriers, our results may offer a principle with which to limit the adverse effects of nanoparticle exposure and offer new therapeutic approaches.

  18. Fibroblast growth factor type 2 signaling is critical for DNA repair in human keratinocyte stem cells.

    PubMed

    Harfouche, Ghida; Vaigot, Pierre; Rachidi, Walid; Rigaud, Odile; Moratille, Sandra; Marie, Mélanie; Lemaitre, Gilles; Fortunel, Nicolas O; Martin, Michèle T

    2010-09-01

    Tissue stem cells must be endowed with superior maintenance and repair systems to ensure genomic stability over multiple generations, which would be less necessary in more differentiated cells. We previously reported that human keratinocyte stem cells were more resistant to ionizing radiation toxicity than their direct progeny, the keratinocyte progenitor cells. In the present study we addressed the mechanisms underlying this difference. Investigations of DNA repair showed that both single and double DNA strand breaks were repaired more rapidly and more efficiently in stem cells than in progenitors. As cell signaling is a key regulatory step in the management of DNA damage, a gene profiling study was performed. Data revealed that several genes of the fibroblast growth factor type 2 (FGF2) signaling pathway were induced by DNA damage in stem cells and not in progenitors. Furthermore, an increased content of the FGF2 protein was found in irradiated stem cells, both for the secreted and the cellular forms of the protein. To examine the role of endogenous FGF2 in DNA repair, stem cells were exposed to FGF2 pathway inhibitors. Blocking the FGF2 receptor (FGF receptor 1) or the kinase (Ras-mitogen-activated protein kinase 1) resulted in a inhibition of single and double DNA strand-break repair in the keratinocyte stem cells. Moreover, supplementing the progenitor cells with exogenous FGF2 activated their DNA repair. We propose that, apart from its well-known role as a strong mitogen and prosurvival factor, FGF2 helps to maintain genomic integrity in stem cells by activating stress-induced DNA repair.

  19. Modular error embedding

    DOEpatents

    Sandford, II, Maxwell T.; Handel, Theodore G.; Ettinger, J. Mark

    1999-01-01

    A method of embedding auxiliary information into the digital representation of host data containing noise in the low-order bits. The method applies to digital data representing analog signals, for example digital images. The method reduces the error introduced by other methods that replace the low-order bits with auxiliary information. By a substantially reverse process, the embedded auxiliary data can be retrieved easily by an authorized user through use of a digital key. The modular error embedding method includes a process to permute the order in which the host data values are processed. The method doubles the amount of auxiliary information that can be added to host data values, in comparison with bit-replacement methods for high bit-rate coding. The invention preserves human perception of the meaning and content of the host data, permitting the addition of auxiliary data in the amount of 50% or greater of the original host data.

  20. Lyn tyrosine kinase promotes silencing of ATM-dependent checkpoint signaling during recovery from DNA double-strand breaks

    SciTech Connect

    Fukumoto, Yasunori Kuki, Kazumasa; Morii, Mariko; Miura, Takahito; Honda, Takuya; Ishibashi, Kenichi; Hasegawa, Hitomi; Kubota, Sho; Ide, Yudai; Yamaguchi, Noritaka; Nakayama, Yuji; Yamaguchi, Naoto

    2014-09-26

    Highlights: • Inhibition of Src family kinases decreased γ-H2AX signal. • Inhibition of Src family increased ATM-dependent phosphorylation of Chk2 and Kap1. • shRNA-mediated knockdown of Lyn increased phosphorylation of Kap1 by ATM. • Ectopic expression of Src family kinase suppressed ATM-mediated Kap1 phosphorylation. • Src is involved in upstream signaling for inactivation of ATM signaling. - Abstract: DNA damage activates the DNA damage checkpoint and the DNA repair machinery. After initial activation of DNA damage responses, cells recover to their original states through completion of DNA repair and termination of checkpoint signaling. Currently, little is known about the process by which cells recover from the DNA damage checkpoint, a process called checkpoint recovery. Here, we show that Src family kinases promote inactivation of ataxia telangiectasia mutated (ATM)-dependent checkpoint signaling during recovery from DNA double-strand breaks. Inhibition of Src activity increased ATM-dependent phosphorylation of Chk2 and Kap1. Src inhibition increased ATM signaling both in G2 phase and during asynchronous growth. shRNA knockdown of Lyn increased ATM signaling. Src-dependent nuclear tyrosine phosphorylation suppressed ATM-mediated Kap1 phosphorylation. These results suggest that Src family kinases are involved in upstream signaling that leads to inactivation of the ATM-dependent DNA damage checkpoint.

  1. DNA damage signaling, impairment of cell cycle progression, and apoptosis triggered by 5-ethynyl-2'-deoxyuridine incorporated into DNA.

    PubMed

    Zhao, Hong; Halicka, H Dorota; Li, Jiangwei; Biela, Ewa; Berniak, Krzysztof; Dobrucki, Jurek; Darzynkiewicz, Zbigniew

    2013-11-01

    The "click chemistry" approach utilizing 5-ethynyl-2'-deoxyuridine (EdU) as a DNA precursor was recently introduced to assess DNA replication and adapted to flow- and imaging-cytometry. In the present study, we observed that EdU, once incorporated into DNA, induces DNA damage signaling (DDS) such as phosphorylation of ATM on Ser1981, of histone H2AX on Ser139, of p53 on Ser15, and of Chk2 on Thr68. It also perturbs progression of cells through the cell cycle and subsequently induces apoptosis. These effects were observed in non-small cell lung adenocarcinoma A549 as well as in B-cell human lymphoblastoid TK6 and WTK1 cells, differing in the status of p53 (wt versus mutated). After 1 h EdU pulse-labeling, the most affected was cells progression through the S phase subsequent to that at which they had incorporated EdU. This indicates that DNA replication using the template containing incorporated EdU is protracted and triggers DDS. Furthermore, progression of cells having DNA pulse-labeled with EdU led to accumulation of cells in G2 , likely by activating G2 checkpoint. Consistent with the latter was activation of p53 and Chk2. Although a correlation was observed in A549 cells between the degree of EdU incorporation and the extent of γH2AX induction, such correlation was weak in TK6 and WTK1 cells. The degree of perturbation of the cell cycle kinetics by the incorporated EdU was different in the wt p53 TK6 cells as compared to their sister WTK1 cell line having mutated p53. The data are thus consistent with the role of p53 in modulating activation of cell cycle checkpoints in response to impaired DNA replication. The confocal microscopy analysis of the 3D images of cells exposed to EdU for 1 h pulse and then grown for 24 or 48 h revealed an increased number of colocalized γH2AX and p53BP1 foci considered to be markers of DNA double-strand breaks and enlarged nuclei.

  2. Visualization of mitochondrial DNA replication in individual cells by EdU signal amplification.

    PubMed

    Haines, Kristine M; Feldman, Eva L; Lentz, Stephen I

    2010-11-15

    Mitochondria are key regulators of cellular energy and mitochondrial biogenesis is an essential component of regulating mitochondria numbers in healthy cells. One approach for monitoring mitochondrial biogenesis is to measure the rate of mitochondrial DNA (mtDNA) replication. We developed a sensitive technique to label newly synthesized mtDNA in individual cells in order to study mtDNA biogenesis. The technique combines the incorporation of 5-ethynyl-2'-deoxyuridine (EdU) with a tyramide signal amplification (TSA) protocol to visualize mtDNA replication within subcellular compartments of neurons. EdU is superior to other thymidine analogs, such as 5-bromo-2-deoxyuridine (BrdU), because the initial click reaction to label EdU does not require the harsh acid treatments or enzyme digests that are required for exposing the BrdU epitope. The milder labeling of EdU allows for direct comparison of its incorporation with other cellular markers. The ability to visualize and quantify mtDNA biogenesis provides an essential tool for investigating the mechanisms used to regulate mitochondrial biogenesis and would provide insight into the pathogenesis associated with drug toxicity, aging, cancer and neurodegenerative diseases. Our technique is applicable to sensory neurons as well as other cell types. The use of this technique to measure mtDNA biogenesis has significant implications in furthering the understanding of both normal cellular physiology as well as impaired disease states.

  3. THE PROTEASOME REGULATES BACTERIAL CpG DNA-INDUCED SIGNALING PATHWAYS IN MURINE MACROPHAGES

    PubMed Central

    Gao, Jian Jun; Shen, Jing; Kolbert, Christopher; Raghavakaimal, Sreekumar; Papasian, Christopher J.; Qureshi, Asaf A.; Vogel, Stefanie N.; Morrison, David C.; Qureshi, Nilofer

    2010-01-01

    Our previous work has provided strong evidence that the proteasome is central to the vast majority of genes induced in mouse macrophages in response to lipopolysaccharide (LPS) stimulation. In the studies presented here, we evaluated the role of the macrophage proteasome in response to a second microbial product CpG DNA (unmethylated bacterial DNA). For these studies, we applied Affymetrix microarray analysis of RNA derived from murine macrophages stimulated with CpG DNA in the presence or absence of proteasome inhibitor, lactacystin. The results of these studies revealed that similar to LPS, a vast majority of those macrophage genes regulated by CpG DNA are also under the control of the proteasome at 4 h. In contrast to LPS stimulation, however, many of these genes were induced much later than 4 h, at 18 h, in response to CpG DNA. Lactacystin treatment of macrophages completely blocked the CpG DNA-induced gene expression of TNF-α and other genes involved in production of inflammatory mediators. These data strongly support the conclusion that, similar to LPS, the macrophage proteasome is a key regulator of CpG DNA-induced signaling pathways. PMID:20160661

  4. Herbivore-Induced DNA Demethylation Changes Floral Signalling and Attractiveness to Pollinators in Brassica rapa

    PubMed Central

    Schlüter, Philipp M.; Schiestl, Florian P.

    2016-01-01

    Plants have to fine-tune their signals to optimise the trade-off between herbivore deterrence and pollinator attraction. An important mechanism in mediating plant-insect interactions is the regulation of gene expression via DNA methylation. However, the effect of herbivore-induced DNA methylation changes on pollinator-relevant plant signalling has not been systematically investigated. Here, we assessed the impact of foliar herbivory on DNA methylation and floral traits in the model crop plant Brassica rapa. Methylation-sensitive amplified fragment length polymorphism (MSAP) analysis showed that leaf damage by the caterpillar Pieris brassicae was associated with genome-wide methylation changes in both leaves and flowers of B. rapa as well as a downturn in flower number, morphology and scent. A comparison to plants with jasmonic acid-induced defence showed similar demethylation patterns in leaves, but both the floral methylome and phenotype differed significantly from P. brassicae infested plants. Standardised genome-wide demethylation with 5-azacytidine in five different B. rapa full-sib groups further resulted in a genotype-specific downturn of floral morphology and scent, which significantly reduced the attractiveness of the plants to the pollinator bee Bombus terrestris. These results suggest that DNA methylation plays an important role in adjusting plant signalling in response to changing insect communities. PMID:27870873

  5. DNA stabilization by the upregulation of estrogen signaling in BRCA gene mutation carriers.

    PubMed

    Suba, Zsuzsanna

    2015-01-01

    Currently available scientific evidence erroneously suggests that mutagenic weakness or loss of the BRCA1/2 genes may liberate the proliferative effects of estrogen signaling, which provokes DNA damage and genomic instability. Conversely, BRCA mutation seems to be an imbalanced defect, crudely inhibiting the upregulation of estrogen receptor expression and liganded transcriptional activity, whereas estrogen receptor-repressor functions become predominant. In BRCA-proficient cases, estrogen signaling orchestrates the activity of cell proliferation and differentiation with high safety, while upregulating the expression and DNA-stabilizing impact of BRCA genes. In turn, BRCA proteins promote estrogen signaling by proper estrogen synthesis via CYP19 gene regulation and by induction of the appropriate expression and transcriptional activity of estrogen receptors. In this exquisitely organized regulatory system, the dysfunction of each player may jeopardize genome stability and lead to severe chronic diseases, such as cancer development. Female organs, such as breast, endometrium, and ovary, exhibiting regular cyclic proliferative activity are particularly vulnerable in case of disturbances in either estrogen signaling or BRCA-mediated DNA repair. BRCA mutation carrier women may apparently be healthy or exhibit clinical signs of deficient estrogen signaling in spite of hyperestrogenism. Even women who enjoy sufficient compensatory DNA-defending activities are at risk of tumor development because many endogenous and environmental factors may jeopardize the mechanisms of extreme compensatory processes. Natural estrogens have numerous benefits in tumor prevention and therapy even in BRCA mutation carriers. There are no toxic effects even in sky-high doses and all physiologic cellular functions are strongly upregulated, while malignant tumor cells are recognized and killed in a Janus-faced manner.

  6. Entrapment of fluorescence signaling DNA enzymes in sol-gel-derived materials for metal ion sensing.

    PubMed

    Shen, Yutu; Mackey, Gillian; Rupcich, Nicholas; Gloster, Darin; Chiuman, William; Li, Yingfu; Brennan, John D

    2007-05-01

    Three fluorescence signaling DNA enzymes (deoxyribozymes or DNAzymes) were successfully immobilized within a series of sol-gel-derived matrixes and used for sensing of various metal ions. The DNAzymes are designed such that binding of appropriate metal ions induces the formation of a catalytic site that cleaves a ribonucleotide linkage within a DNA substrate. A fluorophore (fluorescein) and a quencher (DABCYL, [4-(4-dimethylaminophenylazo)benzoic acid]) were placed on the two deoxythymidines flanking the ribonucleotide to allow the generation of fluorescence upon the catalytic cleavage at the RNA linkage. In general, all DNAzymes retained at least partial catalytic function when entrapped in either hydrophilic or hydrophobic silica-based materials, but displayed slower response times and lower overall signal changes relative to solution. Interestingly, it was determined that maximum sensitivity toward metal ions was obtained when DNAzymes were entrapped into composite materials containing approximately 40% of methyltrimethoxysilane (MTMS) and approximately 60% tetramethoxysilane (TMOS). Highly polar materials derived from sodium silicate, diglycerylsilane, or TMOS had relatively low signal enhancements, while materials with very high levels of MTMS showed significant leaching and low signal enhancements. Entrapment into the hybrid silica material also reduced signal interferences that were related to metal-induced quenching; such interferences were a significant problem for solution-based assays and for polar materials. Extension of the solid-phase DNAzyme assay toward a multiplexed assay format for metal detection is demonstrated, and shows that sol-gel technology can provide new opportunities for the development of DNAzyme-based biosensors.

  7. Expression of tak1 and tram induces synergistic pro-inflammatory signalling and adjuvants DNA vaccines.

    PubMed

    Larsen, Karen Colbjørn; Spencer, Alexandra J; Goodman, Anna L; Gilchrist, Ashley; Furze, Julie; Rollier, Christine S; Kiss-Toth, Endre; Gilbert, Sarah C; Bregu, Migena; Soilleux, Elizabeth J; Hill, Adrian V S; Wyllie, David H

    2009-09-18

    Improving vaccine immunogenicity remains a major challenge in the fight against developing country diseases like malaria and AIDS. We describe a novel strategy to identify new DNA vaccine adjuvants. We have screened components of the Toll-like receptor signalling pathways for their ability to activate pro-inflammatory target genes in transient transfection assays and assessed in vivo adjuvant activity by expressing the activators from the DNA backbone of vaccines. We find that a robust increase in the immune response necessitates co-expression of two activators. Accordingly, the combination of tak1 and tram elicits synergistic reporter activation in transient transfection assays. In a mouse model this combination, but not the individual molecules, induced approximately twofold increases in CD8+ T-cell immune responses. These results indicate that optimal immunogenicity may require activation of distinct innate immune signalling pathways. Thus this strategy offers a novel route to the discovery of a new generation of adjuvants.

  8. Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System

    PubMed Central

    Civade, Raphaël; Dejean, Tony; Valentini, Alice; Roset, Nicolas; Raymond, Jean-Claude; Bonin, Aurélie; Taberlet, Pierre; Pont, Didier

    2016-01-01

    In the last few years, the study of environmental DNA (eDNA) has drawn attention for many reasons, including its advantages for monitoring and conservation purposes. So far, in aquatic environments, most of eDNA research has focused on the detection of single species using species-specific markers. Recently, species inventories based on the analysis of a single generalist marker targeting a larger taxonomic group (eDNA metabarcoding) have proven useful for bony fish and amphibian biodiversity surveys. This approach involves in situ filtering of large volumes of water followed by amplification and sequencing of a short discriminative fragment from the 12S rDNA mitochondrial gene. In this study, we went one step further by investigating the spatial representativeness (i.e. ecological reliability and signal variability in space) of eDNA metabarcoding for large-scale fish biodiversity assessment in a freshwater system including lentic and lotic environments. We tested the ability of this approach to characterize large-scale organization of fish communities along a longitudinal gradient, from a lake to the outflowing river. First, our results confirm that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers. Second, the species list obtained using this approach is comparable to the one obtained when cumulating all traditional sampling sessions since 1995 and 1988 for the lake and the river, respectively. In conclusion, eDNA metabarcoding gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in our study conditions, i.e. longer than a traditional fish sampling site. PMID:27359116

  9. On nanopore DNA sequencing by signal and noise analysis of ionic current

    NASA Astrophysics Data System (ADS)

    Wen, Chenyu; Zeng, Shuangshuang; Zhang, Zhen; Hjort, Klas; Scheicher, Ralph; Zhang, Shi-Li

    2016-05-01

    DNA sequencing, i.e., the process of determining the succession of nucleotides on a DNA strand, has become a standard aid in biomedical research and is expected to revolutionize medicine. With the capability of handling single DNA molecules, nanopore technology holds high promises to become speedier in sequencing at lower cost than what are achievable with the commercially available optics- or semiconductor-based massively parallelized technologies. Despite tremendous progress made with biological and solid-state nanopores, high error rates and large uncertainties persist with the sequencing results. Here, we employ a nano-disk model to quantitatively analyze the sequencing process by examining the variations of ionic current when a DNA strand translocates a nanopore. Our focus is placed on signal-boosting and noise-suppressing strategies in order to attain the single-nucleotide resolution. Apart from decreasing pore diameter and thickness, it is crucial to also reduce the translocation speed and facilitate a stepwise translocation. Our best-case scenario analysis points to severe challenges with employing plain nanopore technology, i.e., without recourse to any signal amplification strategy, in achieving sequencing with the desired single-nucleotide resolution. A conceptual approach based on strand synthesis in the nanopore of the translocating DNA from single-stranded to double-stranded is shown to yield a 10-fold signal amplification. Although it involves no advanced physics and is very simple in mathematics, this simple model captures the essence of nanopore sequencing and is useful in guiding the design and operation of nanopore sequencing.

  10. On nanopore DNA sequencing by signal and noise analysis of ionic current.

    PubMed

    Wen, Chenyu; Zeng, Shuangshuang; Zhang, Zhen; Hjort, Klas; Scheicher, Ralph; Zhang, Shi-Li

    2016-05-27

    DNA sequencing, i.e., the process of determining the succession of nucleotides on a DNA strand, has become a standard aid in biomedical research and is expected to revolutionize medicine. With the capability of handling single DNA molecules, nanopore technology holds high promises to become speedier in sequencing at lower cost than what are achievable with the commercially available optics- or semiconductor-based massively parallelized technologies. Despite tremendous progress made with biological and solid-state nanopores, high error rates and large uncertainties persist with the sequencing results. Here, we employ a nano-disk model to quantitatively analyze the sequencing process by examining the variations of ionic current when a DNA strand translocates a nanopore. Our focus is placed on signal-boosting and noise-suppressing strategies in order to attain the single-nucleotide resolution. Apart from decreasing pore diameter and thickness, it is crucial to also reduce the translocation speed and facilitate a stepwise translocation. Our best-case scenario analysis points to severe challenges with employing plain nanopore technology, i.e., without recourse to any signal amplification strategy, in achieving sequencing with the desired single-nucleotide resolution. A conceptual approach based on strand synthesis in the nanopore of the translocating DNA from single-stranded to double-stranded is shown to yield a 10-fold signal amplification. Although it involves no advanced physics and is very simple in mathematics, this simple model captures the essence of nanopore sequencing and is useful in guiding the design and operation of nanopore sequencing.

  11. Whole transcriptome analysis reveals a role for OGG1-initiated DNA repair signaling in airway remodeling

    PubMed Central

    Aguilera-Aguirre, Leopoldo; Hosoki, Koa; Bacsi, Attila; Radák, Zsolt; Sur, Sanjiv; Hegde, Muralidhar L.; Tian, Bing; Saavedra-Molina, Alfredo; Brasier, Allan R.; Ba, Xueqing; Boldogh, Istvan

    2016-01-01

    Reactive oxygen species (ROS) generated by environmental exposures, and endogenously as by-products of respiration, oxidatively modify biomolecules including DNA. Accumulation of ROS-induced DNA damage has been implicated in various diseases that involve inflammatory processes, and efficient DNA repair is considered critical in preventing such diseases. One of the most abundant DNA base lesions is 7,8-dihydro-8-oxoguanine (8-oxoG), which is repaired by the 8-oxoguanine DNA glycosylase 1 (OGG1)-initiated base-excision repair (OGG1-BER) pathway. Recent studies have shown that the OGG1-BER byproduct 8-oxoG base forms a complex with cytosolic OGG1, activating small GTPases and downstream cell signaling in cultured cells and lungs. This implies that persistent OGG1-BER could result in signaling leading to histological changes in airways. To test this, we mimicked OGG1-BER by repeatedly challenging airways with its repair product 8-oxoG base. Gene expression was analyzed by RNA sequencing (RNA-Seq) and qRT-PCR, and datasets were evaluated by gene ontology and statistical tools. RNA-Seq analysis identified 3252 differentially expressed transcripts (2435 up- and 817 downregulated, Z3-fold change). Among the upregulated transcripts, 2080 mRNAs were identified whose encoded protein products were involved in modulation of the actin family cytoskeleton, extracellular matrix, cell adhesion, cadherin, and cell junctions, affecting biological processes such as tissue development, cell-to-cell adhesion, cell communication, and the immune system. These data are supported by histological observations showing epithelial alterations, subepithelial fibrosis, and collagen deposits in the lungs. These data imply that continuous challenge by the environment and consequent OGG1-BER-driven signaling trigger gene expression consistent with airway remodeling. PMID:26187872

  12. Latent ClpX-recognition signals ensure LexA destruction after DNA damage

    PubMed Central

    Neher, Saskia B.; Flynn, Julia M.; Sauer, Robert T.; Baker, Tania A.

    2003-01-01

    The DNA-damage response genes in bacteria are up-regulated when LexA repressor undergoes autocatalytic cleavage stimulated by activated RecA protein. Intact LexA is stable to intracellular degradation but its auto-cleavage fragments are degraded rapidly. Here, both fragments of LexA are shown to be substrates for the ClpXP protease. ClpXP recognizes these fragments using sequence motifs that flank the auto-cleavage site but are dormant in intact LexA. Furthermore, ClpXP degradation of the LexA-DNA-binding fragment is important to cell survival after DNA damage. These results demonstrate how one protein-processing event can activate latent protease recognition signals, triggering a cascade of protein turnover in response to environmental stress. PMID:12730132

  13. DNA barcodes reveal microevolutionary signals in fire response trait in two legume genera

    PubMed Central

    Bello, Abubakar; Daru, Barnabas H.; Stirton, Charles H.; Chimphango, Samson B. M.; van der Bank, Michelle; Maurin, Olivier; Muasya, A. Muthama

    2015-01-01

    Large-scale DNA barcoding provides a new technique for species identification and evaluation of relationships across various levels (populations and species) and may reveal fundamental processes in recently diverged species. Here, we analysed DNA sequence variation in the recently diverged legumes from the Psoraleeae (Fabaceae) occurring in the Cape Floristic Region (CFR) of southern Africa to test the utility of DNA barcodes in species identification and discrimination. We further explored the phylogenetic signal on fire response trait (reseeding and resprouting) at species and generic levels. We showed that Psoraleoid legumes of the CFR exhibit a barcoding gap yielding the combination of matK and rbcLa (matK + rbcLa) data set as a better barcode than single regions. We found a high score (100 %) of correct identification of individuals to their respective genera but a very low score (<50 %) in identifying them to species. We found a considerable match (54 %) between genetic species and morphologically delimited species. We also found that different lineages showed a weak but significant phylogenetic conservatism in their response to fire as reseeders or resprouters, with more clustering of resprouters than would be expected by chance. These novel microevolutionary patterns might be acting continuously over time to produce multi-scale regularities of biodiversity. This study provides the first insight into the DNA barcoding campaign of land plants in species identification and detection of the phylogenetic signal in recently diverged lineages of the CFR. PMID:26507570

  14. Manufacturing DNA microarrays of high spot homogeneity and reduced background signal

    PubMed Central

    Diehl, Frank; Grahlmann, Susanne; Beier, Markus; Hoheisel, Jörg D.

    2001-01-01

    Analyses on DNA microarrays depend considerably on spot quality and a low background signal of the glass support. By using betaine as an additive to a spotting solution made of saline sodium citrate, both the binding efficiency of spotted PCR products and the homogeneity of the DNA spots is improved significantly on aminated surfaces such as glass slides coated with the widely used poly-l-lysine or aminosilane. In addition, non-specific background signal is markedly diminished. Concomitantly, during the arraying procedure, the betaine reduces evaporation from the microtitre dish wells, which hold the PCR products. Subsequent blocking of the chip surface with succinic anhydride was improved considerably in the presence of the non-polar, non-aqueous solvent 1,2-dichloroethane and the acylating catalyst N-methylimidazole. This procedure prevents the overall background signal that occurs with the frequently applied aqueous solvent 1-methyl-2-pyrrolidone in borate buffer because of DNA that re-dissolves from spots during the blocking process, only to bind again across the entire glass surface. PMID:11266573

  15. Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases

    NASA Astrophysics Data System (ADS)

    Ahmed, Towfiq; Haraldsen, Jason T.; Rehr, John J.; Di Ventra, Massimiliano; Schuller, Ivan; Balatsky, Alexander V.

    2014-03-01

    Nanopore-based sequencing has demonstrated a significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multilayered graphene-based nanopore device architecture for the recognition of single biomolecules. Molecular detection and analysis can be accomplished through the detection of transverse currents as the molecule or DNA base translocates through the nanopore. To increase the overall signal-to-noise ratio and the accuracy, we implement a new ‘multi-point cross-correlation’ technique for identification of DNA bases or other molecules on the single molecular level. We demonstrate that the cross-correlations between each nanopore will greatly enhance the transverse current signal for each molecule. We implement first-principles transport calculations for DNA bases surveyed across a multilayered graphene nanopore system to illustrate the advantages of the proposed geometry. A time-series analysis of the cross-correlation functions illustrates the potential of this method for enhancing the signal-to-noise ratio. This work constitutes a significant step forward in facilitating fingerprinting of single biomolecules using solid state technology.

  16. Plasmonic Enhancement of Raman Signal using Complex Metallic Nanostructures based on DNA Origami

    NASA Astrophysics Data System (ADS)

    Finkelstein, Gleb

    2015-03-01

    DNA-based nanostructures, such as ``DNA origami,'' have recently emerged as one of the leading techniques for precise positioning of nanoscale materials in fields ranging from computer science to biomedical engineering. The origami is composed of a single scaffold DNA strand to which smaller ``staple`` strands are attached through DNA complementarity. The staples help to fold the scaffold strand into the designed structure of a predetermined shape. The resulting templates are highly addressable and have proven to be versatile tools for site-specific placement of various nanocomponents, such as metallic nanoparticles, quantum dots, fluorophores, etc. Building upon massively paralleled assembly mechanism of the origami and its ability to position nanocomponents, one may hope to utilize it for biosensing purposes. One attractive goal is the Raman spectroscopy, which provides a highly specific chemical fingerprint. Unfortunately, the Raman scattering cross section is small; Surface Enhanced Raman Spectroscopy (SERS) enhances the otherwise weak Raman signal by trapping the analyte molecules in the regions of intense electric field produced near rough metallic surfaces. These ``hot spots`` can be understood as resulting from localized surface plasmon modes resonantly exited by the incident laser excitation. We have earlier shown that metallic nanoparticles controllably attached to DNA origami can be further enlarged via an in-solution metallization; this technique allowed us to build metallic structures of complex topology. Recently, we have performed Raman spectroscopy of molecules attached to these metallic assemblies. Specifically, DNA origami is first used to organize the metallic structures, followed by a covalent attachment of Raman-active molecules to the metal. We found that the substrates with four nanoparticles per origami produce a strongly enhanced Raman signal compared to the control samples with only one nanoparticle per origami for the same particle

  17. Rac1 protein signaling is required for DNA damage response stimulated by topoisomerase II poisons.

    PubMed

    Huelsenbeck, Stefanie C; Schorr, Anne; Roos, Wynand P; Huelsenbeck, Johannes; Henninger, Christian; Kaina, Bernd; Fritz, Gerhard

    2012-11-09

    To investigate the potency of the topoisomerase II (topo II) poisons doxorubicin and etoposide to stimulate the DNA damage response (DDR), S139 phosphorylation of histone H2AX (γH2AX) was analyzed using rat cardiomyoblast cells (H9c2). Etoposide caused a dose-dependent increase in the γH2AX level as shown by Western blotting. By contrast, the doxorubicin response was bell-shaped with high doses failing to increase H2AX phosphorylation. Identical results were obtained by immunohistochemical analysis of γH2AX focus formation, comet assay-based DNA strand break analysis, and measuring the formation of the topo II-DNA cleavable complex. At low dose, doxorubicin activated ataxia telangiectasia mutated (ATM) but not ATM and Rad3-related (ATR). Both the lipid-lowering drug lovastatin and the Rac1-specific inhibitor NSC23766 attenuated doxorubicin- and etoposide-stimulated H2AX phosphorylation, induction of DNA strand breaks, and topo II-DNA complex formation. Lovastatin and NSC23766 acted in an additive manner. They did not attenuate doxorubicin-induced increase in p-ATM and p-Chk2 levels. DDR stimulated by topo II poisons was partially blocked by inhibition of type I p21-associated kinases. DDR evoked by the topoisomerase I poison topotecan remained unaffected by lovastatin. The data show that the mechanisms involved in DDR stimulated by topo II poisons are agent-specific with anthracyclines lacking DDR-stimulating activity at high doses. Pharmacological inhibition of Rac1 signaling counteracts doxorubicin- and etoposide-stimulated DDR by disabling the formation of the topo II-DNA cleavable complex. Based on the data we suggest that Rac1-regulated mechanisms are required for DNA damage induction and subsequent activation of the DDR following treatment with topo II but not topo I poisons.

  18. Ultrasensitive Multiplexed Immunoassay for Tumor Biomarkers Based on DNA Hybridization Chain Reaction Amplifying Signal.

    PubMed

    Guo, Jinjin; Wang, Junchun; Zhao, Junqing; Guo, Zilin; Zhang, Yuzhong

    2016-03-23

    In this work, a novel electrochemical immunoassay protocol has been reported for simultaneous determination of multiple tumor biomarkers based on DNA hybridization chain reaction (HCR) for signal amplification. Alpha-fetoprotein (AFP) and prostate specific antigen (PSA) were selected as model biomarkers. The immunoassay protocol contained primary antibodies immobilized on gold nanoparticles (Au NPs), secondary antibodies conjugated with DNA concatemer from HCR of primer, auxiliary probe, and signal probe labeled with signal molecules (methyleneblue (MB) and ferrocene (Fc)). In the presence of target biomarkers, the sandwich immunocomplex was formed between the primary antibodies and secondary antibodies bioconjugates carrying numerous signal molecules. As a result, two well-resolved reduction peaks, one was at -0.35 V (corresponding to MB) and other was at 0.33 V (corresponding to Fc; both vs SCE), were obtained in differential pulse voltammetry, and peak currents changed were related to the level of biomarkers. Under optimal conditions, the electrochemical immunoassay exhibited a wide linear response range (0.5 pg mL(-1) to 50 ng mL(-1)) and low detection limits (PSA, 0.17 pg mL(-1); AFP, 0.25 pg mL(-1)) (at S/N = 3). In addition, the immunoassay was evaluated by analyzing simulate human serum sample, and the recoveries obtained were within 99.4-107.6% for PSA and 97.9-108.2% for AFP, indicating the immnuoassay could be applied to the simultaneous detection of AFP and PSA in human serum samples.

  19. The Caenorhabditis elegans gene unc-89, required fpr muscle M-line assembly, encodes a giant modular protein composed of Ig and signal transduction domains

    PubMed Central

    1996-01-01

    Mutations in the Caenorhabditis elegans gene unc-89 result in nematodes having disorganized muscle structure in which thick filaments are not organized into A-bands, and there are no M-lines. Beginning with a partial cDNA from the C. elegans sequencing project, we have cloned and sequenced the unc-89 gene. An unc-89 allele, st515, was found to contain an 84-bp deletion and a 10-bp duplication, resulting in an in- frame stop codon within predicted unc-89 coding sequence. Analysis of the complete coding sequence for unc-89 predicts a novel 6,632 amino acid polypeptide consisting of sequence motifs which have been implicated in protein-protein interactions. UNC-89 begins with 67 residues of unique sequences, SH3, dbl/CDC24, and PH domains, 7 immunoglobulins (Ig) domains, a putative KSP-containing multiphosphorylation domain, and ends with 46 Ig domains. A polyclonal antiserum raised to a portion of unc-89 encoded sequence reacts to a twitchin-sized polypeptide from wild type, but truncated polypeptides from st515 and from the amber allele e2338. By immunofluorescent microscopy, this antiserum localizes to the middle of A-bands, consistent with UNC-89 being a structural component of the M-line. Previous studies indicate that myofilament lattice assembly begins with positional cues laid down in the basement membrane and muscle cell membrane. We propose that the intracellular protein UNC-89 responds to these signals, localizes, and then participates in assembling an M-line. PMID:8603916

  20. FXR silencing in human colon cancer by DNA methylation and KRAS signaling.

    PubMed

    Bailey, Ann M; Zhan, Le; Maru, Dipen; Shureiqi, Imad; Pickering, Curtis R; Kiriakova, Galina; Izzo, Julie; He, Nan; Wei, Caimiao; Baladandayuthapani, Veerabhadran; Liang, Han; Kopetz, Scott; Powis, Garth; Guo, Grace L

    2014-01-01

    Farnesoid X receptor (FXR) is a bile acid nuclear receptor described through mouse knockout studies as a tumor suppressor for the development of colon adenocarcinomas. This study investigates the regulation of FXR in the development of human colon cancer. We used immunohistochemistry of FXR in normal tissue (n = 238), polyps (n = 32), and adenocarcinomas, staged I-IV (n = 43, 39, 68, and 9), of the colon; RT-quantitative PCR, reverse-phase protein array, and Western blot analysis in 15 colon cancer cell lines; NR1H4 promoter methylation and mRNA expression in colon cancer samples from The Cancer Genome Atlas; DNA methyltransferase inhibition; methyl-DNA immunoprecipitation (MeDIP); bisulfite sequencing; and V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) knockdown assessment to investigate FXR regulation in colon cancer development. Immunohistochemistry and quantitative RT-PCR revealed that expression and function of FXR was reduced in precancerous lesions and silenced in a majority of stage I-IV tumors. FXR expression negatively correlated with phosphatidylinositol-4, 5-bisphosphate 3 kinase signaling and the epithelial-to-mesenchymal transition. The NR1H4 promoter is methylated in ~12% colon cancer The Cancer Genome Atlas samples, and methylation patterns segregate with tumor subtypes. Inhibition of DNA methylation and KRAS silencing both increased FXR expression. FXR expression is decreased early in human colon cancer progression, and both DNA methylation and KRAS signaling may be contributing factors to FXR silencing. FXR potentially suppresses epithelial-to-mesenchymal transition and other oncogenic signaling cascades, and restoration of FXR activity, by blocking silencing mechanisms or increasing residual FXR activity, represents promising therapeutic options for the treatment of colon cancer.

  1. CHK1 and RAD51 activation after DNA damage is regulated via urokinase receptor/TLR4 signaling

    PubMed Central

    Narayanaswamy, Pavan B; Tkachuk, Sergey; Haller, Hermann; Dumler, Inna; Kiyan, Yulia

    2016-01-01

    Mechanisms of DNA damage and repair signaling are not completely understood that hinder the efficiency of cancer therapy. Urokinase-type plasminogen activator receptor (PLAUR) is highly expressed in most solid cancers and serves as a marker of poor prognosis. We show that PLAUR actively promotes DNA repair in cancer cells. On the contrary, downregulation of PLAUR expression results in delayed DNA repair. We found PLAUR to be essential for activation of Checkpoint kinase 1 (CHK1); maintenance of cell cycle arrest after DNA damage in a TP53-dependent manner; expression, nuclear import and recruitment to DNA-damage foci of RAD51 recombinase, the principal protein involved in the homologous recombination repair pathway. Underlying mechanism implies auto-/paracrine signaling of PLAUR/TLR4 receptor complex leading to activation of CHK1 and DNA repair. The signaling is induced by a danger molecule released by DNA-damaged cells and mediates, at least partially, activation of DNA-damage response. This study describes a new mechanism of DNA repair activation initiated by auto-/paracrine signaling of membrane receptors PLAUR/TLR4. It adds to the understanding of role of PLAUR in cancer and provides a rationale for therapeutic targeting of PLAUR/TLR4 interaction in TP53-positive cancers. PMID:27685627

  2. Hh signaling inhibitors from Vitex negundo; naturally occurring inhibitors of the GLI1-DNA complex.

    PubMed

    Arai, Midori A; Fujimatsu, Teruhisa; Uchida, Kyoko; Sadhu, Samir K; Ahmed, Firoj; Ishibashi, Masami

    2013-05-01

    The hedgehog (Hh) signaling pathway has crucial roles in embryonic development, cell maintenance and proliferation, and is also known to contribute to cancer cell growth. New naturally occurring Hh inhibitors (1, 7 and 9) were isolated from Vitex negundo using our previously constructed cell-based assay. Bioactivity guided isolation provided 9 natural compounds including a new diterpene, nishindanol (9). Compounds 7 and 9 showed cytotoxicity against cancer cell lines in which Hh signaling was aberrantly activated. Vitetrifolin D (7; GLI1 transcriptional inhibition IC50 = 20.2 μM) showed inhibition of Hh related protein (PTCH and BCL2) production. Interestingly, the constructed electrophoresis mobility shift assay revealed that vitetrifolin D (7) disrupted GLI1 binding on its DNA binding domain. epi-Sclareol (8; inactive), possessing a similar structure to 7, did not show inhibition of GLI1–DNA complex formation. This is the first example of naturally occurring inhibitors of GLI1–DNA complex formation.

  3. Implementing Modular A Levels.

    ERIC Educational Resources Information Center

    Holding, Gordon

    This document, which is designed for curriculum managers at British further education (FE) colleges, presents basic information on the implementation and perceived benefits of the General Certificate of Education (GCE) modular A (Advanced) levels. The information was synthesized from a survey of 12 FE colleges that introduced the modular A levels…

  4. Modular Buildings Buying Guide.

    ERIC Educational Resources Information Center

    Morris, Susan

    1991-01-01

    Suggests that child care program directors who are expanding their programs or opening new child care centers investigate the possibility of renting, leasing, or purchasing a modular building. Discusses the advantages of modular buildings over conventional building construction or rented space in an occupied building. Provides information about…

  5. Modular tokamak configuration

    SciTech Connect

    Thomson, S.L.

    1985-01-01

    This report is concerned with the modular tokamak configuration, and presents information on the following topics: modularity; external vacuum boundary; vertical maintenance; combined reactor building/biological shield with totally remote maintenance; independent TF coils; minimum TF coil bore; saddle PF coils; and heat transport system in bore.

  6. Persistent DNA damage signaling triggers senescence-associated inflammatory cytokine secretion

    PubMed Central

    Rodier, Francis; Coppé, Jean-Philippe; Patil, Christopher K.; Hoeijmakers, Wieteke A. M.; Muñoz, Denise P.; Raza, Saba R.; Freund, Adam; Campeau, Eric; Davalos, Albert R.; Campisi, Judith

    2009-01-01

    Cellular senescence suppresses cancer by stably arresting the proliferation of damaged cells1. Paradoxically, senescent cells also secrete factors that alter tissue microenvironments2. The pathways regulating this secretion are unknown. We show that damaged human cells develop persistent chromatin lesions bearing hallmarks of DNA double-strand breaks (DSBs), which initiate increased secretion of inflammatory cytokines such as interleukin-6 (IL-6). Cytokine secretion occurred only after establishment of persistent DNA damage signaling, usually associated with senescence, not after transient DNA damage responses (DDR). Initiation and maintenance of this cytokine response required the DDR proteins ATM, NBS1 and CHK2, but not the cell cycle arrest enforcers p53 and pRb. ATM was also essential for IL-6 secretion during oncogene-induced senescence and by damaged cells that bypass senescence. Further, DDR activity and IL-6 were elevated in human cancers, and ATM-depletion suppressed the ability of senescent cells to stimulate IL-6-dependent cancer cell invasiveness. Thus, in addition to orchestrating cell cycle checkpoints and DNA repair, a novel and important role of the DDR is to allow damaged cells to communicate their compromised state to the surrounding tissue. PMID:19597488

  7. Using DNA mechanics to predict intrinsic and extrinsic nucleosome positioning signals

    NASA Astrophysics Data System (ADS)

    Morozov, Alexandre

    2008-03-01

    In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are determined by sequence alone, in vivo competition with other DNA-binding factors and action of chromatin remodeling enzymes play a role that needs to be quantified. We developed a biophysical, DNA mechanics-based model for the sequence dependence of DNA bending energies, and validated it against a collection of in vitro free energies of nucleosome formation and a nucleosome crystal structure; we also successfully designed both strong and poor histone binding sequences ab initio. For in vivo data from S.cerevisiae, the strongest positioning signal came from the competition with other factors rather than intrinsic nucleosome sequence preferences. Based on sequence alone, our model predicts that functional transcription factor binding sites tend to be covered by nucleosomes, yet are uncovered in vivo because functional sites cluster within a single nucleosome footprint and thus make transcription factors bind cooperatively. Similarly a weak enhancement of nucleosome binding in the TATA region becomes a strong depletion when the TATA-binding protein is included, in quantitative agreement with experiment. Our model distinguishes multiple ways in which genomic sequence influences nucleosome positions, and thus provides alternative explanations for several genome-wide experimental findings. In the future our approach will be used to rationally alter gene expression levels in model systems through redesign of nucleosome occupancy profiles.

  8. Mitochondrial DNA variants can mediate methylation status of inflammation, angiogenesis and signaling genes

    PubMed Central

    Atilano, Shari R.; Malik, Deepika; Chwa, Marilyn; Cáceres-Del-Carpio, Javier; Nesburn, Anthony B.; Boyer, David S.; Kuppermann, Baruch D.; Jazwinski, S. Michal; Miceli, Michael V.; Wallace, Douglas C.; Udar, Nitin; Kenney, M. Cristina

    2015-01-01

    Mitochondrial (mt) DNA can be classified into haplogroups representing different geographic and/or racial origins of populations. The H haplogroup is protective against age-related macular degeneration (AMD), while the J haplogroup is high risk for AMD. In the present study, we performed comparison analyses of human retinal cell cybrids, which possess identical nuclei, but mtDNA from subjects with either the H or J haplogroups, and demonstrate differences in total global methylation, and expression patterns for two genes related to acetylation and five genes related to methylation. Analyses revealed that untreated-H and -J cybrids have different expression levels for nuclear genes (CFH, EFEMP1, VEGFA and NFkB2). However, expression levels for these genes become equivalent after treatment with a methylation inhibitor, 5-aza-2′-deoxycytidine. Moreover, sequencing of the entire mtDNA suggests that differences in epigenetic status found in cybrids are likely due to single nucleotide polymorphisms (SNPs) within the haplogroup profiles rather than rare variants or private SNPs. In conclusion, our findings indicate that mtDNA variants can mediate methylation profiles and transcription for inflammation, angiogenesis and various signaling pathways, which are important in several common diseases. PMID:25964427

  9. Kynurenine signaling increases DNA polymerase kappa expression and promotes genomic instability in glioblastoma cells

    PubMed Central

    Bostian, April C.L.; Maddukuri, Leena; Reed, Megan R.; Savenka, Tatsiana; Hartman, Jessica H.; Davis, Lauren; Pouncey, Dakota L.; Miller, Grover P.; Eoff, Robert L.

    2015-01-01

    Over-expression of the translesion synthesis polymerase (TLS pol) hpol κ in glioblastomas has been linked to a poor patient prognosis; however, the mechanism promoting higher expression in these tumors remains unknown. We determined that activation of the aryl hydrocarbon receptor (AhR) pathway in glioblastoma cells leads to increased hpol κ mRNA and protein levels. We blocked nuclear translocation and DNA binding by the AhR in glioblastoma cells using a small-molecule and observed decreased hpol κ expression. Pharmacological inhibition of tryptophan-2,3-dioxygenase (TDO), the enzyme largely responsible for activating the AhR in glioblastomas, led to a decrease in the endogenous AhR agonist kynurenine (Kyn) and a corresponding decrease in hpol κ protein levels. Importantly, we discovered that inhibiting TDO activity, AhR signaling, or suppressing hpol κ expression with RNA interference led to decreased chromosomal damage in glioblastoma cells. Epistasis assays further supported the idea that TDO activity, activation of AhR signaling and the resulting over-expression of hpol κ function primarily in the same pathway to increase endogenous DNA damage. These findings indicate that up-regulation of hpol κ through glioblastoma-specific TDO activity and activation of AhR signaling likely contributes to the high levels of replication stress and genomic instability observed in these tumors. PMID:26651356

  10. A electrogenerated chemiluminescence biosensor for Ramos cancer cell using DNA encapsulated Ru(bpy)₃Cl₂ as signal probe.

    PubMed

    Hun, Xu; Chen, Huaicheng; Wang, Wei

    2011-05-15

    A label-free sensing technology for detection of Ramos cell was developed based on a signal probe Ru(bpy)3Cl2 (Ru) encapsulated by DNA. Gold electrode or magnetic bead as the sensing surface was firstly modified with long-strand DNA with five repeating units. Then two kinds of short-strand DNA are grafted onto the long-strand DNA to form DNA strands A and B (L-A and L-B) through the hybridization, respectively. The addition of aptamer initiates hybridization of L-A and L-B with the aptamer sequence. As the hybridization proceeds, the four kinds of DNA would finally transform into a three-dimensional network structure and the signal probe Ru was encapsulated by DNA simultaneously. When Ramos cells are introduced to interact with the aptamer, the signal probe is released. In order to confirm the generality of this method the ferrocenecarboxylic acid and luminol selected as a signal probe mode were also tested. The Ru used as a signal probe for electrogenerated chemiluminescence (ECL) detection was detailedly studied. With this ECL biosensor, detection limit as low as 58 cells/mL was achieved for Ramos cell. The biosensor also exhibited excellent sensitivity and selectivity.

  11. Unusual sequence length-dependent gold nanoparticles aggregation of the ssDNA sticky end and its application for enzyme-free and signal amplified colorimetric DNA detection

    NASA Astrophysics Data System (ADS)

    He, Hongfei; Dai, Jianyuan; Duan, Zhijuan; Zheng, Baozhan; Meng, Yan; Guo, Yong; Dan Xiao, A1"/>

    2016-08-01

    It is known that the adsorption of short single-stranded DNA (ssDNA) on unmodified gold nanoparticles (AuNPs) is much faster than that for long ssDNA, and thus leads to length-dependent AuNPs aggregation after addition of salt, the color of the solutions sequentially changed from red to blue in accordance with the increase of ssDNA length. However, we found herein that the ssDNA sticky end of hairpin DNA exhibited a completely different adsorption behavior compared to ssDNA, an inverse blue-to-red color variation was observed in the colloid solution with the increase of sticky end length when the length is within a certain range. This unusual sequence length-dependent AuNPs aggregation might be ascribed to the effect of the stem of hairpin DNA. On the basis of this unique phenomenon and catalytic hairpin assembly (CHA) based signal amplification, a novel AuNPs-based colorimetric DNA assay with picomolar sensitivity and specificity was developed. This unusual sequence length-dependent AuNPs aggregation of the ssDNA sticky end introduces a new direction for the AuNPs-based colorimetric assays.

  12. Cell cycle-dependent DNA damage signaling induced by ICRF-193 involves ATM, ATR, CHK2, and BRCA1

    SciTech Connect

    Park, Iha; Avraham, Hava Karsenty . E-mail: havraham@bidmc.harvard.edu

    2006-07-01

    Topoisomerase II is essential for cell proliferation and survival and has been a target of various anticancer drugs. ICRF-193 has long been used as a catalytic inhibitor to study the function of topoisomerase II. Here, we show that ICRF-193 treatment induces DNA damage signaling. Treatment with ICRF-193 induced G2 arrest and DNA damage signaling involving {gamma}-H2AX foci formation and CHK2 phosphorylation. DNA damage by ICRF-193 was further demonstrated by formation of the nuclear foci of 53BP1, NBS1, BRCA1, MDC1, and FANCD2 and increased comet tail moment. The DNA damage signaling induced by ICRF-193 was mediated by ATM and ATR and was restricted to cells in specific cell cycle stages such as S, G2, and mitosis including late and early G1 phases. Downstream signaling of ATM and ATR involved the phosphorylation of CHK2 and BRCA1. Altogether, our results demonstrate that ICRF-193 induces DNA damage signaling in a cell cycle-dependent manner and suggest that topoisomerase II might be essential for the progression of the cell cycle at several stages including DNA decondensation.

  13. Engineering self-contained DNA circuit for proximity recognition and localized signal amplification of target biomolecules.

    PubMed

    Ang, Yan Shan; Yung, Lin-Yue Lanry

    2014-08-01

    Biomolecular interactions have important cellular implications, however, a simple method for the sensing of such proximal events is lacking in the current molecular toolbox. We designed a dynamic DNA circuit capable of recognizing targets in close proximity to initiate a pre-programmed signal transduction process resulting in localized signal amplification. The entire circuit was engineered to be self-contained, i.e. it can self-assemble onto individual target molecules autonomously and form localized signal with minimal cross-talk. α-thrombin was used as a model protein to evaluate the performance of the individual modules and the overall circuit for proximity interaction under physiologically relevant buffer condition. The circuit achieved good selectivity in presence of non-specific protein and interfering serum matrix and successfully detected for physiologically relevant α-thrombin concentration (50 nM-5 μM) in a single mixing step without any further washing. The formation of localized signal at the interaction site can be enhanced kinetically through the control of temperature and probe concentration. This work provides a basic general framework from which other circuit modules can be adapted for the sensing of other biomolecular or cellular interaction of interest.

  14. Control of electrochemical signals from quantum dots conjugated to organic materials by using DNA structure in an analog logic gate.

    PubMed

    Chen, Qi; Yoo, Si-Youl; Chung, Yong-Ho; Lee, Ji-Young; Min, Junhong; Choi, Jeong-Woo

    2016-10-01

    Various bio-logic gates have been studied intensively to overcome the rigidity of single-function silicon-based logic devices arising from combinations of various gates. Here, a simple control tool using electrochemical signals from quantum dots (QDs) was constructed using DNA and organic materials for multiple logic functions. The electrochemical redox current generated from QDs was controlled by the DNA structure. DNA structure, in turn, was dependent on the components (organic materials) and the input signal (pH). Independent electrochemical signals from two different logic units containing QDs were merged into a single analog-type logic gate, which was controlled by two inputs. We applied this electrochemical biodevice to a simple logic system and achieved various logic functions from the controlled pH input sets. This could be further improved by choosing QDs, ionic conditions, or DNA sequences. This research provides a feasible method for fabricating an artificial intelligence system.

  15. Written Reformulation in a Modular Approach.

    ERIC Educational Resources Information Center

    Flottum, Kjersti

    1996-01-01

    Examines the relationship between form and use of the reformulation sequence signalled by "c'est-a-dire" in written French and describes this sequence's various functions. The article attempts to show how a modular approach consisting of structural, semantic, pragmatic, and textual components contributes to a new and accurate description of…

  16. TGF-β1 accelerates the DNA damage response in epithelial cells via Smad signaling.

    PubMed

    Lee, Jeeyong; Kim, Mi-Ra; Kim, Hyun-Ji; An, You Sun; Yi, Jae Youn

    2016-08-05

    The evidence suggests that transforming growth factor-beta (TGF-β) regulates the DNA-damage response (DDR) upon irradiation, and we previously reported that TGF-β1 induced DNA ligase IV (Lig4) expression and enhanced the nonhomologous end-joining repair pathway in irradiated cells. In the present study, we investigated the effects of TGF-β1 on the irradiation-induced DDRs of A431 and HaCaT cells. Cells were pretreated with or without TGF-β1 and irradiated. At 30 min post-irradiation, DDRs were detected by immunoblotting of phospho-ATM, phospho-Chk2, and the presence of histone foci (γH2AX). The levels of all three factors were similar right after irradiation regardless of TGF-β1 pretreatment. However, they soon thereafter exhibited downregulation in TGF-β1-pretreated cells, indicating the acceleration of the DDR. Treatment with a TGF-β type I receptor inhibitor (SB431542) or transfections with siRNAs against Smad2/3 or DNA ligase IV (Lig4) reversed this acceleration of the DDR. Furthermore, the frequency of irradiation-induced apoptosis was decreased by TGF-β1 pretreatment in vivo, but this effect was abrogated by SB431542. These results collectively suggest that TGF-β1 could enhance cell survival by accelerating the DDR via Smad signaling and Lig4 expression.

  17. Structural Basis of Detection and Signaling of DNA Single-Strand Breaks by Human PARP-1

    PubMed Central

    Eustermann, Sebastian; Wu, Wing-Fung; Langelier, Marie-France; Yang, Ji-Chun; Easton, Laura E.; Riccio, Amanda A.; Pascal, John M.; Neuhaus, David

    2015-01-01

    Summary Poly(ADP-ribose)polymerase 1 (PARP-1) is a key eukaryotic stress sensor that responds in seconds to DNA single-strand breaks (SSBs), the most frequent genomic damage. A burst of poly(ADP-ribose) synthesis initiates DNA damage response, whereas PARP-1 inhibition kills BRCA-deficient tumor cells selectively, providing the first anti-cancer therapy based on synthetic lethality. However, the mechanism underlying PARP-1’s function remained obscure; inherent dynamics of SSBs and PARP-1’s multi-domain architecture hindered structural studies. Here we reveal the structural basis of SSB detection and how multi-domain folding underlies the allosteric switch that determines PARP-1’s signaling response. Two flexibly linked N-terminal zinc fingers recognize the extreme deformability of SSBs and drive co-operative, stepwise self-assembly of remaining PARP-1 domains to control the activity of the C-terminal catalytic domain. Automodifcation in cis explains the subsequent release of monomeric PARP-1 from DNA, allowing repair and replication to proceed. Our results provide a molecular framework for understanding PARP inhibitor action and, more generally, allosteric control of dynamic, multi-domain proteins. PMID:26626479

  18. Structural Basis of Detection and Signaling of DNA Single-Strand Breaks by Human PARP-1.

    PubMed

    Eustermann, Sebastian; Wu, Wing-Fung; Langelier, Marie-France; Yang, Ji-Chun; Easton, Laura E; Riccio, Amanda A; Pascal, John M; Neuhaus, David

    2015-12-03

    Poly(ADP-ribose)polymerase 1 (PARP-1) is a key eukaryotic stress sensor that responds in seconds to DNA single-strand breaks (SSBs), the most frequent genomic damage. A burst of poly(ADP-ribose) synthesis initiates DNA damage response, whereas PARP-1 inhibition kills BRCA-deficient tumor cells selectively, providing the first anti-cancer therapy based on synthetic lethality. However, the mechanism underlying PARP-1's function remained obscure; inherent dynamics of SSBs and PARP-1's multi-domain architecture hindered structural studies. Here we reveal the structural basis of SSB detection and how multi-domain folding underlies the allosteric switch that determines PARP-1's signaling response. Two flexibly linked N-terminal zinc fingers recognize the extreme deformability of SSBs and drive co-operative, stepwise self-assembly of remaining PARP-1 domains to control the activity of the C-terminal catalytic domain. Automodification in cis explains the subsequent release of monomeric PARP-1 from DNA, allowing repair and replication to proceed. Our results provide a molecular framework for understanding PARP inhibitor action and, more generally, allosteric control of dynamic, multi-domain proteins.

  19. The danger signal plus DNA damage two-hit hypothesis for chronic inflammation in COPD.

    PubMed

    Aoshiba, Kazutetsu; Tsuji, Takao; Yamaguchi, Kazuhiro; Itoh, Masayuki; Nakamura, Hiroyuki

    2013-12-01

    Inflammation in chronic obstructive pulmonary disease (COPD) is thought to originate from the activation of innate immunity by a danger signal (first hit), although this mechanism does not readily explain why the inflammation becomes chronic. Here, we propose a two-hit hypothesis explaining why inflammation becomes chronic in patients with COPD. A more severe degree of inflammation exists in the lungs of patients who develop COPD than in the lungs of healthy smokers, and the large amounts of reactive oxygen species and reactive nitrogen species released from inflammatory cells are likely to induce DNA double-strand breaks (second hit) in the airways and pulmonary alveolar cells, causing apoptosis and cell senescence. The DNA damage response and senescence-associated secretory phenotype (SASP) are also likely to be activated, resulting in the production of pro-inflammatory cytokines. These pro-inflammatory cytokines further stimulate inflammatory cell infiltration, intensifying cell senescence and SASP through a positive-feedback mechanism. This vicious cycle, characterised by mutually reinforcing inflammation and DNA damage, may cause the inflammation in COPD patients to become chronic. Our hypothesis helps explain why COPD tends to occur in the elderly, why the inflammation worsens progressively, why inflammation continues even after smoking cessation, and why COPD is associated with lung cancer.

  20. Structural basis of detection and signaling of DNA single-strand breaks by human PARP-1

    DOE PAGES

    Eustermann, Sebastian; Wu, Wing -Fung; Langelier, Marie -France; ...

    2015-11-25

    Poly(ADP-ribose)polymerase 1 (PARP-1) is a key eukaryotic stress sensor that responds in seconds to DNA single-strand breaks (SSBs), the most frequent genomic damage. A burst of poly(ADP-ribose) synthesis initiates DNA damage response, whereas PARP-1 inhibition kills BRCA-deficient tumor cells selectively, providing the first anti-cancer therapy based on synthetic lethality. However, the mechanism underlying PARP-1’s function remained obscure; inherent dynamics of SSBs and PARP-1’s multi-domain architecture hindered structural studies. Here we reveal the structural basis of SSB detection and how multi-domain folding underlies the allosteric switch that determines PARP-1’s signaling response. Two flexibly linked N-terminal zinc fingers recognize the extreme deformabilitymore » of SSBs and drive co-operative, stepwise self-assembly of remaining PARP-1 domains to control the activity of the C-terminal catalytic domain. Automodifcation in cis explains the subsequent release of monomeric PARP-1 from DNA, allowing repair and replication to proceed. Finally, our results provide a molecular framework for understanding PARP inhibitor action and, more generally, allosteric control of dynamic, multi-domain proteins.« less

  1. Structural basis of detection and signaling of DNA single-strand breaks by human PARP-1

    SciTech Connect

    Eustermann, Sebastian; Wu, Wing -Fung; Langelier, Marie -France; Yang, Ji -Chun; Easton, Laura E.; Riccio, Amanda A.; Pascal, John M.; Neuhaus, David

    2015-11-25

    Poly(ADP-ribose)polymerase 1 (PARP-1) is a key eukaryotic stress sensor that responds in seconds to DNA single-strand breaks (SSBs), the most frequent genomic damage. A burst of poly(ADP-ribose) synthesis initiates DNA damage response, whereas PARP-1 inhibition kills BRCA-deficient tumor cells selectively, providing the first anti-cancer therapy based on synthetic lethality. However, the mechanism underlying PARP-1’s function remained obscure; inherent dynamics of SSBs and PARP-1’s multi-domain architecture hindered structural studies. Here we reveal the structural basis of SSB detection and how multi-domain folding underlies the allosteric switch that determines PARP-1’s signaling response. Two flexibly linked N-terminal zinc fingers recognize the extreme deformability of SSBs and drive co-operative, stepwise self-assembly of remaining PARP-1 domains to control the activity of the C-terminal catalytic domain. Automodifcation in cis explains the subsequent release of monomeric PARP-1 from DNA, allowing repair and replication to proceed. Finally, our results provide a molecular framework for understanding PARP inhibitor action and, more generally, allosteric control of dynamic, multi-domain proteins.

  2. Successful modular cosmology

    NASA Astrophysics Data System (ADS)

    Kadota, Kenji; Stewart, Ewan D.

    2003-07-01

    We present a modular cosmology scenario where the difficulties encountered in conventional modular cosmology are solved in a self-consistent manner, with definite predictions to be tested by observation. Notably, the difficulty of the dilaton finding its way to a precarious weak coupling minimum is made irrelevant by having eternal modular inflation at the vacuum supersymmetry breaking scale after the dilaton is stabilised. Neither this eternal inflation nor the subsequent non-slow-roll modular inflation destabilise the dilaton from its precarious minimum due to the low energy scale of the inflation and consequent small back reaction on the dilaton potential. The observed flat CMB spectrum is obtained from fluctuations in the angular component of a modulus near a symmetric point, which are hugely magnified by the roll down of the modulus to Planckian values, allowing them to dominate the final curvature perturbation. We also give precise calculations of the spectral index and its running.

  3. Modular tokamak magnetic system

    DOEpatents

    Yang, Tien-Fang

    1988-01-01

    A modular tokamak system comprised of a plurality of interlocking moldules. Each module is comprised of a vacuum vessel section, a toroidal field coil, moldular saddle coils which generate a poloidal magnetic field and ohmic heating coils.

  4. Monitoring the Escape of DNA from a Nanopore Using an Alternating Current Signal

    PubMed Central

    Lathrop, Daniel K.; Ervin, Eric N.; Barrall, Geoffrey A.; Keehan, Michael G.; Kawano, Ryuji; Krupka, Michael A.; White, Henry S.; Hibbs, Andrew H.

    2010-01-01

    We present the use of an alternating current (AC) signal as a means to monitor the conductance of an α-hemolysin (αHL) pore as a DNA hairpin with a polydeoxyadenosine tail is driven into and released from the pore. Specifically, a 12 base pair DNA hairpin attached to a 50-nucleotide poly-A tail (HP-A50) is threaded into an αHL channel using a DC driving voltage. Once the HP-A50 molecule is trapped within the αHL channel, the DC driving voltage is turned off and the conductance of the channel is monitored using an AC voltage. The escape time, defined as the time it takes the HP-A50 molecule to transport out of the αHL channel, is then measured. This escape time has been monitored as a function of AC amplitude (20 to 250 mVac), AC frequency (60–200 kHz), DC drive voltage (0 to 100 mVdc), and temperature (−10 to 20 °C), in order to determine their effect on the predominantly diffusive motion of the DNA through the nanopore. The applied AC voltage used to monitor the conductance of the nanopore has been found to play a significant role in the DNA/nanopore interaction. The experimental results are described by a one-dimensional asymmetric periodic potential model that includes the influence of the AC voltage. An activation enthalpy barrier of 1.74 × 10−19 J and a periodic potential asymmetry parameter of 0.575 are obtained for the diffusion at zero electrical bias of a single nucleotide through αHL. PMID:20099878

  5. A Modular Robotic Architecture

    DTIC Science & Technology

    1990-11-01

    DATES COVERED AD-A232 007 Januar 1991 professional paper5 FUNOING NUMBERS A MODULAR ROBOTIC ARCHITECTURE PR: ZE92 WU: DN300029 PE: 0602936N - S. AUTHOR...mobile robots will help alleviate these problems, and, if made widely available, will promote standardization and compatibility among systems throughout...the industry. The Modular Robotic Architecture (MRA) is a generic control system that meets the above needs by providing developers with a standard set

  6. Modularity and mental architecture.

    PubMed

    Robbins, Philip

    2013-11-01

    Debates about the modularity of cognitive architecture have been ongoing for at least the past three decades, since the publication of Fodor's landmark book The Modularity of Mind. According to Fodor, modularity is essentially tied to informational encapsulation, and as such is only found in the relatively low-level cognitive systems responsible for perception and language. According to Fodor's critics in the evolutionary psychology camp, modularity simply reflects the fine-grained functional specialization dictated by natural selection, and it characterizes virtually all aspects of cognitive architecture, including high-level systems for judgment, decision making, and reasoning. Though both of these perspectives on modularity have garnered support, the current state of evidence and argument suggests that a broader skepticism about modularity may be warranted. WIREs Cogn Sci 2013, 4:641-649. doi: 10.1002/wcs.1255 CONFLICT OF INTEREST: The author has declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website.

  7. [Oligonucleotide derivatives in the nucleic acid hybridization analysis. II. Isothermal signal amplification in process of DNA analysis by minisequencing].

    PubMed

    Dmitrienko, E V; Khomiakova, E A; Pyshnaia; Bragin, A G; Vedernikov, V E; Pyshnyĭ, D V

    2010-01-01

    The isothermal amplification of reporter signal via limited probe extension (minisequencing) upon hybridization of nucleic acids has been studied. The intensity of reporter signal has been shown to increase due to enzymatic labeling of multiple probes upon consecutive hybridization with one DNA template both in homophase and heterophase assays using various kinds of detection signal: radioisotope label, fluorescent label, and enzyme-linked assay. The kinetic scheme of the process has been proposed and kinetic parameters for each step have been determined. The signal intensity has been shown to correlate with physicochemical characteristics of both complexes: probe/DNA and product/DNA. The maximum intensity has been observed at minimal difference between the thermodynamic stability of these complexes, provided the reaction temperature has been adjusted near their melting temperature values; rising or lowering the reaction temperature reduces the amount of reporting product. The signal intensity has been shown to decrease significantly upon hybridization with the DNA template containing single-nucleotide mismatches. Limited probe extension assay is useful not only for detection of DNA template but also for its quantitative characterization.

  8. Slow conformational changes in MutS and DNA direct ordered transitions between mismatch search, recognition and signaling of DNA repair.

    PubMed

    Sharma, Anushi; Doucette, Christopher; Biro, F Noah; Hingorani, Manju M

    2013-11-15

    MutS functions in mismatch repair (MMR) to scan DNA for errors, identify a target site and trigger subsequent events in the pathway leading to error removal and DNA re-synthesis. These actions, enabled by the ATPase activity of MutS, are now beginning to be analyzed from the perspective of the protein itself. This study provides the first ensemble transient kinetic data on MutS conformational dynamics as it works with DNA and ATP in MMR. Using a combination of fluorescence probes (on Thermus aquaticus MutS and DNA) and signals (intensity, anisotropy and resonance energy transfer), we have monitored the timing of key conformational changes in MutS that are coupled to mismatch binding and recognition, ATP binding and hydrolysis, as well as sliding clamp formation and signaling of repair. Significant findings include (a) a slow step that follows weak initial interaction between MutS and DNA, in which concerted conformational changes in both macromolecules control mismatch recognition, and (b) rapid, binary switching of MutS conformations that is concerted with ATP binding and hydrolysis and (c) is stalled after mismatch recognition to control formation of the ATP-bound MutS sliding clamp. These rate-limiting pre- and post-mismatch recognition events outline the mechanism of action of MutS on DNA during initiation of MMR.

  9. DNA Damage Signaling Assessed in Individual Cells in Relation to the Cell Cycle Phase and Induction of Apoptosis

    PubMed Central

    Darzynkiewicz, Zbigniew; Zhao, Hong; Halicka, H. Dorota; Rybak, Paulina; Dobrucki, Jurek; Wlodkowic, Donald

    2012-01-01

    Reviewed are the phosphorylation events reporting activation of protein kinases and the key substrates critical for the DNA damage signaling (DDS). These DDS events are detected immunocytochemically using phospho-specific Abs; flow cytometry or image-assisted cytometry provide the means to quantitatively assess them on a cell by cell basis. The multiparameter analysis of the data is used to correlate these events with each other and relate to the cell cycle phase, DNA replication and induction of apoptosis. Expression of γH2AX as a possible marker of induction of DNA double strand breaks is the most widely studied event of DDS. Reviewed are applications of this multiparameter approach to investigate constitutive DDS reporting DNA damage by endogenous oxidants byproducts of oxidative phosphorylation. Also reviewed are its applications to detect and explore mechanisms of DDS induced by variety of exogenous agents targeting DNA such as exogenous oxidants, ionizing radiation, radiomimetic drugs, UV light, DNA topoisomerase I and II inhibitors, DNA crosslinking drugs and variety of environmental genotoxins. Analysis of DDS induced by these agents provides often a wealth of information about mechanism of induction and the type of DNA damage (lesion) and is reviewed in the context of cell cycle phase specificity, DNA replication, and induction of apoptosis or cell senescence. Critically assessed is interpretation of the data as to whether the observed DDS events report induction of a particular type of DNA lesion. PMID:23137030

  10. Targeting hyperactivated DNA-PKcs by KU0060648 inhibits glioma progression and enhances temozolomide therapy via suppression of AKT signaling

    PubMed Central

    Qu, Yanming; Zhang, Mingshan; Wang, Haoran; Zhang, Zhihua; Zhou, Wei; Fan, Xinyi; Yu, Chunjiang; Zhan, Qimin; Song, Yongmei

    2016-01-01

    The overall survival remains undesirable in clinical glioma treatment. Inhibition of DNA-PKcs activity by its inhibitors suppresses tumor growth and enhances chemosensitivity of several tumors to chemotherapy. However, whether DNA-PKcs could be a potential target in glioma therapy remains unknown. In this study, we reported that the hyperactivated DNA-PKcs was profoundly correlated with glioma malignancy and observe a significant association between DNA-PKcs activation and survival of the glioma patients. Our data also found that inhibition of DNA-PKcs by its inhibitor KU0060648 sensitized glioma cells to TMZ in vitro. Specifically, we demonstrated that KU0060648 interrupted the formation of DNA-PKcs/AKT complex, leading to suppression of AKT signaling and resultantly enhanced TMZ efficacy. Combination of KU0060648 and TMZ substantially inhibited downstream effectors of AKT. The in vivo results were similar to those obtained in vitro. In conclusion, this study indicated that inhibition of DNA-PKcs activity could suppress glioma malignancies and increase TMZ efficacy, which was mainly through regulation of the of AKT signaling. Therefore, DNA-PKcs/AKT axis may be a promising target for improving current glioma therapy. PMID:27487130

  11. Signalign: An Ontology of DNA as Signal for Comparative Gene Structure Prediction Using Information-Coding-and-Processing Techniques.

    PubMed

    Yu, Ning; Guo, Xuan; Gu, Feng; Pan, Yi

    2016-03-01

    Conventional character-analysis-based techniques in genome analysis manifest three main shortcomings-inefficiency, inflexibility, and incompatibility. In our previous research, a general framework, called DNA As X was proposed for character-analysis-free techniques to overcome these shortcomings, where X is the intermediates, such as digit, code, signal, vector, tree, graph network, and so on. In this paper, we further implement an ontology of DNA As Signal, by designing a tool named Signalign for comparative gene structure analysis, in which DNA sequences are converted into signal series, processed by modified method of dynamic time warping and measured by signal-to-noise ratio (SNR). The ontology of DNA As Signal integrates the principles and concepts of other disciplines including information coding theory and signal processing into sequence analysis and processing. Comparing with conventional character-analysis-based methods, Signalign can not only have the equivalent or superior performance, but also enrich the tools and the knowledge library of computational biology by extending the domain from character/string to diverse areas. The evaluation results validate the success of the character-analysis-free technique for improved performances in comparative gene structure prediction.

  12. Analytical Spectroscopy Using Modular Systems

    NASA Astrophysics Data System (ADS)

    Patterson, Brian M.; Danielson, Neil D.; Lorigan, Gary A.; Sommer, André J.

    2003-12-01

    This article describes the development of three analytical spectroscopy experiments that compare the determination of salicylic acid (SA) content in aspirin tablets. The experiments are based on UV vis, fluorescence, and Raman spectroscopies and utilize modular spectroscopic components. Students assemble their own instruments, optimize them with respect to signal-to-noise, generate calibration curves, determine the SA content in retail aspirin tablets, and assign features in the respective spectra to functional groups within the active material. Using this approach in the discovery-based setting, the students gain invaluable insight into method-specific parameters, such as instrumental components, sample preparation, and analytical capability. In addition, the students learn the fundamentals of fiber optics and signal processing using the low-cost CCD based spectroscopic components.

  13. Capicua DNA-binding sites are general response elements for RTK signaling in Drosophila.

    PubMed

    Ajuria, Leiore; Nieva, Claudia; Winkler, Clint; Kuo, Dennis; Samper, Núria; Andreu, María José; Helman, Aharon; González-Crespo, Sergio; Paroush, Ze'ev; Courey, Albert J; Jiménez, Gerardo

    2011-03-01

    RTK/Ras/MAPK signaling pathways play key functions in metazoan development, but how they control expression of downstream genes is not well understood. In Drosophila, it is generally assumed that most transcriptional responses to RTK signal activation depend on binding of Ets-family proteins to specific cis-acting sites in target enhancers. Here, we show that several Drosophila RTK pathways control expression of downstream genes through common octameric elements that are binding sites for the HMG-box factor Capicua, a transcriptional repressor that is downregulated by RTK signaling in different contexts. We show that Torso RTK-dependent regulation of terminal gap gene expression in the early embryo critically depends on Capicua octameric sites, and that binding of Capicua to these sites is essential for recruitment of the Groucho co-repressor to the huckebein enhancer in vivo. We then show that subsequent activation of the EGFR RTK pathway in the neuroectodermal region of the embryo controls dorsal-ventral gene expression by downregulating the Capicua protein, and that this control also depends on Capicua octameric motifs. Thus, a similar mechanism of RTK regulation operates during subdivision of the anterior-posterior and dorsal-ventral embryonic axes. We also find that identical DNA octamers mediate Capicua-dependent regulation of another EGFR target in the developing wing. Remarkably, a simple combination of activator-binding sites and Capicua motifs is sufficient to establish complex patterns of gene expression in response to both Torso and EGFR activation in different tissues. We conclude that Capicua octamers are general response elements for RTK signaling in Drosophila.

  14. A DNA damage signal is required for p53 to activate gadd45.

    PubMed

    Xiao, G; Chicas, A; Olivier, M; Taya, Y; Tyagi, S; Kramer, F R; Bargonetti, J

    2000-03-15

    We provide direct evidence that overexpression of p53 is not sufficient for robust p53-dependent activation of the endogenous gadd45 gene. When p53 was induced in TR9-7 cells in the absence of DNA damage, waf1/p21 and mdm2 mRNA levels were increased, but a change in gadd45 mRNA was barely detectable. Activation of the gadd45 gene was observed when camptothecin was added to cells containing p53 in the absence of a further increase in the p53 level. Phosphorylation of p53 at serine 15 and acetylation at lysine 382 were detected after drug treatment. It has been suggested that p53 posttranslational modification is critical during activation. However, inhibition of these modifications by wortmannin was not sufficient to block the transactivation of gadd45. Interestingly, after camptothecin treatment, increased DNase I sensitivity was detected at the gadd45 promoter, suggesting that an undetermined DNA damage signal is involved in inducing chromatin remodeling at the gadd45 promoter while cooperating with p53 to activate gadd45 transcription.

  15. A cytometric bead assay for sensitive DNA detection based on enzyme-free signal amplification of hybridization chain reaction.

    PubMed

    Ren, Wei; Liu, Hongmei; Yang, Wenxia; Fan, Yunlong; Yang, Lang; Wang, Yucong; Liu, Chenghui; Li, Zhengping

    2013-11-15

    A versatile flow cytometric bead assay (CBA) is developed for sensitive DNA detection by integrating the advantages of hybridization chain reaction (HCR) for enzyme-free signal amplification, flow cytometry for robust and rapid signal readout as well as magnetic beads (MBs) for facile separation. In this HCR-CBA, a biotinylated hairpin DNA (Bio-H1) is firstly immobilized on streptavidin-functionalized MBs. Upon the addition of target DNA, each target would hybridize with one Bio-H1 to open its hairpin structure and subsequently initiate a cascade of hybridization events between two species of fluorescent DNA hairpin probes (H1*/H2*) to form a nicked double helical DNA structure, resulting in amplified accumulation of numerous fluorophores on the MBs. Finally, the fluorescent MBs are directly analyzed by flow cytometry. This technique enables quantitative analysis of the HCR products anchored on the MBs as a function of target DNA concentration, and analysis of each sample can be completed within few minutes. Therefore, the HCR-CBA approach provides a practical DNA assay with greatly improved sensitivity. The detection limit of a model DNA target is 0.5 pM (3σ), which is about 3 orders of magnitude lower compared with traditional hybridization methods without HCR. Furthermore, the signal of complementary target can be clearly distinguished from that of single-base mismatched sequences, indicating the high specificity of the HCR-CBA. Moreover, this strategy is also successfully applied to the DNA analysis in complex biological samples, showing great potential in gene analysis and disease diagnosis in clinical samples.

  16. Cleavable DNA-protein hybrid molecular beacon: A novel efficient signal translator for sensitive fluorescence anisotropy bioassay.

    PubMed

    Hu, Pan; Yang, Bin

    2016-01-15

    Due to its unique features such as high sensitivity, homogeneous format, and independence on fluorescent intensity, fluorescence anisotropy (FA) assay has become a hotspot of study in oligonucleotide-based bioassays. However, until now most FA probes require carefully customized structure designs, and thus are neither generalizable for different sensing systems nor effective to obtain sufficient signal response. To address this issue, a cleavable DNA-protein hybrid molecular beacon was successfully engineered for signal amplified FA bioassay, via combining the unique stable structure of molecular beacon and the large molecular mass of streptavidin. Compared with single DNA strand probe or conventional molecular beacon, the DNA-protein hybrid molecular beacon exhibited a much higher FA value, which was potential to obtain high signal-background ratio in sensing process. As proof-of-principle, this novel DNA-protein hybrid molecular beacon was further applied for FA bioassay using DNAzyme-Pb(2+) as a model sensing system. This FA assay approach could selectively detect as low as 0.5nM Pb(2+) in buffer solution, and also be successful for real samples analysis with good recovery values. Compatible with most of oligonucleotide probes' designs and enzyme-based signal amplification strategies, the molecular beacon can serve as a novel signal translator to expand the application prospect of FA technology in various bioassays.

  17. IL-1α is a DNA damage sensor linking genotoxic stress signaling to sterile inflammation and innate immunity.

    PubMed

    Cohen, Idan; Idan, Cohen; Rider, Peleg; Peleg, Rider; Vornov, Elena; Elena, Voronov; Tomas, Martin; Martin, Tomas; Tudor, Cicerone; Cicerone, Tudor; Wegner, Mareike; Mareike, Wegner; Brondani, Lydia; Lydia, Brondani; Freudenberg, Marina; Marina, Freudenberg; Mittler, Gerhard; Gerhard, Mittler; Ferrando-May, Elisa; Elisa, Ferrando-May; Dinarello, Charles A; Apte, Ron N; Ron, Apte N; Schneider, Robert; Robert, Schneider

    2015-10-06

    Environmental signals can be translated into chromatin changes, which alter gene expression. Here we report a novel concept that cells can signal chromatin damage from the nucleus back to the surrounding tissue through the cytokine interleukin-1alpha (IL-1α). Thus, in addition to its role as a danger signal, which occurs when the cytokine is passively released by cell necrosis, IL-1α could directly sense DNA damage and act as signal for genotoxic stress without loss of cell integrity. Here we demonstrate localization of the cytokine to DNA-damage sites and its subsequent secretion. Interestingly, its nucleo-cytosolic shuttling after DNA damage sensing is regulated by histone deacetylases (HDAC) and IL-1α acetylation. To demonstrate the physiological significance of this newly discovered mechanism, we used IL-1α knockout mice and show that IL-1α signaling after UV skin irradiation and DNA damage is important for triggering a sterile inflammatory cascade in vivo that contributes to efficient tissue repair and wound healing.

  18. Catalytic inhibitors of DNA topoisomerase II suppress the androgen receptor signaling and prostate cancer progression

    PubMed Central

    Li, Haolong; Xie, Ning; Gleave, Martin E.; Dong, Xuesen

    2015-01-01

    Although the new generation of androgen receptor (AR) antagonists like enzalutamide (ENZ) prolong survival of metastatic castration-resistant prostate cancer (CRPC), AR-driven tumors eventually recur indicating that additional therapies are required to fully block AR function. Since DNA topoisomerase II (Topo II) was demonstrated to be essential for AR to initiate gene transcription, this study tested whether catalytic inhibitors of Topo II can block AR signaling and suppress ENZ-resistant CRPC growth. Using multiple prostate cancer cell lines, we showed that catalytic Topo II inhibitors, ICRF187 and ICRF193 inhibited transcription activities of the wild-type AR, mutant ARs (F876L and W741C) and the AR-V7 splice variant. ICRF187 and ICRF193 decreased AR recruitment to target promoters and reduced AR nuclear localization. Both ICRF187 and ICRF193 also inhibited cell proliferation and delayed cell cycling at the G2/M phase. ICRF187 inhibited tumor growth of castration-resistant LNCaP and 22RV1 xenografts as well as ENZ-resistant MR49F xenografts. We conclude that catalytic Topo II inhibitors can block AR signaling and inhibit tumor growth of CRPC xenografts, identifying a potential co-targeting approach using these inhibitors in combination with AR pathway inhibitors in CRPC. PMID:26009876

  19. DNA-PK triggers histone ubiquitination and signaling in response to DNA double-strand breaks produced during the repair of transcription-blocking topoisomerase I lesions.

    PubMed

    Cristini, Agnese; Park, Joon-Hyung; Capranico, Giovanni; Legube, Gaëlle; Favre, Gilles; Sordet, Olivier

    2016-02-18

    Although defective repair of DNA double-strand breaks (DSBs) leads to neurodegenerative diseases, the processes underlying their production and signaling in non-replicating cells are largely unknown. Stabilized topoisomerase I cleavage complexes (Top1cc) by natural compounds or common DNA alterations are transcription-blocking lesions whose repair depends primarily on Top1 proteolysis and excision by tyrosyl-DNA phosphodiesterase-1 (TDP1). We previously reported that stabilized Top1cc produce transcription-dependent DSBs that activate ATM in neurons. Here, we use camptothecin (CPT)-treated serum-starved quiescent cells to induce transcription-blocking Top1cc and show that those DSBs are generated during Top1cc repair from Top1 peptide-linked DNA single-strand breaks generated after Top1 proteolysis and before excision by TDP1. Following DSB induction, ATM activates DNA-PK whose inhibition suppresses H2AX and H2A ubiquitination and the later assembly of activated ATM into nuclear foci. Inhibition of DNA-PK also reduces Top1 ubiquitination and proteolysis as well as resumption of RNA synthesis suggesting that DSB signaling further enhances Top1cc repair. Finally, we show that co-transcriptional DSBs kill quiescent cells. Together, these new findings reveal that DSB production and signaling by transcription-blocking Top1 lesions impact on non-replicating cell fate and provide insights on the molecular pathogenesis of neurodegenerative diseases such as SCAN1 and AT syndromes, which are caused by TDP1 and ATM deficiency, respectively.

  20. Symmetric modular torsatron

    DOEpatents

    Rome, J.A.; Harris, J.H.

    1984-01-01

    A fusion reactor device is provided in which the magnetic fields for plasma confinement in a toroidal configuration is produced by a plurality of symmetrical modular coils arranged to form a symmetric modular torsatron referred to as a symmotron. Each of the identical modular coils is helically deformed and comprise one field period of the torsatron. Helical segments of each coil are connected by means of toroidally directed windbacks which may also provide part of the vertical field required for positioning the plasma. The stray fields of the windback segments may be compensated by toroidal coils. A variety of magnetic confinement flux surface configurations may be produced by proper modulation of the winding pitch of the helical segments of the coils, as in a conventional torsatron, winding the helix on a noncircular cross section and varying the poloidal and radial location of the windbacks and the compensating toroidal ring coils.

  1. Self Evolving Modular Network

    NASA Astrophysics Data System (ADS)

    Tokunaga, Kazuhiro; Kawabata, Nobuyuki; Furukawa, Tetsuo

    We propose a novel modular network called the Self-Evolving Modular Network (SEEM). The SEEM has a modular network architecture with a graph structure and these following advantages: (1) new modules are added incrementally to allow the network to adapt in a self-organizing manner, and (2) graph's paths are formed based on the relationships between the models represented by modules. The SEEM is expected to be applicable to evolving functions of an autonomous robot in a self-organizing manner through interaction with the robot's environment and categorizing large-scale information. This paper presents the architecture and an algorithm for the SEEM. Moreover, performance characteristic and effectiveness of the network are shown by simulations using cubic functions and a set of 3D-objects.

  2. Modular optical detector system

    DOEpatents

    Horn, Brent A.; Renzi, Ronald F.

    2006-02-14

    A modular optical detector system. The detector system is designed to detect the presence of molecules or molecular species by inducing fluorescence with exciting radiation and detecting the emitted fluorescence. Because the system is capable of accurately detecting and measuring picomolar concentrations it is ideally suited for use with microchemical analysis systems generally and capillary chromatographic systems in particular. By employing a modular design, the detector system provides both the ability to replace various elements of the detector system without requiring extensive realignment or recalibration of the components as well as minimal user interaction with the system. In addition, the modular concept provides for the use and addition of a wide variety of components, including optical elements (lenses and filters), light sources, and detection means, to fit particular needs.

  3. Modular Optofluidic Systems (MOPS)

    NASA Astrophysics Data System (ADS)

    Ackermann, Tobias N.; Dietvorst, Jiri; Sanchis, Ana; Salvador, Juan P.; Munoz-Berbel, Xavier; Alvarez-Conde, Erica; Kopp, Daniel; Zappe, Hans; Marco, M.-Pilar; Llobera, Andreu

    2016-12-01

    Elementary PDMS-based building blocks of fluidic, optical and optofluidic components for Lab on a chip (LOC) platforms has here been developed. All individual modules are compatible and can be anchored and released with the help of puzzle-type connectors This approach is a powerful toolbox to create modular optofluidic systems (MOPS), which can be modified/upgraded to user needs and in-situ reconfigurable. In addition, the PDMS can locally be functionalized, defining a modular biosensor. Measurements in absorbance and fluorescence have been pursued as demonstrator.

  4. Modular biowaste monitoring system

    NASA Technical Reports Server (NTRS)

    Fogal, G. L.

    1975-01-01

    The objective of the Modular Biowaste Monitoring System Program was to generate and evaluate hardware for supporting shuttle life science experimental and diagnostic programs. An initial conceptual design effort established requirements and defined an overall modular system for the collection, measurement, sampling and storage of urine and feces biowastes. This conceptual design effort was followed by the design, fabrication and performance evaluation of a flight prototype model urine collection, volume measurement and sampling capability. No operational or performance deficiencies were uncovered as a result of the performance evaluation tests.

  5. Modular total absorption spectrometer

    NASA Astrophysics Data System (ADS)

    Karny, M.; Rykaczewski, K. P.; Fijałkowska, A.; Rasco, B. C.; Wolińska-Cichocka, M.; Grzywacz, R. K.; Goetz, K. C.; Miller, D.; Zganjar, E. F.

    2016-11-01

    The design and performance of the Modular Total Absorption Spectrometer built and commissioned at the Oak Ridge National Laboratory is presented. The active volume of the detector is approximately one ton of NaI(Tl), which results in very high full γ energy peak efficiency of 71% at 6 MeV and nearly flat efficiency of around 81.5% for low energy γ-rays between 300 keV and 1 MeV. In addition to the high peak efficiency, the modular construction of the detector permits the use of a γ-coincidence technique in data analysis as well as β-delayed neutron observation.

  6. DNA Damage Signaling Is Required for Replication of Human Bocavirus 1 DNA in Dividing HEK293 Cells.

    PubMed

    Deng, Xuefeng; Xu, Peng; Zou, Wei; Shen, Weiran; Peng, Jianxin; Liu, Kaiyu; Engelhardt, John F; Yan, Ziying; Qiu, Jianming

    2017-01-01

    Human bocavirus 1 (HBoV1), an emerging human-pathogenic respiratory virus, is a member of the genus Bocaparvovirus of the Parvoviridae family. In human airway epithelium air-liquid interface (HAE-ALI) cultures, HBoV1 infection initiates a DNA damage response (DDR), activating all three phosphatidylinositol 3-kinase-related kinases (PI3KKs): ATM, ATR, and DNA-PKcs. In this context, activation of PI3KKs is a requirement for amplification of the HBoV1 genome (X. Deng, Z. Yan, F. Cheng, J. F. Engelhardt, and J. Qiu, PLoS Pathog, 12:e1005399, 2016, https://doi.org/10.1371/journal.ppat.1005399), and HBoV1 replicates only in terminally differentiated, nondividing cells. This report builds on the previous discovery that the replication of HBoV1 DNA can also occur in dividing HEK293 cells, demonstrating that such replication is likewise dependent on a DDR. Transfection of HEK293 cells with the duplex DNA genome of HBoV1 induces hallmarks of DDR, including phosphorylation of H2AX and RPA32, as well as activation of all three PI3KKs. The large viral nonstructural protein NS1 is sufficient to induce the DDR and the activation of the three PI3KKs. Pharmacological inhibition or knockdown of any one of the PI3KKs significantly decreases both the replication of HBoV1 DNA and the downstream production of progeny virions. The DDR induced by the HBoV1 NS1 protein does not cause obvious damage to cellular DNA or arrest of the cell cycle. Notably, key DNA replication factors and major DNA repair DNA polymerases (polymerase η [Pol η] and polymerase κ [Pol κ]) are recruited to the viral DNA replication centers and facilitate HBoV1 DNA replication. Our study provides the first evidence of the DDR-dependent parvovirus DNA replication that occurs in dividing cells and is independent of cell cycle arrest.

  7. Network-Physics (NP) BEC DIGITAL(#)-VULNERABILITY; ``Q-Computing"=Simple-Arithmetic;Modular-Congruences=SignalXNoise PRODUCTS=Clock-model;BEC-Factorization;RANDOM-# Definition;P=/=NP TRIVIAL Proof!!!

    NASA Astrophysics Data System (ADS)

    Pi, E. I.; Siegel, E.

    2010-03-01

    Siegel[AMS Natl.Mtg.(2002)-Abs.973-60-124] digits logarithmic- law inversion to ONLY BEQS BEC:Quanta/Bosons=#: EMP-like SEVERE VULNERABILITY of ONLY #-networks(VS.ANALOG INvulnerability) via Barabasi NP(VS.dynamics[Not.AMS(5/2009)] critique);(so called)``quantum-computing''(QC) = simple-arithmetic (sansdivision);algorithmiccomplexities:INtractibility/UNdecidabi lity/INefficiency/NONcomputability/HARDNESS(so MIScalled) ``noise''-induced-phase-transition(NIT)ACCELERATION:Cook-Levin theorem Reducibility = RG fixed-points; #-Randomness DEFINITION via WHAT? Query(VS. Goldreich[Not.AMS(2002)] How? mea culpa)= ONLY MBCS hot-plasma v #-clumping NON-random BEC; Modular-Arithmetic Congruences = Signal x Noise PRODUCTS = clock-model; NON-Shor[Physica A,341,586(04)]BEC logarithmic-law inversion factorization: Watkins #-theory U statistical- physics); P=/=NP C-S TRIVIAL Proof: Euclid!!! [(So Miscalled) computational-complexity J-O obviation(3 millennia AGO geometry: NO:CC,``CS'';``Feet of Clay!!!'']; Query WHAT?:Definition: (so MIScalled)``complexity''=UTTER-SIMPLICITY!! v COMPLICATEDNESS MEASURE(S).

  8. Algorithmic-Reducibility = Renormalization-Group Fixed-Points; ``Noise''-Induced Phase-Transitions (NITs) to Accelerate Algorithmics (``NIT-Picking'') Replacing CRUTCHES!!!: Gauss Modular/Clock-Arithmetic Congruences = Signal X Noise PRODUCTS..

    NASA Astrophysics Data System (ADS)

    Siegel, J.; Siegel, Edward Carl-Ludwig

    2011-03-01

    Cook-Levin computational-"complexity"(C-C) algorithmic-equivalence reduction-theorem reducibility equivalence to renormalization-(semi)-group phase-transitions critical-phenomena statistical-physics universality-classes fixed-points, is exploited with Gauss modular/clock-arithmetic/model congruences = signal X noise PRODUCT reinterpretation. Siegel-Baez FUZZYICS=CATEGORYICS(SON of ``TRIZ''): Category-Semantics(C-S) tabular list-format truth-table matrix analytics predicts and implements "noise"-induced phase-transitions (NITs) to accelerate versus to decelerate Harel [Algorithmics(1987)]-Sipser[Intro. Theory Computation(1997) algorithmic C-C: "NIT-picking" to optimize optimization-problems optimally(OOPO). Versus iso-"noise" power-spectrum quantitative-only amplitude/magnitude-only variation stochastic-resonance, this "NIT-picking" is "noise" power-spectrum QUALitative-type variation via quantitative critical-exponents variation. Computer-"science" algorithmic C-C models: Turing-machine, finite-state-models/automata, are identified as early-days once-workable but NOW ONLY LIMITING CRUTCHES IMPEDING latter-days new-insights!!!

  9. Effect of inserted spacer in hepatic cell-penetrating multifunctional peptide component on the DNA intracellular delivery of quaternary complexes based on modular design

    PubMed Central

    Zhang, Luchen; Li, Zhenbo; Sun, Fangli; Xu, Yuhong; Du, Zixiu

    2016-01-01

    A safe and efficient quaternary gene delivery system (named Q-complexes) was constructed based on self-assembly of molecules through noncovalent bonds. This system was formulated through the cooperation and competing interactions of cationic liposomes, multifunctional peptides, and DNA, followed by coating hyaluronic acid on the surface of the ternary complexes. The multifunctional peptide was composed of two functional domains: penetrating hepatic tumor-targeted cell moiety (KRPTMRFRYTWNPMK) and a wrapping gene sequence (polyarginine 16). The effect of spacer insertion between the two domains of multifunctional peptide on the intracellular transfection of Q-complexes was further studied. Experimental results showed that the formulations assembled with various peptides in the spacer elements possessed different intercellular pathways and transfection efficiencies. The Q-complexes containing peptide in the absence of spacer element (Pa) showed the highest gene expression among all samples. The Q-complexes containing peptides with a noncleavable spacer GA (Pc) had no ability of intracellular nucleic acid delivery, whereas those with a cleavable spacer RVRR (Pd) showed moderate transfection activity. These results demonstrated that the different spacers inserted in the multifunctional peptide played an important role in in vitro DNA transfection efficiency. Atomic force microscopy images showed that the morphologies of ternary complexes (LPcD) and Q-complexes (HLcPD) were crystal lamellas, whereas those of other nanocomplexes were spheres. Circular dichroism showed the changed configuration of peptide with spacer GA in nanocomplexes compared with that of its free state, whereas the Pa configuration without spacer in nanocomplexes was consistent with that of its free state. The present study contributed to the structural understanding of Q-complexes, and further effective modification is in progress. PMID:27920533

  10. Post-translational modifications of proliferating cell nuclear antigen: A key signal integrator for DNA damage response (Review).

    PubMed

    Zhu, Qiong; Chang, Yuxiao; Yang, Jin; Wei, Quanfang

    2014-05-01

    Previous studies have shown that the post-translational modifications of proliferating cell nuclear antigen (PCNA) may be crucial in influencing the cellular choice between different pathways, such as the cell cycle checkpoint, DNA repair or apoptosis pathways, in order to maintain genomic stability. DNA damage leads to replication stress and the subsequent induction of PCNA modification by small ubiquitin (Ub)-related modifiers and Ub, which has been identified to affect multiple biological processes of genomic DNA. Thus far, much has been learned concerning the behavior of modified PCNA as a key signal integrator in response to DNA damage. In humans and yeast, modified PCNA activates DNA damage bypass via an error-prone or error-free pathway to prevent the breakage of DNA replication forks, which may potentially induce double-strand breaks and subsequent chromosomal rearrangements. However, the exact mechanisms by which these pathways work and by what means the modified PCNA is involved in these processes remain elusive. Thus, the improved understanding of PCNA modification and its implications for DNA damage response may provide us with more insight into the mechanisms by which human cells regulate aberrant recombination events, and cancer initiation and development. The present review focuses on the post-translational modifications of PCNA and its important functions in mediating mammalian cellular response to different types of DNA damage.

  11. Porcine bocavirus NP1 negatively regulates interferon signaling pathway by targeting the DNA-binding domain of IRF9

    SciTech Connect

    Zhang, Ruoxi; Fang, Liurong; Wang, Dang; Cai, Kaimei; Zhang, Huan; Xie, Lilan; Li, Yi; Chen, Huanchun; Xiao, Shaobo

    2015-11-15

    To subvert host antiviral immune responses, many viruses have evolved countermeasures to inhibit IFN signaling pathway. Porcine bocavirus (PBoV), a newly identified porcine parvovirus, has received attention because it shows clinically high co-infection prevalence with other pathogens in post-weaning multisystemic wasting syndrome (PWMS) and diarrheic piglets. In this study, we screened the structural and non-structural proteins encoded by PBoV and found that the non-structural protein NP1 significantly suppressed IFN-stimulated response element (ISRE) activity and subsequent IFN-stimulated gene (ISG) expression. However, NP1 affected neither the activation and translocation of STAT1/STAT2, nor the formation of the heterotrimeric transcription factor complex ISGF3 (STAT1/STAT2/IRF9). Detailed analysis demonstrated that PBoV NP1 blocked the ISGF3 DNA-binding activity by combining with the DNA-binding domain (DBD) of IRF9. In summary, these results indicate that PBoV NP1 interferes with type I IFN signaling pathway by blocking DNA binding of ISGF3 to attenuate innate immune responses. - Highlights: • Porcine bocavirus (PBoV) NP1 interferes with the IFN α/β signaling pathway. • PBoV NP1 does not prevent STAT1/STAT2 phosphorylation and nuclear translocation. • PBoV NP1 inhibits the DNA-binding activity of ISGF3. • PBoV NP1 interacts with the DNA-binding domain of IRF9.

  12. NF-kappaB activation by camptothecin. A linkage between nuclear DNA damage and cytoplasmic signaling events.

    PubMed

    Huang, T T; Wuerzberger-Davis, S M; Seufzer, B J; Shumway, S D; Kurama, T; Boothman, D A; Miyamoto, S

    2000-03-31

    Activation of the transcription factor NF-kappaB by extracellular signals involves its release from the inhibitor protein IkappaBalpha in the cytoplasm and subsequent nuclear translocation. NF-kappaB can also be activated by the anticancer agent camptothecin (CPT), which inhibits DNA topoisomerase (Topo) I activity and causes DNA double-strand breaks during DNA replication to induce S phase-dependent cytotoxicity. Here we show that CPT activates NF-kappaB by a mechanism that is dependent on initial nuclear DNA damage followed by cytoplasmic signaling events. NF-kappaB activation by CPT is dramatically diminished in cytoplasts and in CEM/C2 cells expressing a mutant Topo I protein that fails to bind CPT. This response is intensified in S phase cell populations and is prevented by the DNA polymerase inhibitor aphidicolin. In addition, CPT activation of NF-kappaB involves degradation of cytoplasmic IkappaBalpha by the ubiquitin-proteasome pathway in a manner that depends on the IkappaB kinase complex. Finally, inhibition of NF-kappaB activation augments CPT-induced apoptosis. These findings elucidate the progression of signaling events that initiates in the nucleus with CPT-Topo I interaction and continues in the cytoplasm resulting in degradation of IkappaBalpha and nuclear translocation of NF-kappaB to attenuate the apoptotic response.

  13. An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes

    PubMed Central

    Huard, Jérémy; Mueller, Stephanie; Gilles, Ernst D; Klingmüller, Ursula; Klamt, Steffen

    2012-01-01

    During liver regeneration, quiescent hepatocytes re-enter the cell cycle to proliferate and compensate for lost tissue. Multiple signals including hepatocyte growth factor, epidermal growth factor, tumor necrosis factor α, interleukin-6, insulin and transforming growth factor β orchestrate these responses and are integrated during the G1 phase of the cell cycle. To investigate how these inputs influence DNA synthesis as a measure for proliferation, we established a large-scale integrated logical model connecting multiple signaling pathways and the cell cycle. We constructed our model based upon established literature knowledge, and successively improved and validated its structure using hepatocyte-specific literature as well as experimental DNA synthesis data. Model analyses showed that activation of the mitogen-activated protein kinase and phosphatidylinositol 3-kinase pathways was sufficient and necessary for triggering DNA synthesis. In addition, we identified key species in these pathways that mediate DNA replication. Our model predicted oncogenic mutations that were compared with the COSMIC database, and proposed intervention targets to block hepatocyte growth factor-induced DNA synthesis, which we validated experimentally. Our integrative approach demonstrates that, despite the complexity and size of the underlying interlaced network, logical modeling enables an integrative understanding of signaling-controlled proliferation at the cellular level, and thus can provide intervention strategies for distinct perturbation scenarios at various regulatory levels. PMID:22443451

  14. DNA Damage Signaling Is Induced in the Absence of Epstein-Barr Virus (EBV) Lytic DNA Replication and in Response to Expression of ZEBRA.

    PubMed

    Wang'ondu, Ruth; Teal, Stuart; Park, Richard; Heston, Lee; Delecluse, Henri; Miller, George

    2015-01-01

    Epstein Barr virus (EBV), like other oncogenic viruses, modulates the activity of cellular DNA damage responses (DDR) during its life cycle. Our aim was to characterize the role of early lytic proteins and viral lytic DNA replication in activation of DNA damage signaling during the EBV lytic cycle. Our data challenge the prevalent hypothesis that activation of DDR pathways during the EBV lytic cycle occurs solely in response to large amounts of exogenous double stranded DNA products generated during lytic viral DNA replication. In immunofluorescence or immunoblot assays, DDR activation markers, specifically phosphorylated ATM (pATM), H2AX (γH2AX), or 53BP1 (p53BP1), were induced in the presence or absence of viral DNA amplification or replication compartments during the EBV lytic cycle. In assays with an ATM inhibitor and DNA damaging reagents in Burkitt lymphoma cell lines, γH2AX induction was necessary for optimal expression of early EBV genes, but not sufficient for lytic reactivation. Studies in lytically reactivated EBV-positive cells in which early EBV proteins, BGLF4, BGLF5, or BALF2, were not expressed showed that these proteins were not necessary for DDR activation during the EBV lytic cycle. Expression of ZEBRA, a viral protein that is necessary for EBV entry into the lytic phase, induced pATM foci and γH2AX independent of other EBV gene products. ZEBRA mutants deficient in DNA binding, Z(R183E) and Z(S186E), did not induce foci of pATM. ZEBRA co-localized with HP1β, a heterochromatin associated protein involved in DNA damage signaling. We propose a model of DDR activation during the EBV lytic cycle in which ZEBRA induces ATM kinase phosphorylation, in a DNA binding dependent manner, to modulate gene expression. ATM and H2AX phosphorylation induced prior to EBV replication may be critical for creating a microenvironment of viral and cellular gene expression that enables lytic cycle progression.

  15. A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signaling pathways in plants

    NASA Technical Reports Server (NTRS)

    Yang, Tianbao; Poovaiah, B. W.

    2002-01-01

    We reported earlier that the tobacco early ethylene-responsive gene NtER1 encodes a calmodulin-binding protein (Yang, T., and Poovaiah, B. W. (2000) J. Biol. Chem. 275, 38467-38473). Here we demonstrate that there is one NtER1 homolog as well as five related genes in Arabidopsis. These six genes are rapidly and differentially induced by environmental signals such as temperature extremes, UVB, salt, and wounding; hormones such as ethylene and abscisic acid; and signal molecules such as methyl jasmonate, H(2)O(2), and salicylic acid. Hence, they were designated as AtSR1-6 (Arabidopsis thaliana signal-responsive genes). Ca(2+)/calmodulin binds to all AtSRs, and their calmodulin-binding regions are located on a conserved basic amphiphilic alpha-helical motif in the C terminus. AtSR1 targets the nucleus and specifically recognizes a novel 6-bp CGCG box (A/C/G)CGCG(G/T/C). The multiple CGCG cis-elements are found in promoters of genes such as those involved in ethylene signaling, abscisic acid signaling, and light signal perception. The DNA-binding domain in AtSR1 is located on the N-terminal 146 bp where all AtSR1-related proteins share high similarity but have no similarity to other known DNA-binding proteins. The calmodulin-binding nuclear proteins isolated from wounded leaves exhibit specific CGCG box DNA binding activities. These results suggest that the AtSR gene family encodes a family of calmodulin-binding/DNA-binding proteins involved in multiple signal transduction pathways in plants.

  16. Sensitive detection for coralyne and mercury ions based on homo-A/T DNA by exonuclease signal amplification.

    PubMed

    Huang, Hailiang; Shi, Shuo; Zheng, Xuyue; Yao, Tianming

    2015-09-15

    Based on specific homo-A/T DNA binding properties, a strategy for coralyne and mercury ions detection was realised by exonuclease-aided signal amplification. Coralyne could specifically bind homo-A DNA and protect it from the hydrolysis of exonuclease I. The coralyne-protected DNA was subsequently used as a trigger strand to hydrolyze DNA2 in exonuclease-aided signal amplification process. Thiazole orange was used to quantify the remainder DNA2. Under the optimal condition, the fluorescence intensity was linearly proportional to the concentration of coralyne in the range of 0.2-100 nM with a limit of detection (LOD) of 0.31 nM, which presented the lowest LOD for coralyne among all reported. With homo-T and Hg(2+) taking the place of homo-A DNA and coralyne, respectively, the system could also be used for Hg(2+) detection. The experiments in real samples also showed good results. This method was label-free, low-cost, easy-operating and highly repeatable for the detection of coralyne and mercury ions. It could also be extended to detect various analytes, such as other metal ions, proteins and small molecules by using appropriate aptamers.

  17. Role of Akt signaling in resistance to DNA-targeted therapy

    PubMed Central

    Avan, Abolfazl; Narayan, Ravi; Giovannetti, Elisa; Peters, Godefridus J

    2016-01-01

    The Akt signal transduction pathway controls most hallmarks of cancer. Activation of the Akt cascade promotes a malignant phenotype and is also widely implicated in drug resistance. Therefore, the modulation of Akt activity is regarded as an attractive strategy to enhance the efficacy of cancer therapy and irradiation. This pathway consists of phosphatidylinositol 3 kinase (PI3K), mammalian target of rapamycin, and the transforming serine-threonine kinase Akt protein isoforms, also known as protein kinase B. DNA-targeted agents, such as platinum agents, taxanes, and antimetabolites, as well as radiation have had a significant impact on cancer treatment by affecting DNA replication, which is aberrantly activated in malignancies. However, the caveat is that they may also trigger the activation of repairing mechanisms, such as upstream and downstream cascade of Akt survival pathway. Thus, each target can theoretically be inhibited in view of improving the potency of conventional treatment. Akt inhibitors, e.g., MK-2206 and perifosine, or PI3K modulators, e.g., LY294002 and Wortmannin, have shown some promising results in favor of sensitizing the cancer cells to the therapy in vitro and in vivo, which have provided the rationale for incorporation of these novel agents into multimodality treatment of different malignancies. Nevertheless, despite the acceptable safety profile of some of these agents in the clinical studies, with regard to the efficacy, the results are still too preliminary. Hence, we need to wait for the upcoming data from the ongoing trials before utilizing them into the standard care of cancer patients. PMID:27777878

  18. Modularity in robotic systems

    NASA Technical Reports Server (NTRS)

    Tesar, Delbert; Butler, Michael S.

    1989-01-01

    Most robotic systems today are designed one at a time, at a high cost of time and money. This wasteful approach has been necessary because the industry has not established a foundation for the continued evolution of intelligent machines. The next generation of robots will have to be generic, versatile machines capable of absorbing new technology rapidly and economically. This approach is demonstrated in the success of the personal computer, which can be upgraded or expanded with new software and hardware at virtually every level. Modularity is perceived as a major opportunity to reduce the 6 to 7 year design cycle time now required for new robotic manipulators, greatly increasing the breadth and speed of diffusion of robotic systems in manufacturing. Modularity and its crucial role in the next generation of intelligent machines are the focus of interest. The main advantages that modularity provides are examined; types of modules needed to create a generic robot are discussed. Structural modules designed by the robotics group at the University of Texas at Austin are examined to demonstrate the advantages of modular design.

  19. MRV - Modular Robotic Vehicle

    NASA Technical Reports Server (NTRS)

    Ridley, Justin; Bluethmann, Bill

    2015-01-01

    The Modular Robotic Vehicle, or MRV, completed in 2013, was developed at the Johnson Space Center in order to advance technologies which have applications for future vehicles both in space and on Earth. With seating for two people, MRV is a fully electric vehicle modeled as a "city car", suited for busy urban environments.

  20. Modular core holder

    SciTech Connect

    Mueller, J.; Cole, C.W.; Hamid, S.; Lucas, J.K.

    1991-03-05

    This patent describes a modular core holder. It comprises: a sleeve, forming an internal cavity for receiving a core. The sleeve including segments; support means, overlying the sleeve, for supporting the sleeve; and access means, positioned between at least two of the segments of the sleeve, for allowing measurement of conditions within the internal cavity.

  1. Modular Perspectives on Bilingualism.

    ERIC Educational Resources Information Center

    Francis, Norbert

    2002-01-01

    This research review traces the current discussion on models of bilingualism to the contributions of Vygotsky and Luria. Proposes that a modular approach to studying the different aspects of bilingual development promises to chart a course toward finding a broader common ground around research findings and interpretations that appear to be…

  2. Modular invariant inflation

    SciTech Connect

    Kobayashi, Tatsuo; Nitta, Daisuke; Urakawa, Yuko

    2016-08-08

    Modular invariance is a striking symmetry in string theory, which may keep stringy corrections under control. In this paper, we investigate a phenomenological consequence of the modular invariance, assuming that this symmetry is preserved as well as in a four dimensional (4D) low energy effective field theory. As a concrete setup, we consider a modulus field T whose contribution in the 4D effective field theory remains invariant under the modular transformation and study inflation drived by T. The modular invariance restricts a possible form of the scalar potenntial. As a result, large field models of inflation are hardly realized. Meanwhile, a small field model of inflation can be still accomodated in this restricted setup. The scalar potential traced during the slow-roll inflation mimics the hilltop potential V{sub ht}, but it also has a non-negligible deviation from V{sub ht}. Detecting the primordial gravitational waves predicted in this model is rather challenging. Yet, we argue that it may be still possible to falsify this model by combining the information in the reheating process which can be determined self-completely in this setup.

  3. A Modular CAI System.

    ERIC Educational Resources Information Center

    Van Der Mast, Charles

    The experimental CAI system which is being tested at Delft University of Technology is structured in a modular manner to account for high changeability. The concept formulated for this project was the outcome of research into technological, organizational, and educational developments in CAI, and the enumeration of the common aspects of the…

  4. Modular invariant inflation

    NASA Astrophysics Data System (ADS)

    Kobayashi, Tatsuo; Nitta, Daisuke; Urakawa, Yuko

    2016-08-01

    Modular invariance is a striking symmetry in string theory, which may keep stringy corrections under control. In this paper, we investigate a phenomenological consequence of the modular invariance, assuming that this symmetry is preserved as well as in a four dimensional (4D) low energy effective field theory. As a concrete setup, we consider a modulus field T whose contribution in the 4D effective field theory remains invariant under the modular transformation and study inflation drived by T. The modular invariance restricts a possible form of the scalar potenntial. As a result, large field models of inflation are hardly realized. Meanwhile, a small field model of inflation can be still accomodated in this restricted setup. The scalar potential traced during the slow-roll inflation mimics the hilltop potential Vht, but it also has a non-negligible deviation from Vht. Detecting the primordial gravitational waves predicted in this model is rather challenging. Yet, we argue that it may be still possible to falsify this model by combining the information in the reheating process which can be determined self-completely in this setup.

  5. Modular, Multilayer Perceptron

    NASA Technical Reports Server (NTRS)

    Cheng, Li-Jen; Liu, Tsuen-Hsi

    1991-01-01

    Combination of proposed modular, multilayer perceptron and algorithm for its operation recognizes new objects after relatively brief retraining sessions. (Perceptron is multilayer, feedforward artificial neural network fully connected and trained via back-propagation learning algorithm.) Knowledge pertaining to each object to be recognized resides in subnetwork of full network, therefore not necessary to retrain full network to recognize each new object.

  6. Regulation of DNA-end resection by hnRNPU-like proteins promotes DNA double-strand break signaling and repair.

    PubMed

    Polo, Sophie E; Blackford, Andrew N; Chapman, J Ross; Baskcomb, Linda; Gravel, Serge; Rusch, Andre; Thomas, Anoushka; Blundred, Rachel; Smith, Philippa; Kzhyshkowska, Julia; Dobner, Thomas; Taylor, A Malcolm R; Turnell, Andrew S; Stewart, Grant S; Grand, Roger J; Jackson, Stephen P

    2012-02-24

    DNA double-strand break (DSB) signaling and repair are critical for cell viability, and rely on highly coordinated pathways whose molecular organization is still incompletely understood. Here, we show that heterogeneous nuclear ribonucleoprotein U-like (hnRNPUL) proteins 1 and 2 play key roles in cellular responses to DSBs. We identify human hnRNPUL1 and -2 as binding partners for the DSB sensor complex MRE11-RAD50-NBS1 (MRN) and demonstrate that hnRNPUL1 and -2 are recruited to DNA damage in an interdependent manner that requires MRN. Moreover, we show that hnRNPUL1 and -2 stimulate DNA-end resection and promote ATR-dependent signaling and DSB repair by homologous recombination, thereby contributing to cell survival upon exposure to DSB-inducing agents. Finally, we establish that hnRNPUL1 and -2 function downstream of MRN and CtBP-interacting protein (CtIP) to promote recruitment of the BLM helicase to DNA breaks. Collectively, these results provide insights into how mammalian cells respond to DSBs.

  7. Focal plane array with modular pixel array components for scalability

    SciTech Connect

    Kay, Randolph R; Campbell, David V; Shinde, Subhash L; Rienstra, Jeffrey L; Serkland, Darwin K; Holmes, Michael L

    2014-12-09

    A modular, scalable focal plane array is provided as an array of integrated circuit dice, wherein each die includes a given amount of modular pixel array circuitry. The array of dice effectively multiplies the amount of modular pixel array circuitry to produce a larger pixel array without increasing die size. Desired pixel pitch across the enlarged pixel array is preserved by forming die stacks with each pixel array circuitry die stacked on a separate die that contains the corresponding signal processing circuitry. Techniques for die stack interconnections and die stack placement are implemented to ensure that the desired pixel pitch is preserved across the enlarged pixel array.

  8. Physalin H from Solanum nigrum as an Hh signaling inhibitor blocks GLI1-DNA-complex formation.

    PubMed

    Arai, Midori A; Uchida, Kyoko; Sadhu, Samir K; Ahmed, Firoj; Ishibashi, Masami

    2014-01-13

    Hedgehog (Hh) signaling plays an important role in embryonic development, cell maintenance and cell proliferation. Moreover, Hh signaling contributes to the growth of cancer cells. Physalins are highly oxidized natural products with a complex structure. Physalins (1-7) were isolated from Solanum nigrum (Solanaceae) collected in Bangladesh by using our cell-based assay. The isolated physalins included the previously reported Hh inhibitors 5 and 6. Compounds 1 and 4 showed strong inhibition of GLI1 transcriptional activity, and exhibited cytotoxicity against cancer cell lines with an aberrant activation of Hh signaling. Compound 1 inhibited the production of the Hh-related proteins patched (PTCH) and BCL2. Analysis of the structures of different physalins showed that the left part of the physalins was important for Hh inhibitory activity. Interestingly, physalin H (1) disrupted GLI1 binding to its DNA binding domain, while the weak inhibitor physalin G (2) did not show inhibition of GLI1-DNA complex formation.

  9. Modular, bluetooth enabled, wireless electroencephalograph (EEG) platform.

    PubMed

    Lovelace, Joseph A; Witt, Tyler S; Beyette, Fred R

    2013-01-01

    A design for a modular, compact, and accurate wireless electroencephalograph (EEG) system is proposed. EEG is the only non-invasive measure for neuronal function of the brain. Using a number of digital signal processing (DSP) techniques, this neuronal function can be acquired and processed into meaningful representations of brain activity. The system described here utilizes Bluetooth to wirelessly transmit the digitized brain signal for an end application use. In this way, the system is portable, and modular in terms of the device to which it can interface. Brain Computer Interface (BCI) has become a popular extension of EEG systems in modern research. This design serves as a platform for applications using BCI capability.

  10. Design and characterization of a mixed-signal PCB for digital-to-analog conversion in a modular and scalable infrared scene projector

    NASA Astrophysics Data System (ADS)

    Benedict, Jacob

    Infra-red (IR) sensors have proven instrumental in a wide variety of fields from military to industrial applications. The proliferation of IR sensors has spawned an intense push for technologies that can test and calibrate the multitudes of IR sensors. One such technology, IR scene projection (IRSP), provides an inexpensive and safe method for the testing of IR sensor devices. Previous efforts have been conducted to develop IRSPs based on super-lattice light emitting diodes (SLEDS). A single-color 512x512 SLEDs system has been developed, produced, and tested as documented in Corey Lange's Master's thesis, and a GOMAC paper by Rodney McGee [1][2]. Current efforts are being undergone to develop a two-color 512x512 SLEDs system designated (TCSA). The following thesis discusses the design and implementation of a custom printed circuit board (PCB), known as the FMC 4DAC, that contains both analog and digital signals. Utilizing two 16-bit digital-to-analog converters (DAC) the purpose of the board is to provide four analog current output channels for driving the TCSA system to a maximum frame rate of 1 kHz. In addition, the board supports a scalable TCSA system architecture. Several copies of the board can be run in parallel to achieve a range of analog channels between 4 and 32.

  11. A Low-Noise, Modular, and Versatile Analog Front-End Intended for Processing In Vitro Neuronal Signals Detected by Microelectrode Arrays

    PubMed Central

    Regalia, Giulia; Biffi, Emilia; Ferrigno, Giancarlo; Pedrocchi, Alessandra

    2015-01-01

    The collection of good quality extracellular neuronal spikes from neuronal cultures coupled to Microelectrode Arrays (MEAs) is a binding requirement to gather reliable data. Due to physical constraints, low power requirement, or the need of customizability, commercial recording platforms are not fully adequate for the development of experimental setups integrating MEA technology with other equipment needed to perform experiments under climate controlled conditions, like environmental chambers or cell culture incubators. To address this issue, we developed a custom MEA interfacing system featuring low noise, low power, and the capability to be readily integrated inside an incubator-like environment. Two stages, a preamplifier and a filter amplifier, were designed, implemented on printed circuit boards, and tested. The system is characterized by a low input-referred noise (<1 μV RMS), a high channel separation (>70 dB), and signal-to-noise ratio values of neuronal recordings comparable to those obtained with the benchmark commercial MEA system. In addition, the system was successfully integrated with an environmental MEA chamber, without harming cell cultures during experiments and without being damaged by the high humidity level. The devised system is of practical value in the development of in vitro platforms to study temporally extended neuronal network dynamics by means of MEAs. PMID:25977683

  12. Potential anti-aging agents suppress the level of constitutive mTOR- and DNA damage- signaling.

    PubMed

    Halicka, H Dorota; Zhao, Hong; Li, Jiangwei; Lee, Yong-Syu; Hsieh, Tze-Chen; Wu, Joseph M; Darzynkiewicz, Zbigniew

    2012-12-01

    Two different mechanisms are considered to be the primary cause of aging. Cumulative DNA damage caused by reactive oxygen species (ROS), the by-products of oxidative phosphorylation, is one of these mechanisms (ROS concept). Constitutive stimulation of mitogen- and nutrient-sensing mTOR/S6 signaling is the second mechanism (TOR concept). The flow- and laser scanning- cytometric methods were developed to measure the level of the constitutive DNA damage/ROS- as well as of mTOR/S6- signaling in individual cells. Specifically, persistent activation of ATM and expression of γH2AX in untreated cells appears to report constitutive DNA damage induced by endogenous ROS. The level of phosphorylation of Ser235/236-ribosomal protein (RP), of Ser2448-mTOR and of Ser65-4EBP1, informs on constitutive signaling along the mTOR/S6 pathway. Potential gero-suppressive agents rapamycin, metformin, 2-deoxyglucose, berberine, resveratrol, vitamin D3 and aspirin, all decreased the level of constitutive DNA damage signaling as seen by the reduced expression of γH2AX in proliferating A549, TK6, WI-38 cells and in mitogenically stimulated human lymphocytes. They all also decreased the level of intracellular ROS and mitochondrial trans-membrane potential ΔΨm, the marker of mitochondrial energizing as well as reduced phosphorylation of mTOR, RP-S6 and 4EBP1. The most effective was rapamycin. Although the primary target of each on these agents may be different the data are consistent with the downstream mechanism in which the decline in mTOR/S6K signaling and translation rate is coupled with a decrease in oxidative phosphorylation, (revealed by ΔΨm) that leads to reduction of ROS and oxidative DNA damage. The decreased rate of translation induced by these agents may slow down cells hypertrophy and alleviate other features of cell aging/senescence. Reduction of oxidative DNA damage may lower predisposition to neoplastic transformation which otherwise may result from errors in repair of DNA

  13. Mitochondrial DNA Signals of Late Glacial Recolonization of Europe from Near Eastern Refugia

    PubMed Central

    Pala, Maria; Olivieri, Anna; Achilli, Alessandro; Accetturo, Matteo; Metspalu, Ene; Reidla, Maere; Tamm, Erika; Karmin, Monika; Reisberg, Tuuli; Kashani, Baharak Hooshiar; Perego, Ugo A.; Carossa, Valeria; Gandini, Francesca; Pereira, Joana B.; Soares, Pedro; Angerhofer, Norman; Rychkov, Sergei; Al-Zahery, Nadia; Carelli, Valerio; Sanati, Mohammad Hossein; Houshmand, Massoud; Hatina, Jiři; Macaulay, Vincent; Pereira, Luísa; Woodward, Scott R.; Davies, William; Gamble, Clive; Baird, Douglas; Semino, Ornella; Villems, Richard; Torroni, Antonio; Richards, Martin B.

    2012-01-01

    Human populations, along with those of many other species, are thought to have contracted into a number of refuge areas at the height of the last Ice Age. European populations are believed to be, to a large extent, the descendants of the inhabitants of these refugia, and some extant mtDNA lineages can be traced to refugia in Franco-Cantabria (haplogroups H1, H3, V, and U5b1), the Italian Peninsula (U5b3), and the East European Plain (U4 and U5a). Parts of the Near East, such as the Levant, were also continuously inhabited throughout the Last Glacial Maximum, but unlike western and eastern Europe, no archaeological or genetic evidence for Late Glacial expansions into Europe from the Near East has hitherto been discovered. Here we report, on the basis of an enlarged whole-genome mitochondrial database, that a substantial, perhaps predominant, signal from mitochondrial haplogroups J and T, previously thought to have spread primarily from the Near East into Europe with the Neolithic population, may in fact reflect dispersals during the Late Glacial period, ∼19–12 thousand years (ka) ago. PMID:22560092

  14. Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana.

    PubMed

    Numa, Hisataka; Kim, Jong-Myong; Matsui, Akihiro; Kurihara, Yukio; Morosawa, Taeko; Ishida, Junko; Mochizuki, Yoshiki; Kimura, Hiroshi; Shinozaki, Kazuo; Toyoda, Tetsuro; Seki, Motoaki; Yoshikawa, Manabu; Habu, Yoshiki

    2010-01-20

    RNA-directed modification of histones is essential for the maintenance of heterochromatin in higher eukaryotes. In plants, cytosine methylation is an additional factor regulating inactive chromatin, but the mechanisms regulating the coexistence of cytosine methylation and repressive histone modification remain obscure. In this study, we analysed the mechanism of gene silencing mediated by MORPHEUS' MOLECULE1 (MOM1) of Arabidopsis thaliana. Transcript profiling revealed that the majority of up-regulated loci in mom1 carry sequences related to transposons and homologous to the 24-nt siRNAs accumulated in wild-type plants that are the hallmarks of RNA-directed DNA methylation (RdDM). Analysis of a single-copy gene, SUPPRESSOR OF drm1 drm2 cmt3 (SDC), revealed that mom1 activates SDC with concomitant reduction of di-methylated histone H3 lysine 9 (H3K9me2) at the tandem repeats in the promoter region without changes in siRNA accumulation and cytosine methylation. The reduction of H3K9me2 is not observed in regions flanking the tandem repeats. The results suggest that MOM1 transduces RdDM signals to repressive histone modification in the core region of RdDM.

  15. Expression, purification, crystallization and preliminary X-ray diffraction analysis of the novel modular DNA-binding protein BurrH in its apo form and in complex with its target DNA.

    PubMed

    Stella, Stefano; Molina, Rafael; Bertonatti, Claudia; Juillerrat, Alexandre; Montoya, Guillermo

    2014-01-01

    Different genome-editing strategies have fuelled the development of new DNA-targeting molecular tools allowing precise gene modifications. Here, the expression, purification, crystallization and preliminary X-ray diffraction of BurrH, a novel DNA-binding protein from Burkholderia rhizoxinica, are reported. Crystallization experiments of BurrH in its apo form and in complex with its target DNA yielded crystals suitable for X-ray diffraction analysis. The crystals of the apo form belonged to the primitive hexagonal space group P3(1) or its enantiomorph P3(2), with unit-cell parameters a = b = 73.28, c = 268.02 Å, α = β = 90, γ = 120°. The BurrH-DNA complex crystallized in the monoclinic space group P2(1), with unit-cell parameters a = 70.15, b = 95.83, c = 76.41 Å, α = γ = 90, β = 109.51°. The self-rotation function and the Matthews coefficient suggested the presence of two protein molecules per asymmetric unit in the apo crystals and one protein-DNA complex in the monoclinic crystals. The crystals diffracted to resolution limits of 2.21 and 2.65 Å, respectively, using synchrotron radiation.

  16. Squalene Inhibits ATM-Dependent Signaling in γIR-Induced DNA Damage Response through Induction of Wip1 Phosphatase.

    PubMed

    Tatewaki, Naoto; Konishi, Tetsuya; Nakajima, Yuki; Nishida, Miyako; Saito, Masafumi; Eitsuka, Takahiro; Sakamaki, Toshiyuki; Ikekawa, Nobuo; Nishida, Hiroshi

    2016-01-01

    Ataxia telangiectasia mutated (ATM) kinase plays a crucial role as a master controller in the cellular DNA damage response. Inhibition of ATM leads to inhibition of the checkpoint signaling pathway. Hence, addition of checkpoint inhibitors to anticancer therapies may be an effective targeting strategy. A recent study reported that Wip1, a protein phosphatase, de-phosphorylates serine 1981 of ATM during the DNA damage response. Squalene has been proposed to complement anticancer therapies such as chemotherapy and radiotherapy; however, there is little mechanistic information supporting this idea. Here, we report the inhibitory effect of squalene on ATM-dependent DNA damage signals. Squalene itself did not affect cell viability and the cell cycle of A549 cells, but it enhanced the cytotoxicity of gamma-irradiation (γIR). The in vitro kinase activity of ATM was not altered by squalene. However, squalene increased Wip1 expression in cells and suppressed ATM activation in γIR-treated cells. Consistent with the potential inhibition of ATM by squalene, IR-induced phosphorylation of ATM effectors such as p53 (Ser15) and Chk1 (Ser317) was inhibited by cell treatment with squalene. Thus, squalene inhibits the ATM-dependent signaling pathway following DNA damage through intracellular induction of Wip1 expression.

  17. Characterization of cDNA clones encoding rabbit and human serum paraoxonase: The mature protein retains its signal sequence

    SciTech Connect

    Hassett, C.; Richter, R.J.; Humbert, R.; Omiecinski, C.J.; Furlong, C.E. ); Chapline, C.; Crabb, J.W. )

    1991-10-22

    Serum paraoxonase hydrolyzes the toxic metabolites of a variety of organophosphorus insecticides. High serum paraoxonase levels appear to protect against the neurotoxic effects of organophosphorus substrates of this enzyme. The amino acid sequence accounting for 42% of rabbit paraoxonase was determined. From these data, two oligonucleotide probes were synthesized and used to screen a rabbit liver cDNA library. Human paraoxonase clones were isolated from a liver cDNA library by using the rabbit cDNA as a hybridization probe. Inserts from three of the longest clones were sequenced, and one full-length clone contained an open reading frame encoding 355 amino acids, four less than the rabbit paraoxonase protein. Amino-terminal sequences derived from purified rabbit and human paraoxonase proteins suggested that the signal sequence is retained, with the exception of the initiator methionine residue. Characterization of the rabbit and human paraoxonase cDNA clones confirms that the signal sequences are not processed, except for the N-terminal methionine residue. The rabbit and human cDNA clones demonstrate striking nucleotide and deduced amino acid similarities (greater than 85%), suggesting an important metabolic role and constraints on the evolution of this protein.

  18. Persistent activation of DNA damage signaling in response to complex mixtures of PAHs in air particulate matter

    SciTech Connect

    Jarvis, Ian W.H.; Bergvall, Christoffer; Bottai, Matteo; Westerholm, Roger; Stenius, Ulla; Dreij, Kristian

    2013-02-01

    Complex mixtures of polycyclic aromatic hydrocarbons (PAHs) are present in air particulate matter (PM) and have been associated with many adverse human health effects including cancer and respiratory disease. However, due to their complexity, the risk of exposure to mixtures is difficult to estimate. In the present study the effects of binary mixtures of benzo[a]pyrene (BP) and dibenzo[a,l]pyrene (DBP) and complex mixtures of PAHs in urban air PM extracts on DNA damage signaling was investigated. Applying a statistical model to the data we observed a more than additive response for binary mixtures of BP and DBP on activation of DNA damage signaling. Persistent activation of checkpoint kinase 1 (Chk1) was observed at significantly lower BP equivalent concentrations in air PM extracts than BP alone. Activation of DNA damage signaling was also more persistent in air PM fractions containing PAHs with more than four aromatic rings suggesting larger PAHs contribute a greater risk to human health. Altogether our data suggests that human health risk assessment based on additivity such as toxicity equivalency factor scales may significantly underestimate the risk of exposure to complex mixtures of PAHs. The data confirms our previous findings with PAH-contaminated soil (Niziolek-Kierecka et al., 2012) and suggests a possible role for Chk1 Ser317 phosphorylation as a biological marker for future analyses of complex mixtures of PAHs. -- Highlights: ► Benzo[a]pyrene (BP), dibenzo[a,l]pyrene (DBP) and air PM PAH extracts were compared. ► Binary mixture of BP and DBP induced a more than additive DNA damage response. ► Air PM PAH extracts were more potent than toxicity equivalency factor estimates. ► Larger PAHs (> 4 rings) contribute more to the genotoxicity of PAHs in air PM. ► Chk1 is a sensitive marker for persistent activation of DNA damage signaling from PAH mixtures.

  19. Biosynthetic Modularity Rules in the Bisintercalator Family of Antitumor Compounds

    PubMed Central

    Fernández, Javier; Marín, Laura; Álvarez-Alonso, Raquel; Redondo, Saúl; Carvajal, Juan; Villamizar, Germán; Villar, Claudio J.; Lombó, Felipe

    2014-01-01

    Diverse actinomycetes produce a family of structurally and biosynthetically related non-ribosomal peptide compounds which belong to the chromodepsipeptide family. These compounds act as bisintercalators into the DNA helix. They give rise to antitumor, antiparasitic, antibacterial and antiviral bioactivities. These compounds show a high degree of conserved modularity (chromophores, number and type of amino acids). This modularity and their high sequence similarities at the genetic level imply a common biosynthetic origin for these pathways. Here, we describe insights about rules governing this modular biosynthesis, taking advantage of the fact that nowadays five of these gene clusters have been made public (thiocoraline, triostin, SW-163 and echinomycin/quinomycin). This modularity has potential application for designing and producing novel genetic engineered derivatives, as well as for developing new chemical synthesis strategies. These would facilitate their clinical development. PMID:24821625

  20. Target-catalyzed autonomous assembly of dendrimer-like DNA nanostructures for enzyme-free and signal amplified colorimetric nucleic acids detection.

    PubMed

    He, Hongfei; Dai, Jianyuan; Duan, Zhijuan; Meng, Yan; Zhou, Cuisong; Long, Yuyin; Zheng, Baozhan; Du, Juan; Guo, Yong; Xiao, Dan

    2016-12-15

    Self-assembly of DNA nanostructures is of great importance in nanomedicine, nanotechnology and biosensing. Herein, a novel target-catalyzed autonomous assembly pathway for the formation of dendrimer-like DNA nanostructures that only employing target DNA and three hairpin DNA probes was proposed. We use the sticky-ended Y shape DNA (Y-DNA) as the assembly monomer and it was synthesized by the catalyzed hairpin assembly (CHA) instead of the DNA strand annealing method. The formed Y-DNA was equipped with three ssDNA sticky ends and two of them were predesigned to be complementary to the third one, then the dendrimer-like DNA nanostructures can be obtained via an autonomous assembly among these sticky-ended Y-DNAs. The resulting nanostructure has been successfully applied to develop an enzyme-free and signal amplified gold nanoparticle (AuNP)-based colorimetric nucleic acids assay.

  1. 3-Nitrobenzanthrone and 3-aminobenzanthrone induce DNA damage and cell signalling in Hepa1c1c7 cells.

    PubMed

    Landvik, N E; Arlt, V M; Nagy, E; Solhaug, A; Tekpli, X; Schmeiser, H H; Refsnes, M; Phillips, D H; Lagadic-Gossmann, D; Holme, J A

    2010-02-03

    3-Nitrobenzanthrone (3-NBA) is a mutagenic and carcinogenic environmental pollutant found in diesel exhaust and urban air pollution. In the present work we have characterised the effects of 3-NBA and its metabolite 3-aminobenzanthrone (3-ABA) on cell death and cytokine release in mouse hepatoma Hepa1c1c7 cells. These effects were related to induced DNA damage and changes in cell signalling pathways. 3-NBA resulted in cell death and caused most DNA damage as judged by the amount of DNA adducts ((32)P-postlabelling assay), single strand (ss)DNA breaks and oxidative DNA lesions (comet assay) detected. An increased phosphorylation of H2AX, chk1, chk2 and partly ATM was observed using flow cytometry and/or Western blotting. Both compounds increased phosphorylation of p53 and MAPKs (ERK, p38 and JNK). However, only 3-NBA caused an accumulation of p53 in the nucleus and a translocation of Bax to the mitochondria. The p53 inhibitor pifithrin-alpha inhibited 3-NBA-induced apoptosis, indicating that cell death was a result of the triggering of DNA signalling pathways. The highest phosphorylation of Akt and degradation of IkappaB-alpha (suggesting activation of NF-kappaB) were also seen after treatment with 3-NBA. In contrast 3-ABA increased IL-6 release, but caused little or no toxicity. Cytokine release was inhibited by PD98059 and curcumin, suggesting that ERK and NF-kappaB play a role in this process. In conclusion, 3-NBA seems to have a higher potency to induce DNA damage compatible with its cytotoxic effects, while 3-ABA seems to have a greater effect on the immune system.

  2. MAP kinase-signaling controls nuclear translocation of tripeptidyl-peptidase II in response to DNA damage and oxidative stress

    SciTech Connect

    Preta, Giulio; Klark, Rainier de; Chakraborti, Shankhamala; Glas, Rickard

    2010-08-27

    Research highlights: {yields} Nuclear translocation of TPPII occurs in response to different DNA damage inducers. {yields} Nuclear accumulation of TPPII is linked to ROS and anti-oxidant enzyme levels. {yields} MAPKs control nuclear accumulation of TPPII. {yields} Inhibited nuclear accumulation of TPPII decreases DNA damage-induced {gamma}-H2AX expression. -- Abstract: Reactive oxygen species (ROS) are a continuous hazard in eukaroytic cells by their ability to cause damage to biomolecules, in particular to DNA. Previous data indicated that the cytosolic serine peptidase tripeptidyl-peptidase II (TPPII) translocates into the nucleus of most tumor cell lines in response to {gamma}-irradiation and ROS production; an event that promoted p53 expression as well as caspase-activation. We here observed that nuclear translocation of TPPII was dependent on signaling by MAP kinases, including p38MAPK. Further, this was caused by several types of DNA-damaging drugs, a DNA cross-linker (cisplatinum), an inhibitor of topoisomerase II (etoposide), and to some extent also by nucleoside-analogues (5-fluorouracil, hydroxyurea). In the minority of tumor cell lines where TPPII was not translocated into the nucleus in response to DNA damage we observed reduced intracellular ROS levels, and the expression levels of redox defense systems were increased. Further, treatment with the ROS-inducer {gamma}-hexa-chloro-cyclohexane ({gamma}-HCH, lindane), an inhibitor of GAP junctions, restored nuclear translocation of TPPII in these cell lines upon {gamma}-irradiation. Moreover, blocking nuclear translocation of TPPII in etoposide-treated cells, by using a peptide-derived inhibitor (Z-Gly-Leu-Ala-OH), attenuated expression of {gamma}-H2AX in {gamma}-irradiated melanoma cells. Our results indicated a role for TPPII in MAPK-dependent DNA damage signaling.

  3. ATIS - A modular approach

    NASA Astrophysics Data System (ADS)

    Kirson, Allan

    The author describes a modular approach to the design of an in-vehicle navigation and route guidance system that supports a phased implementation of the technology, and anticipates expected differences in implementation in different parts of the world and for different makes and models of vehicle. A series of sensors in the vehicle are used to determine the vehicle's position by dead reckoning and map-matching. The system then calculates the best route to the selected destination, taking into account the real-time traffic information received from a traffic management center, and presents route guidance instructions to the user as the route is traversed. Attention is given to modularity considerations, vehicle positioning, driver support, vehicle-to-infrastructure communications, and the role of standards.

  4. Quantum spaces are modular

    NASA Astrophysics Data System (ADS)

    Freidel, Laurent; Leigh, Robert G.; Minic, Djordje

    2016-11-01

    At present, our notion of space is a classical concept. Taking the point of view that quantum theory is more fundamental than classical physics, and that space should be given a purely quantum definition, we revisit the notion of Euclidean space from the point of view of quantum mechanics. Since space appears in physics in the form of labels on relativistic fields or Schrödinger wave functionals, we propose to define Euclidean quantum space as a choice of polarization for the Heisenberg algebra of quantum theory. We show, following Mackey, that generically, such polarizations contain a fundamental length scale and that contrary to what is implied by the Schrödinger polarization, they possess topologically distinct spectra. These are the modular spaces. We show that they naturally come equipped with additional geometrical structures usually encountered in the context of string theory or generalized geometry. Moreover, we show how modular space reconciles the presence of a fundamental scale with translation and rotation invariance. We also discuss how the usual classical notion of space comes out as a form of thermodynamical limit of modular space while the Schrödinger space is a singular limit.

  5. HER2 Signaling Drives DNA Anabolism and Proliferation through SRC-3 Phosphorylation and E2F1-Regulated Genes.

    PubMed

    Nikolai, Bryan C; Lanz, Rainer B; York, Brian; Dasgupta, Subhamoy; Mitsiades, Nicholas; Creighton, Chad J; Tsimelzon, Anna; Hilsenbeck, Susan G; Lonard, David M; Smith, Carolyn L; O'Malley, Bert W

    2016-03-15

    Approximately 20% of early-stage breast cancers display amplification or overexpression of the ErbB2/HER2 oncogene, conferring poor prognosis and resistance to endocrine therapy. Targeting HER2(+) tumors with trastuzumab or the receptor tyrosine kinase (RTK) inhibitor lapatinib significantly improves survival, yet tumor resistance and progression of metastatic disease still develop over time. Although the mechanisms of cytosolic HER2 signaling are well studied, nuclear signaling components and gene regulatory networks that bestow therapeutic resistance and limitless proliferative potential are incompletely understood. Here, we use biochemical and bioinformatic approaches to identify effectors and targets of HER2 transcriptional signaling in human breast cancer. Phosphorylation and activity of the Steroid Receptor Coactivator-3 (SRC-3) is reduced upon HER2 inhibition, and recruitment of SRC-3 to regulatory elements of endogenous genes is impaired. Transcripts regulated by HER2 signaling are highly enriched with E2F1 binding sites and define a gene signature associated with proliferative breast tumor subtypes, cell-cycle progression, and DNA replication. We show that HER2 signaling promotes breast cancer cell proliferation through regulation of E2F1-driven DNA metabolism and replication genes together with phosphorylation and activity of the transcriptional coactivator SRC-3. Furthermore, our analyses identified a cyclin-dependent kinase (CDK) signaling node that, when targeted using the CDK4/6 inhibitor palbociclib, defines overlap and divergence of adjuvant pharmacologic targeting. Importantly, lapatinib and palbociclib strictly block de novo synthesis of DNA, mostly through disruption of E2F1 and its target genes. These results have implications for rational discovery of pharmacologic combinations in preclinical models of adjuvant treatment and therapeutic resistance.

  6. Doped Graphene for DNA Analysis: the Electrochemical Signal is Strongly Influenced by the Kind of Dopant and the Nucleobase Structure

    NASA Astrophysics Data System (ADS)

    Tian, Huidi; Wang, Lu; Sofer, Zdenek; Pumera, Martin; Bonanni, Alessandra

    2016-09-01

    Doping graphene with heteroatoms can alter the electronic and electrochemical properties of the starting material. Contrasting properties should be expected when the doping is carried out with electron donating species (n-type dopants) or with electron withdrawing species (p-type dopants). This in turn can have a profound influence on the electroanalytical performance of the doped material being used for the detection of specific probes. Here we investigate the electrochemical oxidation of DNA bases adenine, guanine, thymine and cytosine on two heteroatom-doped graphene platforms namely boron-doped graphene (p-type dopant) and nitrogen-doped graphene (n-type dopant). We found that overall, boron–doped graphene provided the best response in terms of electrochemical signal sensitivity for all bases. This is due to the electron deficiency of boron-doped graphene, which can promote the oxidation of DNA bases, as opposed to nitrogen-doped graphene which possesses an excess of electrons. Moreover, also the structure of the nucleobase was found to have significant influence on the obtained signal. Our study may open new frontiers in the electrochemical detection of DNA bases which is the first step for label-free DNA analysis.

  7. Doped Graphene for DNA Analysis: the Electrochemical Signal is Strongly Influenced by the Kind of Dopant and the Nucleobase Structure.

    PubMed

    Tian, Huidi; Wang, Lu; Sofer, Zdenek; Pumera, Martin; Bonanni, Alessandra

    2016-09-14

    Doping graphene with heteroatoms can alter the electronic and electrochemical properties of the starting material. Contrasting properties should be expected when the doping is carried out with electron donating species (n-type dopants) or with electron withdrawing species (p-type dopants). This in turn can have a profound influence on the electroanalytical performance of the doped material being used for the detection of specific probes. Here we investigate the electrochemical oxidation of DNA bases adenine, guanine, thymine and cytosine on two heteroatom-doped graphene platforms namely boron-doped graphene (p-type dopant) and nitrogen-doped graphene (n-type dopant). We found that overall, boron-doped graphene provided the best response in terms of electrochemical signal sensitivity for all bases. This is due to the electron deficiency of boron-doped graphene, which can promote the oxidation of DNA bases, as opposed to nitrogen-doped graphene which possesses an excess of electrons. Moreover, also the structure of the nucleobase was found to have significant influence on the obtained signal. Our study may open new frontiers in the electrochemical detection of DNA bases which is the first step for label-free DNA analysis.

  8. Phosphatidylinositol 3-Kinase (PI3K) Signaling via Glycogen Synthase Kinase-3 (Gsk-3) Regulates DNA Methylation of Imprinted Loci*

    PubMed Central

    Popkie, Anthony P.; Zeidner, Leigh C.; Albrecht, Ashley M.; D'Ippolito, Anthony; Eckardt, Sigrid; Newsom, David E.; Groden, Joanna; Doble, Bradley W.; Aronow, Bruce; McLaughlin, K. John; White, Peter; Phiel, Christopher J.

    2010-01-01

    Glycogen synthase kinase-3 (Gsk-3) isoforms, Gsk-3α and Gsk-3β, are constitutively active, largely inhibitory kinases involved in signal transduction. Underscoring their biological significance, altered Gsk-3 activity has been implicated in diabetes, Alzheimer disease, schizophrenia, and bipolar disorder. Here, we demonstrate that deletion of both Gsk-3α and Gsk-3β in mouse embryonic stem cells results in reduced expression of the de novo DNA methyltransferase Dnmt3a2, causing misexpression of the imprinted genes Igf2, H19, and Igf2r and hypomethylation of their corresponding imprinted control regions. Treatment of wild-type embryonic stem cells and neural stem cells with the Gsk-3 inhibitor, lithium, phenocopies the DNA hypomethylation at these imprinted loci. We show that inhibition of Gsk-3 by phosphatidylinositol 3-kinase (PI3K)-mediated activation of Akt also results in reduced DNA methylation at these imprinted loci. Finally, we find that N-Myc is a potent Gsk-3-dependent regulator of Dnmt3a2 expression. In summary, we have identified a signal transduction pathway that is capable of altering the DNA methylation of imprinted loci. PMID:21047779

  9. Doped Graphene for DNA Analysis: the Electrochemical Signal is Strongly Influenced by the Kind of Dopant and the Nucleobase Structure

    PubMed Central

    Tian, Huidi; Wang, Lu; Sofer, Zdenek; Pumera, Martin; Bonanni, Alessandra

    2016-01-01

    Doping graphene with heteroatoms can alter the electronic and electrochemical properties of the starting material. Contrasting properties should be expected when the doping is carried out with electron donating species (n-type dopants) or with electron withdrawing species (p-type dopants). This in turn can have a profound influence on the electroanalytical performance of the doped material being used for the detection of specific probes. Here we investigate the electrochemical oxidation of DNA bases adenine, guanine, thymine and cytosine on two heteroatom-doped graphene platforms namely boron-doped graphene (p-type dopant) and nitrogen-doped graphene (n-type dopant). We found that overall, boron–doped graphene provided the best response in terms of electrochemical signal sensitivity for all bases. This is due to the electron deficiency of boron-doped graphene, which can promote the oxidation of DNA bases, as opposed to nitrogen-doped graphene which possesses an excess of electrons. Moreover, also the structure of the nucleobase was found to have significant influence on the obtained signal. Our study may open new frontiers in the electrochemical detection of DNA bases which is the first step for label-free DNA analysis. PMID:27623951

  10. Endothelin-1 protects human melanocytes from UV-induced DNA damage by activating JNK and p38 signalling pathways.

    PubMed

    von Koschembahr, Anne M; Swope, Viki B; Starner, Renny J; Abdel-Malek, Zalfa A

    2015-04-01

    Endothelin-1 is a paracrine factor with mitogenic, melanogenic and survival effects on cultured human melanocytes. We report that endothelin-1 signalling reduced the generation and enhanced the repair of ultraviolet radiation (UV)-induced DNA photoproducts, and inhibited apoptosis of human melanocytes, without increasing cAMP levels, melanin content or proliferation. Treatment with endothelin-1 activated the MAP kinases JNK and p38, as evidenced by phosphorylation of their target, activating transcription factor-2 (ATF-2). Endothelin-1 also enhanced the phosphorylation of JNK, p38 and ATF-2 by UV. The effects of endothelin-1 were dependent on increasing intracellular calcium mobilization by endothelin B receptor signalling. Activation of both JNK and p38 was required for reducing DNA photoproducts, but only JNK partially contributed to the survival effect of endothelin-1. ATF-2 activation depended mainly on JNK, yet was not sufficient for the effect of endothelin-1 on UV-induced DNA damage, suggesting the requirement for other JNK and p38 targets for this effect. Our results underscore the significance of endothelin-1 and endothelin B receptor signalling in reducing the genotoxic effects of UV via activating JNK and p38, hence restoring genomic stability of melanocytes.

  11. Gefitinib Radiosensitizes Stem-Like Glioma Cells: Inhibition of Epidermal Growth Factor Receptor-Akt-DNA-PK Signaling, Accompanied by Inhibition of DNA Double-Strand Break Repair

    SciTech Connect

    Kang, Khong Bee; Zhu Congju; Wong Yinling; Gao Qiuhan; Ty, Albert; Wong, Meng Cheong

    2012-05-01

    Purpose: We compared radiosensitivity of brain tumor stem cells (BTSCs) with matched nonstem glioma cells, and determined whether gefitinib enhanced BTSC radiosensitivity by inhibiting epidermal growth factor receptor (EGFR)-Akt-DNA-dependent protein kinase (DNA-PK) signaling, followed by enhanced DNA double-stand breaks (DSBs) and inhibition of DSB repair. Methods and Materials: Radiosensitivity of stem-like gliomaspheres and nonstem glioma cells (obtained at patient neurosurgical resection) were evaluated by clonogenic assays, {gamma}-H{sub 2}AX immunostaining and cell cycle distribution. Survival of irradiated and nonirradiated NOD-SCID mice intracranially implanted with stem-like gliomaspheres were monitored. Glioma cells treated with gefitinib, irradiation, or both were assayed for clonogenic survival, {gamma}-H{sub 2}AX immunostaining, DNA-PKcs expression, and phosphorylation of EGFR and Akt. Results: Stem-like gliomaspheres displayed BTSC characteristics of self-renewal; differentiation into lineages of neurons, oligodendrocytes, and astrocytes; and initiation of glioma growth in NOD-SCID mice. Irradiation dose-dependently reduced clonogenic survival, induced G{sub 2}/M arrest and increased {gamma}-H{sub 2}AX immunostaining of nonstem glioma cells, but not stem-like gliomaspheres. There was no difference in survival of irradiated and nonirradiated mice implanted with stem-like gliomaspheres. The addition of gefitinib significantly inhibited clonogenic survival, increased {gamma}-H{sub 2}AX immunostaining, and reduced DNA-PKcs expression of irradiated stem-like gliomaspheres, without affecting irradiated-nonstem glioma cells. Gefitinib alone, and when combined with irradiation, inhibited phosphorylation of EGFR (Y1068 and Y1045) and Akt (S473) in stem-like gliomaspheres. In nonstem glioma cells, gefitinib alone inhibited EGFR Y1068 phosphorylation, with further inhibition by combined gefitinib and irradiation. Conclusions: Stem-like gliomaspheres are

  12. Gestational Diabetes Alters Offspring DNA Methylation Profiles in Human and Rat: Identification of Key Pathways Involved in Endocrine System Disorders, Insulin Signaling, Diabetes Signaling, and ILK Signaling.

    PubMed

    Petropoulos, Sophie; Guillemin, Claire; Ergaz, Zivanit; Dimov, Sergiy; Suderman, Matthew; Weinstein-Fudim, Liza; Ornoy, Asher; Szyf, Moshe

    2015-06-01

    Gestational diabetes is associated with risk for metabolic disease later in life. Using a cross-species approach in rat and humans, we examined the hypothesis that gestational diabetes during pregnancy triggers changes in the methylome of the offspring that might be mediating these risks. We show in a gestation diabetes rat model, the Cohen diabetic rat, that gestational diabetes triggers wide alterations in DNA methylation in the placenta in both candidate diabetes genes and genome-wide promoters, thus providing evidence for a causal relationship between diabetes during pregnancy and DNA methylation alterations. There is a significant overlap between differentially methylated genes in the placenta and the liver of the rat offspring. Several genes differentially methylated in rat placenta exposed to maternal diabetes are also differentially methylated in the human placenta of offspring exposed to gestational diabetes in utero. DNA methylation changes inversely correlate with changes in expression. The changes in DNA methylation affect known functional gene pathways involved in endocrine function, metabolism, and insulin responses. These data provide support to the hypothesis that early-life exposures and their effects on metabolic disease are mediated by DNA methylation changes. This has important diagnostic and therapeutic implications.

  13. Efficient algorithm and systolic architecture for modular division

    NASA Astrophysics Data System (ADS)

    Chen, Chuanpeng; Qin, Zhongping

    2011-06-01

    A new efficient modular division algorithm suitable for systolic implementation and its systolic architecture is proposed in this article. With a new exit condition of while loop and a new updating method of a control variable, the new algorithm reduces the average of iteration numbers by more than 14.3% compared to the algorithm proposed by Chen, Bai and Chen. Based on the new algorithm, we design a fast systolic architecture with an optimised core computing cell. Compared to the architecture proposed by Chen, Bai and Chen, our systolic architecture has reduced the critical path delay by about 18% and the total computational time for one modular division by almost 30%, with the cost of about 1% more cells. Moreover, by the addition of a flag signal and three logic gates, the proposed systolic architecture can also perform Montgomery modular multiplication and a fast unified modular divider/multiplier is realised.

  14. Genotoxicity of radiofrequency signals. I. Investigation of DNA damage and micronuclei induction in cultured human blood cells.

    PubMed

    Tice, Raymond R; Hook, Graham G; Donner, Maria; McRee, Donald I; Guy, Arthur W

    2002-02-01

    As part of a comprehensive investigation of the potential genotoxicity of radiofrequency (RF) signals emitted by cellular telephones, in vitro studies evaluated the induction of DNA and chromosomal damage in human blood leukocytes and lymphocytes, respectively. The signals were voice modulated 837 MHz produced by an analog signal generator or by a time division multiple access (TDMA) cellular telephone, 837 MHz generated by a code division multiple access (CDMA) cellular telephone (not voice modulated), and voice modulated 1909.8 MHz generated by a global system of mobile communication (GSM)-type personal communication systems (PCS) cellular telephone. DNA damage (strand breaks/alkali labile sites) was assessed in leukocytes using the alkaline (pH>13) single cell gel electrophoresis (SCG) assay. Chromosomal damage was evaluated in lymphocytes mitogenically stimulated to divide postexposure using the cytochalasin B-binucleate cell micronucleus assay. Cells were exposed at 37+/-1 degrees C, for 3 or 24 h at average specific absorption rates (SARs) of 1.0-10.0 W/kg. Exposure for either 3 or 24 h did not induce a significant increase in DNA damage in leukocytes, nor did exposure for 3 h induce a significant increase in micronucleated cells among lymphocytes. However, exposure to each of the four RF signal technologies for 24 h at an average SAR of 5.0 or 10.0 W/kg resulted in a significant and reproducible increase in the frequency of micronucleated lymphocytes. The magnitude of the response (approximately four fold) was independent of the technology, the presence or absence of voice modulation, and the frequency (837 vs. 1909.8 MHz). This research demonstrates that, under extended exposure conditions, RF signals at an average SAR of at least 5.0 W/kg are capable of inducing chromosomal damage in human lymphocytes.

  15. The TOTEM modular trigger system

    NASA Astrophysics Data System (ADS)

    Bagliesi, M. G.; Berretti, M.; Cecchi, R.; Greco, V.; Lami, S.; Latino, G.; Oliveri, E.; Pedreschi, E.; Scribano, A.; Spinella, F.; Turini, N.

    2010-05-01

    The TOTEM experiment will measure the total cross-section with the luminosity independent method and study elastic and diffractive scattering at the LHC. We are developing a modular trigger system, based on programmable logic, that will select meaningful events within 2.5 μs. The trigger algorithm is based on a tree structure in order to obtain information compression. The trigger primitive is generated directly on the readout chip, VFAT, that has a specific fast output that gives low resolution hits information. In two of the TOTEM detectors, Roman Pots and T2, a coincidence chip will perform track recognition directly on the detector readout boards, while for T1 the hits are transferred from the VFATs to the trigger hardware. Starting from more than 2000 bits delivered by the detector electronics, we extract, in a first step, six trigger patterns of 32 LVDS signals each; we build, then, on a dedicated board, a 1-bit (L1) trigger signal for the TOTEM experiment and 16 trigger bits to the CMS experiment global trigger system for future common data taking.

  16. Robotic hand with modular extensions

    DOEpatents

    Salisbury, Curt Michael; Quigley, Morgan

    2015-01-20

    A robotic device is described herein. The robotic device includes a frame that comprises a plurality of receiving regions that are configured to receive a respective plurality of modular robotic extensions. The modular robotic extensions are removably attachable to the frame at the respective receiving regions by way of respective mechanical fuses. Each mechanical fuse is configured to trip when a respective modular robotic extension experiences a predefined load condition, such that the respective modular robotic extension detaches from the frame when the load condition is met.

  17. Decreased T cell ERK pathway signaling may contribute to the development of lupus through effects on DNA methylation and gene expression.

    PubMed

    Oelke, Kurt; Richardson, Bruce

    2004-01-01

    T cells from patients with active lupus have multiple biochemical abnormalities. One of these is DNA hypomethylation, which in model systems alters gene expression and induces lupus-like autoimmunity. Recent reports indicate that DNA methylation is regulated in part by the ERK pathway, and that ERK pathway signaling is diminished in lupus T cells. This suggests a model in which defective T cell ERK pathway signaling contributes to the development of autoimmunity by decreasing DNA methyltransferase expression, modifying DNA methylation patterns and altering gene expression. This mechanism could contribute to idiopathic and drug-induced lupus.

  18. Identifying the North American plum species phylogenetic signal using nuclear, mitochondrial, and chloroplast DNA markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Premise of the study: Prunus L. phylogeny has extensively studied using cpDNA sequences. CpDNA has a slow rate of evolution which is beneficial to determine species relationships at a deeper level. However, a limitation of the chloroplast based phylogenies is its transfer by interspecific hybridizat...

  19. Quantifying environmental DNA signals for aquatic invasive species across multiple detection platforms.

    PubMed

    Nathan, Lucas M; Simmons, Megan; Wegleitner, Benjamin J; Jerde, Christopher L; Mahon, Andrew R

    2014-11-04

    The use of molecular surveillance techniques has become popular among aquatic researchers and managers due to the improved sensitivity and efficiency compared to traditional sampling methods. Rapid expansion in the use of environmental DNA (eDNA), paired with the advancement of molecular technologies, has resulted in new detection platforms and techniques. In this study we present a comparison of three eDNA surveillance platforms: traditional polymerase chain reaction (PCR), quantitative PCR (qPCR), and digital droplet PCR (ddPCR) in which water samples were collected over a 24 h time period from mesocosm experiments containing a population gradient of invasive species densities. All platforms reliably detected the presence of DNA, even at low target organism densities within the first hour. The two quantitative platforms (qPCR and ddPCR) produced similar estimates of DNA concentrations. The analyses completed with ddPCR was faster from sample collection through analyses and cost approximately half the expenditure of qPCR. Although a new platform for eDNA surveillance of aquatic species, ddPCR was consistent with more commonly used qPCR and a cost-effective means of estimating DNA concentrations. Use of ddPCR by researchers and managers should be considered in future eDNA surveillance applications.

  20. Modular biometric system

    NASA Astrophysics Data System (ADS)

    Hsu, Charles; Viazanko, Michael; O'Looney, Jimmy; Szu, Harold

    2009-04-01

    Modularity Biometric System (MBS) is an approach to support AiTR of the cooperated and/or non-cooperated standoff biometric in an area persistent surveillance. Advanced active and passive EOIR and RF sensor suite is not considered here. Neither will we consider the ROC, PD vs. FAR, versus the standoff POT in this paper. Our goal is to catch the "most wanted (MW)" two dozens, separately furthermore ad hoc woman MW class from man MW class, given their archrivals sparse front face data basis, by means of various new instantaneous input called probing faces. We present an advanced algorithm: mini-Max classifier, a sparse sample realization of Cramer-Rao Fisher bound of the Maximum Likelihood classifier that minimize the dispersions among the same woman classes and maximize the separation among different man-woman classes, based on the simple feature space of MIT Petland eigen-faces. The original aspect consists of a modular structured design approach at the system-level with multi-level architectures, multiple computing paradigms, and adaptable/evolvable techniques to allow for achieving a scalable structure in terms of biometric algorithms, identification quality, sensors, database complexity, database integration, and component heterogenity. MBS consist of a number of biometric technologies including fingerprints, vein maps, voice and face recognitions with innovative DSP algorithm, and their hardware implementations such as using Field Programmable Gate arrays (FPGAs). Biometric technologies and the composed modularity biometric system are significant for governmental agencies, enterprises, banks and all other organizations to protect people or control access to critical resources.

  1. DNA.

    ERIC Educational Resources Information Center

    Felsenfeld, Gary

    1985-01-01

    Structural form, bonding scheme, and chromatin structure of and gene-modification experiments with deoxyribonucleic acid (DNA) are described. Indicates that DNA's double helix is variable and also flexible as it interacts with regulatory and other molecules to transfer hereditary messages. (DH)

  2. Modular gear bearings

    NASA Technical Reports Server (NTRS)

    Vranish, John M. (Inventor)

    2009-01-01

    A gearing system using modular gear bearing components. Each component is composed of a core, one or more modules attached to the core and two or more fastening modules rigidly attaching the modules to the core. The modules, which are attached to the core, may consist of gears, rollers or gear bearing components. The core orientation affects the orientation of the modules attached to the core. This is achieved via the keying arrangement of the core and the component modules that attach to the core. Such an arrangement will also facilitate the phase tuning of gear modules with respect to the core and other gear modules attached to the core.

  3. Modularity of music processing.

    PubMed

    Peretz, Isabelle; Coltheart, Max

    2003-07-01

    The music faculty is not a monolithic entity that a person either has or does not. Rather, it comprises a set of neurally isolable processing components, each having the potential to be specialized for music. Here we propose a functional architecture for music processing that captures the typical properties of modular organization. The model rests essentially on the analysis of music-related deficits in neurologically impaired individuals, but provides useful guidelines for exploring the music faculty in normal people, using methods such as neuroimaging.

  4. Modular Biometric Monitoring System

    NASA Technical Reports Server (NTRS)

    Chmiel, Alan J. (Inventor); Humphreys, Bradley T. (Inventor)

    2017-01-01

    A modular system for acquiring biometric data includes a plurality of data acquisition modules configured to sample biometric data from at least one respective input channel at a data acquisition rate. A representation of the sampled biometric data is stored in memory of each of the plurality of data acquisition modules. A central control system is in communication with each of the plurality of data acquisition modules through a bus. The central control system is configured to control communication of data, via the bus, with each of the plurality of data acquisition modules.

  5. Modular space station facilities.

    NASA Technical Reports Server (NTRS)

    Parker, P. J.

    1973-01-01

    The modular space station will operate as a general purpose laboratory (GPL). In addition, the space station will be able to support many attached or free-flying research and application modules that would be dedicated to specific projects like astronomy or earth observations. The GPL primary functions have been organized into functional laboratories including an electrical/electronics laboratory, a mechanical sciences laboratory, an experiment and test isolation laboratory, a hard data process facility, a data evaluation facility, an optical sciences laboratory, a biomedical and biosciences laboratory, and an experiment/secondary command and control center.

  6. Modular and Hierarchically Modular Organization of Brain Networks

    PubMed Central

    Meunier, David; Lambiotte, Renaud; Bullmore, Edward T.

    2010-01-01

    Brain networks are increasingly understood as one of a large class of information processing systems that share important organizational principles in common, including the property of a modular community structure. A module is topologically defined as a subset of highly inter-connected nodes which are relatively sparsely connected to nodes in other modules. In brain networks, topological modules are often made up of anatomically neighboring and/or functionally related cortical regions, and inter-modular connections tend to be relatively long distance. Moreover, brain networks and many other complex systems demonstrate the property of hierarchical modularity, or modularity on several topological scales: within each module there will be a set of sub-modules, and within each sub-module a set of sub-sub-modules, etc. There are several general advantages to modular and hierarchically modular network organization, including greater robustness, adaptivity, and evolvability of network function. In this context, we review some of the mathematical concepts available for quantitative analysis of (hierarchical) modularity in brain networks and we summarize some of the recent work investigating modularity of structural and functional brain networks derived from analysis of human neuroimaging data. PMID:21151783

  7. Extracellular signal-related kinase positively regulates ataxia telangiectasia mutated, homologous recombination repair, and the DNA damage response.

    PubMed

    Golding, Sarah E; Rosenberg, Elizabeth; Neill, Steven; Dent, Paul; Povirk, Lawrence F; Valerie, Kristoffer

    2007-02-01

    The accurate joining of DNA double-strand breaks by homologous recombination repair (HRR) is critical to the long-term survival of the cell. The three major mitogen-activated protein (MAP) kinase (MAPK) signaling pathways, extracellular signal-regulated kinase (ERK), p38, and c-Jun-NH(2)-kinase (JNK), regulate cell growth, survival, and apoptosis. To determine the role of MAPK signaling in HRR, we used a human in vivo I-SceI-based repair system. First, we verified that this repair platform is amenable to pharmacologic manipulation and show that the ataxia telangiectasia mutated (ATM) kinase is critical for HRR. The ATM-specific inhibitor KU-55933 compromised HRR up to 90% in growth-arrested cells, whereas this effect was less pronounced in cycling cells. Then, using well-characterized MAPK small-molecule inhibitors, we show that ERK1/2 and JNK signaling are important positive regulators of HRR in growth-arrested cells. On the other hand, inhibition of the p38 MAPK pathway generated an almost 2-fold stimulation of HRR. When ERK1/2 signaling was stimulated by oncogenic RAF-1, an approximately 2-fold increase in HRR was observed. KU-55933 partly blocked radiation-induced ERK1/2 phosphorylation, suggesting that ATM regulates ERK1/2 signaling. Furthermore, inhibition of MAP/ERK kinase (MEK)/ERK signaling resulted in severely reduced levels of phosphorylated (S1981) ATM foci but not gamma-H2AX foci, and suppressed ATM phosphorylation levels >85% throughout the cell cycle. Collectively, these results show that MAPK signaling positively and negatively regulates HRR in human cells. More specifically, ATM-dependent signaling through the RAF/MEK/ERK pathway is critical for efficient HRR and for radiation-induced ATM activation, suggestive of a regulatory feedback loop between ERK and ATM.

  8. DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli

    PubMed Central

    Fulcrand, Geraldine; Dages, Samantha; Zhi, Xiaoduo; Chapagain, Prem; Gerstman, Bernard S.; Dunlap, David; Leng, Fenfei

    2016-01-01

    Escherichia coli lac repressor (LacI) is a paradigmatic transcriptional factor that controls the expression of lacZYA in the lac operon. This tetrameric protein specifically binds to the O1, O2 and O3 operators of the lac operon and forms a DNA loop to repress transcription from the adjacent lac promoter. In this article, we demonstrate that upon binding to the O1 and O2 operators at their native positions LacI constrains three (−) supercoils within the 401-bp DNA loop of the lac promoter and forms a topological barrier. The stability of LacI-mediated DNA topological barriers is directly proportional to its DNA binding affinity. However, we find that DNA supercoiling modulates the basal expression from the lac operon in E. coli. Our results are consistent with the hypothesis that LacI functions as a topological barrier to constrain free, unconstrained (−) supercoils within the 401-bp DNA loop of the lac promoter. These constrained (−) supercoils enhance LacI’s DNA-binding affinity and thereby the repression of the promoter. Thus, LacI binding is superhelically modulated to control the expression of lacZYA in the lac operon under varying growth conditions. PMID:26763930

  9. DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli.

    PubMed

    Fulcrand, Geraldine; Dages, Samantha; Zhi, Xiaoduo; Chapagain, Prem; Gerstman, Bernard S; Dunlap, David; Leng, Fenfei

    2016-01-14

    Escherichia coli lac repressor (LacI) is a paradigmatic transcriptional factor that controls the expression of lacZYA in the lac operon. This tetrameric protein specifically binds to the O1, O2 and O3 operators of the lac operon and forms a DNA loop to repress transcription from the adjacent lac promoter. In this article, we demonstrate that upon binding to the O1 and O2 operators at their native positions LacI constrains three (-) supercoils within the 401-bp DNA loop of the lac promoter and forms a topological barrier. The stability of LacI-mediated DNA topological barriers is directly proportional to its DNA binding affinity. However, we find that DNA supercoiling modulates the basal expression from the lac operon in E. coli. Our results are consistent with the hypothesis that LacI functions as a topological barrier to constrain free, unconstrained (-) supercoils within the 401-bp DNA loop of the lac promoter. These constrained (-) supercoils enhance LacI's DNA-binding affinity and thereby the repression of the promoter. Thus, LacI binding is superhelically modulated to control the expression of lacZYA in the lac operon under varying growth conditions.

  10. Signal amplification strategies for DNA and protein detection based on polymeric nanocomposites and polymerization: A review.

    PubMed

    Zhou, Shaohong; Yuan, Liang; Hua, Xin; Xu, Lingling; Liu, Songqin

    2015-06-02

    Demand is increasing for ultrasensitive bioassays for disease diagnosis, environmental monitoring and other research areas. This requires novel signal amplification strategies to maximize the signal output. In this review, we focus on a series of significant signal amplification strategies based on polymeric nanocomposites and polymerization. Some common polymers are used as carriers to increase the local concentration of signal probes and/or biomolecules on their surfaces or in their interiors. Some polymers with special fluorescence and optical properties can efficiently transfer the excitation energy from a single site to the whole polymer backbone. This results in superior fluorescence signal amplification due to the resulting collective effort (integration of signal). Recent polymerization-based signal amplification strategies that employ atom transfer radical polymerization (ATRP) and photo-initiated polymerization are also summarized. Several distinctive applications of polymers in ultrasensitive bioanalysis are highlighted.

  11. Near-infrared silver cluster optically signaling oligonucleotide hybridization and assembling two DNA hosts.

    PubMed

    Petty, Jeffrey T; Nicholson, David A; Sergev, Orlin O; Graham, Stuart K

    2014-09-16

    Silver clusters with ~10 atoms form within DNA strands, and the conjugates are chemical sensors. The DNA host hybridizes with short oligonucleotides, and the cluster moieties optically respond to these analytes. Our studies focus on how the cluster adducts perturb the structure of their DNA hosts. Our sensor is comprised of an oligonucleotide with two components: a 5'-cluster domain that complexes silver clusters and a 3'-recognition site that hybridizes with a target oligonucleotide. The single-stranded sensor encapsulates an ~11 silver atom cluster with violet absorption at 400 nm and with minimal emission. The recognition site hybridizes with complementary oligonucleotides, and the violet cluster converts to an emissive near-infrared cluster with absorption at 730 nm. Our key finding is that the near-infrared cluster coordinates two of its hybridized hosts. The resulting tertiary structure was investigated using intermolecular and intramolecular variants of the same dimer. The intermolecular dimer assembles in concentrated (~5 μM) DNA solutions. Strand stoichiometries and orientations were chromatographically determined using thymine-modified complements that increase the overall conjugate size. The intramolecular dimer develops within a DNA scaffold that is founded on three linked duplexes. The high local cluster concentrations and relative strand arrangements again favor the antiparallel dimer for the near-infrared cluster. When the two monomeric DNA/violet cluster conjugates transform to one dimeric DNA/near-infrared conjugate, the DNA strands accumulate silver. We propose that these correlated changes in DNA structure and silver stoichiometry underlie the violet to near-infrared cluster transformation.

  12. Chromatin and DNA replication.

    PubMed

    MacAlpine, David M; Almouzni, Geneviève

    2013-08-01

    The size of a eukaryotic genome presents a unique challenge to the cell: package and organize the DNA to fit within the confines of the nucleus while at the same time ensuring sufficient dynamics to allow access to specific sequences and features such as genes and regulatory elements. This is achieved via the dynamic nucleoprotein organization of eukaryotic DNA into chromatin. The basic unit of chromatin, the nucleosome, comprises a core particle with 147 bp of DNA wrapped 1.7 times around an octamer of histones. The nucleosome is a highly versatile and modular structure, both in its composition, with the existence of various histone variants, and through the addition of a series of posttranslational modifications on the histones. This versatility allows for both short-term regulatory responses to external signaling, as well as the long-term and multigenerational definition of large functional chromosomal domains within the nucleus, such as the centromere. Chromatin organization and its dynamics participate in essentially all DNA-templated processes, including transcription, replication, recombination, and repair. Here we will focus mainly on nucleosomal organization and describe the pathways and mechanisms that contribute to assembly of this organization and the role of chromatin in regulating the DNA replication program.

  13. Modular radiochemistry synthesis system

    SciTech Connect

    Satyamurthy, Nagichettiar; Barrio, Jorge R.; Amarasekera, Bernard; Van Dam, R. Michael; Olma, Sebastian; Williams, Dirk; Eddings, Mark; Shen, Clifton Kwang-Fu

    2015-12-15

    A modular chemical production system includes multiple modules for performing a chemical reaction, particularly of radiochemical compounds, from a remote location. One embodiment comprises a reaction vessel including a moveable heat source with the position thereof relative to the reaction vessel being controllable from a remote position. Alternatively the heat source may be fixed in location and the reaction vial is moveable into and out of the heat source. The reaction vessel has one or more sealing plugs, the positioning of which in relationship to the reaction vessel is controllable from a remote position. Also the one or more reaction vessel sealing plugs can include one or more conduits there through for delivery of reactants, gases at atmospheric or an elevated pressure, inert gases, drawing a vacuum and removal of reaction end products to and from the reaction vial, the reaction vial with sealing plug in position being operable at elevated pressures. The modular chemical production system is assembled from modules which can each include operating condition sensors and controllers configured for monitoring and controlling the individual modules and the assembled system from a remote position. Other modules include, but are not limited to a Reagent Storage and Delivery Module, a Cartridge Purification Module, a Microwave Reaction Module, an External QC/Analysis/Purification Interface Module, an Aliquotting Module, an F-18 Drying Module, a Concentration Module, a Radiation Counting Module, and a Capillary Reactor Module.

  14. Modular radiochemistry synthesis system

    SciTech Connect

    Satyamurthy, Nagichettiar; Barrio, Jorge R.; Amarasekera, Bernard; Van Dam, Michael R.; Olma, Sebastian; Williams, Dirk; Eddings, Mark; Shen, Clifton Kwang-Fu

    2016-11-01

    A modular chemical production system includes multiple modules for performing a chemical reaction, particularly of radiochemical compounds, from a remote location. One embodiment comprises a reaction vessel including a moveable heat source with the position thereof relative to the reaction vessel being controllable from a remote position. Alternatively the heat source may be fixed in location and the reaction vial is moveable into and out of the heat source. The reaction vessel has one or more sealing plugs, the positioning of which in relationship to the reaction vessel is controllable from a remote position. Also the one or more reaction vessel sealing plugs can include one or more conduits there through for delivery of reactants, gases at atmospheric or an elevated pressure, inert gases, drawing a vacuum and removal of reaction end products to and from the reaction vial, the reaction vial with sealing plug in position being operable at elevated pressures. The modular chemical production system is assembled from modules which can each include operating condition sensors and controllers configured for monitoring and controlling the individual modules and the assembled system from a remote position. Other modules include, but are not limited to a Reagent Storage and Delivery Module, a Cartridge Purification Module, a Microwave Reaction Module, an External QC/Analysis/Purification Interface Module, an Aliquotting Module, an F-18 Drying Module, a Concentration Module, a Radiation Counting Module, and a Capillary Reactor Module.

  15. Modular Robotic Vehicle

    NASA Technical Reports Server (NTRS)

    Borroni-Bird, Christopher E. (Inventor); Vitale, Robert L. (Inventor); Lee, Chunhao J. (Inventor); Ambrose, Robert O. (Inventor); Bluethmann, William J. (Inventor); Junkin, Lucien Q. (Inventor); Lutz, Jonathan J. (Inventor); Guo, Raymond (Inventor); Lapp, Anthony Joseph (Inventor); Ridley, Justin S. (Inventor)

    2015-01-01

    A modular robotic vehicle includes a chassis, driver input devices, an energy storage system (ESS), a power electronics module (PEM), modular electronic assemblies (eModules) connected to the ESS via the PEM, one or more master controllers, and various embedded controllers. Each eModule includes a drive wheel containing a propulsion-braking module, and a housing containing propulsion and braking control assemblies with respective embedded propulsion and brake controllers, and a mounting bracket covering a steering control assembly with embedded steering controllers. The master controller, which is in communication with each eModule and with the driver input devices, communicates with and independently controls each eModule, by-wire, via the embedded controllers to establish a desired operating mode. Modes may include a two-wheel, four-wheel, diamond, and omni-directional steering modes as well as a park mode. A bumper may enable docking with another vehicle, with shared control over the eModules of the vehicles.

  16. Modular radiochemistry synthesis system

    DOEpatents

    Satyamurthy, Nagichettiar; Barrio, Jorge R; Amarasekera, Bernard; Van Dam, R. Michael; Olma, Sebastian; Williams, Dirk; Eddings, Mark A; Shen, Clifton Kwang-Fu

    2015-02-10

    A modular chemical production system includes multiple modules for performing a chemical reaction, particularly of radiochemical compounds, from a remote location. One embodiment comprises a reaction vessel including a moveable heat source with the position thereof relative to the reaction vessel being controllable from a remote position. Alternatively the heat source may be fixed in location and the reaction vial is moveable into and out of the heat source. The reaction vessel has one or more sealing plugs, the positioning of which in relationship to the reaction vessel is controllable from a remote position. Also the one or more reaction vessel sealing plugs can include one or more conduits there through for delivery of reactants, gases at atmospheric or an elevated pressure, inert gases, drawing a vacuum and removal of reaction end products to and from the reaction vial, the reaction vial with sealing plug in position being operable at elevated pressures. The modular chemical production system is assembled from modules which can each include operating condition sensors and controllers configured for monitoring and controlling the individual modules and the assembled system from a remote position. Other modules include, but are not limited to a Reagent Storage and Delivery Module, a Cartridge Purification Module, a Microwave Reaction Module, an External QC/Analysis/Purification Interface Module, an Aliquotting Module, an F-18 Drying Module, a Concentration Module, a Radiation Counting Module, and a Capillary Reactor Module.

  17. Modular antenna design study

    NASA Technical Reports Server (NTRS)

    Ribble, J. W.

    1981-01-01

    The mechanical design of a modular antenna concept was developed sufficiently to allow manufacture of a working demonstration model of a module, to predict mass properties, and to make performance estimates for antenna reflectors composed of these modules. The primary features of this concept are: (1) each module is an autonomous structural element which can be attached to adjacent modules through a three point connection; (2) the upper surface is a folding hexagonal truss plate mechanism which serves as the supporting structure for a reflective surface; and (3) the entire truss and surface can be folded into a cylindrical envelope in which all truss elements are essentially parallel. The kinematic studies and engineering demonstration model fully verified the deployment kinematics, stowing philosophy, and deployment sequencing for large antenna modules. It was established that such modules can be stowed in packages as small as 25 cm in diameter, using 1.27 cm diameter structural tubes. The development activity indicates that this deployable modular approach towards building large structures in space will support erection of 450 m apertures for operation up to 3 GHz with a single space shuttle flight.

  18. Modular reflector concept study

    NASA Technical Reports Server (NTRS)

    Vaughan, D. H.

    1981-01-01

    A study was conducted to evaluate the feasibility of space erecting a 100 meter paraboloidal radio frequency reflector by joining a number of individually deployed structural modules. Three module design concepts were considered: (1) the deployable cell module (DCM); (2) the modular paraboloidal erectable truss antenna (Mod-PETA); and (3) the modular erectable truss antenna (META). With the space shuttle (STS) as the launch system, the methodology of packaging and stowing in the orbiter, and of dispensing, deploying and joining, in orbit, were studied and the necessary support equipment identified. The structural performance of the completed reflectors was evaluated and their overall operational capability and feasibility were evaluated and compared. The potential of the three concepts to maintain stable shape in the space environment was determined. Their ability to operate at radio frequencies of 1 GHz and higher was assessed assuming the reflector surface to consist of a number of flat, hexagonal facets. A parametric study was performed to determine figure degradation as a function of reflector size, flat facet size, and f/D ratio.

  19. Numerical analysis of intensity signals resulting from genotyping pooled DNA samples in beef cattle and broiler chicken.

    PubMed

    Reverter, A; Henshall, J M; McCulloch, R; Sasazaki, S; Hawken, R; Lehnert, S A

    2014-05-01

    Pooled genomic DNA has been proposed as a cost-effective approach in genomewide association studies (GWAS). However, algorithms for genotype calling of biallelic SNP are not adequate with pooled DNA samples because they assume the presence of 2 fluorescent signals, 1 for each allele, and operate under the expectation that at most 2 copies of the variant allele can be found for any given SNP and DNA sample. We adapt analytical methodology from 2-channel gene expression microarray technology to SNP genotyping of pooled DNA samples. Using 5 datasets from beef cattle and broiler chicken of varying degrees of complexity in terms of design and phenotype, continuous and dichotomous, we show that both differential hybridization (M = green minus red intensity signal) and abundance (A = average of red and green intensities) provide useful information in the prediction of SNP allele frequencies. This is predominantly true when making inference about extreme SNP that are either nearly fixed or highly polymorphic. We propose the use of model-based clustering via mixtures of bivariate normal distributions as an optimal framework to capture the relationship between hybridization intensity and allele frequency from pooled DNA samples. The range of M and A values observed here are in agreement with those reported within the context of gene expression microarray and also with those from SNP array data within the context of analytical methodology for the identification of copy number variants. In particular, we confirm that highly polymorphic SNP yield a strong signal from both channels (red and green) while lowly or nonpolymorphic SNP yield a strong signal from 1 channel only. We further confirm that when the SNP allele frequencies are known, either because the individuals in the pools or from a closely related population are themselves genotyped, a multiple regression model with linear and quadratic components can be developed with high prediction accuracy. We conclude that when

  20. Quantum modular forms, mock modular forms, and partial theta functions

    NASA Astrophysics Data System (ADS)

    Kimport, Susanna

    Defined by Zagier in 2010, quantum modular forms have been the subject of an explosion of recent research. Many of these results are aimed at discovering examples of these functions, which are defined on the rational numbers and have "nice" modularity properties. Though the subject is in its early stages, numerous results (including Zagier's original examples) show these objects naturally arising from many areas of mathematics as limits of other modular-like functions. One such family of examples is due to Folsom, Ono, and Rhoades, who connected these new objects to partial theta functions (introduced by Rogers in 1917) and mock modular forms (about which there is a rich theory, whose origins date back to Ramanujan in 1920). In this thesis, we build off of the work of Folsom, Ono, and Rhoades by providing an infinite family of quantum modular forms of arbitrary positive half-integral weight. Further, this family of quantum modular forms "glues" mock modular forms to partial theta functions and is constructed from a so-called "universal" mock theta function by extending a method of Eichler and Zagier (originally defined for holomorphic Jacobi forms) into a non-holomorphic setting. In addition to the infinite family, we explore the weight 1/2 and 3/2 functions in more depth. For both of these weights, we are able to explicitly write down the quantum modular form, as well as the corresponding "errors to modularity," which can be shown to be Mordell integrals of specific theta functions and, as a consequence, are real-analytic functions. Finally, we turn our attention to the partial theta functions associated with these low weight examples. Berndt and Kim provide asymptotic expansions for a certain class of partial theta functions as q approaches 1 radially within the unit disk. Here, we extend this work to not only obtain asymptotic expansions for this class of functions as q approaches any root of unity, but also for a certain class of derivatives of these functions

  1. Spacecraft Modularity for Serviceable Satellites

    NASA Technical Reports Server (NTRS)

    Rossetti, Dino; Keer, Beth; Panek, John; Ritter, Bob; Reed, Benjamin; Cepollina, Frank

    2015-01-01

    Spacecraft modularity has been a topic of interest at NASA since the 1970s, when the Multi-­-Mission Modular Spacecraft (MMS) was developed at the Goddard Space Flight Center. Since then, modular concepts have been employed for a variety of spacecraft and, as in the case of the Hubble Space Telescope (HST) and the International Space Station (ISS), have been critical to the success of on-­- orbit servicing. Modularity is even more important for future robotic servicing. Robotic satellite servicing technologies under development by NASA can extend mission life and reduce lifecycle cost and risk. These are optimized when the target spacecraft is designed for servicing, including advanced modularity. This paper will explore how spacecraft design, as demonstrated by the Reconfigurable Operational spacecraft for Science and Exploration (ROSE) spacecraft architecture, and servicing technologies can be developed in parallel to fully take advantage of the promise of both.

  2. Spacecraft Modularity for Serviceable Satellites

    NASA Technical Reports Server (NTRS)

    Reed, Benjamin B.; Rossetti, Dino; Keer, Beth; Panek, John; Cepollina, Frank; Ritter, Robert

    2015-01-01

    Spacecraft modularity has been a topic of interest at NASA since the 1970s, when the Multi-Mission Modular Spacecraft (MMS) was developed at the Goddard Space Flight Center. Since then, modular concepts have been employed for a variety of spacecraft and, as in the case of the Hubble Space Telescope (HST) and the International Space Station (ISS), have been critical to the success of on-orbit servicing. Modularity is even more important for future robotic servicing. Robotic satellite servicing technologies under development by NASA can extend mission life and reduce life-cycle cost and risk. These are optimized when the target spacecraft is designed for servicing, including advanced modularity. This paper will explore how spacecraft design, as demonstrated by the Reconfigurable Operational spacecraft for Science and Exploration (ROSE) spacecraft architecture, and servicing technologies can be developed in parallel to fully take advantage of the promise of both.

  3. DNA Damage-Induced HSPC Malfunction Depends on ROS Accumulation Downstream of IFN-1 Signaling and Bid Mobilization.

    PubMed

    Tasdogan, Alpaslan; Kumar, Suresh; Allies, Gabriele; Bausinger, Julia; Beckel, Franziska; Hofemeister, Helmut; Mulaw, Medhanie; Madan, Vikas; Scharfetter-Kochanek, Karin; Feuring-Buske, Michaela; Doehner, Konstanze; Speit, Günter; Stewart, A Francis; Fehling, Hans Joerg

    2016-12-01

    Mouse mutants with an impaired DNA damage response frequently exhibit a set of remarkably similar defects in the HSPC compartment that are of largely unknown molecular basis. Using Mixed-Lineage-Leukemia-5 (Mll5)-deficient mice as prototypical examples, we have identified a mechanistic pathway linking DNA damage and HSPC malfunction. We show that Mll5 deficiency results in accumulation of DNA damage and reactive oxygen species (ROS) in HSPCs. Reduction of ROS efficiently reverses hematopoietic defects, establishing ROS as a major cause of impaired HSPC function. The Ink4a/Arf locus also contributes to HSPC phenotypes, at least in part via promotion of ROS. Strikingly, toxic ROS levels in Mll5(-/-) mice are critically dependent on type 1 interferon (IFN-1) signaling, which triggers mitochondrial accumulation of full-length Bid. Genetic inactivation of Bid diminishes ROS levels and reverses HSPC defects in Mll5(-/-) mice. Overall, therefore, our findings highlight an unexpected IFN-1 > Bid > ROS pathway underlying DNA damage-associated HSPC malfunction.

  4. Autophagy Promotes the Repair of Radiation-Induced DNA Damage in Bone Marrow Hematopoietic Cells via Enhanced STAT3 Signaling.

    PubMed

    Xu, Fei; Li, Xin; Yan, Lili; Yuan, Na; Fang, Yixuan; Cao, Yan; Xu, Li; Zhang, Xiaoying; Xu, Lan; Ge, Chaorong; An, Ni; Jiang, Gaoyue; Xie, Jialing; Zhang, Han; Jiang, Jiayi; Li, Xiaotian; Yao, Lei; Zhang, Suping; Zhou, Daohong; Wang, Jianrong

    2017-03-01

    Autophagy protects hematopoietic cells from radiation damage in part by promoting DNA damage repair. However, the molecular mechanisms by which autophagy regulates DNA damage repair remain largely elusive. Here, we report that this radioprotective effect of autophagy depends on STAT3 signaling in murine bone marrow mononuclear cells (BM-MNCs). Specifically, we found that STAT3 activation and nuclear translocation in BM-MNCs were increased by activation of autophagy with an mTOR inhibitor and decreased by knockout of the autophagy gene Atg7. The autophagic regulation of STAT3 activation is likely mediated by induction of KAP1 degradation, because we showed that KAP1 directly interacted with STAT3 in the cytoplasm and knockdown of KAP1 increased the phosphorylation and nuclear translocation of STAT3. Subsequently, activated STAT3 transcriptionally upregulated the expression of BRCA1, which increased the ability of BM-MNCs to repair radiation-induced DNA damage. This novel finding that activation of autophagy can promote DNA damage repair in BM-MNCs via the ATG-KAP1-STAT3-BRCA1 pathway suggests that autophagy plays an important role in maintaining genomic integrity of BM-MNCs and its activation may confer protection of BM-MNCs against radiation-induced genotoxic stress.

  5. Differential Processing of Low and High LET Radiation Induced DNA Damage: Investigation of Switch from ATM to ATR Signaling

    NASA Technical Reports Server (NTRS)

    Saha, Janapriya; Wang, Minli; Hada, Megumi; Cucinotta, Francis A.

    2011-01-01

    The members of the phosphatidylinositol kinase-like kinase family of proteins namely ataxia-telangiectasia mutated (ATM) and ATM- and Rad3-related (ATR) are directly responsible for the maintenance of genomic integrity by mounting DDR through signaling and facilitating the recruitment of repair factors at the sites of DNA damage along with coordinating the deployment of cell cycle checkpoints to permit repair by phosphorylating Checkpoint kinase Chk1, Chk2 and p53. High LET radiation from GCR (Galactic Cosmic Rays) consisting mainly of protons and high energy and charged (HZE) particles from SPE (Solar Particle Event) pose a major health risk for astronauts on their space flight missions. The determination of these risks and the design of potential safeguards require sound knowledge of the biological consequences of lesion induction and the capability of the cells to counter them. We here strive to determine the coordination of ATM and ATR kinases at the break sites directly affecting checkpoint signaling and DNA repair and whether differential processing of breaks induced by low and high LET radiation leads to possible augmentation of swap of these damage sensors at the sites of DNA damage. Exposure of cells to IR triggers rapid autophosphorylation of serine-1981 that causes dimer dissociation and initiates monomer formation of ATM. ATM kinase activity depends on the disruption of the dimer, which allows access and phosphorylation of downstream ATM substrates like Chk2. Evidence suggests that ATM is activated by the alterations in higher-order chromatin structure although direct binding of ATM to DSB ends may be a crucial step in its activation. On the other hand, in case of ATR, RPA (replication protein A)-coated ssDNA (single-stranded DNA) generated as a result of stalled DNA replication or during processing of chromosomal lesions is crucial for the localization of ATR to sites of DNA damage in association with ATR-interacting protein (ATRIP). Although the

  6. Modular robotics overview of the `state of the art`

    SciTech Connect

    Kress, R.L.; Jansen, J.F.; Hamel, W.R.

    1996-08-01

    The design of a robotic arm processing modular components and reconfigurable links is the general goal of a modular robotics development program. The impetus behind the pursuit of modular design is the remote engineering paradigm of improved reliability and availability provided by the ability to remotely maintain and repair a manipulator operating in a hazardous environment by removing and replacing worn or failed modules. Failed components can service off- line and away from hazardous conditions. The desire to reconfigure an arm to perform different tasks is also an important driver for the development of a modular robotic manipulator. In order to bring to fruition a truly modular manipulator, an array of technical challenges must be overcome. These range from basic mechanical and electrical design considerations such as desired kinematics, actuator types, and signal and transmission types and routings, through controls issues such as the need for control algorithms capable of stable free space and contact control, to computer and sensor design issues like consideration of the use of embedded processors and redundant sensors. This report presents a brief overview of the state of the art of technical issues relevant of modular robotic arm design. The focus is on breadth of coverage, rather than depth, in order to provide a reference frame for future development.

  7. Modular Flooring System

    NASA Technical Reports Server (NTRS)

    Thate, Robert

    2012-01-01

    The modular flooring system (MFS) was developed to provide a portable, modular, durable carpeting solution for NASA fs Robotics Alliance Project fs (RAP) outreach efforts. It was also designed to improve and replace a modular flooring system that was too heavy for safe use and transportation. The MFS was developed for use as the flooring for various robotics competitions that RAP utilizes to meet its mission goals. One of these competitions, the FIRST Robotics Competition (FRC), currently uses two massive rolls of broadloom carpet for the foundation of the arena in which the robots are contained during the competition. The area of the arena is approximately 30 by 72 ft (approximately 9 by 22 m). This carpet is very cumbersome and requires large-capacity vehicles, and handling equipment and personnel to transport and deploy. The broadloom carpet sustains severe abuse from the robots during a regular three-day competition, and as a result, the carpet is not used again for competition. Similarly, broadloom carpets used for trade shows at convention centers around the world are typically discarded after only one use. This innovation provides a green solution to this wasteful practice. Each of the flooring modules in the previous system weighed 44 lb (.20 kg). The improvements in the overall design of the system reduce the weight of each module by approximately 22 lb (.10 kg) (50 %), and utilize an improved "module-to-module" connection method that is superior to the previous system. The MFS comprises 4-by-4-ft (.1.2-by- 1.2-m) carpet module assemblies that utilize commercially available carpet tiles that are bonded to a lightweight substrate. The substrate surface opposite from the carpeted surface has a module-to-module connecting interface that allows for the modules to be connected, one to the other, as the modules are constructed. This connection is hidden underneath the modules, creating a smooth, co-planar flooring surface. The modules are stacked and strapped

  8. In search of antiaging modalities: evaluation of mTOR- and ROS/DNA damage-signaling by cytometry.

    PubMed

    Darzynkiewicz, Zbigniew; Zhao, Hong; Halicka, H Dorota; Li, Jiangwei; Lee, Yong-Syu; Hsieh, Tze-Chen; Wu, Joseph M

    2014-05-01

    This review presents the evidence in support of the IGF-1/mTOR/S6K1 signaling as the primary factor contributing to aging and cellular senescence. Reviewed are also specific interactions between mTOR/S6K1 and ROS-DNA damage signaling pathways. Outlined are critical sites along these pathways, including autophagy, as targets for potential antiaging (gero-suppressive) and/or chemopreventive agents. Presented are applications of flow- and laser scanning- cytometry utilizing phospho-specific Abs, to monitor activation along these pathways in response to the reported antiaging drugs rapamycin, metformin, berberine, resveratrol, vitamin D3, 2-deoxyglucose, and acetylsalicylic acid. Specifically, effectiveness of these agents to attenuate the level of constitutive mTOR signaling was tested by cytometry and confirmed by Western blotting through measuring phosphorylation of the mTOR-downstream targets including ribosomal protein S6. The ratiometric analysis of phosphorylated to total protein along the mTOR pathway offers a useful parameter reporting the effects of gero-suppressive agents. In parallel, their ability to suppress the level of constitutive DNA damage signaling induced by endogenous ROS was measured. While the primary target of each of these agents may be different the data obtained on several human cancer cell lines, WI-38 fibroblasts and normal lymphocytes suggest common downstream mechanism in which the decline in mTOR/S6K1 signaling and translation rate is coupled with a reduction of oxidative phosphorylation and ROS that leads to decreased oxidative DNA damage. The combined assessment of constitutive γH2AX expression, mitochondrial activity (ROS, ΔΨm), and mTOR signaling provides an adequate gamut of cell responses to test effectiveness of gero-suppressive agents. Described is also an in vitro model of induction of cellular senescence by persistent replication stress, its quantitative analysis by laser scanning cytometry, and application to detect the

  9. DNA damage in mammalian neural stem cells leads to astrocytic differentiation mediated by BMP2 signaling through JAK-STAT.

    PubMed

    Schneider, Leonid; Pellegatta, Serena; Favaro, Rebecca; Pisati, Federica; Roncaglia, Paola; Testa, Giuseppe; Nicolis, Silvia K; Finocchiaro, Gaetano; d'Adda di Fagagna, Fabrizio

    2013-01-01

    The consequences of DNA damage generation in mammalian somatic stem cells, including neural stem cells (NSCs), are poorly understood despite their potential relevance for tissue homeostasis. Here, we show that, following ionizing radiation-induced DNA damage, NSCs enter irreversible proliferative arrest with features of cellular senescence. This is characterized by increased cytokine secretion, loss of stem cell markers, and astrocytic differentiation. We demonstrate that BMP2 is necessary to induce expression of the astrocyte marker GFAP in irradiated NSCs via a noncanonical signaling pathway engaging JAK-STAT. This is promoted by ATM and antagonized by p53. Using a SOX2-Cre reporter mouse model for cell-lineage tracing, we demonstrate irradiation-induced NSC differentiation in vivo. Furthermore, glioblastoma assays reveal that irradiation therapy affects the tumorigenic potential of cancer stem cells by ablating self-renewal and inducing astroglial differentiation.

  10. Dub3 controls DNA damage signalling by direct deubiquitination of H2AX.

    PubMed

    Delgado-Díaz, M Rocío; Martín, Yusé; Berg, Anna; Freire, Raimundo; Smits, Veronique A J

    2014-07-01

    A crucial event in the DNA damage response is the phosphorylation and subsequent ubiquitination of H2AX, required for the recruitment of proteins involved in DNA repair. Here we identify a novel regulator of this process, the ubiquitin hydrolase Dub3. Overexpression of wild type, but not catalytic inactive, Dub3 decreases the DNA damage-induced mono-ubiquitination of H2A(X) whereas downregulation of Dub3 has the opposite effect. Dub3 overexpression abrogates focus formation of 53BP1 and BRCA1 in response to genotoxic stress. However, focus formation of MDC1 and γH2AX, earlier events in this response, are unaffected by Dub3 overexpression. We show that Dub3 counteracts H2AX E3 ligases RNF8 and RNF168. Moreover, Dub3 and H2AX interact and Dub3 deubiquitinates H2AX in vitro. Importantly, overexpression of Dub3 delays H2AX dephosphorylation and recovery of MDC1 focus formation at later time points after DNA damage, whereas H2AX dephosphorylation at later time points is faster after Dub3 depletion. Altogether these results show that Dub3 regulates a correct DNA damage response by controlling H2AX ubiquitination.

  11. Cis-acting signals modulate the efficiency of programmed DNA elimination in Paramecium tetraurelia

    PubMed Central

    Ferro, Diana; Lepennetier, Gildas; Catania, Francesco

    2015-01-01

    In Paramecium, the regeneration of a functional somatic genome at each sexual event relies on the elimination of thousands of germline DNA sequences, known as Internal Eliminated Sequences (IESs), from the zygotic nuclear DNA. Here, we provide evidence that IESs’ length and sub-terminal bases jointly modulate IES excision by affecting DNA conformation in P. tetraurelia. Our study reveals an excess of complementary base pairing between IESs’ sub-terminal and contiguous sites, suggesting that IESs may form DNA loops prior to cleavage. The degree of complementary base pairing between IESs’ sub-terminal sites (termed Cin-score) is positively associated with IES length and is shaped by natural selection. Moreover, it escalates abruptly when IES length exceeds 45 nucleotides (nt), indicating that only sufficiently large IESs may form loops. Finally, we find that IESs smaller than 46 nt are favored targets of the cellular surveillance systems, presumably because of their relatively inefficient excision. Our findings extend the repertoire of cis-acting determinants for IES recognition/excision and provide unprecedented insights into the distinct selective pressures that operate on IESs and somatic DNA regions. This information potentially moves current models of IES evolution and of mechanisms of IES recognition/excision forward. PMID:26304543

  12. Highly specific electronic signal transduction mediated by DNA/metal self-assembly.

    SciTech Connect

    Dentinger, Paul M.; Pathak, Srikant

    2003-11-01

    Highly specific interactions between DNA could potentially be amplified if the DNA interactions were utilized to assemble large scale parts. Fluidic assembly of microsystem parts has the potential for rapid and accurate placement of otherwise difficult to handle pieces. Ideally, each part would have a different chemical interaction that allowed it to interact with the substrate only in specific areas. One easy way to obtain a multiple chemical permutations is to use synthetic DNA oligomers. Si parts were prepared using silicon-on-insulator technology microfabrication techniques. Several surface chemistry protocols were developed to react commercial oligonucleotides to the parts. However, no obvious assembly was achieved. It was thought that small defects on the surface did not allow the microparts to be in close enough proximity for DNA hybridization, and this was. in part, confirmed by interferometry. To assist in the hybridization, plastic, pliable parts were manufactured and a new chemistry was developed. However, assembly was still absent even with the application of force. It is presently thought that one of three mechanisms is preventing the assembly. The surfaces of the two solid substrates can not get in close enough proximity, the surface chemistry lacks sufficient density to keep the parts from separating, or DNA interactions in close proximity on solid substrates are forbidden. These possibilities are discussed in detail.

  13. Quantum dot monolayer for surface plasmon resonance signal enhancement and DNA hybridization detection.

    PubMed

    Ghrera, Aditya Sharma; Pandey, Manoj Kumar; Malhotra, Bansi Dhar

    2016-06-15

    We report results of studies relating to the fabrication of a surface plasmon resonance (SPR)-based nucleic acid sensor for quantification of DNA sequence specific to chronic myelogeneous leukemia (CML). The SPR disk surface has been modified with octadecanethiol self-assembled monolayer followed by deposition of the tri-n-octylphosphine oxide capped cadmium selenide quantum dots (QD) Langmuir monolayer. The deposition is performed via Langmuir-Blodgett (LB) technique. For the sensor chip preparation, covalent immobilization of the thiol-terminated DNA probe sequence (pDNA) using displacement reaction is accomplished. This integrated SPR chip has been used to detect target complementary DNA concentration by monitoring the change in coupling angle via hybridization. It is revealed that this biosensor exhibits high sensitivity (0.7859 m(0)pM(-1)) towards complementary DNA and can be used to detect it in the concentration range, 180 pM to 5 pM with detection limit as 4.21 pM. The results of kinetic studies yield the values of hybridization and dissociation rate constants as 9.6 × 10(4) M(-1) s(-1) and 2.3 × 10(-2) s(-1), respectively, with the equilibrium constant for hybridization as 4.2 × 10(6) M(-1).

  14. A protein interaction between β-catenin and Dnmt1 regulates Wnt Signaling and DNA methylation in colorectal cancer cells

    PubMed Central

    Song, Jing; Du, Zhanwen; Ravasz, Mate; Dong, Bohan; Wang, Zhenghe; Ewing, Rob M.

    2015-01-01

    Aberrant activation of the Wnt signaling pathway is an important step in the initiation and progression of tumor development in diverse cancers. The central effector of canonical Wnt signaling, β-catenin (CTNNB1), is a multifunctional protein, and has been extensively studied with respect to its roles in cell-cell adhesion and in regulation of Wnt-driven transcription. Here, a novel mass spectrometry-based proteomics technique in colorectal cancer cells expressing stabilized β-catenin, was used to identify a protein-protein interaction between β-catenin and DNA methyltransferase I (Dnmt1) protein, the primary regulator of DNA methylation patterns in mammalian cells. Dnmt1 and β-catenin strongly co-localized in the nuclei of colorectal cancer cells, and the interaction is mediated by the central domain of the Dnmt1 protein. Dnmt1 protein abundance is dependent upon the levels of β-catenin, and is increased in cells expressing stabilized mutant β-catenin. Conversely, the Dnmt1 regulates the levels of nuclear β-catenin and β-catenin/TCF driven transcription. In addition, lysine-specific demethylase 1 (LSD1/KDM1A), a regulator of DNMT1 stability, was identified as a component of the Dnmt1/β-catenin protein complex and perturbation of the Dnmt1/β-catenin interaction altered DNA methylation. In summary, a functional protein-protein interaction was identified between two critically important oncoproteins, in turn revealing a link between Wnt signaling and downstream nuclear functions mediated by Dnmt1. PMID:25753001

  15. The actin depolymerizing factor (ADF)/cofilin signaling pathway and DNA damage responses in cancer.

    PubMed

    Chang, Chun-Yuan; Leu, Jyh-Der; Lee, Yi-Jang

    2015-02-13

    The actin depolymerizing factor (ADF)/cofilin protein family is essential for actin dynamics, cell division, chemotaxis and tumor metastasis. Cofilin-1 (CFL-1) is a primary non-muscle isoform of the ADF/cofilin protein family accelerating the actin filamental turnover in vitro and in vivo. In response to environmental stimulation, CFL-1 enters the nucleus to regulate the actin dynamics. Although the purpose of this cytoplasm-nucleus transition remains unclear, it is speculated that the interaction between CFL-1 and DNA may influence various biological responses, including DNA damage repair. In this review, we will discuss the possible involvement of CFL-1 in DNA damage responses (DDR) induced by ionizing radiation (IR), and the implications for cancer radiotherapy.

  16. Self-DNA, STING-dependent signaling and the origins of autoinflammatory disease.

    PubMed

    Ahn, Jeonghyun; Barber, Glen N

    2014-12-01

    Self-DNA has long been considered a key cause of inflammatory and autoimmune disease, although the exact origin and general mechanisms of action have remained to be elucidated. Recently, new insight has been gained into our understanding of those innate immune pathways and sensors that are responsible for instigating self-DNA triggered autoinflammatory events in the cell. One such sensor referred to as STING (for stimulator of interferon genes) has been found to be seminal for controlling cytosolic-DNA induced cytokine production, and may be responsible for a wide variety of inflammatory diseases including systemic lupus erythematosus (SLE), Aicardi-Goutieres syndrome (AGS) and STING-associated vasculopathy with onset of infancy (SAVI). STING may also be involved with augmenting certain types of carcinogen induced cancer. Aside from generating valuable information into mechanisms underlining innate immune gene regulation, these findings offer new opportunities to generate innovative therapeutics which may help treat such diseases.

  17. Modular arctic structures system

    SciTech Connect

    Reusswig, G. H.

    1984-12-04

    A modular and floatable offshore exploration and production platform system for use in shallow arctic waters is disclosed. A concrete base member is floated to the exploration or production site, and ballated into a predredged cavity. The cavity and base are sized to provide a stable horizontal base 30 feet below the mean water/ice plane. An exploration or production platform having a massive steel base is floated to the site and ballasted into position on the base. Together, the platform, base and ballast provide a massive gravity structure that is capable of resisting large ice and wave forces that impinge on the structure. The steel platform has a sloping hourglass profile to deflect horizontal ice loads vertically, and convert the horizontal load to a vertical tensile stress, which assists in breaking the ice as it advances toward the structure.

  18. Modular small hydro configuration

    NASA Astrophysics Data System (ADS)

    1981-09-01

    Smaller sites (those under 750 kilowatts) which previously were not attractive to develop using equipment intended for application at larger scale sites, were the focal point in the conception of a system which utilizes standard industrial components which are generally available within short procurement times. Such components were integrated into a development scheme for sites having 20 feet to 150 feet of head. The modular small hydro configuration maximizes the use of available components and minimizes modification of existing civil works. A key aspect of the development concept is the use of a vertical turbine multistage pump, used in the reverse mode as a hydraulic turbine. The configuration allows for automated operation and control of the hydroelectric facilities with sufficient flexibility for inclusion of potential hydroelectric sites into dispersed storage and generation (DSG) utility grid systems.

  19. Modular Optical PDV System

    SciTech Connect

    Araceli Rutkowski, David Esquibel

    2008-12-11

    A modular optical photon Doppler velocimetry (PDV) detector system has been developed by using readily available optical components with a 20-GHz Miteq optical detector into eight channels of single-wide modules integrated into a 3U rack unit (1U = 1.75 inches) with a common power supply. Optical fibers were precisely trimmed, welded, and timed within each unit. This system has been used to collect dynamic velocity data on various physics experiments. An optical power meter displays the laser input power to the module and optical power at the detector. An adjustable micro-electromechanical system (MEMS) optical attenuator is used to adjust the amount of unshifted light entering the detector. Front panel LEDs show the presence of power to the module. A fully loaded chassis with eight channels consumes 45 watts of power. Each chassis requires 1U spacing above and below for heat management. Modules can be easily replaced.

  20. Modular weapon control unit

    SciTech Connect

    Boccabella, M.F.; McGovney, G.N.

    1997-01-01

    The goal of the Modular Weapon Control Unit (MWCU) program was to design and develop a reconfigurable weapon controller (programmer/sequencer) that can be adapted to different weapon systems based on the particular requirements for that system. Programmers from previous systems are conceptually the same and perform similar tasks. Because of this commonality and the amount of re-engineering necessary with the advent of every new design, the idea of a modular, adaptable system has emerged. Also, the controller can be used in more than one application for a specific weapon system. Functionality has been divided into a Processor Module (PM) and an Input/Output Module (IOM). The PM will handle all operations that require calculations, memory, and timing. The IOM will handle interfaces to the rest of the system, input level shifting, output drive capability, and detection of interrupt conditions. Configuration flexibility is achieved in two ways. First, the operation of the PM is determined by a surface mount Read-Only Memory (ROM). Other surface-mount components can be added or neglected as necessary for functionality. Second, IOMs consist of configurable input buffers, configurable output drivers, and configurable interrupt generation. Further, these modules can be added singly or in groups to a Processor Module to achieve the required I/O configuration. The culmination of this LDRD was the building of both Processor Module and Input/Output Module. The MWCU was chosen as a test system to evaluate Low-Temperature Co-fired Ceramic (LTCC) technology, desirable for high component density and good thermal characteristics.

  1. eyelid antagonizes wingless signaling during Drosophila development and has homology to the Bright family of DNA-binding proteins

    PubMed Central

    Treisman, Jessica E.; Luk, Alvin; Rubin, Gerald M.; Heberlein, Ulrike

    1997-01-01

    In Drosophila, pattern formation at multiple stages of embryonic and imaginal development depends on the same intercellular signaling pathways. We have identified a novel gene, eyelid (eld), which is required for embryonic segmentation, development of the notum and wing margin, and photoreceptor differentiation. In these tissues, eld mutations have effects opposite to those caused by wingless (wg) mutations. eld encodes a widely expressed nuclear protein with a region homologous to a novel family of DNA-binding domains. Based on this homology and on the phenotypic analysis, we suggest that Eld could act as a transcription factor antagonistic to the Wg pathway. PMID:9271118

  2. Intelligent subsystem interface for modular hardware system

    NASA Technical Reports Server (NTRS)

    Krening, Douglas N. (Inventor); Lannan, Gregory B. (Inventor); Schneiderwind, Michael J. (Inventor); Schneiderwind, Robert A. (Inventor); Caffrey, Robert T. (Inventor)

    2000-01-01

    A single chip application specific integrated circuit (ASIC) which provides a flexible, modular interface between a subsystem and a standard system bus. The ASIC includes a microcontroller/microprocessor, a serial interface for connection to the bus, and a variety of communications interface devices available for coupling to the subsystem. A three-bus architecture, utilizing arbitration, provides connectivity within the ASIC and between the ASIC and the subsystem. The communication interface devices include UART (serial), parallel, analog, and external device interface utilizing bus connections paired with device select signals. A low power (sleep) mode is provided as is a processor disable option.

  3. Modular platform for low-light microscopy

    PubMed Central

    Kim, Tae Jin; Tuerkcan, Silvan; Ceballos, Andrew; Pratx, Guillem

    2015-01-01

    Cell imaging using low-light techniques such as bioluminescence, radioluminescence, and low-excitation fluorescence has received increased attention, particularly due to broad commercialization of highly sensitive detectors. However, the dim signals are still regarded as difficult to image using conventional microscopes, where the only low-light microscope in the market is primarily optimized for bioluminescence imaging. Here, we developed a novel modular microscope that is cost-effective and suitable for imaging different low-light luminescence modes. Results show that this microscope system features excellent aberration correction capabilities and enhanced image resolution, where bioluminescence, radioluminescence and epifluorescence images were captured and compared with the commercial bioluminescence microscope. PMID:26601020

  4. Real-time colorimetric detection of target DNA using isothermal target and signaling probe amplification and gold nanoparticle cross-linking assay.

    PubMed

    Jung, Cheulhee; Chung, Ji Won; Kim, Un Ok; Kim, Min Hwan; Park, Hyun Gyu

    2011-01-15

    We describe a facile gold nanoparticle (AuNP)-mediated colorimetric method for real-time detection of target DNA in conjugation with our unique isothermal target and signaling probe amplification (iTPA) method, comprising novel ICA (isothermal chain amplification) and CPT (cycling probe technology). Under isothermal conditions, the iTPA simultaneously amplifies the target and signaling probe through two displacement events induced by a combination of four specially designed primers, the strand displacement activity of DNA polymerase, and the RNA degrading activity of RNase H. The resulting target amplicons are hybridized with gold nanoparticle cross-linking assay (GCA) probes having a DNA-RNA-DNA chimeric form followed by RNA cleavage by RNase H in the CPT step. The intact GCA probes were designed to cross-link two sets of DNA-AuNPs conjugates in the absence of target DNA, inducing aggregation (blue color) of AuNPs. On the contrary, the presence of target DNA leads to cleavage of the GCA probes in proportion to the amount of amplified target DNA and the solution remains red in color without aggregation of AuNPs. Relying on this strategy, 10(2) copies of target Chlamydia trachomatis plasmid were successfully detected in a colorimetric manner. Importantly, all the procedures employed up to the final detection of the target DNA were performed under isothermal conditions without requiring any detection instruments. Therefore, this strategy would greatly benefit convenient, real-time monitoring technology of target DNA under restricted environments.

  5. Two-color, 30 second microwave-accelerated Metal-Enhanced Fluorescence DNA assays: a new Rapid Catch and Signal (RCS) technology.

    PubMed

    Dragan, Anatoliy I; Golberg, Karina; Elbaz, Amit; Marks, Robert; Zhang, Yongxia; Geddes, Chris D

    2011-03-07

    For analyses of DNA fragment sequences in solution we introduce a 2-color DNA assay, utilizing a combination of the Metal-Enhanced Fluorescence (MEF) effect and microwave-accelerated DNA hybridization. The assay is based on a new "Catch and Signal" technology, i.e. the simultaneous specific recognition of two target DNA sequences in one well by complementary anchor-ssDNAs, attached to silver island films (SiFs). It is shown that fluorescent labels (Alexa 488 and Alexa 594), covalently attached to ssDNA fragments, play the role of biosensor recognition probes, demonstrating strong response upon DNA hybridization, locating fluorophores in close proximity to silver NPs, which is ideal for MEF. Subsequently the emission dramatically increases, while the excited state lifetime decreases. It is also shown that 30s microwave irradiation of wells, containing DNA molecules, considerably (~1000-fold) speeds up the highly selective hybridization of DNA fragments at ambient temperature. The 2-color "Catch and Signal" DNA assay platform can radically expedite quantitative analysis of genome DNA sequences, creating a simple and fast bio-medical platform for nucleic acid analysis.

  6. A new way to detect the interaction of DNA and anticancer drugs based on the decreased resonance light scattering signal and its potential application.

    PubMed

    Chen, Zhanguang; Song, Tianhe; Peng, Yurui; Chen, Xi; Chen, Junhui; Zhang, Guomin; Qian, Sihua

    2011-10-07

    A novel assay has been developed to detect the interaction of DNA and anticancer drugs based on the decreased resonance light scattering (RLS) technique. The proposed method can be used to study those drugs which do not produce a RLS-signal after binding to DNA. RLS was used to monitor the interaction of five anticancer drugs with DNA. The reaction between anticancer drugs and DNA took place in BR buffer solution. From the RLS assay, the sequence of five anticancer drugs activities was as follows: CTX < MTX < Pt < MMC < 5-Fu. Mammary cancer cell DNA (mcDNA) was involved to validate the RLS assay. The results showed that the sensitivities of the five anticancer drugs targeting both mcDNA and ctDNA increased in the same order. However the sensitivity of each drug to mcDNA was higher than that to ctDNA It is a significant innovation of the RLS method to detect the interaction of DNA and anticancer drugs and to obtain drug sensitivity, which provides new strategies to screen DNA targeted anticancer drugs.

  7. STING Negatively Regulates Double-Stranded DNA-Activated JAK1-STAT1 Signaling via SHP-1/2 in B Cells.

    PubMed

    Dong, Guanjun; You, Ming; Ding, Liang; Fan, Hongye; Liu, Fei; Ren, Deshan; Hou, Yayi

    2015-05-01

    Recognition of cytosolic DNA initiates a series of innate immune responses by inducing IFN-I production and subsequent triggering JAK1-STAT1 signaling which plays critical roles in the pathogenesis of infection, inflammation and autoimmune diseases through promoting B cell activation and antibody responses. The stimulator of interferon genes protein (STING) has been demonstrated to be a critical hub of type I IFN induction in cytosolic DNA-sensing pathways. However, it still remains unknown whether cytosolic DNA can directly activate the JAK1-STAT1 signaling or not. And the role of STING is also unclear in this response. In the present study, we found that dsDNA directly triggered the JAK1-STAT1 signaling by inducing phosphorylation of the Lyn kinase. Moreover, this response is not dependent on type I IFN receptors. Interestingly, STING could inhibit dsDNA-triggered activation of JAK1-STAT1 signaling by inducing SHP-1 and SHP-2 phosphorylation. In addition, compared with normal B cells, the expression of STING was significantly lower and the phosphorylation level of JAK1 was significantly higher in B cells from MRL/lpr lupus-prone mice, highlighting the close association between STING low-expression and JAK1-STAT1 signaling activation in B cells in autoimmune diseases. Our data provide a molecular insight into the novel role of STING in dsDNA-mediated inflammatory disorders.

  8. DNA

    ERIC Educational Resources Information Center

    Stent, Gunther S.

    1970-01-01

    This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)

  9. The DNA damage response and immune signaling alliance: Is it good or bad? Nature decides when and where.

    PubMed

    Pateras, Ioannis S; Havaki, Sophia; Nikitopoulou, Xenia; Vougas, Konstantinos; Townsend, Paul A; Panayiotidis, Michalis I; Georgakilas, Alexandros G; Gorgoulis, Vassilis G

    2015-10-01

    The characteristic feature of healthy living organisms is the preservation of homeostasis. Compelling evidence highlight that the DNA damage response and repair (DDR/R) and immune response (ImmR) signaling networks work together favoring the harmonized function of (multi)cellular organisms. DNA and RNA viruses activate the DDR/R machinery in the host cells both directly and indirectly. Activation of DDR/R in turn favors the immunogenicity of the incipient cell. Hence, stimulation of DDR/R by exogenous or endogenous insults triggers innate and adaptive ImmR. The immunogenic properties of ionizing radiation, a prototypic DDR/R inducer, serve as suitable examples of how DDR/R stimulation alerts host immunity. Thus, critical cellular danger signals stimulate defense at the systemic level and vice versa. Disruption of DDR/R-ImmR cross talk compromises (multi)cellular integrity, leading to cell-cycle-related and immune defects. The emerging DDR/R-ImmR concept opens up a new avenue of therapeutic options, recalling the Hippocrates quote "everything in excess is opposed by nature."

  10. Association of the circadian factor Period 2 to p53 influences p53's function in DNA-damage signaling

    PubMed Central

    Gotoh, Tetsuya; Vila-Caballer, Marian; Liu, Jingjing; Schiffhauer, Samuel; Finkielstein, Carla V.

    2015-01-01

    Circadian period proteins influence cell division and death by associating with checkpoint components, although their mode of regulation has not been firmly established. hPer2 forms a trimeric complex with hp53 and its negative regulator Mdm2. In unstressed cells, this association leads to increased hp53 stability by blocking Mdm2-dependent ubiquitination and transcription of hp53 target genes. Because of the relevance of hp53 in checkpoint signaling, we hypothesize that hPer2 association with hp53 acts as a regulatory module that influences hp53's downstream response to genotoxic stress. Unlike the trimeric complex, whose distribution was confined to the nuclear compartment, hPer2/hp53 was identified in both cytosol and nucleus. At the transcriptional level, a reporter containing the hp21WAF1/CIP1 promoter, a target of hp53, remained inactive in cells expressing a stable form of the hPer2/hp53 complex even when treated with γ-radiation. Finally, we established that hPer2 directly acts on the hp53 node, as checkpoint components upstream of hp53 remained active in response to DNA damage. Quantitative transcriptional analyses of hp53 target genes demonstrated that unbound hp53 was absolutely required for activation of the DNA-damage response. Our results provide evidence of the mode by which the circadian tumor suppressor hPer2 modulates hp53 signaling in response to genotoxic stress. PMID:25411341

  11. Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution.

    PubMed

    Luo, Zhipu; Dauter, Miroslawa; Dauter, Zbigniew

    2014-07-01

    A large number of Z-DNA hexamer duplex structures and a few oligomers of different lengths are available, but here the first crystal structure of the d(CGCGCGCGCGCG)2 dodecameric duplex is presented. Two synchrotron data sets were collected; one was used to solve the structure by the single-wavelength anomalous dispersion (SAD) approach based on the anomalous signal of P atoms, the other set, extending to an ultrahigh resolution of 0.75 Å, served to refine the atomic model to an R factor of 12.2% and an R(free) of 13.4%. The structure consists of parallel duplexes arranged into practically infinitely long helices packed in a hexagonal fashion, analogous to all other known structures of Z-DNA oligomers. However, the dodecamer molecule shows a high level of flexibility, especially of the backbone phosphate groups, with six out of 11 phosphates modeled in double orientations corresponding to the two previously observed Z-DNA conformations: Z(I), with the phosphate groups inclined towards the inside of the helix, and Z(II), with the phosphate groups rotated towards the outside of the helix.

  12. Detection of single-nucleotide polymorphisms with novel leaky surface acoustic wave biosensors, DNA ligation and enzymatic signal amplification.

    PubMed

    Xu, Qinghua; Chang, Kai; Lu, Weiping; Chen, Wei; Ding, Yi; Jia, Shuangrong; Zhang, Kejun; Li, Fake; Shi, Jianfeng; Cao, Liang; Deng, Shaoli; Chen, Ming

    2012-03-15

    This manuscript describes a new technique for detecting single-nucleotide polymorphisms (SNPs) by integrating a leaky surface acoustic wave (LSAW) biosensor, enzymatic DNA ligation and enzymatic signal amplification. In this technique, the DNA target is hybridized with a capture probe immobilized on the surface of a LSAW biosensor. Then, the hybridized sequence is ligated to biotinylated allele-specific detection probe using Taq DNA ligase. The ligation does not take place if there is a single-nucleotide mismatch between the target and the capture probe. The ligated detection probe is transformed into a streptavidin-horseradish peroxidase (SA-HRP) terminal group via a biotin-streptavidin complex. Then, the SA-HRP group catalyzes the polymerization of 3,3-diaminobenzidine (DAB) to form a surface precipitate, thus effectively increasing the sensitivity of detecting surface mass changes and allowing detection of SNPs. Optimal detection conditions were found to be: 0.3 mol/L sodium ion concentration in PBS, pH 7.6, capture probe concentration 0.5 μmol/L and target sequence concentration 1.0 μmol/L. The detection limit was found to be 1 × 10(-12)mol/L. Using this technique, we were able to detect a single-point mutation at nucleotide A2293G in Japanese encephalitis virus.

  13. Homocysteine Triggers Inflammatory Responses in Macrophages through Inhibiting CSE-H2S Signaling via DNA Hypermethylation of CSE Promoter

    PubMed Central

    Li, Jiao-Jiao; Li, Qian; Du, Hua-Ping; Wang, Ya-Li; You, Shou-Jiang; Wang, Fen; Xu, Xing-Shun; Cheng, Jian; Cao, Yong-Jun; Liu, Chun-Feng; Hu, Li-Fang

    2015-01-01

    Hyperhomocysteinemia (HHcy) is an independent risk factor of atherosclerosis and other cardiovascular diseases. Unfortunately, Hcy-lowering strategies were found to have limited effects in reducing cardiovascular events. The underlying mechanisms remain unclear. Increasing evidence reveals a role of inflammation in the pathogenesis of HHcy. Homocysteine (Hcy) is a precursor of hydrogen sulfide (H2S), which is formed via the transsulfuration pathway catalyzed by cystathionine β-synthase and cystathionine γ-lyase (CSE) and serves as a novel modulator of inflammation. In the present study, we showed that methionine supplementation induced mild HHcy in mice, associated with the elevations of TNF-α and IL-1β in the plasma and reductions of plasma H2S level and CSE expression in the peritoneal macrophages. H2S-releasing compound GYY4137 attenuated the increases of TNF-α and IL-1β in the plasma of HHcy mice and Hcy-treated raw264.7 cells while CSE inhibitor PAG exacerbated it. Moreover, the in vitro study showed that Hcy inhibited CSE expression and H2S production in macrophages, accompanied by the increases of DNA methyltransferase (DNMT) expression and DNA hypermethylation in cse promoter region. DNMT inhibition or knockdown reversed the decrease of CSE transcription induced by Hcy in macrophages. In sum, our findings demonstrate that Hcy may trigger inflammation through inhibiting CSE-H2S signaling, associated with increased promoter DNA methylation and transcriptional repression of cse in macrophages. PMID:26047341

  14. Wavelet analysis of frequency chaos game signal: a time-frequency signature of the C. elegans DNA.

    PubMed

    Messaoudi, Imen; Oueslati, Afef Elloumi; Lachiri, Zied

    2014-12-01

    Challenging tasks are encountered in the field of bioinformatics. The choice of the genomic sequence's mapping technique is one the most fastidious tasks. It shows that a judicious choice would serve in examining periodic patterns distribution that concord with the underlying structure of genomes. Despite that, searching for a coding technique that can highlight all the information contained in the DNA has not yet attracted the attention it deserves. In this paper, we propose a new mapping technique based on the chaos game theory that we call the frequency chaos game signal (FCGS). The particularity of the FCGS coding resides in exploiting the statistical properties of the genomic sequence itself. This may reflect important structural and organizational features of DNA. To prove the usefulness of the FCGS approach in the detection of different local periodic patterns, we use the wavelet analysis because it provides access to information that can be obscured by other time-frequency methods such as the Fourier analysis. Thus, we apply the continuous wavelet transform (CWT) with the complex Morlet wavelet as a mother wavelet function. Scalograms that relate to the organism Caenorhabditis elegans (C. elegans) exhibit a multitude of periodic organization of specific DNA sequences.

  15. Processivity factor of KSHV contains a nuclear localization signal and binding domains for transporting viral DNA polymerase into the nucleus

    SciTech Connect

    Chen Yali; Ciustea, Mihai; Ricciardi, Robert P. . E-mail: ricciardi@biochem.dental.upenn.edu

    2005-09-30

    Kaposi's sarcoma-associated human herpesvirus (KSHV) encodes a processivity factor (PF-8, ORF59) that forms homodimers and binds to viral DNA polymerase (Pol-8, ORF9). PF-8 is essential for stabilizing Pol-8 on template DNA so that Pol-8 can incorporate nucleotides continuously. Here, the intracellular interaction of these two viral proteins was examined by confocal immunofluorescence microscopy. When individually expressed, PF-8 was observed exclusively in the nucleus, whereas Pol-8 was found only in the cytoplasm. However, when co-expressed, Pol-8 was co-translocated with PF-8 into the nucleus. Mutational analysis revealed that PF-8 contains a nuclear localization signal (NLS) as well as domains located at the N-terminus and the C-proximal regions that are required for Pol-8 binding. This study suggests that the mechanism that enables PF-8 to transport Pol-8 into the nucleus is the first critical step required for Pol-8 and PF-8 to function processively in KSHV DNA synthesis.

  16. Development of DNA Damage Response Signaling Biomarkers using Automated, Quantitative Image Analysis

    PubMed Central

    Nikolaishvilli-Feinberg, Nana; Cohen, Stephanie M.; Midkiff, Bentley; Zhou, Yingchun; Olorvida, Mark; Ibrahim, Joseph G.; Omolo, Bernard; Shields, Janiel M.; Thomas, Nancy E.; Groben, Pamela A.; Kaufmann, William K.

    2014-01-01

    The DNA damage response (DDR) coordinates DNA repair with cell cycle checkpoints to ameliorate or mitigate the pathological effects of DNA damage. Automated quantitative analysis (AQUA) and Tissue Studio are commercial technologies that use digitized immunofluorescence microscopy images to quantify antigen expression in defined tissue compartments. Because DDR is commonly activated in cancer and may reflect genetic instability within the lesion, a method to quantify DDR in cancer offers potential diagnostic and/or prognostic value. In this study, both AQUA and Tissue Studio algorithms were used to quantify the DDR in radiation-damaged skin fibroblasts, melanoma cell lines, moles, and primary and metastatic melanomas. Digital image analysis results for three markers of DDR (γH2AX, P-ATM, P-Chk2) correlated with immunoblot data for irradiated fibroblasts, whereas only γH2AX and P-Chk2 correlated with immunoblot data in melanoma cell lines. Melanoma cell lines displayed substantial variation in γH2AX and P-Chk2 expression, and P-Chk2 expression was significantly correlated with radioresistance. Moles, primary melanomas, and melanoma metastases in brain, lung and liver displayed substantial variation in γH2AX expression, similar to that observed in melanoma cell lines. Automated digital analysis of immunofluorescent images stained for DDR biomarkers may be useful for predicting tumor response to radiation and chemotherapy. PMID:24309508

  17. Regulation of DNA damage following termination of Hedgehog (HH) survival signaling at the level of the GLI genes in human colon cancer.

    PubMed

    Agyeman, Akwasi; Mazumdar, Tapati; Houghton, Janet A

    2012-08-01

    Transcriptional regulation of the Hedgehog (HH) signaling response is mediated by GLI genes (GLI1, GLI2) downstream of SMO, that are also activated by oncogenic signaling pathways. We have demonstrated the importance of targeting GLI downstream of SMO in the induction of cell death in human colon carcinoma cells. In HT29 cells inhibition of GLI1/GLI2 by the small molecule inhibitor GANT61 induced DNA double strand breaks (DSBs) and activation of ATM, MDC1 and NBS1; γH2AX and MDC1, NBS1 and MDC1 co-localized in nuclear foci. Early activation of ATM was decreased by 24 hr, when p-NBS1(Ser343), activated by ATM, was significantly reduced in cell extracts. Bound γH2AX was detected in isolated chromatin fractions or nuclei during DNA damage but not during DNA repair. MDC1 was tightly bound to chromatin at 32 hr as cells accumulated in early S-phase prior to becoming subG1, and during DNA repair. Limited binding of NBS1 was detected at all times during DNA damage but was strongly bound during DNA repair. Transient overexpression of NBS1 protected HT29 cells from GANT61-induced cell death, while knockdown of H2AX by H2AXshRNA delayed DNA damage signaling. Data demonstrate following GLI1/GLI2 inhibition: 1) induction of DNA damage in cells that are also resistant to SMO inhibitors, 2) dynamic interactions between γH2AX, MDC1 and NBS1 in single cell nuclei and in isolated chromatin fractions, 3) expression and chromatin binding properties of key mediator proteins that mark DNA damage or DNA repair, and 4) the importance of NBS1 in the DNA damage response mechanism.

  18. ExpressYourself: a modular platform for processing and visualizing microarray data

    PubMed Central

    Luscombe, Nicholas M.; Royce, Thomas E.; Bertone, Paul; Echols, Nathaniel; Horak, Christine E.; Chang, Joseph T.; Snyder, Michael; Gerstein, Mark

    2003-01-01

    DNA microarrays are widely used in biological research; by analyzing differential hybridization on a single microarray slide, one can detect changes in mRNA expression levels, increases in DNA copy numbers and the location of transcription factor binding sites on a genomic scale. Having performed the experiments, the major challenge is to process large, noisy datasets in order to identify the specific array elements that are significantly differentially hybridized. This normally requires aggregating different, often incompatible programs into a multi-step pipeline. Here we present ExpressYourself, a fully integrated platform for processing microarray data. In completely automated fashion, it will correct the background array signal, normalize the Cy5 and Cy3 signals, score levels of differential hybridization, combine the results of replicate experiments, filter problematic regions of the array and assess the quality of individual and replicate experiments. ExpressYourself is designed with a highly modular architecture so various types of microarray analysis algorithms can readily be incorporated as they are developed; for example, the system currently implements several normalization methods, including those that simultaneously consider signal intensity and slide location. The processed data are presented using a web-based graphical interface to facilitate comparison with the original images of the array slides. In particular, Express Yourself is able to regenerate images of the original microarray after applying various steps of processing, which greatly facilities identification of position-specific artifacts. The program is freely available for use at http://bioinfo.mbb.yale.edu/expressyourself. PMID:12824348

  19. Expansion Mechanisms and Evolutionary History on Genes Encoding DNA Glycosylases and Their Involvement in Stress and Hormone Signaling

    PubMed Central

    Jiang, Shu-Ye; Ramachandran, Srinivasan

    2016-01-01

    DNA glycosylases catalyze the release of methylated bases. They play vital roles in the base excision repair pathway and might also function in DNA demethylation. At least three families of DNA glycosylases have been identified, which included 3′-methyladenine DNA glycosylase (MDG) I, MDG II, and HhH-GPD (Helix–hairpin–Helix and Glycine/Proline/aspartate (D)). However, little is known on their genome-wide identification, expansion, and evolutionary history as well as their expression profiling and biological functions. In this study, we have genome-widely identified and evolutionarily characterized these family members. Generally, a genome encodes only one MDG II gene in most of organisms. No MDG I or MDG II gene was detected in green algae. However, HhH-GPD genes were detectable in all available organisms. The ancestor species contain small size of MDG I and HhH-GPD families. These two families were mainly expanded through the whole-genome duplication and segmental duplication. They were evolutionarily conserved and were generally under purifying selection. However, we have detected recent positive selection among the Oryza genus, which might play roles in species divergence. Further investigation showed that expression divergence played important roles in gene survival after expansion. All of these family genes were expressed in most of developmental stages and tissues in rice plants. High ratios of family genes were downregulated by drought and fungus pathogen as well as abscisic acid (ABA) and jasmonic acid (JA) treatments, suggesting a negative regulation in response to drought stress and pathogen infection through ABA- and/or JA-dependent hormone signaling pathway. PMID:27026054

  20. Expansion Mechanisms and Evolutionary History on Genes Encoding DNA Glycosylases and Their Involvement in Stress and Hormone Signaling.

    PubMed

    Jiang, Shu-Ye; Ramachandran, Srinivasan

    2016-04-25

    DNA glycosylases catalyze the release of methylated bases. They play vital roles in the base excision repair pathway and might also function in DNA demethylation. At least three families of DNA glycosylases have been identified, which included 3'-methyladenine DNA glycosylase (MDG) I, MDG II, and HhH-GPD (Helix-hairpin-Helix and Glycine/Proline/aspartate (D)). However, little is known on their genome-wide identification, expansion, and evolutionary history as well as their expression profiling and biological functions. In this study, we have genome-widely identified and evolutionarily characterized these family members. Generally, a genome encodes only one MDG II gene in most of organisms. No MDG I or MDG II gene was detected in green algae. However, HhH-GPD genes were detectable in all available organisms. The ancestor species contain small size of MDG I and HhH-GPD families. These two families were mainly expanded through the whole-genome duplication and segmental duplication. They were evolutionarily conserved and were generally under purifying selection. However, we have detected recent positive selection among the Oryza genus, which might play roles in species divergence. Further investigation showed that expression divergence played important roles in gene survival after expansion. All of these family genes were expressed in most of developmental stages and tissues in rice plants. High ratios of family genes were downregulated by drought and fungus pathogen as well as abscisic acid (ABA) and jasmonic acid (JA) treatments, suggesting a negative regulation in response to drought stress and pathogen infection through ABA- and/or JA-dependent hormone signaling pathway.

  1. Spacecraft Modularity for Serviceable Satellites

    NASA Technical Reports Server (NTRS)

    Rossetti, Dino; Keer, Beth; Panek, John; Reed, Benjamin; Cepollina, Frank; Ritter, Robert

    2015-01-01

    Satellite servicing has been a proven capability of NASA since the first servicing missions in the 1980s with astronauts on the space shuttle. This capability enabled the on-orbit assembly of the International Space Station (ISS) and saved the Hubble Space Telescope (HST) mission following the discovery of the flawed primary mirror. The effectiveness and scope of servicing opportunities, especially using robotic servicers, is a function of how cooperative a spacecraft is. In this paper, modularity will be presented as a critical design aspect for a spacecraft that is cooperative from a servicing perspective. Different features of modularity are discussed using examples from HST and the Multimission Modular Spacecraft (MMS) program from the 1980s and 1990s. The benefits of modularity will be presented including those directly related to servicing and those outside of servicing including reduced costs and increased flexibility. The new Reconfigurable Operational spacecraft for Science and Exploration (ROSE) concept is introduced as an affordable implementation of modularity that provides cost savings and flexibility. Key aspects of the ROSE architecture are discussed such as the module design and the distributed avionics architecture. The ROSE concept builds on the experience from MMS and due to its modularity, would be highly suitable as a future client for on-orbit servicing.

  2. Modular Isotopic Thermoelectric Generator

    SciTech Connect

    Schock, Alfred

    1981-04-03

    Advanced RTG concepts utilizing improved thermoelectric materials and converter concepts are under study at Fairchild for DOE. The design described here is based on DOE's newly developed radioisotope heat source, and on an improved silicon-germanium material and a multicouple converter module under development at Syncal. Fairchild's assignment was to combine the above into an attractive power system for use in space, and to assess the specific power and other attributes of that design. The resultant design is highly modular, consisting of standard RTG slices, each producing ~24 watts at the desired output voltage of 28 volt. Thus, the design could be adapted to various space missions over a wide range of power levels, with little or no redesign. Each RTG slice consists of a 250-watt heat source module, eight multicouple thermoelectric modules, and standard sections of insulator, housing, radiator fins, and electrical circuit. The design makes it possible to check each thermoelectric module for electrical performance, thermal contact, leaktightness, and performance stability, after the generator is fully assembled; and to replace any deficient modules without disassembling the generator or perturbing the others. The RTG end sections provide the spring-loaded supports required to hold the free-standing heat source stack together during launch vibration. Details analysis indicates that the design offers a substantial improvement in specific power over the present generator of RTGs, using the same heat source modules. There are three copies in the file.

  3. Modular Approach to Spintronics.

    PubMed

    Camsari, Kerem Yunus; Ganguly, Samiran; Datta, Supriyo

    2015-06-11

    There has been enormous progress in the last two decades, effectively combining spintronics and magnetics into a powerful force that is shaping the field of memory devices. New materials and phenomena continue to be discovered at an impressive rate, providing an ever-increasing set of building blocks that could be exploited in designing transistor-like functional devices of the future. The objective of this paper is to provide a quantitative foundation for this building block approach, so that new discoveries can be integrated into functional device concepts, quickly analyzed and critically evaluated. Through careful benchmarking against available theory and experiment we establish a set of elemental modules representing diverse materials and phenomena. These elemental modules can be integrated seamlessly to model composite devices involving both spintronic and nanomagnetic phenomena. We envision the library of modules to evolve both by incorporating new modules and by improving existing modules as the field progresses. The primary contribution of this paper is to establish the ground rules or protocols for a modular approach that can build a lasting bridge between materials scientists and circuit designers in the field of spintronics and nanomagnetics.

  4. The Modular Adaptive Ribosome

    PubMed Central

    Yadav, Anupama; Radhakrishnan, Aparna; Panda, Anshuman; Singh, Amartya; Sinha, Himanshu; Bhanot, Gyan

    2016-01-01

    The ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner. We show through large data analyses that although many ribosomal proteins are essential with consistent effect on growth in different conditions in yeast and similar expression across cell and tissue types in mice and humans, some ribosomal proteins are used in an environment specific manner. The latter set of variable ribosomal proteins further function in a coordinated manner forming modules, which are adapted to different environmental cues in different organisms. We show that these environment specific modules of ribosomal proteins in yeast have differential genetic interactions with other pathways and their 5’UTRs show differential signatures of selection in yeast strains, presumably to facilitate adaptation. Similarly, we show that in higher metazoans such as mice and humans, different modules of ribosomal proteins are expressed in different cell types and tissues. A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans. Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments. PMID:27812193

  5. The Modular Adaptive Ribosome.

    PubMed

    Yadav, Anupama; Radhakrishnan, Aparna; Panda, Anshuman; Singh, Amartya; Sinha, Himanshu; Bhanot, Gyan

    2016-01-01

    The ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner. We show through large data analyses that although many ribosomal proteins are essential with consistent effect on growth in different conditions in yeast and similar expression across cell and tissue types in mice and humans, some ribosomal proteins are used in an environment specific manner. The latter set of variable ribosomal proteins further function in a coordinated manner forming modules, which are adapted to different environmental cues in different organisms. We show that these environment specific modules of ribosomal proteins in yeast have differential genetic interactions with other pathways and their 5'UTRs show differential signatures of selection in yeast strains, presumably to facilitate adaptation. Similarly, we show that in higher metazoans such as mice and humans, different modules of ribosomal proteins are expressed in different cell types and tissues. A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans. Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments.

  6. Modular Approach to Spintronics

    PubMed Central

    Camsari, Kerem Yunus; Ganguly, Samiran; Datta, Supriyo

    2015-01-01

    There has been enormous progress in the last two decades, effectively combining spintronics and magnetics into a powerful force that is shaping the field of memory devices. New materials and phenomena continue to be discovered at an impressive rate, providing an ever-increasing set of building blocks that could be exploited in designing transistor-like functional devices of the future. The objective of this paper is to provide a quantitative foundation for this building block approach, so that new discoveries can be integrated into functional device concepts, quickly analyzed and critically evaluated. Through careful benchmarking against available theory and experiment we establish a set of elemental modules representing diverse materials and phenomena. These elemental modules can be integrated seamlessly to model composite devices involving both spintronic and nanomagnetic phenomena. We envision the library of modules to evolve both by incorporating new modules and by improving existing modules as the field progresses. The primary contribution of this paper is to establish the ground rules or protocols for a modular approach that can build a lasting bridge between materials scientists and circuit designers in the field of spintronics and nanomagnetics. PMID:26066079

  7. Polychlorinated biphenyl quinone induces oxidative DNA damage and repair responses: The activations of NHEJ, BER and NER via ATM-p53 signaling axis

    SciTech Connect

    Dong, Hui; Shi, Qiong; Song, Xiufang; Fu, Juanli; Hu, Lihua; Xu, Demei; Su, Chuanyang; Xia, Xiaomin; Song, Erqun; Song, Yang

    2015-07-01

    Our previous studies demonstrated that polychlorinated biphenyl (PCB) quinone induced oxidative DNA damage in HepG2 cells. To promote genomic integrity, DNA damage response (DDR) coordinates cell-cycle transitions, DNA repair and apoptosis. PCB quinone-induced cell cycle arrest and apoptosis have been documented, however, whether PCB quinone insult induce DNA repair signaling is still unknown. In this study, we identified the activation of DDR and corresponding signaling events in HepG2 cells upon the exposure to a synthetic PCB quinone, PCB29-pQ. Our data illustrated that PCB29-pQ induces the phosphorylation of p53, which was mediated by ataxia telangiectasia mutated (ATM) protein kinase. The observed phosphorylated histone H2AX (γ-H2AX) foci and the elevation of 8-hydroxy-2′-deoxyguanosine (8-OHdG) indicated that DDR was stimulated by PCB29-pQ treatment. Additionally, we found PCB29-pQ activates non-homologous end joining (NHEJ), base excision repair (BER) and nucleotide excision repair (NER) signalings. However, these repair pathways are not error-free processes and aberrant repair of DNA damage may cause the potential risk of carcinogenesis and mutagenesis. - Highlights: • Polychlorinated biphenyl quinone induces oxidative DNA damage in HepG2 cells. • The elevation of γ-H2AX and 8-OHdG indicates the activation of DNA damage response. • ATM-p53 signaling acts as the DNA damage sensor and effector. • Polychlorinated biphenyl quinone activates NHEJ, BER and NER signalings.

  8. A label-free signal amplification assay for DNA detection based on exonuclease III and nucleic acid dye SYBR Green I.

    PubMed

    Zheng, Aihua; Luo, Ming; Xiang, Dongshan; Xiang, Xia; Ji, Xinghu; He, Zhike

    2013-09-30

    We have developed a new fluorescence method for specific single-stranded DNA sequences with exonuclease III (Exo III) and nucleic acid dye SYBR Green I. It is demonstrated by a reverse transcription oligonucleotide sequence (target DNA, 27 bases) of RNA fragment of human immunodeficiency virus (HIV) as a model system. In the absence of the target DNA, the hairpin-probe is in the stem-closed structure, the fluorescence of SYBR Green I is very strong. In the presence of the target DNA, the hairpin-probe hybridizes with the target DNA to form double-stranded structure with a blunt 3'-terminus. Thus, in the presence of Exo III, only the 3'-terminus of probe is subjected to digestion. Exo III catalyzes the stepwise removal of mononucleotides from this terminus, releasing the target DNA. The released target DNA then hybridizes with another probe, whence the cycle starts anew. The signal of SYBR Green I decreases greatly. This system provides a detection limit of 160 pM, which is comparable to the existing signal amplification methods that utilized Exo III as a signal amplification nuclease. Due to the unique property of Exo III, this method shows excellent detection selectivity for single-base discrimination. More importantly, superiors to other methods based on Exo III, these probes have the advantages of easier to design, synthesize, purify and thus are much cheaper and more applicable. This new approach could be widely applied to sensitive and selective nucleic acids detection.

  9. Robust modular product family design

    NASA Astrophysics Data System (ADS)

    Jiang, Lan; Allada, Venkat

    2001-10-01

    This paper presents a modified Taguchi methodology to improve the robustness of modular product families against changes in customer requirements. The general research questions posed in this paper are: (1) How to effectively design a product family (PF) that is robust enough to accommodate future customer requirements. (2) How far into the future should designers look to design a robust product family? An example of a simplified vacuum product family is used to illustrate our methodology. In the example, customer requirements are selected as signal factors; future changes of customer requirements are selected as noise factors; an index called quality characteristic (QC) is set to evaluate the product vacuum family; and the module instance matrix (M) is selected as control factor. Initially a relation between the objective function (QC) and the control factor (M) is established, and then the feasible M space is systemically explored using a simplex method to determine the optimum M and the corresponding QC values. Next, various noise levels at different time points are introduced into the system. For each noise level, the optimal values of M and QC are computed and plotted on a QC-chart. The tunable time period of the control factor (the module matrix, M) is computed using the QC-chart. The tunable time period represents the maximum time for which a given control factor can be used to satisfy current and future customer needs. Finally, a robustness index is used to break up the tunable time period into suitable time periods that designers should consider while designing product families.

  10. Diabetes-Induced Oxidative DNA Damage Alters p53-p21CIP1/Waf1 Signaling in the Rat Testis

    PubMed Central

    Al-Bader, Maie M.

    2015-01-01

    Diabetes is increasingly becoming a major cause of large-scale morbidity and mortality. Diabetes-induced oxidative stress alters numerous intracellular signaling pathways. Although testicular dysfunction is a major concern in diabetic men, the mechanistic alterations in the testes that lead to hypogonadism are not yet clear. Oxidative mitochondrial DNA damage, as indicated by 7,8-dihydro-8-oxo-2′-deoxyguanosine, and phosphorylation of p53 at ser315 residue (p-p53ser315) increased in a stage- and cell-specific manner in the testes of rats that were diabetic for 1 month (DM1). Prolongation of diabetes for 3 months (DM3) led to an increase in nuclear oxidative DNA damage in conjunction with a decrease in the expression of p-p53ser315. The nuclei of pachytene and preleptotene spermatocytes, steps 1, 11, and 12 spermatids, secondary spermatocytes and the Sertoli cells, and the meiotic figures showed an increase in the expression of p-p53ser315. An increase in the expression of a downstream target of p53 and protein 21cyclin-dependent kinase interacting protein 1/wild-type p53-activated factor 1 (p21CIP1/Waf1) in both diabetic groups did not show any time-dependent effects but occurred concurrent with an upregulation of p-p53ser315 in DM1 and a downregulation of the protein in DM3. In diabetic groups, the expression of p21CIP1/Waf1 was mainly cytoplasmic but also perinuclear in pachytene spermatocytes and round spermatids. The cytoplasmic localization of p21CIP1/Waf1 may be suggestive of an antiapoptotic role for the protein. The perinuclear localization is probably related to the cell cycle arrest meant for DNA damage repair. Diabetes upregulates p21CIP1/Waf1 signaling in testicular germ cells in association with alteration in p-p53ser315 expression, probably to counteract DNA damage-induced cell death. PMID:24828139

  11. The mtDNA NARP mutation activates the actin-Nrf2 signaling of antioxidant defenses

    SciTech Connect

    Dassa, Emmanuel Philippe; Paupe, Vincent; Goncalves, Sergio; Rustin, Pierre

    2008-04-11

    An efficient handling of superoxides by antioxidant defenses is a crucial issue for cells with respiratory chain deficient mitochondria. We used human cultured skin fibroblasts to delineate the mechanism controlling the expression of antioxidant defenses in the case of a severe ATPase deficiency resulting from an 8993T>G mutation in the mitochondrial ATPase6 gene. We observed the nuclear translocation of the transcription factor Nrf2 associated with thinning of the actin stress fibers. The mobilization of the Nrf2 signaling pathway could be mimicked by a chemical blockade of the ATPase with a specific inhibitor, oligomycin. Interestingly enough, Nrf2 nuclear translocation was not observed in the case of a severe cytochrome oxidase deficiency, indicating that studying the status of this signaling pathway could throw some light on the importance of the oxidative insult associated with different respiratory chain defects.

  12. Parts & pools: a framework for modular design of synthetic gene circuits.

    PubMed

    Marchisio, Mario Andrea

    2014-01-01

    Published in 2008, Parts & Pools represents one of the first attempts to conceptualize the modular design of bacterial synthetic gene circuits with Standard Biological Parts (DNA segments) and Pools of molecules referred to as common signal carriers (e.g., RNA polymerases and ribosomes). The original framework for modeling bacterial components and designing prokaryotic circuits evolved over the last years and brought, first, to the development of an algorithm for the automatic design of Boolean gene circuits. This is a remarkable achievement since gene digital circuits have a broad range of applications that goes from biosensors for health and environment care to computational devices. More recently, Parts & Pools was enabled to give a proper formal description of eukaryotic biological circuit components. This was possible by employing a rule-based modeling approach, a technique that permits a faithful calculation of all the species and reactions involved in complex systems such as eukaryotic cells and compartments. In this way, Parts & Pools is currently suitable for the visual and modular design of synthetic gene circuits in yeast and mammalian cells too.

  13. Inter-module credit assignment in modular reinforcement learning.

    PubMed

    Samejima, Kazuyuki; Doya, Kenji; Kawato, Mitsuo

    2003-09-01

    Critical issues in modular or hierarchical reinforcement learning (RL) are (i) how to decompose a task into sub-tasks, (ii) how to achieve independence of learning of sub-tasks, and (iii) how to assure optimality of the composite policy for the entire task. The second and last requirements are often under trade-off. We propose a method for propagating the reward for the entire task achievement between modules. This is done in the form of a 'modular reward', which is calculated from the temporal difference of the module gating signal and the value of the succeeding module. We implement modular reward for a multiple model-based reinforcement learning (MMRL) architecture and show its effectiveness in simulations of a pursuit task with hidden states and a continuous-time non-linear control task.

  14. Probing plant-pathogen interactions and downstream defense signaling using DNA microarrays.

    PubMed

    Wan, Jinrong; Dunning, F Mark; Bent, Andrew F

    2002-11-01

    The interaction between a plant and a pathogen activates a wide variety of defense responses. The recent development of microarray-based expression profiling methods, together with the availability of genomic and/or EST (expressed sequence tag) sequence data for some plant species, has allowed significant progress in the characterization of plant pathogenesis-related responses. The small number of expression profiling studies completed to date have already identified an amazing number of genes that had not previously been implicated in plant defense. Some of these genes can be associated with defense signal transduction or antimicrobial action, but the functional contribution of many others remains uncertain. Initial expression profiling work has also revealed similarities and distinctions between different defense signaling pathways, and cross-talk (both overlap and interference) between pathogenesis-related responses and plant responses to other stresses. Potential transcriptional cis-regulatory elements upstream of co-regulated genes can also be identified. Whole-genome arrays are only now becoming available, and many interactions remain to be studied (e.g. different pathogen species, plant genotypes, mutants, time-points after infection). Expression profiling technologies, in combination with other genomic tools, will have a substantial impact on our understanding of plant-pathogen interactions and defense signaling pathways.

  15. Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling

    PubMed Central

    Nelson, Glyn; Hall, Philip; Miwa, Satomi; Kirkwood, Thomas B. L.; Shanley, Daryl P.

    2015-01-01

    Unrepaired or inaccurately repaired DNA damage can lead to a range of cell fates, such as apoptosis, cellular senescence or cancer, depending on the efficiency and accuracy of DNA damage repair and on the downstream DNA damage signalling. DNA damage repair and signalling have been studied and modelled in detail separately, but it is not yet clear how they integrate with one another to control cell fate. In this study, we have created an integrated stochastic model of DNA damage repair by non-homologous end joining and of gamma irradiation-induced cellular senescence in human cells that are not apoptosis-prone. The integrated model successfully explains the changes that occur in the dynamics of DNA damage repair after irradiation. Simulations of p53/p21 dynamics after irradiation agree well with previously published experimental studies, further validating the model. Additionally, the model predicts, and we offer some experimental support, that low-dose fractionated irradiation of cells leads to temporal patterns in p53/p21 that lead to significant cellular senescence. The integrated model is valuable for studying the processes of DNA damage induced cell fate and predicting the effectiveness of DNA damage related medical interventions at the cellular level. PMID:26020242

  16. Electrochemiluminescence Biosensor Based on 3-D DNA Nanomachine Signal Probe Powered by Protein-Aptamer Binding Complex for Ultrasensitive Mucin 1 Detection.

    PubMed

    Jiang, Xinya; Wang, Haijun; Wang, Huijun; Zhuo, Ying; Yuan, Ruo; Chai, Yaqin

    2017-04-04

    Herein, we fabricated a novel electrochemiluminescence (ECL) biosensor for ultrasensitive detection of mucin 1 (MUC1) based on a three-dimensional (3-D) DNA nanomachine signal probe powered by protein-aptamer binding complex. The assembly of 3-D DNA nanomachine signal probe achieved the cyclic reuse of target protein based on the protein-aptamer binding complex induced catalyzed hairpin assembly (CHA), which overcame the shortcoming of protein conversion with enzyme cleavage or polymerization in the traditional examination of protein. In addition, CoFe2O4, a mimic peroxidase, was used as the nanocarrier of the 3-D DNA nanomachine signal probe to catalyze the decomposition of coreactant H2O2 to generate numerous reactive hydroxyl radical OH(•) as the efficient accelerator of N-(aminobutyl)-N-(ethylisoluminol) (ABEI) ECL reaction to amplify the luminescence signal. Simultaneously, the assembly of 3-D DNA nanomachine signal probe was executed in solution, which led to abundant luminophore ABEI be immobilized around the CoFe2O4 surface with amplified ECL signal output since the CHA reaction was occurred unencumberedly in all directions under homogeneous environment. The prepared ECL biosensor showed a favorable linear response for MUC1 detection with a relatively low detection limit of 0.62 fg mL(-1). With excellent sensitivity, the strategy may provide an efficient method for clinical application, especially in trace protein determination.

  17. Homogeneous electrochemical immunoassay of aflatoxin B1 in foodstuff using proximity-hybridization-induced omega-like DNA junctions and exonuclease III-triggered isothermal cycling signal amplification.

    PubMed

    Tang, Juan; Huang, Yapei; Liu, Huiqiong; Zhang, Cengceng; Tang, Dianping

    2016-12-01

    A new homogeneous electrochemical immunosensing platform was designed for sensitive detection of aflatoxin B1 (AFB1) in foodstuff. The system consisted of anti-AFB1 antibody labeled DNA1 (Ab-DNA1), AFB1-bovine serum albumin (BSA)-conjugated DNA2 (AFB1-DNA2), and methylene blue functionalized hairpin DNA. Owing to a specific antigen-antibody reaction between anti-AFB1 and AFB1-BSA, the immunocomplex formed assisted the proximity hybridization of DNA1 with DNA2, thus resulting in the formation of an omega-like DNA junction. Thereafter, the junction opened the hairpin DNA to construct a new double-stranded DNA, which could be readily cleaved by exonuclease III to release the omega-like DNA junction and methylene blue. The dissociated DNA junction could repeatedly hybridize with residual hairpin DNA molecules with exonuclease III-based isothermal cycling amplification, thereby releasing numerous free methylene blue molecules into the detection solution. The as-produced free methylene blue molecules could be captured by a negatively charged indium tin oxide electrode, each of which could produce an electronic signal within the applied potentials. On introduction of target AFB1, the analyte competed with AFB1-DNA2 for the conjugated anti-AFB1 on the Ab-DNA1, subsequently decreasing the amount of omega-like DNA junctions formed, hence causing methylene blue labeled hairpin DNA to move far away from the electrode surface. Under optimal conditions the detectable electrochemical signal decreased with increasing amount of target AFB1 in a dynamic working range of 0.01-30 ng mL(-1) with a detection limit of 4.8 pg mL(-1). In addition, the precision and reproducibility of this system were acceptable. Finally, the method was further evaluated for analysis of naturally contaminated or AFB1-spiked peanut samples, giving results that matched well with those obtained with a commercial AFB1 ELISA kit.

  18. Modular Stirling Radioisotope Generator

    NASA Technical Reports Server (NTRS)

    Schmitz, Paul C.; Mason, Lee S.; Schifer, Nicholas A.

    2016-01-01

    High-efficiency radioisotope power generators will play an important role in future NASA space exploration missions. Stirling Radioisotope Generators (SRGs) have been identified as a candidate generator technology capable of providing mission designers with an efficient, high-specific-power electrical generator. SRGs high conversion efficiency has the potential to extend the limited Pu-238 supply when compared with current Radioisotope Thermoelectric Generators (RTGs). Due to budgetary constraints, the Advanced Stirling Radioisotope Generator (ASRG) was canceled in the fall of 2013. Over the past year a joint study by NASA and the Department of Energy (DOE) called the Nuclear Power Assessment Study (NPAS) recommended that Stirling technologies continue to be explored. During the mission studies of the NPAS, spare SRGs were sometimes required to meet mission power system reliability requirements. This led to an additional mass penalty and increased isotope consumption levied on certain SRG-based missions. In an attempt to remove the spare power system, a new generator architecture is considered, which could increase the reliability of a Stirling generator and provide a more fault-tolerant power system. This new generator called the Modular Stirling Radioisotope Generator (MSRG) employs multiple parallel Stirling convertor/controller strings, all of which share the heat from the General Purpose Heat Source (GPHS) modules. For this design, generators utilizing one to eight GPHS modules were analyzed, which provided about 50 to 450 W of direct current (DC) to the spacecraft, respectively. Four Stirling convertors are arranged around each GPHS module resulting in from 4 to 32 Stirling/controller strings. The convertors are balanced either individually or in pairs, and are radiatively coupled to the GPHS modules. Heat is rejected through the housing/radiator, which is similar in construction to the ASRG. Mass and power analysis for these systems indicate that specific

  19. Modular Stirling Radioisotope Generator

    NASA Technical Reports Server (NTRS)

    Schmitz, Paul C.; Mason, Lee S.; Schifer, Nicholas A.

    2015-01-01

    High efficiency radioisotope power generators will play an important role in future NASA space exploration missions. Stirling Radioisotope Generators (SRG) have been identified as a candidate generator technology capable of providing mission designers with an efficient, high specific power electrical generator. SRGs high conversion efficiency has the potential to extend the limited Pu-238 supply when compared with current Radioisotope Thermoelectric Generators (RTG). Due to budgetary constraints, the Advanced Stirling Radioisotope Generator (ASRG) was canceled in the fall of 2013. Over the past year a joint study by NASA and DOE called the Nuclear Power Assessment Study (NPAS) recommended that Stirling technologies continue to be explored. During the mission studies of the NPAS, spare SRGs were sometimes required to meet mission power system reliability requirements. This led to an additional mass penalty and increased isotope consumption levied on certain SRG-based missions. In an attempt to remove the spare power system, a new generator architecture is considered which could increase the reliability of a Stirling generator and provide a more fault-tolerant power system. This new generator called the Modular Stirling Radioisotope Generator (MSRG) employs multiple parallel Stirling convertor/controller strings, all of which share the heat from the General Purpose Heat Source (GPHS) modules. For this design, generators utilizing one to eight GPHS modules were analyzed, which provide about 50 to 450 watts DC to the spacecraft, respectively. Four Stirling convertors are arranged around each GPHS module resulting in from 4 to 32 Stirling/controller strings. The convertors are balanced either individually or in pairs, and are radiatively coupled to the GPHS modules. Heat is rejected through the housing/radiator which is similar in construction to the ASRG. Mass and power analysis for these systems indicate that specific power may be slightly lower than the ASRG and

  20. A Signal, from Human mtDNA, of Postglacial Recolonization in Europe

    PubMed Central

    Torroni, Antonio; Bandelt, Hans-Jürgen; Macaulay, Vincent; Richards, Martin; Cruciani, Fulvio; Rengo, Chiara; Martinez-Cabrera, Vicente; Villems, Richard; Kivisild, Toomas; Metspalu, Ene; Parik, Jüri; Tolk, Helle-Viivi; Tambets, Kristiina; Forster, Peter; Karger, Bernd; Francalacci, Paolo; Rudan, Pavao; Janicijevic, Branka; Rickards, Olga; Savontaus, Marja-Liisa; Huoponen, Kirsi; Laitinen, Virpi; Koivumäki, Satu; Sykes, Bryan; Hickey, Eileen; Novelletto, Andrea; Moral, Pedro; Sellitto, Daniele; Coppa, Alfredo; Al-Zaheri, Nadia; Santachiara-Benerecetti, A. Silvana; Semino, Ornella; Scozzari, Rosaria

    2001-01-01

    Mitochondrial HVS-I sequences from 10,365 subjects belonging to 56 populations/geographical regions of western Eurasia and northern Africa were first surveyed for the presence of the T→C transition at nucleotide position 16298, a mutation which has previously been shown to characterize haplogroup V mtDNAs. All mtDNAs with this mutation were then screened for a number of diagnostic RFLP sites, revealing two major subsets of mtDNAs. One is haplogroup V proper, and the other has been termed “pre*V,” since it predates V phylogenetically. The rather uncommon pre*V tends to be scattered throughout Europe (and northwestern Africa), whereas V attains two peaks of frequency: one situated in southwestern Europe and one in the Saami of northern Scandinavia. Geographical distributions and ages support the scenario that pre*V originated in Europe before the Last Glacial Maximum (LGM), whereas the more recently derived haplogroup V arose in a southwestern European refugium soon after the LGM. The arrival of V in eastern/central Europe, however, occurred much later, possibly with (post-)Neolithic contacts. The distribution of haplogroup V mtDNAs in modern European populations would thus, at least in part, reflect the pattern of postglacial human recolonization from that refugium, affecting even the Saami. Overall, the present study shows that the dissection of mtDNA variation into small and well-defined evolutionary units is an essential step in the identification of spatial frequency patterns. Mass screening of a few markers identified using complete mtDNA sequences promises to be an efficient strategy for inferring features of human prehistory. PMID:11517423

  1. A signal, from human mtDNA, of postglacial recolonization in Europe.

    PubMed

    Torroni, A; Bandelt, H J; Macaulay, V; Richards, M; Cruciani, F; Rengo, C; Martinez-Cabrera, V; Villems, R; Kivisild, T; Metspalu, E; Parik, J; Tolk, H V; Tambets, K; Forster, P; Karger, B; Francalacci, P; Rudan, P; Janicijevic, B; Rickards, O; Savontaus, M L; Huoponen, K; Laitinen, V; Koivumäki, S; Sykes, B; Hickey, E; Novelletto, A; Moral, P; Sellitto, D; Coppa, A; Al-Zaheri, N; Santachiara-Benerecetti, A S; Semino, O; Scozzari, R

    2001-10-01

    Mitochondrial HVS-I sequences from 10,365 subjects belonging to 56 populations/geographical regions of western Eurasia and northern Africa were first surveyed for the presence of the T-->C transition at nucleotide position 16298, a mutation which has previously been shown to characterize haplogroup V mtDNAs. All mtDNAs with this mutation were then screened for a number of diagnostic RFLP sites, revealing two major subsets of mtDNAs. One is haplogroup V proper, and the other has been termed "pre*V," since it predates V phylogenetically. The rather uncommon pre*V tends to be scattered throughout Europe (and northwestern Africa), whereas V attains two peaks of frequency: one situated in southwestern Europe and one in the Saami of northern Scandinavia. Geographical distributions and ages support the scenario that pre*V originated in Europe before the Last Glacial Maximum (LGM), whereas the more recently derived haplogroup V arose in a southwestern European refugium soon after the LGM. The arrival of V in eastern/central Europe, however, occurred much later, possibly with (post-)Neolithic contacts. The distribution of haplogroup V mtDNAs in modern European populations would thus, at least in part, reflect the pattern of postglacial human recolonization from that refugium, affecting even the Saami. Overall, the present study shows that the dissection of mtDNA variation into small and well-defined evolutionary units is an essential step in the identification of spatial frequency patterns. Mass screening of a few markers identified using complete mtDNA sequences promises to be an efficient strategy for inferring features of human prehistory.

  2. Molecular Buffers Permit Sensitivity Tuning and Inversion of Riboswitch Signals.

    PubMed

    Rugbjerg, Peter; Genee, Hans Jasper; Jensen, Kristian; Sarup-Lytzen, Kira; Sommer, Morten Otto Alexander

    2016-07-15

    Predictable integration of foreign biological signals and parts remains a key challenge in the systematic engineering of synthetic cellular actuations, and general methods to improve signal transduction and sensitivity are needed. To address this problem we modeled and built a molecular signal buffer network in Saccharomyces cerevisiae inspired by chemical pH buffer systems. The molecular buffer system context-insulates a riboswitch enabling synthetic control of colony formation and modular signal manipulations. The riboswitch signal is relayed to a transcriptional activation domain of a split transcription factor, while interacting DNA-binding domains mediate the transduction of signal and form an interacting molecular buffer. The molecular buffer system enables modular signal inversion through integration with repressor modules. Further, tuning of input sensitivity was achieved through perturbation of the buffer pair ratio guided by a mathematical model. Such buffered signal tuning networks will be useful for domestication of RNA-based sensors enabling tunable outputs and library-wide selections for drug discovery and metabolic engineering.

  3. Large-scale genomic analyses link reproductive ageing to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair

    PubMed Central

    Lunetta, Kathryn L.; Pervjakova, Natalia; Chasman, Daniel I.; Stolk, Lisette; Finucane, Hilary K.; Sulem, Patrick; Bulik-Sullivan, Brendan; Esko, Tõnu; Johnson, Andrew D.; Elks, Cathy E.; Franceschini, Nora; He, Chunyan; Altmaier, Elisabeth; Brody, Jennifer A.; Franke, Lude L.; Huffman, Jennifer E.; Keller, Margaux F.; McArdle, Patrick F.; Nutile, Teresa; Porcu, Eleonora; Robino, Antonietta; Rose, Lynda M.; Schick, Ursula M.; Smith, Jennifer A.; Teumer, Alexander; Traglia, Michela; Vuckovic, Dragana; Yao, Jie; Zhao, Wei; Albrecht, Eva; Amin, Najaf; Corre, Tanguy; Hottenga, Jouke-Jan; Mangino, Massimo; Smith, Albert V.; Tanaka, Toshiko; Abecasis, Goncalo; Andrulis, Irene L.; Anton-Culver, Hoda; Antoniou, Antonis C.; Arndt, Volker; Arnold, Alice M.; Barbieri, Caterina; Beckmann, Matthias W.; Beeghly-Fadiel, Alicia; Benitez, Javier; Bernstein, Leslie; Bielinski, Suzette J.; Blomqvist, Carl; Boerwinkle, Eric; Bogdanova, Natalia V.; Bojesen, Stig E.; Bolla, Manjeet K.; Borresen-Dale, Anne-Lise; Boutin, Thibaud S; Brauch, Hiltrud; Brenner, Hermann; Brüning, Thomas; Burwinkel, Barbara; Campbell, Archie; Campbell, Harry; Chanock, Stephen J.; Chapman, J. Ross; Chen, Yii-Der Ida; Chenevix-Trench, Georgia; Couch, Fergus J.; Coviello, Andrea D.; Cox, Angela; Czene, Kamila; Darabi, Hatef; De Vivo, Immaculata; Demerath, Ellen W.; Dennis, Joe; Devilee, Peter; Dörk, Thilo; dos-Santos-Silva, Isabel; Dunning, Alison M.; Eicher, John D.; Fasching, Peter A.; Faul, Jessica D.; Figueroa, Jonine; Flesch-Janys, Dieter; Gandin, Ilaria; Garcia, Melissa E.; García-Closas, Montserrat; Giles, Graham G.; Girotto, Giorgia G.; Goldberg, Mark S.; González-Neira, Anna; Goodarzi, Mark O.; Grove, Megan L.; Gudbjartsson, Daniel F.; Guénel, Pascal; Guo, Xiuqing; Haiman, Christopher A.; Hall, Per; Hamann, Ute; Henderson, Brian E.; Hocking, Lynne J.; Hofman, Albert; Homuth, Georg; Hooning, Maartje J.; Hopper, John L.; Hu, Frank B.; Huang, Jinyan; Humphreys, Keith; Hunter, David J.; Jakubowska, Anna; Jones, Samuel E.; Kabisch, Maria; Karasik, David; Knight, Julia A.; Kolcic, Ivana; Kooperberg, Charles; Kosma, Veli-Matti; Kriebel, Jennifer; Kristensen, Vessela; Lambrechts, Diether; Langenberg, Claudia; Li, Jingmei; Li, Xin; Lindström, Sara; Liu, Yongmei; Luan, Jian’an; Lubinski, Jan; Mägi, Reedik; Mannermaa, Arto; Manz, Judith; Margolin, Sara; Marten, Jonathan; Martin, Nicholas G.; Masciullo, Corrado; Meindl, Alfons; Michailidou, Kyriaki; Mihailov, Evelin; Milani, Lili; Milne, Roger L.; Müller-Nurasyid, Martina; Nalls, Michael; Neale, Ben M.; Nevanlinna, Heli; Neven, Patrick; Newman, Anne B.; Nordestgaard, Børge G.; Olson, Janet E.; Padmanabhan, Sandosh; Peterlongo, Paolo; Peters, Ulrike; Petersmann, Astrid; Peto, Julian; Pharoah, Paul D.P.; Pirastu, Nicola N.; Pirie, Ailith; Pistis, Giorgio; Polasek, Ozren; Porteous, David; Psaty, Bruce M.; Pylkäs, Katri; Radice, Paolo; Raffel, Leslie J.; Rivadeneira, Fernando; Rudan, Igor; Rudolph, Anja; Ruggiero, Daniela; Sala, Cinzia F.; Sanna, Serena; Sawyer, Elinor J.; Schlessinger, David; Schmidt, Marjanka K.; Schmidt, Frank; Schmutzler, Rita K.; Schoemaker, Minouk J.; Scott, Robert A.; Seynaeve, Caroline M.; Simard, Jacques; Sorice, Rossella; Southey, Melissa C.; Stöckl, Doris; Strauch, Konstantin; Swerdlow, Anthony; Taylor, Kent D.; Thorsteinsdottir, Unnur; Toland, Amanda E.; Tomlinson, Ian; Truong, Thérèse; Tryggvadottir, Laufey; Turner, Stephen T.; Vozzi, Diego; Wang, Qin; Wellons, Melissa; Willemsen, Gonneke; Wilson, James F.; Winqvist, Robert; Wolffenbuttel, Bruce B.H.R.; Wright, Alan F.; Yannoukakos, Drakoulis; Zemunik, Tatijana; Zheng, Wei; Zygmunt, Marek; Bergmann, Sven; Boomsma, Dorret I.; Buring, Julie E.; Ferrucci, Luigi; Montgomery, Grant W.; Gudnason, Vilmundur; Spector, Tim D.; van Duijn, Cornelia M; Alizadeh, Behrooz Z.; Ciullo, Marina; Crisponi, Laura; Easton, Douglas F.; Gasparini, Paolo P.; Gieger, Christian; Harris, Tamara B.; Hayward, Caroline; Kardia, Sharon L.R.; Kraft, Peter; McKnight, Barbara; Metspalu, Andres; Morrison, Alanna C.; Reiner, Alex P.; Ridker, Paul M.; Rotter, Jerome I.; Toniolo, Daniela; Uitterlinden, André G.; Ulivi, Sheila; Völzke, Henry; Wareham, Nicholas J.; Weir, David R.; Yerges-Armstrong, Laura M.; Price, Alkes L.; Stefansson, Kari; Visser, Jenny A.; Ong, Ken K.; Chang-Claude, Jenny; Murabito, Joanne M.; Perry, John R.B.; Murray, Anna

    2015-01-01

    Menopause timing has a substantial impact on infertility and risk of disease, including breast cancer, but the underlying mechanisms are poorly understood. We report a dual strategy in ~70,000 women to identify common and low-frequency protein-coding variation associated with age at natural menopause (ANM). We identified 44 regions with common variants, including two harbouring additional rare missense alleles of large effect. We found enrichment of signals in/near genes involved in delayed puberty, highlighting the first molecular links between the onset and end of reproductive lifespan. Pathway analyses revealed a major association with DNA damage-response (DDR) genes, including the first common coding variant in BRCA1 associated with any complex trait. Mendelian randomisation analyses supported a causal effect of later ANM on breast cancer risk (~6% risk increase per-year, P=3×10−14), likely mediated by prolonged sex hormone exposure, rather than DDR mechanisms. PMID:26414677

  4. Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair.

    PubMed

    Day, Felix R; Ruth, Katherine S; Thompson, Deborah J; Lunetta, Kathryn L; Pervjakova, Natalia; Chasman, Daniel I; Stolk, Lisette; Finucane, Hilary K; Sulem, Patrick; Bulik-Sullivan, Brendan; Esko, Tõnu; Johnson, Andrew D; Elks, Cathy E; Franceschini, Nora; He, Chunyan; Altmaier, Elisabeth; Brody, Jennifer A; Franke, Lude L; Huffman, Jennifer E; Keller, Margaux F; McArdle, Patrick F; Nutile, Teresa; Porcu, Eleonora; Robino, Antonietta; Rose, Lynda M; Schick, Ursula M; Smith, Jennifer A; Teumer, Alexander; Traglia, Michela; Vuckovic, Dragana; Yao, Jie; Zhao, Wei; Albrecht, Eva; Amin, Najaf; Corre, Tanguy; Hottenga, Jouke-Jan; Mangino, Massimo; Smith, Albert V; Tanaka, Toshiko; Abecasis, Gonçalo R; Andrulis, Irene L; Anton-Culver, Hoda; Antoniou, Antonis C; Arndt, Volker; Arnold, Alice M; Barbieri, Caterina; Beckmann, Matthias W; Beeghly-Fadiel, Alicia; Benitez, Javier; Bernstein, Leslie; Bielinski, Suzette J; Blomqvist, Carl; Boerwinkle, Eric; Bogdanova, Natalia V; Bojesen, Stig E; Bolla, Manjeet K; Borresen-Dale, Anne-Lise; Boutin, Thibaud S; Brauch, Hiltrud; Brenner, Hermann; Brüning, Thomas; Burwinkel, Barbara; Campbell, Archie; Campbell, Harry; Chanock, Stephen J; Chapman, J Ross; Chen, Yii-Der Ida; Chenevix-Trench, Georgia; Couch, Fergus J; Coviello, Andrea D; Cox, Angela; Czene, Kamila; Darabi, Hatef; De Vivo, Immaculata; Demerath, Ellen W; Dennis, Joe; Devilee, Peter; Dörk, Thilo; Dos-Santos-Silva, Isabel; Dunning, Alison M; Eicher, John D; Fasching, Peter A; Faul, Jessica D; Figueroa, Jonine; Flesch-Janys, Dieter; Gandin, Ilaria; Garcia, Melissa E; García-Closas, Montserrat; Giles, Graham G; Girotto, Giorgia G; Goldberg, Mark S; González-Neira, Anna; Goodarzi, Mark O; Grove, Megan L; Gudbjartsson, Daniel F; Guénel, Pascal; Guo, Xiuqing; Haiman, Christopher A; Hall, Per; Hamann, Ute; Henderson, Brian E; Hocking, Lynne J; Hofman, Albert; Homuth, Georg; Hooning, Maartje J; Hopper, John L; Hu, Frank B; Huang, Jinyan; Humphreys, Keith; Hunter, David J; Jakubowska, Anna; Jones, Samuel E; Kabisch, Maria; Karasik, David; Knight, Julia A; Kolcic, Ivana; Kooperberg, Charles; Kosma, Veli-Matti; Kriebel, Jennifer; Kristensen, Vessela; Lambrechts, Diether; Langenberg, Claudia; Li, Jingmei; Li, Xin; Lindström, Sara; Liu, Yongmei; Luan, Jian'an; Lubinski, Jan; Mägi, Reedik; Mannermaa, Arto; Manz, Judith; Margolin, Sara; Marten, Jonathan; Martin, Nicholas G; Masciullo, Corrado; Meindl, Alfons; Michailidou, Kyriaki; Mihailov, Evelin; Milani, Lili; Milne, Roger L; Müller-Nurasyid, Martina; Nalls, Michael; Neale, Benjamin M; Nevanlinna, Heli; Neven, Patrick; Newman, Anne B; Nordestgaard, Børge G; Olson, Janet E; Padmanabhan, Sandosh; Peterlongo, Paolo; Peters, Ulrike; Petersmann, Astrid; Peto, Julian; Pharoah, Paul D P; Pirastu, Nicola N; Pirie, Ailith; Pistis, Giorgio; Polasek, Ozren; Porteous, David; Psaty, Bruce M; Pylkäs, Katri; Radice, Paolo; Raffel, Leslie J; Rivadeneira, Fernando; Rudan, Igor; Rudolph, Anja; Ruggiero, Daniela; Sala, Cinzia F; Sanna, Serena; Sawyer, Elinor J; Schlessinger, David; Schmidt, Marjanka K; Schmidt, Frank; Schmutzler, Rita K; Schoemaker, Minouk J; Scott, Robert A; Seynaeve, Caroline M; Simard, Jacques; Sorice, Rossella; Southey, Melissa C; Stöckl, Doris; Strauch, Konstantin; Swerdlow, Anthony; Taylor, Kent D; Thorsteinsdottir, Unnur; Toland, Amanda E; Tomlinson, Ian; Truong, Thérèse; Tryggvadottir, Laufey; Turner, Stephen T; Vozzi, Diego; Wang, Qin; Wellons, Melissa; Willemsen, Gonneke; Wilson, James F; Winqvist, Robert; Wolffenbuttel, Bruce B H R; Wright, Alan F; Yannoukakos, Drakoulis; Zemunik, Tatijana; Zheng, Wei; Zygmunt, Marek; Bergmann, Sven; Boomsma, Dorret I; Buring, Julie E; Ferrucci, Luigi; Montgomery, Grant W; Gudnason, Vilmundur; Spector, Tim D; van Duijn, Cornelia M; Alizadeh, Behrooz Z; Ciullo, Marina; Crisponi, Laura; Easton, Douglas F; Gasparini, Paolo P; Gieger, Christian; Harris, Tamara B; Hayward, Caroline; Kardia, Sharon L R; Kraft, Peter; McKnight, Barbara; Metspalu, Andres; Morrison, Alanna C; Reiner, Alex P; Ridker, Paul M; Rotter, Jerome I; Toniolo, Daniela; Uitterlinden, André G; Ulivi, Sheila; Völzke, Henry; Wareham, Nicholas J; Weir, David R; Yerges-Armstrong, Laura M; Price, Alkes L; Stefansson, Kari; Visser, Jenny A; Ong, Ken K; Chang-Claude, Jenny; Murabito, Joanne M; Perry, John R B; Murray, Anna

    2015-11-01

    Menopause timing has a substantial impact on infertility and risk of disease, including breast cancer, but the underlying mechanisms are poorly understood. We report a dual strategy in ∼70,000 women to identify common and low-frequency protein-coding variation associated with age at natural menopause (ANM). We identified 44 regions with common variants, including two regions harboring additional rare missense alleles of large effect. We found enrichment of signals in or near genes involved in delayed puberty, highlighting the first molecular links between the onset and end of reproductive lifespan. Pathway analyses identified major association with DNA damage response (DDR) genes, including the first common coding variant in BRCA1 associated with any complex trait. Mendelian randomization analyses supported a causal effect of later ANM on breast cancer risk (∼6% increase in risk per year; P = 3 × 10(-14)), likely mediated by prolonged sex hormone exposure rather than DDR mechanisms.

  5. Improving signal-to-noise performance for DNA translocation in solid-state nanopores at MHz bandwidths

    NASA Astrophysics Data System (ADS)

    Machielse, Bartholomeus; Balan, Adrian; Niedzwiecki, David; Lin, Jianxun; Ong, Peijie; Engelke, Rebecca; Shepard, Kenneth; Drndic, Marija

    2015-03-01

    DNA sequencing using solid-state nanopores is impeded by the relatively high noise and low bandwidth of the current state-of-the-art translocation measurements. We measure the ion current noise through Si3N4 nanopores at bandwidths up to 1 MHz. At these bandwidths, the input-referred current noise is dominated by the amplifier's voltage noise acting across the total capacitance at the amplifier input. By reducing the nanopore membrane capacitance we are able to transition to a regime in which current noise is dominated by the effects of the capacitance of the amplifier itself. Advances in bandwidth and signal-to-noise ratio necessary for DNA sequencing will require lower capacitance devices as well as new amplifier designs with reduced input capacitance and noise characteristics. This work was supported by NIH Grants R21HG004767 and R01HG006879. We gratefully acknowledge use of the TEM in the NSF-MRSEC electron microscopy facility. We thank Andrew Sharo, Matthew Puster, Dr. Kimberly Venta, and Prof. Jacob Rosenstein.

  6. ENHANCING NETWORK SECURITY USING 'LEARNING-FROM-SIGNALS' AND FRACTIONAL FOURIER TRANSFORM BASED RF-DNA FINGERPRINTS

    SciTech Connect

    Buckner, Mark A; Bobrek, Miljko; Farquhar, Ethan; Harmer, Paul K; Temple, Michael A

    2011-01-01

    Wireless Access Points (WAP) remain one of the top 10 network security threats. This research is part of an effort to develop a physical (PHY) layer aware Radio Frequency (RF) air monitoring system with multi-factor authentication to provide a first-line of defense for network security--stopping attackers before they can gain access to critical infrastructure networks through vulnerable WAPs. This paper presents early results on the identification of OFDM-based 802.11a WiFi devices using RF Distinct Native Attribute (RF-DNA) fingerprints produced by the Fractional Fourier Transform (FRFT). These fingerprints are input to a "Learning from Signals" (LFS) classifier which uses hybrid Differential Evolution/Conjugate Gradient (DECG) optimization to determine the optimal features for a low-rank model to be used for future predictions. Results are presented for devices under the most challenging conditions of intra-manufacturer classification, i.e., same-manufacturer, same-model, differing only in serial number. The results of Fractional Fourier Domain (FRFD) RF-DNA fingerprints demonstrate significant improvement over results based on Time Domain (TD), Spectral Domain (SD) and even Wavelet Domain (WD) fingerprints.

  7. Modular Power Standard for Space Explorations Missions

    NASA Technical Reports Server (NTRS)

    Oeftering, Richard C.; Gardner, Brent G.

    2016-01-01

    Future human space exploration will most likely be composed of assemblies of multiple modular spacecraft elements with interconnected electrical power systems. An electrical system composed of a standardized set modular building blocks provides significant development, integration, and operational cost advantages. The modular approach can also provide the flexibility to configure power systems to meet the mission needs. A primary goal of the Advanced Exploration Systems (AES) Modular Power System (AMPS) project is to establish a Modular Power Standard that is needed to realize these benefits. This paper is intended to give the space exploration community a "first look" at the evolving Modular Power Standard and invite their comments and technical contributions.

  8. Eigenvalue Spectra of Modular Networks

    NASA Astrophysics Data System (ADS)

    Peixoto, Tiago P.

    2013-08-01

    A large variety of dynamical processes that take place on networks can be expressed in terms of the spectral properties of some linear operator which reflects how the dynamical rules depend on the network topology. Often, such spectral features are theoretically obtained by considering only local node properties, such as degree distributions. Many networks, however, possess large-scale modular structures that can drastically influence their spectral characteristics and which are neglected in such simplified descriptions. Here, we obtain in a unified fashion the spectrum of a large family of operators, including the adjacency, Laplacian, and normalized Laplacian matrices, for networks with generic modular structure, in the limit of large degrees. We focus on the conditions necessary for the merging of the isolated eigenvalues with the continuous band of the spectrum, after which the planted modular structure can no longer be easily detected by spectral methods. This is a crucial transition point which determines when a modular structure is strong enough to affect a given dynamical process. We show that this transition happens in general at different points for the different matrices, and hence the detectability threshold can vary significantly, depending on the operator chosen. Equivalently, the sensitivity to the modular structure of the different dynamical processes associated with each matrix will be different, given the same large-scale structure present in the network. Furthermore, we show that, with the exception of the Laplacian matrix, the different transitions coalesce into the same point for the special case where the modules are homogeneous but separate otherwise.

  9. A novel role for the DNA repair gene Rad51 in Netrin-1 signalling

    PubMed Central

    Glendining, K. A.; Markie, D.; Gardner, R. J. M.; Franz, E. A.; Robertson, S. P.; Jasoni, C. L.

    2017-01-01

    Mutations in RAD51 have recently been linked to human Congenital Mirror Movements (CMM), a developmental disorder of the motor system. The only gene previously linked to CMM encodes the Netrin-1 receptor DCC, which is important for formation of corticospinal and callosal axon tracts. Thus, we hypothesised that Rad51 has a novel role in Netrin-1-mediated axon development. In mouse primary motor cortex neurons, Rad51 protein was redistributed distally down the axon in response to Netrin-1, further suggesting a functional link between the two. We next manipulated Rad51 expression, and assessed Netrin-1 responsiveness. Rad51 siRNA knockdown exaggerated Netrin-1-mediated neurite branching and filopodia formation. RAD51 overexpression inhibited these responses, whereas overexpression of the CMM-linked R250Q mutation, a predicted loss-of-function, had no effect. Thus, Rad51 appears to negatively regulate Netrin-1 signalling. Finally, we examined whether Rad51 might operate by modulating the expression of the Unc5 family, known negative regulators of Netrin-1-responsiveness. Unc5b and Unc5c transcripts were downregulated in response to Rad51 knockdown, and upregulated with RAD51 overexpression, but not R250Q. Thus, Rad51 negatively regulates Netrin-1 signalling, at least in part, by modulating the expression of Unc5s. Imbalance of positive and negative influences is likely to lead to aberrant motor system development resulting in CMMs. PMID:28057929

  10. DNA synthesis during endomitosis is stimulated by insulin via the PI3K/Akt and TOR signaling pathways in the silk gland cells of Bombyx mori.

    PubMed

    Li, Yaofeng; Chen, Xiangyun; Tang, Xiaofang; Zhang, Chundong; Wang, La; Chen, Peng; Pan, Minhui; Lu, Cheng

    2015-03-18

    Silk gland cells undergo multiple endomitotic cell cycles during silkworm larval ontogeny. Our previous study demonstrated that feeding is required for continued endomitosis in the silk gland cells of silkworm larvae. Furthermore, the insulin signaling pathway is closely related to nutritional signals. To investigate whether the insulin signaling pathway is involved in endomitosis in silk gland cells, in this study, we initially analyzed the effects of bovine insulin on DNA synthesis in endomitotic silk gland cells using 5-bromo-2'-deoxyuridine (BrdU) labeling technology, and found that bovine insulin can stimulate DNA synthesis. Insulin signal transduction is mainly mediated via phosphoinositide 3-kinase (PI3K)/Akt, the target of rapamycin (TOR) and the extracellular signal-regulated kinase (ERK) pathways in vertebrates. We ascertained that these three pathways are involved in DNA synthesis in endomitotic silk gland cells using specific inhibitors against each pathway. Moreover, we investigated whether these three pathways are involved in insulin-stimulated DNA synthesis in endomitotic silk gland cells, and found that the PI3K/Akt and TOR pathways, but not the ERK pathway, are involved in this process. These results provide an important theoretical foundation for the further investigations of the mechanism underlying efficient endomitosis in silk gland cells.

  11. Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

    PubMed Central

    Leaché, Adam D.; Chavez, Andreas S.; Jones, Leonard N.; Grummer, Jared A.; Gottscho, Andrew D.; Linkem, Charles W.

    2015-01-01

    Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both “recent” and “deep” timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking. We compared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a species-rich and diverse group containing nine genera that began diversifying approximately 55 Ma. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice or evolved once and was subsequently lost in Callisaurus. PMID:25663487

  12. DNA-only cascade: a universal tool for signal amplification, enhancing the detection of target analytes.

    PubMed

    Bone, Simon M; Hasick, Nicole J; Lima, Nicole E; Erskine, Simon M; Mokany, Elisa; Todd, Alison V

    2014-09-16

    Diagnostic tests performed in the field or at the site of patient care would benefit from using a combination of inexpensive, stable chemical reagents and simple instrumentation. Here, we have developed a universal "DNA-only Cascade" (DoC) to quantitatively detect target analytes with increased speed. The DoC utilizes quasi-circular structures consisting of temporarily inactivated deoxyribozymes (DNAzymes). The catalytic activity of the DNAzymes is restored in a universal manner in response to a broad range of environmental and biological targets. The present study demonstrates DNAzyme activation in the presence of metal ions (Pb(2+)), small molecules (deoxyadenosine triphosphate) and nucleic acids homologous to genes from Meningitis-causing bacteria. Furthermore, DoC efficiently discriminates nucleic acid targets differing by a single nucleotide. When detection of analytes is orchestrated by functional nucleic acids, the inclusion of DoC reagents substantially decreases time for detection and allows analyte quantification. The detection of nucleic acids using DoC was further characterized for its capability to be multiplexed and retain its functionality following long-term exposure to ambient temperatures and in a background of complex medium (human serum).

  13. Product modular design incorporating preventive maintenance issues

    NASA Astrophysics Data System (ADS)

    Gao, Yicong; Feng, Yixiong; Tan, Jianrong

    2016-03-01

    Traditional modular design methods lead to product maintenance problems, because the module form of a system is created according to either the function requirements or the manufacturing considerations. For solving these problems, a new modular design method is proposed with the considerations of not only the traditional function related attributes, but also the maintenance related ones. First, modularity parameters and modularity scenarios for product modularity are defined. Then the reliability and economic assessment models of product modularity strategies are formulated with the introduction of the effective working age of modules. A mathematical model used to evaluate the difference among the modules of the product so that the optimal module of the product can be established. After that, a multi-objective optimization problem based on metrics for preventive maintenance interval different degrees and preventive maintenance economics is formulated for modular optimization. Multi-objective GA is utilized to rapidly approximate the Pareto set of optimal modularity strategy trade-offs between preventive maintenance cost and preventive maintenance interval difference degree. Finally, a coordinate CNC boring machine is adopted to depict the process of product modularity. In addition, two factorial design experiments based on the modularity parameters are constructed and analyzed. These experiments investigate the impacts of these parameters on the optimal modularity strategies and the structure of module. The research proposes a new modular design method, which may help to improve the maintainability of product in modular design.

  14. Modular Control of Treadmill vs Overground Running

    PubMed Central

    Farina, Dario; Kersting, Uwe Gustav

    2016-01-01

    Motorized treadmills have been widely used in locomotion studies, although a debate remains concerning the extrapolation of results obtained from treadmill experiments to overground locomotion. Slight differences between treadmill (TRD) and overground running (OVG) kinematics and muscle activity have previously been reported. However, little is known about differences in the modular control of muscle activation in these two conditions. Therefore, we aimed at investigating differences between motor modules extracted from TRD and OVG by factorization of multi-muscle electromyographic (EMG) signals. Twelve healthy men ran on a treadmill and overground at their preferred speed while we recorded tibial acceleration and surface EMG from 11 ipsilateral lower limb muscles. We extracted motor modules representing relative weightings of synergistic muscle activations by non-negative matrix factorization from 20 consecutive gait cycles. Four motor modules were sufficient to accurately reconstruct the EMG signals in both TRD and OVG (average reconstruction quality = 92±3%). Furthermore, a good reconstruction quality (80±7%) was obtained also when muscle weightings of one condition (either OVG or TRD) were used to reconstruct the EMG data from the other condition. The peak amplitudes of activation signals showed a similar timing (pattern) across conditions. The magnitude of peak activation for the module related to initial contact was significantly greater for OVG, whereas peak activation for modules related to leg swing and preparation to landing were greater for TRD. We conclude that TRD and OVG share similar muscle weightings throughout motion. In addition, modular control for TRD and OVG is achieved with minimal temporal adjustments, which were dependent on the phase of the running cycle. PMID:27064978

  15. Inherent controllability in modular ALMRs

    SciTech Connect

    Sackett, J.I.; Sevy, R.H.; Wei, T.Y.C.

    1989-01-01

    As part of recent development efforts on advanced reactor designs ANL has proposed the IFR (Integral Fast Reactor) concept. The IFR concept is currently being applied to modular sized reactors which would be built in multiple power paks together with an integrated fuel cycle facility. It has been amply demonstrated that the concept as applied to the modular designs has significant advantages in regard to ATWS transients. Attention is now being focussed on determining whether or not those advantages deriving from the traits of the IFR can be translated to the operational/DBA (design basis accident) class of transients. 5 refs., 3 figs., 3 tabs.

  16. Modular multivariable control improves hydrocracking

    SciTech Connect

    Chia, T.L.; Lefkowitz, I.; Tamas, P.D.

    1996-10-01

    Modular multivariable control (MMC), a system of interconnected, single process variable controllers, can be a user-friendly, reliable and cost-effective alternative to centralized, large-scale multivariable control packages. MMC properties and features derive directly from the properties of the coordinated controller which, in turn, is based on internal model control technology. MMC was applied to a hydrocracking unit involving two process variables and three controller outputs. The paper describes modular multivariable control, MMC properties, tuning considerations, application at the DCS level, constraints handling, and process application and results.

  17. Modular multichannel surface plasmon spectrometer

    NASA Astrophysics Data System (ADS)

    Neuert, G.; Kufer, S.; Benoit, M.; Gaub, H. E.

    2005-05-01

    We have developed a modular multichannel surface plasmon resonance (SPR) spectrometer on the basis of a commercially available hybrid sensor chip. Due to its modularity this inexpensive and easy to use setup can readily be adapted to different experimental environments. High temperature stability is achieved through efficient thermal coupling of individual SPR units. With standard systems the performance of the multichannel instrument was evaluated. The absorption kinetics of a cysteamine monolayer, as well as the concentration dependence of the specific receptor-ligand interaction between biotin and streptavidin was measured.

  18. Modular Firewalls for Storage Areas

    NASA Technical Reports Server (NTRS)

    Fedor, O. H.; Owens, L. J.

    1986-01-01

    Giant honeycomb structures assembled in modular units. Flammable materials stored in cells. Walls insulated with firebrick to prevent spread of fire among cells. Portable, modular barrier withstands heat of combustion for limited time and confines combustion products horizontally to prevent fire from spreading. Barrier absorbs heat energy by ablation and not meant to be reused. Designed to keep fires from spreading among segments of solid rocket propellant in storage, barrier erected between storage units of other flammable or explosive materials; tanks of petroleum or liquid natural gas. Barrier adequate for most industrial purposes.

  19. Modular assembly of thick multifunctional cardiac patches

    PubMed Central

    Fleischer, Sharon; Shapira, Assaf; Feiner, Ron; Dvir, Tal

    2017-01-01

    In cardiac tissue engineering cells are seeded within porous biomaterial scaffolds to create functional cardiac patches. Here, we report on a bottom-up approach to assemble a modular tissue consisting of multiple layers with distinct structures and functions. Albumin electrospun fiber scaffolds were laser-patterned to create microgrooves for engineering aligned cardiac tissues exhibiting anisotropic electrical signal propagation. Microchannels were patterned within the scaffolds and seeded with endothelial cells to form closed lumens. Moreover, cage-like structures were patterned within the scaffolds and accommodated poly(lactic-co-glycolic acid) (PLGA) microparticulate systems that controlled the release of VEGF, which promotes vascularization, or dexamethasone, an anti-inflammatory agent. The structure, morphology, and function of each layer were characterized, and the tissue layers were grown separately in their optimal conditions. Before transplantation the tissue and microparticulate layers were integrated by an ECM-based biological glue to form thick 3D cardiac patches. Finally, the patches were transplanted in rats, and their vascularization was assessed. Because of the simple modularity of this approach, we believe that it could be used in the future to assemble other multicellular, thick, 3D, functional tissues. PMID:28167795

  20. A sandwich-hybridization assay for simultaneous determination of HIV and tuberculosis DNA targets based on signal amplification by quantum dots-PowerVision™ polymer coding nanotracers.

    PubMed

    Yan, Zhongdan; Gan, Ning; Zhang, Huairong; Wang, De; Qiao, Li; Cao, Yuting; Li, Tianhua; Hu, Futao

    2015-09-15

    A novel sandwich-hybridization assay for simultaneous electrochemical detection of multiple DNA targets related to human immune deficiency virus (HIV) and tuberculosis (TB) was developed based on the different quantum dots-PowerVision(TM) polymer nanotracers. The polymer nanotracers were respectively fabricated by immobilizing SH-labeled oligonucleotides (s-HIV or s-TB), which can partially hybrid with virus DNA (HIV or TB), on gold nanoparticles (Au NPs) and then modified with PowerVision(TM) (PV) polymer-encapsulated quantum dots (CdS or PbS) as signal tags. PV is a dendrimer enzyme linked polymer, which can immobilize abundant QDs to amplify the stripping voltammetry signals from the metal ions (Pb or Cd). The capture probes were prepared through the immobilization of SH-labeled oligonucleotides, which can complementary with HIV and TB DNA, on the magnetic Fe3O4@Au (GMPs) beads. After sandwich-hybridization, the polymer nanotracers together with HIV and TB DNA targets were simultaneously introduced onto the surface of GMPs. Then the two encoding metal ions (Cd(2+) and Pb(2+)) were used to differentiate two viruses DNA due to the different subsequent anodic stripping voltammetric peaks at -0.84 V (Cd) and -0.61 V (Pb). Because of the excellent signal amplification of the polymer nanotracers and the great specificity of DNA targets, this assay could detect targets DNA as low as 0.2 femtomolar and exhibited excellent selectivity with the dynamitic range from 0.5 fM to 500 pM. Those results demonstrated that this electrochemical coding assay has great potential in applications for screening more viruses DNA while changing the probes.

  1. Expression of Caveolin 1 is enhanced by DNA demethylation during adipocyte differentiation. status of insulin signaling.

    PubMed

    Palacios-Ortega, Sara; Varela-Guruceaga, Maider; Milagro, Fermín Ignacio; Martínez, José Alfredo; de Miguel, Carlos

    2014-01-01

    Caveolin 1 (Cav-1) is an essential constituent of adipocyte caveolae which binds the beta subunit of the insulin receptor (IR) and is implicated in the regulation of insulin signaling. We have found that, during adipocyte differentiation of 3T3-L1 cells the promoter, exon 1 and first intron of the Cav-1 gene undergo a demethylation process that is accompanied by a strong induction of Cav-1 expression, indicating that epigenetic mechanisms must have a pivotal role in this differentiation process. Furthermore, IR, PKB-Akt and Glut-4 expression are also increased during the differentiation process suggesting a coordinated regulation with Cav-1. Activation of Cav-1 protein by phosphorylation arises during the differentiation process, yet in fully mature adipocytes insulin is no longer able to significantly increase Cav-1 phosphorylation. However, these long-term differentiated cells are still able to respond adequately to insulin, increasing IR and PKB-Akt phosphorylation and glucose uptake. The activation of Cav-1 during the adipocyte differentiation process could facilitate the maintenance of insulin sensitivity by these fully mature adipocytes isolated from additional external stimuli. However, under the influence of physiological conditions associated to obesity, such as chronic inflammation and hypoxia, insulin sensitivity would finally be compromised.

  2. Expression of Caveolin 1 Is Enhanced by DNA Demethylation during Adipocyte Differentiation. Status of Insulin Signaling

    PubMed Central

    Palacios-Ortega, Sara; Varela-Guruceaga, Maider; Milagro, Fermín Ignacio; Martínez, José Alfredo; de Miguel, Carlos

    2014-01-01

    Caveolin 1 (Cav-1) is an essential constituent of adipocyte caveolae which binds the beta subunit of the insulin receptor (IR) and is implicated in the regulation of insulin signaling. We have found that, during adipocyte differentiation of 3T3-L1 cells the promoter, exon 1 and first intron of the Cav-1 gene undergo a demethylation process that is accompanied by a strong induction of Cav-1 expression, indicating that epigenetic mechanisms must have a pivotal role in this differentiation process. Furthermore, IR, PKB-Akt and Glut-4 expression are also increased during the differentiation process suggesting a coordinated regulation with Cav-1. Activation of Cav-1 protein by phosphorylation arises during the differentiation process, yet in fully mature adipocytes insulin is no longer able to significantly increase Cav-1 phosphorylation. However, these long-term differentiated cells are still able to respond adequately to insulin, increasing IR and PKB-Akt phosphorylation and glucose uptake. The activation of Cav-1 during the adipocyte differentiation process could facilitate the maintenance of insulin sensitivity by these fully mature adipocytes isolated from additional external stimuli. However, under the influence of physiological conditions associated to obesity, such as chronic inflammation and hypoxia, insulin sensitivity would finally be compromised. PMID:24751908

  3. A signal-on electrochemical aptasensor for ultrasensitive detection of endotoxin using three-way DNA junction-aided enzymatic recycling and graphene nanohybrid for amplification

    NASA Astrophysics Data System (ADS)

    Bai, Lijuan; Chai, Yaqin; Pu, Xiaoyun; Yuan, Ruo

    2014-02-01

    Endotoxin, also known as lipopolysaccharide (LPS), is able to induce a strong immune response on its internalization into mammalian cells. To date, aptamer-based biosensors for LPS detection have been rarely reported. This work describes a new signal-on electrochemical aptasensor for the ultrasensitive detection of LPS by combining the three-way DNA hybridization process and nanotechnology-based amplification. With the help of DNA1 (associated with the concentration of target LPS), the capture probe hybridizes with DNA1 and the assistant probe to open its hairpin structure and form a ternary ``Y'' junction structure. The DNA1 can be released from the structure in the presence of nicking endonuclease to initiate the next hybridization process. Then a great deal of cleaved capture probe produced in the cyclic process can bind with DNA2-nanocomposite, which contains the electroactive toluidine blue (Tb) with the amplification materials graphene (Gra) and gold nanoparticles (AuNPs). Thus, an enhanced electrochemical signal can be easily read out. With the cascade signal amplification, this newly designed protocol provides an ultrasensitive electrochemical detection of LPS down to the femtogram level (8.7 fg mL-1) with a linear range of 6 orders of magnitude (from 10 fg mL-1 to 50 ng mL-1). Moreover, the high sensitivity and specificity make this method versatile for the detection of other biomolecules by changing the corresponding sequences of the capture probe and the assistant probe.

  4. A signal-on electrochemical aptasensor for ultrasensitive detection of endotoxin using three-way DNA junction-aided enzymatic recycling and graphene nanohybrid for amplification.

    PubMed

    Bai, Lijuan; Chai, Yaqin; Pu, Xiaoyun; Yuan, Ruo

    2014-03-07

    Endotoxin, also known as lipopolysaccharide (LPS), is able to induce a strong immune response on its internalization into mammalian cells. To date, aptamer-based biosensors for LPS detection have been rarely reported. This work describes a new signal-on electrochemical aptasensor for the ultrasensitive detection of LPS by combining the three-way DNA hybridization process and nanotechnology-based amplification. With the help of DNA1 (associated with the concentration of target LPS), the capture probe hybridizes with DNA1 and the assistant probe to open its hairpin structure and form a ternary "Y" junction structure. The DNA1 can be released from the structure in the presence of nicking endonuclease to initiate the next hybridization process. Then a great deal of cleaved capture probe produced in the cyclic process can bind with DNA2-nanocomposite, which contains the electroactive toluidine blue (Tb) with the amplification materials graphene (Gra) and gold nanoparticles (AuNPs). Thus, an enhanced electrochemical signal can be easily read out. With the cascade signal amplification, this newly designed protocol provides an ultrasensitive electrochemical detection of LPS down to the femtogram level (8.7 fg mL(-1)) with a linear range of 6 orders of magnitude (from 10 fg mL(-1) to 50 ng mL(-1)). Moreover, the high sensitivity and specificity make this method versatile for the detection of other biomolecules by changing the corresponding sequences of the capture probe and the assistant probe.

  5. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 1 2014-10-01 2014-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212 Modular transmitters. (a) Single modular transmitters consist of a completely...

  6. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212 Modular transmitters. (a) Single modular transmitters consist of a completely...

  7. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212 Modular transmitters. (a) Single modular transmitters consist of a completely...

  8. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 1 2013-10-01 2013-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212 Modular transmitters. (a) Single modular transmitters consist of a completely...

  9. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 1 2011-10-01 2011-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212 Modular transmitters. (a) Single modular transmitters consist of a completely...

  10. 48 CFR 3417.70 - Modular contracting.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 7 2013-10-01 2012-10-01 true Modular contracting. 3417... REGULATION CONTRACTING METHODS AND CONTRACT TYPES SPECIAL CONTRACTING METHODS Modular Contracting 3417.70 Modular contracting. (a) FSA—May incrementally conduct successive procurements of modules of...

  11. Retroactivity in the Context of Modularly Structured Biomolecular Systems.

    PubMed

    Pantoja-Hernández, Libertad; Martínez-García, Juan Carlos

    2015-01-01

    Synthetic biology has intensively promoted the technical implementation of modular strategies in the fabrication of biological devices. Modules are considered as networks of reactions. The behavior displayed by biomolecular systems results from the information processes carried out by the interconnection of the involved modules. However, in natural systems, module wiring is not a free-of-charge process; as a consequence of interconnection, a reactive phenomenon called retroactivity emerges. This phenomenon is characterized by signals that propagate from downstream modules (the modules that receive the incoming signals upon interconnection) to upstream ones (the modules that send the signals upon interconnection). Such retroactivity signals, depending of their strength, may change and sometimes even disrupt the behavior of modular biomolecular systems. Thus, analysis of retroactivity effects in natural biological and biosynthetic systems is crucial to achieve a deeper understanding of how this interconnection between functionally characterized modules takes place and how it impacts the overall behavior of the involved cell. By discussing the modules interconnection in natural and synthetic biomolecular systems, we propose that such systems should be considered as quasi-modular.

  12. Retroactivity in the Context of Modularly Structured Biomolecular Systems

    PubMed Central

    Pantoja-Hernández, Libertad; Martínez-García, Juan Carlos

    2015-01-01

    Synthetic biology has intensively promoted the technical implementation of modular strategies in the fabrication of biological devices. Modules are considered as networks of reactions. The behavior displayed by biomolecular systems results from the information processes carried out by the interconnection of the involved modules. However, in natural systems, module wiring is not a free-of-charge process; as a consequence of interconnection, a reactive phenomenon called retroactivity emerges. This phenomenon is characterized by signals that propagate from downstream modules (the modules that receive the incoming signals upon interconnection) to upstream ones (the modules that send the signals upon interconnection). Such retroactivity signals, depending of their strength, may change and sometimes even disrupt the behavior of modular biomolecular systems. Thus, analysis of retroactivity effects in natural biological and biosynthetic systems is crucial to achieve a deeper understanding of how this interconnection between functionally characterized modules takes place and how it impacts the overall behavior of the involved cell. By discussing the modules interconnection in natural and synthetic biomolecular systems, we propose that such systems should be considered as quasi-modular. PMID:26137457

  13. Modular Instruction Under Restricted Conditions.

    ERIC Educational Resources Information Center

    Utomo, Tjipto; Ruijter, Kees

    1984-01-01

    Describes the evaluation and reconstruction of a transport phenomena course given at the Bandung Institute of Technology which had a 70 percent failure rate. Discusses the teacher-paced modular instruction technique designed to replace the original course material and its results in terms of student performance over a three-year period. (JM)

  14. Rapidly Deployed Modular Telemetry System

    NASA Technical Reports Server (NTRS)

    Varnavas, Kosta A. (Inventor); Sims, William Herbert, III (Inventor)

    2013-01-01

    The present invention is a telemetry system, and more specifically is a rapidly deployed modular telemetry apparatus which utilizes of SDR technology and the FPGA programming capability to reduce the number of hardware components and programming required to deploy a telemetry system.

  15. Sub-femtomolar DNA detection based on layered molybdenum disulfide/multi-walled carbon nanotube composites, Au nanoparticle and enzyme multiple signal amplification.

    PubMed

    Huang, Ke-Jing; Liu, Yu-Jie; Wang, Hai-Bo; Wang, Ya-Ya; Liu, Yan-Ming

    2014-05-15

    A novel 2-dimensional graphene analog molybdenum disulfide/multi-walled carbon nanotube (MoS2/MWCNT) was synthesized by a simple hydrothermal method to achieve excellent electrochemical properties. An ultrasensitive electrochemical DNA biosensor was subsequently constructed by assembling a thiol-tagged DNA probe on a MoS2/MWCNT and gold nanoparticle (AuNP)-modified electrode that has already been coupled with glucose oxidase (GOD). In this work, GOD was used as a redox marker. The heteronanostructure formed on the biosensor surface appeared relatively good conductor for accelerating the electron transfer, while the modification of GOD and AuNPs provided multiple signal amplification for electrochemical biosensing. The multiple signal amplification strategy produced an ultrasensitive electrochemical detection of DNA down to 0.79 fM with a linear range from 10 fM to 10(7)fM, and appeared high selectivity to differentiate three-base mismatched DNA and one-base mismatched DNA. The developed approach provided a simple and reliable method for DNA detection with high sensitivity and specificity, and would open new opportunities for sensitive detection of other biorecognition events.

  16. Some improvements on RNS Montgomery modular multiplication

    NASA Astrophysics Data System (ADS)

    Bajard, Jean-Claude; Didier, Laurent-Stephane; Kornerup, Peter; Rico, Fabien

    2000-11-01

    In Residue Number Systems (RNS), an integer X is represented by its residues {x0,...,xn-1} modulo a base of relatively prime numbers {m0,...,mn-1}. Thus a large number can be represented as a set of small integers. Addition and multiplication can be easily parallelized, there is no carry propagation. The time is reduced to the evaluation of these operations with small numbers. This representation is useful in cryptography and digital signal processing. Furthermore, in these two domains, modular multiplication (A X B mod N) is frequently used. So, in 1998, we have presented in IEEE journal of transactions on computers, a new modular multiplication algorithm in RNS. This algorithm is based on the Montgomery algorithm, using the associated Mixed Radix representation, for the weighted digits. It was the first algorithm of this type. In this paper, we present two remarks. First, if we develop the different expressions due to the algorithm, we obtain some mathematical simplifications that allow us to suppress some Mixed Radix occurrence in the basic iteration simply with a new initialization of our variables. Thus, in this new version, the complexity of each basic iteration, becomes equivalent to two products of small integers instead of three. The second remark is that, most of the time, modular multiplications are done with the same modulo N. We can precompute some values and reduce the complexity of each basic iteration to one multiplication of two small integers. Thus, the basic iteration is three times faster, and the global computation, due to the initialization, is 8/5 time faster than the original version. Sometime after the last basic iteration a Mixed Radix conversion can be needed. Classical parallel methods are linear. We propose an algorithmic parallel algorithm for this translation from RNS to Mixed Radix. For this, we use a result that comes from an RNS division algorithm, we published in Journal of VLSI signal processing systems 1998. We obtain in a

  17. A modular tyrosine kinase deoxyribozyme with discrete aptamer and catalyst domains.

    PubMed

    Dokukin, Victor; Silverman, Scott K

    2014-08-25

    We assess the utility of integrating a predetermined aptamer DNA module adjacent to a random catalytic DNA region for identifying new deoxyribozymes by in vitro selection. By placing a known ATP aptamer next to an N40 random region, an explicitly modular DNA catalyst for tyrosine side chain phosphorylation is identified. The results have implications for broader identification of deoxyribozymes that function with small-molecule substrates.

  18. Self-catalytic growth of unmodified gold nanoparticles as conductive bridges mediated gap-electrical signal transduction for DNA hybridization detection.

    PubMed

    Zhang, Jing; Nie, Huagui; Wu, Zhan; Yang, Zhi; Zhang, Lijie; Xu, Xiangju; Huang, Shaoming

    2014-01-21

    A simple and sensitive gap-electrical biosensor based on self-catalytic growth of unmodified gold nanoparticles (AuNPs) as conductive bridges has been developed for amplifying DNA hybridization events. In this strategy, the signal amplification degree of such conductive bridges is closely related to the variation of the glucose oxidase (GOx)-like catalytic activity of AuNPs upon interaction with single- and double-stranded DNA (ssDNA and dsDNA), respectively. In the presence of target DNA, the obtained dsDNA product cannot adsorb onto the surface of AuNPs due to electrostatic interaction, which makes the unmodified AuNPs exhibit excellent GOx-like catalytic activity. Such catalytic activity can enlarge the diameters of AuNPs in the glucose and HAuCl4 solution and result in a connection between most of the AuNPs and a conductive gold film formation with a dramatically increased conductance. For the control sample, the catalytic activity sites of AuNPs are fully blocked by ssDNA due to the noncovalent interaction between nucleotide bases and AuNPs. Thus, the growth of the assembled AuNPs will not happen and the conductance between microelectrodes will be not changed. Under the optimal experimental conditions, the developed strategy exhibited a sensitive response to target DNA with a high signal-to-noise ratio. Moreover, this strategy was also demonstrated to provide excellent differentiation ability for single-nucleotide polymorphism. Such performances indicated the great potential of this label-free electrical strategy for clinical diagnostics and genetic analysis under real biological sample separation.

  19. Quasispecies Theory for Evolution of Modularity

    PubMed Central

    Park, Jeong-Man; Niestemski, Liang Ren; Deem, Michael W.

    2015-01-01

    Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here develop a quasispecies theory for the dynamics of modularity in populations of these systems. We show how the steady-state fitness in a randomly changing environment can be computed. We derive a fluctuation dissipation relation for the rate of change of modularity and use it to derive a relationship between rate of environmental changes and rate of growth of modularity. We also find a principle of least action for the evolved modularity at steady state. Finally, we compare our predictions to simulations of protein evolution and find them to be consistent. PMID:25679649

  20. Quasispecies theory for evolution of modularity

    NASA Astrophysics Data System (ADS)

    Park, Jeong-Man; Niestemski, Liang Ren; Deem, Michael W.

    2015-01-01

    Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here develop a quasispecies theory for the dynamics of modularity in populations of these systems. We show how the steady-state fitness in a randomly changing environment can be computed. We derive a fluctuation dissipation relation for the rate of change of modularity and use it to derive a relationship between rate of environmental changes and rate of growth of modularity. We also find a principle of least action for the evolved modularity at steady state. Finally, we compare our predictions to simulations of protein evolution and find them to be consistent.

  1. Global DNA cytosine methylation as an evolving trait: phylogenetic signal and correlated evolution with genome size in angiosperms

    PubMed Central

    Alonso, Conchita; Pérez, Ricardo; Bazaga, Pilar; Herrera, Carlos M.

    2015-01-01

    DNA cytosine methylation is a widespread epigenetic mechanism in eukaryotes, and plant genomes commonly are densely methylated. Genomic methylation can be associated with functional consequences such as mutational events, genomic instability or altered gene expression, but little is known on interspecific variation in global cytosine methylation in plants. In this paper, we compare global cytosine methylation estimates obtained by HPLC and use a phylogenetically-informed analytical approach to test for significance of evolutionary signatures of this trait across 54 angiosperm species in 25 families. We evaluate whether interspecific variation in global cytosine methylation is statistically related to phylogenetic distance and also whether it is evolutionarily correlated with genome size (C-value). Global cytosine methylation varied widely between species, ranging between 5.3% (Arabidopsis) and 39.2% (Narcissus). Differences between species were related to their evolutionary trajectories, as denoted by the strong phylogenetic signal underlying interspecific variation. Global cytosine methylation and genome size were evolutionarily correlated, as revealed by the significant relationship between the corresponding phylogenetically independent contrasts. On average, a ten-fold increase in genome size entailed an increase of about 10% in global cytosine methylation. Results show that global cytosine methylation is an evolving trait in angiosperms whose evolutionary trajectory is significantly linked to changes in genome size, and suggest that the evolutionary implications of epigenetic mechanisms are likely to vary between plant lineages. PMID:25688257

  2. Hyperactivation of NF-κB via the MEK signaling is indispensable for the inhibitory effect of cAMP on DNA damage-induced cell death.

    PubMed

    Kloster, Martine M; Naderi, Elin H; Carlsen, Harald; Blomhoff, Heidi K; Naderi, Soheil

    2011-04-21

    With cAMP signaling having a profound inhibitory effect on DNA damage-induced apoptosis in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) cells, understanding how this signaling pathway affects the survival capacity of the cell has important implications for cancer therapy. We have recently shown that p53 is critical for the inhibitory effect of cAMP on genotoxic agents-mediated apoptosis in BCP-ALLs. Here, we show that elevation of cAMP levels in cells exposed to DNA damage enhances the nuclear translocation and DNA binding of NF-κB by accelerating the phosphorylation of IKKβ and thereby phosphorylation and degradation of IκBα. Furthermore, we show that the ability of cAMP to potentiate the ionizing radiation-induced activation of NF-κB requires the activity of MEK. Importantly, pharmacological or genetic ablation of NF-κB reversed the inhibitory effect of cAMP on DNA damage-induced apoptosis, demonstrating that, in addition to p53, cAMP relies on the activity of NF-κB to provide cells with a survival advantage in the face of DNA damage. Collectively, our results uncover a novel and important interaction between the cAMP and NF-κB pathways that may have implications for the targeted treatment of lymphoid malignancies, such as BCP-ALL, in which aberrant NF-κB activity functions as a driving force for treatment resistance.

  3. Genome Protection by the 9-1-1 Complex Subunit HUS1 Requires Clamp Formation, DNA Contacts, and ATR Signaling-independent Effector Functions*

    PubMed Central

    Lim, Pei Xin; Patel, Darshil R.; Poisson, Kelsey E.; Basuita, Manpreet; Tsai, Charlton; Lyndaker, Amy M.; Hwang, Bor-Jang; Lu, A-Lien; Weiss, Robert S.

    2015-01-01

    The RAD9A-HUS1-RAD1 (9-1-1) complex is a heterotrimeric clamp that promotes checkpoint signaling and repair at DNA damage sites. In this study, we elucidated HUS1 functional residues that drive clamp assembly, DNA interactions, and downstream effector functions. First, we mapped a HUS1-RAD9A interface residue that was critical for 9-1-1 assembly and DNA loading. Next, we identified multiple positively charged residues in the inner ring of HUS1 that were crucial for genotoxin-induced 9-1-1 chromatin localization and ATR signaling. Finally, we found two hydrophobic pockets on the HUS1 outer surface that were important for cell survival after DNA damage. Interestingly, these pockets were not required for 9-1-1 chromatin localization or ATR-mediated CHK1 activation but were necessary for interactions between HUS1 and its binding partner MYH, suggesting that they serve as interaction domains for the recruitment and coordination of downstream effectors at damage sites. Together, these results indicate that, once properly loaded onto damaged DNA, the 9-1-1 complex executes multiple, separable functions that promote genome maintenance. PMID:25911100

  4. Genome Protection by the 9-1-1 Complex Subunit HUS1 Requires Clamp Formation, DNA Contacts, and ATR Signaling-independent Effector Functions.

    PubMed

    Lim, Pei Xin; Patel, Darshil R; Poisson, Kelsey E; Basuita, Manpreet; Tsai, Charlton; Lyndaker, Amy M; Hwang, Bor-Jang; Lu, A-Lien; Weiss, Robert S

    2015-06-12

    The RAD9A-HUS1-RAD1 (9-1-1) complex is a heterotrimeric clamp that promotes checkpoint signaling and repair at DNA damage sites. In this study, we elucidated HUS1 functional residues that drive clamp assembly, DNA interactions, and downstream effector functions. First, we mapped a HUS1-RAD9A interface residue that was critical for 9-1-1 assembly and DNA loading. Next, we identified multiple positively charged residues in the inner ring of HUS1 that were crucial for genotoxin-induced 9-1-1 chromatin localization and ATR signaling. Finally, we found two hydrophobic pockets on the HUS1 outer surface that were important for cell survival after DNA damage. Interestingly, these pockets were not required for 9-1-1 chromatin localization or ATR-mediated CHK1 activation but were necessary for interactions between HUS1 and its binding partner MYH, suggesting that they serve as interaction domains for the recruitment and coordination of downstream effectors at damage sites. Together, these results indicate that, once properly loaded onto damaged DNA, the 9-1-1 complex executes multiple, separable functions that promote genome maintenance.

  5. A new system for the amplification of biological signals: RecA and complimentary single strand DNA probes on a leaky surface acoustic wave biosensor.

    PubMed

    Zhang, Liqun; Wang, Yunxia; Chen, Ming; Luo, Yang; Deng, Kun; Chen, Dong; Fu, Weiling

    2014-10-15

    This research describes a new amplification signals system of the leaky surface acoustic wave (LSAW) bis-peptide nucleic acid (bis-PNA) biosensor for the simple, sensitive and rapid detection of the target double-stranded DNA (dsDNA). The system consists of a RecA protein-coated complementary single-stranded DNA (cssDNA) probe complex that amplifies the biological signal to improve the sensitivity of the biosensor. The bis-PNA probe for detecting HPV was first immobilized on a gold surface membrane of the detection channel. After the probe was completely hybridized with the corresponding target DNA, different concentrations of the "RecA protein-complementary single strand DNA probe" were added to react with the bis-PNA/dsDNA complex. The phase shift of the LSAW biosensors, which was measured and found to be most significant when the RecA protein was 45 μg/mL and the ATPγS was 2.5 mmol/L. Compared with other concentrations (P<0.01) of RecA and ATPγS, the value of the phase shift was (11.74 ± 1.03) degrees and the ratio of the phase shift and hybridization time clearly outperformed that of the other concentrations. Compared to the direct hybridization of the bis-PNA probe and the target DNA sequence, the sensitivity was effectively improved and the detection time was significantly shortened. PNA binding adjacent to the area of the target sequence homologous to the probe significantly increased the yield of the hybridization reaction between the PNA/dsDNA complex and the RecA protein-coated cssDNA probe. In this condition, the phase shift was significantly obvious and the detection time was significantly shortened. In conclusion, the combination of the RecA protein-coated cssDNA probe and the LSAW bis-PNA biosensor provides sensitivity and simple and rapid detection of clinical trace pathogenic microorganisms.

  6. RECK impedes DNA repair by inhibiting the erbB/JAB1/Rad51 signaling axis and enhances chemosensitivity of breast cancer cells

    PubMed Central

    Hong, Kun-Jing; Hsu, Ming-Chuan; Hung, Wen-Chun

    2015-01-01

    The reversion-inducing cysteine-rich protein with kazal motif (RECK) is an endogenous matrix metalloproteinase (MMP) inhibitor and a tumor suppressor. Its expression is dramatically down-regulated in human cancers. Our recent results suggest a novel MMP-independent anti-cancer activity of RECK by inhibiting the erbB signaling. Activation of the erbB signaling is associated with chemotherapeutic resistance, however, whether RECK could modulate drug sensitivity is still unknown. Here we demonstrated that expression of RECK induced the activation of ATM and ATR pathways, and the formation of γ-H2AX foci in breast cancer cells. RECK inhibited the erbB signaling and attenuated the expression of the downstream molecules Jun activation domain-binding protein 1 (JAB1) and the DNA repair protein RAD51 to impede DNA repair and to increase drug sensitivity. Treatment of epidermal growth factor or over-expression of HER-2 effectively reversed the inhibitory effect of RECK. In addition, ectopic expression of JAB1 counteracted RECK-induced RAD51 reduction and drug sensitization. Our results elucidate a novel function of RECK to modulate DNA damage response and drug resistance by inhibiting the erbB/Jab1/RAD51 signaling axis. Restoration of RECK expression in breast cancer cells may increase sensitivity to chemotherapeutic agents. PMID:26396917

  7. Relaxation labeling using modular operators

    SciTech Connect

    Duncan, J.S.; Frei, W.

    1983-01-01

    Probabilistic relaxation labeling has been shown to be useful in image processing, pattern recognition, and artificial intelligence. The approaches taken to date have been encumbered with computationally extensive summations which generally prevent real-time operation and/or easy hardware implementation. The authors present a new and unique approach to the relaxation labeling problem using modular, VLSI-oriented hierarchical complex operators. One of the fundamental concepts of this work is the representation of the probability distribution of the possible labels for a given object (pixel) as an ellipse, which may be summed with neighboring object's distribution ellipses, resulting in a new, relaxed label space. The mathematical development of the elliptical approach will be presented and compared to more classical approaches, and a hardware block diagram that shows the implementation of the relaxation scheme using vlsi chips will be presented. Finally, results will be shown which illustrate applications of the modular scheme, iteratively, to both edges and lines. 13 references.

  8. Modular hydrodam: concept definition study

    SciTech Connect

    Not Available

    1981-07-01

    The purpose of this investigation was to explore the potential for developing economical new ultra low-head (6 to 10 ft) sites using an innovative concept known as the Modular Hydrodam (MH). This concept combines the benefits of shop fabrication, installation of equipment in truck transportable, waterproof power modules, and prefabricated gate sections that can be located between the power modules. The size and weight of the power module permits it to be fully assembled and checked out in the manufacturer's shop. The module can then be broken down into four pieces and shipped by truck to the site. Once in place, concrete ballast will be added, as necessary, to prevent flotation. The following aspects were investigated: tubular and cross flow turbines; modularized components; the use of a cable support system for horizontal stability of the dam and powerhouse; and construction in the wet as well as in the dry.

  9. Modular Stellarator Fusion Reactor concept

    SciTech Connect

    Miller, R.L.; Krakowski, R.A.

    1981-08-01

    A preliminary conceptual study is made of the Modular Stellarator Reactor (MSR). A steady-state ignited, DT-fueled, magnetic fusion reactor is proposed for use as a central electric-power station. The MSR concept combines the physics of the classic stellarator confinement topology with an innovative, modular-coil design. Parametric tradeoff calculations are described, leading to the selection of an interim design point for a 4-GWt plant based on Alcator transport scaling and an average beta value of 0.04 in an l = 2 system with a plasma aspect ratio of 11. The physics basis of the design point is described together with supporting magnetics, coil-force, and stress computations. The approach and results presented herein will be modified in the course of ongoing work to form a firmer basis for a detailed conceptual design of the MSR.

  10. Modular Platforms for Optofluidic Systems

    NASA Astrophysics Data System (ADS)

    Brammer, Marko; Mappes, Timo

    2013-02-01

    Optofluidics is increasingly gaining impact in a number of different fields of research, namely biology and medicine, environmental monitoring and green energy. However, the market for optofluidic products is still in the early development phase. In this manuscript, we discuss modular platforms as a potential concept to facilitate the transfer of optofluidic sensing systems to an industrial implementation. We present microfluidic and optical networks as a basis for the interconnection of optofluidic sensor modules. Finally, we show the potential for entire optofluidic networks.

  11. Modular Platforms for Optofluidic Systems

    NASA Astrophysics Data System (ADS)

    Brammer, Marko; Mappes, Timo

    2014-01-01

    Optofluidics is increasingly gaining impact in a number of different fields of research, namely biology and medicine, environmental monitoring and green energy. However, the market for optofluidic products is still in the early development phase. In this manuscript, we discuss modular platforms as a potential concept to facilitate the transfer of optofluidic sensing systems to an industrial implementation. We present microfluidic and optical networks as a basis for the interconnection of optofluidic sensor modules. Finally, we show the potential for entire optofluidic networks

  12. CAMAC modular programmable function generator

    SciTech Connect

    Turner, G.W.; Suehiro, S.; Hendricks, R.W.

    1980-12-01

    A CAMAC modular programmable function generator has been developed. The device contains a 1024 word by 12-bit memory, a 12-bit digital-to-analog converter with a 600 ns settling time, an 18-bit programmable frequency register, and two programmable trigger output registers. The trigger registers can produce programmed output logic transitions at various (binary) points in the output function curve, and are used to synchronize various other data acquisition devices with the function curve.

  13. Multidimensional bioseparation with modular microfluidics

    DOEpatents

    Chirica, Gabriela S.; Renzi, Ronald F.

    2013-08-27

    A multidimensional chemical separation and analysis system is described including a prototyping platform and modular microfluidic components capable of rapid and convenient assembly, alteration and disassembly of numerous candidate separation systems. Partial or total computer control of the separation system is possible. Single or multiple alternative processing trains can be tested, optimized and/or run in parallel. Examples related to the separation and analysis of human bodily fluids are given.

  14. Oxidative DNA damage and augmentation of poly(ADP-ribose) polymerase/nuclear factor-kappa B signaling in patients with type 2 diabetes and microangiopathy.

    PubMed

    Adaikalakoteswari, Antonysunil; Rema, Mohan; Mohan, Viswanathan; Balasubramanyam, Muthuswamy

    2007-01-01

    Although oxidative stress and the subsequent DNA damage is one of the obligatory signals for poly(ADP-ribose) polymerase (PARP) activation and nuclear factor-kappa B (NFkappaB) alterations, these molecular aspects have not been collectively examined in epidemiological and clinical settings. Therefore, this study attempts to assess the oxidative DNA damage and its downstream effector signals in peripheral blood lymphocytes from Type 2 diabetes subjects without and with microangiopathy along with age-matched non-diabetic subjects. The basal DNA damage, lipid peroxidation and protein carbonyl content were significantly (p<0.05) higher in patients with and without microangiopathy compared to control subjects. Formamido Pyrimidine Glycosylase (FPG)-sensitive DNA strand breaks which represents reliable indicator of oxidative DNA damage were also significantly (p<0.001) higher in diabetic patients with (19.41+/-2.5) and without microangiopathy (16.53+/-2.0) compared to control subjects (1.38+/-0.85). Oxidative DNA damage was significantly correlated to poor glycemic control. PARP mRNA expression and PARP activity were significantly (p<0.05) increased in cells from diabetic patients with (0.31+/-0.03 densitometry units; 0.22+/-0.02PARPunits/mgprotein, respectively) and without (0.35+/-0.02; 0.42+/-0.05) microangiopathy compared to control (0.19+/-0.02; 0.11+/-0.02) subjects. Diabetic subjects with and without microangiopathy exhibited a significantly (p<0.05) higher (80%) NFkappaB binding activity compared to control subjects. In diabetic patients, FPG-sensitive DNA strand breaks correlated positively with PARP gene expression, PARP activity and NFkappaB binding activity. This study provides a comprehensive molecular evidence for increased oxidative stress and genomic instability in Type 2 diabetic subjects even prior to vascular pathology and hence reveals a window of opportunity for early therapeutic intervention.

  15. Estimation of inter-modular connectivity from the local field potentials in a hierarchical modular network

    NASA Astrophysics Data System (ADS)

    Cui, Xue-Mei; Kim, Won Sup; Hwang, Dong-Uk; Han, Seung Kee

    2015-05-01

    We propose a method of estimating inter-modular connectivity in a hierarchical modular network. The method is based on an analysis of inverse phase synchronization applied to the local field potentials on a hierarchical modular network of phase oscillators. For a strong-coupling strength, the inverse phase synchronization index of the local field potentials for two modules depends linearly on the corresponding inter-modular connectivity defined as the number of links connecting the modules. The method might enable us to estimate the inter-modular connectivity in various complex systems from the inverse phase synchronization index of the mesoscopic modular activities.

  16. Mitogen-activated protein kinase signal transduction and DNA repair network are involved in aluminum-induced DNA damage and adaptive response in root cells of Allium cepa L.

    PubMed Central

    Panda, Brahma B.; Achary, V. Mohan M.

    2014-01-01

    In the current study, we studied the role of signal transduction in aluminum (Al3+)-induced DNA damage and adaptive response in root cells of Allium cepa L. The root cells in planta were treated with Al3+ (800 μM) for 3 h without or with 2 h pre-treatment of inhibitors of mitogen-activated protein kinase (MAPK), and protein phosphatase. Also, root cells in planta were conditioned with Al3+ (10 μM) for 2 h and then subjected to genotoxic challenge of ethyl methane sulfonate (EMS; 5 mM) for 3 h without or with the pre-treatment of the aforementioned inhibitors as well as the inhibitors of translation, transcription, DNA replication and repair. At the end of treatments, roots cells were assayed for cell death and/or DNA damage. The results revealed that Al3+ (800 μM)-induced significant DNA damage and cell death. On the other hand, conditioning with low dose of Al3+ induced adaptive response conferring protection of root cells from genotoxic stress caused by EMS-challenge. Pre-treatment of roots cells with the chosen inhibitors prior to Al3+-conditioning prevented or reduced the adaptive response to EMS genotoxicity. The results of this study suggested the involvement of MAPK and DNA repair network underlying Al-induced DNA damage and adaptive response to genotoxic stress in root cells of A. cepa. PMID:24926302

  17. Modular Activating Receptors in Innate and Adaptive Immunity.

    PubMed

    Berry, Richard; Call, Matthew E

    2017-03-14

    Triggering of cell-mediated immunity is largely dependent on the recognition of foreign or abnormal molecules by a myriad of cell surface-bound receptors. Many activating immune receptors do not possess any intrinsic signaling capacity but instead form noncovalent complexes with one or more dimeric signaling modules that communicate with a common set of kinases to initiate intracellular information-transfer pathways. This modular architecture, where the ligand binding and signaling functions are detached from one another, is a common theme that is widely employed throughout the innate and adaptive arms of immune systems. The evolutionary advantages of this highly adaptable platform for molecular recognition are visible in the variety of ligand-receptor interactions that can be linked to common signaling pathways, the diversification of receptor modules in response to pathogen challenges, and the amplification of cellular responses through incorporation of multiple signaling motifs. Here we provide an overview of the major classes of modular activating immune receptors and outline the current state of knowledge regarding how these receptors assemble, recognize their ligands, and ultimately trigger intracellular signal transduction pathways that activate immune cell effector functions.

  18. Localization of single-copy T-DNA insertion in transgenic shallots (Allium cepa) by using ultra-sensitive FISH with tyramide signal amplification.

    PubMed

    Khrustaleva, L I; Kik, C

    2001-03-01

    The sensitivity of fluorescence in situ hybridization (FISH) for mapping plant chromosomes of single-copy DNA sequences is limited. We have adapted for plant cytogenetics a new signal-amplification method termed tyramide-FISH (Tyr-FISH). Until present this technique has only been applied to human chromosomes. The method is based on enzymatic deposition of fluorochrome-conjugated tyramide. With Tyr-FISH it was possible to detect target T-DNA sequences on plant metaphase chromosomes as small as 710 bp without using a cooled CCD camera. Short detection time and high sensitivity, in combination with a low background, make the Tyr-FISH method very suitable for routine application in plant cytogenetic research. With Tyr-FISH we analysed the position of T-DNA inserts in transgenic shallots. We found that the inserts were preferentially located in the distal region of metaphase chromosomes. Sequential fluorescence in situ hybridization with a 375 bp satellite sequence suggested that a specific T-DNA insert was located within the satellite sequence hybridization region on a metaphase chromosome. Analysis of less-condensed prophase and interphase chromosomes revealed that the T-DNA was integrated outside the satellite DNA-hybridization region in a more proximal euchromatin region.

  19. ATP puts the brake on DNA double-strand break repair: a new study shows that ATP switches the Mre11-Rad50-Nbs1 repair factor between signaling and processing of DNA ends.

    PubMed

    Hopfner, Karl-Peter

    2014-12-01

    DNA double-strand breaks (DSBs) are one of the most deleterious forms of DNA damage and can result in cell inviability or chromosomal aberrations. The Mre11-Rad50-Nbs1 (MRN) ATPase-nuclease complex is a central player in the cellular response to DSBs and is implicated in the sensing and nucleolytic processing of DSBs, as well as in DSB signaling by activating the cell cycle checkpoint kinase ATM. ATP binding to Rad50 switches MRN from an open state with exposed Mre11 nuclease sites to a closed state with partially buried nuclease sites. The functional meaning of this switch remained unclear. A new study shows that ATP binding to Rad50 promotes DSB recognition, tethering, and ATM activation, while ATP hydrolysis opens the nuclease active sites to promote processing of DSBs. MRN thus emerges as functional switch that may coordinate the temporal transition from signaling to processing of DSBs.

  20. Modularized Evolution in Archaeal Methanogens Phylogenetic Forest

    PubMed Central

    Li, Jun; Wong, Chi-Fat; Wong, Mabel Ting; Huang, He; Leung, Frederick C.

    2014-01-01

    Methanogens are methane-producing archaea that plays a key role in the global carbon cycle. To date, the evolutionary history of methanogens and closely related nonmethanogen species remains unresolved among studies conducted upon different genetic markers, attributing to horizontal gene transfers (HGTs). With an effort to decipher both congruent and conflicting evolutionary events, reconstruction of coevolved gene clusters and hierarchical structure in the archaeal methanogen phylogenetic forest, comprehensive evolution, and network analyses were performed upon 3,694 gene families from 41 methanogens and 33 closely related archaea. Our results show that 1) greater than 50% of genes are in topological dissonance with others; 2) the prevalent interorder HGTs, even for core genes, in methanogen genomes led to their scrambled phylogenetic relationships; 3) most methanogenesis-related genes have experienced at least one HGT; 4) greater than 20% of the genes in methanogen genomes were transferred horizontally from other archaea, with genes involved in cell-wall synthesis and defense system having been transferred most frequently; 5) the coevolution network contains seven statistically robust modules, wherein the central module has the highest average node strength and comprises a majority of the core genes; 6) different coevolutionary module genes boomed in different time and evolutionary lineage, constructing diversified pan-genome structures; 7) the modularized evolution is also closely related to the vertical evolution signals and the HGT rate of the genes. Overall, this study presented a modularized phylogenetic forest that describes a combination of complicated vertical and nonvertical evolutionary processes for methanogenic archaeal species. PMID:25502908

  1. Phosphoproteomic Profiling Reveals Epstein-Barr Virus Protein Kinase Integration of DNA Damage Response and Mitotic Signaling

    PubMed Central

    Li, Renfeng; Pinto, Sneha M.; Shaw, Patrick G.; Huang, Tai-Chung; Wan, Jun; Qian, Jiang; Gowda, Harsha; Wu, Xinyan; Lv, Dong-Wen; Zhang, Kun; Manda, Srikanth S.; Pandey, Akhilesh; Hayward, S. Diane

    2015-01-01

    Epstein-Barr virus (EBV) is etiologically linked to infectious mononucleosis and several human cancers. EBV encodes a conserved protein kinase BGLF4 that plays a key role in the viral life cycle. To provide new insight into the host proteins regulated by BGLF4, we utilized stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics to compare site-specific phosphorylation in BGLF4-expressing Akata B cells. Our analysis revealed BGLF4-mediated hyperphosphorylation of 3,046 unique sites corresponding to 1,328 proteins. Frequency analysis of these phosphosites revealed a proline-rich motif signature downstream of BGLF4, indicating a broader substrate recognition for BGLF4 than its cellular ortholog cyclin-dependent kinase 1 (CDK1). Further, motif analysis of the hyperphosphorylated sites revealed enrichment in ATM, ATR and Aurora kinase substrates while functional analyses revealed significant enrichment of pathways related to the DNA damage response (DDR), mitosis and cell cycle. Phosphorylation of proteins associated with the mitotic spindle assembly checkpoint (SAC) indicated checkpoint activation, an event that inactivates the anaphase promoting complex/cyclosome, APC/C. Furthermore, we demonstrated that BGLF4 binds to and directly phosphorylates the key cellular proteins PP1, MPS1 and CDC20 that lie upstream of SAC activation and APC/C inhibition. Consistent with APC/C inactivation, we found that BGLF4 stabilizes the expression of many known APC/C substrates. We also noted hyperphosphorylation of 22 proteins associated the nuclear pore complex, which may contribute to nuclear pore disassembly and SAC activation. A drug that inhibits mitotic checkpoint activation also suppressed the accumulation of extracellular EBV virus. Taken together, our data reveal that, in addition to the DDR, manipulation of mitotic kinase signaling and SAC activation are mechanisms associated with lytic EBV replication. All MS data have been deposited in

  2. A Cross-Cancer Genetic Association Analysis of the DNA repair and DNA Damage Signaling Pathways for Lung, Ovary, Prostate, Breast and Colorectal Cancer

    PubMed Central

    Scarbrough, Peter M.; Weber, Rachel Palmieri; Iversen, Edwin S.; Brhane, Yonathan; Amos, Christopher I.; Kraft, Peter; Hung, Rayjean J.; Sellers, Thomas A.; Witte, John S.; Pharoah, Paul; Henderson, Brian E.; Gruber, Stephen B.; Hunter, David J.; Garber, Judy E.; Joshi, Amit D.; McDonnell, Kevin; Easton, Doug F.; Eeles, Ros; Kote-Jarai, Zsofia; Muir, Kenneth; Doherty, Jennifer A.; Schildkraut, Joellen M.

    2015-01-01

    Background DNA damage is an established mediator of carcinogenesis, though GWAS have identified few significant loci. This cross-cancer site, pooled analysis was performed to increase the power to detect common variants of DNA repair genes associated with cancer susceptibility. Methods We conducted a cross-cancer analysis of 60,297 SNPs, at 229 DNA repair gene regions, using data from the NCI Genetic Associations and Mechanisms in Oncology (GAME-ON) Network. Our analysis included data from 32 GWAS and 48,734 controls and 51,537 cases across five cancer sites (breast, colon, lung, ovary, and prostate). Because of the unavailability of individual data, data were analyzed at the aggregate level. Meta-analysis was performed using the Association analysis for SubSETs (ASSET) software. To test for genetic associations that might escape individual variant testing due to small effect sizes, pathway analysis of eight DNA repair pathways was performed using hierarchical modeling. Results We identified three susceptibility DNA repair genes, RAD51B (p < 5.09 × 10−6), MSH5 (p < 5.09 × 10−6) and BRCA2 (p = 5.70 × 10−6). Hierarchical modeling identified several pleiotropic associations with cancer risk in the base excision repair, nucleotide excision repair, mismatch repair, and homologous recombination pathways. Conclusions Only three susceptibility loci were identified which had all been previously reported. In contrast, hierarchical modeling identified several pleiotropic cancer risk associations in key DNA repair pathways. Impact Results suggest that many common variants in DNA repair genes are likely associated with cancer susceptibility through small effect sizes that do not meet stringent significance testing criteria. PMID:26637267

  3. Modular Design in Treaty Verification Equipment

    SciTech Connect

    Macarthur, Duncan Whittemore; Benz, Jacob; Tolk, Keith; Weber, Tom

    2015-01-27

    It is widely believed that modular design is a good thing. However, there are often few explicit arguments, or even an agreed range of definitions, to back up this belief. In this paper, we examine the potential range of design modularity, the implications of various amounts of modularity, and the advantages and disadvantages of each level of modular construction. We conclude with a comparison of the advantages and disadvantages of each type, as well as discuss many caveats that should be observed to take advantage of the positive features of modularity and minimize the effects of the negative. The tradeoffs described in this paper will be evaluated during the conceptual design to determine what amount of modularity should be included.

  4. Modular microrobot for swimming in heterogeneous environments

    NASA Astrophysics Data System (ADS)

    Cheang, U. Kei; Meshkati, Meshkati; Fu, Henry; Kim, Minjun; Drexel University Team; University of Nevada, Reno Team

    2015-11-01

    One of the difficulties in navigating in vivo is to overcome many types of environments. This includes blood vessels of different diameters, fluids with different mechanical properties, and physical barriers. Inspired by conventional modular robotics, we demonstrate modular microrobotics using magnetic particles as the modular units to change size and shape through docking and undocking. Much like the vast variety of microorganisms navigating many different bio-environments, modular microswimmers have the ability to dynamically adapt different environments by reconfiguring the swimmers' physical characteristics. We model the docking as magnetic assembly and undocking mechanisms as deformation by hydrodynamic forces. We characterize the swimming capability of the modular microswimmer with different size and shapes. Finally, we demonstrate modular microrobotics by assembling a three-bead microswimmer into a nine-bead microswimmer, and then disassemble it into several independently swimming microswimmers..

  5. Convergence of multiple signaling pathways is required to coordinately up-regulate mtDNA and mitochondrial biogenesis during T cell activation

    PubMed Central

    D’Souza, Anthony D.; Parikh, Neal; Kaech, Susan M.; Shadel, Gerald S.

    2009-01-01

    The quantity and activity of mitochondria vary dramatically in tissues and are modulated in response to changing cellular energy demands and environmental factors. The amount of mitochondrial DNA (mtDNA), which encodes essential subunits of the oxidative phosphorylation complexes required for cellular ATP production, is also tightly regulated, but by largely unknown mechanisms. Using murine T cells as a model system, we have addressed how specific signaling pathways influence mitochondrial biogenesis and mtDNA levels. T cell receptor (TCR) activation results in a large increase in mitochondrial mass and membrane potential and a corresponding increase of mtDNA copy number, indicating the vital role for mitochondrial function for the growth and proliferation of these cells. Independent activation of protein kinase C (via PMA) or calcium-related pathways (via ionomycin) had differential and sub-maximal effects on these mitochondrial parameters, as did activation of naïve T cells with proliferative cytokines. Thus, the robust mitochondrial biogenesis response observed upon TCR activation requires synergy of multiple downstream signaling pathways. One such pathway involves AMP-activated protein kinase (AMPK), which we show has an unprecedented role in negatively regulating mitochondrial biogenesis that is mammalian target of rapamycin (mTOR)-dependent. That is, inhibition of AMPK after TCR signaling commences results in excessive, but uncoordinated mitochondrial proliferation. We propose that mitochondrial biogenesis is not under control of a master regulatory circuit, but rather requires the convergence of multiple signaling pathways with distinct downstream consequences on the organelle’s structure, composition, and function. PMID:17890163

  6. Irreparable telomeric DNA damage and persistent DDR signalling as a shared causative mechanism of cellular senescence and ageing.

    PubMed

    Rossiello, Francesca; Herbig, Utz; Longhese, Maria Pia; Fumagalli, Marzia; d'Adda di Fagagna, Fabrizio

    2014-06-01

    The DNA damage response (DDR) orchestrates DNA repair and halts cell cycle. If damage is not resolved, cells can enter into an irreversible state of proliferative arrest called cellular senescence. Organismal ageing in mammals is associated with accumulation of markers of cellular senescence and DDR persistence at telomeres. Since the vast majority of the cells in mammals are non-proliferating, how do they age? Are telomeres involved? Also oncogene activation causes cellular senescence due to altered DNA replication and DDR activation in particular at the telomeres. Is there a common mechanism shared among apparently distinct types of cellular senescence? And what is the role of telomeric DNA damage?

  7. Modular, Hierarchical Learning By Artificial Neural Networks

    NASA Technical Reports Server (NTRS)

    Baldi, Pierre F.; Toomarian, Nikzad

    1996-01-01

    Modular and hierarchical approach to supervised learning by artificial neural networks leads to neural networks more structured than neural networks in which all neurons fully interconnected. These networks utilize general feedforward flow of information and sparse recurrent connections to achieve dynamical effects. The modular organization, sparsity of modular units and connections, and fact that learning is much more circumscribed are all attractive features for designing neural-network hardware. Learning streamlined by imitating some aspects of biological neural networks.

  8. Suppressor of Cytokine Signaling (SOCS) Genes Are Silenced by DNA Hypermethylation and Histone Deacetylation and Regulate Response to Radiotherapy in Cervical Cancer Cells

    PubMed Central

    Kim, Moon-Hong; Kim, Moon-Sun; Kim, Wonwoo; Kang, Mi Ae; Cacalano, Nicholas A.; Kang, Soon-Beom; Shin, Young-Joo; Jeong, Jae-Hoon

    2015-01-01

    Suppressor of cytokine signaling (SOCS) family is an important negative regulator of cytokine signaling and deregulation of SOCS has been involved in many types of cancer. All cervical cancer cell lines tested showed lower expression of SOCS1, SOCS3, and SOCS5 than normal tissue or cell lines. The immunohistochemistry result for SOCS proteins in human cervical tissue also confirmed that normal tissue expressed higher level of SOCS proteins than neighboring tumor. Similar to the regulation of SOCS in other types of cancer, DNA methylation contributed to SOCS1 downregulation in CaSki, ME-180, and HeLa cells. However, the expression of SOCS3 or SOCS5 was not recovered by the inhibition of DNA methylation. Histone deacetylation may be another regulatory mechanism involved in SOCS1 and SOCS3 expression, however, SOCS5 expression was neither affected by DNA methylation nor histone deacetylation. Ectopic expression of SOCS1 or SOCS3 conferred radioresistance to HeLa cells, which implied SOCS signaling regulates the response to radiation in cervical cancer. In this study, we have shown that SOCS expression repressed by, in part, epigenetically and altered SOCS1 and SOCS3 expression could contribute to the radiosensitive phenotype in cervical cancer. PMID:25849377

  9. Modular cryogenic interconnects for multi-qubit devices

    SciTech Connect

    Colless, J. I.; Reilly, D. J.

    2014-11-15

    We have developed a modular interconnect platform for the control and readout of multiple solid-state qubits at cryogenic temperatures. The setup provides 74 filtered dc-bias connections, 32 control and readout connections with −3 dB frequency above 5 GHz, and 4 microwave feed lines that allow low loss (less than 3 dB) transmission 10 GHz. The incorporation of a radio-frequency interposer enables the platform to be separated into two printed circuit boards, decoupling the simple board that is bonded to the qubit chip from the multilayer board that incorporates expensive connectors and components. This modular approach lifts the burden of duplicating complex interconnect circuits for every prototype device. We report the performance of this platform at milli-Kelvin temperatures, including signal transmission and crosstalk measurements.

  10. Membrane-bound mucin modular domains: from structure to function.

    PubMed

    Jonckheere, Nicolas; Skrypek, Nicolas; Frénois, Frédéric; Van Seuningen, Isabelle

    2013-06-01

    Mucins belong to a heterogeneous family of large O-glycoproteins composed of a long peptidic chain called apomucin on which are linked hundreds of oligosaccharidic chains. Among mucins, membrane-bound mucins are modular proteins and have a structural organization usually containing Pro/Thr/Ser-rich O-glycosylated domains (PTS), EGF-like and SEA domains. Via these modular domains, the membrane-bound mucins participate in cell signalling and cell interaction with their environment in normal and pathological conditions. Moreover, the recent knowledge of these domains and their biological activities led to the development of new therapeutic approaches involving mucins. In this review, we show 3D structures of EGF and SEA domains. We also describe the functional features of the evolutionary conserved domains of membrane-bound mucins and discuss consequences of splice events.

  11. Programming DNA tube circumferences.

    PubMed

    Yin, Peng; Hariadi, Rizal F; Sahu, Sudheer; Choi, Harry M T; Park, Sung Ha; Labean, Thomas H; Reif, John H

    2008-08-08

    Synthesizing molecular tubes with monodisperse, programmable circumferences is an important goal shared by nanotechnology, materials science, and supermolecular chemistry. We program molecular tube circumferences by specifying the complementarity relationships between modular domains in a 42-base single-stranded DNA motif. Single-step annealing results in the self-assembly of long tubes displaying monodisperse circumferences of 4, 5, 6, 7, 8, 10, or 20 DNA helices.

  12. A label-free, PCR-free and signal-on electrochemical DNA biosensor for Leishmania major based on gold nanoleaves.

    PubMed

    Moradi, M; Sattarahmady, N; Rahi, A; Hatam, G R; Sorkhabadi, S M Rezayat; Heli, H

    2016-12-01

    Detection of leishmaniasis is important in clinical diagnoses. In the present study, identification of Leishmania parasites was performed by a label-free, PCR-free and signal-on ultrasensitive electrochemical DNA biosensor. Gold nanoleaves were firstly electrodeposited by an electrodeposition method using spermidine as a shape directing agent. The biosensor was fabricated by immobilization of a Leishmania major specific DNA probe onto gold nanoleaves, and methylene blue was employed as a marker. Hybridization of the complementary single stranded DNA sequence with the biosensor under the selected conditions was then investigated. The biosensor could detect a synthetic DNA target in a range of 1.0×10(-10) to 1.0×10(-19)molL(-1) with a limit of detection of 1.8×10(-20)molL(-1), and genomic DNA in a range of 0.5-20ngμL(-1) with a limit of detection of 0.07ngμL(-1). The biosensor could distinguish Leishmania major from a non-complementary-sequence oligonucleotide and the tropica species with a high selectivity. The biosensor was applicable to detect Leishmania major in patient samples.

  13. A T7exonuclease-assisted target recycling amplification with graphene oxide acting as the signal amplifier for fluorescence polarization detection of human immunodeficiency virus (HIV) DNA.

    PubMed

    Wang, Lijun; Tian, Jianniao; Yang, Wen; Zhao, Yanchun; Zhao, Shulin

    2016-03-01

    We report a fluorescence polarization (FP) platform for human immunodeficiency virus (HIV) DNA detection based on T7exonuclease-assisted target recycling amplification with graphene oxide (GO) acting as a FP signal amplifier. In the sensing method, the presence of the target DNA leads to target recycling with the assistance of T7exonuclease, furthermore, the amplification products are absorbed onto the surface of GO, so the all FP values are enhanced by GO. More importantly, this FP sensor exhibits high detection sensitivity; under optimal conditions, the change in FP is linear with the concentration of the target DNA within a concentration range of 50-2000 pmol/L, and the detection limit of this method is as low as 38.6 pmol/L. This FP sensor also exhibits high selectivity, even single-base mismatched DNA can be effectively discriminated from complementary target DNA. Above all, the proposed FP sensor may serve as a general platform for the sensitive assay of disease-related genes.

  14. Interplay with the Mre11-Rad50-Nbs1 complex and phosphorylation by GSK3β implicate human B-Myb in DNA-damage signaling

    PubMed Central

    Henrich, Sarah Marie; Usadel, Clemens; Werwein, Eugen; Burdova, Kamila; Janscak, Pavel; Ferrari, Stefano; Hess, Daniel; Klempnauer, Karl-Heinz

    2017-01-01

    B-Myb, a highly conserved member of the Myb transcription factor family, is expressed ubiquitously in proliferating cells and controls the cell cycle dependent transcription of G2/M-phase genes. Deregulation of B-Myb has been implicated in oncogenesis and loss of genomic stability. We have identified B-Myb as a novel interaction partner of the Mre11-Rad50-Nbs1 (MRN) complex, a key player in the repair of DNA double strand breaks. We show that B-Myb directly interacts with the Nbs1 subunit of the MRN complex and is recruited transiently to DNA-damage sites. In response to DNA-damage B-Myb is phosphorylated by protein kinase GSK3β and released from the MRN complex. A B-Myb mutant that cannot be phosphorylated by GSK3β disturbs the regulation of pro-mitotic B-Myb target genes and leads to inappropriate mitotic entry in response to DNA-damage. Overall, our work suggests a novel function of B-Myb in the cellular DNA-damage signalling. PMID:28128338

  15. Cascading dynamics in modular networks

    NASA Astrophysics Data System (ADS)

    Galstyan, Aram; Cohen, Paul

    2007-03-01

    In this paper we study a simple cascading process in a structured heterogeneous population, namely, a network composed of two loosely coupled communities. We demonstrate that under certain conditions the cascading dynamics in such a network has a two-tiered structure that characterizes activity spreading at different rates in the communities. We study the dynamics of the model using both simulations and an analytical approach based on annealed approximation and obtain good agreement between the two. Our results suggest that network modularity might have implications in various applications, such as epidemiology and viral marketing.

  16. Integrated modular engine - Reliability assessment

    NASA Astrophysics Data System (ADS)

    Parsley, R. C.; Ward, T. B.

    1992-07-01

    A major driver in the increased interest in integrated modular engine configurations is the desire for ultra reliability for future rocket propulsion systems. The concept of configuring multiple sets of turbomachinery networked to multiple thrust chamber assemblies has been identified as an approach with potential to achieve significant reliability enhancement. This paper summarizes the results of a reliability study comparing networked systems vs. discrete engine installations, both with and without major module and engine redundancy. The study was conducted for gas generator, expander, and staged combustion cycles. The results are representative of either booster or upper-stage applications and are indicative of either plug or nonplug installation philosophies.

  17. Modular design attitude control system

    NASA Technical Reports Server (NTRS)

    Chichester, F. D.

    1984-01-01

    A sequence of single axismodels and a series of reduced state linear observers of minimum order are used to reconstruct inaccessible variables pertaining to the modular attitude control of a rigid body flexible suspension model of a flexible spacecraft. The single axis models consist of two, three, four, and five rigid bodies, each interconnected by a flexible shaft passing through the mass centers of the bodies. Modal damping is added to each model. Reduced state linear observers are developed for synthesizing the inaccessible modal state variables for each modal model.

  18. Modular passive solar heating system

    SciTech Connect

    Hunter, B.D.

    1985-03-19

    A modular passive solar energy storage system comprises a plurality of heat tubes which are arranged to form a flat plate solar collector and are releasably connected to a water reservoir by, and are part of, double-walled heat exchangers which penetrate to the water reservoir and enhance the heat transfer characteristics between the collector and the reservoir. The flat plate collector-heat exchanger disassembly, the collector housing, and the reservoir are integrated into a relatively light weight, unitary structural system in which the reservoir is a primary structural element. In addition to light weight, the system features high efficiency and ease of assembly and maintenance.

  19. Investigation of switch from ATM to ATR signaling at the sites of DNA damage induced by low and high LET radiation.

    PubMed

    Saha, Janapriya; Wang, Minli; Cucinotta, Francis A

    2013-12-01

    Upon induction of DNA damage by ionizing radiation (IR), members of the phosphatidylinositol 3-kinase-like kinase family of proteins namely ataxia-telangiectasia mutated (ATM), DNA-PKcs, and ATM- and Rad3-related (ATR) maintain genomic integrity by mounting DNA damage response (DDR). Recent reports suggest that activation of ATM and ATR are oppositely regulated by the length of single stranded overhangs generated during end processing by nucleases at the break sites. These stretches of single stranded overhangs hold the clue for the transition from ATM to ATR signaling at broken DNA ends. We investigated whether differential processing of breaks induced by low and high LET radiation augments the phenomenon of switching from ATM to ATR kinase and hence a concomitant NHEJ to HR transition at the sites of DNA damage. 82-6 human fibroblasts were irradiated with 1 or 2Gy of γ-rays and particle radiation of increasing LET in order to increase the complexity and variability of DNA double strand breaks (DSB) structures. The activation kinetics of ATM and ATR kinases along with their downstream substrates were determined utilizing Western blotting and immunofluorescence techniques. Our data provide evidence of a potential switch from ATM to ATR kinase signaling in cells treated with γ-rays at approximately 2h post irradiation, with induction and completion of resection denoted by Rad51 foci resolution kinetics and observed with a significant decline of phosphorylated ATR kinase 8h after IR. On the other hand, irradiation with high LET 600MeV/u (56)Fe (180keV/μm) and 170MeV/u (28)Si (99keV/μm) particles show a similar Rad51 foci decay kinetics, however, exhibiting prolonged resection, evident by the persistent phosphorylated ATM and ATR kinase until 24h post irradiation. This residual effect, however, was significantly reduced for 250MeV/u (16)O particles of moderate LET (25keV/μm) and absent for γ-rays. Hence, our results support the hypothesis that the transition

  20. Integrating DNA strand displacement circuitry to the nonlinear hybridization chain reaction.

    PubMed

    Zhang, Zhuo; Fan, Tsz Wing; Hsing, I-Ming

    2017-02-23

    Programmable and modular attributes of DNA molecules allow one to develop versatile sensing platforms that can be operated isothermally and enzyme-free. In this work, we present an approach to integrate upstream DNA strand displacement circuits that can be turned on by a sequence-specific microRNA analyte with a downstream nonlinear hybridization chain reaction for a cascading hyperbranched nucleic acid assembly. This system provides a two-step amplification strategy for highly sensitive detection of the miRNA analyte, conducive for multiplexed detection. Multiple miRNA analytes were tested with our integrated circuitry using the same downstream signal amplification setting, showing the decoupling of nonlinear self-assembly with the analyte sequence. Compared with the reported methods, our signal amplification approach provides an additional control module for higher-order DNA self-assembly and could be developed into a promising platform for the detection of critical nucleic-acid based biomarkers.

  1. Mineralocorticoid Receptor (MR) trans-Activation of Inflammatory AP-1 Signaling: DEPENDENCE ON DNA SEQUENCE, MR CONFORMATION, AND AP-1 FAMILY MEMBER EXPRESSION.

    PubMed

    Dougherty, Edward J; Elinoff, Jason M; Ferreyra, Gabriela A; Hou, Angela; Cai, Rongman; Sun, Junfeng; Blaine, Kevin P; Wang, Shuibang; Danner, Robert L

    2016-11-04

    Glucocorticoids are commonly used to treat inflammatory disorders. The glucocorticoid receptor (GR) can tether to inflammatory transcription factor complexes, such as NFκB and AP-1, and trans-repress the transcription of cytokines, chemokines, and adhesion molecules. In contrast, aldosterone and the mineralocorticoid receptor (MR) primarily promote cardiovascular inflammation by incompletely understood mechanisms. Although MR has been shown to weakly repress NFκB, its role in modulating AP-1 has not been established. Here, the effects of GR and MR on NFκB and AP-1 signaling were directly compared using a variety of ligands, two different AP-1 consensus sequences, GR and MR DNA-binding domain mutants, and siRNA knockdown or overexpression of core AP-1 family members. Both GR and MR repressed an NFκB reporter without influencing p65 or p50 binding to DNA. Likewise, neither GR nor MR affected AP-1 binding, but repression or activation of AP-1 reporters occurred in a ligand-, AP-1 consensus sequence-, and AP-1 family member-specific manner. Notably, aldosterone interactions with both GR and MR demonstrated a potential to activate AP-1. DNA-binding domain mutations that eliminated the ability of GR and MR to cis-activate a hormone response element-driven reporter variably affected the strength and polarity of these responses. Importantly, MR modulation of NFκB and AP-1 signaling was consistent with a trans-mechanism, and AP-1 effects were confirmed for specific gene targets in primary human cells. Steroid nuclear receptor trans-effects on inflammatory signaling are context-dependent and influenced by nuclear receptor conformation, DNA sequence, and the expression of heterologous binding partners. Aldosterone activation of AP-1 may contribute to its proinflammatory effects in the vasculature.

  2. Highly sensitive aptasensor based on synergetic catalysis activity of MoS2-Au-HE composite using cDNA-Au-GOD for signal amplification.

    PubMed

    Song, Hai-Yan; Kang, Tian-Fang; Lu, Li-Ping; Cheng, Shui-Yuan

    2017-03-01

    Single or few-layer nanosheets of MoS2 (MoS2 nanosheets) and a composite composed of MoS2 nanosheets, Au nanoparticles (AuNPs) and hemin (HE) (denoted as MoS2-Au-HE) were prepared. The composites possessed high synergetic catalysis activity towards the electroreduction of hydrogen peroxide. Furthermore, glucose oxidase (GOD) and AuNPs were used as marker of the complementary DNA (cDNA) strand of kanamycin aptamer to prepare a conjugate (reffered as cDNA-Au-GOD) that was designed as the signal probe. Both cDNA-Au-GOD and MoS2-Au-HE were applied to fabricate aptasensor for kanamycin. MoS2-Au-HE acted as solid platform for kanamycin aptamer and signal transmitters. AuNPs were employed as the supporter of cDNA and GOD which catalyze dissolved oxygen to produce hydrogen peroxide in the presence of glucose. Then cathodic peak current of H2O2 was recorded by differential pulse voltammetry (DPV). The electrochemical reduction of H2O2 was catalyzed by MoS2-Au-HE that was modified onto the surface of a glassy carbon electrode (GCE). The cathodic peak current of H2O2 was highly linearly decreased with an increase of kanamycin concentrations from 1.0ng/L to 1.0×10(5)ng/L, with a detection limit of 0.8ng/L. This aptasensor can be used to detect kanamycin in milk with high specificity, sensitivity and selectivity.

  3. Thermal stress and cellular signaling processes in hemocytes of native (Mytilus californianus) and invasive (M. galloprovincialis) mussels: cell cycle regulation and DNA repair.

    PubMed

    Yao, Cui-Luan; Somero, George N

    2013-06-01

    In a previous study using hemocytes from native and invasive congeners of Mytilus (Mytilus californianus and Mytilus galloprovincialis, respectively) we showed that DNA damage and cell signaling transduction processes related to the cellular stress response and apoptosis were induced by acute temperature stress. The present study extends this work by examining effects of acute heat- and cold stress on total hemocyte counts (THCs) and expression of key regulatory molecules involved in responding to stress: tumor suppressor factor (p53), cell cycle arrest activator (p21), and a DNA base excision repair enzyme (apurinic/apyrimidinic endonuclease (APE)). Hyperthermia (28 °C, 32 °C) led to significant decreases of THCs in both species. The extent of decrease in THC was temperature-, time-, and species-dependent; lower THC values were found in M. californianus, the more cold-adapted species. Western blot analyses of hemocyte extracts with antibodies specific for p53 protein, several site-specific phosphorylation states of p53, p21 protein, and APE indicated that heat- and cold (2 °C) stress induced a time-dependent activation of stress-related proteins in response to DNA damage; these stress-induced changes could govern cell cycle arrest or DNA damage repair. Our results show that the downstream regulatory response to temperature-induced cell damage may play an important role in deciding cellular fate following heat- and cold stress. Compared to M. californianus, the more warm-adapted M. galloprovincialis appears to have a higher temperature tolerance due to a lesser reduction in THC, faster signaling activation and transduction, and stronger DNA repair ability following heat stress.

  4. Compact stellarators with modular coils.

    PubMed

    Garabedian, P R

    2000-07-18

    Compact stellarator designs with modular coils and only two or three field periods are now available; these designs have both good stability and quasiaxial symmetry providing adequate transport for a magnetic fusion reactor. If the bootstrap current assumes theoretically predicted values a three field period configuration is optimal, but if that net current turns out to be lower, a device with two periods and just 12 modular coils might be better. There are also attractive designs with quasihelical symmetry and four or five periods whose properties depend less on the bootstrap current. Good performance requires that there be a satisfactory magnetic well in the vacuum field, which is a property lacking in a stellarator-tokamak hybrid that has been proposed for a proof of principle experiment. In this paper, we present an analysis of stability for these configurations that is based on a mountain pass theorem asserting that, if two solutions of the problem of magnetohydrodynamic equilibrium can be found, then there has to be an unstable solution. We compare results of our theory of equilibrium, stability, and transport with recently announced measurements from the large LHD experiment in Japan.

  5. Compact stellarators with modular coils

    PubMed Central

    Garabedian, P. R.

    2000-01-01

    Compact stellarator designs with modular coils and only two or three field periods are now available; these designs have both good stability and quasiaxial symmetry providing adequate transport for a magnetic fusion reactor. If the bootstrap current assumes theoretically predicted values a three field period configuration is optimal, but if that net current turns out to be lower, a device with two periods and just 12 modular coils might be better. There are also attractive designs with quasihelical symmetry and four or five periods whose properties depend less on the bootstrap current. Good performance requires that there be a satisfactory magnetic well in the vacuum field, which is a property lacking in a stellarator-tokamak hybrid that has been proposed for a proof of principle experiment. In this paper, we present an analysis of stability for these configurations that is based on a mountain pass theorem asserting that, if two solutions of the problem of magnetohydrodynamic equilibrium can be found, then there has to be an unstable solution. We compare results of our theory of equilibrium, stability, and transport with recently announced measurements from the large LHD experiment in Japan. PMID:10899993

  6. Learning modular policies for robotics

    PubMed Central

    Neumann, Gerhard; Daniel, Christian; Paraschos, Alexandros; Kupcsik, Andras; Peters, Jan

    2014-01-01

    A promising idea for scaling robot learning to more complex tasks is to use elemental behaviors as building blocks to compose more complex behavior. Ideally, such building blocks are used in combination with a learning algorithm that is able to learn to select, adapt, sequence and co-activate the building blocks. While there has been a lot of work on approaches that support one of these requirements, no learning algorithm exists that unifies all these properties in one framework. In this paper we present our work on a unified approach for learning such a modular control architecture. We introduce new policy search algorithms that are based on information-theoretic principles and are able to learn to select, adapt and sequence the building blocks. Furthermore, we developed a new representation for the individual building block that supports co-activation and principled ways for adapting the movement. Finally, we summarize our experiments for learning modular control architectures in simulation and with real robots. PMID:24966830

  7. A modular BLSS simulation model

    NASA Technical Reports Server (NTRS)

    Rummel, John D.; Volk, Tyler

    1987-01-01

    A bioregenerative life support system (BLSS) for extraterrestrial use will be faced with coordination problems more acute than those in any ecosystem found on Earth. A related problem in BLSS design is providing an interface between the various life support processors, one that will allow for their coordination while still allowing for system expansion. A modular model is presented of a BLSS that interfaces system processors only with the material storage reservoirs, allowing those reservoirs to act as the principal buffers in the system and thus minimizing difficulties with processor coordination. The modular nature of the model allows independent development of the detailed submodels that exist within the model framework. Using this model, BLSS dynamics were investigated under normal conditions and under various failure modes. Partial and complete failures of various components, such as the waste processors or the plants themselves, drive transient responses in the model system, allowing the examination of the effectiveness of the system reservoirs as buffers. The results from simulations help to determine control strategies and BLSS design requirements. An evolved version could be used as an interactive control aid in a future BLSS.

  8. Decentralized and Modular Electrical Architecture

    NASA Astrophysics Data System (ADS)

    Elisabelar, Christian; Lebaratoux, Laurence

    2014-08-01

    This paper presents the studies made on the definition and design of a decentralized and modular electrical architecture that can be used for power distribution, active thermal control (ATC), standard inputs-outputs electrical interfaces.Traditionally implemented inside central unit like OBC or RTU, these interfaces can be dispatched in the satellite by using MicroRTU.CNES propose a similar approach of MicroRTU. The system is based on a bus called BRIO (Bus Réparti des IO), which is composed, by a power bus and a RS485 digital bus. BRIO architecture is made with several miniature terminals called BTCU (BRIO Terminal Control Unit) distributed in the spacecraft.The challenge was to design and develop the BTCU with very little volume, low consumption and low cost. The standard BTCU models are developed and qualified with a configuration dedicated to ATC, while the first flight model will fly on MICROSCOPE for PYRO actuations and analogue acquisitions. The design of the BTCU is made in order to be easily adaptable for all type of electric interface needs.Extension of this concept is envisaged for power conditioning and distribution unit, and a Modular PCDU based on BRIO concept is proposed.

  9. NMR analysis of the architecture and functional remodeling of a modular multidomain protein, RPA.

    PubMed

    Brosey, Chris A; Chagot, Marie-Eve; Ehrhardt, Mark; Pretto, Dalyir I; Weiner, Brian E; Chazin, Walter J

    2009-05-13

    Modular proteins with multiple domains tethered by flexible linkers have variable global architectures. Using the eukaryotic ssDNA binding protein, Replication Protein A (RPA), we demonstrate that NMR spectroscopy is a powerful tool to characterize the remodeling of architecture in different functional states. The first direct evidence is obtained for the remodeling of RPA upon binding ssDNA, including an alteration in the availability of the RPA32N domain that may help explain its damage-dependent phosphorylation.

  10. The Iterative Structure Analysis of Montgomery Modular Multiplication

    NASA Astrophysics Data System (ADS)

    Jinbo, Wang

    2007-09-01

    Montgomery modular multiplication (MMM) plays a crucial role in the implementation of modular exponentiations of public-key cryptography. In this paper, we discuss the iterative structure and extend the iterative bound condition of MMM. It can be applied to complicated modular exponentiations. Based on the iterative condition of MMM, we can directly use non-modular additions, subtractions and even simple multiplications instead of the modular forms, which make modular exponentiation operation very efficient but more importantly iterative applicability of MMM.

  11. Improving the count rate performance of a modular cylindrical SPECT system

    SciTech Connect

    Li, Y.J.; Hollinger, E.F.; Liu, J.; Chang, W.

    1996-12-31

    We recently proposed a design of a modular cylindrical cardiac SPECT system. one special feature of this system is an integrated provision for transmission imaging. To meet the clinical demands of obtaining transmission images, this system must be able to achieve a very high count rate (CR). To explore methods for achieving a high CR capability on a modular cylindrical detector system, we have used our existing modular cylindrical brain SPECT system to examine the feasibility of two approaches. First, we use digital-signal-processing (DSP) boards, in parallel, to execute real time position calculations. Second, we use local encoding and triggering circuits to perform analog signal processing, including identifying the detector module and digitizing the pulse signals. The results of our preliminary investigations indicate that applying the multiple-DSP parallel position calculation and local triggering techniques in a modular SPECT system can improve the CR capability significantly. Applying local triggering increased the CR capability by 15% at a CR capability of 200 kcps. Because we have used slow-speed DSP boards during this proof-of-concept testing, we have not yet met the CR requirements for transmission imaging. However, these results indicate that by using state-of-the-art DSP boards the CR capability of this modular SPECT system can be increased to over 300 kcps.

  12. Signal Transduction Mechanism for Serotonin 5-HT2B Receptor-Mediated DNA Synthesis and Proliferation in Primary Cultures of Adult Rat Hepatocytes.

    PubMed

    Naito, Kota; Tanaka, Chizuru; Mitsuhashi, Manami; Moteki, Hajime; Kimura, Mitsutoshi; Natsume, Hideshi; Ogihara, Masahiko

    2016-01-01

    The involvement of serotonin (5-hydroxytryptamine; 5-HT) and the 5-HT2 receptor subtypes in the induction of DNA synthesis and proliferation was investigated in primary cultures of adult rat hepatocytes to elucidate the intracellular signal transduction mechanisms. Hepatocyte parenchymal cells maintained in a serum-free, defined medium, synthesized DNA and proliferated in the presence of 5-HT or a selective 5-HT2B receptor agonist, BW723C86, but not in the presence of 5-HT2A, or 5-HT2C receptor agonists (TCB-2 and CP809101, respectively), in a time- and dose-dependent manner. A selective 5-HT2B receptor antagonist, LY272015 (10(-7) M), and a specific phospholipase C (PLC) inhibitor, U-73122 (10(-6) M), as well as specific inhibitors of growth-related signal transducers-including AG1478, LY294002, PD98059, and rapamycin-completely inhibited 5-HT (10(-6) M)- or BW723C86 (10(-6) M)-induced hepatocyte DNA synthesis and proliferation. Both 5-HT and BW723C86 were shown to significantly stimulate the phosphorylation of epidermal growth factor (EGF)/transforming growth factor (TGF)-α receptor tyrosine kinase (p175 kDa) and extracellular signal-regulated kinase (ERK) 2 on Western blot analysis. These results suggest that the proliferative mechanism of activating 5-HT is mediated mainly through 5-HT2B receptor-stimulated Gq/PLC and EGF/TGF-α-receptor/phosphatidylinositol 3-kinase (PI3K)/ERK2/mammalian target of rapamycin (mTOR) signaling pathways in primary cultured hepatocytes.

  13. E7449: A dual inhibitor of PARP1/2 and tankyrase1/2 inhibits growth of DNA repair deficient tumors and antagonizes Wnt signaling

    PubMed Central

    Wu, Jiayi; Chang, Paul; Kolber-Simonds, Donna; Ackermann, Karen; Twine, Natalie C.; Shie, Jue-Lon; Miu, Jingzang Tao; Huang, Kuan-Chun; Moniz, George A.; Nomoto, Kenichi

    2015-01-01

    Inhibition of Poly(ADP-ribose) Polymerase1 (PARP1) impairs DNA damage repair, and early generation PARP1/2 inhibitors (olaparib, niraparib, etc.) have demonstrated clinical proof of concept for cancer treatment. Here, we describe the development of the novel PARP inhibitor E7449, a potent PARP1/2 inhibitor that also inhibits PARP5a/5b, otherwise known as tankyrase1 and 2 (TNKS1 and 2), important regulators of canonical Wnt/β-catenin signaling. E7449 inhibits PARP enzymatic activity and additionally traps PARP1 onto damaged DNA; a mechanism previously shown to augment cytotoxicity. Cells deficient in DNA repair pathways beyond homologous recombination were sensitive to E7449 treatment. Chemotherapy was potentiated by E7449 and single agent had significant antitumor activity in BRCA-deficient xenografts. Additionally, E7449 inhibited Wnt/β-catenin signaling in colon cancer cell lines, likely through TNKS inhibition. Consistent with this possibility, E7449 stabilized axin and TNKS proteins resulting in β-catenin de-stabilization and significantly altered expression of Wnt target genes. Notably, hair growth mediated by Wnt signaling was inhibited by E7449. A pharmacodynamic effect of E7449 on Wnt target genes was observed in tumors, although E7449 lacked single agent antitumor activity in vivo, a finding typical for selective TNKS inhibitors. E7449 antitumor activity was increased through combination with MEK inhibition. Particularly noteworthy was the lack of toxicity, most significantly the lack of intestinal toxicity reported for other TNKS inhibitors. E7449 represents a novel dual PARP1/2 and TNKS1/2 inhibitor which has the advantage of targeting Wnt/β-catenin signaling addicted tumors. E7449 is currently in early clinical development. PMID:26513298

  14. Modular Construction: The Wave of the Future.

    ERIC Educational Resources Information Center

    Savage, Chuck

    1989-01-01

    Modular construction of school buildings offers speed of construction, with 100 percent contractor responsibility for the completed structures. Under negotiated terms, modular projects can be purchased outright or through long-term leasing arrangements that provide ownership at the end of the lease period. (MLF)

  15. Modular Buildings Are Here To Stay.

    ERIC Educational Resources Information Center

    Williams, Steven; Roman, Michael I.; Tiernan, Maury; Savage, Chuck; Airikka, Robert; Brosius, Jerry L.

    2000-01-01

    Presents several examples of modular building construction being used be school districts to support their need for more space, building flexibility, and enhancement of the learning environment. Comparisons with traditionally built school facilities are offered as are answers to commonly held myths concerning modular construction. (GR)

  16. Detectability thresholds of general modular graphs

    NASA Astrophysics Data System (ADS)

    Kawamoto, Tatsuro; Kabashima, Yoshiyuki

    2017-01-01

    We investigate the detectability thresholds of various modular structures in the stochastic block model. Our analysis reveals how the detectability threshold is related to the details of the modular pattern, including the hierarchy of the clusters. We show that certain planted structures are impossible to infer regardless of their fuzziness.

  17. The Modular Clock Algorithm for Blind Rendezvous

    DTIC Science & Technology

    2009-03-26

    Theory . . . . . . . . . . . . . . . . . . . . . . . 20 Strategies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 vi Page...50 Random Strategy vs. Modular Clock Algorithm . . . . . . . . . . . . . . 53 Modified Modular Clock Algorithm...Spectrum has become such a precious commodity that the auction of five blocks of 700 MHz spectrum raised $20 billion dollars from big market players

  18. Modular Building Institute 2000 Educational Showcase.

    ERIC Educational Resources Information Center

    Modular Building Inst., Charlottesville, VA.

    This publication contains brief articles concerned with modular school structures. The articles offer examples of such structures at actual schools. The articles in this issue are: (1) "Elementary K-8 Modular Courtyard"; (2) "School District #33, Chilliwack, BC"; (3) "New Elementary School for Briarwood, NY"; (4) "Addition to Queens Intermediate…

  19. A Modular Laser Graphics Projection System

    NASA Astrophysics Data System (ADS)

    Newswanger, Craig D.

    1984-05-01

    WED Enterprises has designed and built a modular projection system for the presentation of animated laser shows. This system was designed specifically for use in Disney theme shows. Its modular design allows it to be adapted to many show situations with simple hardware and software adjustments. The primary goals were superior animation, long life, low maintenance and stand alone operation.

  20. 48 CFR 39.103 - Modular contracting.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 1 2013-10-01 2013-10-01 false Modular contracting. 39.103 Section 39.103 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION SPECIAL... extent practicable, use modular contracting to acquire major systems (see 2.101) of...

  1. 48 CFR 39.103 - Modular contracting.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 1 2011-10-01 2011-10-01 false Modular contracting. 39.103 Section 39.103 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION SPECIAL... extent practicable, use modular contracting to acquire major systems (see 2.101) of...

  2. Modularity maximization using completely positive programming

    NASA Astrophysics Data System (ADS)

    Yazdanparast, Sakineh; Havens, Timothy C.

    2017-04-01

    Community detection is one of the most prominent problems of social network analysis. In this paper, a novel method for Modularity Maximization (MM) for community detection is presented which exploits the Alternating Direction Augmented Lagrangian (ADAL) method for maximizing a generalized form of Newman's modularity function. We first transform Newman's modularity function into a quadratic program and then use Completely Positive Programming (CPP) to map the quadratic program to a linear program, which provides the globally optimal maximum modularity partition. In order to solve the proposed CPP problem, a closed form solution using the ADAL merged with a rank minimization approach is proposed. The performance of the proposed method is evaluated on several real-world data sets used for benchmarks community detection. Simulation results shows the proposed technique provides outstanding results in terms of modularity value for crisp partitions.

  3. Finding network communities using modularity density

    NASA Astrophysics Data System (ADS)

    Botta, Federico; del Genio, Charo I.

    2016-12-01

    Many real-world complex networks exhibit a community structure, in which the modules correspond to actual functional units. Identifying these communities is a key challenge for scientists. A common approach is to search for the network partition that maximizes a quality function. Here, we present a detailed analysis of a recently proposed function, namely modularity density. We show that it does not incur in the drawbacks suffered by traditional modularity, and that it can identify networks without ground-truth community structure, deriving its analytical dependence on link density in generic random graphs. In addition, we show that modularity density allows an easy comparison between networks of different sizes, and we also present some limitations that methods based on modularity density may suffer from. Finally, we introduce an efficient, quadratic community detection algorithm based on modularity density maximization, validating its accuracy against theoretical predictions and on a set of benchmark networks.

  4. The emergence of modularity in biological systems

    NASA Astrophysics Data System (ADS)

    Lorenz, Dirk M.; Jeng, Alice; Deem, Michael W.

    2011-06-01

    In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to explain modular organization of biology, with a focus on explaining how biology may spontaneously organize to a structured form. That is, we seek to explain how biology nucleated from among the many possibilities in chemistry. The emergence of modular organization of biological structure will be described as a symmetry-breaking phase transition, with modularity as the order parameter. Experimental support for this description will be reviewed. Examples will be presented from pathogen structure, metabolic networks, gene networks, and protein-protein interaction networks. Additional examples will be presented from ecological food networks, developmental pathways, physiology, and social networks.

  5. Nucleotide excision repair-dependent DNA double-strand break formation and ATM signaling activation in mammalian quiescent cells.

    PubMed

    Wakasugi, Mitsuo; Sasaki, Takuma; Matsumoto, Megumi; Nagaoka, Miyuki; Inoue, Keiko; Inobe, Manabu; Horibata, Katsuyoshi; Tanaka, Kiyoji; Matsunaga, Tsukasa

    2014-10-10

    Histone H2A variant H2AX is phosphorylated at Ser(139) in response to DNA double-strand break (DSB) and single-stranded DNA (ssDNA) formation. UV light dominantly induces pyrimidine photodimers, which are removed from the mammalian genome by nucleotide excision repair (NER). We previously reported that in quiescent G0 phase cells, UV induces ATR-mediated H2AX phosphorylation plausibly caused by persistent ssDNA gap intermediates during NER. In this study, we have found that DSB is also generated following UV irradiation in an NER-dependent manner and contributes to an earlier fraction of UV-induced H2AX phosphorylation. The NER-dependent DSB formation activates ATM kinase and triggers the accumulation of its downstream factors, MRE11, NBS1, and MDC1, at UV-damaged sites. Importantly, ATM-deficient cells exhibited enhanced UV sensitivity under quiescent conditions compared with asynchronously growing conditions. Finally, we show that the NER-dependent H2AX phosphorylation is also observed in murine peripheral T lymphocytes, typical nonproliferating quiescent cells in vivo. These results suggest that in vivo quiescent cells may suffer from NER-mediated secondary DNA damage including ssDNA and DSB.

  6. Direct electrochemical DNA detection originated from the self-redox signal of sulfonated polyaniline enhanced by graphene oxide in neutral solution.

    PubMed

    Yang, Tao; Meng, Le; Wang, Xinxing; Wang, Longlong; Jiao, Kui

    2013-11-13

    In this paper, a type of direct DNA impedance detection using the self-redox signal change of sulfonated polyaniline (SPAN) enhanced by graphene oxide (GNO) was reported, here SPAN is a copolymer obtained from aniline and m-aminobenzenesulfonic acid. The resulting nanocomposite was characterized by scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, cyclic voltammetry, and electrochemical impedance spectroscopy. The π-π planar structure of GNO and the carboxyl groups on the surface of GNO ensured it could act as an excellent substrate for adsorption and polymerization of aniline monomer. Because of the existence of GNO, the electrochemical activities of SPAN were enhanced obviously. Because of abundant sulfonic acid groups, the resulting nanocomposite showed obvious self-redox signal even at physiological pH, which is beneficial for biosensing field. DNA probes with amine groups could be covalently attached to the modified electrode surface through the acyl chloride cross-linking reaction of sulfonic groups and amines. When the flexible probe DNA was successfully grafted, the electrode was coated and electron transfer between electrode and buffer was restrained. Thus, the inner impedance value of SPAN (rather than using outer classic EIS probe, [Fe(CN)6](3-/4-)) increased significantly. After hybridization, the rigid helix opened the electron channel, which induced impedance value decreased dramatically. As an initial application of this system, the PML/RARA fusion gene sequence formed from promyelocytic leukemia (PML) and retinoic acid receptor alpha (RARA) was successfully detected.

  7. Histone H4 expression is cooperatively maintained by IKKβ and Akt1 which attenuates cisplatin-induced apoptosis through the DNA-PK/RIP1/IAPs signaling cascade

    PubMed Central

    Wang, Ruixue; Zheng, Xuelian; Zhang, Lei; Zhou, Bin; Hu, Huaizhong; Li, Zhiping; Zhang, Lin; Lin, Yong; Wang, Xia

    2017-01-01

    While chromatin remodeling mediated by post-translational modification of histone is extensively studied in carcinogenesis and cancer cell’s response to chemotherapy and radiotherapy, little is known about the role of histone expression in chemoresistance. Here we report a novel chemoresistance mechanism involving histone H4 expression. Extended from our previous studies showing that concurrent blockage of the NF-κB and Akt signaling pathways sensitizes lung cancer cells to cisplatin-induced apoptosis, we for the first time found that knockdown of Akt1 and the NF-κB-activating kinase IKKβ cooperatively downregulated histone H4 expression, which increased cisplatin-induced apoptosis in lung cancer cells. The enhanced cisplatin cytotoxicity in histone H4 knockdown cells was associated with proteasomal degradation of RIP1, accumulation of cellular ROS and degradation of IAPs (cIAP1 and XIAP). The cisplatin-induced DNA-PK activation was suppressed in histone H4 knockdown cells, and inhibiting DNA-PK reduced expression of RIP1 and IAPs in cisplatin-treated cells. These results establish a novel mechanism by which NF-κB and Akt contribute to chemoresistance involving a signaling pathway consisting of histone H4, DNA-PK, RIP1 and IAPs that attenuates ROS-mediated apoptosis, and targeting this pathway may improve the anticancer efficacy of platinum-based chemotherapy. PMID:28139737

  8. DNA-based hybridization chain reaction and biotin-streptavidin signal amplification for sensitive detection of Escherichia coli O157:H7 through ELISA.

    PubMed

    Guo, Qi; Han, Jiao-Jiao; Shan, Shan; Liu, Dao-Feng; Wu, Song-Song; Xiong, Yong-Hua; Lai, Wei-Hua

    2016-12-15

    This study reported on a novel sandwich enzyme linked immunosorbent assay (ELISA) for the sensitive determination of Escherichia coli O157:H7 (E. coli O157:H7) by using DNA-based hybridization chain reaction (HCR) and biotin-streptavidin signal amplification. The anti-E. coli O157:H7 polyclonal antibody (pAb) was immobilized in the ELISA wells. The anti-E. coli O157:H7 monoclonal antibody (mAb) and initiator strand (DNA1) were labeled on gold nanoparticle (AuNP) to form a mAb-AuNP-DNA1 complex. In the presence of the target E. coli O157:H7, the sandwiched immunocomplex, which is pAb-E. coli O157:H7-mAb-AuNP-DNA1, could be formed. Two types of biotinylated hairpin were subsequently added in the ELISA well. A nicked double-stranded DNA (dsDNA) that contained abundant biotins was formed after HCR. Detection was performed after adding horseradish peroxidase-streptavidin and substrate/chromogen solution. Under optimal conditions, E. coli O157:H7 could be detected in the range of 5×10(2) CFU/mL to 1×10(7) CFU/mL; the limit of detection was 1.08×10(2) CFU/mL in pure culture. The LOD of the novel ELISA was 185 times lower than that of traditional ELISA. The proposed method is considerably specific and can be applied in the detection of whole milk samples inoculated with E. coli O157:H7. The coefficient of variation of in pure culture and in whole milk was 0.99-5.88% and 0.76-5.38%, respectively. This method offers a promising application in the detection of low concentrations of food-borne pathogens.

  9. Miniature modular microwave end-to-end receiver

    NASA Technical Reports Server (NTRS)

    Sukamto, Lin M. (Inventor); Cooley, Thomas W. (Inventor); Janssen, Michael A. (Inventor); Parks, Gary S. (Inventor)

    1993-01-01

    An end-to-end microwave receiver system contained in a single miniature hybrid package mounted on a single heatsink is presented. It includes an input end connected to a microwave receiver antenna and an output end which produces a digital count proportional to the amplitude of a signal of a selected microwave frequency band received at the antenna and corresponding to one of the water vapor absorption lines near frequencies of 20 GHz or 30 GHz. The hybrid package is on the order of several centimeters in length and a few centimeters in height and width. The package includes an L-shaped carrier having a base surface, a vertical wall extending up from the base surface and forming a corner therewith, and connection pins extending through the vertical wall. Modular blocks rest on the base surface against the vertical wall and support microwave monolithic integrated circuits on top surfaces thereof connected to the external connection pins. The modular blocks lie end-to-end on the base surface so as to be modularly removable by sliding along the base surface beneath the external connection pins away from the vertical wall.

  10. Small Modular Reactors: Institutional Assessment

    SciTech Connect

    Joseph Perkowski, Ph.D.

    2012-06-01

    ? Objectives include, among others, a description of the basic development status of “small modular reactors” (SMRs) focused primarily on domestic activity; investigation of the domestic market appeal of modular reactors from the viewpoints of both key energy sector customers and also key stakeholders in the financial community; and consideration of how to proceed further with a pro-active "core group" of stakeholders substantially interested in modular nuclear deployment in order to provide the basis to expedite design/construction activity and regulatory approval. ? Information gathering was via available resources, both published and personal communications with key individual stakeholders; published information is limited to that already in public domain (no confidentiality); viewpoints from interviews are incorporated within. Discussions at both government-hosted and private-hosted SMR meetings are reflected herein. INL itself maintains a neutral view on all issues described. Note: as per prior discussion between INL and CAP, individual and highly knowledgeable senior-level stakeholders provided the bulk of insights herein, and the results of those interviews are the main source of the observations of this report. ? Attachment A is the list of individual stakeholders consulted to date, including some who provided significant earlier assessments of SMR institutional feasibility. ? Attachments B, C, and D are included to provide substantial context on the international status of SMR development; they are not intended to be comprehensive and are individualized due to the separate nature of the source materials. Attachment E is a summary of the DOE requirements for winning teams regarding the current SMR solicitation. Attachment F deserves separate consideration due to the relative maturity of the SMART SMR program underway in Korea. Attachment G provides illustrative SMR design features and is intended for background. Attachment H is included for overview

  11. Modular multi-engine thrust control assembly

    SciTech Connect

    Sakurai, S.

    1986-02-04

    This patent describes a modular thrust control lever assembly for controling forward/reverse thrust generated by an aircraft engine. It includes an electric/electronic engine thrust control system, an inhibit mechanism for preventing inadverent or premature establishment of at least one of forward and reverse engine thrust. It consists of a (a) housing; (b) a control lever assembly pivotally mounted within the housing for fore and aft pivotal movement in a single vertical plane; (c) movable inhibit mechanism normally mounted in the path of movement of the laterally projecting roller on the control lever assembly between at least one of the maximum thrust limit positions of the assembly and the adjacent intermediate idle thrust position; (d) a electric/electronic engine thrust control system including an mechanism for reconfiguring the thrust controls of the engine upon movement of the thrust control lever assembly to the adjacent intermediate idle thrust position; (e) a mechanism responsive to the output signal for shifting the inhibit mechanism out of the path of movement of the control lever assembly.

  12. Modular reconfigurable matched spectral filter spectrometer

    NASA Astrophysics Data System (ADS)

    Schundler, Elizabeth; Engel, James R.; Gruber, Thomas; Vaillancourt, Robert; Benedict-Gill, Ryan; Mansur, David J.; Dixon, John; Potter, Kevin; Newbry, Scott

    2015-06-01

    OPTRA is currently developing a modular, reconfigurable matched spectral filter (RMSF) spectrometer for the monitoring of greenhouse gases. The heart of this spectrometer will be the RMSF core, which is a dispersive spectrometer that images the sample spectrum from 2000 - 3333 cm-1 onto a digital micro-mirror device (DMD) such that different columns correspond to different wavebands. By applying masks to this DMD, a matched spectral filter can be applied in hardware. The core can then be paired with different fore-optics or detector modules to achieve active in situ or passive remote detection of the chemicals of interest. This results in a highly flexible system that can address a wide variety of chemicals by updating the DMD masks and a wide variety of applications by swapping out fore-optic and detector modules. In either configuration, the signal on the detector is effectively a dot-product between the applied mask and the sample spectrum that can be used to make detection and quantification determinations. Using this approach significantly reduces the required data bandwidth of the sensor without reducing the information content, therefore making it ideal for remote, unattended systems. This paper will focus on the design of the RMSF core.

  13. BESST: A Miniature, Modular Radiometer

    NASA Technical Reports Server (NTRS)

    Warden, Robert; Good, William; Baldwin-Stevens, Erik

    2010-01-01

    A new radiometer assembly has been developed that incorporates modular design principles in order to provide flexibility and versatility. The assembly, shown in Figure 1, is made up of six modules plus a central cubical frame. A small thermal imaging detector is used to determine the temperature of remote objects. To improve the accuracy of the temperature reading, frequent calibration is required. The detector must view known temperature targets before viewing the remote object. Calibration is achieved by using a motorized fold mirror to select the desired scene the detector views. The motor steps the fold mirror through several positions, which allows the detector to view the calibration targets or the remote object. The details, features, and benefits of the radiometer are described in this paper.

  14. A bioinspired modular aquatic robot

    NASA Astrophysics Data System (ADS)

    Tallapragada, Phanindra; Pollard, Beau

    2016-11-01

    Several bio inspired swimming robots exist which seek to emulate the morphology of fish and the flapping motion of the tail and fins or other appendages and body of aquatic creatures. The locomotion of such robots and the aquatic animals that they seek to emulate is determined to a large degree by the changes in the shape of the body, which produce periodic changes in the momentum of the body and the creation and interaction of the vorticity field in the fluid with the body. We demonstrate an underactuated robot which swims due to the periodic changes in the angular momentum of the robot effected by the motion of an internal rotor. The robot is modular, unactuated tail like segments can be easily added to the robot. These segments modulate the interaction of the body with the fluid to produce a variety of passive shape changes that can allow the robot to swim in different modes.

  15. Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays.

    PubMed

    Lam, Kathy N; van Bakel, Harm; Cote, Atina G; van der Ven, Anton; Hughes, Timothy R

    2011-06-01

    C2H2 zinc fingers (C2H2-ZFs) are the most prevalent type of vertebrate DNA-binding domain, and typically appear in tandem arrays (ZFAs), with sequential C2H2-ZFs each contacting three (or more) sequential bases. C2H2-ZFs can be assembled in a modular fashion, providing one explanation for their remarkable evolutionary success. Given a set of modules with defined three-base specificities, modular assembly also presents a way to construct artificial proteins with specific DNA-binding preferences. However, a recent survey of a large number of three-finger ZFAs engineered by modular assembly reported high failure rates (∼70%), casting doubt on the generality of modular assembly. Here, we used protein-binding microarrays to analyze 28 ZFAs that failed in the aforementioned study. Most (17) preferred specific sequences, which in all but one case resembled the intended target sequence. Like natural ZFAs, the engineered ZFAs typically yielded degenerate motifs, binding dozens to hundreds of related individual sequences. Thus, the failure of these proteins in previous assays is not due to lack of sequence-specific DNA-binding activity. Our findings underscore the relevance of individual C2H2-ZF sequence specificities within tandem arrays, and support the general ability of modular assembly to produce ZFAs with sequence-specific DNA-binding activity.

  16. MODULAR MANIPULATOR FOR ROBOTICS APPLICATIONS

    SciTech Connect

    Joseph W. Geisinger, Ph.D.

    2001-07-31

    ARM Automation, Inc. is developing a framework of modular actuators that can address the DOE's wide range of robotics needs. The objective of this effort is to demonstrate the effectiveness of this technology by constructing a manipulator from these actuators within a glovebox for Automated Plutonium Processing (APP). At the end of the project, the system of actuators was used to construct several different manipulator configurations, which accommodate common glovebox tasks such as repackaging. The modular nature and quickconnects of this system simplify installation into ''hot'' boxes and any potential modifications or repair therein. This work focused on the development of self-contained robotic actuator modules including the embedded electronic controls for the purpose of building a manipulator system. Both of the actuators developed under this project contain the control electronics, sensors, motor, gear train, wiring, system communications and mechanical interfaces of a complete robotics servo device. Test actuators and accompanying DISC{trademark}s underwent validation testing at The University of Texas at Austin and ARM Automation, Inc. following final design and fabrication. The system also included custom links, an umbilical cord, an open architecture PC-based system controller, and operational software that permitted integration into a completely functional robotic manipulator system. The open architecture on which this system is based avoids proprietary interfaces and communication protocols which only serve to limit the capabilities and flexibility of automation equipment. The system was integrated and tested in the contractor's facility for intended performance and operations. The manipulator was tested using the full-scale equipment and process mock-ups. The project produced a practical and operational system including a quantitative evaluation of its performance and cost.

  17. Androgen receptor in Sertoli cells regulates DNA double-strand break repair and chromosomal synapsis of spermatocytes partially through intercellular EGF-EGFR signaling.

    PubMed

    Chen, Su-Ren; Hao, Xiao-Xia; Zhang, Yan; Deng, Shou-Long; Wang, Zhi-Peng; Wang, Yu-Qian; Wang, Xiu-Xia; Liu, Yi-Xun

    2016-04-05

    Spermatogenesis does not progress beyond the pachytene stages of meiosis in Sertoli cell-specific AR knockout (SCARKO) mice. However, further evidence of meiotic arrest and underlying paracrine signals in SCARKO testes is still lacking. We utilized co-immunostaining of meiotic surface spreads to examine the key events during meiotic prophase I. SCARKO spermatocytes exhibited a failure in chromosomal synapsis observed by SCP1/SCP3 double-staining and CREST foci quantification. In addition, DNA double-strand breaks (DSBs) were formed but were not repaired in the mutant spermatocytes, as revealed by γ-H2AX staining and DNA-dependent protein kinase (DNA-PK) activity examination. The later stages of DSB repair, such as the accumulation of the RAD51 strand exchange protein and the localization of mismatch repair protein MLH1, were correspondingly altered in SCARKO spermatocytes. Notably, the expression of factors that guide RAD51 loading onto sites of DSBs, including TEX15, BRCA1/2 and PALB2, was severely impaired when either AR was down-regulated or EGF was up-regulated. We observed that some ligands in the epidermal growth factor (EGF) family were over-expressed in SCARKO Sertoli cells and that some receptors in the EGF receptor (EGFR) family were ectopically activated in the mutant spermatocytes. When EGF-EGFR signaling was repressed to approximately normal by the specific inhibitor AG1478 in the cultured SCARKO testis tissues, the arrested meiosis was partially rescued, and functional haploid cells were generated. Based on these data, we propose that AR in Sertoli cells regulates DSB repair and chromosomal synapsis of spermatocytes partially through proper intercellular EGF-EGFR signaling.

  18. Systems Biology Model of Interactions between Tissue Growth Factors and DNA Damage Pathways: Low Dose Response and Cross-Talk in TGFβ and ATM Signaling

    SciTech Connect

    Cucinotta, Francis A

    2016-09-01

    The etiology of radiation carcinogenesis has been described in terms of aberrant changes that span several levels of biological organization. Growth factors regulate many important cellular and tissue functions including apoptosis, differentiation and proliferation. A variety of genetic and epigenetic changes of growth factors have been shown to contribute to cancer initiation and progression. It is known that cellular and tissue damage to ionizing radiation is in part initiated by the production of reactive oxygen species, which can activate cytokine signaling, and the DNA damage response pathways, most notably the ATM signaling pathway. Recently the transforming growth factor β (TGFβ) pathway has been shown to regulate or directly interact with the ATM pathway in the response to radiation. The relevance of this interaction with the ATM pathway is not known although p53 becomes phosphorylated and DNA damage responses are involved. However, growth factor interactions with DNA damage responses have not been elucidated particularly at low doses and further characterization of their relationship to cancer processes is warranted. Our goal will be to use a systems biology approach to mathematically and experimentally describe the low dose responses and cross-talk between the ATM and TGFβ pathways initiated by low and high LET radiation. We will characterize ATM and TGFβ signaling in epithelial and fibroblast cells using 2D models and ultimately extending to 3D organotypic cell culture models to begin to elucidate possible differences that may occur for different cell types and/or inter-cellular communication. We will investigate the roles of the Smad and Activating transcription factor 2 (ATF2) proteins as the potential major contributors to crosstalk between the TGFβ and ATM pathways, and links to cell cycle control and/or the DNA damage response, and potential differences in their responses at low and high doses. We have developed various experimental approaches

  19. Systems Biology Model of Interactions Between Tissue Growth Factors and DNA Damage Pathways: Low Dose Response and Cross-Talk in TGFbeta and ATM Signaling

    SciTech Connect

    O'Neill, Peter; Anderson, Jennifer

    2014-10-02

    The etiology of radiation carcinogenesis has been described in terms of aberrant changes that span several levels of biological organization. Growth factors regulate many important cellular and tissue functions including apoptosis, differentiation and proliferation. A variety of genetic and epigenetic changes of growth factors have been shown to contribute to cancer initiation and progression. It is known that cellular and tissue damage to ionizing radiation is in part initiated by the production of reactive oxygen species, which can activate cytokine signaling, and the DNA damage response pathways, most notably the ATM signaling pathway. Recently the transforming growth factor β (TGFβ) pathway has been shown to regulate or directly interact with the ATM pathway in the response to radiation. The relevance of this interaction with the ATM pathway is not known although p53 becomes phosphorylated and DNA damage responses are involved. However, growth factor interactions with DNA damage responses have not been elucidated particularly at low doses and further characterization of their relationship to cancer processes is warranted. Our goal will be to use a systems biology approach to mathematically and experimentally describe the low dose responses and cross-talk between the ATM and TGFβ pathways initiated by low and high LET radiation. We will characterize ATM and TGFβ signaling in epithelial and fibroblast cells using 2D models and ultimately extending to 3D organotypic cell culture models to begin to elucidate possible differences that may occur for different cell types and/or inter-cellular communication. We will investigate the roles of the Smad and Activating transcription factor 2 (ATF2) proteins as the potential major contributors to cross- talk between the TGFβ and ATM pathways, and links to cell cycle control and/or the DNA damage response, and potential differences in their responses at low and high doses. We have developed various experimental

  20. The opportunistic pathogen Pseudomonas aeruginosa activates the DNA double-strand break signaling and repair pathway in infected cells.

    PubMed

    Elsen, Sylvie; Collin-Faure, Véronique; Gidrol, Xavier; Lemercier, Claudie

    2013-11-01

    Highly hazardous DNA double-strand breaks can be induced in eukaryotic cells by a number of agents including pathogenic bacterial strains. We have investigated the genotoxic potential of Pseudomonas aeruginosa, an opportunistic pathogen causing devastating nosocomial infections in cystic fibrosis or immunocompromised patients. Our data revealed that infection of immune or epithelial cells by P. aeruginosa triggered DNA strand breaks and phosphorylation of histone H2AX (γH2AX), a marker of DNA double-strand breaks. Moreover, it induced formation of discrete nuclear repair foci similar to gamma-irradiation-induced foci, and containing γH2AX and 53BP1, an adaptor protein mediating the DNA-damage response pathway. Gene deletion, mutagenesis, and complementation in P. aeruginosa identified ExoS bacterial toxin as the major factor involved in γH2AX induction. Chemical inhibition of several kinases known to phosphorylate H2AX demonstrated that Ataxia Telangiectasia Mutated (ATM) was the principal kinase in P. aeruginosa-induced H2AX phosphorylation. Finally, infection led to ATM kinase activation by an auto-phosphorylation mechanism. Together, these data show for the first time that infection by P. aeruginosa activates the DNA double-strand break repair machinery of the host cells. This novel information sheds new light on the consequences of P. aeruginosa infection in mammalian cells. As pathogenic Escherichia coli or carcinogenic Helicobacter pylori can alter genome integrity through DNA double-strand breaks, leading to chromosomal instability and eventually cancer, our findings highlight possible new routes for further investigations of P. aeruginosa in cancer biology and they identify ATM as a potential target molecule for drug design.

  1. Possible signaling cascades involved in attenuation of alloxan-induced oxidative stress and hyperglycemia in mice by ethanolic extract of Syzygium jambolanum: drug-DNA interaction with calf thymus DNA as target.

    PubMed

    Samadder, Asmita; Chakraborty, Debrup; De, Arnab; Bhattacharyya, Soumya Sundar; Bhadra, Kakali; Khuda-Bukhsh, Anisur Rahman

    2011-10-09

    We injected alloxan (100 mg/kg b.w.) in mice (Mus musculus) intra-peritoneally to induce hyperglycemia and divided the hyperglycemic mice into two sub-groups: one was fed ethanolic extract of Syzygium jambolanum (EESJ) (20 mg/kg b.w. for 8 weeks) and the other 85% ethyl alcohol ("vehicle"-control). Chromatographic and mass spectroscopic studies of EESJ revealed two principal components, one corresponding to an iridoid glycoside. We estimated blood glucose, glycosylated hemoglobin, glucokinase, and fructosamine and analyzed the expression of marker proteins like insulin, GLUT2, and GLUT4. We also studied anti-oxidant biomarkers like lipid peroxidase, superoxide dismutase, total thiole and catalase. We assayed generation of reactive oxygen species (ROS) and several inflammatory and apoptotic signal proteins like NFkB, IFNγ, iNOS, Bcl(2,) Bax, STAT1 and Caspase3. We further evaluated the effects of hyperglycemia on DNA through comet assay and DNA fragmentation study and assessed drug-DNA interaction by comparative analysis of circular dichroism (CD) spectral data and melting temperature profiles (T(m)) of calf thymus DNA treated with or without EESJ. We observed an elevation of all biomarkers for oxidative stress, generation of ROS and activation of NFkB and down regulation in expression of insulin, GLUT2 and glucokinase in hyperglycemic mice. Administration of EESJ reversed these changes. Histo-pathological observations of pancreas, liver and kidney also revealed relevant changes. Data of CD and (T(m)) indicated an interaction of EESJ with calf thymus DNA, indicating change in structure and conformation. Thus, EESJ has anti-oxidant as well as anti-hyperglycemic activities in diabetic mice, and potentially useful in management of hyperglycemia.

  2. Size reduction of complex networks preserving modularity

    SciTech Connect

    Arenas, A.; Duch, J.; Fernandez, A.; Gomez, S.

    2008-12-24

    The ubiquity of modular structure in real-world complex networks is being the focus of attention in many trials to understand the interplay between network topology and functionality. The best approaches to the identification of modular structure are based on the optimization of a quality function known as modularity. However this optimization is a hard task provided that the computational complexity of the problem is in the NP-hard class. Here we propose an exact method for reducing the size of weighted (directed and undirected) complex networks while maintaining invariant its modularity. This size reduction allows the heuristic algorithms that optimize modularity for a better exploration of the modularity landscape. We compare the modularity obtained in several real complex-networks by using the Extremal Optimization algorithm, before and after the size reduction, showing the improvement obtained. We speculate that the proposed analytical size reduction could be extended to an exact coarse graining of the network in the scope of real-space renormalization.

  3. Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree.

    PubMed

    Moore, Andrew D; Grath, Sonja; Schüler, Andreas; Huylmans, Ann K; Bornberg-Bauer, Erich

    2013-05-01

    Modularity is a hallmark of molecular evolution. Whether considering gene regulation, the components of metabolic pathways or signaling cascades, the ability to reuse autonomous modules in different molecular contexts can expedite evolutionary innovation. Similarly, protein domains are the modules of proteins, and modular domain rearrangements can create diversity with seemingly few operations in turn allowing for swift changes to an organism's functional repertoire. Here, we assess the patterns and functional effects of modular rearrangements at high resolution. Using a well resolved and diverse group of pancrustaceans, we illustrate arrangement diversity within closely related organisms, estimate arrangement turnover frequency and establish, for the first time, branch-specific rate estimates for fusion, fission, domain addition and terminal loss. Our results show that roughly 16 new arrangements arise per million years and that between 64% and 81% of these can be explained by simple, single-step modular rearrangement events. We find evidence that the frequencies of fission and terminal deletion events increase over time, and that modular rearrangements impact all levels of the cellular signaling apparatus and thus may have strong adaptive potential. Novel arrangements that cannot be explained by simple modular rearrangements contain a significant amount of repeat domains that occur in complex patterns which we term "supra-repeats". Furthermore, these arrangements are significantly longer than those with a single-step rearrangement solution, suggesting that such arrangements may result from multi-step events. In summary, our analysis provides an integrated view and initial quantification of the patterns and functional impact of modular protein evolution in a well resolved phylogenetic tree. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.

  4. Rational design of efficient modular cells.

    PubMed

    Trinh, Cong T; Liu, Yan; Conner, David J

    2015-11-01

    The modular cell design principle is formulated to devise modular (chassis) cells. These cells can be assembled with exchangeable production modules in a plug-and-play fashion to build microbial cell factories for efficient combinatorial biosynthesis of novel molecules, requiring minimal iterative strain optimization steps. A modular cell is designed to be auxotrophic, containing core metabolic pathways that are necessary but insufficient to support cell growth and maintenance. To be functional, it must tightly couple with an exchangeable production module containing auxiliary metabolic pathways that not only complement cell growth but also enhance production of targeted molecules. We developed a MODCELL (modular cell) framework based on metabolic pathway analysis to implement the modular cell design principle. MODCELL identifies genetic modifications and requirements to construct modular cell candidates and their associated exchangeable production modules. By defining the degree of similarity and coupling metrics, MODCELL can evaluate which exchangeable production module(s) can be tightly coupled with a modular cell candidate. We first demonstrated how MODCELL works in a step-by-step manner for example metabolic networks, and then applied it to design modular Escherichia coli cells for efficient combinatorial biosynthesis of five alcohols (ethanol, propanol, isopropanol, butanol and isobutanol) and five butyrate esters (ethyl butyrate, propyl butyrate, isopropyl butyrate, butyl butyrate and isobutyl butyrate) from pentose sugars (arabinose and xylose) and hexose sugars (glucose, mannose, and galactose) under anaerobic conditions. We identified three modular cells, MODCELL1, MODCELL2 and MODCELL3, that can couple well with Group 1 of modules (ethanol, isobutanol, butanol, ethyl butyrate, isobutyl butyrate, butyl butyrate), Group 2 (isopropanol, isopropyl butyrate), and Group 3 (propanol, isopropanol), respectively. We validated the design of MODCELL1 for anaerobic

  5. Rapid Detection of Herpes Simplex Virus DNA in Genital Ulcers by Real-Time PCR Using SYBR Green I Dye as the Detection Signal

    PubMed Central

    Aldea, Carmen; Alvarez, Carmen P.; Folgueira, Lola; Delgado, Rafael; Otero, Joaquín R.

    2002-01-01

    We have evaluated a real-time PCR procedure based on the LightCycler technology for rapid detection of herpes simplex virus (HSV) in genital lesions. Two sets of primers, corresponding to the thymidine kinase and DNA polymerase regions, were used for the amplification reactions in separate capillaries containing the SYBR Green I dye as detection signal. In 28 of 118 samples (24%), HSV was isolated by conventional cell culture. All cell culture-positive samples were also positive by real-time PCR. Six additional cell culture-negative samples were positive by PCR with both sets of primers. Total processing time was less than 3 h. Real-time PCR using SYBR Green I as detection signal is a sensitive procedure for the rapid diagnosis of HSV in genital lesions. PMID:11880439

  6. ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors

    PubMed Central

    Starick, Stephan R.; Ibn-Salem, Jonas; Jurk, Marcel; Hernandez, Céline; Love, Michael I.; Chung, Ho-Ryun; Vingron, Martin; Thomas-Chollier, Morgane; Meijsing, Sebastiaan H.

    2015-01-01

    The classical DNA recognition sequence of the glucocorticoid receptor (GR) appears to be present at only a fraction of bound genomic regions. To identify sequences responsible for recruitment of this transcription factor (TF) to individual loci, we turned to the high-resolution ChIP-exo approach. We exploited this signal by determining footprint profiles of TF binding at single-base-pair resolution using ExoProfiler, a computational pipeline based on DNA binding motifs. When applied to our GR and the few available public ChIP-exo data sets, we find that ChIP-exo footprints are protein- and recognition sequence-specific signatures of genomic TF association. Furthermore, we show that ChIP-exo captures information about TFs other than the one directly targeted by the antibody in the ChIP procedure. Consequently, the shape of the ChIP-exo footprint can be used to discriminate between direct and indirect (tethering to other DNA-bound proteins) DNA association of GR. Together, our findings indicate that the absence of classical recognition sequences can be explained by direct GR binding to a broader spectrum of sequences than previously known, either as a homodimer or as a heterodimer binding together with a member of the ETS or TEAD families of TFs, or alternatively by indirect recruitment via FOX or STAT proteins. ChIP-exo footprints also bring structural insights and locate DNA:protein cross-link points that are compatible with crystal structures of the studied TFs. Overall, our generically applicable footprint-based approach uncovers new structural and functional insights into the diverse ways of genomic cooperation and association of TFs. PMID:25720775

  7. Fluorescent trimethyl-substituted naphthyridine as a label-free signal reporter for one-step and highly sensitive fluorescent detection of DNA in serum samples.

    PubMed

    Wang, Jiamian; Wang, Xiuyun; Wu, Shuo; Che, Ruping; Luo, Pinchen; Meng, Changgong

    2017-01-15

    A facile label-free sensing method is developed for the one-step and highly sensitive fluorescent detection of DNA, which couples the specific C-C mismatch bonding and fluorescent quenching property of a trimethyl-substituted naphthyridine dye (ATMND) with the exonuclease III (Exo III) assisted cascade target recycling amplification strategy. In the absence of target DNA, the DNA hairpin probe with a C-C mismatch in the stem and more than 4 bases overhung at the 3' terminus could entrap and quench the fluorescence of ATMND and resist the digestion of Exo III, thus showing a low fluorescence background. In the presence of the target, however, the hybridization event between the two protruding segments and the target triggers the digestion reaction of Exo III, recycles the initial target, and simultaneously releases both the secondary target analogue and the ATMND caged in the stem. The released initial and secondary targets take part in another cycle of digestion, thus leading to the release of a huge amount of free ATMND for signal transducing. Based on the fluorescence recovery, the as-proposed label-free fluorescent sensing strategy shows very good analytical performances towards DNA detection, such as a wide linear range from 10pM to 1μM, a low limit of detection of 6pM, good selectivity, and a facile one-step operation at room temperature. Practical sample analysis in serum samples indicates the method has good precision and accuracy, which may thus have application potentials for point-of-care screening of DNA in complex clinical and environmental samples.

  8. The gravity duals of modular Hamiltonians

    NASA Astrophysics Data System (ADS)

    Jafferis, Daniel L.; Suh, S. Josephine

    2016-09-01

    In this work, we investigate modular Hamiltonians defined with respect to arbitrary spatial regions in quantum field theory states which have semi-classical gravity duals. We find prescriptions in the gravity dual for calculating the action of the modular Hamiltonian on its defining state, including its dual metric, and also on small excitations around the state. Curiously, use of the covariant holographic entanglement entropy formula leads us to the conclusion that the modular Hamiltonian, which in the quantum field theory acts only in the causal completion of the region, does not commute with bulk operators whose entire gauge-invariant description is space-like to the causal completion of the region.

  9. Generalized epidemic process on modular networks

    NASA Astrophysics Data System (ADS)

    Chung, Kihong; Baek, Yongjoo; Kim, Daniel; Ha, Meesoon; Jeong, Hawoong

    2014-05-01

    Social reinforcement and modular structure are two salient features observed in the spreading of behavior through social contacts. In order to investigate the interplay between these two features, we study the generalized epidemic process on modular networks with equal-sized finite communities and adjustable modularity. Using the analytical approach originally applied to clique-based random networks, we show that the system exhibits a bond-percolation type continuous phase transition for weak social reinforcement, whereas a discontinuous phase transition occurs for sufficiently strong social reinforcement. Our findings are numerically verified using the finite-size scaling analysis and the crossings of the bimodality coefficient.

  10. A Modular Approach to Redundant Robot Control

    SciTech Connect

    Anderson, R.J.

    1997-12-01

    This paper describes a modular approach for computing redundant robot kinematics. First some conventional redundant control methods are presented and shown to be `passive control laws`, i.e. they can be represented by a network consisting of passive elements. These networks are then put into modular form by applying scattering operator techniques. Additional subnetwork modules can then be added to further shape the motion. Modules for obstacle detection, joint limit avoidance, proximity sensing, and for imposing nonlinear velocity constraints are presented. The resulting redundant robot control system is modular, flexible and robust.

  11. A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation.

    PubMed

    Wan, Guohui; Hu, Xiaoxiao; Liu, Yunhua; Han, Cecil; Sood, Anil K; Calin, George A; Zhang, Xinna; Lu, Xiongbin

    2013-10-30

    A prompt and efficient DNA damage response (DDR) eliminates the detrimental effects of DNA lesions in eukaryotic cells. Basic and preclinical studies suggest that the DDR is one of the primary anti-cancer barriers during tumorigenesis. The DDR involves a complex network of processes that detect and repair DNA damage, in which long non-coding RNAs (lncRNAs), a new class of regulatory RNAs, may play an important role. In the current study, we identified a novel lncRNA, lncRNA-JADE, that is induced after DNA damage in an ataxia-telangiectasia mutated (ATM)-dependent manner. LncRNA-JADE transcriptionally activates Jade1, a key component in the HBO1 (human acetylase binding to ORC1) histone acetylation complex. Consequently, lncRNA-JADE induces histone H4 acetylation in the DDR. Markedly higher levels of lncRNA-JADE were observed in human breast tumours in comparison with normal breast tissues. Knockdown of lncRNA-JADE significantly inhibited breast tumour growth in vivo. On the basis of these results, we propose that lncRNA-JADE is a key functional link that connects the DDR to histone H4 acetylation, and that dysregulation of lncRNA-JADE may contribute to breast tumorigenesis.

  12. Cytogenetic responses to ionizing radiation exposure of human fibroblasts with knocked-down expressions of various DNA damage signaling genes

    NASA Astrophysics Data System (ADS)

    Zhang, Ye; Rohde, Larry; Wu, Honglu

    Changes of gene expression profile are one of the most important biological responses in living cells after ionizing radiation (IR) exposure. Although some studies have demonstrated that genes with up-regulated expression induced by IR may play important roles in DNA damage sensing, cell cycle checkpoint and chromosomal repair, the relationship between the regulation of gene expression by IR and its impact on cytogenetic responses to ionizing radiation has not been systematically studied. Here, the expression of 25 genes selected based on their transcriptional changes in response to IR or from their known DNA repair roles were individually knocked down by siRNA transfection in human fibroblast cells. Chromosome aberrations (CA) and micronuclei (MN) formation were measured as the cytogenetic endpoints. Our results showed that the yields of MN and/or CA formation were significantly increased by suppressed expression of some of the selected genes in DSB and other DNA repair pathways. Knocked-down expression of other genes showed significant impact on cell cycle progression, possibly because of severe impairment of DNA damage repair. Of these 11 genes that affected the cytogenetic response, 9 were up-regulated in the cells exposed to gamma radiation, suggesting that genes transcriptionally modulated by IR were critical to regulating the biological consequences after IR. Failure to express these IR-responsive genes, such as by gene mutation, could seriously change the outcome of the post IR scenario and lead to carcinogenesis.

  13. Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling

    PubMed Central

    Chaki, Moumita; Airik, Rannar; Ghosh, Amiya K.; Giles, Rachel H.; Chen, Rui; Slaats, Gisela G.; Wang, Hui; Hurd, Toby W.; Zhou, Weibin; Cluckey, Andrew; Gee, Heon-Yung; Ramaswami, Gokul; Hong, Chen-Jei; Hamilton, Bruce A.; Červenka, Igor; Ganji, Ranjani Sri; Bryja, Vitezslav; Arts, Heleen H.; van Reeuwijk, Jeroen; Oud, Machteld M.; Letteboer, Stef J.F.; Roepman, Ronald; Husson, Hervé; Ibraghimov-Beskrovnaya, Oxana; Ysunaga, Takayuki; Walz, Gerd; Eley, Lorraine; Sayer, John A.; Schermer, Bernhard; Liebau, Max C.; Benzing, Thomas; Le Corre, Stephanie; Drummond, Iain; Joles, Jaap A.; Janssen, Sabine; Allen, Susan J.; Natarajan, Sivakumar; O Toole, John F.; Attanasio, Massimo; Saunier, Sophie; Antignac, Corinne; Koenekoop, Robert K.; Ren, Huanan; Lopez, Irma; Nayir, Ahmet; Stoetzel, Corinne; Dollfus, Helene; Massoudi, Rustin; Gleeson, Joseph G.; Andreoli, Sharon P.; Doherty, Dan G.; Lindstrad, Anna; Golzio, Christelle; Katsanis, Nicholas; Pape, Lars; Abboud, Emad B.; Al-Rajhi, Ali A.; Lewis, Richard A.; Lupski, James R.; Omran, Heymut; Lee, Eva; Wang, Shaohui; Sekiguchi, JoAnn M.; Saunders, Rudel; Johnson, Colin A.; Garner, Elizabeth; Vanselow, Katja; Andersen, Jens S.; Shlomai, Joseph; Nurnberg, Gudrun; Nurnberg, Peter; Levy, Shawn; Smogorzewska, Agata; Otto, Edgar A.; Hildebrandt, Friedhelm

    2012-01-01

    SUMMARY Nephronophthisis-related ciliopathies (NPHP-RC) are degenerative recessive diseases that affect kidney, retina and brain. Genetic defects in NPHP gene products that localize to cilia and centrosomes defined them as ‘ciliopathies’. However, disease mechanisms remain poorly understood. Here we identify by whole exome resequencing, mutations of MRE11, ZNF423, and CEP164 as causing NPHP-RC. All three genes function within the DNA damage response (DDR) pathway, hitherto not implicated in ciliopathies. We demonstrate that, upon induced DNA damage, the NPHP-RC proteins ZNF423, CEP164 and NPHP10 colocalize to nuclear foci positive for TIP60, known to activate ATM at sites of DNA damage. We show that knockdown of CEP164 or ZNF423 causes sensitivity to DNA damaging agents, and that cep164 knockdown in zebrafish results in dysregulated DDR and an NPHP-RC phenotype. We identify TTBK2, CCDC92, NPHP3 and DVL3 as novel CEP164 interaction partners. Our findings link degenerative diseases of kidney and retina, disorders of increasing prevalence, to mechanisms of DDR. PMID:22863007

  14. Modular optimization code package: MOZAIK

    NASA Astrophysics Data System (ADS)

    Bekar, Kursat B.

    This dissertation addresses the development of a modular optimization code package, MOZAIK, for geometric shape optimization problems in nuclear engineering applications. MOZAIK's first mission, determining the optimal shape of the D2O moderator tank for the current and new beam tube configurations for the Penn State Breazeale Reactor's (PSBR) beam port facility, is used to demonstrate its capabilities and test its performance. MOZAIK was designed as a modular optimization sequence including three primary independent modules: the initializer, the physics and the optimizer, each having a specific task. By using fixed interface blocks among the modules, the code attains its two most important characteristics: generic form and modularity. The benefit of this modular structure is that the contents of the modules can be switched depending on the requirements of accuracy, computational efficiency, or compatibility with the other modules. Oak Ridge National Laboratory's discrete ordinates transport code TORT was selected as the transport solver in the physics module of MOZAIK, and two different optimizers, Min-max and Genetic Algorithms (GA), were implemented in the optimizer module of the code package. A distributed memory parallelism was also applied to MOZAIK via MPI (Message Passing Interface) to execute the physics module concurrently on a number of processors for various states in the same search. Moreover, dynamic scheduling was enabled to enhance load balance among the processors while running MOZAIK's physics module thus improving the parallel speedup and efficiency. In this way, the total computation time consumed by the physics module is reduced by a factor close to M, where M is the number of processors. This capability also encourages the use of MOZAIK for shape optimization problems in nuclear applications because many traditional codes related to radiation transport do not have parallel execution capability. A set of computational models based on the

  15. M@IA: a modular open-source application for microarray workflow and integrative datamining.

    PubMed

    Le Béchec, Antony; Zindy, Pierre; Sierocinski, Thomas; Petritis, Dimitri; Bihouée, Audrey; Le Meur, Nolwenn; Léger, Jean; Théret, Nathalie

    2008-01-01

    Microarray technology is a widely used approach to gene expression analysis. Many tools for microarray management and data analysis have been developed, and recently new methods have been proposed for deciphering biological pathways by integrating microarray data with other data sources. However, to improve microarray analysis and provide meaningful gene interaction networks, integrated software solutions are still needed. Therefore, we developed M@IA, an environment for DNA microarray data analysis allowing gene network reconstruction. M@IA is a microarray integrated application which includes all of the steps of a microarray study, from MIAME-compliant raw data storage and processing gene expression analysis. Furthermore, M@IA allows automatic gene annotation based on ontology, metabolic/signalling pathways, protein interaction, miRNA and transcriptional factor associations, as well as integrative analysis of gene interaction networks. Statistical and graphical methods facilitate analysis, yielding new hypotheses on gene expression data. To illustrate our approach, we applied M@IA modules to microarray data taken from an experiment on liver tissue. We integrated differentially expressed genes with additional biological information, thus identifying new molecular interaction networks that are associated with fibrogenesis. M@IA is a new application for microarray management and data analysis, offering functional insights into microarray data by the combination of gene expression data and biological knowledge annotation based on interactive graphs. M@IA is an interactive multi-user interface based on a flexible modular architecture and it is freely available for academic users at http://maia.genouest.org.

  16. H2AX phosphorylation in response to DNA double-strand break formation during bystander signalling: effect of microRNA knockdown.

    PubMed

    Dickey, Jennifer S; Zemp, Franz J; Altamirano, Alvin; Sedelnikova, Olga A; Bonner, William M; Kovalchuk, Olga

    2011-02-01

    Upon DNA double-strand break (DSB) formation, hundreds of H2AX molecules in the chromatin flanking the break site are phosphorylated on serine residue 139, termed gamma-H2AX, so that virtually every DSB site in a nucleus can be visualised within 10 min of its formation using an antibody to gamma-H2AX. One application of this sensitive assay is to examine the induction of DNA double-strand damage in subtle non-targeted cellular effects such as the bystander effect. Here whether microRNA (miRNA) serve as a primary signalling mechanism for bystander effect propagation by comparing matched human colon carcinoma cell lines with wild-type or depleted levels of mature miRNAs was investigated. No major differences were found in the levels of induced gamma-H2AX foci in the tested cell lines, indicating that though miRNAs play a role in bystander effect manifestation, they appear not to be the primary bystander signalling molecules in the formation of bystander effect-induced DSBs.

  17. Neuronal DNA damage response‐associated dysregulation of signalling pathways and cholesterol metabolism at the earliest stages of Alzheimer‐type pathology

    PubMed Central

    Simpson, Julie E.; Ince, Paul G.; Minett, Thais; Matthews, Fiona E.; Heath, Paul R.; Shaw, Pamela J.; Goodall, Emily; Garwood, Claire J.; Ratcliffe, Laura E.; Brayne, Carol; Rattray, Magnus

    2015-01-01

    Aims Oxidative damage and an associated DNA damage response (DDR) are evident in mild cognitive impairment and early Alzheimer's disease, suggesting that neuronal dysfunction resulting from oxidative DNA damage may account for some of the cognitive impairment not fully explained by Alzheimer‐type pathology. Methods Frontal cortex (Braak stage 0–II) was obtained from the Medical Research Council's Cognitive Function and Ageing Study cohort. Neurones were isolated from eight cases (four high and four low DDR) by laser capture microdissection and changes in the transcriptome identified by microarray analysis. Results Two thousand three hundred seventy‐eight genes were significantly differentially expressed (1690 up‐regulated, 688 down‐regulated, P < 0.001) in cases with a high neuronal DDR. Functional grouping identified dysregulation of cholesterol biosynthesis, insulin and Wnt signalling, and up‐regulation of glycogen synthase kinase 3β. Candidate genes were validated by quantitative real‐time polymerase chain reaction. Cerebrospinal fluid levels of 24(S)‐hydroxycholesterol associated with neuronal DDR across all Braak stages (r s = 0.30, P = 0.03). Conclusions A persistent neuronal DDR may result in increased cholesterol biosynthesis, impaired insulin and Wnt signalling, and increased GSK3β, thereby contributing to neuronal dysfunction independent of Alzheimer‐type pathology in the ageing brain. PMID:26095650

  18. A sequence-specific DNA binding small molecule triggers the release of immunogenic signals and phagocytosis in a model of B-cell lymphoma

    PubMed Central

    Kang, JeenJoo S.; Dervan, Peter B.

    2016-01-01

    Means to cause an immunogenic cell death could lead to significant insight into how cancer escapes immune control. In this study, we screened a library of five pyrrole–imidazole polyamides coding for different DNA sequences in a model of B-cell lymphoma for the upregulation of surface calreticulin, a pro-phagocytosis signal implicated in immunogenic cell death. We found that hairpin polyamide 1 triggers the release of the damage-associated molecular patterns calreticulin, ATP and HMGB1 in a slow necrotic-type cell death. Consistent with this signaling, we observed an increase in the rate of phagocytosis by macrophages after the cancer cells were exposed to polyamide 1. The DNA sequence preference of polyamide 1 is 5′-WGGGTW-3′ (where W = A/T), indicated by the pairing rules and confirmed by the Bind-n-Seq method. The close correspondence of this sequence with the telomere-repeat sequence suggests a potential mechanism of action through ligand binding at the telomere. This study reveals a chemical means to trigger an inflammatory necrotic cell death in cancer cells. PMID:26537405

  19. A signal-on fluorescent aptasensor based on single-stranded DNA-sensitized luminescence of terbium (III) for label-free detection of breast cancer cells.

    PubMed

    Cai, Shuxian; Li, Guangwen; Zhang, Xi; Xia, Yaokun; Chen, Mei; Wu, Dongzhi; Chen, Qiuxiang; Zhang, Jing; Chen, Jinghua

    2015-06-01

    Breast cancer is the most common type of malignant tumor in women. Recently, it has been shown that detection of breast cancer tumor cells outside the primitive tumor is an effective early diagnosis with great prognostic and clinical utility. For this purpose, we developed a signal-on fluorescence aptasensor for label-free, facile and sensitive detection of MCF-7 breast cancer cells. Due to target-aptamer specific recognition and single-stranded DNA-sensitized luminescence of terbium (III), the proposed aptasensor exhibits excellent sensitivity with detection limit as low as 70 cells mL(-1). Compared with common organic dyes and the emerging nano-technological probes, the combination of terbium (III) and single-stranded DNA signal probe (Tb(3+)-SP) serves as a more powerful bio-probe because of its stable optical property, good biocompatibility and free from complex synthesis. The feasibility investigations have illustrated the potential applicability of this aptasensor for selective and sensitive detection of MCF-7 breast cancer cells. Moreover, this proposed aptasensor can be also extended for the determination of other tumor cancers or bio-molecules by altering corresponding aptamers. Taken together, this easy-to-perform aptasensor may represent a promising way for early screening and detection of tumor cancers or other bio-molecules in clinical diagnosis.

  20. Modular digital holographic fringe data processing system

    NASA Technical Reports Server (NTRS)

    Downward, J. G.; Vavra, P. C.; Schebor, F. S.; Vest, C. M.

    1985-01-01

    A software architecture suitable for reducing holographic fringe data into useful engineering data is developed and tested. The results, along with a detailed description of the proposed architecture for a Modular Digital Fringe Analysis System, are presented.

  1. Modular Solar Electric Power (MSEP) Systems (Presentation)

    SciTech Connect

    Hassani, V.

    2000-06-18

    This presentation discusses the development and deployment of Modular Solar Electric Power (MSEP) systems, the feasibility of application of existing binary power cycles to solar trough technology, and identification of next action items.

  2. Modular biowaste monitoring system conceptual design

    NASA Technical Reports Server (NTRS)

    Fogal, G. L.

    1974-01-01

    The objective of the study was to define requirements and generate a conceptual design for a Modular Biowaste Monitoring System for specifically supporting shuttle life science experimental and diagnostic programs.

  3. A 3-d modular gripper design tool

    SciTech Connect

    Brown, R.G.; Brost, R.C.

    1997-01-01

    Modular fixturing kits are precisely machined sets of components used for flexible, short-turnaround construction of fixtures for a variety of manufacturing purposes. A modular vise is a parallel-jaw vise, where each jaw is a modular fixture plate with a regular grid of precisely positioned holes. A modular vise can be used to locate and hold parts for machining, assembly, and inspection tasks. To fixture a part, one places pins in some of the holes so that when the vise is closed, the part is reliably located and completely constrained. The modular vise concept can be adapted easily to the design of modular parallel-jaw grippers for robots. By attaching a grid plate to each jaw of a parallel-jaw gripper, the authors gain the ability to easily construct high-quality grasps for a wide variety of parts from a standard set of hardware. Wallack and Canny developed a previous algorithm for planning planar grasp configurations for the modular vise. In this paper, the authors expand this work to produce a 3-d fixture/gripper design tool. They describe several analyses added to the planar algorithm to improve its utility, including a three-dimensional grasp quality metric based on geometric and force information, three-dimensional geometric loading analysis, and inter-gripper interference analysis to determine the compatibility of multiple grasps for handing the part from one gripper to another. Finally, the authors describe two applications which combine the utility of modular vise-style grasping with inter-gripper interference: The first is the design of a flexible part-handling subsystem for a part cleaning workcell under development at Sandia National Laboratories; the second is the automatic design of grippers that support the assembly of multiple products on a single assembly line.

  4. Modular Programming Techniques for Distributed Computing Tasks

    DTIC Science & Technology

    2004-08-01

    Modular Programming Techniques for Distributed Computing Tasks Anthony Cowley, Hwa-Chow Hsu, Camillo J. Taylor GRASP Laboratory University of...network, distributed computing , software design 1. INTRODUCTION As efforts to field sensor networks, or teams of mobile robots, become more...TITLE AND SUBTITLE Modular Programming Techniques for Distributed Computing Tasks 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER

  5. Optimal Network Modularity for Information Diffusion

    NASA Astrophysics Data System (ADS)

    Nematzadeh, Azadeh; Ferrara, Emilio; Flammini, Alessandro; Ahn, Yong-Yeol

    2014-08-01

    We investigate the impact of community structure on information diffusion with the linear threshold model. Our results demonstrate that modular structure may have counterintuitive effects on information diffusion when social reinforcement is present. We show that strong communities can facilitate global diffusion by enhancing local, intracommunity spreading. Using both analytic approaches and numerical simulations, we demonstrate the existence of an optimal network modularity, where global diffusion requires the minimal number of early adopters.

  6. Adaptive Coupled Oscillators for Modular Robots

    NASA Astrophysics Data System (ADS)

    Hartono, Pitoyo; Nakane, Aito

    In this research we physically built several robotics modules that are able to self-discover a connection topology which allows them to generate a coordinated behavior as an integrated modular robot. We consider that this self-configurability of hardware module can potentially simplify the costly designing process of complicated robots and at the same time improve the resiliency of modular robots in the face of internal and external changes.

  7. The Error-Prone DNA Polymerase κ Promotes Temozolomide Resistance in Glioblastoma through Rad17-Dependent Activation of ATR-Chk1 Signaling.

    PubMed

    Peng, Chenghao; Chen, Zhengxin; Wang, Shuai; Wang, Hong-Wei; Qiu, Wenjin; Zhao, Lin; Xu, Ran; Luo, Hui; Chen, Yuanyuan; Chen, Dan; You, Yongping; Liu, Ning; Wang, Huibo

    2016-04-15

    The acquisition of drug resistance is a persistent clinical problem limiting the successful treatment of human cancers, including glioblastoma (GBM). However, the molecular mechanisms by which initially chemoresponsive tumors develop therapeutic resistance remain poorly understood. In this study, we report that Pol κ, an error-prone polymerase that participates in translesion DNA synthesis, was significantly upregulated in GBM cell lines and tumor tissues following temozolomide treatment. Overexpression of Pol κ in temozolomide-sensitive GBM cells conferred resistance to temozolomide, whereas its inhibition markedly sensitized resistant cells to temozolomide in vitro and in orthotopic xenograft mouse models. Mechanistically, depletion of Pol κ disrupted homologous recombination (HR)-mediated repair and restart of stalled replication forks, impaired the activation of ATR-Chk1 signaling, and delayed cell-cycle re-entry and progression. Further investigation of the relationship between Pol κ and temozolomide revealed that Pol κ inactivation facilitated temozolomide-induced Rad17 ubiquitination and proteasomal degradation, subsequently silencing ATR-Chk1 signaling and leading to defective HR repair and the reversal of temozolomide resistance. Moreover, overexpression of Rad17 in Pol κ-depleted GBM cells restored HR efficiency, promoted the clearance of temozolomide-induced DNA breaks, and desensitized cells to the cytotoxic effects of temozolomide observed in the absence of Pol κ. Finally, we found that Pol κ overexpression correlated with poor prognosis in GBM patients undergoing temozolomide therapy. Collectively, our findings identify a potential mechanism by which GBM cells develop resistance to temozolomide and suggest that targeting the DNA damage tolerance pathway may be beneficial for overcoming resistance. Cancer Res; 76(8); 2340-53. ©2016 AACR.

  8. Employment of bromophenol red and bovine serum albumin as luminol signal co-enhancer in chemiluminescent detection of sequence-specific DNA.

    PubMed

    Yu, Xiaoqian; Sheng, Yingying; Zhao, Yanjun; Fan, Aiping

    2016-01-01

    Bromophenol red, known as chemical indicator, was found to act as a novel potent signal enhancer of the peroxidase-catalyzed luminol-H2O2 chemiluminescent (CL) reaction. It was found interestingly that bovine serum albumin (BSA) played a role in the enhanced chemiluminescent reaction (ECR). The addition of 2.5 mg mL(-1) BSA into bromophenol red-enhance CL system showed 36 times stronger CL signal than that without addition of BSA. Mechanism study showed that the luminophors in the ECR were still 3-aminophthalate ion in an excited state (3-APA*). In addition, singlet oxygen ((1)O2) and hydroxyl radical ((∙)OH) played a role in the ECR. The possible mechanism was discussed in the present study. The effect of pH, reaction time, and concentration of bromophenol red, BSA, luminol, and H2O2 on CL intensity of the peroxidase-catalyzed CL reaction was studied. The detection limit value (LOD) of HRP and streptavidin-modified HRP in the proposed ECR with bromophenol red and BSA was 0.20 ng mL(-1) and 0.05 ng mL(-1), respectively. This novel luminol-H2O2-HRP-bromophenol red-BSA CL system was applied to the CL detection of sequence-specific DNA based on a magnetic separation process. As low as 0.4 fmol of target DNA could be sensitively detected using the proposed CL system without any amplification process. The obtained results demonstrate very promising perspectives for using bromophenol red and BSA to improve the sensitivity of CL detection of sequence-specific DNA. In addition, this novel ECR system can also be generalized for CL immunoassay, CL western blotting, and so on.

  9. γH2AX foci on apparently intact mitotic chromosomes: not signatures of misrejoining events but signals of unresolved DNA damage.

    PubMed

    Martín, Marta; Terradas, Mariona; Hernández, Laia; Genescà, Anna

    2014-01-01

    The presence of γH2AX foci on apparently intact mitotic chromosomes is controversial because they challenge the assumed relationship between γH2AX foci and DNA double-strand breaks (DSBs). In this work, we show that after irradiation during interphase, a variety of γH2AX foci are scored in mitotic cells. Surprisingly, approximately 80% of the γH2AX foci spread over apparently undamaged chromatin at Terminal or Interstitial positions and they can display variable sizes, thus being classified as Small, Medium and Big foci. Chromosome and chromatid breaks that reach mitosis are spotted with Big (60%) and Medium (30%) Terminal γH2AX foci, but very rarely are they signaled with Small γH2AX foci. To evaluate if Interstitial γH2AX foci might be signatures of misrejoining, an mFISH analysis was performed on the same slides. The results show that Interstitial γH2AX foci lying on apparently intact chromatin do not mark sites of misrejoining, and that misrejoined events were never signaled by a γH2AX foci during mitosis. Finally, when analyzing the presence of other DNA-damage response (DDR) factors we found that all γH2AX foci-regardless their coincidence with a visible break-always colocalized with MRE11, but not with 53BP1. This pattern suggests that these γH2AX foci may be hallmarks of both microscopically visible and invisible DNA damage, in which an active, although incomplete or halted DDR is taking place.

  10. Bipartite Recognition of DNA by TCF/Pangolin Is Remarkably Flexible and Contributes to Transcriptional Responsiveness and Tissue Specificity of Wingless Signaling

    PubMed Central

    Archbold, Hilary C.; Broussard, Chris; Chang, Mikyung V.; Cadigan, Ken M.

    2014-01-01

    The T-cell factor (TCF) family of transcription factors are major mediators of Wnt/β-catenin signaling in metazoans. All TCFs contain a High Mobility Group (HMG) domain that possesses specific DNA binding activity. In addition, many TCFs contain a second DNA binding domain, the C-clamp, which binds to DNA motifs referred to as Helper sites. While HMG and Helper sites are both important for the activation of several Wnt dependent cis-regulatory modules (W-CRMs), the rules of what constitutes a functional HMG-Helper site pair are unknown. In this report, we employed a combination of in vitro binding, reporter gene analysis and bioinformatics to address this question, using the Drosophila family member TCF/Pangolin (TCF/Pan) as a model. We found that while there were constraints for the orientation and spacing of HMG-Helper pairs, the presence of a Helper site near a HMG site in any orientation increased binding and transcriptional response, with some orientations displaying tissue-specific patterns. We found that altering an HMG-Helper site pair from a sub-optimal to optimal orientation/spacing dramatically increased the responsiveness of a W-CRM in several fly tissues. In addition, we used the knowledge gained to bioinformatically identify two novel W-CRMs, one that was activated by Wnt/β-catenin signaling in the prothoracic gland, a tissue not previously connected to this pathway. In sum, this work extends the importance of Helper sites in fly W-CRMs and suggests that the type of HMG-Helper pair is a major factor in setting the threshold for Wnt activation and tissue-responsiveness. PMID:25188465

  11. Bipartite recognition of DNA by TCF/Pangolin is remarkably flexible and contributes to transcriptional responsiveness and tissue specificity of wingless signaling.

    PubMed

    Archbold, Hilary C; Broussard, Chris; Chang, Mikyung V; Cadigan, Ken M

    2014-09-01

    The T-cell factor (TCF) family of transcription factors are major mediators of Wnt/β-catenin signaling in metazoans. All TCFs contain a High Mobility Group (HMG) domain that possesses specific DNA binding activity. In addition, many TCFs contain a second DNA binding domain, the C-clamp, which binds to DNA motifs referred to as Helper sites. While HMG and Helper sites are both important for the activation of several Wnt dependent cis-regulatory modules (W-CRMs), the rules of what constitutes a functional HMG-Helper site pair are unknown. In this report, we employed a combination of in vitro binding, reporter gene analysis and bioinformatics to address this question, using the Drosophila family member TCF/Pangolin (TCF/Pan) as a model. We found that while there were constraints for the orientation and spacing of HMG-Helper pairs, the presence of a Helper site near a HMG site in any orientation increased binding and transcriptional response, with some orientations displaying tissue-specific patterns. We found that altering an HMG-Helper site pair from a sub-optimal to optimal orientation/spacing dramatically increased the responsiveness of a W-CRM in several fly tissues. In addition, we used the knowledge gained to bioinformatically identify two novel W-CRMs, one that was activated by Wnt/β-catenin signaling in the prothoracic gland, a tissue not previously connected to this pathway. In sum, this work extends the importance of Helper sites in fly W-CRMs and suggests that the type of HMG-Helper pair is a major factor in setting the threshold for Wnt activation and tissue-responsiveness.

  12. A 3-d modular gripper design tool

    SciTech Connect

    Brown, R.G.; Brost, R.C.

    1997-02-01

    Modular fixturing kits are sets of components used for flexible, rapid construction of fixtures. A modular vise is a parallel-jaw vise, each jaw of which is a modular fixture plate with a regular grid of precisely positioned holes. To fixture a part, one places pins in some of the holes so that when the vise is closed, the part is reliably located and completely constrained. The modular vise concept can be adapted easily to the design of modular parallel-jaw grippers for robots. By attaching a grid-plate to each jaw of a parallel-jaw gripper, one gains the ability to easily construct high-quality grasps for a wide variety of parts from a standard set of hardware. Wallack and Canny developed an algorithm for planning planar grasp configurations for the modular vise. In this paper, the authors expand this work to produce a 3-d fixture/gripper design tool. They describe several analyses they have added to the planar algorithm, including a 3-d grasp quality metric based on force information, 3-d geometric loading analysis, and inter-gripper interference analysis. Finally, the authors describe two applications of their code. One of these is an internal application at Sandia, while the other shows a potential use of the code for designing part of an agile assembly line.

  13. Managing in an age of modularity.

    PubMed

    Baldwin, C Y; Clark, K B

    1997-01-01

    Modularity is a familiar principle in the computer industry. Different companies can independently design and produce components, suck as disk drives or operating software, and those modules will fit together into a complex and smoothly functioning product because the module makers obey a given set of design rules. Modularity in manufacturing is already common in many companies. But now a number of them are beginning to extend the approach into the design of their products and services. Modularity in design should tremendously boost the rate of innovation in many industries as it did in the computer industry. As businesses as diverse as auto manufacturing and financial services move toward modular designs, the authors say, competitive dynamics will change enormously. No longer will assemblers control the final product: suppliers of key modules will gain leverage and even take on responsibility for design rules. Companies will compete either by specifying the dominant design rules (as Microsoft does) or by producing excellent modules (as disk drive maker Quantum does). Leaders in a modular industry will control less, so they will have to watch the competitive environment closely for opportunities to link up with other module makers. They will also need to know more: engineering details that seemed trivial at the corporate level may now play a large part in strategic decisions. Leaders will also become knowledge managers internally because they will need to coordinate the efforts of development groups in order to keep them focused on the modular strategies the company is pursuing.

  14. Functional Modularity of Background Activities in Normal and Epileptic Brain Networks

    NASA Astrophysics Data System (ADS)

    Chavez, M.; Valencia, M.; Navarro, V.; Latora, V.; Martinerie, J.

    2010-03-01

    We analyze the connectivity structure of weighted brain networks extracted from spontaneous magnetoencephalographic signals of healthy subjects and epileptic patients (suffering from absence seizures) recorded at rest. We find that, for the activities in the 5-14 Hz range, healthy brains exhibit a sparse connectivity, whereas the brain networks of patients display a rich connectivity with a clear modular structure. Our results suggest that modularity plays a key role in the functional organization of brain areas during normal and pathological neural activities at rest.

  15. Modular Wideband Active Vibration Absorber

    NASA Technical Reports Server (NTRS)

    Smith, David R.; Zewari, Wahid; Lee, Kenneth Y.

    1999-01-01

    A comparison of space experiments with previous missions shows a common theme. Some of the recent experiments are based on the scientific fundamentals of instruments of prior years. However, the main distinguishing characteristic is the embodiment of advances in engineering and manufacturing in order to extract clearer and sharper images and extend the limits of measurement. One area of importance to future missions is providing vibration free observation platforms at acceptable costs. It has been shown by researchers that vibration problems cannot be eliminated by passive isolation techniques alone. Therefore, various organizations have conducted research in the area of combining active and passive vibration control techniques. The essence of this paper is to present progress in what is believed to be a new concept in this arena. It is based on the notion that if one active element in a vibration transmission path can provide a reasonable vibration attenuation, two active elements in series may provide more control options and better results. The paper presents the functions of a modular split shaft linear actuator developed by NASA's Goddard Space Flight Center and University of Massachusetts Lowell. It discusses some of the control possibilities facilitated by the device. Some preliminary findings and problems are also discussed.

  16. Modular verification of concurrent systems

    SciTech Connect

    Sobel, A.E.K.

    1986-01-01

    During the last ten years, a number of authors have proposed verification techniques that allow one to prove properties of individual processes by using global assumptions about the behavior of the remaining processes in the distributed program. As a result, one must justify these global assumptions before drawing any conclusions regarding the correctness of the entire program. This justification is often the most difficult part of the proof and presents a serious obstacle to hierarchical program development. This thesis develops a new approach to the verification of concurrent systems. The approach is modular and supports compositional development of programs since the proofs of each individual process of a program are completely isolated from all others. The generality of this approach is illustrated by applying it to a representative set of contemporary concurrent programming languages, namely: CSP, ADA, Distributed Processes, and a shared variable language. In addition, it is also shown how the approach may be used to deal with a number of other constructs that have been proposed for inclusion in concurrent languages: FORK and JOIN primitives, nested monitor calls, path expressions, atomic transactions, and asynchronous message passing. These results allow argument that the approach is universal and can be used to design proof systems for any concurrent language.

  17. Theory for the Emergence of Modularity in Complex Systems

    NASA Astrophysics Data System (ADS)

    Deem, Michael; Park, Jeong-Man

    2013-03-01

    Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here develop a theory for the dynamics of modularity in these systems. We find a principle of least action for the evolved modularity at long times. In addition, we find a fluctuation dissipation relation for the rate of change of modularity at short times. We discuss a number of biological and social systems that can be understood with this framework. The modularity of the protein-protein interaction network increases when yeast are exposed to heat shock, and the modularity of the protein-protein networks in both yeast and E. coli appears to have increased over evolutionary time. Food webs in low-energy, stressful environments are more modular than those in plentiful environments, arid ecologies are more modular during droughts, and foraging of sea otters is more modular when food is limiting. The modularity of social networks changes over time: stock brokers instant messaging networks are more modular under stressful market conditions, criminal networks are more modular under increased police pressure, and world trade network modularity has decreased

  18. MicroRNA-101 suppresses progression of lung cancer through the PTEN/AKT signaling pathway by targeting DNA methyltransferase 3A

    PubMed Central

    Wang, Lumin; Yao, Jiayi; Sun, Hongfei; He, Kang; Tong, Dongdong; Song, Tusheng; Huang, Chen

    2017-01-01

    It is well established that transcriptional silencing of critical tumor suppressor genes by DNA methylation is a fundamental process in the initiation of lung cancer. However, the involvement of microRNAs (miRNAs) in restoring abnormal DNA methylation patterns in lung cancer is not well understood. Therefore, and since miRNA-101 is complementary to the 3′-untranslated region of DNA methyltransferase 3A (DNMT3A), we investigated whether miRNA-101 could restore normal DNA methylation patterns in lung cancer cell lines. Bioinformatics has indicated that DNMT3A is a major target of miR-101. In addition, the overexpression of miR-101 downregulates DNMT3A. Using a methylation-specific polymerase chain reaction assay, we demonstrated that methylation of the phosphatase and tensin homolog (PTEN) promoter was reduced in A549 cells transfected with miR-101, but not in the transfected control. Furthermore, overexpression of miR-101 and silencing of DNMT3A suppressed lung cell proliferation and S/G2 transition, and increased apoptosis through the PTEN/AKT pathway in vitro. Furthermore, we observed the opposite phenomenon in A549 cells transfected with a miR-101 inhibitor. Subsequent investigation revealed that overexpression of miR-101 significantly inhibited the tumorigenicity of A549 cells in a nude mouse xenograft model. These results demonstrate that miR-101 affects lung cancer progression through the PTEN/AKT signaling pathway by targeting DNMT3A in lung cells, suggesting that miR-101 may be a novel potential therapeutic strategy in lung cancer treatment. PMID:28123563

  19. Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling.

    PubMed

    Nones, Katia; Waddell, Nic; Song, Sarah; Patch, Ann-Marie; Miller, David; Johns, Amber; Wu, Jianmin; Kassahn, Karin S; Wood, David; Bailey, Peter; Fink, Lynn; Manning, Suzanne; Christ, Angelika N; Nourse, Craig; Kazakoff, Stephen; Taylor, Darrin; Leonard, Conrad; Chang, David K; Jones, Marc D; Thomas, Michelle; Watson, Clare; Pinese, Mark; Cowley, Mark; Rooman, Ilse; Pajic, Marina; Butturini, Giovanni; Malpaga, Anna; Corbo, Vincenzo; Crippa, Stefano; Falconi, Massimo; Zamboni, Giuseppe; Castelli, Paola; Lawlor, Rita T; Gill, Anthony J; Scarpa, Aldo; Pearson, John V; Biankin, Andrew V; Grimmond, Sean M

    2014-09-01

    The importance of epigenetic modifications such as DNA methylation in tumorigenesis is increasingly being appreciated. To define the genome-wide pattern of DNA methylation in pancreatic ductal adenocarcinomas (PDAC), we captured the methylation profiles of 167 untreated resected PDACs and compared them to a panel of 29 adjacent nontransformed pancreata using high-density arrays. A total of 11,634 CpG sites associated with 3,522 genes were significantly differentially methylated (DM) in PDAC and were capable of segregating PDAC from non-malignant pancreas, regardless of tumor cellularity. As expected, PDAC hypermethylation was most prevalent in the 5' region of genes (including the proximal promoter, 5'UTR and CpG islands). Approximately 33% DM genes showed significant inverse correlation with mRNA expression levels. Pathway analysis revealed an enrichment of aberrantly methylated genes involved in key molecular mechanisms important to PDAC: TGF-β, WNT, integrin signaling, cell adhesion, stellate cell activation and axon guidance. Given the recent discovery that SLIT-ROBO mutations play a clinically important role in PDAC, the role of epigenetic perturbation of axon guidance was pursued in more detail. Bisulfite amplicon deep sequencing and qRT-PCR expression analyses confirmed recurrent perturbation of axon guidance pathway genes SLIT2, SLIT3, ROBO1, ROBO3, ITGA2 and MET and suggests epigenetic suppression of SLIT-ROBO signaling and up-regulation of MET and ITGA2 expression. Hypomethylation of MET and ITGA2 correlated with high gene expression, which was associated with poor survival. These data suggest that aberrant methylation plays an important role in pancreatic carcinogenesis affecting core signaling pathways with potential implications for the disease pathophysiology and therapy.

  20. Fitness, environmental changes and the growth of modularity- a quasispecies theory for the evolutionary dynamics of modularity

    NASA Astrophysics Data System (ADS)

    Niestemski, Liang; Park, Jeong-Man; Deem, Michael

    2015-03-01

    Although the modularity of a biological system is demonstrated and recognized, the evolution of the modularity is not well understood. We here present a quasispecies theory for the evolutionary dynamics of modularity. Complemented with numerical models, this analytical theory shows the calculation of the steady-state fitness in a randomly changing environment, the relationship between rate of environmental changes and rate of growth of modularity, as well as a principle of least action for the evolved modularity at steady state.

  1. Structural basis for the Smad5 MH1 domain to recognize different DNA sequences

    PubMed Central

    Chai, Nan; Li, Wan-Xin; Wang, Jue; Wang, Zhi-Xin; Yang, Shi-Ming; Wu, Jia-Wei

    2015-01-01

    Smad proteins are important intracellular mediators of TGF-β signalling, which transmit signals directly from cell surface receptors to the nucleus. The MH1 domain of Smad plays a key role in DNA recognition. Two types of DNA sequence were identified as Smad binding motifs: the Smad binding element (SBE) and the GC-rich sequence. Here we report the first crystal structure of the Smad5 MH1 domain in complex with the GC-rich sequence. Compared with the Smad5-MH1/SBE complex structure, the Smad5 MH1 domain contacts the GC-rich site with the same β-hairpin, but the detailed interaction modes are different. Conserved β-hairpin residues make base specific contacts with the minimal GC-rich site, 5′-GGC-3′. The assembly of Smad5-MH1 on the GC-rich DNA also results in distinct DNA conformational changes. Moreover, the crystal structure of Smad5-MH1 in complex with a composite DNA sequence demonstrates that the MH1 domain is targeted to each binding site (GC-rich or SBE) with modular binding modes, and the length of the DNA spacer affects the MH1 assembly. In conclusion, our work provides the structural basis for the recognition and binding specificity of the Smad MH1 domain with the DNA targets. PMID:26304548

  2. Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: the molecular choreography.

    PubMed

    Thompson, Larry H

    2012-01-01

    The faithful maintenance of chromosome continuity in human cells during DNA replication and repair is critical for preventing the conversion of normal diploid cells to an oncogenic state. The evolution of higher eukaryotic cells endowed them with a large genetic investment in the molecular machinery that ensures chromosome stability. In mammalian and other vertebrate cells, the elimination of double-strand breaks with minimal nucleotide sequence change involves the spatiotemporal orchestration of a seemingly endless number of proteins ranging in their action from the nucleotide level to nucleosome organization and chromosome architecture. DNA DSBs trigger a myriad of post-translational modifications that alter catalytic activities and the specificity of protein interactions: phosphorylation, acetylation, methylation, ubiquitylation, and SUMOylation, followed by the reversal of these changes as repair is completed. "Superfluous" protein recruitment to damage sites, functional redundancy, and alternative pathways ensure that DSB repair is extremely efficient, both quantitatively and qualitatively. This review strives to integrate the information about the molecular mechanisms of DSB repair that has emerged over the last two decades with a focus on DSBs produced by the prototype agent ionizing radiation (IR). The exponential growth of molecular studies, heavily driven by RNA knockdown technology, now reveals an outline of how many key protein players in genome stability and cancer biology perform their interwoven tasks, e.g. ATM, ATR, DNA-PK, Chk1, Chk2, PARP1/2/3, 53BP1, BRCA1, BRCA2, BLM, RAD51, and the MRE11-RAD50-NBS1 complex. Thus, the nature of the intricate coordination of repair processes with cell cycle progression is becoming apparent. This review also links molecular abnormalities to cellular pathology as much a possible and provides a framework of temporal relationships.

  3. Advanced Modular Inverter Technology Development

    SciTech Connect

    Adam Szczepanek

    2006-02-04

    Electric and hybrid-electric vehicle systems require an inverter to convert the direct current (DC) output of the energy generation/storage system (engine, fuel cells, or batteries) to the alternating current (AC) that vehicle propulsion motors use. Vehicle support systems, such as lights and air conditioning, also use the inverter AC output. Distributed energy systems require an inverter to provide the high quality AC output that energy system customers demand. Today's inverters are expensive due to the cost of the power electronics components, and system designers must also tailor the inverter for individual applications. Thus, the benefits of mass production are not available, resulting in high initial procurement costs as well as high inverter maintenance and repair costs. Electricore, Inc. (www.electricore.org) a public good 501 (c) (3) not-for-profit advanced technology development consortium assembled a highly qualified team consisting of AeroVironment Inc. (www.aerovironment.com) and Delphi Automotive Systems LLC (Delphi), (www.delphi.com), as equal tiered technical leads, to develop an advanced, modular construction, inverter packaging technology that will offer a 30% cost reduction over conventional designs adding to the development of energy conversion technologies for crosscutting applications in the building, industry, transportation, and utility sectors. The proposed inverter allows for a reduction of weight and size of power electronics in the above-mentioned sectors and is scalable over the range of 15 to 500kW. The main objective of this program was to optimize existing AeroVironment inverter technology to improve power density, reliability and producibility as well as develop new topology to reduce line filter size. The newly developed inverter design will be used in automotive and distribution generation applications. In the first part of this program the high-density power stages were redesigned, optimized and fabricated. One of the main tasks

  4. Femtosecond near-infrared laser microirradiation reveals a crucial role for PARP signaling on factor assemblies at DNA damage sites

    PubMed Central

    Saquilabon Cruz, Gladys Mae; Kong, Xiangduo; Silva, Bárbara Alcaraz; Khatibzadeh, Nima; Thai, Ryan; Berns, Michael W.; Yokomori, Kyoko

    2016-01-01

    Laser microirradiation is a powerful tool for real-time single-cell analysis of the DNA damage response (DDR). It is often found, however, that factor recruitment or modification profiles vary depending on the laser system employed. This is likely due to an incomplete understanding of how laser conditions/dosages affect the amounts and types of damage and the DDR. We compared different irradiation conditions using a femtosecond near-infrared laser and found distinct damage site recruitment thresholds for 53BP1 and TRF2 correlating with the dose-dependent increase of strand breaks and damage complexity. Low input-power microirradiation that induces relatively simple strand breaks led to robust recruitment of 53BP1 but not TRF2. In contrast, increased strand breaks with complex damage including crosslinking and base damage generated by high input-power microirradiation resulted in TRF2 recruitment to damage sites with no 53BP1 clustering. We found that poly(ADP-ribose) polymerase (PARP) activation distinguishes between the two damage states and that PARP activation is essential for rapid TRF2 recruitment while suppressing 53BP1 accumulation at damage sites. Thus, our results reveal that careful titration of laser irradiation conditions allows induction of varying amounts and complexities of DNA damage that are gauged by differential PARP activation regulating protein assembly at the damage site. PMID:26424850

  5. Endomorphisms on half-sided modular inclusions

    SciTech Connect

    Svegstrup, Rolf Dyre

    2006-12-15

    In algebraic quantum field theory we consider nets of von Neumann algebras indexed over regions of the space time. Wiesbrock [''Conformal quantum field theory and half-sided modular inclusions of von Neumann algebras,'' Commun. Math. Phys. 158, 537-543 (1993)] has shown that strongly additive nets of von Neumann algebras on the circle are in correspondence with standard half-sided modular inclusions. We show that a finite index endomorphism on a half-sided modular inclusion extends to a finite index endomorphism on the corresponding net of von Neumann algebras on the circle. Moreover, we present another approach to encoding endomorphisms on nets of von Neumann algebras on the circle into half-sided modular inclusions. There is a natural way to associate a weight to a Moebius covariant endomorphism. The properties of this weight have been studied by Bertozzini et al. [''Covariant sectors with infinite dimension and positivity of the energy,'' Commun. Math. Phys. 193, 471-492 (1998)]. In this paper we show the converse, namely, how to associate a Moebius covariant endomorphism to a given weight under certain assumptions, thus obtaining a correspondence between a class of weights on a half-sided modular inclusion and a subclass of the Moebius covariant endomorphisms on the associated net of von Neumann algebras. This allows us to treat Moebius covariant endomorphisms in terms of weights on half-sided modular inclusions. As our aim is to provide a framework for treating endomorphisms on nets of von Neumann algebras in terms of the apparently simpler objects of weights on half-sided modular inclusions, we lastly give some basic results for manipulations with such weights.

  6. Teleoperated Modular Robots for Lunar Operations

    NASA Technical Reports Server (NTRS)

    Globus, Al; Hornby, Greg; Larchev, Greg; Hancher, Matt; Cannon, Howard; Lohn, Jason

    2004-01-01

    Solar system exploration is currently carried out by special purpose robots exquisitely designed for the anticipated tasks. However, all contingencies for in situ resource utilization (ISRU), human habitat preparation, and exploration will be difficult to anticipate. Furthermore, developing the necessary special purpose mechanisms for deployment and other capabilities is difficult and error prone. For example, the Galileo high gain antenna never opened, severely restricting the quantity of data returned by the spacecraft. Also, deployment hardware is used only once. To address these problems, we are developing teleoperated modular robots for lunar missions, including operations in transit from Earth. Teleoperation of lunar systems from Earth involves a three second speed-of-light delay, but experiment suggests that interactive operations are feasible.' Modular robots typically consist of many identical modules that pass power and data between them and can be reconfigured for different tasks providing great flexibility, inherent redundancy and graceful degradation as modules fail. Our design features a number of different hub, link, and joint modules to simplify the individual modules, lower structure cost, and provide specialized capabilities. Modular robots are well suited for space applications because of their extreme flexibility, inherent redundancy, high-density packing, and opportunities for mass production. Simple structural modules can be manufactured from lunar regolith in situ using molds or directed solar sintering. Software to direct and control modular robots is difficult to develop. We have used genetic algorithms to evolve both the morphology and control system for walking modular robots3 We are currently using evolvable system technology to evolve controllers for modular robots in the ISS glove box. Development of lunar modular robots will require software and physical simulators, including regolith simulation, to enable design and test of robot

  7. Modular Manufacturing Simulator: Users Manual

    NASA Technical Reports Server (NTRS)

    1997-01-01

    The Modular Manufacturing Simulator (MMS) has been developed for the beginning user of computer simulations. Consequently, the MMS cannot model complex systems that require branching and convergence logic. Once a user becomes more proficient in computer simulation and wants to add more complexity, the user is encouraged to use one of the many available commercial simulation systems. The (MMS) is based on the SSE5 that was developed in the early 1990's by the University of Alabama in Huntsville (UAH). A recent survey by MSFC indicated that the simulator has been a major contributor to the economic impact of the MSFC technology transfer program. Many manufacturers have requested additional features for the SSE5. Consequently, the following features have been added to the MMS that are not available in the SSE5: runs under Windows, print option for both input parameters and output statistics, operator can be fixed at a station or assigned to a group of stations, operator movement based on time limit, part limit, or work-in-process (WIP) limit at next station. The movement options for a moveable operators are: go to station with largest WIP, rabbit chase where operator moves in circular sequence between stations, and push/pull where operator moves back and forth between stations. This user's manual contains the necessary information for installing the MMS on a PC, a description of the various MMS commands, and the solutions to a number of sample problems using the MMS. Also included in the beginning of this report is a brief discussion of technology transfer.

  8. Local modularity for community detection in complex networks

    NASA Astrophysics Data System (ADS)

    Xiang, Ju; Hu, Tao; Zhang, Yan; Hu, Ke; Li, Jian-Ming; Xu, Xiao-Ke; Liu, Cui-Cui; Chen, Shi

    2016-02-01

    Community detection is a topic of interest in the study of complex networks such as the protein-protein interaction networks and metabolic networks. In recent years, various methods were proposed to detect community structures of the networks. Here, a kind of local modularity with tunable parameter is derived from the Newman-Girvan modularity by a special self-loop strategy that depends on the community division of the networks. By the self-loop strategy, one can easily control the definition of modularity, and the resulting modularity can be optimized by using the existing modularity optimization algorithms. The local modularity is used as the target function for community detection, and a self-consistent method is proposed for the optimization of the local modularity. We analyze the behaviors of the local modularity and show the validity of the local modularity in detecting community structures on various networks.

  9. MagArray Biochips for Protein and DNA Detection with Magnetic Nanotags: Design, Experiment, and Signal-to-Noise Ratio

    NASA Astrophysics Data System (ADS)

    Osterfeld, Sebastian J.; Wang, Shan X.

    MagArray™ chips contain arrays of magnetic sensors, which can be used to detect surface binding reactions of biological molecules that have been labeled with 10 to 100 nm sized magnetic particles. Although MagArray chips are in some ways similar to fluorescence-based DNA array chips, the use of magnetic labeling tags leads to many distinct advantages, such as better background rejection, no label bleaching, inexpensive chip readers, potentially higher sensitivity, ability to measure multiple binding reactions in homogeneous assays simultaneously and in real-time, and seamless integration with magnetic separation techniques. So far, the technology of MagArray chips has been successfully used to perform quantitative analytic bioassays of both protein and nucleic acid targets. The potential of this technology, especially for point-of-care testing (POCT) and portable molecular diagnostics, appears promising, and it is likely that this technology will see significant further performance gains in the near future.

  10. Telomere attrition induces a DNA double-strand break damage signal that reactivates p53 transcription in HTLV-I leukemic cells.

    PubMed

    Datta, A; Nicot, C

    2008-02-14

    Persistent inhibition of telomerase induces a severe telomere shortening in human T-cell leukemia virus type-1-infected cells which signals a DNA double-strand break damage response, formation of telomere dysfunction-induced foci and activates the ATM pathway. In turn, activation of ATM and its downstream effectors led to an increased phosphorylation and acetylation on specific residues of p53 known to be involved in transcriptional activation. Disruption of Mdm2-p53 complexes coupled with increased proteasomal degradation of MDMX further enhanced reactivation of p53 transcription, ultimately leading to senescence of tumor cells. Induction of senescence in these T-cells was associated with an increased expression of p21, p16 and activation of GSK3beta. Our results support the cancer-aging model and demonstrate that the halt of aging in cancer cells can be reversed through reactivation of p53.

  11. A upconversion luminescene biosensor based on dual-signal amplification for the detection of short DNA species of c-erbB-2 oncogene

    PubMed Central

    Lan, Jianming; Liu, Yingxin; Li, Li; Wen, Fadi; Wu, Fang; Han, Zhizhong; Sun, Weiming; Li, Chunyan; Chen, Jinghua

    2016-01-01

    High-sensitivity detection of trace amounts of c-erbB-2 oncogene was reported to be equal to or surpass the ability of CA 15-3 for early diagnosis and/or follow-up recurrent screening of breast cancer. Therefore, in the current study, by using upconversion nanoparticles (UCNPs), rare earth-doped NaYF4:Yb3+/Er3+ as the luminescent labels, a upconversion luminescent (UCL) biosensor based on dual-signal amplification of exonuclease III (ExoIII)-assisted target cycles and long-range self-assembly DNA concatamers was developed for the detection of c-erbB-2 oncogene. The proposed biosensor exhibited ultrasensitive detection with limit as low as 40 aM, which may express the potential of being used in trace analysis of c-erbB-2 oncogene and early diagnosis of breast cancer. PMID:27098295

  12. The complexity of DNA double strand break is a crucial factor for activating ATR signaling pathway for G2/M checkpoint regulation regardless of ATM function.

    PubMed

    Xue, Lian; Furusawa, Yoshiya; Okayasu, Ryuichi; Miura, Masahiko; Cui, Xing; Liu, Cuihua; Hirayama, Ryoichi; Matsumoto, Yoshitaka; Yajima, Hirohiko; Yu, Dong

    2015-01-01

    DNA double strand break (DSB) repair pathway choice following ionizing radiation (IR) is currently an appealing research topic, which is still largely unclear. Our recent paper indicated that the complexity of DSBs is a critical factor that enhances DNA end resection. It has been well accepted that the RPA-coated single strand DNA produced by resection is a signaling structure for ATR activation. Therefore, taking advantage of high linear energy transfer (LET) radiation to effectively produce complex DSBs, we investigated how the complexity of DSB influences the function of ATR pathway on the G2/M checkpoint regulation. Human skin fibroblast cells with or without ATM were irradiated with X rays or heavy ion particles, and dual-parameter flow cytometry was used to quantitatively assess the mitotic entry at early period post radiation by detecting the cells positive for phosphor histone H3. In ATM-deficient cells, ATR pathway played a pivotal role and functioned in a dose- and LET-dependent way to regulate the early G2/M arrest even as low as 0.2Gy for heavy ion radiation, which indicated that ATR pathway could be rapidly activated and functioned in an ATM-independent, but DSB complexity-dependent manner following exposure to IR. Furthermore, ATR pathway also functioned more efficiently in ATM-proficient cells to block G2 to M transition at early period of particle radiation exposure. Accordingly, in contrast to ATM inhibitor, ATR inhibitor had a more effective radiosensitizing effect on survival fraction following heavy ion beams as compared with X ray radiation. Taken together, our results reveal that the complexity of DSBs is a crucial factor for the activation of ATR pathway for G2/M checkpoint regulation, and ATM-dependent end resection is not essential for the activation.

  13. A signal-amplified electrochemical DNA biosensor incorporated with a colorimetric internal control for Vibrio cholerae detection using shelf-ready reagents.

    PubMed

    Low, Kim-Fatt; Zain, Zainiharyati Mohd; Yean, Chan Yean

    2017-01-15

    A novel enzyme/nanoparticle-based DNA biosensing platform with dual colorimetric/electrochemical approach has been developed for the sequence-specific detection of the bacterium Vibrio cholerae, the causative agent of acute diarrheal disease in cholera. This assay platform exploits the use of shelf-stable and ready-to-use (shelf-ready) reagents to greatly simplify the bioanalysis procedures, allowing the assay platform to be more amenable to point-of-care applications. To assure maximum diagnosis reliability, an internal control (IC) capable of providing instant validation of results was incorporated into the assay. The microbial target, single-stranded DNA amplified with asymmetric PCR, was quantitatively detected via electrochemical stripping analysis of gold nanoparticle-loaded latex microspheres as a signal-amplified hybridization tag, while the incorporated IC was analyzed using a simplified horseradish peroxidase enzyme-based colorimetric scheme by simple visual observation of enzymatic color development. The platform showed excellent diagnostic sensitivity and specificity (100%) when challenged with 145 clinical isolate-spiked fecal specimens. The limits of detection were 0.5ng/ml of genomic DNA and 10 colony-forming units (CFU)/ml of bacterial cells with dynamic ranges of 0-100ng/ml (R(2)=0.992) and log10 (1-10(4) CFU/ml) (R(2)=0.9918), respectively. An accelerated stability test revealed that the assay reagents were stable at temperatures of 4-37°C, with an estimated ambient shelf life of 200 days. The versatility of the biosensing platform makes it easily adaptable for quantitative detection of other microbial pathogens.

  14. Protection by taurine against INOS-dependent DNA damage in heavily exercised skeletal muscle by inhibition of the NF-κB signaling pathway.

    PubMed

    Sugiura, Hiromichi; Okita, Shinya; Kato, Toshihiro; Naka, Toru; Kawanishi, Shosuke; Ohnishi, Shiho; Oshida, Yoshiharu; Ma, Ning

    2013-01-01

    Taurine protects against tissue damage in a variety of models involving inflammation, especially the muscle. We set up a heavy exercise bout protocol for rats consisting of climbing ran on a treadmill to examine the effect of an intraabdominal dose of taurine (300 mg/kg/day) administered 1 h before heavy exercise for ten consecutive days. Each group ran on the treadmill at 20 m/min, 25% grade, for 20 min or until exhaustion within 20 min once each 10 days. Exhaustion was the point when an animal was unable to right itself when placed on its side. The muscle damage was associated with an increased accumulation of 8-nitroguanine and 8-OHdG in the nuclei of skeletal muscle cells. The immunoreactivities for NF-κB and iNOS were also increased in the exercise group. Taurine ameliorated heavy exercise-induced muscle DNA damage to a significant extent since it reduced the accumulation of 8-nitroguanine and 8-OHdG, possibly by down-regulating the expression of iNOS through a modulatory action on NF-κB signaling pathway. This study demonstrates for the first time that taurine can protect against intense exercise-induced nitrosative inflammation and ensuing DNA damage in the skeletal muscle of rats by preventing iNOS expression and the nitrosative stress generated by heavy exercise.

  15. Modular synthetic inverters from zinc finger proteins and small RNAs

    DOE PAGES

    Hsia, Justin; Holtz, William J.; Maharbiz, Michel M.; ...

    2016-02-17

    Synthetic zinc finger proteins (ZFPs) can be created to target promoter DNA sequences, repressing transcription. The binding of small RNA (sRNA) to ZFP mRNA creates an ultrasensitive response to generate higher effective Hill coefficients. Here we combined three “off the shelf” ZFPs and three sRNAs to create new modular inverters in E. coli and quantify their behavior using induction fold. We found a general ordering of the effects of the ZFPs and sRNAs on induction fold that mostly held true when combining these parts. We then attempted to construct a ring oscillator using our new inverters. In conclusion, our chosenmore » parts performed insufficiently to create oscillations, but we include future directions for improvement upon our work presented here.« less

  16. Modular synthetic inverters from zinc finger proteins and small RNAs

    SciTech Connect

    Hsia, Justin; Holtz, William J.; Maharbiz, Michel M.; Arcak, Murat; Keasling, Jay D.; Rao, Christopher V.

    2016-02-17

    Synthetic zinc finger proteins (ZFPs) can be created to target promoter DNA sequences, repressing transcription. The binding of small RNA (sRNA) to ZFP mRNA creates an ultrasensitive response to generate higher effective Hill coefficients. Here we combined three “off the shelf” ZFPs and three sRNAs to create new modular inverters in E. coli and quantify their behavior using induction fold. We found a general ordering of the effects of the ZFPs and sRNAs on induction fold that mostly held true when combining these parts. We then attempted to construct a ring oscillator using our new inverters. In conclusion, our chosen parts performed insufficiently to create oscillations, but we include future directions for improvement upon our work presented here.

  17. The generation of zinc finger proteins by modular assembly

    PubMed Central

    Bhakta, Mital; Segal, David J.

    2015-01-01

    The modular assembly (MA) method of generating engineered zinc finger proteins (ZFPs) was the first practical method for creating custom DNA-binding proteins. As such, MA has enabled a vast exploration of sequence-specific methods and reagents, ushering in the modern era of zinc finger-based applications that are described in this volume. The first zinc finger nuclease to cleave an endogenous site was created using MA, as was the first artificial transcription factor to enter phase II clinical trials. In recent years, other excellent methods have been developed that improved the affinity and specificity of the engineered ZFPs. However, MA is still used widely for many applications. This chapter will describe methods and give guidance for the creation of ZFPs using MA. Such ZFPs might be useful as starting materials to perform other methods described in this volume. Here, we also describe a single-strand annealing recombination assay for the initial testing of zinc finger nucleases. PMID:20680825

  18. Modularized functions of the Fanconi anemia core complex.

    PubMed

    Huang, Yaling; Leung, Justin W C; Lowery, Megan; Matsushita, Nobuko; Wang, Yucai; Shen, Xi; Huong, Do; Takata, Minoru; Chen, Junjie; Li, Lei

    2014-06-26

    The Fanconi anemia (FA) core complex provides the essential E3 ligase function for spatially defined FANCD2 ubiquitination and FA pathway activation. Of the seven FA gene products forming the core complex, FANCL possesses a RING domain with demonstrated E3 ligase activity. The other six components do not have clearly defined roles. Through epistasis analyses, we identify three functional modules in the FA core complex: a catalytic module consisting of FANCL, FANCB, and FAAP100 is absolutely required for the E3 ligase function, and the FANCA-FANCG-FAAP20 and the FANCC-FANCE-FANCF modules provide nonredundant and ancillary functions that help the catalytic module bind chromatin or sites of DNA damage. Disruption of the catalytic module causes complete loss of the core complex function, whereas loss of any ancillary module component does not. Our work reveals the roles of several FA gene products with previously undefined functions and a modularized assembly of the FA core complex.

  19. The cAMP signaling system inhibits the repair of {gamma}-ray-induced DNA damage by promoting Epac1-mediated proteasomal degradation of XRCC1 protein in human lung cancer cells

    SciTech Connect

    Cho, Eun-Ah; Juhnn, Yong-Sung

    2012-06-01

    Highlights: Black-Right-Pointing-Pointer cAMP signaling system inhibits repair of {gamma}-ray-induced DNA damage. Black-Right-Pointing-Pointer cAMP signaling system inhibits DNA damage repair by decreasing XRCC1 expression. Black-Right-Pointing-Pointer cAMP signaling system decreases XRCC1 expression by promoting its proteasomal degradation. Black-Right-Pointing-Pointer The promotion of XRCC1 degradation by cAMP signaling system is mediated by Epac1. -- Abstract: Cyclic AMP is involved in the regulation of metabolism, gene expression, cellular growth and proliferation. Recently, the cAMP signaling system was found to modulate DNA-damaging agent-induced apoptosis by regulating the expression of Bcl-2 family proteins and inhibitors of apoptosis. Thus, we hypothesized that the cAMP signaling may modulate DNA repair activity, and we investigated the effects of the cAMP signaling system on {gamma}-ray-induced DNA damage repair in lung cancer cells. Transient expression of a constitutively active mutant of stimulatory G protein (G{alpha}sQL) or treatment with forskolin, an adenylyl cyclase activator, augmented radiation-induced DNA damage and inhibited repair of the damage in H1299 lung cancer cells. Expression of G{alpha}sQL or treatment with forskolin or isoproterenol inhibited the radiation-induced expression of the XRCC1 protein, and exogenous expression of XRCC1 abolished the DNA repair-inhibiting effect of forskolin. Forskolin treatment promoted the ubiquitin and proteasome-dependent degradation of the XRCC1 protein, resulting in a significant decrease in the half-life of the protein after {gamma}-ray irradiation. The effect of forskolin on XRCC1 expression was not inhibited by PKA inhibitor, but 8-pCPT-2 Prime -O-Me-cAMP, an Epac-selective cAMP analog, increased ubiquitination of XRCC1 protein and decreased XRCC1 expression. Knockdown of Epac1 abolished the effect of 8-pCPT-2 Prime -O-Me-cAMP and restored XRCC1 protein level following {gamma}-ray irradiation. From

  20. A modular PMAD system for small spacecraft

    NASA Astrophysics Data System (ADS)

    Button, Robert M.

    1997-01-01

    Current trends in satellite design are focused on developing small, reliable, and inexpensive spacecraft. To that end, a modular power management and distribution system (PMAD) is proposed which will help transition the aerospace industry towards an assembly line approach to building spacecraft. The modular system is based on an innovative DC voltage boost converter called the Series Connected Boost Unit (SCBU). The SCBU uses existing DC-DC converters and adds a unique series connection. This simple modification provides the SCBU topology with many advantages over existing boost converters. Efficiencies of 94-98%, power densities above 1,000 We/kg, and inherent fault tolerance are just a few of the characteristics presented. Limitations of the SCBU technology are presented, and it is shown that the SCBU makes an ideal photovoltaic array regulator. A modular design based on the series connected boost unit is outlined and functional descriptions of the components are given.

  1. A Modular PMAD System for Small Spacecraft

    NASA Technical Reports Server (NTRS)

    Button, Robert M.

    1998-01-01

    Current trends in satellite design are focused on developing small, reliable, and inexpensive spacecraft. To that end, a modular power management and distribution system (PMAD) is proposed which will help transition the aerospace industry towards an assembly line approach to building spacecraft. The modular system is based on an innovative DC voltage boost converter