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Sample records for operator dna insight

  1. New Insights into the Phage Genetic Switch: Effects of Bacteriophage Lambda Operator Mutations on DNA Looping and Regulation of PR, PL, and PRM.

    Science.gov (United States)

    Lewis, Dale E A; Gussin, Gary N; Adhya, Sankar

    2016-11-06

    One of the best understood systems in genetic regulatory biology is the so-called "genetic switch" that determines the choice the phage-encoded CI repressor binds cooperatively to tripartite operators, OL and OR, in a defined pattern, thus blocking the transcription at two lytic promoters, PL and PR, and auto-regulating the promoter, PRM, which directs CI synthesis by the prophage. Fine-tuning of the maintenance of lysogeny is facilitated by interactions between CI dimers bound to OR and OL through the formation of a loop by the intervening DNA segment. By using a purified in vitro transcription system, we have genetically dissected the roles of individual operator sites in the formation of the DNA loop and thus have gained several new and unexpected insights into the system. First, although both OR and OL are tripartite, the presence of only a single active CI binding site in one of the two operators is sufficient for DNA loop formation. Second, in PL, unlike in PR, the promoter distal operator site, OL3, is sufficient to directly repress PL. Third, DNA looping mediated by the formation of CI octamers arising through the interaction of pairs of dimers bound to adjacent operator sites in OR and OL does not require OR and OL to be aligned "in register", that is, CI bound to "out-of-register" sub-operators, for example, OL1~Ol2 and OR2~OR3, can also mediate loop formation. Finally, based on an examination of the mechanism of activation of PRM when only OR1 or OR2 are wild type, we hypothesize that RNA polymerase bound at PR interferes with DNA loop formation. Thus, the formation of DNA loops involves potential interactions between proteins bound at numerous cis-acting sites, which therefore very subtly contribute to the regulation of the "switch".

  2. Insights into DNA signals for nucleosome positioning

    Institute of Scientific and Technical Information of China (English)

    Zhiming DAI; Xianhua DAI; Jihua FENG; Qian XIANG; Yangyang DENG; Jiang WANG

    2008-01-01

    The nucleosome is the fundamental unit of eukaryotic genomes. Its positioning in the promoter region plays a central role in regulating gene transcription. Experimental evidence suggests that the genomic DNA sequence is one important determinant of nucleosome positioning. Several approaches have been developed to predict nucleosome positions based on DNA sequence features, but the results indicate that there is room for improvement. This paper presents a new computational approach to predict genome-wide nucleosome locations in promoter regions. Importantly, the proposed approach outperforms existing approaches in yeast. Further anal-ysis demonstrates that DNA signals for nucleosome posi-tioning vary with species and composition of histones. Analysis of individual genes reveals that the role of the underlying DNA sequence in nucleosome positioning var-ies with genes.

  3. Controlling gene expression by DNA mechanics: emerging insights and challenges.

    Science.gov (United States)

    Levens, David; Baranello, Laura; Kouzine, Fedor

    2016-11-01

    Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions. The double helix is a fiber that responds to flexural and torsional stress, which if accumulated, can affect promoter output as well as change DNA and chromatin structure. The relationship between DNA mechanics and the control of early transcription initiation events has been under-investigated. Genomic techniques to display topological stress and conformational variation in DNA across the mammalian genome provide an exciting new insight on the role of DNA mechanics in the early stages of the transcription cycle. Without understanding how torsional and flexural stresses are generated, transmitted, and dissipated, no model of transcription will be complete and accurate.

  4. DNA Methylation in Basal Metazoans: Insights from Ctenophores.

    Science.gov (United States)

    Dabe, Emily C; Sanford, Rachel S; Kohn, Andrea B; Bobkova, Yelena; Moroz, Leonid L

    2015-12-01

    Epigenetic modifications control gene expression without altering the primary DNA sequence. However, little is known about DNA methylation in invertebrates and its evolution. Here, we characterize two types of genomic DNA methylation in ctenophores, 5-methyl cytosine (5-mC) and the unconventional form of methylation 6-methyl adenine (6-mA). Using both bisulfite sequencing and an ELISA-based colorimetric assay, we experimentally confirmed the presence of 5-mC DNA methylation in ctenophores. In contrast to other invertebrates studied, Mnemiopsis leidyi has lower levels of genome-wide 5-mC methylation, but higher levels of 5-mC methylation in promoters when compared with gene bodies. Phylogenetic analysis showed that ctenophores have distinct forms of DNA methyltransferase 1 (DNMT1); the zf-CXXC domain type, which localized DNMT1 to CpG sites, and is a metazoan specific innovation. We also show that ctenophores encode the full repertoire of putative enzymes for 6-mA DNA methylation, and these genes are expressed in the aboral organ of Mnemiopsis. Using an ELISA-based colorimetric assay, we experimentally confirmed the presence of 6-mA methylation in the genomes of three different species of ctenophores, M. leidyi, Beroe abyssicola, and Pleurobrachia bachei. The functional role of this novel epigenomic mark is currently unknown. In summary, despite their compact genomes, there is a wide variety of epigenomic mechanisms employed by basal metazoans that provide novel insights into the evolutionary origins of biological novelties. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  5. Logic Gate Operation by DNA Translocation through Biological Nanopores.

    Directory of Open Access Journals (Sweden)

    Hiroki Yasuga

    Full Text Available Logical operations using biological molecules, such as DNA computing or programmable diagnosis using DNA, have recently received attention. Challenges remain with respect to the development of such systems, including label-free output detection and the rapidity of operation. Here, we propose integration of biological nanopores with DNA molecules for development of a logical operating system. We configured outputs "1" and "0" as single-stranded DNA (ssDNA that is or is not translocated through a nanopore; unlabeled DNA was detected electrically. A negative-AND (NAND operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA. In addition, this operation was executed in a four-droplet network. DNA molecules and associated information were transferred among droplets via biological nanopores. This system would facilitate linking of molecules and electronic interfaces. Thus, it could be applied to molecular robotics, genetic engineering, and even medical diagnosis and treatment.

  6. A novel image encryption algorithm based on DNA subsequence operation.

    Science.gov (United States)

    Zhang, Qiang; Xue, Xianglian; Wei, Xiaopeng

    2012-01-01

    We present a novel image encryption algorithm based on DNA subsequence operation. Different from the traditional DNA encryption methods, our algorithm does not use complex biological operation but just uses the idea of DNA subsequence operations (such as elongation operation, truncation operation, deletion operation, etc.) combining with the logistic chaotic map to scramble the location and the value of pixel points from the image. The experimental results and security analysis show that the proposed algorithm is easy to be implemented, can get good encryption effect, has a wide secret key's space, strong sensitivity to secret key, and has the abilities of resisting exhaustive attack and statistic attack.

  7. A Novel Image Encryption Algorithm Based on DNA Subsequence Operation

    Science.gov (United States)

    Zhang, Qiang; Xue, Xianglian; Wei, Xiaopeng

    2012-01-01

    We present a novel image encryption algorithm based on DNA subsequence operation. Different from the traditional DNA encryption methods, our algorithm does not use complex biological operation but just uses the idea of DNA subsequence operations (such as elongation operation, truncation operation, deletion operation, etc.) combining with the logistic chaotic map to scramble the location and the value of pixel points from the image. The experimental results and security analysis show that the proposed algorithm is easy to be implemented, can get good encryption effect, has a wide secret key's space, strong sensitivity to secret key, and has the abilities of resisting exhaustive attack and statistic attack. PMID:23093912

  8. A Novel Image Encryption Algorithm Based on DNA Subsequence Operation

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

    2012-01-01

    Full Text Available We present a novel image encryption algorithm based on DNA subsequence operation. Different from the traditional DNA encryption methods, our algorithm does not use complex biological operation but just uses the idea of DNA subsequence operations (such as elongation operation, truncation operation, deletion operation, etc. combining with the logistic chaotic map to scramble the location and the value of pixel points from the image. The experimental results and security analysis show that the proposed algorithm is easy to be implemented, can get good encryption effect, has a wide secret key's space, strong sensitivity to secret key, and has the abilities of resisting exhaustive attack and statistic attack.

  9. Next-generation sequencing offers new insights into DNA degradation

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren; Orlando, Ludovic Antoine Alexandre; Willerslev, Eske

    2012-01-01

    The processes underlying DNA degradation are central to various disciplines, including cancer research, forensics and archaeology. The sequencing of ancient DNA molecules on next-generation sequencing platforms provides direct measurements of cytosine deamination, depurination and fragmentation r...

  10. Rupture of DNA aptamer: New insights from simulations

    Energy Technology Data Exchange (ETDEWEB)

    Mishra, Rakesh Kumar; Nath, Shesh; Kumar, Sanjay [Department of Physics, Banaras Hindu University, Varanasi 221 005 (India)

    2015-10-28

    Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a crucial role in biological processes. Because of thermal fluctuations, it can lower the stability of DNA, whereas, in case of DNA aptamer, small molecules, e.g., adenosinemonophosphate and adenosinetriphosphate, form additional hydrogen bonds with base-pockets termed as “binding-pockets,” which enhance the stability. Using the Langevin dynamics simulations of coarse grained model of DNA followed by atomistic simulations, we investigated the influence of base-pocket and binding-pocket on the stability of DNA aptamer. Striking differences have been reported here for the separation induced by temperature and force, which require further investigation by single molecule experiments.

  11. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA

    DEFF Research Database (Denmark)

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela

    2015-01-01

    An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ss......DNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained...

  12. Insights on protein-DNA recognition by coarse grain modelling

    Science.gov (United States)

    Poulain, Pierre; Saladin, Adrien; Hartmann, Brigitte; Prévost, Chantal

    2008-01-01

    Coarse grain modelling of macromolecules is a new approach potentially well adapted to answer numerous issues, ranging from physics to biology. We propose here an original DNA coarse grain model specifically dedicated to protein–DNA docking, a crucial, but still largely unresolved, question in molecular biology. Using a representative set of protein–DNA complexes, we first show that our model is able to predict the interaction surface between the macromolecular partners taken in their bound form. In a second part, the impact of the DNA sequence and electrostatics, together with the DNA and protein conformations on docking is investigated. Our results strongly suggest that the overall DNA structure mainly contributes in discriminating the interaction site on cognate proteins. Direct electrostatic interactions between phosphate groups and amino acids side chains strengthen the binding. Overall, this work demonstrates that coarse grain modelling can reveal itself a precious auxiliary for a general and complete description and understanding of protein–DNA association mechanisms. PMID:18478582

  13. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA.

    Science.gov (United States)

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela; Gamba, Cristina; Barnett, Ross; Samaniego, José Alfredo; Madrigal, Jazmín Ramos; Orlando, Ludovic; Gilbert, M Thomas P

    2015-12-01

    An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ssDNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained DNA, but this enrichment is less pronounced when dsDNA preparations successfully recover short endogenous DNA fragments (mean size < 70 bp). Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method.

  14. Mitochondrial DNA damage and animal longevity: insights from comparative studies.

    Science.gov (United States)

    Pamplona, Reinald

    2011-03-02

    Chemical reactions in living cells are under strict enzyme control and conform to a tightly regulated metabolic program. However, uncontrolled and potentially deleterious endogenous reactions occur, even under physiological conditions. Aging, in this chemical context, could be viewed as an entropic process, the result of chemical side reactions that chronically and cumulatively degrade the function of biological systems. Mitochondria are a main source of reactive oxygen species (ROS) and chemical sidereactions in healthy aerobic tissues and are the only known extranuclear cellular organelles in animal cells that contain their own DNA (mtDNA). ROS can modify mtDNA directly at the sugar-phosphate backbone or at the bases, producing many different oxidatively modified purines and pyrimidines, as well as single and double strand breaks and DNA mutations. In this scenario, natural selection tends to decrease the mitochondrial ROS generation, the oxidative damage to mtDNA, and the mitochondrial mutation rate in long-lived species, in agreement with the mitochondrial oxidative stress theory of aging.

  15. Insights into the Initiation of Eukaryotic DNA Replication.

    Science.gov (United States)

    Bruck, Irina; Perez-Arnaiz, Patricia; Colbert, Max K; Kaplan, Daniel L

    2015-01-01

    The initiation of DNA replication is a highly regulated event in eukaryotic cells to ensure that the entire genome is copied once and only once during S phase. The primary target of cellular regulation of eukaryotic DNA replication initiation is the assembly and activation of the replication fork helicase, the 11-subunit assembly that unwinds DNA at a replication fork. The replication fork helicase, called CMG for Cdc45-Mcm2-7, and GINS, assembles in S phase from the constituent Cdc45, Mcm2-7, and GINS proteins. The assembly and activation of the CMG replication fork helicase during S phase is governed by 2 S-phase specific kinases, CDK and DDK. CDK stimulates the interaction between Sld2, Sld3, and Dpb11, 3 initiation factors that are each required for the initiation of DNA replication. DDK, on the other hand, phosphorylates the Mcm2, Mcm4, and Mcm6 subunits of the Mcm2-7 complex. Sld3 recruits Cdc45 to Mcm2-7 in a manner that depends on DDK, and recent work suggests that Sld3 binds directly to Mcm2-7 and also to single-stranded DNA. Furthermore, recent work demonstrates that Sld3 and its human homolog Treslin substantially stimulate DDK phosphorylation of Mcm2. These data suggest that the initiation factor Sld3/Treslin coordinates the assembly and activation of the eukaryotic replication fork helicase by recruiting Cdc45 to Mcm2-7, stimulating DDK phosphorylation of Mcm2, and binding directly to single-stranded DNA as the origin is melted.

  16. Insights into the Initiation of Eukaryotic DNA Replication

    Science.gov (United States)

    Bruck, Irina; Perez-Arnaiz, Patricia; Colbert, Max K; Kaplan, Daniel L

    2015-01-01

    The initiation of DNA replication is a highly regulated event in eukaryotic cells to ensure that the entire genome is copied once and only once during S phase. The primary target of cellular regulation of eukaryotic DNA replication initiation is the assembly and activation of the replication fork helicase, the 11-subunit assembly that unwinds DNA at a replication fork. The replication fork helicase, called CMG for Cdc45-Mcm2–7, and GINS, assembles in S phase from the constituent Cdc45, Mcm2–7, and GINS proteins. The assembly and activation of the CMG replication fork helicase during S phase is governed by 2 S-phase specific kinases, CDK and DDK. CDK stimulates the interaction between Sld2, Sld3, and Dpb11, 3 initiation factors that are each required for the initiation of DNA replication. DDK, on the other hand, phosphorylates the Mcm2, Mcm4, and Mcm6 subunits of the Mcm2–7 complex. Sld3 recruits Cdc45 to Mcm2–7 in a manner that depends on DDK, and recent work suggests that Sld3 binds directly to Mcm2–7 and also to single-stranded DNA. Furthermore, recent work demonstrates that Sld3 and its human homolog Treslin substantially stimulate DDK phosphorylation of Mcm2. These data suggest that the initiation factor Sld3/Treslin coordinates the assembly and activation of the eukaryotic replication fork helicase by recruiting Cdc45 to Mcm2–7, stimulating DDK phosphorylation of Mcm2, and binding directly to single-stranded DNA as the origin is melted. PMID:26710261

  17. DNA markers provide insight about common lime in historicalplantings

    DEFF Research Database (Denmark)

    Hansen, Ole Kim; Thomsen, Pernille; Rasmussen, Christine Waage

    2014-01-01

    nurseries in the Netherlands and Germany. It also provides evidence that it is possible to obtain the same genetic material as originally planted when common lime trees are to be replaced in historical plantings. Furthermore, the utility of DNA markers in the management of plant material in parks......As part of the restoration process of an avenue of common lime (Tilia × europaea) from 1760 in the Royal Danish Gardens, all remaining trees were genotyped with DNA markers before they were felled. As such, information about the nature of the plant material (clonal versus non-clonal) and mode...

  18. Thermodynamic and structural insights into CSL-DNA complexes

    Energy Technology Data Exchange (ETDEWEB)

    Friedmann, David R.; Kovall, Rhett A. (UCIN-MED)

    2010-10-28

    The Notch pathway is an intercellular signaling mechanism that plays important roles in cell fates decisions throughout the developing and adult organism. Extracellular complexation of Notch receptors with ligands ultimately results in changes in gene expression, which is regulated by the nuclear effector of the pathway, CSL (C-promoter binding factor 1 (CBF-1), suppressor of hairless (Su(H)), lin-12 and glp-1 (Lag-1)). CSL is a DNA binding protein that is involved in both repression and activation of transcription from genes that are responsive to Notch signaling. One well-characterized Notch target gene is hairy and enhancer of split-1 (HES-1), which is regulated by a promoter element consisting of two CSL binding sites oriented in a head-to-head arrangement. Although previous studies have identified in vivo and consensus binding sites for CSL, and crystal structures of these complexes have been determined, to date, a quantitative description of the energetics that underlie CSL-DNA binding is unknown. Here, we provide a thermodynamic and structural analysis of the interaction between CSL and the two individual sites that comprise the HES-1 promoter element. Our comprehensive studies that analyze binding as a function of temperature, salt, and pH reveal moderate, but distinct, differences in the affinities of CSL for the two HES-1 binding sites. Similarly, our structural results indicate that overall CSL binds both DNA sites in a similar manner; however, minor changes are observed in both the conformation of CSL and DNA. Taken together, our results provide a quantitative and biophysical basis for understanding how CSL interacts with DNA sites in vivo.

  19. New Insights into DNA Polymerase Function Revealed by Phosphonoacetic Acid-Sensitive T4 DNA Polymerases.

    Science.gov (United States)

    Zhang, Likui

    2017-09-15

    The bacteriophage T4 DNA polymerase (pol) and the closely related RB69 DNA pol have been developed into model enzymes to study family B DNA pols. While all family B DNA pols have similar structures and share conserved protein motifs, the molecular mechanism underlying natural drug resistance of nonherpes family B DNA pols and drug sensitivity of herpes DNA pols remains unknown. In the present study, we constructed T4 phages containing G466S, Y460F, G466S/Y460F, P469S, and V475W mutations in DNA pol. These amino acid substitutions replace the residues in drug-resistant T4 DNA pol with residues found in drug-sensitive herpes family DNA pols. We investigated whether the T4 phages expressing the engineered mutant DNA pols were sensitive to the antiviral drug phosphonoacetic acid (PAA) and characterized the in vivo replication fidelity of the phage DNA pols. We found that G466S substitution marginally increased PAA sensitivity, whereas Y460F substitution conferred resistance. The phage expressing a double mutant G466S/Y460F DNA pol was more PAA-sensitive. V475W T4 DNA pol was highly sensitive to PAA, as was the case with V478W RB69 DNA pol. However, DNA replication was severely compromised, which resulted in the selection of phages expressing more robust DNA pols that have strong ability to replicate DNA and contain additional amino acid substitutions that suppress PAA sensitivity. Reduced replication fidelity was observed in all mutant phages expressing PAA-sensitive DNA pols. These observations indicate that PAA sensitivity and fidelity are balanced in DNA pols that can replicate DNA in different environments.

  20. DNA methylation in psychosis: insights into etiology and treatment.

    Science.gov (United States)

    Castellani, Christina A; Melka, Melkaye G; Diehl, Eric J; Laufer, Benjamin I; O'Reilly, Richard L; Singh, Shiva M

    2015-01-01

    Evidence for involvement of DNA methylation in psychosis forms the focus of this perspective. Of interest are results from two independent sets of experiments including rats treated with antipsychotic drugs and monozygotic twins discordant for schizophrenia. The results show that DNA methylation is increased in rats treated with antipsychotic drugs, reflecting the global effect of the drugs. Some of these changes are also seen in affected schizophrenic twins that were treated with antipsychotics. The genes and pathways identified in the unrelated experiments are relevant to neurodevelopment and psychiatric disorders. The common cause is hypothesized to be aberrations resulting from medication use. However, this needs to be established by future studies that address the origin of methylation changes in psychosis.

  1. Controlling gene expression by DNA mechanics: emerging insights and challenges

    OpenAIRE

    Levens, David; Baranello, Laura; Kouzine, Fedor

    2016-01-01

    Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and o...

  2. Recognition rules for binding of homeodomains to operator DNA.

    Science.gov (United States)

    Chirgadze, Yu N; Sivozhelezov, V S; Polozov, R V; Stepanenko, V A; Ivanov, V V

    2012-01-01

    The spatial arrangement of interfaces between homeodomain transcription factors and operator DNA has been considered. We analyzed the binding contacts for a representative set of 22 complexes of homeodomain transcription factors with a double-stranded operator DNA in the region of the major groove. It was shown that the recognition of DNA by the recognizing _-helix of protein is governed by two contact groups. Invariant protein-DNA group of contacts includes six contacts, formed by atomic groups of coding and non-coding DNA chains with the groups of amino acids. The recognizing _-helix forms contacts by polar groups of residues Trp2 (NE1), Asn5, and Lys9 with the canonical sequence T(1)A(2)A(3)T(4) of the coding DNA chain, and contacts by residues Lys0, Arg7 and Lys11 with the sequence A(4)X(5)X(6)X(7) of a non-coding DNA chain, where X is any nucleotide. Variable protein-DNA group of contacts comprises two groups bound with the sequence T(3)A(4)X(5)X(6) of the non- coding DNA-chain. These contacts are mainly with the bases and specify the binding pattern of individual homeodomains. The invariant contact group represents a recognition pattern for transcription factors of the homeodomain family: multiple adenine-asparagine contact and six position-specific phosphate contacts mainly with lysine or arginine. Within this group, we have found three most significant invariant contacts which allow deducing the recognition rules for homeodomains. These rules are inherent for different taxonomic groups of the homeodomain family and can distinguishing members of this family from any other family of transcription factors.

  3. Color image encryption scheme using CML and DNA sequence operations.

    Science.gov (United States)

    Wang, Xing-Yuan; Zhang, Hui-Li; Bao, Xue-Mei

    2016-06-01

    In this paper, an encryption algorithm for color images using chaotic system and DNA (Deoxyribonucleic acid) sequence operations is proposed. Three components for the color plain image is employed to construct a matrix, then perform confusion operation on the pixels matrix generated by the spatiotemporal chaos system, i.e., CML (coupled map lattice). DNA encoding rules, and decoding rules are introduced in the permutation phase. The extended Hamming distance is proposed to generate new initial values for CML iteration combining color plain image. Permute the rows and columns of the DNA matrix and then get the color cipher image from this matrix. Theoretical analysis and experimental results prove the cryptosystem secure and practical, and it is suitable for encrypting color images of any size. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  4. Optically controlled multiple switching operations of DNA biopolymer devices

    Energy Technology Data Exchange (ETDEWEB)

    Hung, Chao-You; Tu, Waan-Ting; Lin, Yi-Tzu [Institute of Photonics Technologies, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Fruk, Ljiljana [Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA (United Kingdom); Hung, Yu-Chueh, E-mail: ychung@ee.nthu.edu.tw [Institute of Photonics Technologies, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan (China)

    2015-12-21

    We present optically tunable operations of deoxyribonucleic acid (DNA) biopolymer devices, where a single high-resistance state, write-once read-many-times memory state, write-read-erase memory state, and single low-resistance state can be achieved by controlling UV irradiation time. The device is a simple sandwich structure with a spin-coated DNA biopolymer layer sandwiched by two electrodes. Upon irradiation, the electrical properties of the device are adjusted owing to a phototriggered synthesis of silver nanoparticles in DNA biopolymer, giving rise to multiple switching scenarios. This technique, distinct from the strategy of doping of pre-formed nanoparticles, enables a post-film fabrication process for achieving optically controlled memory device operations, which provides a more versatile platform to fabricate organic memory and optoelectronic devices.

  5. Linguistic isolates in Portugal: insights from the mitochondrial DNA pattern.

    Science.gov (United States)

    Mairal, Quim; Santos, Cristina; Silva, Marina; Marques, Sofia L; Ramos, Amanda; Aluja, Maria Pilar; Amorim, Antonio; Prata, Maria João; Alvarez, Luis

    2013-12-01

    Miranda do Douro, located in the northeastern region of Portugal, has notable characteristics not only from a geographic or naturalistic point of view, but also from a cultural perspective. A remarkable one is the coexistence of two different languages: Portuguese and Mirandese, the second being an Astur-Leonese dialect. The current persistence of the Astur-Leonese dialect in this population falls on the singularity of the region: relative isolation, implying difficulties to communicate with other Portuguese regions, while the same location facilitated the establishment of social and commercial relationships with adjacent Spanish territories, origin of the Astur-Leonese language. The objective of this study was to characterize the population from Miranda through the analysis of maternal lineages in order to evaluate whether its mitochondrial DNA diversity fitted the patterns previously reported for other populations from the Iberian Peninsula. Viewing that, the entire control region of mitochondrial DNA from 121 individuals was examined. Miranda showed a haplogroup composition usual for a Western European population, in the sense that as high as 63.6% of sequences belonged to macro-haplogroup R0. Lineages ascribed to have an African (L2a and L1b) origin, were detected, but reaching an amount commonly found in Portugal. Miranda also presented a few haplogroups typically found in Jewish populations, while rarely observed in other Iberian populations. The finding can be explained by gene flow with crypto-Jew communities that since long are known to be established in the region where Miranda is located. In Miranda, both genetic and nucleotide diversities presented low values (0.9292 ± 0.0180 and 0.01101 ± 0.00614 respectively) when compared to populations from its micro-geographical framework, which constitute a sign of population isolation that certainly provided conditions for the survival of the Astur-Leonese dialect in the region. Copyright © 2013 Elsevier

  6. Conservation and divergence of DNA methylation in eukaryotes: new insights from single base-resolution DNA methylomes.

    Science.gov (United States)

    Su, Zhixi; Han, Leng; Zhao, Zhongming

    2011-02-01

    DNA methylation is one of the most important heritable epigenetic modifications of the genome and is involved in the regulation of many cellular processes. Aberrant DNA methylation has been frequently reported to influence gene expression and subsequently cause various human diseases, including cancer. Recent rapid advances in next-generation sequencing technologies have enabled investigators to profile genome methylation patterns at single-base resolution. Remarkably, more than 20 eukaryotic methylomes have been generated thus far, with a majority published since November 2009. Analysis of this vast amount of data has dramatically enriched our knowledge of biological function, conservation and divergence of DNA methylation in eukaryotes. Even so, many specific functions of DNA methylation and their underlying regulatory systems still remain unknown to us. Here, we briefly introduce current approaches for DNA methylation profiling and then systematically review the features of whole genome DNA methylation patterns in eight animals, six plants and five fungi. Our systematic comparison provides new insights into the conservation and divergence of DNA methylation in eukaryotes and their regulation of gene expression. This work aims to summarize the current state of available methylome data and features informatively.

  7. Supreme audit court of auditors' insights on operational audit challenges

    Directory of Open Access Journals (Sweden)

    Sadegh Jamali

    2012-04-01

    Full Text Available Operational audit plays an important role on managing governmental budget. It helps control government spending and other important budgetary issues. This paper presents an empirical study to find out the possible barriers on implementing operational audit. The proposed study distributes some questionnaires among supreme audit court of auditors and analyzes the questions. The results indicate that many governmental organizations are not strongly committed to rules and regulations. There are not sufficient standards on auditing programs and many governmental agencies do not even use operational budgeting system since they are not aware of the benefits of such system. There are some of the most important challenges of having operational budgeting and paper suggests some guidelines for having better regulation on removing the main barriers.

  8. Stiffness of DNA nanotubes: insights for the design of dsDNA materials

    Science.gov (United States)

    Weitekamp, Paul; Schiffels, Daniel; Iteen, Alex; Fygenson, Deborah

    2011-03-01

    DNA is increasingly used as a material in the design and construction of elaborate structures with nanoscale precision and functionalities. Whether self-assembled from tiles of short, synthetic oligomers or woven from purified genomic strands, most DNA nanostructures are based on parallel arrays of double-stranded DNA (dsDNA) held together by Holliday junction-like cross-links. There is considerable evidence that the double-helices thus intertwined are largely B-form in structure, but the mechanical integrity of the resulting nanostructures has gone largely unexplored. Here we present a systematic study of the stiffness of DNA nanotubes varying parameters such as helix number, cross-link density and strand complexity. We find stiffness is a useful reporter of structural quality for nanotubes and extract design principles for optimizing mechanical integrity of dsDNA materials.

  9. Insights into early pig domestication provided by ancient DNA analysis

    Science.gov (United States)

    Caliebe, Amke; Nebel, Almut; Makarewicz, Cheryl; Krawczak, Michael; Krause-Kyora, Ben

    2017-01-01

    Pigs (Sus scrofa) were first domesticated between 8,500 and 8,000 cal BC in the Near East, from where they were subsequently brought into Europe by agriculturalists. Soon after the arrival of the first domestic pigs in northern Europe (~4500 BC), farmers are thought to have started to incorporate local wild boars into their swine herds. This husbandry strategy ultimately resulted in the domestication of European wild boars. Here, we set out to provide a more precise geographic and temporal framework of the early management of suid populations in northern Europe, drawing upon mitochondrial DNA haplotype data from 116 Neolithic Sus specimens. We developed a quantitative mathematical model tracing the haplotypes of the domestic pigs back to their most likely geographic origin. Our modelling results suggest that, between 5000 and 4000 BC, almost all matrilines in the north originated from domesticated animals from the south of central Europe. In the following period (4000–3000 BC), an estimated 78–100% of domesticates in the north were of northern matrilineal origin, largely from local wild boars. These findings point towards a dramatic change in suid management strategies taking place throughout south-central and northern Europe after 4000 BC. PMID:28300151

  10. The smooth (tractor) operator: insights of knowledge engineering.

    Science.gov (United States)

    Cullen, Ralph H; Smarr, Cory-Ann; Serrano-Baquero, Daniel; McBride, Sara E; Beer, Jenay M; Rogers, Wendy A

    2012-11-01

    The design of and training for complex systems requires in-depth understanding of task demands imposed on users. In this project, we used the knowledge engineering approach (Bowles et al., 2004) to assess the task of mowing in a citrus grove. Knowledge engineering is divided into four phases: (1) Establish goals. We defined specific goals based on the stakeholders involved. The main goal was to identify operator demands to support improvement of the system. (2) Create a working model of the system. We reviewed product literature, analyzed the system, and conducted expert interviews. (3) Extract knowledge. We interviewed tractor operators to understand their knowledge base. (4) Structure knowledge. We analyzed and organized operator knowledge to inform project goals. We categorized the information and developed diagrams to display the knowledge effectively. This project illustrates the benefits of knowledge engineering as a qualitative research method to inform technology design and training.

  11. Nuclear DNA replication initiation in kinetoplastid parasites: new insights into an ancient process.

    Science.gov (United States)

    Tiengwe, Calvin; Marques, Catarina A; McCulloch, Richard

    2014-01-01

    Nuclear DNA replication is, arguably, the central cellular process in eukaryotes, because it drives propagation of life and intersects with many other genome reactions. Perhaps surprisingly, our understanding of nuclear DNA replication in kinetoplastids was limited until a clutch of studies emerged recently, revealing new insight into both the machinery and genome-wide coordination of the reaction. Here, we discuss how these studies suggest that the earliest acting components of the kinetoplastid nuclear DNA replication machinery - the factors that demarcate sites of the replication initiation, termed origins - are diverged from model eukaryotes. In addition, we discuss how origin usage and replication dynamics relate to the highly unusual organisation of transcription in the genome of Trypanosoma brucei.

  12. Interaction of vasicine with calf thymus DNA: Molecular docking, spectroscopic and differential scanning calorimetric insights

    Science.gov (United States)

    R. S., Sai Murali; R. S., Sai Siddhardha; Rajesh Babu, D.; Venketesh, S.; Basavaraju, R.; Nageswara Rao, G.

    2017-06-01

    The present study brings out the interaction between vasicine, an alkaloid and Adhatoda vasica Nees with double stranded DNA. The physico-chemical interaction between small molecules and nucleic acids is a major area of focus in screening drugs against various cancers. Molecular probing in our study using Molecular Operating Environment (MOE) has revealed interaction of vasicine with DNA double helix. Here we report the interaction of vasicine with Calf thymus DNA. We present for the first time the results obtained from UV-visible, fluorescence spectroscopic and differential scanning calorimetric techniques that suggest a moderate to strong electrostatic, hydrophobic and van der Waals interactions mediating the DNA binding properties of vasicine, leading to disruption of DNA secondary structure.

  13. Microscopic insight into the DNA condensation process of a zwitterion-functionalized polycation.

    Science.gov (United States)

    Sun, Hui; Zhou, Li; Chen, Xiaolu; Han, Xia; Wang, Rui; Liu, Honglai

    2016-11-01

    Zwitterion-functionalized polycations are ideal gene carriers with long circulation, high cellular uptaking and low cell viability. However, the trade-off between the DNA condensation efficiency and the cell viability must be addressed. The purpose of this study is to provide a microscopic insight into the DNA condensation process and to explore the effect of a zwitterionic block of zwitterion-functionalized polycation, which is of great significance in designing novel gene delivery systems. Poly[2-(dimethylamino)ethyl methacrylate-b-(sulfobetaine methacrylate)] (PDMAEMA-b-PSBMA) copolymers were synthesized and used as the model systems. Different from the conventional concept that the PSBMA zwitterionic block act only as the "stealthy" groups, the subtle differences in physical and colloidal characteristics between the polycation/DNA polyplexes show that the PSBMA segment is capable of wrapping DNA attributed to the quaternary ammonium cations, without compromising the DNA condensation capability. On the other hand, the incorporation of PSBMA block reduces the surface charge of the polyplexes, which substantially result in the inefficient transfection and the reduced cytotoxicity.

  14. Insights into the conformation of aminofluorene-deoxyguanine adduct in a DNA polymerase active site.

    Science.gov (United States)

    Vaidyanathan, Vaidyanathan G; Liang, Fengting; Beard, William A; Shock, David D; Wilson, Samuel H; Cho, Bongsup P

    2013-08-09

    The active site conformation of the mutagenic fluoroaminofluorene-deoxyguanine adduct (dG-FAF, N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene) has been investigated in the presence of Klenow fragment of Escherichia coli DNA polymerase I (Kfexo(-)) and DNA polymerase β (pol β) using (19)F NMR, insertion assay, and surface plasmon resonance. In a single nucleotide gap, the dG-FAF adduct adopts both a major-groove- oriented and base-displaced stacked conformation, and this heterogeneity is retained upon binding pol β. The addition of a non-hydrolysable 2'-deoxycytosine-5'-[(α,β)-methyleno]triphosphate (dCMPcPP) nucleotide analog to the binary complex results in an increase of the major groove conformation of the adduct at the expense of the stacked conformation. Similar results were obtained with the addition of an incorrect dAMPcPP analog but with formation of the minor groove binding conformer. In contrast, dG-FAF adduct at the replication fork for the Kfexo(-) complex adopts a mix of the major and minor groove conformers with minimal effect upon the addition of non-hydrolysable nucleotides. For pol β, the insertion of dCTP was preferred opposite the dG-FAF adduct in a single nucleotide gap assay consistent with (19)F NMR data. Surface plasmon resonance binding kinetics revealed that pol β binds tightly with DNA in the presence of correct dCTP, but the adduct weakens binding with no nucleotide specificity. These results provide molecular insights into the DNA binding characteristics of FAF in the active site of DNA polymerases and the role of DNA structure and sequence on its coding potential.

  15. Archaeal Genome Guardians Give Insights into Eukaryotic DNA Replication and Damage Response Proteins

    Directory of Open Access Journals (Sweden)

    David S. Shin

    2014-01-01

    Full Text Available As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the biochemical, geochemical, and physical limitations to adaptive strategies allowing organisms to thrive under environmental stress relevant to determining the boundaries for life as we know it. Specifically, archaeal enzyme structures have informed the architecture and mechanisms of key DNA repair proteins and complexes. With added abilities to temperature-trap flexible complexes and reveal core domains of transient and dynamic complexes, these structures provide insights into mechanisms of maintaining genome integrity despite extreme environmental stress. The DNA damage response protein structures noted in this review therefore inform the basis for genome integrity in the face of environmental stress, with implications for all domains of life as well as for biomanufacturing, astrobiology, and medicine.

  16. Atomic Insight into the Altered O6-Methylguanine-DNA Methyltransferase Protein Architecture in Gastric Cancer.

    Directory of Open Access Journals (Sweden)

    Naveed Anjum Chikan

    Full Text Available O6-methylguanine-DNA methyltransferase (MGMT is one of the major DNA repair protein that counteracts the alkalyting agent-induced DNA damage by replacing O6-methylguanine (mutagenic lesion back to guanine, eventually suppressing the mismatch errors and double strand crosslinks. Exonic alterations in the form of nucleotide polymorphism may result in altered protein structure that in turn can lead to the loss of function. In the present study, we focused on the population feared for high exposure to alkylating agents owing to their typical and specialized dietary habits. To this end, gastric cancer patients pooled out from the population were selected for the mutational screening of a specific error prone region of MGMT gene. We found that nearly 40% of the studied neoplastic samples harbored missense mutation at codon151 resulting into Serine to Isoleucine variation. This variation resulted in bringing about the structural disorder, subsequently ensuing into a major stoichiometric variance in recognition domain, substrate binding and selectivity loop of the active site of the MGMT protein, as observed under virtual microscope of molecular dynamics simulation (MDS. The atomic insight into MGMT protein by computational approach showed a significant change in the intra molecular hydrogen bond pattern, thus leading to the observed structural anomalies. To further examine the mutational implications on regulatory plugs of MGMT that holds the protein in a DNA-Binding position, a MDS based analysis was carried out on, all known physically interacting amino acids essentially clustered into groups based on their position and function. The results generated by physical-functional clustering of protein indicated that the identified mutation in the vicinity of the active site of MGMT protein causes the local and global destabilization of a protein by either eliminating the stabilizing salt bridges in cluster C3, C4, and C5 or by locally destabilizing the

  17. Insights from the DNA databases: approaches to the phylogenetic structure of Acanthamoeba.

    Science.gov (United States)

    Fuerst, Paul A

    2014-11-01

    Species of Acanthamoeba have been traditionally described using morphology (primarily cyst structure), or cytology of nuclear division (used by Pussard and Pons, 1977). Twenty-plus putative species were proposed based on such criteria. Morphology, however, is often plastic, dependent upon culture conditions. DNA sequences of the nuclear small subunit (18S) rRNA that can be used for the study of the phylogeny of Acanthamoeba have increased from a single sequence in 1986 to more than 1800 in 2013. Some of the patterns of the sequence data for Acanthamoeba are reviewed, and some of the insights that this data illuminates are illustrated. In particular, the data suggest the existence of 20 or more genotypic types, a number not dissimilar to the number of named species of Acanthamoeba. However, molecular studies make clear that the relationship between phylogenetic relatedness and species names as we know them for Acanthamoeba is tenuous at best.

  18. DNA for crime investigation: European co-operation model.

    Science.gov (United States)

    Fiodorova, Anna

    2014-01-01

    The article presents DNA related data exchange mechanism established within the framework of the European Union for the transnational crime investigation. First of all, it provides with the comprehensive overview of legal and practical state of play, pointing out that approved legal basis seeks to ensure legality and reliability in this area by establishing information exchange purposes and competent authorities involved, setting up technical requirements for the DNA analysis and DNA data bases, laying down provisions on accreditation of forensic service providers, foreseeing at least minimum common data protection requirements. Secondly, it reveals that despite being the most exhaustive international regulation on DNA related data exchange among law enforcement and judicial authorities it misses effective data protection mechanism, does not harmonize neither backgrounds for DNA collection in criminal process in general nor storage requirements and that results the variation in categories of subjects related to the crime investigation and included in data bases of different Member States. These gaps make the use of data collected and stored in another Member State vulnerable from the perspective of different rules on evidences' legality within the criminal process. The article also reveals the model's weakness in terms of assessment of its efficiency as statistics gathered for the time being show only number of coincidences (hits) of searched DNA profiles, but not the impact on crime investigation and its results.

  19. Translesion Synthesis: Insights into the Selection and Switching of DNA Polymerases

    Directory of Open Access Journals (Sweden)

    Linlin Zhao

    2017-01-01

    Full Text Available DNA replication is constantly challenged by DNA lesions, noncanonical DNA structures and difficult-to-replicate DNA sequences. Two major strategies to rescue a stalled replication fork and to ensure continuous DNA synthesis are: (1 template switching and recombination-dependent DNA synthesis; and (2 translesion synthesis (TLS using specialized DNA polymerases to perform nucleotide incorporation opposite DNA lesions. The former pathway is mainly error-free, and the latter is error-prone and a major source of mutagenesis. An accepted model of translesion synthesis involves DNA polymerase switching steps between a replicative DNA polymerase and one or more TLS DNA polymerases. The mechanisms that govern the selection and exchange of specialized DNA polymerases for a given DNA lesion are not well understood. In this review, recent studies concerning the mechanisms of selection and switching of DNA polymerases in eukaryotic systems are summarized.

  20. Mutations altering the interplay between GkDnaC helicase and DNA reveal an insight into helicase unwinding.

    Directory of Open Access Journals (Sweden)

    Yu-Hua Lo

    Full Text Available Replicative helicases are essential molecular machines that utilize energy derived from NTP hydrolysis to move along nucleic acids and to unwind double-stranded DNA (dsDNA. Our earlier crystal structure of the hexameric helicase from Geobacillus kaustophilus HTA426 (GkDnaC in complex with single-stranded DNA (ssDNA suggested several key residues responsible for DNA binding that likely play a role in DNA translocation during the unwinding process. Here, we demonstrated that the unwinding activities of mutants with substitutions at these key residues in GkDnaC are 2-4-fold higher than that of wild-type protein. We also observed the faster unwinding velocities in these mutants using single-molecule experiments. A partial loss in the interaction of helicase with ssDNA leads to an enhancement in helicase efficiency, while their ATPase activities remain unchanged. In strong contrast, adding accessory proteins (DnaG or DnaI to GkDnaC helicase alters the ATPase, unwinding efficiency and the unwinding velocity of the helicase. It suggests that the unwinding velocity of helicase could be modulated by two different pathways, the efficiency of ATP hydrolysis or protein-DNA interaction.

  1. Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease.

    Science.gov (United States)

    Probst, Markus; Aeschimann, Walter; Chau, Thi T H; Langenegger, Simon M; Stocker, Achim; Häner, Robert

    2016-09-06

    The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal structures of three DNA-organized chromophore aggregates. DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with the recently described binding domain of the restriction enzyme BpuJI. Crystal structures of these complexes were determined at 2.7, 1.9 and 1.6 Å resolutions. The structures reveal aromatic stacking interactions between pyrene and/or phenanthrene units within the framework of the B-DNA duplex. In hybrids containing a single modification in each DNA strand near the end of the duplex, the two polyaromatic hydrocarbons are engaged in a face-to-face stacking orientation. Due to crystal packing and steric effects, the terminal GC base pair is disrupted in all three crystal structures, which results in a non-perfect stacking arrangement of the aromatic chromophores in two of the structures. In a hybrid containing a total of three pyrenes, crystal lattice induced end-to-end stacking of individual DNA duplexes leads to the formation of an extended aromatic π-stack containing four co-axially arranged pyrenes. The aromatic planes of the stacked pyrenes are oriented in a parallel way. The study demonstrates the value of co-crystallization of chemically modified DNA with the recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed structural insight into DNA-assembled oligochromophores.

  2. Characterisation of full-length cDNA sequences provides insights into the Eimeria tenellatranscriptome

    Directory of Open Access Journals (Sweden)

    Amiruddin Nadzirah

    2012-01-01

    Full Text Available Abstract Background Eimeria tenella is an apicomplexan parasite that causes coccidiosis in the domestic fowl. Infection with this parasite is diagnosed frequently in intensively reared poultry and its control is usually accorded a high priority, especially in chickens raised for meat. Prophylactic chemotherapy has been the primary method used for the control of coccidiosis. However, drug efficacy can be compromised by drug-resistant parasites and the lack of new drugs highlights demands for alternative control strategies including vaccination. In the long term, sustainable control of coccidiosis will most likely be achieved through integrated drug and vaccination programmes. Characterisation of the E. tenella transcriptome may provide a better understanding of the biology of the parasite and aid in the development of a more effective control for coccidiosis. Results More than 15,000 partial sequences were generated from the 5' and 3' ends of clones randomly selected from an E. tenella second generation merozoite full-length cDNA library. Clustering of these sequences produced 1,529 unique transcripts (UTs. Based on the transcript assembly and subsequently primer walking, 433 full-length cDNA sequences were successfully generated. These sequences varied in length, ranging from 441 bp to 3,083 bp, with an average size of 1,647 bp. Simple sequence repeat (SSR analysis identified CAG as the most abundant trinucleotide motif, while codon usage analysis revealed that the ten most infrequently used codons in E. tenella are UAU, UGU, GUA, CAU, AUA, CGA, UUA, CUA, CGU and AGU. Subsequent analysis of the E. tenella complete coding sequences identified 25 putative secretory and 60 putative surface proteins, all of which are now rational candidates for development as recombinant vaccines or drug targets in the effort to control avian coccidiosis. Conclusions This paper describes the generation and characterisation of full-length cDNA sequences from E

  3. Inhibitory Effect of Bridged Nucleosides on Thermus aquaticus DNA Polymerase and Insight into the Binding Interactions.

    Directory of Open Access Journals (Sweden)

    Sung-Kun Kim

    Full Text Available Modified nucleosides have the potential to inhibit DNA polymerases for the treatment of viral infections and cancer. With the hope of developing potent drug candidates by the modification of the 2',4'-position of the ribose with the inclusion of a bridge, efforts were focused on the inhibition of Taq DNA polymerase using quantitative real time PCR, and the results revealed the significant inhibitory effects of 2',4'-bridged thymidine nucleoside on the polymerase. Study on the mode of inhibition revealed the competitive mechanism with which the 2',4'-bridged thymidine operates. With a Ki value of 9.7 ± 1.1 μM, the 2',4'-bridged thymidine proved to be a very promising inhibitor. Additionally, docking analysis showed that all the nucleosides including 2',4'-bridged thymidine were able to dock in the active site, indicating that the substrate analogs reflect a structural complementarity to the enzyme active site. The analysis also provided evidence that Asp610 was a key binding site for 2',4'-bridged thymidine. Molecular dynamics (MD simulations were performed to further understand the conformational variations of the binding. The root-mean-square deviation (RMSD values for the peptide backbone of the enzyme and the nitrogenous base of the inhibitor stabilized within 0.8 and 0.2 ns, respectively. Furthermore, the MD analysis indicates substantial conformational change in the ligand (inhibitor as the nitrogenous base rotated anticlockwise with respect to the sugar moiety, complemented by the formation of several new hydrogen bonds where Arg587 served as a pivot axis for binding formation. In conclusion, the active site inhibition of Taq DNA polymerase by 2',4'-bridged thymidine suggests the potential of bridged nucleosides as drug candidates.

  4. Structure and operation of the DNA-translocating type I DNA restriction enzymes.

    Science.gov (United States)

    Kennaway, Christopher K; Taylor, James E; Song, Chun Feng; Potrzebowski, Wojciech; Nicholson, William; White, John H; Swiderska, Anna; Obarska-Kosinska, Agnieszka; Callow, Philip; Cooper, Laurie P; Roberts, Gareth A; Artero, Jean-Baptiste; Bujnicki, Janusz M; Trinick, John; Kneale, G Geoff; Dryden, David T F

    2012-01-01

    Type I DNA restriction/modification (RM) enzymes are molecular machines found in the majority of bacterial species. Their early discovery paved the way for the development of genetic engineering. They control (restrict) the influx of foreign DNA via horizontal gene transfer into the bacterium while maintaining sequence-specific methylation (modification) of host DNA. The endonuclease reaction of these enzymes on unmethylated DNA is preceded by bidirectional translocation of thousands of base pairs of DNA toward the enzyme. We present the structures of two type I RM enzymes, EcoKI and EcoR124I, derived using electron microscopy (EM), small-angle scattering (neutron and X-ray), and detailed molecular modeling. DNA binding triggers a large contraction of the open form of the enzyme to a compact form. The path followed by DNA through the complexes is revealed by using a DNA mimic anti-restriction protein. The structures reveal an evolutionary link between type I RM enzymes and type II RM enzymes.

  5. Insights into the quality of DnaA boxes and their cooperativity

    DEFF Research Database (Denmark)

    Hansen, Flemming G.; Christensen, Bjarke Bak; Nielsen, Christina Bang;

    2006-01-01

    Plasmids carrying the mioC promoter region with its two DnaA boxes are as efficient in titration of DnaA protein as plasmids carrying a replicationinactivated oriC region with its five DnaA boxes. The two DnaA boxes upstream of the mioC promoter were mutated in various ways to study the cooperati......Plasmids carrying the mioC promoter region with its two DnaA boxes are as efficient in titration of DnaA protein as plasmids carrying a replicationinactivated oriC region with its five DnaA boxes. The two DnaA boxes upstream of the mioC promoter were mutated in various ways to study...... the cooperativity between the DnaA boxes, and to study in vivo the in vitrodefined 9mer DnaA box consensus sequence TTA/TTNCACA). The quality and cooperativity of the DnaA oxes were determined in two complementary ways: as titration of DnaA protein leading to derepression of the dnaA promoter, and as repression...... of the mioC promoter caused by the DnaA protein binding to the DnaA boxes. Titration of DnaA protein correlated with repression of the mioC promoter. The level of titration and repression with the normal promoter-proximal box (TTTTCCACA) depends strongly on the presence and the quality of a DnaA box...

  6. Insight into F plasmid DNA segregation revealed by structures of SopB and SopB–DNA complexes

    OpenAIRE

    2010-01-01

    Accurate DNA segregation is essential for genome transmission. Segregation of the prototypical F plasmid requires the centromere-binding protein SopB, the NTPase SopA and the sopC centromere. SopB displays an intriguing range of DNA-binding properties essential for partition; it binds sopC to form a partition complex, which recruits SopA, and it also coats DNA to prevent non-specific SopA–DNA interactions, which inhibits SopA polymerization. To understand the myriad functions of SopB, we dete...

  7. Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights.

    Science.gov (United States)

    Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji

    2016-12-13

    Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

  8. Algebraic characterization of RNA operations for DNA-based computation

    Institute of Scientific and Technical Information of China (English)

    LI Shuchao

    2004-01-01

    Any RNA strand can be presented by a word in the language X*, where X={A,C,G,U}. By encoding A as 010, C as 000, G as 111, and U as 101, the RNA operations can be considered as the performance of concatenation, union, reverse, complement, in terms of the algebraic characterization. The concatenation and union play the roles of multiplication and addition over some algebraic structures, respectively. The rest of the operations turn out to be the homomorphisms or anti-homomorphisms of these algebraic structures. Using this technique, we find the relationship among these RNA operations.

  9. Linearly programmed DNA-based molecular computer operated on magnetic particle surface in test-tube

    Institute of Scientific and Technical Information of China (English)

    ZHAO Jian; ZHANG Zhizhou; SHI Yongyong; Li Xiuxia; HE Lin

    2004-01-01

    The postgenomic era has seen an emergence of new applications of DNA manipulation technologies, including DNA-based molecular computing. Surface DNA computing has already been reported in a number of studies that, however, all employ different mechanisms other than automaton functions. Here we describe a programmable DNA surface-computing device as a Turing machine-like finite automaton. The laboratory automaton is primarily composed of DNA (inputs, output-detectors, transition molecules as software), DNA manipulating enzymes and buffer system that solve artificial computational problems autonomously. When fluoresceins were labeled in the 5′ end of (-) strand of the input molecule, direct observation of all reaction intermediates along the time scale was made so that the dynamic process of DNA computing could be conveniently visualized. The features of this study are: (i) achievement of finite automaton functions by linearly programmed DNA computer operated on magnetic particle surface and (ii) direct detection of all DNA computing intermediates by capillary electrophoresis. Since DNA computing has the massive parallelism and feasibility for automation, this achievement sets a basis for large-scale implications of DNA computing for functional genomics in the near future.

  10. Nanotechnology - DNA operations%纳米技术-DNA操作

    Institute of Scientific and Technical Information of China (English)

    张阳德; 潘爱华

    2003-01-01

    The discovery of PCR opened a new area of biological research. The impact can be oberved not only by the great progress in the field of molecular biology, but also in may achievements in other related fields of science.Molecular biology techniques have been implemented successfully in biology,biotechnology,medical science,diagnostics, and so on. PCR amplification have been used to design the new laboratory devices and analyse amplified DNA fragments. And according to the nature and construction of DNA molecules and the potential computable methods,some studies have been conclucted conceming mimicing living systevms, as well as developing and constructing artificial nanodevices, such as biomolecular sensors and artifical cells.%PCR的发现为生物学的研究开辟了一个崭新的领域,在分子生物学及其相关的领域取得了巨大进步.分子的生物学技术已成功应用于生物学、生物科技、医学、诊断学等,利用PCR扩增技术设计新的实验方法和分析扩增的DNA片段,根据DNA分子的性质、结构和潜在性的可计算方法,研究模拟活生物,构造人工纳米装置,如生物分子感应器和人造细胞.

  11. Lac repressor: Crystallization of intact tetramer and its complexes with inducer and operator DNA

    Energy Technology Data Exchange (ETDEWEB)

    Pace, H.C.; Lu, P. (Univ. of Pennsylvania, Philadelphia (USA)); Lewis, M. (Univ. of Pennsylvania, Philadelphia, (USA) Smith Kline and French Labs., King of Prussia, PA (USA))

    1990-03-01

    The intact lac repressor tetramer, which regulates expression of the lac operon in Escherichia coli, has been crystallized in the native form, with an inducer, and in a ternary complex with operator DNA and an anti-inducer. The crystals without DNA diffract to better than 3.5 {angstrom}. They belong to the monoclinic space group C2 and have cell dimensions a = 164.7 {angstrom}, b = 75.6 {angstrom}, and c = 161.2 {angstrom}, with {alpha} = {gamma} = 90{degree} and {beta} = 125.5{degree}. Cocrystals have been obtained with a number of different lac operator-related DNA fragments. The complex with a blunt-ended 16-base-pair strand yielded tetragonal bipyramids that diffract to 6.5 {angstrom}. These protein-DNA cocrystals crack upon exposure to the gratuitous inducer isopropyl {beta}-D-thiogalactoside, suggesting a conformational change in the repressor-operator complex.

  12. Communications During Critical Mission Operations: Preparing for InSight's Landing on Mars

    Science.gov (United States)

    Asmar, Sami; Oudrhiri, Kamal; Kurtik, Susan; Weinstein-Weiss, Stacy

    2014-01-01

    Radio communications with deep space missions are often taken for granted due to the impressively successful records since, for decades, the technology and infrastructure have been developed for ground and flight systems to optimize telemetry and commanding. During mission-critical events such as the entry, descent, and landing of a spacecraft on the surface of Mars, the signal's level and frequency dynamics vary significantly and typically exceed the threshold of the budgeted links. The challenge is increased when spacecraft shed antennas with heat shields and other hardware during those risky few minutes. We have in the past successfully received signals on Earth during critical events even ones not intended for ground reception. These included the UHF signal transmitted by Curiosity to Marsorbiting assets. Since NASA's Deep Space Network does not operate in the UHF band, large radio telescopes around the world are utilized. The Australian CSIRO Parkes Radio Telescope supported the Curiosity UHF signal reception and DSN receivers, tools, and expertise were used in the process. In preparation for the InSight mission's landing on Mars in 2016, preparations are underway to support the UHF communications. This paper presents communication scenarios with radio telescopes, and the DSN receiver and tools. It also discusses the usefulness of the real-time information content for better response time by the mission team towards successful mission operations.

  13. New insights on the mechanism of quinoline-based DNA Methyltransferase inhibitors.

    Science.gov (United States)

    Gros, Christina; Fleury, Laurence; Nahoum, Virginie; Faux, Céline; Valente, Sergio; Labella, Donatella; Cantagrel, Frédéric; Rilova, Elodie; Bouhlel, Mohamed Amine; David-Cordonnier, Marie-Hélène; Dufau, Isabelle; Ausseil, Frédéric; Mai, Antonello; Mourey, Lionel; Lacroix, Laurent; Arimondo, Paola B

    2015-03-06

    Among the epigenetic marks, DNA methylation is one of the most studied. It is highly deregulated in numerous diseases, including cancer. Indeed, it has been shown that hypermethylation of tumor suppressor genes promoters is a common feature of cancer cells. Because DNA methylation is reversible, the DNA methyltransferases (DNMTs), responsible for this epigenetic mark, are considered promising therapeutic targets. Several molecules have been identified as DNMT inhibitors and, among the non-nucleoside inhibitors, 4-aminoquinoline-based inhibitors, such as SGI-1027 and its analogs, showed potent inhibitory activity. Here we characterized the in vitro mechanism of action of SGI-1027 and two analogs. Enzymatic competition studies with the DNA substrate and the methyl donor cofactor, S-adenosyl-l-methionine (AdoMet), displayed AdoMet non-competitive and DNA competitive behavior. In addition, deviations from the Michaelis-Menten model in DNA competition experiments suggested an interaction with DNA. Thus their ability to interact with DNA was established; although SGI-1027 was a weak DNA ligand, analog 5, the most potent inhibitor, strongly interacted with DNA. Finally, as 5 interacted with DNMT only when the DNA duplex was present, we hypothesize that this class of chemical compounds inhibit DNMTs by interacting with the DNA substrate.

  14. Insights into specific DNA recognition during the assembly of a viral genome packaging machine.

    Science.gov (United States)

    de Beer, Tonny; Fang, Jenny; Ortega, Marcos; Yang, Qin; Maes, Levi; Duffy, Carol; Berton, Nancy; Sippy, Jean; Overduin, Michael; Feiss, Michael; Catalano, Carlos Enrique

    2002-05-01

    Terminase enzymes mediate genome "packaging" during the reproduction of DNA viruses. In lambda, the gpNu1 subunit guides site-specific assembly of terminase onto DNA. The structure of the dimeric DNA binding domain of gpNu1 was solved using nuclear magnetic resonance spectroscopy. Its fold contains a unique winged helix-turn-helix (wHTH) motif within a novel scaffold. Surprisingly, a predicted P loop ATP binding motif is in fact the wing of the DNA binding motif. Structural and genetic analysis has identified determinants of DNA recognition specificity within the wHTH motif and the DNA recognition sequence. The structure reveals an unexpected DNA binding mode and provides a mechanistic basis for the concerted action of gpNu1 and Escherichia coli integration host factor during assembly of the packaging machinery.

  15. Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil

    Directory of Open Access Journals (Sweden)

    Masaru Tsunoda

    2010-01-01

    Full Text Available Hydroxyl radicals are potent mutagens that attack DNA to form various base and ribose derivatives. One of the major damaged thymine derivatives is 5-formyluracil (fU, which induces pyrimidine transition during replication. In order to establish the structural basis for such mutagenesis, the crystal structures of two kinds of DNA d(CGCGRATfUCGCG with R = A/G have been determined by X-ray crystallography. The fU residues form a Watson-Crick-type pair with A and two types of pairs (wobble and reversed wobble with G, the latter being a new type of base pair between ionized thymine base and guanine base. In silico structural modeling suggests that the DNA polymerase can accept the reversed wobble pair with G, as well as the Watson-Crick pair with A.

  16. Structure of an aprataxin-DNA complex with insights into AOA1 neurodegenerative disease

    Energy Technology Data Exchange (ETDEWEB)

    Tumbale, Percy; Appel, C Denise; Kraehenbuehl, Rolf; Robertson, Patrick D; Williams, Jessica S; Krahn, Joe; Ahel, Ivan; Williams, R Scott [NIEHS; (Manchester)

    2012-09-17

    DNA ligases finalize DNA replication and repair through DNA nick-sealing reactions that can abort to generate cytotoxic 5'-adenylation DNA damage. Aprataxin (Aptx) catalyzes direct reversal of 5'-adenylate adducts to protect genome integrity. Here the structure of a Schizosaccharomyces pombe Aptx-DNA-AMP-Zn2+ complex reveals active site and DNA interaction clefts formed by fusing a histidine triad (HIT) nucleotide hydrolase with a DNA minor groove-binding C2HE zinc finger (Znf). An Aptx helical 'wedge' interrogates the base stack for sensing DNA ends or DNA nicks. The HIT-Znf, the wedge and an '[F/Y]PK' pivot motif cooperate to distort terminal DNA base-pairing and direct 5'-adenylate into the active site pocket. Structural and mutational data support a wedge-pivot-cut HIT-Znf catalytic mechanism for 5'-adenylate adduct recognition and removal and suggest that mutations affecting protein folding, the active site pocket and the pivot motif underlie Aptx dysfunction in the neurodegenerative disorder ataxia with oculomotor apraxia 1 (AOA1).

  17. Structural and mechanistic insight into DNA unwinding by Deinococcus radiodurans UvrD.

    Directory of Open Access Journals (Sweden)

    Meike Stelter

    Full Text Available DNA helicases are responsible for unwinding the duplex DNA, a key step in many biological processes. UvrD is a DNA helicase involved in several DNA repair pathways. We report here crystal structures of Deinococcus radiodurans UvrD (drUvrD in complex with DNA in different nucleotide-free and bound states. These structures provide us with three distinct snapshots of drUvrD in action and for the first time trap a DNA helicase undergoing a large-scale spiral movement around duplexed DNA. Our structural data also improve our understanding of the molecular mechanisms that regulate DNA unwinding by Superfamily 1A (SF1A helicases. Our biochemical data reveal that drUvrD is a DNA-stimulated ATPase, can translocate along ssDNA in the 3'-5' direction and shows ATP-dependent 3'-5', and surprisingly also, 5'-3' helicase activity. Interestingly, we find that these translocase and helicase activities of drUvrD are modulated by the ssDNA binding protein. Analysis of drUvrD mutants indicate that the conserved β-hairpin structure of drUvrD that functions as a separation pin is critical for both drUvrD's 3'-5' and 5'-3' helicase activities, whereas the GIG motif of drUvrD involved in binding to the DNA duplex is essential for the 5'-3' helicase activity only. These special features of drUvrD may reflect its involvement in a wide range of DNA repair processes in vivo.

  18. Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics.

    Directory of Open Access Journals (Sweden)

    Suryani Lukman

    Full Text Available The transcription factor p53 regulates cellular integrity in response to stress. p53 is mutated in more than half of cancerous cells, with a majority of the mutations localized to the DNA binding domain (DBD. In order to map the structural and dynamical features of the DBD, we carried out multiple copy molecular dynamics simulations (totaling 0.8 μs. Simulations show the loop 1 to be the most dynamic element among the DNA-contacting loops (loops 1-3. Loop 1 occupies two major conformational states: extended and recessed; the former but not the latter displays correlations in atomic fluctuations with those of loop 2 (~24 Å apart. Since loop 1 binds to the major groove whereas loop 2 binds to the minor groove of DNA, our results begin to provide some insight into the possible mechanism underpinning the cooperative nature of DBD binding to DNA. We propose (1 a novel mechanism underlying the dynamics of loop 1 and the possible tread-milling of p53 on DNA and (2 possible mutations on loop 1 residues to restore the transcriptional activity of an oncogenic mutation at a distant site.

  19. New Insights into Cooperative Binding of Homeodomain Transcription Factors PREP1 and PBX1 to DNA

    Science.gov (United States)

    Zucchelli, Chiara; Ferrari, Elena; Blasi, Francesco; Musco, Giovanna; Bruckmann, Chiara

    2017-01-01

    PREP1 and PBX1 are homeodomain (HD) transcription factors that play crucial roles in embryonic development. Here, we present the first biophysical characterization of a PREP1 HD, and the NMR spectroscopic study of its DNA binding pocket. The data show that residues flanking the HD participate in DNA binding. The kinetic parameters for DNA binding of individual PREP1 and PBX1 HDs, and of their combination, show that isolated PREP1 and PBX1 HDs bind to DNA in a cooperative manner. A novel PREP1 motif, flanking the HD at the C-terminus, is required for cooperativity. PMID:28094776

  20. Mitochondrial DNA disease—molecular insights and potential routes to a cure

    Energy Technology Data Exchange (ETDEWEB)

    Russell, Oliver; Turnbull, Doug, E-mail: doug.turnbull@newcastle.ac.uk

    2014-07-01

    Mitochondrial DNA diseases are common neurological conditions caused by mutations in the mitochondrial genome or nuclear genes responsible for its maintenance. Current treatments for these disorders are focussed on the management of the symptoms, rather than the correction of biochemical defects caused by the mutation. This review focuses on the molecular effects of mutations, the symptoms they cause and current work focusing on the development of targeted treatments for mitochondrial DNA disease. - Highlights: • We discuss several common disease causing mtDNA mutations. • We highlight recent work linking pathogenicity to deletion size and heteroplasmy. • We discuss recent advances in the development of targeted mtDNA disease treatments.

  1. Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching.

    Directory of Open Access Journals (Sweden)

    Paul J Holland

    Full Text Available BACKGROUND: In Escherichia coli, cytotoxic DNA methyl lesions on the N1 position of purines and N3 position of pyrimidines are primarily repaired by the 2-oxoglutarate (2-OG iron(II dependent dioxygenase, AlkB. AlkB repairs 1-methyladenine (1-meA and 3-methylcytosine (3-meC lesions, but it also repairs 1-methylguanine (1-meG and 3-methylthymine (3-meT at a much less efficient rate. How the AlkB enzyme is able to locate and identify methylated bases in ssDNA has remained an open question. METHODOLOGY/PRINCIPAL FINDINGS: We determined the crystal structures of the E. coli AlkB protein holoenzyme and the AlkB-ssDNA complex containing a 1-meG lesion. We coupled this to site-directed mutagenesis of amino acids in and around the active site, and tested the effects of these mutations on the ability of the protein to bind both damaged and undamaged DNA, as well as catalyze repair of a methylated substrate. CONCLUSIONS/SIGNIFICANCE: A comparison of our substrate-bound AlkB-ssDNA complex with our unliganded holoenzyme reveals conformational changes of residues within the active site that are important for binding damaged bases. Site-directed mutagenesis of these residues reveals novel insight into their roles in DNA damage recognition and repair. Our data support a model that the AlkB protein utilizes at least two distinct conformations in searching and binding methylated bases within DNA: a "searching" mode and "repair" mode. Moreover, we are able to functionally separate these modes through mutagenesis of residues that affect one or the other binding state. Finally, our mutagenesis experiments show that amino acid D135 of AlkB participates in both substrate specificity and catalysis.

  2. Cryptanalysis of an Image Encryption Algorithm Based on DNA Sequence Operation and Hyper-chaotic System

    Science.gov (United States)

    Xu, Ming

    2017-06-01

    Recently, chaotic image cipher using DNA sequence operation has been studied extensively. However, corresponding cryptanalysis is lacking, which impedes its further development. This paper cryptanalyzes a newly proposed chaotic image cipher based on DNA sequence operation. In this paper, we firstly analyze the security defects of the proposal. Then by applying chosen-plaintext attack, we show that all the secret parameters can be revealed. The effectiveness of the proposed chosen-plaintext attack is supported both by rigorous theoretical analysis and experimental results.

  3. DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas

    Directory of Open Access Journals (Sweden)

    Gavery Mackenzie R

    2010-08-01

    Full Text Available Abstract Background DNA methylation is an epigenetic mechanism with important regulatory functions in animals. While the mechanism itself is evolutionarily ancient, the distribution and function of DNA methylation is diverse both within and among phylogenetic groups. Although DNA methylation has been well studied in mammals, there are limited data on invertebrates, particularly molluscs. Here we characterize the distribution and investigate potential functions of DNA methylation in the Pacific oyster (Crassostrea gigas. Results Methylation sensitive PCR and bisulfite sequencing PCR approaches were used to identify CpG methylation in C. gigas genes and demonstrated that this species possesses intragenic methylation. In silico analysis of CpGo/e ratios in publicly available sequence data suggests that DNA methylation is a common feature of the C. gigas genome, and that specific functional categories of genes have significantly different levels of methylation. Conclusions The Pacific oyster genome displays intragenic DNA methylation and contains genes necessary for DNA methylation in animals. Results of this investigation suggest that DNA methylation has regulatory functions in Crassostrea gigas, particularly in gene families that have inducible expression, including those involved in stress and environmental responses.

  4. A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics.

    Science.gov (United States)

    Rosario, Karyna; Duffy, Siobain; Breitbart, Mya

    2012-10-01

    Despite their small size and limited protein-coding capacity, the rapid evolution rates of single-stranded DNA (ssDNA) viruses have led to their emergence as serious plant and animal pathogens. Recently, metagenomics has revealed an unprecedented diversity of ssDNA viruses, expanding their known environmental distributions and host ranges. This review summarizes and contrasts the basic characteristics of known circular ssDNA viral groups, providing a resource for analyzing the wealth of ssDNA viral sequences identified through metagenomics. Since ssDNA viruses are largely identified based on conserved rolling circle replication proteins, this review highlights distinguishing motifs and catalytic residues important for replication. Genomes identified through metagenomics have demonstrated unique ssDNA viral genome architectures and revealed characteristics that blur the boundaries between previously well-defined groups. Metagenomic discovery of ssDNA viruses has created both a challenge to current taxonomic classification schemes and an opportunity to revisit hypotheses regarding the evolutionary history of these viruses.

  5. Effect of temperature on DNA double helix: An insight from molecular dynamics simulation

    Indian Academy of Sciences (India)

    Sangeeta Kundu; Sanchita Mukherjee; Dhananjay Bhattacharyya

    2012-07-01

    The three-dimensional structure of DNA contains various sequence-dependent structural information, which control many cellular processes in life, such as replication, transcription, DNA repair, etc. For the above functions, DNA double helices need to unwind or melt locally, which is different from terminal melting, as often seen in molecular dynamics (MD) simulations or even in many DNA crystal structures. We have carried out detailed MD simulations of DNA double helices of regular oligonucleotide fragments as well as in polymeric constructs with water and charge-neutralizing counter-ions at several different temperatures. We wanted to eliminate the end-effect or terminal melting propensity by employing MD simulation of DNA oligonucleotides in such a manner that gives rise to properties of polymeric DNA of infinite length. The polymeric construct is expected to allow us to see local melting at elevated temperatures. Comparative structural analysis of oligonucleotides and its corresponding virtual polymer at various temperatures ranging from 300 K to 400 K is discussed. The general behaviour, such as volume expansion coefficients of both the simulations show high similarity, indicating polymeric construct, does not give many artificial constraints. Local melting of a polymer, even at elevated temperature, may need a high nucleation energy that was not available in the short (7 ns) simulations. We expected to observe such nucleation followed by cooperative melting of the polymers in longer MD runs. Such simulations of different polymeric sequences would facilitate us to predict probable melting origins in a polymeric DNA.

  6. Structure of the FANCI-FANCD2 Complex: Insights into the Fanconi Anemia DNA Repair Pathway

    Energy Technology Data Exchange (ETDEWEB)

    Joo, Woo; Xu, Guozhou; Persky, Nicole S.; Smogorzewska, Agata; Rudge, Derek G.; Buzovetsky, Olga; Elledge, Stephen J.; Pavletich, Nikola P. (Harvard-Med); (Cornell); (MSKCC)

    2011-08-29

    Fanconi anemia is a cancer predisposition syndrome caused by defects in the repair of DNA interstrand cross-links (ICLs). Central to this pathway is the Fanconi anemia I-Fanconi anemia D2 (FANCI-FANCD2) (ID) complex, which is activated by DNA damage-induced phosphorylation and monoubiquitination. The 3.4 angstrom crystal structure of the {approx}300 kilodalton ID complex reveals that monoubiquitination and regulatory phosphorylation sites map to the I-D interface, suggesting that they occur on monomeric proteins or an opened-up complex and that they may serve to stabilize I-D heterodimerization. The 7.8 angstrom electron-density map of FANCI-DNA crystals and in vitro data show that each protein has binding sites for both single- and double-stranded DNA, suggesting that the ID complex recognizes DNA structures that result from the encounter of replication forks with an ICL.

  7. Structure of the FANCI-FANCD2 Complex: Insights into the Fanconi Anemia DNA Repair Pathway

    Energy Technology Data Exchange (ETDEWEB)

    W Joo; G Xu; n Persky; A Smogorzewska; D Rudge; O Buzovetsky; S Elledge; N Pavletich

    2011-12-31

    Fanconi anemia is a cancer predisposition syndrome caused by defects in the repair of DNA interstrand cross-links (ICLs). Central to this pathway is the Fanconi anemia I-Fanconi anemia D2 (FANCI-FANCD2) (ID) complex, which is activated by DNA damage-induced phosphorylation and monoubiquitination. The 3.4 angstrom crystal structure of the {approx}300 kilodalton ID complex reveals that monoubiquitination and regulatory phosphorylation sites map to the I-D interface, suggesting that they occur on monomeric proteins or an opened-up complex and that they may serve to stabilize I-D heterodimerization. The 7.8 angstrom electron-density map of FANCI-DNA crystals and in vitro data show that each protein has binding sites for both single- and double-stranded DNA, suggesting that the ID complex recognizes DNA structures that result from the encounter of replication forks with an ICL.

  8. Sharks and people: insight into the global practices of tourism operators and their attitudes to shark behaviour.

    Science.gov (United States)

    Richards, Kirsty; O'Leary, Bethan C; Roberts, Callum M; Ormond, Rupert; Gore, Mauvis; Hawkins, Julie P

    2015-02-15

    Shark tourism is a popular but controversial activity. We obtained insights into this industry via a global e-mailed questionnaire completed by 45 diving/snorkelling operators who advertised shark experiences (shark operators) and 49 who did not (non-shark operators). 42% of shark operators used an attractant to lure sharks and 93% stated they had a formal code of conduct which 86% enforced "very strictly". While sharks were reported to normally ignore people, 9 operators had experienced troublesome behaviour from them. Whilst our research corroborates previous studies indicating minimal risk to humans from most shark encounters, a precautionary approach to provisioning is required to avoid potential ecological and societal effects of shark tourism. Codes of conduct should always stipulate acceptable diver behaviour and appropriate diver numbers and shark operators should have a moral responsibility to educate their customers about the need for shark conservation.

  9. Low Mitochondrial DNA Diversity in an Ancient Population from China: Insight into Social Organization at the Fujia Site.

    Science.gov (United States)

    Dong, Yu; Li, Chunxiang; Luan, Fengshi; Li, Zhenguang; Li, Hongjie; Cui, Yinqiu; Zhou, Hui; Malhi, Ripan S

    2015-01-01

    To gain insight into the social organization of a population associated with the Dawenkou period, we performed ancient DNA analysis of 18 individuals from human remains from the Fujia site in Shandong Province, China. Directly radiocarbon dated to 4800-4500 cal BP, the Fujia site is assumed to be associated with a transitional phase from matrilineal clans to patrilineal monogamous families. Our results reveal a low mitochondrial DNA diversity from the site and population. Combined with Y chromosome data, the pattern observed at the Fujia site is most consistent with a matrilineal community. The patterns also suggest that the bond of marriage was de-emphasized compared with the bonds of descent at Fujia.

  10. Structural insight into β-Clamp and its interaction with DNA Ligase in Helicobacter pylori.

    Science.gov (United States)

    Pandey, Preeti; Tarique, Khaja Faisal; Mazumder, Mohit; Rehman, Syed Arif Abdul; Kumari, Nilima; Gourinath, Samudrala

    2016-08-08

    Helicobacter pylori, a gram-negative and microaerophilic bacterium, is the major cause of chronic gastritis, gastric ulcers and gastric cancer. Owing to its central role, DNA replication machinery has emerged as a prime target for the development of antimicrobial drugs. Here, we report 2Å structure of β-clamp from H. pylori (Hpβ-clamp), which is one of the critical components of DNA polymerase III. Despite of similarity in the overall fold of eubacterial β-clamp structures, some distinct features in DNA interacting loops exists that have not been reported previously. The in silico prediction identified the potential binders of β-clamp such as alpha subunit of DNA pol III and DNA ligase with identification of β-clamp binding regions in them and validated by SPR studies. Hpβ-clamp interacts with DNA ligase in micromolar binding affinity. Moreover, we have successfully determined the co-crystal structure of β-clamp with peptide from DNA ligase (not reported earlier in prokaryotes) revealing the region from ligase that interacts with β-clamp.

  11. Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase.

    Directory of Open Access Journals (Sweden)

    Jérémie Piton

    Full Text Available Mycobacterium tuberculosis DNA gyrase, an indispensable nanomachine involved in the regulation of DNA topology, is the only type II topoisomerase present in this organism and is hence the sole target for quinolone action, a crucial drug active against multidrug-resistant tuberculosis. To understand at an atomic level the quinolone resistance mechanism, which emerges in extensively drug resistant tuberculosis, we performed combined functional, biophysical and structural studies of the two individual domains constituting the catalytic DNA gyrase reaction core, namely the Toprim and the breakage-reunion domains. This allowed us to produce a model of the catalytic reaction core in complex with DNA and a quinolone molecule, identifying original mechanistic properties of quinolone binding and clarifying the relationships between amino acid mutations and resistance phenotype of M. tuberculosis DNA gyrase. These results are compatible with our previous studies on quinolone resistance. Interestingly, the structure of the entire breakage-reunion domain revealed a new interaction, in which the Quinolone-Binding Pocket (QBP is blocked by the N-terminal helix of a symmetry-related molecule. This interaction provides useful starting points for designing peptide based inhibitors that target DNA gyrase to prevent its binding to DNA.

  12. Novel insights into DNA methylation features in spermatozoa: stability and peculiarities.

    Directory of Open Access Journals (Sweden)

    Csilla Krausz

    Full Text Available Data about the entire sperm DNA methylome are limited to two sperm donors whereas studies dealing with a greater number of subjects focused only on a few genes or were based on low resolution arrays. This implies that information about what we can consider as a normal sperm DNA methylome and whether it is stable among different normozoospermic individuals is still missing. The definition of the DNA methylation profile of normozoospermic men, the entity of inter-individual variability and the epigenetic characterization of quality-fractioned sperm subpopulations in the same subject (intra-individual variability are relevant for a better understanding of pathological conditions. We addressed these questions by using the high resolution Infinium 450K methylation array and compared normal sperm DNA methylomes against somatic and cancer cells. Our study, based on the largest number of subjects (n = 8 ever considered for such a large number of CpGs (n = 487,517, provided clear evidence for i a highly conserved DNA methylation profile among normozoospermic subjects; ii a stable sperm DNA methylation pattern in different quality-fractioned sperm populations of the same individual. The latter finding is particularly relevant if we consider that different quality fractioned sperm subpopulations show differences in their structural features, metabolic and genomic profiles. We demonstrate, for the first time, that DNA methylation in normozoospermic men remains highly uniform regardless the quality of sperm subpopulations. In addition, our analysis provided both confirmatory and novel data concerning the sperm DNA methylome, including its peculiar features in respect to somatic and cancer cells. Our description about a highly polarized sperm DNA methylation profile, the clearly distinct genomic and functional organization of hypo- versus hypermethylated loci as well as the association of histone-enriched hypomethylated loci with embryonic development

  13. Proteomics insights into DNA damage response and translating this knowledge to clinical strategies

    DEFF Research Database (Denmark)

    von Stechow, Louise; Olsen, Jesper V

    2017-01-01

    Spectrometry (MS)-based proteomics emerged as method of choice for global studies of proteins and their posttranslational modifications (PTMs). MS-based studies of the DDR have aided in delineating DNA damage-induced signalling responses. Those studies identified changes in abundance, interactions...... and modification of proteins in the context of genotoxic stress. Here we review ground-breaking MS-based proteomics studies, which analysed changes in protein abundance, protein-protein and protein-DNA interactions, phosphorylation, acetylation, ubiquitylation, SUMOylation and Poly(ADP-ribose)ylation (PARylation......Genomic instability is a critical driver in the process of cancer formation. At the same time, inducing DNA damage by irradiation or genotoxic compounds constitutes a key therapeutic strategy to kill fast-dividing cancer cells. Sensing of DNA lesions initiates a complex set of signalling pathways...

  14. On the path to genetic novelties: insights from programmed DNA elimination and RNA splicing.

    Science.gov (United States)

    Catania, Francesco; Schmitz, Jürgen

    2015-01-01

    Understanding how genetic novelties arise is a central goal of evolutionary biology. To this end, programmed DNA elimination and RNA splicing deserve special consideration. While programmed DNA elimination reshapes genomes by eliminating chromatin during organismal development, RNA splicing rearranges genetic messages by removing intronic regions during transcription. Small RNAs help to mediate this class of sequence reorganization, which is not error-free. It is this imperfection that makes programmed DNA elimination and RNA splicing excellent candidates for generating evolutionary novelties. Leveraging a number of these two processes' mechanistic and evolutionary properties, which have been uncovered over the past years, we present recently proposed models and empirical evidence for how splicing can shape the structure of protein-coding genes in eukaryotes. We also chronicle a number of intriguing similarities between the processes of programmed DNA elimination and RNA splicing, and highlight the role that the variation in the population-genetic environment may play in shaping their target sequences.

  15. Novel insights into the apoptosis mechanism of DNA topoisomerase I inhibitor isoliquiritigenin on HCC tumor cell

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ze-xin; Li, Jian; Li, Yan; You, Kun; Xu, Hongwei; Wang, Jianguo, E-mail: wangjianguoxx@163.com

    2015-08-21

    The inhibitory effect of DNA topoisomerase (Top I) by isoliquiritigenin(ISO) were investigated and their interaction mechanism was evaluated using methods including UV–vis absorption, fluorescence, coupled with molecular simulation, and using the MTT method of inhibition rate of HCC tumor cell SNU475 proliferation assay, finally, the interaction of ISO with calf thymus DNA was investigated by melting measurements and molecular docking studies. It was found that isoliquiritigenin reversibly inhibited DNA Top I in a competitive manner with the concentrations of ISO resulting in 50% activity lost (IC{sub 50}) were estimated to be 0.178 ± 0.12 mM. Isoliquiritigenin exhibited a strong ability to quench the intrinsic fluorescence of Top I through a static quenching procedure. The positive values of enthalpy change and entropy change suggested that the binding of isoliquiritigenin to Top I was driven mainly by hydrophobic interactions. The molecular docking results revealed isoliquiritigenin actually interacted with the primary amino acid residues on the active site of Top I, and the detection results of fluorescence staining and the inhibitory effect on the growth of HCC SUN475 showed that isoliquiritigenin induced the apoptosis cells increased gradually. The interaction of ISO with DNA can cause the denaturation temperature to be increased, which indicated that the stabilization of the DNA helix was increased in the presence of ISO, which indicated that the results provide strong evidence for intercalative binding of ISO with DNA. - Highlights: • ISO reversibly inhibits TOP I activity in an A dose dependent manner. • Hydrophobic interactions play a major role in ISO–TOP I interaction. • ISO has a high affinity close to the active site pocket of TOP I. • The binding of ISO to DNA induces the stability of the structure of DNA.

  16. Structural insight into DNA binding and oligomerization of the multifunctional Cox protein of bacteriophage P2.

    Science.gov (United States)

    Berntsson, Ronnie P-A; Odegrip, Richard; Sehlén, Wilhelmina; Skaar, Karin; Svensson, Linda M; Massad, Tariq; Högbom, Martin; Haggård-Ljungquist, Elisabeth; Stenmark, Pål

    2014-02-01

    The Cox protein from bacteriophage P2 is a small multifunctional DNA-binding protein. It is involved in site-specific recombination leading to P2 prophage excision and functions as a transcriptional repressor of the P2 Pc promoter. Furthermore, it transcriptionally activates the unrelated, defective prophage P4 that depends on phage P2 late gene products for lytic growth. In this article, we have investigated the structural determinants to understand how P2 Cox performs these different functions. We have solved the structure of P2 Cox to 2.4 Å resolution. Interestingly, P2 Cox crystallized in a continuous oligomeric spiral with its DNA-binding helix and wing positioned outwards. The extended C-terminal part of P2 Cox is largely responsible for the oligomerization in the structure. The spacing between the repeating DNA-binding elements along the helical P2 Cox filament is consistent with DNA binding along the filament. Functional analyses of alanine mutants in P2 Cox argue for the importance of key residues for protein function. We here present the first structure from the Cox protein family and, together with previous biochemical observations, propose that P2 Cox achieves its various functions by specific binding of DNA while wrapping the DNA around its helical oligomer.

  17. Super DNAging-New insights into DNA integrity, genome stability and telomeres in the oldest old.

    Science.gov (United States)

    Franzke, Bernhard; Neubauer, Oliver; Wagner, Karl-Heinz

    2015-01-01

    Reductions in DNA integrity, genome stability, and telomere length are strongly associated with the aging process, age-related diseases as well as the age-related loss of muscle mass. However, in people reaching an age far beyond their statistical life expectancy the prevalence of diseases, such as cancer, cardiovascular disease, diabetes or dementia, is much lower compared to "averagely" aged humans. These inverse observations in nonagenarians (90-99 years), centenarians (100-109 years) and super-centenarians (110 years and older) require a closer look into dynamics underlying DNA damage within the oldest old of our society. Available data indicate improved DNA repair and antioxidant defense mechanisms in "super old" humans, which are comparable with much younger cohorts. Partly as a result of these enhanced endogenous repair and protective mechanisms, the oldest old humans appear to cope better with risk factors for DNA damage over their lifetime compared to subjects whose lifespan coincides with the statistical life expectancy. This model is supported by study results demonstrating superior chromosomal stability, telomere dynamics and DNA integrity in "successful agers". There is also compelling evidence suggesting that life-style related factors including regular physical activity, a well-balanced diet and minimized psycho-social stress can reduce DNA damage and improve chromosomal stability. The most conclusive picture that emerges from reviewing the literature is that reaching "super old" age appears to be primarily determined by hereditary/genetic factors, while a healthy lifestyle additionally contributes to achieving the individual maximum lifespan in humans. More research is required in this rapidly growing population of super old people. In particular, there is need for more comprehensive investigations including short- and long-term lifestyle interventions as well as investigations focusing on the mechanisms causing DNA damage, mutations, and telomere

  18. Insights into the error bypass of 1-Nitropyrene DNA adduct by DNA polymerase ι: A QM/MM study

    Science.gov (United States)

    Li, Yanwei; Bao, Lei; Zhang, Ruiming; Tang, Xiaowen; Zhang, Qingzhu; Wang, Wenxing

    2017-10-01

    The error bypass mechanism of DNA polymerase ι toward N-(deoxyguanosin-8-yl)-1-aminopyrene adduction was studied by using quantum mechanics/molecular mechanics method. The most favorable mechanism highlights three elementary steps: proton transfer from dC to dATP, phosphoryl transfer, and deprotonation of dAMP. The phosphoryl transfer step was found to be rate-determining. The calculated average barrier (23.8 kcal mol-1) is in accordance with the experimental value (21.5 kcal mol-1). Electrostatic influence analysis indicates that residues Asp126 and Lys207 significantly suppress the error bypass while Glu127 facilitates the process. These results highlight the origins of the mutagenicity of nitrated polycyclic aromatic hydrocarbons in molecular detail.

  19. Biochemical and Structural Insights into the Mechanism of DNA Recognition by Arabidopsis ETHYLENE INSENSITIVE3.

    Directory of Open Access Journals (Sweden)

    Jinghui Song

    Full Text Available Gaseous hormone ethylene regulates numerous stress responses and developmental adaptations in plants by controlling gene expression via transcription factors ETHYLENE INSENSITIVE3 (EIN3 and EIN3-Like1 (EIL1. However, our knowledge regarding to the accurate definition of DNA-binding domains (DBDs within EIN3 and also the mechanism of specific DNA recognition by EIN3 is limited. Here, we identify EIN3 82-352 and 174-306 as the optimal and core DBDs, respectively. Results from systematic biochemical analyses reveal that both the number of EIN3-binding sites (EBSs and the spacing length between two EBSs affect the binding affinity of EIN3; accordingly, a new DNA probe which has higher affinity with EIN3 than ERF1 is also designed. Furthermore, we show that palindromic repeat sequences in ERF1 promoter are not necessary for EIN3 binding. Finally, we provide, to our knowledge, the first crystal structure of EIN3 core DBD, which contains amino acid residues essential for DNA binding and signaling. Collectively, these data suggest the detailed mechanism of DNA recognition by EIN3 and provide an in-depth view at molecular level for the transcriptional regulation mediated by EIN3.

  20. Magic-angle spinning NMR of intact bacteriophages: Insights into the capsid, DNA and their interface

    Science.gov (United States)

    Abramov, Gili; Morag, Omry; Goldbourt, Amir

    2015-04-01

    Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses.

  1. Structural Insight into Processive Human Mitochondrial DNA Synthesis and Disease-Related Polymerase Mutations

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young-Sam; Kennedy, W. Dexter; Yin, Y. Whitney; (Texas)

    2010-09-07

    Human mitochondrial DNA polymerase (Pol {gamma}) is the sole replicase in mitochondria. Pol {gamma} is vulnerable to nonselective antiretroviral drugs and is increasingly associated with mutations found in patients with mitochondriopathies. We determined crystal structures of the human heterotrimeric Pol {gamma} holoenzyme and, separately, a variant of its processivity factor, Pol {gamma}B. The holoenzyme structure reveals an unexpected assembly of the mitochondrial DNA replicase where the catalytic subunit Pol {gamma}A interacts with its processivity factor primarily via a domain that is absent in all other DNA polymerases. This domain provides a structural module for supporting both the intrinsic processivity of the catalytic subunit alone and the enhanced processivity of holoenzyme. The Pol {gamma} structure also provides a context for interpreting the phenotypes of disease-related mutations in the polymerase and establishes a foundation for understanding the molecular basis of toxicity of anti-retroviral drugs targeting HIV reverse transcriptase.

  2. Charge-Transfer Excited States in Aqueous DNA: Insights from Many-Body Green's Function Theory

    Science.gov (United States)

    Yin, Huabing; Ma, Yuchen; Mu, Jinglin; Liu, Chengbu; Rohlfing, Michael

    2014-06-01

    Charge-transfer (CT) excited states play an important role in the excited-state dynamics of DNA in aqueous solution. However, there is still much controversy on their energies. By ab initio many-body Green's function theory, together with classical molecular dynamics simulations, we confirm the existence of CT states at the lower energy side of the optical absorption maximum in aqueous DNA as observed in experiments. We find that the hydration shell can exert strong effects (˜1 eV) on both the electronic structure and CT states of DNA molecules through dipole electric fields. In this case, the solvent cannot be simply regarded as a macroscopic screening medium as usual. The influence of base stacking and base pairing on the CT states is also discussed.

  3. Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants.

    Science.gov (United States)

    Vidya, T N C; Sukumar, Raman; Melnick, Don J

    2009-03-07

    Recent phylogeographic studies of the endangered Asian elephant (Elephas maximus) reveal two highly divergent mitochondrial DNA (mtDNA) lineages, an elucidation of which is central to understanding the species's evolution. Previous explanations for the divergent clades include introgression of mtDNA haplotypes between ancestral species, allopatric divergence of the clades between Sri Lanka or the Sunda region and the mainland, historical trade of elephants, and retention of divergent lineages due to large population sizes. However, these studies lacked data from India and Myanmar, which host approximately 70 per cent of all extant Asian elephants. In this paper, we analyse mtDNA sequence data from 534 Asian elephants across the species's range to explain the current distribution of the two divergent clades. Based on phylogenetic reconstructions, estimates of times of origin of clades, probable ancestral areas of origin inferred from dispersal-vicariance analyses and the available fossil record, we believe both clades originated from Elephas hysudricus. This probably occurred allopatrically in different glacial refugia, the alpha clade in the Myanmar region and the beta clade possibly in southern India-Sri Lanka, 1.6-2.1Myr ago. Results from nested clade and dispersal-vicariance analyses indicate a subsequent isolation and independent diversification of the beta clade in both Sri Lanka and the Sunda region, followed by northward expansion of the clade. We also find more recent population expansions in both clades based on mismatch distributions. We therefore suggest a contraction-expansion scenario during severe climatic oscillations of the Quaternary, with range expansions from different refugia during warmer interglacials leading to the varying geographical overlaps of the two mtDNA clades. We also demonstrate that trade in Asian elephants has not substantially altered the species's mtDNA population genetic structure.

  4. A novel chaos-based image encryption algorithm using DNA sequence operations

    Science.gov (United States)

    Chai, Xiuli; Chen, Yiran; Broyde, Lucie

    2017-01-01

    An image encryption algorithm based on chaotic system and deoxyribonucleic acid (DNA) sequence operations is proposed in this paper. First, the plain image is encoded into a DNA matrix, and then a new wave-based permutation scheme is performed on it. The chaotic sequences produced by 2D Logistic chaotic map are employed for row circular permutation (RCP) and column circular permutation (CCP). Initial values and parameters of the chaotic system are calculated by the SHA 256 hash of the plain image and the given values. Then, a row-by-row image diffusion method at DNA level is applied. A key matrix generated from the chaotic map is used to fuse the confused DNA matrix; also the initial values and system parameters of the chaotic system are renewed by the hamming distance of the plain image. Finally, after decoding the diffused DNA matrix, we obtain the cipher image. The DNA encoding/decoding rules of the plain image and the key matrix are determined by the plain image. Experimental results and security analyses both confirm that the proposed algorithm has not only an excellent encryption result but also resists various typical attacks.

  5. Structuring polymers for delivery of DNA-based therapeutics: updated insights.

    Science.gov (United States)

    Gupta, Madhu; Tiwari, Shailja; Vyas, Suresh

    2012-01-01

    Gene therapy offers greater opportunities for treating numerous incurable diseases from genetic disorders, infections, and cancer. However, development of appropriate delivery systems could be one of the most important factors to overcome numerous biological barriers for delivery of various therapeutic molecules. A number of nonviral polymer-mediated vectors have been developed for DNA delivery and offer the potential to surmount the associated problems of their viral counterpart. To address the concerns associated with safety issues, a wide range of polymeric vectors are available and have been utilized successfully to deliver their therapeutics in vivo. Today's research is mainly focused on the various natural or synthetic polymer-based delivery carriers that protect the DNA molecule from degradation, which offer specific targeting to the desired cells after systemic administration, have transfection efficiencies equivalent to virus-mediated gene delivery, and have long-term gene expression through sustained-release mechanisms. This review explores an updated overview of different nonviral polymeric delivery system for delivery of DNA-based therapeutics. These polymeric carriers have been evaluated in vitro and in vivo and are being utilized in various stages of clinical evaluation. Continued research and understanding of the principles of polymer-based gene delivery systems will enable us to develop new and efficient delivery systems for the delivery of DNA-based therapeutics to achieve the goal of efficacious and specific gene therapy for a vast array of clinical disorders as the therapeutic solutions of tomorrow.

  6. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Binladen, Jonas; Miller, Webb;

    2007-01-01

    , and subsequently be interpreted to enable characterization of the aDNA damage behind the observed phenotypes. Through comparative analyses on 390,965 bp of modern chloroplast and 131,474 bp of ancient woolly mammoth GS20 sequence data we conclusively demonstrate that in this sample at least, a permafrost preserved...

  7. Recognition rules for binding of Zn-Cys2His2 transcription factors to operator DNA.

    Science.gov (United States)

    Polozov, R V; Sivozhelezov, V S; Chirgadze, Yu N; Ivanov, V V

    2015-01-01

    The molecules of Zn-finger transcription factors consist of several similar small protein units. We analyzed the crystal structures 46 basic units of 22 complexes of Zn-Cys2His2 family with the fragments of operator DNA. We showed that the recognition of DNA occurs via five protein contacts. The canonical binding positions of the recognizing α-helix were -1, 3, 6, and 7, which make contacts with the tetra-nucleotide sequence ZXYZ of the coding DNA strand; here the canonical binding triplet is underlined. The non-coding DNA strand forms only one contact at α-helix position 2. We have discovered that there is a single highly conservative contact His7α with the phosphate group of nucleotide Z, which precedes each triplet XYZ of the coding DNA chain. This particular contact is invariant for the all Zn-Cys2His2 family with high frequency of occurrence 83%, which we considered as an invariant recognition rule. We have also selected a previously unreported Zn-Cys2His2-Arg subfamily of 21 Zn-finger units bound with DNA triplets, which make two invariant contacts with residues Arg6α and His7α with the coding DNA chain. These contacts show frequency of occurrence 100 and 90%, and are invariant recognition rule. Three other variable protein-DNA contacts are formed mainly with the bases and specify the recognition patterns of individual factor units. The revealed recognition rules are inherent for the Zn-Cys2His2 family and Zn-Cys2His2-Arg subfamily of different taxonomic groups and can distinguish members of these families from any other family of transcription factors.

  8. Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3.

    Science.gov (United States)

    Gong, Bei; Shin, Minsang; Sun, Jiali; Jung, Che-Hun; Bolt, Edward L; van der Oost, John; Kim, Jeong-Sun

    2014-11-18

    Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a "Cascade" ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called "interference." After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum, with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3' to 5' nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3' to 5' translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems.

  9. Binding of PFOS to serum albumin and DNA: insight into the molecular toxicity of perfluorochemicals

    Directory of Open Access Journals (Sweden)

    Ma Yin-Sheng

    2009-02-01

    Full Text Available Abstract Background Health risk from exposure of perfluorochemicals (PFCs to wildlife and human has been a subject of great interest for understanding their molecular mechanism of toxicity. Although much work has been done, the toxigenicity of PFCs remains largely unknown. In this work, the non-covalent interactions between perfluorooctane sulfonate (PFOS and serum albumin (SA and DNA were investigated under normal physiological conditions, aiming to elucidate the toxigenicity of PFCs. Results In equilibrium dialysis assay, the bindings of PFOS to SA correspond to the Langmuir isothermal model with two-step sequence model. The saturation binding number of PFOS was 45 per molecule of SA and 1 per three base-pairs of DNA, respectively. ITC results showed that all the interactions were spontaneous driven by entropy change. Static quenching of the fluorescence of SA was observed when interacting with PFOS, indicating PFOS bound Trp residue of SA. CD spectra of SA and DNA changed obviously in the presence of PFOS. At normal physiological conditions, 1.2 mmol/l PFOS reduces the binding ratio of Vitamin B2 to SA by more than 30%. Conclusion The ion bond, van der Waals force and hydrophobic interaction contributed to PFOS binding to peptide chain of SA and to the groove bases of DNA duplex. The non-covalent interactions of PFOS with SA and DNA alter their secondary conformations, with the physiological function of SA to transport Vitamin B2 being inhibited consequently. This work provides a useful experimental method for further studying the toxigenicity of PFCs.

  10. Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies.

    Science.gov (United States)

    Gallagher, William M; Bergin, Orla E; Rafferty, Mairin; Kelly, Zoë D; Nolan, Ilse-Maria; Fox, Edward J P; Culhane, Aedin C; McArdle, Linda; Fraga, Mario F; Hughes, Linda; Currid, Caroline A; O'Mahony, Fiona; Byrne, Aileen; Murphy, Alison A; Moss, Catherine; McDonnell, Susan; Stallings, Raymond L; Plumb, Jane A; Esteller, Manel; Brown, Robert; Dervan, Peter A; Easty, David J

    2005-11-01

    The incidence of melanoma is increasing rapidly, with advanced lesions generally failing to respond to conventional chemotherapy. Here, we utilized DNA microarray-based gene expression profiling techniques to identify molecular determinants of melanoma progression within a unique panel of isogenic human melanoma cell lines. When a poorly tumorigenic cell line, derived from an early melanoma, was compared with two increasingly aggressive derivative cell lines, the expression of 66 genes was significantly changed. A similar pattern of differential gene expression was found with an independently derived metastatic cell line. We further examined these melanoma progression-associated genes via use of a tailored TaqMan Low Density Array (LDA), representing the majority of genes within our cohort of interest. Considerable concordance was seen between the transcriptomic profiles determined by DNA microarray and TaqMan LDA approaches. A range of novel markers were identified that correlated here with melanoma progression. Most notable was TSPY, a Y chromosome-specific gene that displayed extensive down-regulation in expression between the parental and derivative cell lines. Examination of a putative CpG island within the TSPY gene demonstrated that this region was hypermethylated in the derivative cell lines, as well as metastatic melanomas from male patients. Moreover, treatment of the derivative cell lines with the DNA methyltransferase inhibitor, 2'-deoxy-5-azacytidine (DAC), restored expression of the TSPY gene to levels comparable with that found in the parental cells. Additional DNA microarray studies uncovered a subset of 13 genes from the above-mentioned 66 gene cohort that displayed re-activation of expression following DAC treatment, including TSPY, CYBA and MT2A. DAC suppressed tumor cell growth in vitro. Moreover, systemic treatment of mice with DAC attenuated growth of melanoma xenografts, with consequent re-expression of TSPY mRNA. Overall, our data support

  11. Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic

    Science.gov (United States)

    Perry, Kay; Hwang, Young; Bushman, Frederic D.; Van Duyne, Gregory D.

    2010-01-01

    Summary Poxviruses encode their own type IB topoisomerases (TopIBs) which release superhelical tension generated by replication and transcription of their genomes. To investigate the reaction catalyzed viral TopIBs, we have determined the structure of a variola virus topoisomerase-DNA complex trapped as a vanadate transition state mimic. The structure reveals how the viral TopIB enzymes are likely to position the DNA duplex for ligation following relaxation of supercoils and identifies the sources of friction observed in single molecule experiments that argue against free rotation. The structure also identifies a conformational change in the leaving group sugar that must occur prior to cleavage and reveals a mechanism for promoting ligation following relaxation of supercoils that involves a novel Asp-minor groove interaction. Overall, the new structural data support a common catalytic mechanism for the TopIB superfamily but indicate distinct methods for controlling duplex rotation in the small vs. large enzyme subfamilies. PMID:20152159

  12. A quantitative model of human DNA base excision repair. I. mechanistic insights

    OpenAIRE

    Sokhansanj, Bahrad A.; Rodrigue, Garry R.; Fitch, J. Patrick; David M Wilson

    2002-01-01

    Base excision repair (BER) is a multistep process involving the sequential activity of several proteins that cope with spontaneous and environmentally induced mutagenic and cytotoxic DNA damage. Quantitative kinetic data on single proteins of BER have been used here to develop a mathematical model of the BER pathway. This model was then employed to evaluate mechanistic issues and to determine the sensitivity of pathway throughput to altered enzyme kinetics. Notably, the model predicts conside...

  13. Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys.

    Science.gov (United States)

    Han, Lu; Zhu, Songbiao; Ning, Chao; Cai, Dawei; Wang, Kai; Chen, Quanjia; Hu, Songmei; Yang, Junkai; Shao, Jing; Zhu, Hong; Zhou, Hui

    2014-11-30

    The donkey (Equus asinus) is an important domestic animal that provides a reliable source of protein and method of transportation for many human populations. However, the process of domestication and the dispersal routes of the Chinese donkey are still unclear, as donkey remains are sparse in the archaeological record and often confused with horse remains. To explore the maternal origins and dispersal route of Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene fragments of 21 suspected donkey remains from four archaeological sites in China were amplified and sequenced. Molecular methods of species identification show that 17 specimens were donkeys and three samples had the maternal genetic signature of horses. One sample that dates to about 20,000 years before present failed to amplify. In this study, the phylogenetic analysis reveals that ancient Chinese donkeys have high mitochondrial DNA diversity and two distinct mitochondrial maternal lineages, known as the Somali and Nubian lineages. These results indicate that the maternal origin of Chinese domestic donkeys was probably related to the African wild ass, which includes the Nubian wild ass (Equus africanus africanus) and the Somali wild ass (Equus africanus somaliensis). Combined with historical records, the results of this study implied that domestic donkeys spread into west and north China before the emergence of the Han dynasty. The number of Chinese domestic donkeys had increased primarily to meet demand for the expansion of trade, and they were likely used as commodities or for shipping goods along the Silk Road during the Tang Dynasty, when the Silk Road reached its golden age. This study is the first to provide valuable ancient animal DNA evidence for early trade between African and Asian populations. The ancient DNA analysis of Chinese donkeys also sheds light on the dynamic process of the maternal origin, domestication, and dispersal route of ancient Chinese donkeys.

  14. 18S ribosomal DNA sequences provide insight into the phylogeny of patellogastropod limpets (Mollusca: Gastropoda).

    Science.gov (United States)

    Yoon, Sook Hee; Kim, Won

    2007-02-28

    To investigate the phylogeny of Patellogastropoda, the complete 18S rDNA sequences of nine patellogastropod limpets Cymbula canescens (Gmelin, 1791), Helcion dunkeri (Krauss, 1848), Patella rustica Linnaeus, 1758, Cellana toreuma (Reeve, 1855), Cellana nigrolineata (Reeve, 1854), Nacella magellanica Gmelin, 1791, Nipponacmea concinna (Lischke, 1870), Niveotectura pallida (Gould, 1859), and Lottia dorsuosa Gould, 1859 were determined. These sequences were then analyzed along with the published 18S rDNA sequences of 35 gastropods, one bivalve, and one chiton species. Phylogenetic trees were constructed by maximum parsimony, maximum likelihood, and Bayesian inference. The results of our 18S rDNA sequence analysis strongly support the monophyly of Patellogastropoda and the existence of three subgroups. Of these, two subgroups, the Patelloidea and Acmaeoidea, are closely related, with branching patterns that can be summarized as [(Cymbula + Helcion) + Patella] and [(Nipponacmea + Lottia) + Niveotectura]. The remaining subgroup, Nacelloidea, emerges as basal and paraphyletic, while its genus Cellana is monophyletic. Our analysis also indicates that the Patellogastropoda have a sister relationship with the order Cocculiniformia within the Gastropoda.

  15. Insights into the Determination of the Templating Nucleotide at the Initiation of φ29 DNA Replication.

    Science.gov (United States)

    del Prado, Alicia; Lázaro, José M; Longás, Elisa; Villar, Laurentino; de Vega, Miguel; Salas, Margarita

    2015-11-06

    Bacteriophage φ29 from Bacillus subtilis starts replication of its terminal protein (TP)-DNA by a protein-priming mechanism. To start replication, the DNA polymerase forms a heterodimer with a free TP that recognizes the replication origins, placed at both 5' ends of the linear chromosome, and initiates replication using as primer the OH-group of Ser-232 of the TP. The initiation of φ29 TP-DNA replication mainly occurs opposite the second nucleotide at the 3' end of the template. Earlier analyses of the template position that directs the initiation reaction were performed using single-stranded and double-stranded oligonucleotides containing the replication origin sequence without the parental TP. Here, we show that the parental TP has no influence in the determination of the nucleotide used as template in the initiation reaction. Previous studies showed that the priming domain of the primer TP determines the template position used for initiation. The results obtained here using mutant TPs at the priming loop where Ser-232 is located indicate that the aromatic residue Phe-230 is one of the determinants that allows the positioning of the penultimate nucleotide at the polymerization active site to direct insertion of the initiator dAMP during the initiation reaction. The role of Phe-230 in limiting the internalization of the template strand in the polymerization active site is discussed.

  16. A Reversible DNA Logic Gate Platform Operated by One- and Two-Photon Excitations.

    Science.gov (United States)

    Tam, Dick Yan; Dai, Ziwen; Chan, Miu Shan; Liu, Ling Sum; Cheung, Man Ching; Bolze, Frederic; Tin, Chung; Lo, Pik Kwan

    2016-01-04

    We demonstrate the use of two different wavelength ranges of excitation light as inputs to remotely trigger the responses of the self-assembled DNA devices (D-OR). As an important feature of this device, the dependence of the readout fluorescent signals on the two external inputs, UV excitation for 1 min and/or near infrared irradiation (NIR) at 800 nm fs laser pulses, can mimic function of signal communication in OR logic gates. Their operations could be reset easily to its initial state. Furthermore, these DNA devices exhibit efficient cellular uptake, low cytotoxicity, and high bio-stability in different cell lines. They are considered as the first example of a photo-responsive DNA logic gate system, as well as a biocompatible, multi-wavelength excited system in response to UV and NIR. This is an important step to explore the concept of photo-responsive DNA-based systems as versatile tools in DNA computing, display devices, optical communication, and biology. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Soldier Quality of Life (Operational) and Readiness at Contingency Base Camps: Insights From Qualitative Interviews

    Science.gov (United States)

    2017-03-13

    domains. To address this gap, the research team interviewed 31 active duty Soldiers from Fort Drum, NY and Fort Bliss, TX. A majority of the Soldiers had... activities . Billets drive sleep quality Field feeding drives nutrition Hygiene and MWR drive activities that restore readiness 8UNCLASSIFIED What is...or have some place where they can kick back and relax helps facilitate that.” 26UNCLASSIFIED Insight: Connection Soldiers look for ways to affiliate

  18. New insights into the activation mechanism of store-operated calcium channels:roles of STIM and Orai

    Institute of Scientific and Technical Information of China (English)

    Rui-wei GUO; Lan HUANG

    2008-01-01

    The activation of Ca2+ entry through store-operated channels by agonists that deplete Ca2+ from the endoplasmic reticulum (ER)is a ubiquitous signaling mechanism,the molecular basis of which has remained elusive for the past two decades.Store-operated Ca2+-release-activated Ca2+(CRAC)channels constitute the sole pathway for Ca2+ entry following antigen-receptor engagement.In a set of breakthrough studies over the past two years,stromal interaction molecule l(STIM1,tbe ER Ca2+ sensor) and Orail(a pore-forming subunit of the CRAC channel)have been identified.Here we review these recent studies and the insights they provide into the mechanism of store-operated Ca2+ channels(SOCCs).

  19. Insights into the Evolutionary History of an Extinct South American Freshwater Snail Based on Historical DNA

    Science.gov (United States)

    Strong, Ellen E.; Rumi, Alejandra; Peso, Juana G.

    2016-01-01

    Highly oxygenated freshwater habitats in the High Paraná River (Argentina–Paraguay) were home to highly endemic snails of the genus Aylacostoma, which face extinction owing to the impoundment of the Yacyretá Reservoir in the 1990s. Two species, A. chloroticum and A. brunneum, are currently included in an ongoing ex situ conservation programme, whereas A. guaraniticum and A. stigmaticum are presumed extinct. Consequently, the validity and affinities of the latter two have remained enigmatic. Here, we provide the first molecular data on the extinct A. stigmaticum by means of historical DNA analysis. We describe patterns of molecular evolution based on partial sequences of the mitochondrial 12S ribosomal RNA gene from the extinct species and from those being bred within the ex situ programme. We further use this gene to derive a secondary structure model, to examine the specific status of A. stigmaticum and to explore the evolutionary history of these snails. The secondary structure model based on A. stigmaticum revealed that most polymorphic sites are located in unpaired regions. Our results support the view that the mitochondrial 12S region is an efficient marker for the discrimination of species, and the extinct A. stigmaticum is recognized here as a distinct evolutionary genetic species. Molecular phylogenetic analyses revealed a sister group relationship between A. chloroticum and A. brunneum, and estimated divergence times suggest that diversification of Aylacostoma in the High Paraná River might have started in the late Miocene via intra-basin speciation due to a past marine transgression. Finally, our findings reveal that DNA may be obtained from dried specimens at least 80 years after their collection, and confirms the feasibility of extracting historical DNA from museum collections for elucidating evolutionary patterns and processes in gastropods. PMID:28033407

  20. Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny.

    Science.gov (United States)

    Yu, Xiang-Qin; Drew, Bryan T; Yang, Jun-Bo; Gao, Lian-Ming; Li, De-Zhu

    2017-01-01

    Schima is an ecologically and economically important woody genus in tea family (Theaceae). Unresolved species delimitations and phylogenetic relationships within Schima limit our understanding of the genus and hinder utilization of the genus for economic purposes. In the present study, we conducted comparative analysis among the complete chloroplast (cp) genomes of 11 Schima species. Our results indicate that Schima cp genomes possess a typical quadripartite structure, with conserved genomic structure and gene order. The size of the Schima cp genome is about 157 kilo base pairs (kb). They consistently encode 114 unique genes, including 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, with 17 duplicated in the inverted repeat (IR). These cp genomes are highly conserved and do not show obvious expansion or contraction of the IR region. The percent variability of the 68 coding and 93 noncoding (>150 bp) fragments is consistently less than 3%. The seven most widely touted DNA barcode regions as well as one promising barcode candidate showed low sequence divergence. Eight mutational hotspots were identified from the 11 cp genomes. These hotspots may potentially be useful as specific DNA barcodes for species identification of Schima. The 58 cpSSR loci reported here are complementary to the microsatellite markers identified from the nuclear genome, and will be leveraged for further population-level studies. Phylogenetic relationships among the 11 Schima species were resolved with strong support based on the cp genome data set, which corresponds well with the species distribution pattern. The data presented here will serve as a foundation to facilitate species identification, DNA barcoding and phylogenetic reconstructions for future exploration of Schima.

  1. A quantitative model of human DNA base excision repair. I. Mechanistic insights.

    Science.gov (United States)

    Sokhansanj, Bahrad A; Rodrigue, Garry R; Fitch, J Patrick; Wilson, David M

    2002-04-15

    Base excision repair (BER) is a multistep process involving the sequential activity of several proteins that cope with spontaneous and environmentally induced mutagenic and cytotoxic DNA damage. Quantitative kinetic data on single proteins of BER have been used here to develop a mathematical model of the BER pathway. This model was then employed to evaluate mechanistic issues and to determine the sensitivity of pathway throughput to altered enzyme kinetics. Notably, the model predicts considerably less pathway throughput than observed in experimental in vitro assays. This finding, in combination with the effects of pathway cooperativity on model throughput, supports the hypothesis of cooperation during abasic site repair and between the apurinic/apyrimidinic (AP) endonuclease, Ape1, and the 8-oxoguanine DNA glycosylase, Ogg1. The quantitative model also predicts that for 8-oxoguanine and hydrolytic AP site damage, short-patch Polbeta-mediated BER dominates, with minimal switching to the long-patch subpathway. Sensitivity analysis of the model indicates that the Polbeta-catalyzed reactions have the most control over pathway throughput, although other BER reactions contribute to pathway efficiency as well. The studies within represent a first step in a developing effort to create a predictive model for BER cellular capacity.

  2. Evolution of the B3 DNA binding superfamily: new insights into REM family gene diversification.

    Directory of Open Access Journals (Sweden)

    Elisson A C Romanel

    Full Text Available BACKGROUND: The B3 DNA binding domain includes five families: auxin response factor (ARF, abscisic acid-insensitive3 (ABI3, high level expression of sugar inducible (HSI, related to ABI3/VP1 (RAV and reproductive meristem (REM. The release of the complete genomes of the angiosperm eudicots Arabidopsis thaliana and Populus trichocarpa, the monocot Orysa sativa, the bryophyte Physcomitrella patens,the green algae Chlamydomonas reinhardtii and Volvox carteri and the red algae Cyanidioschyzon melorae provided an exceptional opportunity to study the evolution of this superfamily. METHODOLOGY: In order to better understand the origin and the diversification of B3 domains in plants, we combined comparative phylogenetic analysis with exon/intron structure and duplication events. In addition, we investigated the conservation and divergence of the B3 domain during the origin and evolution of each family. CONCLUSIONS: Our data indicate that showed that the B3 containing genes have undergone extensive duplication events, and that the REM family B3 domain has a highly diverged DNA binding. Our results also indicate that the founding member of the B3 gene family is likely to be similar to the ABI3/HSI genes found in C. reinhardtii and V. carteri. Among the B3 families, ABI3, HSI, RAV and ARF are most structurally conserved, whereas the REM family has experienced a rapid divergence. These results are discussed in light of their functional and evolutionary roles in plant development.

  3. DNA polymerase conformational dynamics and the role of fidelity-conferring residues: Insights from computational simulations

    Directory of Open Access Journals (Sweden)

    Massimiliano eMeli

    2016-05-01

    Full Text Available Herein we investigate the molecular bases of DNA polymerase I conformational dynamics that underlie the replication fidelity of the enzyme. Such fidelity is determined by conformational changes that promote the rejection of incorrect nucleotides before the chemical ligation step. We report a comprehensive atomic resolution study of wild type and mutant enzymes in different bound states and starting from different crystal structures, using extensive molecular dynamics (MD simulations that cover a total timespan of ~ 5 microseconds. The resulting trajectories are examined via a combination of novel methods of internal dynamics and energetics analysis, aimed to reveal the principal molecular determinants for the (destabilization of a certain conformational state. Our results show that the presence of fidelity-decreasing mutations or the binding of incorrect nucleotides in ternary complexes tend to favor transitions from closed towards open structures, passing through an ensemble of semi-closed intermediates. The latter ensemble includes the experimentally observed ajar conformation which, consistent with previous experimental observations, emerges as a molecular checkpoint for the selection of the correct nucleotide to incorporate. We discuss the implications of our results for the understanding of the relationships between the structure, dynamics and function of DNA polymerase I at the atomistic level.

  4. Insights and Opportunities: Challenges of Canadian First Nations Drinking Water Operators

    Directory of Open Access Journals (Sweden)

    Heather M. Murphy

    2015-06-01

    Full Text Available Providing safe drinking water continues to be a challenge in Canadian First Nations communities. In 2011, in Ontario and British Columbia, only 45 percent and 51 percent of 143 and 160 First Nations had water systems with a fully trained certified operator, respectively. The objective of this research was to investigate the issues of operator training, retention, and job satisfaction through semi-structured interviews and surveys of water system operators in Ontario and British Columbia. Operators reported the lack of funding for operation and maintenance, and a lack of support from band council as challenges in performing their jobs. Of those who reported being unsatisfied with their position, wages, hours of work, and lack of funding or support were cited as primary reasons.

  5. New insight into the molecular mechanisms of the biological effects of DNA minor groove binders.

    Directory of Open Access Journals (Sweden)

    Xinbo Zhang

    Full Text Available BACKGROUND: Bisbenzimides, or Hoechst 33258 (H258, and its derivative Hoechst 33342 (H342 are archetypal molecules for designing minor groove binders, and widely used as tools for staining DNA and analyzing side population cells. They are supravital DNA minor groove binders with AT selectivity. H342 and H258 share similar biological effects based on the similarity of their chemical structures, but also have their unique biological effects. For example, H342, but not H258, is a potent apoptotic inducer and both H342 and H258 can induce transgene overexpression in in vitro studies. However, the molecular mechanisms by which Hoechst dyes induce apoptosis and enhance transgene overexpression are unclear. METHODOLOGY/PRINCIPAL FINDINGS: To determine the molecular mechanisms underlying different biological effects between H342 and H258, microarray technique coupled with bioinformatics analyses and multiple other techniques has been utilized to detect differential global gene expression profiles, Hoechst dye-specific gene expression signatures, and changes in cell morphology and levels of apoptosis-associated proteins in malignant mesothelioma cells. H342-induced apoptosis occurs in a dose-dependent fashion and is associated with morphological changes, caspase-3 activation, cytochrome c mitochondrial translocation, and cleavage of apoptosis-associated proteins. The antagonistic effect of H258 on H342-induced apoptosis indicates a pharmacokinetic basis for the two dyes' different biological effects. Differential global gene expression profiles induced by H258 and H342 are accompanied by unique gene expression signatures determined by DNA microarray and bioinformatics software, indicating a genetic basis for their different biological effects. CONCLUSIONS/SIGNIFICANCE: A unique gene expression signature associated with H342-induced apoptosis provides a new avenue to predict and classify the therapeutic class of minor groove binders in the drug

  6. Application of environmental DNA analysis to inform invasive fish eradication operations

    Science.gov (United States)

    Davison, Phillip I.; Copp, Gordon H.; Créach, Véronique; Vilizzi, Lorenzo; Britton, J. R.

    2017-04-01

    Environmental DNA (eDNA) detection of non-native species has considerable potential to inform management decisions, including identifying the need for population control and/or eradication. An invasive species of European concern is the Asian cyprinid fish, topmouth gudgeon ( Pseudorasbora parva) . Here, eDNA analyses were applied at a commercial angling venue in southern England to inform operations aiming to eradicate P. parva, which had only ever been observed in one of the venue's seven unconnected angling ponds. Eradication of P. parva was initially attempted by repeated depletion of the population using fish traps (crayfish traps fitted with 5 mm mesh netting) and the introduction of native predators over a 4-year period. The very low number of P. parva captured following these eradication efforts suggested a possible population crash. Conventional PCR analysis of water samples using species-specific primers was applied to all seven ponds to confirm that P. parva was present in only one pond, that the eradication attempt had indeed failed and that the species' distribution in the pond appeared to be restricted to three bankside locations. The continued presence of P. parva at these locations was confirmed by subsequent trapping. Water samples from an adjacent, unconnected stream were also analysed using the eDNA methodology, but no DNA of P. parva was detected. The results suggest that further management action to eradicate P. parva be focused on the pond shown to contain the isolated P. parva population and thereby eliminate the risk of further dispersal. This study is the first to apply eDNA analysis to assess the efficacy of an eradication attempt and to provide evidence that the species was unlikely to be present in the other ponds, thus reducing the resources needed to control the species.

  7. New Insights into 5hmC DNA Modification: Generation, Distribution and Function

    Directory of Open Access Journals (Sweden)

    Dong-Qiao Shi

    2017-07-01

    Full Text Available Dynamic DNA modifications, such as methylation/demethylation on cytosine, are major epigenetic mechanisms to modulate gene expression in both eukaryotes and prokaryotes. In addition to the common methylation on the 5th position of the pyrimidine ring of cytosine (5mC, other types of modifications at the same position, such as 5-hydroxymethyl (5hmC, 5-formyl (5fC, and 5-carboxyl (5caC, are also important. Recently, 5hmC, a product of 5mC demethylation by the Ten-Eleven Translocation family proteins, was shown to regulate many cellular and developmental processes, including the pluripotency of embryonic stem cells, neuron development, and tumorigenesis in mammals. Here, we review recent advances on the generation, distribution, and function of 5hmC modification in mammals and discuss its potential roles in plants.

  8. DNA barcode libraries provide insight into continental patterns of avian diversification.

    Directory of Open Access Journals (Sweden)

    Darío A Lijtmaer

    Full Text Available BACKGROUND: The causes for the higher biodiversity in the Neotropics as compared to the Nearctic and the factors promoting species diversification in each region have been much debated. The refuge hypothesis posits that high tropical diversity reflects high speciation rates during the Pleistocene, but this conclusion has been challenged. The present study investigates this matter by examining continental patterns of avian diversification through the analysis of large-scale DNA barcode libraries. METHODOLOGY AND PRINCIPAL FINDINGS: Standardized COI datasets from the avifaunas of Argentina, the Nearctic, and the Palearctic were analyzed. Average genetic distances between closest congeners and sister species were higher in Argentina than in North America reflecting a much higher percentage of recently diverged species in the latter region. In the Palearctic genetic distances between closely related species appeared to be more similar to those of the southern Neotropics. Average intraspecific variation was similar in Argentina and North America, while the Palearctic fauna had a higher value due to a higher percentage of variable species. Geographic patterning of intraspecific structure was more complex in the southern Neotropics than in the Nearctic, while the Palearctic showed an intermediate level of complexity. CONCLUSIONS AND SIGNIFICANCE: DNA barcodes can reveal continental patterns of diversification. Our analysis suggests that avian species are older in Argentina than in the Nearctic, supporting the idea that the greater diversity of the Neotropical avifauna is not caused by higher recent speciation rates. Species in the Palearctic also appear to be older than those in the Nearctic. These results, combined with the patterns of geographic structuring found in each region, suggest a major impact of Pleistocene glaciations in the Nearctic, a lesser effect in the Palearctic and a mild effect in the southern Neotropics.

  9. Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication.

    Science.gov (United States)

    Kimura, Birgitta; Marshall, Fiona B; Chen, Shanyuan; Rosenbom, Sónia; Moehlman, Patricia D; Tuross, Noreen; Sabin, Richard C; Peters, Joris; Barich, Barbara; Yohannes, Hagos; Kebede, Fanuel; Teclai, Redae; Beja-Pereira, Albano; Mulligan, Connie J

    2011-01-07

    Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.

  10. New insights into the promoterless transcription of DNA coligo templates by RNA polymerase III.

    Science.gov (United States)

    Lama, Lodoe; Seidl, Christine I; Ryan, Kevin

    2014-01-01

    Chemically synthesized DNA can carry small RNA sequence information but converting that information into small RNA is generally thought to require large double-stranded promoters in the context of plasmids, viruses and genes. We previously found evidence that circularized oligodeoxynucleotides (coligos) containing certain sequences and secondary structures can template the synthesis of small RNA by RNA polymerase III in vitro and in human cells. By using immunoprecipitated RNA polymerase III we now report corroborating evidence that this enzyme is the sole polymerase responsible for coligo transcription. The immobilized polymerase enabled experiments showing that coligo transcripts can be formed through transcription termination without subsequent 3' end trimming. To better define the determinants of productive transcription, a structure-activity relationship study was performed using over 20 new coligos. The results show that unpaired nucleotides in the coligo stem facilitate circumtranscription, but also that internal loops and bulges should be kept small to avoid secondary transcription initiation sites. A polymerase termination sequence embedded in the double-stranded region of a hairpin-encoding coligo stem can antagonize transcription. Using lessons learned from new and old coligos, we demonstrate how to convert poorly transcribed coligos into productive templates. Our findings support the possibility that coligos may prove useful as chemically synthesized vectors for the ectopic expression of small RNA in human cells.

  11. Polyphyly of the fern family Tectariaceae sensu Ching: Insights from cpDNA sequence data

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Tectariaceae are a pantropical fern family of about 20 genera, among which 8 are distributed in China. The morphological distinctiveness of the family is widely recognized, yet relatively little systematic research has been conducted on members of Tectariaceae. Phylogenetic analyses of chloroplast DNA sequence data (rbcL and atpB) from 15 species representing all 8 genera in China were carried out under parsimony criteria and Bayesian inference. The phylogenetic reconstructions indicated that the fern family Tectariaceae as traditionally circumscribed are polyphyletic. Ctenitis, Dryopsis, Lastreopsis clustered with and should be included within the newly-defined Dryopteridaceae, and Pleocnemia is also tentatively assigned to it. A narrowly monophyletic Tectariaceae is identified, which includes Ctenitopsis, Hemigramma, Pteridrys, Quercifilix, and Tectaria. In the single rbcL analysis, Arthropteris clustered with the above-mentioned monophyletic Tectariaceae. Although further investigations are still needed to identify infrafamilial relationships within the monophyletic Tectariaceae and to redefine several problematic genera, we propose a working concept here that better reflects the inferred evolutionary history of this group.

  12. Polyphyly of the fern family Tectariaceae sensu Ching: insights from cpDNA sequence data.

    Science.gov (United States)

    Liu, HongMei; Zhang, XianChun; Chen, ZhiDuan; Dong, ShiYong; Qiu, YinLong

    2007-12-01

    Tectariaceae are a pantropical fern family of about 20 genera, among which 8 are distributed in China. The morphological distinctiveness of the family is widely recognized, yet relatively little systematic research has been conducted on members of Tectariaceae. Phylogenetic analyses of chloroplast DNA sequence data (rbcL and atpB) from 15 species representing all 8 genera in China were carried out under parsimony criteria and Bayesian inference. The phylogenetic reconstructions indicated that the fern family Tectariaceae as traditionally circumscribed are polyphyletic. Ctenitis, Dryopsis, Lastreopsis clustered with and should be included within the newly-defined Dryopteridaceae, and Pleocnemia is also tentatively assigned to it. A narrowly monophyletic Tectariaceae is identified, which includes Ctenitopsis, Hemigramma, Pteridrys, Quercifilix, and Tectaria. In the single rbcL analysis, Arthropteris clustered with the above-mentioned monophyletic Tectariaceae. Although further investigations are still needed to identify infrafamilial relationships within the monophyletic Tectariaceae and to redefine several problematic genera, we propose a working concept here that better reflects the inferred evolutionary history of this group.

  13. DNA methylation fingerprint of neuroblastoma reveals new biological and clinical insights

    Science.gov (United States)

    Gómez, Soledad; Castellano, Giancarlo; Mayol, Gemma; Queiros, Ana; Martín-Subero, José I.; Lavarino, Cinzia

    2015-01-01

    Neuroblastoma (NB) is one of the most frequently occurring extracranial solid tumors of childhood (Maris et al., 2007 [1]; Brodeur, 2003 [2]). Probability of cure varies according to patient's age, extent of disease and tumor biology (Maris et al., 2007 [1]; Brodeur, 2003 [2]; Cohn et al., 2009 [3]). However, the etiology of this developmental tumor is unknown. Recent evidence has shown that pediatric solid tumors, including NB, harbor a paucity of recurrent genetic mutations, with a significant proportion of recurrent events converging on epigenetic mechanisms (Cheung et al., 2012 [4]; Molenaar et al., 2012 [5]; Pugh et al., 2013 [6]; Sausen et al., 2013 [7]. We have analyzed the DNA methylome of neuroblastoma using high-density microarrays (Infinium Human Methylation 450k BeadChip) to define the epigenetic landscape of this pediatric tumor and its potential clinicopathological impact. Here, we provide the detail of methods and quality control parameters of the microarray data used for the study. Methylation data has been deposited at NCBI Gene Expression Omnibus data repository, accession number GSE54719; superseries record GSE54721. PMID:26484286

  14. The structure of a DnaA/HobA complex from Helicobacter pylori provides insight into regulation of DNA replication in bacteria

    OpenAIRE

    Natrajan, Ganesh; Noirot-Gros, Marie Francoise; Zawilak-Pawlik, Anna; Kapp, Ulrike; Terradot, Laurent

    2009-01-01

    Bacterial DNA replication requires DnaA, an AAA+ ATPase that initiates replication at a specific chromosome region, oriC, and is regulated by species-specific regulators that directly bind DnaA. HobA is a DnaA binding protein, recently identified as an essential regulator of DNA replication in Helicobacter pylori. We report the crystal structure of HobA in complex with domains I and II of DnaA (DnaAI–II) from H. pylori, the first structure of DnaA bound to one of its regulators. Biochemical c...

  15. Some insights in novel risk modeling of liquefied natural gas carrier maintenance operations

    Science.gov (United States)

    Nwaoha, T. C.; John, Andrew

    2016-06-01

    This study discusses the analysis of various modeling approaches and maintenance techniques applicable to the Liquefied Natural Gas (LNG) carrier operations in the maritime environment. Various novel modeling techniques are discussed; including genetic algorithms, fuzzy logic and evidential reasoning. We also identify the usefulness of these algorithms in the LNG carrier industry in the areas of risk assessment and maintenance modeling.

  16. Desert Rats 2010 Operations Tests: Insights from the Geology Crew Members

    Science.gov (United States)

    Bleacher, J. E.; Hurtado, J. M., Jr.; Young, K. E.; Rice, J.; Garry, W. B.; Eppler, D.

    2011-01-01

    Desert Research and Technology Studies (Desert RATS) is a multi-year series of tests of NASA hardware and operations deployed in the high desert of Arizona. Conducted annually since 1997, these activities exercise planetary surface hardware and operations in relatively harsh conditions where long-distance, multi-day roving is achievable. Such activities not only test vehicle subsystems, they also stress communications and operations systems and enable testing of science operations approaches that advance human and robotic surface exploration capabilities. Desert RATS 2010 tested two crewed rovers designed as first-generation prototypes of small pressurized vehicles, consistent with exploration architecture designs. Each rover provided the internal volume necessary for crewmembers to live and work for periods up to 14 days, as well as allowing for extravehicular activities (EVAs) through the use of rear-mounted suit ports. The 2010 test was designed to simulate geologic science traverses over a 14-day period through a volcanic field that is analogous to volcanic terrains observed throughout the Solar System. The test was conducted between 31 August and 13 September 2010. Two crewmembers lived in and operated each rover for a week with a "shift change" on day 7, resulting in a total of eight test subjects for the two-week period. Each crew consisted of an engineer/commander and an experienced field geologist. Three of the engineer/commanders were experienced astronauts with at least one Space Shuttle flight. The field geologists were drawn from the scientific community, based on funded and published field expertise.

  17. Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase.

    Science.gov (United States)

    Xia, Shuangluo; Wang, Mina; Blaha, Gregor; Konigsberg, William H; Wang, Jimin

    2011-10-25

    We have captured a preinsertion ternary complex of RB69 DNA polymerase (RB69pol) containing the 3' hydroxyl group at the terminus of an extendable primer (ptO3') and a nonhydrolyzable 2'-deoxyuridine 5'-α,β-substituted triphosphate, dUpXpp, where X is either NH or CH(2), opposite a complementary templating dA nucleotide residue. Here we report four structures of these complexes formed by three different RB69pol variants with catalytically inert Ca(2+) and four other structures with catalytically competent Mn(2+) or Mg(2+). These structures provide new insights into why the complete divalent metal-ion coordination complexes at the A and B sites are required for nucleotidyl transfer. They show that the metal ion in the A site brings ptO3' close to the α-phosphorus atom (Pα) of the incoming dNTP to enable phosphodiester bond formation through simultaneous coordination of both ptO3' and the nonbridging Sp oxygen of the dNTP's α-phosphate. The coordination bond length of metal ion A as well as its ionic radius determines how close ptO3' can approach Pα. These variables are expected to affect the rate of bond formation. The metal ion in the B site brings the pyrophosphate product close enough to Pα to enable pyrophosphorolysis and assist in the departure of the pyrophosphate. In these dUpXpp-containing complexes, ptO3' occupies the vertex of a distorted metal ion A coordination octahedron. When ptO3' is placed at the vertex of an undistorted, idealized metal ion A octahedron, it is within bond formation distance to Pα. This geometric relationship appears to be conserved among DNA polymerases of known structure.

  18. Kinetic insights over a PEMFC operating on stationary and oscillatory states.

    Science.gov (United States)

    Mota, Andressa; Gonzalez, Ernesto R; Eiswirth, Markus

    2011-12-01

    Kinetic investigations in the oscillatory state have been carried out in order to shed light on the interplay between the complex kinetics exhibited by a proton exchange membrane fuel cell fed with poisoned H(2) (108 ppm of CO) and the other in serie process. The apparent activation energy (E(a)) in the stationary state was investigated in order to clarify the E(a) observed in the oscillatory state. The apparent activation energy in the stationary state, under potentiostatic control, rendered (a) E(a) ≈ 50-60 kJ mol(-1) over 0.8 V proton conductivity in the membrane. The dependence of the period-one oscillations on the temperature yielded a genuine Arrhenius dependence with two E(a) values: (a) E(a) around 70 kJ mol(-1), at high temperatures, and (b) E(a) around 10-15 kJ mol(-1), at lower temperatures. The latter E(a) indicates the presence of protonic mass transport coupled to the essential oscillatory mechanism. These insights point in the right direction to predict spatial couplings between anode and cathode as having the highest strength as well as to speculate the most likely candidates to promote spatial inhomogeneities.

  19. Human Factors Engineering (HFE) insights for advanced reactors based upon operating experience

    Energy Technology Data Exchange (ETDEWEB)

    Higgins, J.; Nasta, K.

    1997-01-01

    The NRC Human Factors Engineering Program Review Model (HFE PRM, NUREG-0711) was developed to support a design process review for advanced reactor design certification under 10CFR52. The HFE PRM defines ten fundamental elements of a human factors engineering program. An Operating Experience Review (OER) is one of these elements. The main purpose of an OER is to identify potential safety issues from operating plant experience and ensure that they are addressed in a new design. Broad-based experience reviews have typically been performed in the past by reactor designers. For the HFE PRM the intent is to have a more focussed OER that concentrates on HFE issues or experience that would be relevant to the human-system interface (HSI) design process for new advanced reactors. This document provides a detailed list of HFE-relevant operating experience pertinent to the HSI design process for advanced nuclear power plants. This document is intended to be used by NRC reviewers as part of the HFE PRM review process in determining the completeness of an OER performed by an applicant for advanced reactor design certification. 49 refs.

  20. Passive BCI in Operational Environments: Insights, Recent Advances, and Future Trends.

    Science.gov (United States)

    Arico, Pietro; Borghini, Gianluca; Di Flumeri, Gianluca; Sciaraffa, Nicolina; Colosimo, Alfredo; Babiloni, Fabio

    2017-07-01

    This minireview aims to highlight recent important aspects to consider and evaluate when passive brain-computer interface (pBCI) systems would be developed and used in operational environments, and remarks future directions of their applications. Electroencephalography (EEG) based pBCI has become an important tool for real-time analysis of brain activity since it could potentially provide covertly-without distracting the user from the main task-and objectively-not affected by the subjective judgment of an observer or the user itself-information about the operator cognitive state. Different examples of pBCI applications in operational environments and new adaptive interface solutions have been presented and described. In addition, a general overview regarding the correct use of machine learning techniques (e.g., which algorithm to use, common pitfalls to avoid, etc.) in the pBCI field has been provided. Despite recent innovations on algorithms and neurotechnology, pBCI systems are not completely ready to enter the market yet, mainly due to limitations of the EEG electrodes technology, and algorithms reliability and capability in real settings. High complexity and safety critical systems (e.g., airplanes, ATM interfaces) should adapt their behaviors and functionality accordingly to the user' actual mental state. Thus, technologies (i.e., pBCIs) able to measure in real time the user's mental states would result very useful in such "high risk" environments to enhance human machine interaction, and so increase the overall safety.

  1. jMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units.

    Directory of Open Access Journals (Sweden)

    Martin Jones

    Full Text Available BACKGROUND: DNA barcoding and other DNA sequence-based techniques for investigating and estimating biodiversity require explicit methods for associating individual sequences with taxa, as it is at the taxon level that biodiversity is assessed. For many projects, the bioinformatic analyses required pose problems for laboratories whose prime expertise is not in bioinformatics. User-friendly tools are required for both clustering sequences into molecular operational taxonomic units (MOTU and for associating these MOTU with known organismal taxonomies. RESULTS: Here we present jMOTU, a Java program for the analysis of DNA barcode datasets that uses an explicit, determinate algorithm to define MOTU. We demonstrate its usefulness for both individual specimen-based Sanger sequencing surveys and bulk-environment metagenetic surveys using long-read next-generation sequencing data. jMOTU is driven through a graphical user interface, and can analyse tens of thousands of sequences in a short time on a desktop computer. A companion program, Taxonerator, that adds traditional taxonomic annotation to MOTU, is also presented. Clustering and taxonomic annotation data are stored in a relational database, and are thus amenable to subsequent data mining and web presentation. CONCLUSIONS: jMOTU efficiently and robustly identifies the molecular taxa present in survey datasets, and Taxonerator decorates the MOTU with putative identifications. jMOTU and Taxonerator are freely available from http://www.nematodes.org/.

  2. A reversible DNA-silver nanoclusters-based molecular fluorescence switch and its use for logic gate operation.

    Science.gov (United States)

    Huang, Zhenzhen; Ren, Jinsong; Qu, Xiaogang

    2012-03-01

    Molecule-like silver nanoclusters (AgNCs) with few to tens of atoms are highly sensitive to the sequence and structure of DNA stabilizers. In this paper, a novel pH-triggered reversible molecular fluorescence switch is developed by taking advantage of the DNA-dependent fluorescence pH response of AgNCs. The DNA-AgNCs fluorescence switch simultaneously addresses concerns of simple construction strategy, efficient design and organic-solvent-free operation. Moreover, the excellent photostability and biocompatibility of AgNCs provide great potential for application of the DNA-AgNCs fluorescence switch in the development of functional molecular devices. Specifically, we apply the DNA-AgNCs fluorescence switch combined with the DNA sequence-dependent pH response pattern of AgNCs for construction of molecular logic gates.

  3. Insights on the Bayesian spectral density method for operational modal analysis

    Science.gov (United States)

    Au, Siu-Kui

    2016-01-01

    This paper presents a study on the Bayesian spectral density method for operational modal analysis. The method makes Bayesian inference of the modal properties by using the sample power spectral density (PSD) matrix averaged over independent sets of ambient data. In the typical case with a single set of data, it is divided into non-overlapping segments and they are assumed to be independent. This study is motivated by a recent paper that reveals a mathematical equivalence of the method with the Bayesian FFT method. The latter does not require averaging concepts or the independent segment assumption. This study shows that the equivalence does not hold in reality because the theoretical long data asymptotic distribution of the PSD matrix may not be valid. A single time history can be considered long for the Bayesian FFT method but not necessarily for the Bayesian PSD method, depending on the number of segments.

  4. Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations.

    Science.gov (United States)

    Feng, Lingyan; Zhao, Andong; Ren, Jinsong; Qu, Xiaogang

    2013-09-01

    Left-handed Z-DNA has been identified as a transient structure occurred during transcription. DNA B-Z transition has attracted much attention because of not only Z-DNA biological importance but also their relation to disease and DNA nanotechnology. Recently, photoluminescent carbon dots, especially highly luminescent nitrogen-doped carbon dots, have attracted much attention on their applications to bioimaging and gene/drug delivery because of carbon dots with low toxicity, highly stable photoluminescence and controllable surface function. However, it is still unknown whether carbon dots can influence DNA conformation or structural transition, such as B-Z transition. Herein, based on our previous series work on DNA interactions with carbon nanotubes, we report the first example that photoluminescent carbon dots can induce right-handed B-DNA to left-handed Z-DNA under physiological salt conditions with sequence and conformation selectivity. Further studies indicate that carbon dots would bind to DNA major groove with GC preference. Inspired by carbon dots lighting up Z-DNA and DNA nanotechnology, several types of DNA logic gates have been designed and constructed based on fluorescence resonance energy transfer between photoluminescent carbon dots and DNA intercalators.

  5. SECURITY CO-OPERATION IN THE SOUTHERN AFRICAN DEVELOPMENT COMMUNITY: INSIGHTS FROM THE NEW INSTITUTIONALISM

    Directory of Open Access Journals (Sweden)

    Anthoni Van Nieuwkerk

    2011-08-01

    Full Text Available This article focuses on the institutional dimensions of security cooperationas it manifests in the Southern African Development Community(SADC. As the quotations above suggest, security co-operation, as part of a biggerproject of regional integration, is not obvious. Indeed, should southern Africansbelieve their politicians when the latter claim that SADC is ‘forging ahead’ on theroad to formal integration? Slabbert is not convinced. Not only academics, but civilsociety increasingly question its raison d’ etre. For many, it is unclear whether orhow SADC provides human security to the people of the region. Instead, SADCmembers’ positions on the key regional challenges (trade, growth and development,security and stability are driven by national interest rather than regional interest – asrealists argue, national interests (a must-have are hard and measurable; regional cooperation(often a nice-to-have is hard to measure. Or should we accept a regionalconsciousness shaped by a shared historical experience – a problematic assumption?

  6. Are positive and negative reinforcement "different"? Insights from a free-operant differential outcomes effect.

    Science.gov (United States)

    Magoon, Michael A; Critchfield, Thomas S; Merrill, Dustin; Newland, M Christopher; Schneider, W Joel

    2017-01-01

    Although theoretical discussions typically assume that positive and negative reinforcement differ, the literature contains little unambiguous evidence that they produce differential behavioral effects. To test whether the two types of consequences control behavior differently, we pitted money-gain positive reinforcement and money-loss-avoidance negative reinforcement, scheduled through identically programmed variable-cycle schedules, against each other in concurrent schedules. Contingencies of response-produced feedback, normally different in positive and negative reinforcement, were made symmetrical. Steeper matching slopes were produced compared to a baseline consisting of all positive reinforcement. This free-operant differential outcomes effect supports the notion that that stimulus-presentation positive reinforcement and stimulus-elimination negative reinforcement are functionally "different." However, a control experiment showed that the feedback asymmetry of more traditional positive and negative reinforcement schedules also is sufficient to create a "difference" when the type of consequence is held constant. We offer these findings as a small step in meeting the very large challenge of moving negative reinforcement theory beyond decades of relative quiescence.

  7. Structure of the MecI repressor from Staphylococcus aureus in complex with the cognate DNA operator of mec

    Energy Technology Data Exchange (ETDEWEB)

    Safo, Martin K., E-mail: msafo@vcu.edu [Department of Medicinal Chemistry, School of Pharmacy and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23298 (United States); Ko, Tzu-Ping [Institute of Biological Chemistry, Academia Sinica, Taipei 11529,Taiwan (China); Musayev, Faik N. [Department of Medicinal Chemistry, School of Pharmacy and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23298 (United States); Zhao, Qixun [Department of Medicine and Department of Microbiology/Immunology, Virginia Commonwealth University, Richmond, Virginia 23298 (United States); Wang, Andrew H.-J. [Institute of Biological Chemistry, Academia Sinica, Taipei 11529,Taiwan (China); Archer, Gordon L. [Department of Medicine and Department of Microbiology/Immunology, Virginia Commonwealth University, Richmond, Virginia 23298 (United States); Department of Medicinal Chemistry, School of Pharmacy and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23298 (United States)

    2006-04-01

    The up-and-down binding of dimeric MecI to mecA dyad DNA may account for the cooperative effect of the repressor. The dimeric repressor MecI regulates the mecA gene that encodes the penicillin-binding protein PBP-2a in methicillin-resistant Staphylococcus aureus (MRSA). MecI is similar to BlaI, the repressor for the blaZ gene of β-lactamase. MecI and BlaI can bind to both operator DNA sequences. The crystal structure of MecI in complex with the 32 base-pair cognate DNA of mec was determined to 3.8 Å resolution. MecI is a homodimer and each monomer consists of a compact N-terminal winged-helix domain, which binds to DNA, and a loosely packed C-terminal helical domain, which intertwines with its counter-monomer. The crystal contains horizontal layers of virtual DNA double helices extending in three directions, which are separated by perpendicular DNA segments. Each DNA segment is bound to two MecI dimers. Similar to the BlaI–mec complex, but unlike the MecI–bla complex, the MecI repressors bind to both sides of the mec DNA dyad that contains four conserved sequences of TACA/TGTA. The results confirm the up-and-down binding to the mec operator, which may account for cooperative effect of the repressor.

  8. Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations

    OpenAIRE

    Feng, Lingyan; Zhao, Andong; Ren, Jinsong; Qu, Xiaogang

    2013-01-01

    Left-handed Z-DNA has been identified as a transient structure occurred during transcription. DNA B-Z transition has attracted much attention because of not only Z-DNA biological importance but also their relation to disease and DNA nanotechnology. Recently, photoluminescent carbon dots, especially highly luminescent nitrogen-doped carbon dots, have attracted much attention on their applications to bioimaging and gene/drug delivery because of carbon dots with low toxicity, highly stable photo...

  9. The structure of a DnaA/HobA complex from Helicobacter pylori provides insight into regulation of DNA replication in bacteria

    Science.gov (United States)

    Natrajan, Ganesh; Noirot-Gros, Marie Francoise; Zawilak-Pawlik, Anna; Kapp, Ulrike; Terradot, Laurent

    2009-01-01

    Bacterial DNA replication requires DnaA, an AAA+ ATPase that initiates replication at a specific chromosome region, oriC, and is regulated by species-specific regulators that directly bind DnaA. HobA is a DnaA binding protein, recently identified as an essential regulator of DNA replication in Helicobacter pylori. We report the crystal structure of HobA in complex with domains I and II of DnaA (DnaAI–II) from H. pylori, the first structure of DnaA bound to one of its regulators. Biochemical characterization of the complex formed shows that a tetramer of HobA binds four DnaAI–II molecules, and that DnaAI–II is unable to oligomerize by itself. Mutagenesis and protein–protein interaction studies demonstrate that some of the residues located at the HobA-DnaAI–II interface in the structure are necessary for complex formation. Introduction of selected mutations into H. pylori shows that the disruption of the interaction between HobA and DnaA is lethal for the bacteria. Remarkably, the DnaA binding site of HobA is conserved in DiaA from Escherichia coli, suggesting that the structure of the HobA/DnaA complex represents a model for DnaA regulation in other Gram-negative bacteria. Our data, together with those from other studies, indicate that HobA could play a crucial scaffolding role during the initiation of replication in H. pylori by organizing the first step of DnaA oligomerization and attachment to oriC. PMID:19940251

  10. Insights into the Thwaites Glacier grounding zone from Operation IceBridge aerogravity

    Science.gov (United States)

    Tinto, K. J.; Bell, R. E.; Cochran, J. R.; Elieff, S.; Frearson, N.

    2010-12-01

    Operation IceBridge acquired 1500 km of geophysical data, at 10 km spacing, in front of the Thwaites Glacier grounding line during the 2009 season. The gravity anomalies recorded by the survey have been used to model the bathymetry of the sea floor in front of the glacier, an area inaccessible to previous surveys. The resulting map reveals previously unseen detail of the Thwaites grounding zone, as well as the spatial extent of features that were formerly only known as points affecting the ice surface. The modeled bathymetry in front of Thwaites Glacier is marked by an undulating ridge running sub-parallel to the grounding line, 40 km seaward. The highest peak on the ridge is in contact with the overlying ice shelf, hindering its flow. Ridge elevation decreases to the west, with a maximum ridge depth of 850 m and an average relief of 350 m. This is comparable in scale to the recently identified ridge crossing the channel of nearby Pine Island Glacier (Jenkins et al., 2010). The present-day grounding line of Thwaites appears to be marked by a more subdued ridge, in which we have identified a 20 km wide hollow, to a water depth of 1200 m. Our model shows that this hollow corresponds to a landward bight in the grounding line, in the region through which the fast ice flow of Thwaites Glacier is focused. This correlation was not visible on previous, coarser scale maps of the grounding line, and shows a clear relationship between the bathymetry and ice flow. Gravity inversions have been constrained by nearby marine surveys, satellite images of the ice rise at the peak of the ridge and radar and laser data from the IceBridge survey to constrain ice thickness. The absolute values of predicted bathymetry are dependent on the density of the rocks in the subsurface, for example the presence or absence of volcanic material or loose sediments. Some models of the geology of the survey area are also proposed. Uncertainty of underlying geology may account for ~100 m errors in the

  11. Structure of the Mecl Repressor from Staphylococcus aureus in Complex with the Cognate DNA Operator of mec

    Energy Technology Data Exchange (ETDEWEB)

    Safo,M.; Ko, T.; Musayev, F.; Zhao, Q.; Wang, A.; Archer, G.

    2006-01-01

    The dimeric repressor MecI regulates the mecA gene that encodes the penicillin-binding protein PBP-2a in methicillin-resistant Staphylococcus aureus (MRSA). MecI is similar to BlaI, the repressor for the blaZ gene of {beta}-lactamase. MecI and BlaI can bind to both operator DNA sequences. The crystal structure of MecI in complex with the 32 base-pair cognate DNA of mec was determined to 3.8 Angstroms resolution. MecI is a homodimer and each monomer consists of a compact N-terminal winged-helix domain, which binds to DNA, and a loosely packed C-terminal helical domain, which intertwines with its counter-monomer. The crystal contains horizontal layers of virtual DNA double helices extending in three directions, which are separated by perpendicular DNA segments. Each DNA segment is bound to two MecI dimers. Similar to the BlaI-mec complex, but unlike the MecI-bla complex, the MecI repressors bind to both sides of the mec DNA dyad that contains four conserved sequences of TACA/TGTA. The results confirm the up-and-down binding to the mec operator, which may account for cooperative effect of the repressor.

  12. Intrinsic disorder in the partitioning protein KorB persists after co-operative complex formation with operator DNA and KorA.

    Science.gov (United States)

    Hyde, Eva I; Callow, Philip; Rajasekar, Karthik V; Timmins, Peter; Patel, Trushar R; Siligardi, Giuliano; Hussain, Rohanah; White, Scott A; Thomas, Christopher M; Scott, David J

    2017-08-30

    The ParB protein, KorB, from the RK2 plasmid is required for DNA partitioning and transcriptional repression. It acts co-operatively with other proteins, including the repressor KorA. Like many multifunctional proteins, KorB contains regions of intrinsically disordered structure, existing in a large ensemble of interconverting conformations. Using NMR spectroscopy, circular dichroism and small-angle neutron scattering, we studied KorB selectively within its binary complexes with KorA and DNA, and within the ternary KorA/KorB/DNA complex. The bound KorB protein remains disordered with a mobile C-terminal domain and no changes in the secondary structure, but increases in the radius of gyration on complex formation. Comparison of wild-type KorB with an N-terminal deletion mutant allows a model of the ensemble average distances between the domains when bound to DNA. We propose that the positive co-operativity between KorB, KorA and DNA results from conformational restriction of KorB on binding each partner, while maintaining disorder. © 2017 The Author(s).

  13. DNA Bipedal Motor Achieves a Large Number of Steps Due to Operation Using Microfluidics-Based Interface.

    Science.gov (United States)

    Tomov, Toma E; Tsukanov, Roman; Glick, Yair; Berger, Yaron; Liber, Miran; Avrahami, Dorit; Gerber, Doron; Nir, Eyal

    2017-04-25

    Realization of bioinspired molecular machines that can perform many and diverse operations in response to external chemical commands is a major goal in nanotechnology, but current molecular machines respond to only a few sequential commands. Lack of effective methods for introduction and removal of command compounds and low efficiencies of the reactions involved are major reasons for the limited performance. We introduce here a user interface based on a microfluidics device and single-molecule fluorescence spectroscopy that allows efficient introduction and removal of chemical commands and enables detailed study of the reaction mechanisms involved in the operation of synthetic molecular machines. The microfluidics provided 64 consecutive DNA strand commands to a DNA-based motor system immobilized inside the microfluidics, driving a bipedal walker to perform 32 steps on a DNA origami track. The microfluidics enabled removal of redundant strands, resulting in a 6-fold increase in processivity relative to an identical motor operated without strand removal and significantly more operations than previously reported for user-controlled DNA nanomachines. In the motor operated without strand removal, redundant strands interfere with motor operation and reduce its performance. The microfluidics also enabled computer control of motor direction and speed. Furthermore, analysis of the reaction kinetics and motor performance in the absence of redundant strands, made possible by the microfluidics, enabled accurate modeling of the walker processivity. This enabled identification of dynamic boundaries and provided an explanation, based on the "trap state" mechanism, for why the motor did not perform an even larger number of steps. This understanding is very important for the development of future motors with significantly improved performance. Our universal interface enables two-way communication between user and molecular machine and, relying on concepts similar to that of solid

  14. Genetic and biochemical evidences reveal novel insights into the mechanism underlying Saccharomyces cerevisiae Sae2-mediated abrogation of DNA replication stress

    Indian Academy of Sciences (India)

    INDRAJEET GHODKE; K MUNIYAPPA

    2016-12-01

    In Saccharomyces cerevisiae, the Mre11-Rad50-Xrs2 (MRX) protein complex plays pivotal roles in double-strandbreak (DSB) repair, replication stress and telomere length maintenance. Another protein linked to DSB repair is Sae2,which regulates MRX persistence at DSBs. However, very little is known about its role in DNA replication stress andrepair. Here, we reveal a crucial role for Sae2 in DNA replication stress. We show that different mutant alleles of SAE2cause hypersensitivity to genotoxic agents, and when combined with Δmre11 or nuclease-defective mre11 mutantalleles, the double mutants are considerably more sensitive suggesting that the sae2 mutations synergize with mre11mutations. Biochemical studies demonstrate that Sae2 exists as a dimer in solution, associates preferentially withsingle-stranded and branched DNA structures, exhibits structure-specific endonuclease activity and cleaves thesesubstrates from the 5′ end. Furthermore, we show that the nuclease activity is indeed intrinsic to Sae2. Interestingly,sae2G270D protein possesses DNA-binding activity, but lacks detectable nuclease activity. Altogether, our data suggesta direct role for Sae2 nuclease activity in processing of the DNA structures that arise during replication and DNAdamage and provide insights into the mechanism underlying Mre11-Sae2-mediated abrogation of replication stress-relateddefects in S. cerevisiae.

  15. Surfactant-cobalt(III) complexes: The impact of hydrophobicity on interaction with HSA and DNA - insights from experimental and theoretical approach.

    Science.gov (United States)

    Veeralakshmi, Selvakumar; Sabapathi, Gopal; Nehru, Selvan; Venuvanalingam, Ponnambalam; Arunachalam, Sankaralingam

    2017-05-01

    To develop surfactant-based metallodrugs, it is very important to know about their hydrophobicity, micelle forming capacity, their interaction with biomacromolecules such as proteins and nucleic acids, and biological activities. Here, diethylenetriamine (dien) and tetradecylamine ligand (TA) based surfactant-cobalt(III) complexes with single chain domain, [Co(dien)(TA)Cl2]ClO4 (1) and double chain domain [Co(dien)(TA)2Cl](ClO4)2 (2) were chosen to study the effect of hydrophobicity on the interaction with human serum albumin and calf thymus DNA. The obtained results showed that (i) single chain surfactant-cobalt(III) complex (1) interact with HSA and DNA via electrostatic interaction and groove binding, respectively; (ii) double chain surfactant-cobalt(III) complex (2) interact with HSA and DNA via hydrophobic interaction and partial intercalation, respectively, due to the play of hydrophobicity by single and double chain domains. Further it is noted that, double chain surfactant-cobalt(III) complex interact strongly with HSA and DNA, compared single chain surfactant-cobalt(III) complex due to their more hydrophobicity nature. DFT and molecular docking studies offer insights into the mechanism and mode of binding towards the molecular target CT-DNA and HSA. Hence, the present findings will create new avenue towards the use of hydrophobic metallodrugs for various therapeutic applications. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. A structural insight into major groove directed binding of nitrosourea derivative nimustine with DNA: a spectroscopic study.

    Directory of Open Access Journals (Sweden)

    Shweta Agarwal

    Full Text Available Nitrosourea therapeutics occupies a definite place in cancer therapy but its exact mechanism of action has yet to be established. Nimustine, a chloroethyl nitrosourea derivative, is used to treat various types of malignancy including gliomas. The present work focuses on the understanding of nimustine interaction with DNA to delineate its mechanism at molecular level. Attenuated total reflection-Fourier transform infrared (ATR-FTIR has been used to determine the binding sites of nimustine on DNA. Circular dichroism (CD spectroscopy has been used to confirm conformational variations in DNA molecule upon nimustine-DNA interaction. Thermodynamic parameters of nimustine-DNA reaction have been calculated by isothermal titration calorimetry. Results of the present study demonstrate that nimustine is not a simple alkylating agent rather it causes major grove-directed-alkylation. Spectroscopic data suggest binding of nimustine with nitrogenous bases guanine (C6 = O6 and thymine (C4 = O4 in DNA major groove. CD spectra of nimustine-DNA complexes point toward the perturbation of native B-conformation of DNA and its partial transition into C-form. Thermodynamically, nimustine-DNA interaction is an entropy driven endothermic reaction, which suggests hydrophobic interaction of nimustine in DNA-major groove pocket. Spectral results suggest base binding and local conformational changes in DNA upon nimustine interaction. Investigation of drug-DNA interaction is an essential part of rational drug designing that also provides information about the drug's action at molecular level. Results, demonstrated here, may contribute in the development of new nitrosourea therapeutics with better efficacy and fewer side effects.

  17. ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors.

    Science.gov (United States)

    Starick, Stephan R; Ibn-Salem, Jonas; Jurk, Marcel; Hernandez, Céline; Love, Michael I; Chung, Ho-Ryun; Vingron, Martin; Thomas-Chollier, Morgane; Meijsing, Sebastiaan H

    2015-06-01

    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. © 2015 Starick et al.; Published by Cold Spring Harbor Laboratory Press.

  18. DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetic structure of whitebark pine (Pinus albicaulis).

    Science.gov (United States)

    Richardson, B A; Brunsfeld, S J; Klopfenstein, N B

    2002-02-01

    Uniparentally inherited mitochondrial (mt)DNA and chloroplast (cp)DNA microsatellites (cpSSRs) were used to examine population genetic structure and biogeographic patterns of bird-dispersed seed and wind-disseminated pollen of whitebark pine (Pinus albicaulis Engelm.). Sampling was conducted from 41 populations throughout the range of the species. Analyses provide evidence for an ancestral haplotype and two derived mtDNA haplotypes with distinct regional distributions. An abrupt contact zone between mtDNA haplotypes in the Cascade Range suggests postglacial biogeographic movements. Among three cpSSR loci, 42 haplotypes were detected within 28 cpSSR sample populations that were aggregated into six regions. Analysis of molecular variance (amova) was used to determine the hierarchical genetic structure of cpSSRs. amova and population pairwise comparisons (FST ) of cpSSR, and geographical distribution of mtDNA haplotypes provide insights into historical changes in biogeography. The genetic data suggest that whitebark pine has been intimately tied to climatic change and associated glaciation, which has led to range movements facilitated by seed dispersal by Clark's nutcracker (Nucifraga columbiana Wilson). The two hypotheses proposed to explain the genetic structure are: (i) a northward expansion into Canada and the northern Cascades in the early Holocene; and (ii) historical gene flow between Idaho and the Oregon Cascades when more continuous habitat existed in Central Oregon during the late Pleistocene. Genetic structure and insights gained from historical seed movements provide a basis on which to develop recovery plans for a species that is at risk from multiple threats.

  19. Insights into the mechanism of DNA recognition by the methylated LINE binding protein EhMLBP of Entamoeba histolytica.

    Science.gov (United States)

    Lavi, Tal; Siman-Tov, Rama; Ankri, Serge

    2009-08-01

    EhMLBP is an essential Entamoeba histolytica protein that binds preferentially to methylated long interspersed nuclear elements and rDNA. In an effort to identify more EhMLBP DNA substrates, we developed an affinity-based technique in which the C-terminal DNA binding domain of EhMLBP (GST-CterEhMLBP) was used as the ligand. Bioinformatic analysis of the DNA sequences that were isolated by this affinity method revealed the presence of a 29-nucleotide consensus motif that includes a stretch of ten adenines. Gel retardation analysis showed that EhMLBP binds to the consensus motif with a preference for its methylated form. Four DNA sequences, namely those that encoded either dihydrouridine synthetase, RAP GTPase activating protein, serine/threonine protein kinase or leucine-rich repeat containing protein (LRPP) were then selected for further analysis. In vivo binding of EhMLBP to these genes was confirmed by chromatin immunoprecipitation. The presence of methylated cytosines was detected in DNA encoding LRPP and to a lower extent in the other genes. EhMLBP binds preferentially to the methylated forms of these DNA targets. The ability of the consensus motif to compete with EhMLBP binding to its DNA substrates indicates that the adenine stretch is involved in the mechanism of DNA recognition. The results of this investigation extend our existing knowledge on the number of DNA sequences that are recognized by EhMLBP and reinforce the notion that this protein is an innate methylated DNA binding protein in E. histolytica.

  20. A bacterial antirepressor with SH3 domain topology mimics operator DNA in sequestering the repressor DNA recognition helix

    OpenAIRE

    León, Esther; Navarro-Avilés, Gloria; Santiveri, Clara M.; Flores-Flores, Cesar; Rico, Manuel; González, Carlos; Murillo, Francisco J; Elías-Arnanz, Montserrat; Jiménez, María Angeles; Padmanabhan, S.

    2010-01-01

    Direct targeting of critical DNA-binding elements of a repressor by its cognate antirepressor is an effective means to sequester the repressor and remove a transcription initiation block. Structural descriptions for this, though often proposed for bacterial and phage repressor–antirepressor systems, are unavailable. Here, we describe the structural and functional basis of how the Myxococcus xanthus CarS antirepressor recognizes and neutralizes its cognate repressors to turn on a photo-inducib...

  1. DNA supercoiling during transcription.

    Science.gov (United States)

    Ma, Jie; Wang, Michelle D

    2016-11-01

    The twin-supercoiled-domain model describes how transcription can drive DNA supercoiling, and how DNA supercoiling, in turn plays an important role in regulating gene transcription. In vivo and in vitro experiments have disclosed many details of the complex interactions in this relationship, and recently new insights have been gained with the help of genome-wide DNA supercoiling mapping techniques and single molecule methods. This review summarizes the general mechanisms of the interplay between DNA supercoiling and transcription, considers the biological implications, and focuses on recent important discoveries and technical advances in this field. We highlight the significant impact of DNA supercoiling in transcription, but also more broadly in all processes operating on DNA.

  2. DNA supercoiling during transcription

    Science.gov (United States)

    Ma, Jie; Wang, Michelle D.

    2017-01-01

    The twin-supercoiled-domain model describes how transcription can drive DNA supercoiling, and how DNA supercoiling, in turn plays an important role in regulating gene transcription. In vivo and in vitro experiments have disclosed many details of the complex interactions in this relationship, and recently new insights have been gained with the help of genome-wide DNA supercoiling mapping techniques and single molecule methods. This review summarizes the general mechanisms of the interplay between DNA supercoiling and transcription, considers the biological implications, and focuses on recent important discoveries and technical advances in this field. We highlight the significant impact of DNA supercoiling in transcription, but also more broadly in all processes operating on DNA.

  3. Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions.

    Science.gov (United States)

    Shaytan, Alexey K; Armeev, Grigoriy A; Goncearenco, Alexander; Zhurkin, Victor B; Landsman, David; Panchenko, Anna R

    2016-01-16

    An octamer of histone proteins wraps about 200bp of DNA into two superhelical turns to form nucleosomes found in chromatin. Although the static structure of the nucleosomal core particle has been solved, details of the dynamic interactions between histones and DNA remain elusive. We performed extensively long unconstrained, all-atom microsecond molecular dynamics simulations of nucleosomes including linker DNA segments and full-length histones in explicit solvent. For the first time, we were able to identify and characterize the rearrangements in nucleosomes on a microsecond timescale including the coupling between the conformation of the histone tails and the DNA geometry. We found that certain histone tail conformations promoted DNA bulging near its entry/exit sites, resulting in the formation of twist defects within the DNA. This led to a reorganization of histone-DNA interactions, suggestive of the formation of initial nucleosome sliding intermediates. We characterized the dynamics of the histone tails upon their condensation on the core and linker DNA and showed that tails may adopt conformationally constrained positions due to the insertion of "anchoring" lysines and arginines into the DNA minor grooves. Potentially, these phenomena affect the accessibility of post-translationally modified histone residues that serve as important sites for epigenetic marks (e.g., at H3K9, H3K27, H4K16), suggesting that interactions of the histone tails with the core and linker DNA modulate the processes of histone tail modifications and binding of the effector proteins. We discuss the implications of the observed results on the nucleosome function and compare our results to different experimental studies.

  4. Predictors of Outcome in Traumatic Brain Injury: New Insight Using Receiver Operating Curve Indices and Bayesian Network Analysis.

    Directory of Open Access Journals (Sweden)

    Zsolt Zador

    Full Text Available Traumatic brain injury remains a global health problem. Understanding the relative importance of outcome predictors helps optimize our treatment strategies by informing assessment protocols, clinical decisions and trial designs. In this study we establish importance ranking for outcome predictors based on receiver operating indices to identify key predictors of outcome and create simple predictive models. We then explore the associations between key outcome predictors using Bayesian networks to gain further insight into predictor importance.We analyzed the corticosteroid randomization after significant head injury (CRASH trial database of 10008 patients and included patients for whom demographics, injury characteristics, computer tomography (CT findings and Glasgow Outcome Scale (GCS were recorded (total of 13 predictors, which would be available to clinicians within a few hours following the injury in 6945 patients. Predictions of clinical outcome (death or severe disability at 6 months were performed using logistic regression models with 5-fold cross validation. Predictive performance was measured using standardized partial area (pAUC under the receiver operating curve (ROC and we used Delong test for comparisons. Variable importance ranking was based on pAUC targeted at specificity (pAUCSP and sensitivity (pAUCSE intervals of 90-100%. Probabilistic associations were depicted using Bayesian networks.Complete AUC analysis showed very good predictive power (AUC = 0.8237, 95% CI: 0.8138-0.8336 for the complete model. Specificity focused importance ranking highlighted age, pupillary, motor responses, obliteration of basal cisterns/3rd ventricle and midline shift. Interestingly when targeting model sensitivity, the highest-ranking variables were age, severe extracranial injury, verbal response, hematoma on CT and motor response. Simplified models, which included only these key predictors, had similar performance (pAUCSP = 0.6523, 95% CI: 0

  5. Moa's Ark or volant ghosts of Gondwana? Insights from nineteen years of ancient DNA research on the extinct moa (Aves: Dinornithiformes) of New Zealand.

    Science.gov (United States)

    Allentoft, Morten E; Rawlence, Nicolas J

    2012-01-20

    The moa (Aves: Dinornithiformes) of New Zealand represent one of the extinct iconic taxa that define the field of ancient DNA (aDNA), and after almost two decades of genetic scrutiny of bones, feathers, coprolites, mummified tissue, eggshell, and sediments, our knowledge of these prehistoric giants has increased significantly. Thanks to molecular and morphological-based research, the insights that have been obtained into moa phylogenetics, phylogeography, and palaeobiology exceeds that of any other extinct taxon. This review documents the strengths of applying a multidisciplinary approach when studying extinct taxa but also shows that cross-disciplinary controversies still remain at the most fundamental levels, with highly conflicting interpretations derived from aDNA and morphology. Moa species diversity, for example, is still heavily debated, as well as their relationship with other ratites and the mode of radiation. In addition to increasing our knowledge on a lineage of extinct birds, further insights into these aspects can clarify some of the basal splits in avian evolution, and the evolutionary implications of the breakup of the prehistoric supercontinent Gondwana. Did a flightless moa ancestor drift away on proto New Zealand (Moa's Ark) or did a volant ancestor arrive by flight? Here we provide an overview of 19 years of aDNA research on moa, critically assess the attempts and controversies in placing the moa lineage among palaeognath birds, and discuss the factors that facilitated the extensive radiation of moa. Finally, we identify the most obvious gaps in the current knowledge to address the future potential research areas in moa genetics.

  6. Insights into the processes behind the contamination of degraded human teeth and bone samples with exogenous sources of DNA

    DEFF Research Database (Denmark)

    Gilbert, M. T. P.; Hansen, Anders J.; Willerslev, E.

    2006-01-01

    A principal problem facing human DNA studies that use old and degraded remains is contamination from other sources of human DNA. In this study we have attempted to contaminate deliberately bones and teeth sampled from a medieval collection excavated in Trondheim, Norway, in order to investigate...... and are difficult to decontaminate using the tested protocol. We believe that this is largely due to the porous nature of bone and teeth facilitating the deep penetration of the contaminant DNA. To simulate a more realistic handling situation, 27 further teeth were directly handled and washed, then decontaminated...

  7. Insights into N-calls of mitochondrial DNA sequencing using MitoChip v2.0

    Directory of Open Access Journals (Sweden)

    Blakely Emma L

    2011-10-01

    Full Text Available Abstract Background Developments in DNA resequencing microarrays include mitochondrial DNA (mtDNA sequencing and mutation detection. Failure by the microarray to identify a base, compared to the reference sequence, is designated an 'N-call.' This study re-examined the N-call distribution of mtDNA samples sequenced by the Affymetrix MitoChip v.2.0, based on the hypothesis that N-calls may represent insertions or deletions (indels in mtDNA. Findings We analysed 16 patient mtDNA samples using MitoChip. N-calls by the proprietary GSEQ software were significantly reduced when either of the freeware on-line algorithms ResqMi or sPROFILER was utilized. With sPROFILER, this decrease in N-calls had no effect on the homoplasmic or heteroplasmic mutation levels compared to GSEQ software, but ResqMi produced a significant change in mutation load, as well as producing longer N-cell stretches. For these reasons, further analysis using ResqMi was not attempted. Conventional DNA sequencing of the longer N-calls stretches from sPROFILER revealed 7 insertions and 12 point mutations. Moreover, analysis of single-base N-calls of one mtDNA sample found 3 other point mutations. Conclusions Our study is the first to analyse N-calls produced from GSEQ software for the MitoChipv2.0. By narrowing the focus to longer stretches of N-calls revealed by sPROFILER, conventional sequencing was able to identify unique insertions and point mutations. Shorter N-calls also harboured point mutations, but the absence of deletions among N-calls suggests that probe confirmation affects binding and thus N-calling. This study supports the contention that the GSEQ is more capable of assigning bases when used in conjunction with sPROFILER.

  8. Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding

    Energy Technology Data Exchange (ETDEWEB)

    Tewary, Sunil K.; Liang, Lingfei; Lin, Zihan; Lynn, Annie [Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 (United States); Cotmore, Susan F. [Departments of Laboratory Medicine, Yale University Medical School, New Haven, CT 06510 (United States); Tattersall, Peter [Departments of Laboratory Medicine, Yale University Medical School, New Haven, CT 06510 (United States); Departments of Genetics, Yale University Medical School, New Haven, CT 06510 (United States); Zhao, Haiyan, E-mail: zhaohy@ku.edu [Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 (United States); Tang, Liang, E-mail: tangl@ku.edu [Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 (United States)

    2015-02-15

    Members of the Parvoviridae family all encode a non-structural protein 1 (NS1) that directs replication of single-stranded viral DNA, packages viral DNA into capsid, and serves as a potent transcriptional activator. Here we report the X-ray structure of the minute virus of mice (MVM) NS1 N-terminal domain at 1.45 Å resolution, showing that sites for dsDNA binding, ssDNA binding and cleavage, nuclear localization, and other functions are integrated on a canonical fold of the histidine-hydrophobic-histidine superfamily of nucleases, including elements specific for this Protoparvovirus but distinct from its Bocaparvovirus or Dependoparvovirus orthologs. High resolution structural analysis reveals a nickase active site with an architecture that allows highly versatile metal ligand binding. The structures support a unified mechanism of replication origin recognition for homotelomeric and heterotelomeric parvoviruses, mediated by a basic-residue-rich hairpin and an adjacent helix in the initiator proteins and by tandem tetranucleotide motifs in the replication origins. - Highlights: • The structure of a parvovirus replication initiator protein has been determined; • The structure sheds light on mechanisms of ssDNA binding and cleavage; • The nickase active site is preconfigured for versatile metal ligand binding; • The binding site for the double-stranded replication origin DNA is identified; • A single domain integrates multiple functions in virus replication.

  9. Molecular interactions of UvrB protein and DNA from Helicobacter pylori: Insight into a molecular modeling approach.

    Science.gov (United States)

    Bavi, Rohit; Kumar, Raj; Rampogu, Shailima; Son, Minky; Park, Chanin; Baek, Ayoung; Kim, Hyong-Ha; Suh, Jung-Keun; Park, Seok Ju; Lee, Keun Woo

    2016-08-01

    Helicobacter pylori (H. pylori) persevere in the human stomach, an environment in which they encounter many DNA-damaging conditions, including gastric acidity. The pathogenicity of H. pylori is enhanced by its well-developed DNA repair mechanism, thought of as 'machinery,' such as nucleotide excision repair (NER). NER involves multi-enzymatic excinuclease proteins (UvrABC endonuclease), which repair damaged DNA in a sequential manner. UvrB is the central component in prokaryotic NER, essential for damage recognition. Therefore, molecular modeling studies of UvrB protein from H. pylori are carried out with homology modeling and molecular dynamics (MD) simulations. The results reveal that the predicted structure is bound to a DNA hairpin with 3-bp stem, an 11-nucleotide loop, and 3-nt 3' overhang. In addition, a mutation of the Y96A variant indicates reduction in the binding affinity for DNA. Free-energy calculations demonstrate the stability of the complex and help identify key residues in various interactions based on residue decomposition analysis. Stability comparative studies between wild type and mutant protein-DNA complexes indicate that the former is relatively more stable than the mutant form. This predicted model could also be useful in designing new inhibitors for UvrB protein, as well as preventing the pathogenesis of H. pylori.

  10. Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering.

    Science.gov (United States)

    Marcaida, María José; Prieto, Jesús; Redondo, Pilar; Nadra, Alejandro D; Alibés, Andreu; Serrano, Luis; Grizot, Sylvestre; Duchateau, Philippe; Pâques, Frédéric; Blanco, Francisco J; Montoya, Guillermo

    2008-11-04

    Homing endonucleases, also known as meganucleases, are sequence-specific enzymes with large DNA recognition sites. These enzymes can be used to induce efficient homologous gene targeting in cells and plants, opening perspectives for genome engineering with applications in a wide series of fields, ranging from biotechnology to gene therapy. Here, we report the crystal structures at 2.0 and 2.1 A resolution of the I-DmoI meganuclease in complex with its substrate DNA before and after cleavage, providing snapshots of the catalytic process. Our study suggests that I-DmoI requires only 2 cations instead of 3 for DNA cleavage. The structure sheds light onto the basis of DNA binding, indicating key residues responsible for nonpalindromic target DNA recognition. In silico and in vivo analysis of the I-DmoI DNA cleavage specificity suggests that despite the relatively few protein-base contacts, I-DmoI is highly specific when compared with other meganucleases. Our data open the door toward the generation of custom endonucleases for targeted genome engineering using the monomeric I-DmoI scaffold.

  11. Challenges and progress in making DNA-based monitoring operational AIS early detection as testbed

    Science.gov (United States)

    The ability of DNA barcoding to find additional species in hard-to-sample locations or hard-to-identify samples is well established. Nevertheless, adoption of DNA barcoding into regular monitoring programs has been slow, in part due to issues of standardization and interpretation...

  12. Challenges and progress in making DNA-based AIS early detection monitoring operational

    Science.gov (United States)

    The ability of DNA barcoding to find additional species in hard-to-sample locations or hard-to-identify samples is well established. Nevertheless, adoption of DNA barcoding into regular monitoring programs has been slow, in part due to issues of standardization and interpretation...

  13. What determines water-bridge lifetimes at the surface of DNA? Insight from systematic molecular dynamics analysis of water kinetics for various DNA sequences.

    Science.gov (United States)

    Yonetani, Yoshiteru; Kono, Hidetoshi

    2012-01-01

    The lifetime during which a water molecule resides at the surface of a biomolecule varies according to the hydration site. What determines this variety of lifetimes? Despite many previous studies, there is still no uniform picture quantitatively explaining this phenomenon. Here we calculate the lifetime for a particular hydration pattern in the DNA minor groove, the water bridge, for various DNA sequences to show that the water-bridge lifetime varies from 1 to ~300ps in a sequence-dependent manner. We find that it follows 1/k(V(step))P(m), where P(m) and V(step) are two crucial factors, namely the probability of forming a specific hydrogen bond in which more than one donor atom participates, and the structural fluctuation of DNA, respectively. This relationship provides a picture of the water kinetics with atomistic detail and shows that water dissociation occurs when a particular hydrogen-bonding pattern appears. The rate constant of water dissociation k can be described as a function of the structural fluctuations of DNA. This picture is consistent with the model of Laage and Hynes proposing that hydrogen-bond switching occurs when an unusual number of hydrogen bonds are formed. The two new factors suggested here are discussed in the context of the surface's geometry and electrostatic nature, which were previously proposed as the determinants of water lifetimes.

  14. Journey of DNA Evidence in Legal Arena: An Insight on Its Legal Perspective Worldwide and Highlight on Admissibility in India

    Directory of Open Access Journals (Sweden)

    Ramakant Gupta

    2016-01-01

    Full Text Available DNA profiling is one of the powerful breakthroughs in forensics. This specialized technique has made the identification of an individual possible even by a tiny shred of tissue or drop of blood thus, has strongly revolutionized various criminal investigations. Rape, paternity, and murder cases are the type of criminal cases commonly solved by the use of this technique. It has been recently introduced to forensic odontology and is also used frequently. Although this is a powerful and reliable scientific technique but its forensic use is a major contribution to the debate on law reform. The application of DNA profiling in the criminal justice system, i.e., the admissibility of DNA evidence in court of law is an important issue which is being faced by the courts and forensic experts worldwide today. Thus, a proper legal outlook is required while dealing with this kind of scientific evidence. Therefore, this review intends to make forensic experts/odontologists aware about the admissibility of DNA evidence in court, with a highlight on the laws related to the admissibility of evidence worldwide, having a special focus on the laws related to admissibility of evidence in Indian judicial system. For this review, the literature was overviewed from articles on DNA evidence and admissibility retrieved by searches on electronic databases such as Google, PubMed, and EMBASE from 1975 through July 2015.

  15. Novel permutation-diffusion image encryption algorithm with chaotic dynamic S-box and DNA sequence operation

    Science.gov (United States)

    Tian, Ye; Lu, Zhimao

    2017-08-01

    The development of the computer network makes image files transportation via network become more and more convenient. This paper is concerned with the image encryption algorithm design based on the chaotic S-box mechanism. This paper proposes an Image Encryption algorithm involving both chaotic dynamic S-boxes and DNA sequence operation(IESDNA). The contribution of this paper is three folded: Firstly, we design an external 256-bit key to get large key space; secondly, we design a chaotic system to scramble image pixels; thirdly, DNA sequence operations are adopted to diffuse the scrambled image pixels. Experimental results show that our proposed image encryption algorithm can meet multiple cryptographic criteria and obtain good image encryption effect.

  16. FurA from Anabaena PCC 7120: New insights on its regulation and the interaction with DNA

    Science.gov (United States)

    Hernández, J. A.; López-Gomollón, S.; Pellicer, S.; Martín, B.; Sevilla, E.; Bes, M. T.; Peleato, M. L.; Fillat, M. F.

    2006-08-01

    Fur (ferric uptake regulator) proteins are global regulatory proteins involved in the maintenance of iron homeostasis. They recognize specific DNA sequences denoted iron boxes. It is assumed that Fur proteins act as classical repressors. Under iron-rich conditions, Fur dimers complexed with ferrous ions bind to iron boxes, preventing transcription. In addition to iron homeostasis, Fur proteins control the concerted response to oxidative and acidic stresses in heterotrophic prokaryotes. Our group studies the interaction between Fur proteins and target DNA sequences. Moreover, the regulation of FurA in the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120, whose genome codes for three fur homologues has been investigated. We present an overview about the different factors involved in the regulation of FurA and analyze the parameters that influence FurA-DNA interaction in the cyanobacterium Anabaena PCC 7120.

  17. Insights Into Finding a Mismatch Through the Structure of a Mispaired DNA Bound By a Rhodium Intercalator

    Energy Technology Data Exchange (ETDEWEB)

    Pierre, V.C.; Kaiser, J.T.; Barton, J.K.; /Caltech

    2007-07-12

    We report the 1.1-angstrom resolution crystal structure of a bulky rhodium complex bound to two different DNA sites, mismatched and matched in the oligonucleotide 5'-(dCGGAAATTCCCG){sub 2}-3'. At the AC mismatch site, the structure reveals ligand insertion from the minor groove with ejection of both mismatched bases and elucidates how destabilized mispairs in DNA may be recognized. This unique binding mode contrasts with major groove intercalation, observed at a matched site, where doubling of the base pair rise accommodates stacking of the intercalator. Mass spectral analysis reveals different photocleavage products associated with the two binding modes in the crystal, with only products characteristic of mismatch binding in solution. This structure, illustrating two clearly distinct binding modes for a molecule with DNA, provides a rationale for the interrogation and detection of mismatches.

  18. The action of the bacterial toxin microcin B17. Insight into the cleavage-religation reaction of DNA gyrase.

    Science.gov (United States)

    Pierrat, Olivier A; Maxwell, Anthony

    2003-09-12

    We have examined the effects of the bacterial toxin microcin B17 (MccB17) on the reactions of Escherichia coli DNA gyrase. MccB17 slows down but does not completely inhibit the DNA supercoiling and relaxation reactions of gyrase. A kinetic analysis of the cleavage-religation equilibrium of gyrase was performed to determine the effect of the toxin on the forward (cleavage) and reverse (religation) reactions. A simple mechanism of two consecutive reversible reactions with a nicked DNA intermediate was used to simulate the kinetics of cleavage and religation. The action of MccB17 on the kinetics of cleavage and religation was compared with that of the quinolones ciprofloxacin and oxolinic acid. With relaxed DNA as substrate, only a small amount of gyrase cleavage complex is observed with MccB17 in the absence of ATP, whereas the presence of the nucleotide significantly enhances the effect of the toxin on both the cleavage and religation reactions. In contrast, ciprofloxacin, oxolinic acid, and Ca2+ show lesser dependence on ATP to stabilize the cleavage complex. MccB17 enhances the overall rate of DNA cleavage by increasing the forward rate constant (k2) of the second equilibrium. In contrast, ciprofloxacin increases the amount of cleaved DNA by a combined effect on the forward and reverse rate constants of both equilibria. Based on these results and on the observations that MccB17 only slowly inhibits the supercoiling and relaxation reactions, we suggest a model of the interaction of MccB17 with gyrase.

  19. DNA

    Science.gov (United States)

    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)

  20. The NMR solution structure of a mutant of the Max b/HLH/LZ free of DNA: insights into the specific and reversible DNA binding mechanism of dimeric transcription factors.

    Science.gov (United States)

    Sauvé, Simon; Tremblay, Luc; Lavigne, Pierre

    2004-09-17

    Basic region-helix1-loop-helix2-leucine zipper (b/H(1)LH(2)/LZ) transcription factors bind specific DNA sequence in their target gene promoters as dimers. Max, a b/H(1)LH(2)/LZ transcription factor, is the obligate heterodimeric partner of the related b/H(1)LH(2)/LZ proteins of the Myc and Mad families. These heterodimers specifically bind E-box DNA sequence (CACGTG) to activate (e.g. c-Myc/Max) and repress (e.g. Mad1/Max) transcription. Max can also homodimerize and bind E-box sequences in c-Myc target gene promoters. While the X-ray structure of the Max b/H(1)LH(2)/LZ/DNA complex and that of others have been reported, the precise sequence of events leading to the reversible and specific binding of these important transcription factors is still largely unknown. In order to provide insights into the DNA binding mechanism, we have solved the NMR solution structure of a covalently homodimerized version of a Max b/H(1)LH(2)/LZ protein with two stabilizing mutations in the LZ, and characterized its backbone dynamics from (15)N spin-relaxation measurements in the absence of DNA. Apart from minor differences in the pitch of the LZ, possibly resulting from the mutations in the construct, we observe that the packing of the helices in the H(1)LH(2) domain is almost identical to that of the two crystal structures, indicating that no important conformational change in these helices occurs upon DNA binding. Conversely to the crystal structures of the DNA complexes, the first 14 residues of the basic region are found to be mostly unfolded while the loop is observed to be flexible. This indicates that these domains undergo conformational changes upon DNA binding. On the other hand, we find the last four residues of the basic region form a persistent helical turn contiguous to H(1). In addition, we provide evidence of the existence of internal motions in the backbone of H(1) that are of larger amplitude and longer time-scale (nanoseconds) than the ones in the H(2) and LZ domain

  1. Relative toxicities of DNA cross-links and monoadducts: new insights from studies of decarbamoyl mitomycin C and mitomycin C.

    Science.gov (United States)

    Palom, Yolanda; Suresh Kumar, Gopinatha; Tang, Li-Qian; Paz, Manuel M; Musser, Steven M; Rockwell, Sara; Tomasz, Maria

    2002-11-01

    Mitomycin C (MC), a cytotoxic anticancer drug and bifunctional DNA DNA alkylating agent, induces cross-linking of the complementary strands of DNA. The DNA interstrand cross-links (ICLs) are thought to be the critical cytotoxic lesions produced by MC. Decarbamoyl mitomycin C (DMC) has been regarded as a monofunctional mitomycin, incapable of causing ICLs. Paradoxically, DMC is slightly more toxic than MC to hypoxic EMT6 mouse mammary tumor cells as well as to CHO cells. To resolve this paradox, EMT6 cells were treated with MC or DMC under hypoxia at equimolar concentrations and the resulting DNA adducts were analyzed using HPLC and UV detection. MC treatment generated both intrastrand and interstrand cross-link adducts and four monoadducts, as shown previously. DMC generated two stereoisomeric monoadducts and two stereoisomeric ICL adducts, all of which were structurally characterized; one was identical with that formed with MC, the other was new and unique to DMC. Overall, adduct frequencies were strikingly higher (20-30-fold) with DMC than with MC. Although DMC monoadducts greatly exceeded DMC cross-link adducts ( approximately 10:1 ratio), the latter were equal or higher in number than the cross-link adducts from MC. DMC displayed a much higher monoadduct:cross-link ratio than MC. The similar cytotoxicities of the two drug show a correlation with their similar DNA cross-link adduct frequencies, but not with their total adduct or monoadduct frequencies. This provides specific experimental evidence that the ICLs rather than the monoadducts are critical factors in the cell death induced by MC. In vitro, overall alkylation of calf thymus DNA by DMC was much less efficient than by MC. Nevertheless, ICLs formed with DMC were clearly detectable. The chemical pathway of the cross-linking was shown to be analogous to that occurring with MC. These results also suggest that the differential sensitivity of Fanconi's Anemia cells to MC and DMC is related to factors other

  2. Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome.

    Science.gov (United States)

    Pett, Walker; Ryan, Joseph F; Pang, Kevin; Mullikin, James C; Martindale, Mark Q; Baxevanis, Andreas D; Lavrov, Dennis V

    2011-08-01

    Recent advances in sequencing technology have led to a rapid accumulation of mitochondrial DNA (mtDNA) sequences, which now represent the wide spectrum of animal diversity. However, one animal phylum--Ctenophora--has, to date, remained completely unsampled. Ctenophores, a small group of marine animals, are of interest due to their unusual biology, controversial phylogenetic position, and devastating impact as invasive species. Using data from the Mnemiopsis leidyi genome sequencing project, we Polymerase Chain Reaction (PCR) amplified and analyzed its complete mitochondrial (mt-) genome. At just over 10 kb, the mt-genome of M. leidyi is the smallest animal mtDNA ever reported and is among the most derived. It has lost at least 25 genes, including atp6 and all tRNA genes. We show that atp6 has been relocated to the nuclear genome and has acquired introns and a mitochondrial targeting presequence, while tRNA genes have been genuinely lost, along with nuclear-encoded mt-aminoacyl tRNA synthetases. The mt-genome of M. leidyi also displays extremely high rates of sequence evolution, which likely led to the degeneration of both protein and rRNA genes. In particular, encoded rRNA molecules possess little similarity with their homologs in other organisms and have highly reduced secondary structures. At the same time, nuclear encoded mt-ribosomal proteins have undergone expansions, likely to compensate for the reductions in mt-rRNA. The unusual features identified in M. leidyi mtDNA make this organism an interesting system for the study of various aspects of mitochondrial biology, particularly protein and tRNA import and mt-ribosome structures, and add to its value as an emerging model species. Furthermore, the fast-evolving M. leidyi mtDNA should be a convenient molecular marker for species- and population-level studies.

  3. Extreme Mitochondrial Evolution in the Ctenophore Mnemiopsis leidyi: Insights from mtDNA and the Nuclear Genome

    Science.gov (United States)

    Pett, Walker; Ryan, Joseph F.; Pang, Kevin; Mullikin, James C.; Martindale, Mark Q.; Baxevanis, Andreas D.; Lavrov, Dennis V.

    2012-01-01

    Recent advances in sequencing technology have led to a rapid accumulation of mitochondrial DNA (mtDNA) sequences, which now represent the wide spectrum of animal diversity. However, one animal phylum – Ctenophora – has, to date, remained completely unsampled. Ctenophores, a small group of marine animals, are of interest due to their unusual biology, controversial phylogenetic position, and devastating impact as an invasive species. Using data from the Mnemiopsis leidyi genome sequencing project, we PCR amplified and analyzed its complete mitochondrial (mt-) genome. At just over 10kb, the mt-genome of M. leidyi is the smallest animal mtDNA ever reported and is among the most derived. It has lost at least 25 genes, including atp6 and all tRNA genes. We show that atp6 has been relocated to the nuclear genome and has acquired introns and a mitochondrial targeting presequence, while tRNA genes have been genuinely lost, along with nuclear-encoded mt-aminoacyl tRNA synthetases. The mt-genome of M. leidyi also displays extremely high rates of sequence evolution, which likely led to the degeneration of both protein and rRNA genes. In particular, encoded rRNA molecules possess little similarity with their homologues in other organisms and have highly reduced secondary structures. At the same time, nuclear encoded mt-ribosomal proteins have undergone expansions, probably to compensate for the reductions in mt-rRNA. The unusual features identified in M. leidyi mtDNA make this organism an interesting system for the study of various aspects of mitochondrial biology, particularly protein and tRNA import and mt-ribosome structures, and add to its value as an emerging model species. Furthermore, the fast-evolving M. leidyi mtDNA should be a convenient molecular marker for species- and population-level studies. PMID:21985407

  4. Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum.

    Science.gov (United States)

    Veluchamy, Alaguraj; Lin, Xin; Maumus, Florian; Rivarola, Maximo; Bhavsar, Jaysheel; Creasy, Todd; O'Brien, Kimberly; Sengamalay, Naomi A; Tallon, Luke J; Smith, Andrew D; Rayko, Edda; Ahmed, Ikhlak; Le Crom, Stéphane; Farrant, Gregory K; Sgro, Jean-Yves; Olson, Sue A; Bondurant, Sandra Splinter; Allen, Andrew E; Allen, Andrew; Rabinowicz, Pablo D; Sussman, Michael R; Bowler, Chris; Tirichine, Leïla

    2013-01-01

    DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.

  5. High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites

    DEFF Research Database (Denmark)

    Lorenzen, Eline D; Arctander, Peter; Siegismund, Hans R

    2008-01-01

    Patterns of genetic differentiation in the plains zebra (Equus quagga) were analysed using mitochondrial DNA control region variation and seven microsatellites. The six morphologically defined subspecies of plains zebra lacked the population genetic structure indicative of distinct evolutionary...... units. Both marker sets showed high levels of genetic variation and very low levels of differentiation. There was no geographical structuring of mitochondrial DNA haplotypes in the phylogenetic tree, and the plains zebra showed the lowest overall differentiation recorded in any African ungulate studied...... so far. Arid-adapted African ungulates have shown significant regional genetic structuring in support of the Pleistocene refuge theory. This was not the case in the zebra, and the data are discussed in relation to the impact of Pleistocene climate change on a nonbovid member of the savannah ungulate...

  6. Crystal structure of a KSHV-SOX-DNA complex: insights into the molecular mechanisms underlying DNase activity and host shutoff.

    Science.gov (United States)

    Bagnéris, Claire; Briggs, Louise C; Savva, Renos; Ebrahimi, Bahram; Barrett, Tracey E

    2011-07-01

    The early lytic phase of Kaposi's sarcoma herpesvirus infection is characterized by viral replication and the global degradation (shutoff) of host mRNA. Key to both activities is the virally encoded alkaline exonuclease KSHV SOX. While the DNase activity of KSHV SOX is required for the resolution of viral genomic DNA as a precursor to encapsidation, its exact involvement in host shutoff remains to be determined. We present the first crystal structure of a KSHV SOX-DNA complex that has illuminated the catalytic mechanism underpinning both its endo and exonuclease activities. We further illustrate that KSHV SOX, similar to its Epstein-Barr virus homologue, has an intrinsic RNase activity in vitro that although an element of host shutoff, cannot solely account for the phenomenon.

  7. Novel insights into the pathophysiology of varicocele and its association with reactive oxygen species and sperm DNA fragmentation

    Directory of Open Access Journals (Sweden)

    Chak-Lam Cho

    2016-01-01

    Full Text Available Varicocele has been associated with reduced male reproductive potential. With the advances in biomolecular techniques, it has been possible to better understand the mechanisms involved in testicular damage provoked by varicocele. Current evidence suggests the central role of reactive oxygen species (ROS and the resultant oxidative stress (OS in the pathogenesis of varicocele-associated male subfertility although the mechanisms have not yet been fully described and it is likely to be multifactorial. Excessive ROS is associated with sperm DNA fragmentation, which may mediate the clinical manifestation of poor sperm function and fertilization outcome related to varicocele. Testing of ROS/OS and DNA fragmentation has the potential to provide additional diagnostic and prognostic information compared to conventional semen analysis and may guide therapeutic management strategies in individual patient.

  8. Novel insights into the pathophysiology of varicocele and its association with reactive oxygen species and sperm DNA fragmentation

    Science.gov (United States)

    Cho, Chak-Lam; Esteves, Sandro C; Agarwal, Ashok

    2016-01-01

    Varicocele has been associated with reduced male reproductive potential. With the advances in biomolecular techniques, it has been possible to better understand the mechanisms involved in testicular damage provoked by varicocele. Current evidence suggests the central role of reactive oxygen species (ROS) and the resultant oxidative stress (OS) in the pathogenesis of varicocele-associated male subfertility although the mechanisms have not yet been fully described and it is likely to be multifactorial. Excessive ROS is associated with sperm DNA fragmentation, which may mediate the clinical manifestation of poor sperm function and fertilization outcome related to varicocele. Testing of ROS/OS and DNA fragmentation has the potential to provide additional diagnostic and prognostic information compared to conventional semen analysis and may guide therapeutic management strategies in individual patient. PMID:26732105

  9. Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants.

    Science.gov (United States)

    Kosa, Peter; Valach, Matus; Tomaska, Lubomir; Wolfe, Kenneth H; Nosek, Jozef

    2006-01-01

    We determined complete mitochondrial DNA sequences of the two yeast species, Candida orthopsilosis and Candida metapsilosis, and compared them with the linear mitochondrial genome of their close relative, C.parapsilosis. Mitochondria of all the three species harbor compact genomes encoding the same set of genes arranged in the identical order. Differences in the length of these genomes result mainly from the presence/absence of introns. Multiple alterations were identified also in the sequences of the ribosomal and transfer RNAs, and proteins. However, the most striking feature of C.orthopsilosis and C.metapsilosis is the existence of strains differing in the molecular form of the mitochondrial genome (circular-mapping versus linear). Their analysis opens a unique window for understanding the role of mitochondrial telomeres in the stability and evolution of molecular architecture of the genome. Our results indicate that the circular-mapping mitochondrial genome derived from the linear form by intramolecular end-to-end fusions. Moreover, we suggest that the linear mitochondrial genome evolved from a circular-mapping form present in a common ancestor of the three species and, at the same time, the emergence of mitochondrial telomeres enabled the formation of linear monomeric DNA forms. In addition, comparison of isogenic C.metapsilosis strains differing in the form of the organellar genome suggests a possibility that, under some circumstances, the linearity and/or the presence of telomeres provide a competitive advantage over a circular-mapping mitochondrial genome.

  10. The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations

    Science.gov (United States)

    Manara, Richard M. A.; Tomasio, Susana; Khalid, Syma

    2015-01-01

    Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is “exonuclease sequencing”, in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein.

  11. Exploration of cell cycle regulation and modulation of the DNA methylation mechanism of pelargonidin: Insights from the molecular modeling approach.

    Science.gov (United States)

    Karthi, Natesan; Karthiga, Arumugasamy; Kalaiyarasu, Thangaraj; Stalin, Antony; Manju, Vaiyapuri; Singh, Sanjeev Kumar; Cyril, Ravi; Lee, Sang-Myeong

    2017-10-01

    Pelargonidin is an anthocyanidin isolated from plant resources. It shows strong cytotoxicity toward various cancer cell lines, even though the carcinogenesis-modulating pathway of pelargonidin is not yet known. One of our previous reports showed that pelargonidin arrests the cell cycle and induces apoptosis in HT29 cells. Flowcytometry and immunoblot analysis confirmed that pelargonidin specifically inhibits the activation of CDK1 and blocks the G2-M transition of the cell cycle. In addition, DNA fragmentation was observed along with induction of cytochrome c release-mediated apoptosis. Hence, the aim of the present study was to investigate the molecular mechanism of pelargonidin's action on cell cycle regulators CDK1, CDK4, and CDK6 as well as the substrate-binding domain of DNMT1 and DNMT3A, which regulate the epigenetic signals related to DNA methylation. The results of docking analysis, binding free energy calculation, and molecular dynamics simulation correlated with the experimental results, and pelargonidin showed a specific interaction with CDK1. In this context, pelargonidin may also inhibit the recognition of DNA and catalytic binding by DNMT1 and DNMT3A. The HOMO-LUMO analysis mapped the functional groups of pelargonidin. Prediction of pharmacological descriptors suggested that pelargonidin can serve as a multitarget inhibitor for cancer treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Yersinia pestis DNA from skeletal remains from the 6(th) century AD reveals insights into Justinianic Plague.

    Science.gov (United States)

    Harbeck, Michaela; Seifert, Lisa; Hänsch, Stephanie; Wagner, David M; Birdsell, Dawn; Parise, Katy L; Wiechmann, Ingrid; Grupe, Gisela; Thomas, Astrid; Keim, Paul; Zöller, Lothar; Bramanti, Barbara; Riehm, Julia M; Scholz, Holger C

    2013-01-01

    Yersinia pestis, the etiologic agent of the disease plague, has been implicated in three historical pandemics. These include the third pandemic of the 19(th) and 20(th) centuries, during which plague was spread around the world, and the second pandemic of the 14(th)-17(th) centuries, which included the infamous epidemic known as the Black Death. Previous studies have confirmed that Y. pestis caused these two more recent pandemics. However, a highly spirited debate still continues as to whether Y. pestis caused the so-called Justinianic Plague of the 6(th)-8(th) centuries AD. By analyzing ancient DNA in two independent ancient DNA laboratories, we confirmed unambiguously the presence of Y. pestis DNA in human skeletal remains from an Early Medieval cemetery. In addition, we narrowed the phylogenetic position of the responsible strain down to major branch 0 on the Y. pestis phylogeny, specifically between nodes N03 and N05. Our findings confirm that Y. pestis was responsible for the Justinianic Plague, which should end the controversy regarding the etiology of this pandemic. The first genotype of a Y. pestis strain that caused the Late Antique plague provides important information about the history of the plague bacillus and suggests that the first pandemic also originated in Asia, similar to the other two plague pandemics.

  13. Yersinia pestis DNA from skeletal remains from the 6(th century AD reveals insights into Justinianic Plague.

    Directory of Open Access Journals (Sweden)

    Michaela Harbeck

    Full Text Available Yersinia pestis, the etiologic agent of the disease plague, has been implicated in three historical pandemics. These include the third pandemic of the 19(th and 20(th centuries, during which plague was spread around the world, and the second pandemic of the 14(th-17(th centuries, which included the infamous epidemic known as the Black Death. Previous studies have confirmed that Y. pestis caused these two more recent pandemics. However, a highly spirited debate still continues as to whether Y. pestis caused the so-called Justinianic Plague of the 6(th-8(th centuries AD. By analyzing ancient DNA in two independent ancient DNA laboratories, we confirmed unambiguously the presence of Y. pestis DNA in human skeletal remains from an Early Medieval cemetery. In addition, we narrowed the phylogenetic position of the responsible strain down to major branch 0 on the Y. pestis phylogeny, specifically between nodes N03 and N05. Our findings confirm that Y. pestis was responsible for the Justinianic Plague, which should end the controversy regarding the etiology of this pandemic. The first genotype of a Y. pestis strain that caused the Late Antique plague provides important information about the history of the plague bacillus and suggests that the first pandemic also originated in Asia, similar to the other two plague pandemics.

  14. Yersinia pestis DNA from Skeletal Remains from the 6th Century AD Reveals Insights into Justinianic Plague

    Science.gov (United States)

    Harbeck, Michaela; Seifert, Lisa; Hänsch, Stephanie; Wagner, David M.; Birdsell, Dawn; Parise, Katy L.; Wiechmann, Ingrid; Grupe, Gisela; Thomas, Astrid; Keim, Paul; Zöller, Lothar; Bramanti, Barbara; Riehm, Julia M.; Scholz, Holger C.

    2013-01-01

    Yersinia pestis, the etiologic agent of the disease plague, has been implicated in three historical pandemics. These include the third pandemic of the 19th and 20th centuries, during which plague was spread around the world, and the second pandemic of the 14th–17th centuries, which included the infamous epidemic known as the Black Death. Previous studies have confirmed that Y. pestis caused these two more recent pandemics. However, a highly spirited debate still continues as to whether Y. pestis caused the so-called Justinianic Plague of the 6th–8th centuries AD. By analyzing ancient DNA in two independent ancient DNA laboratories, we confirmed unambiguously the presence of Y. pestis DNA in human skeletal remains from an Early Medieval cemetery. In addition, we narrowed the phylogenetic position of the responsible strain down to major branch 0 on the Y. pestis phylogeny, specifically between nodes N03 and N05. Our findings confirm that Y. pestis was responsible for the Justinianic Plague, which should end the controversy regarding the etiology of this pandemic. The first genotype of a Y. pestis strain that caused the Late Antique plague provides important information about the history of the plague bacillus and suggests that the first pandemic also originated in Asia, similar to the other two plague pandemics. PMID:23658525

  15. The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations.

    Science.gov (United States)

    Manara, Richard M A; Tomasio, Susana; Khalid, Syma

    2015-01-27

    Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is "exonuclease sequencing", in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein.

  16. An enzyme-free and DNA-based Feynman gate for logically reversible operation.

    Science.gov (United States)

    Zhou, Chunyang; Wang, Kun; Fan, Daoqing; Wu, Changtong; Liu, Dali; Liu, Yaqing; Wang, Erkang

    2015-06-28

    A logically reversible Feynman gate was successfully realized under enzyme-free conditions by integrating graphene oxide and DNA for the first time. The gate has a one-to-one mapping function to identify inputs from the corresponding outputs. This type of reversible logic gate may have great potential applications in information processing and biosensing systems.

  17. Noncovalent interactions of a benzo[a]pyrene diol epoxide with DNA base pairs: insight into the formation of adducts of (+)-BaP DE-2 with DNA.

    Science.gov (United States)

    Hargis, Jacqueline C; Schaefer, Henry F; Houk, K N; Wheeler, Steven E

    2010-02-01

    Noncovalent complexes of a tumorigenic benzo[a]pyrene diol epoxide with the guanine-cytosine (GC) and adenine-thymine (AT) base pairs have been examined computationally. (+)-BaP DE-2 forms covalent adducts with DNA via nucleophilic attack on the (+)-BaP DE-2 epoxide. Computational results predict five thermodynamically accessible complexes of AT with (+)-BaP DE-2 that are compatible with intact DNA. Among these, two are expected to lead to adenine adducts. In the lowest energy AT...(+)-BaP DE-2 complex, which has a gas-phase interaction energy of -20.9 kcal mol(-1), the exocyclic NH(2) of adenine is positioned for backside epoxide attack and formation of a trans adduct. The most energetically favorable complex leading to formation of a cis ring-opened adduct lies only 0.6 kcal mol(-1) higher in energy. For GC...(+)-BaP DE-2, there are only two thermodynamically accessible complexes. The higher-lying complex, bound in the gas phase by 24.4 kcal mol(-1) relative to separated GC and (+)-BaP DE-2, would lead to a trans ring-opened N(2)-guanine adduct. In the global minimum energy GC...(+)-BaP DE-2 complex, bound by 27.3 kcal mol(-1), the exocyclic NH(2) group of cytosine is positioned for cis epoxide addition. However, adducts of (+)-BaP DE-2 with cytosine are rarely observed experimentally. The paucity of cytosine adducts, despite the predicted thermodynamic stability of this GC...(+)-BaP DE-2 complex, is attributed to the electrostatic destabilization of the benzylic cation intermediate thought to precede cis addition.

  18. Domain movements of the enhancer-dependent sigma factor drive DNA delivery into the RNA polymerase active site: insights from single molecule studies.

    Science.gov (United States)

    Sharma, Amit; Leach, Robert N; Gell, Christopher; Zhang, Nan; Burrows, Patricia C; Shepherd, Dale A; Wigneshweraraj, Sivaramesh; Smith, David Alastair; Zhang, Xiaodong; Buck, Martin; Stockley, Peter G; Tuma, Roman

    2014-04-01

    Recognition of bacterial promoters is regulated by two distinct classes of sequence-specific sigma factors, σ(70) or σ(54), that differ both in their primary sequence and in the requirement of the latter for activation via enhancer-bound upstream activators. The σ(54) version controls gene expression in response to stress, often mediating pathogenicity. Its activator proteins are members of the AAA+ superfamily and use adenosine triphosphate (ATP) hydrolysis to remodel initially auto-inhibited holoenzyme promoter complexes. We have mapped this remodeling using single-molecule fluorescence spectroscopy. Initial remodeling is nucleotide-independent and driven by binding both ssDNA during promoter melting and activator. However, DNA loading into the RNA polymerase active site depends on co-operative ATP hydrolysis by the activator. Although the coupled promoter recognition and melting steps may be conserved between σ(70) and σ(54), the domain movements of the latter have evolved to require an activator ATPase.

  19. New Insights into p53 Signaling and Cancer Cell Response to DNA Damage: Implications for Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Razmik Mirzayans

    2012-01-01

    Full Text Available Activation of the p53 signaling pathway by DNA-damaging agents was originally proposed to result either in cell cycle checkpoint activation to promote survival or in apoptotic cell death. This model provided the impetus for numerous studies focusing on the development of p53-based cancer therapies. According to recent evidence, however, most p53 wild-type human cell types respond to ionizing radiation by undergoing stress-induced premature senescence (SIPS and not apoptosis. SIPS is a sustained growth-arrested state in which cells remain viable and secrete factors that may promote cancer growth and progression. The p21WAF1 (hereafter p21 protein has emerged as a key player in the p53 pathway. In addition to its well-studied role in cell cycle checkpoints, p21 regulates p53 and its upstream kinase (ATM, controls gene expression, suppresses apoptosis, and induces SIPS. Herein, we review these and related findings with human solid tumor-derived cell lines, report new data demonstrating dynamic behaviors of p53 and p21 in the DNA damage response, and examine the gain-of-function properties of cancer-associated p53 mutations. We point out obstacles in cancer-therapeutic strategies that are aimed at reactivating the wild-type p53 function and highlight some alternative approaches that target the apoptotic threshold in cancer cells with differing p53 status.

  20. Analysis of medieval mtDNA from Napole cemetery provides new insights into the early history of Polish state.

    Science.gov (United States)

    Płoszaj, Tomasz; Jędrychowska-Dańska, Krystyna; Masłowska, Alicja; Kozłowski, Tomasz; Chudziak, Wojciech; Bojarski, Jacek; Robaszkiewicz, Agnieszka; Witas, Henryk W

    2017-02-01

    Contemporary historical anthropology and classical archaeology are concerned not only with such fundamental issues as the origins of ancient human populations and migration routes, but also with the formation and development of inter-population relations and the mixing of gene pools as a result of inter-breeding between individuals representing different cultural units. The contribution of immigrants to the analysed autochthonous population and their effect on the gene pool of that population has proven difficult to evaluate with classical morphological methods. The burial of one individual in the studied Napole cemetery located in central Poland had the form of a chamber grave, which is typical of Scandinavian culture from that period. However, this fact cannot be interpreted as absolute proof that the individual (in the biological sense) was allochtonous. This gives rise to the question as to who was actually buried in that cemetery. The ancient DNA results indicate that one of the individuals had an mtDNA haplotype typical of Iron Age northern Europe, which suggests that he could have arrived from that area at a later period. This seems to indirectly confirm the claims of many anthropologists that the development of the early medieval Polish state was significantly and directly influenced by the Scandinavians.

  1. Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera

    Science.gov (United States)

    Mutanen, Marko; Kivelä, Sami M.; Vos, Rutger A.; Doorenweerd, Camiel; Ratnasingham, Sujeevan; Hausmann, Axel; Huemer, Peter; Dincă, Vlad; van Nieukerken, Erik J.; Lopez-Vaamonde, Carlos; Vila, Roger; Aarvik, Leif; Decaëns, Thibaud; Efetov, Konstantin A.; Hebert, Paul D. N.; Johnsen, Arild; Karsholt, Ole; Pentinsaari, Mikko; Rougerie, Rodolphe; Segerer, Andreas; Tarmann, Gerhard; Zahiri, Reza; Godfray, H. Charles J.

    2016-01-01

    The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the

  2. Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania

    Science.gov (United States)

    Larson, Greger; Cucchi, Thomas; Fujita, Masakatsu; Matisoo-Smith, Elizabeth; Robins, Judith; Anderson, Atholl; Rolett, Barry; Spriggs, Matthew; Dolman, Gaynor; Kim, Tae-Hun; Thuy, Nguyen Thi Dieu; Randi, Ettore; Doherty, Moira; Due, Rokus Awe; Bollt, Robert; Djubiantono, Tony; Griffin, Bion; Intoh, Michiko; Keane, Emile; Kirch, Patrick; Li, Kuang-Ti; Morwood, Michael; Pedriña, Lolita M.; Piper, Philip J.; Rabett, Ryan J.; Shooter, Peter; Van den Bergh, Gert; West, Eric; Wickler, Stephen; Yuan, Jing; Cooper, Alan; Dobney, Keith

    2007-01-01

    Human settlement of Oceania marked the culmination of a global colonization process that began when humans first left Africa at least 90,000 years ago. The precise origins and dispersal routes of the Austronesian peoples and the associated Lapita culture remain contentious, and numerous disparate models of dispersal (based primarily on linguistic, genetic, and archeological data) have been proposed. Here, through the use of mtDNA from 781 modern and ancient Sus specimens, we provide evidence for an early human-mediated translocation of the Sulawesi warty pig (Sus celebensis) to Flores and Timor and two later separate human-mediated dispersals of domestic pig (Sus scrofa) through Island Southeast Asia into Oceania. Of the later dispersal routes, one is unequivocally associated with the Neolithic (Lapita) and later Polynesian migrations and links modern and archeological Javan, Sumatran, Wallacean, and Oceanic pigs with mainland Southeast Asian S. scrofa. Archeological and genetic evidence shows these pigs were certainly introduced to islands east of the Wallace Line, including New Guinea, and that so-called “wild” pigs within this region are most likely feral descendants of domestic pigs introduced by early agriculturalists. The other later pig dispersal links mainland East Asian pigs to western Micronesia, Taiwan, and the Philippines. These results provide important data with which to test current models for human dispersal in the region. PMID:17360400

  3. Deeper insight into maternal genetic assessments and demographic history for Egyptian indigenous chicken populations using mtDNA analysis

    Directory of Open Access Journals (Sweden)

    Marwa A. Eltanany

    2016-09-01

    Full Text Available This study principally sought to reveal the demographic expansion of Egyptian indigenous chickens (EIC using representative breeds: Sinai (North, Fayoumi (Middle and Dandarawi (South of Egypt as well as to deeply clarify their genetic diversity, possible matrilineal origin and dispersal routes. A total of 33 partial mitochondrial DNA sequences were generated from EIC and compared with a worldwide reference dataset of 1290 wild and domestic chicken sequences. Study populations had 12 polymorphic variable sites and 7 haplotypes. A lack of maternal substructure between EIC was detected (FST = 0.003. The unimodal mismatch distribution and negative values of Tajima’s D (−0.659 and Fu’s Fs (−0.157 indicated demographic expansion among EIC and pointed to Fayoumi as the oldest EIC population. Egyptian haplotypes were clustered phylogenetically into two divergent clades. Their phylogeography revealed an ancient single maternal lineage of Egyptian chickens likely derived from Indian-Subcontinent. Moreover, a recent maternal commercial heritage possibly originated in Yunnan-Province and/or surrounding areas was admixed restrictedly into Sinai. It is implied that Egypt was an entry point for Indian chicken into Africa and its further dispersal route to Europe. This study provides a clue supporting the previous assumption that urged utilizing consistent founder populations having closely related progenitors for synthetizing a stabilized homogenous crossbreed as a sustainable discipline in breeding program.

  4. A device that operates within a self-assembled 3D DNA crystal

    Science.gov (United States)

    Hao, Yudong; Kristiansen, Martin; Sha, Ruojie; Birktoft, Jens J.; Hernandez, Carina; Mao, Chengde; Seeman, Nadrian C.

    2017-08-01

    Structural DNA nanotechnology finds applications in numerous areas, but the construction of objects, 2D and 3D crystalline lattices and devices is prominent among them. Each of these components has been developed individually, and most of them have been combined in pairs. However, to date there are no reports of independent devices contained within 3D crystals. Here we report a three-state 3D device whereby we change the colour of the crystals by diffusing strands that contain dyes in or out of the crystals through the mother-liquor component of the system. Each colouring strand is designed to pair with an extended triangle strand by Watson-Crick base pairing. The arm that contains the dyes is quite flexible, but it is possible to establish the presence of the duplex proximal to the triangle by X-ray crystallography. We modelled the transition between the red and blue states through a simple kinetic model.

  5. DNA translocation by type III restriction enzymes: a comparison of current models of their operation derived from ensemble and single-molecule measurements.

    Science.gov (United States)

    Dryden, David T F; Edwardson, J M; Henderson, Robert M

    2011-06-01

    Much insight into the interactions of DNA and enzymes has been obtained using a number of single-molecule techniques. However, recent results generated using two of these techniques-atomic force microscopy (AFM) and magnetic tweezers (MT)-have produced apparently contradictory results when applied to the action of the ATP-dependent type III restriction endonucleases on DNA. The AFM images show extensive looping of the DNA brought about by the existence of multiple DNA binding sites on each enzyme and enzyme dimerisation. The MT experiments show no evidence for looping being a requirement for DNA cleavage, but instead support a diffusive sliding of the enzyme on the DNA until an enzyme-enzyme collision occurs, leading to cleavage. Not only do these two methods appear to disagree, but also the models derived from them have difficulty explaining some ensemble biochemical results on DNA cleavage. In this 'Survey and Summary', we describe several different models put forward for the action of type III restriction enzymes and their inadequacies. We also attempt to reconcile the different models and indicate areas for further experimentation to elucidate the mechanism of these enzymes.

  6. Influence of climate warming on arctic mammals? New insights from ancient DNA studies of the collared lemming Dicrostonyx torquatus.

    Directory of Open Access Journals (Sweden)

    Stefan Prost

    Full Text Available BACKGROUND: Global temperature increased by approximately half a degree (Celsius within the last 150 years. Even this moderate warming had major impacts on Earth's ecological and biological systems, especially in the Arctic where the magnitude of abiotic changes even exceeds those in temperate and tropical biomes. Therefore, understanding the biological consequences of climate change on high latitudes is of critical importance for future conservation of the species living in this habitat. The past 25,000 years can be used as a model for such changes, as they were marked by prominent climatic changes that influenced geographical distribution, demographic history and pattern of genetic variation of many extant species. We sequenced ancient and modern DNA of the collared lemming (Dicrostonyx torquatus, which is a key species of the arctic biota, from a single site (Pymva Shor, Northern Pre Urals, Russia to see if climate warming events after the Last Glacial Maximum had detectable effects on the genetic variation of this arctic rodent species, which is strongly associated with a cold and dry climate. RESULTS: Using three dimensional network reconstructions we found a dramatic decline in genetic diversity following the LGM. Model-based approaches such as Approximate Bayesian Computation and Markov Chain Monte Carlo based Bayesian inference show that there is evidence for a population decline in the collared lemming following the LGM, with the population size dropping to a minimum during the Greenland Interstadial 1 (Bølling/Allerød warming phase at 14.5 kyrs BP. CONCLUSION: Our results show that previous climate warming events had a strong influence on genetic diversity and population size of collared lemmings. Due to its already severely compromised genetic diversity a similar population reduction as a result of the predicted future climate change could completely abolish the remaining genetic diversity in this population. Local population

  7. Acetaldehyde as a drug of abuse: insight into AM281 administration on operant-conflict paradigm in rats.

    Science.gov (United States)

    Plescia, Fulvio; Brancato, Anna; Marino, Rosa A M; Cannizzaro, Carla

    2013-01-01

    Increasing evidence focuses on acetaldehyde (ACD) as the mediator of the rewarding and motivational properties of ethanol. Indeed, ACD stimulates dopamine release in the nucleus accumbens and it is self-administered under different conditions. Besides the dopaminergic transmission, the endocannabinoid system has been reported to play an important role in ethanol central effects, modulating primary alcohol rewarding effect, drug-seeking, and relapse behavior. Drug motivational properties are highlighted in operant paradigms which include response-contingent punishment, a behavioral equivalent of compulsive drug use despite adverse consequences. The aim of this study was thus to characterize ACD motivational and rewarding properties employing an operant-conflict paradigm in which rats, trained to lever press in order to get ACD solution (0.9%), undergo extinction, reinstatement and conflict sessions, according to a modified Geller-Seifter procedure. Furthermore, the role played by CB1 receptor system in modulating ACD-induced effects were investigated through the administration of CB1 receptor antagonist, AM281 (1 mg/kg, i.p.) during the extinction-, relapse-, and conflict-experiments. Our results indicate that ACD is able to induce and maintain an operant behavior, a high number of responses during extinction, an increase in the lever presses during the reinstatement phase, and a higher emission of punished responses during the conflict experiments, when compared to controls. The administration of AM281 is able to decrease ACD-seeking behavior during extinction, the number of lever presses during reinstatement and to strongly decrease the punished responses for ACD. Our data strengthen the idea that ACD may be responsible for the central effects of ethanol, and pinpoint at the CB1 system as one of the neural substrates underlying its addictive properties.

  8. The effect of different operations modes on science capabilities during the 2010 Desert RATS test: Insights from the geologist crewmembers

    Science.gov (United States)

    Bleacher, Jacob E.; Hurtado, José M.; Young, Kelsey E.; Rice, James W.; Garry, W. Brent

    2013-10-01

    The 2010 Desert RATS field test utilized two Space Exploration Vehicles (prototype planetary rovers) and four crewmembers (2 per rover) to conduct a geologic traverse across northern Arizona while testing continuous and twice-per-day communications paired with operation modes of separating and exploring individually (Divide & Conquer) and exploring together (Lead & Follow), respectively. This report provides qualitative conclusions from the geologist crewmembers involved in this test as to how these modes of communications and operations affected our ability to conduct field geology. Each mode of communication and operation provided beneficial capabilities that might be further explored for future Human Spaceflight Missions to other solar system objects. We find that more frequent interactions between crews and an Apollo-style Science Team on the Earth best enables scientific progress during human exploration. However, during multiple vehicle missions, this communication with an Earth-based team of scientists, who represent "more minds on the problem", should not come at the exclusion of (or significantly decrease) communication between the crewmembers in different vehicles who have the "eyes on the ground". Inter-crew communications improved when discussions with a backroom were infrequent. Both aspects are critical and cannot be mutually exclusive. Increased vehicle separation distances best enable encounters with multiple geologic units. However, seemingly redundant visits by multiple vehicles to the same feature can be utilized to provide improved process-related observations about the development and modification of the local terrain. We consider the value of data management, transfer, and accessibility to be the most important lesson learned. Crews and backrooms should have access to all data and related interpretations within the mission in as close to real-time conditions as possible. This ensures that while on another planetary surface, crewmembers are as

  9. Acetaldehyde as a drug of abuse: insight into AM281 administration on operant-conflict paradigm in rats.

    Directory of Open Access Journals (Sweden)

    Fulvio ePlescia

    2013-06-01

    Full Text Available Increasing evidence focuses on acetaldehyde (ACD as the mediator of the rewarding and motivational properties of ethanol. Indeed, ACD stimulates dopamine release in the nucleus accumbens and it is self-administered under different conditions. Besides the dopaminergic transmission, the endocannabinoid system has been reported to play an important role in ethanol central effects, modulating primary alcohol rewarding effect, drug-seeking and relapse behaviour. Drug motivational properties are highlighted in operant paradigms which include response-contingent punishment, a behavioural equivalent of compulsive drug use despite adverse consequences.The aim of this study was thus to characterize ACD motivational and rewarding properties employing an operant-conflict paradigm in which rats, trained to lever press in order to get ACD solution (0.9%, undergo extinction, reinstatement and conflict sessions, according to a modified Geller-Seifter procedur. Furthermore the role played by CB1 receptor system in modulating ACD-induced effects were investigated through the administration of CB1 receptor antagonist, AM281 (1 mg/kg, i.p. during the extinction-, relapse- and conflict experiments.Our results indicate that ACD is able to induce and maintain an operant behaviour, a high number of responses during extinction, an increase in the lever presses during the reinstatement phase, and a higher emission of punished responses during the conflict experiments, when compared to controls.The administration of AM281 is able to decrease ACD-seeking behaviour during extinction, the number of lever presses during reinstatement and to strongly decrease the punished responses for ACD. Our data strengthen the idea that ACD may be responsible for the central effects of ethanol, and pinpoint at the CB1 system as one of the neural substrates underlying its addictive properties.

  10. Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies.

    Science.gov (United States)

    Liu, Shixin; Chistol, Gheorghe; Bustamante, Carlos

    2014-05-06

    Ring NTPases represent a large and diverse group of proteins that couple their nucleotide hydrolysis activity to a mechanical task involving force generation and some type of transport process in the cell. Because of their shape, these enzymes often operate as gates that separate distinct cellular compartments to control and regulate the passage of chemical species across them. In this manner, ions and small molecules are moved across membranes, biopolymer substrates are segregated between cells or moved into confined spaces, double-stranded nucleic acids are separated into single strands to provide access to the genetic information, and polypeptides are unfolded and processed for recycling. Here we review the recent advances in the characterization of these motors using single-molecule manipulation and detection approaches. We describe the various mechanisms by which ring motors convert chemical energy to mechanical force or torque and coordinate the activities of individual subunits that constitute the ring. We also examine how single-molecule studies have contributed to a better understanding of the structural elements involved in motor-substrate interaction, mechanochemical coupling, and intersubunit coordination. Finally, we discuss how these molecular motors tailor their operation-often through regulation by other cofactors-to suit their unique biological functions.

  11. New insight into multifunctional role of peroxiredoxin family protein: Determination of DNA protection properties of bacterioferritin comigratory protein under hyperthermal and oxidative stresses

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sangmin, E-mail: taeinlee2011@kangwon.ac.kr [Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, South Korea (Korea, Republic of); Chung, Jeong Min [Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, South Korea (Korea, Republic of); Yun, Hyung Joong; Won, Jonghan [Advanced Nano Surface Research Group, Korea Basic Science Institute, 169-148 Gwahak-ro, Daejeon, 305-333 (Korea, Republic of); Jung, Hyun Suk, E-mail: hsjung@kangwon.ac.kr [Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, South Korea (Korea, Republic of)

    2016-01-22

    Bacterioferritin comigratory protein (BCP) is a monomeric conformer acting as a putative thiol-dependent bacterial peroxidase, however molecular basis of DNA-protection via DNA-binding has not been clearly understood. In this study, we characterized the DNA binding properties of BCP using various lengths and differently shaped architectures of DNA. An electrophoretic mobility shift assay and electron microscopy analysis showed that recombinant TkBCP bound to DNA of a circular shape (double-stranded DNA and single-stranded DNA) and a linear shape (16–1000 bp) as well as various architectures of DNA. In addition, DNA protection experiments indicated that TkBCP can protect DNA against hyperthermal and oxidative stress by removing highly reactive oxygen species (ROS) or by protecting DNA from thermal degradation. Based on these results, we suggest that TkBCP is a multi-functional DNA-binding protein which has DNA chaperon and antioxidant functions. - Highlights: • Bacterioferritin comigratory protein (BCP) protects DNA from oxidative stress by reducing ROS. • TkBCP does not only scavenge ROS, but also protect DNA from hyperthermal stress. • BCP potentially adopts the multi-functional role in DNA binding activities and anti-oxidant functions.

  12. The Vertebrate Brain, Evidence of Its Modular Organization and Operating System: Insights into the Brain's Basic Units of Structure, Function, and Operation and How They Influence Neuronal Signaling and Behavior.

    Science.gov (United States)

    Baslow, Morris H

    2011-01-01

    The human brain is a complex organ made up of neurons and several other cell types, and whose role is processing information for use in eliciting behaviors. However, the composition of its repeating cellular units for both structure and function are unresolved. Based on recent descriptions of the brain's physiological "operating system", a function of the tri-cellular metabolism of N-acetylaspartate (NAA) and N-acetylaspartylglutamate (NAAG) for supply of energy, and on the nature of "neuronal words and languages" for intercellular communication, insights into the brain's modular structural and functional units have been gained. In this article, it is proposed that the basic structural unit in brain is defined by its physiological operating system, and that it consists of a single neuron, and one or more astrocytes, oligodendrocytes, and vascular system endothelial cells. It is also proposed that the basic functional unit in the brain is defined by how neurons communicate, and consists of two neurons and their interconnecting dendritic-synaptic-dendritic field. Since a functional unit is composed of two neurons, it requires two structural units to form a functional unit. Thus, the brain can be envisioned as being made up of the three-dimensional stacking and intertwining of myriad structural units which results not only in its gross structure, but also in producing a uniform distribution of binary functional units. Since the physiological NAA-NAAG operating system for supply of energy is repeated in every structural unit, it is positioned to control global brain function.

  13. Rescue of a Plant Negative-Strand RNA Virus from Cloned cDNA: Insights into Enveloped Plant Virus Movement and Morphogenesis.

    Directory of Open Access Journals (Sweden)

    Qiang Wang

    2015-10-01

    Full Text Available Reverse genetics systems have been established for all major groups of plant DNA and positive-strand RNA viruses, and our understanding of their infection cycles and pathogenesis has benefitted enormously from use of these approaches. However, technical difficulties have heretofore hampered applications of reverse genetics to plant negative-strand RNA (NSR viruses. Here, we report recovery of infectious virus from cloned cDNAs of a model plant NSR, Sonchus yellow net rhabdovirus (SYNV. The procedure involves Agrobacterium-mediated transcription of full-length SYNV antigenomic RNA and co-expression of the nucleoprotein (N, phosphoprotein (P, large polymerase core proteins and viral suppressors of RNA silencing in Nicotiana benthamiana plants. Optimization of core protein expression resulted in up to 26% recombinant SYNV (rSYNV infections of agroinfiltrated plants. A reporter virus, rSYNV-GFP, engineered by inserting a green fluorescence protein (GFP gene between the N and P genes was able to express GFP during systemic infections and after repeated plant-to-plant mechanical passages. Deletion analyses with rSYNV-GFP demonstrated that SYNV cell-to-cell movement requires the sc4 protein and suggested that uncoiled nucleocapsids are infectious movement entities. Deletion analyses also showed that the glycoprotein is not required for systemic infection, although the glycoprotein mutant was defective in virion morphogenesis. Taken together, we have developed a robust reverse genetics system for SYNV that provides key insights into morphogenesis and movement of an enveloped plant virus. Our study also provides a template for developing analogous systems for reverse genetic analysis of other plant NSR viruses.

  14. Rescue of a Plant Negative-Strand RNA Virus from Cloned cDNA: Insights into Enveloped Plant Virus Movement and Morphogenesis.

    Science.gov (United States)

    Wang, Qiang; Ma, Xiaonan; Qian, ShaSha; Zhou, Xin; Sun, Kai; Chen, Xiaolan; Zhou, Xueping; Jackson, Andrew O; Li, Zhenghe

    2015-10-01

    Reverse genetics systems have been established for all major groups of plant DNA and positive-strand RNA viruses, and our understanding of their infection cycles and pathogenesis has benefitted enormously from use of these approaches. However, technical difficulties have heretofore hampered applications of reverse genetics to plant negative-strand RNA (NSR) viruses. Here, we report recovery of infectious virus from cloned cDNAs of a model plant NSR, Sonchus yellow net rhabdovirus (SYNV). The procedure involves Agrobacterium-mediated transcription of full-length SYNV antigenomic RNA and co-expression of the nucleoprotein (N), phosphoprotein (P), large polymerase core proteins and viral suppressors of RNA silencing in Nicotiana benthamiana plants. Optimization of core protein expression resulted in up to 26% recombinant SYNV (rSYNV) infections of agroinfiltrated plants. A reporter virus, rSYNV-GFP, engineered by inserting a green fluorescence protein (GFP) gene between the N and P genes was able to express GFP during systemic infections and after repeated plant-to-plant mechanical passages. Deletion analyses with rSYNV-GFP demonstrated that SYNV cell-to-cell movement requires the sc4 protein and suggested that uncoiled nucleocapsids are infectious movement entities. Deletion analyses also showed that the glycoprotein is not required for systemic infection, although the glycoprotein mutant was defective in virion morphogenesis. Taken together, we have developed a robust reverse genetics system for SYNV that provides key insights into morphogenesis and movement of an enveloped plant virus. Our study also provides a template for developing analogous systems for reverse genetic analysis of other plant NSR viruses.

  15. Self-Assembly Model of DNA Molecular Logical Operators%DNA分子并行自组装逻辑运算模型

    Institute of Scientific and Technical Information of China (English)

    佘辉; 游自立; 张文政; 霍家佳

    2013-01-01

    Since Aldeman successful implemented DNA computing to solve HPP problem, the potential of calculation of DNA molecules was noticed by many scientists. We use it to solve logic operations based on the Self-Assembly Model. It was used DNA enzymes to dispose the product of the DNA to find the results of DNA logical operations. After the above experiment, it showed that the DNA molecule calculation model is feasible.%自从Aldeman成功地实现了用DNA计算解决汉密尔顿路径问题,DNA分子的计算潜力得到了许多科学家的高度关注.本文提出一种可实现的高并行性自组装的逻辑运算模型.通过DNA互补配对的特性使计算分子自行识别组装,利用DNA内切酶等处理DNA产物完成对DNA分子逻辑运算结果的筛选.实验表明该DNA分子计算模型是可行的.

  16. FBH1 co-operates with MUS81 in inducing DNA double-strand breaks and cell death following replication stress

    DEFF Research Database (Denmark)

    Fugger, Kasper; Chu, Wai Kit; Haahr, Peter

    2013-01-01

    The molecular events occurring following the disruption of DNA replication forks are poorly characterized, despite extensive use of replication inhibitors such as hydroxyurea in the treatment of malignancies. Here, we identify a key role for the FBH1 helicase in mediating DNA double-strand break...... formation following replication inhibition. We show that FBH1-deficient cells are resistant to killing by hydroxyurea, and exhibit impaired activation of the pro-apoptotic factor p53, consistent with decreased DNA double-strand break formation. Similar findings were obtained in murine ES cells carrying...... disrupted alleles of Fbh1. We also show that FBH1 through its helicase activity co-operates with the MUS81 nuclease in promoting the endonucleolytic DNA cleavage following prolonged replication stress. Accordingly, MUS81 and EME1-depleted cells show increased resistance to the cytotoxic effects...

  17. Reactions of potent antitumor complex trans-[Ru(III)Cl4(indazole)2]- with a DNA-relevant nucleobase and thioethers: insight into biological action.

    Science.gov (United States)

    Egger, Alexander; Arion, Vladimir B; Reisner, Erwin; Cebrián-Losantos, Berta; Shova, Sergiu; Trettenhahn, Günter; Keppler, Bernhard K

    2005-01-10

    Reactions of the complex trans-[RuCl(4)(Hind)(2)](-) (Hind = indazole), which is of clinical relevance today, with both the DNA model nucleobase 9-methyladenine (made) and the thioethers R(2)S (R = Me, Et), as models of the methionine residue in biological molecules possibly acting as nitrogen-competing sulfur-donor ligands for ruthenium atom, have been investigated to get insight into details of mechanism leading to antitumor activity. Three novel ruthenium complexes, viz., [Ru(III)Cl(3)(Hind)(2)(made)], 1, [Ru(II)Cl(2)(Hind)(2)(Me(2)S)(2)], 2, and [Ru(II)Cl(2)(Hind)(2)(Et(2)S)(2)], 3, have been isolated as solids. Oxidation of 2 and 3 with hydrogen peroxide in the presence of 12 M HCl in chloroform afforded the monothioether adducts, viz., [Ru(III)Cl(3)(Hind)(2)(Me(2)S)], 4, and [Ru(III)Cl(3)(Hind)(2)(Et(2)S)], 5. By dissolution of 2 or 3 in DMSO, replacement of both R(2)S ligands by DMSO molecules occurred with isolation of trans,trans,trans-[Ru(II)Cl(2)(Hind)(2)(DMSO)(2)], 6. The products were characterized by elemental analysis, IR, UV-vis, electrospray mass spectrometry, cyclic voltammetry, and X-ray crystallography (1.CH(2)Cl(2).CH(3)OH and 1.1.1H(2)O.0.9CH(3)OH, 2, and 5). The first crystallographic evidence for the monofunctional coordination of the 9-methyladenine ligand to ruthenium via N7 and the self-pairing of the complex molecules via H-bonding, using the usual Watson-Crick pairing donor and acceptor sites of two adjacent 9-methyladenine ligands, is reported. The electrochemical behavior of 1-5 has been studied in DMF and DMSO by cyclic voltammetry. The redox potential values have been interpreted on the basis of the Lever's parametrization method. The E(L) parameter was estimated for 9-methyladenine at 0.18 V, showing that this ligand behaves as a weaker net electron donor than imidazole (E(L) = 0.12 V). The kinetics of the reductively induced stepwise replacement of chlorides by DMF in 4 and 5 were studied by digital simulation of the cyclic

  18. Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: insights from molecular dynamics simulation and free energy analysis.

    Science.gov (United States)

    Chen, Lin; Zhang, Ji-Long; Yu, Li-Ying; Zheng, Qing-Chuan; Chu, Wen-Ting; Xue, Qiao; Zhang, Hong-Xing; Sun, Chia-Chung

    2012-10-18

    Cren7, a novel chromatin protein highly conserved among crenarchaea, plays an important role in genome packaging and gene regulation. However, the detail dynamical structural characteristic of the Cren7-DNA complex and the detail study of the DNA in the complex have not been done. Focused on two specific Cren7-DNA complexes (PDB codes 3LWH and 3LWI ), we applied molecular dynamics (MD) simulations at four different temperatures (300, 350, 400, and 450 K) and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation at 300 and 350 K to examine the role of Cren7 protein in enhancing the stability of DNA duplexes via protein-DNA interactions, and to study the structural transition in DNA. The simulation results indicate that Cren7 stabilizes DNA duplex in a certain temperature range in the binary complex compared with the unbound DNA molecules. At the same time, DNA molecules were found to undergo B-like to A-like form transitions with increased temperature. The results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on the structure of DNA molecules. Our work can give important information to understand the interactions of proteins with nucleic acids and other ligands.

  19. Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae.

    Science.gov (United States)

    Jeon, Junhyun; Choi, Jaeyoung; Lee, Gir-Won; Park, Sook-Young; Huh, Aram; Dean, Ralph A; Lee, Yong-Hwan

    2015-02-24

    DNA methylation is an important epigenetic modification that regulates development of plants and mammals. To investigate the roles of DNA methylation in fungal development, we profiled genome-wide methylation patterns at single-nucleotide resolution during vegetative growth, asexual reproduction, and infection-related morphogenesis in a model plant pathogenic fungus, Magnaporthe oryzae. We found that DNA methylation occurs in and around genes as well as transposable elements and undergoes global reprogramming during fungal development. Such reprogramming of DNA methylation suggests that it may have acquired new roles other than controlling the proliferation of TEs. Genetic analysis of DNA methyltransferase deletion mutants also indicated that proper reprogramming in methylomes is required for asexual reproduction in the fungus. Furthermore, RNA-seq analysis showed that DNA methylation is associated with transcriptional silencing of transposable elements and transcript abundance of genes in context-dependent manner, reinforcing the role of DNA methylation as a genome defense mechanism. This comprehensive approach suggests that DNA methylation in fungi can be a dynamic epigenetic entity contributing to fungal development and genome defense. Furthermore, our DNA methylomes provide a foundation for future studies exploring this key epigenetic modification in fungal development and pathogenesis.

  20. DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetic structure of whitebark pine (Pinus albicaulis)

    Science.gov (United States)

    Bryce A. Richardson; Steven J. Runsfeld; Ned B. Klopfenstein

    2002-01-01

    Uniparentally inherited mitochondrial (mt)DNA and chloroplast (cp)DNA microsatellites (cpSSRs) were used to examine population genetic structure and biogeographic patterns of bird-dispersed seed and wind-disseminated pollen of whitebark pine (Pinus albicaulis Engelm.). Sampling was conducted from 41 populations throughout the range of the species....

  1. A novel mitochondrial DNA deletion in a patient with Pearson syndrome and neonatal diabetes mellitus provides insight into disease etiology, severity and progression.

    Science.gov (United States)

    Chen, Xin-Yu; Zhao, Si-Yu; Wang, Yan; Wang, Dong; Dong, Chang-Hu; Yang, Ying; Wang, Zhi-Hua; Wu, Yuan-Ming

    2016-07-01

    Pearson syndrome (PS) is a rare, mitochondrial DNA (mtDNA) deletion disorder mainly affecting hematopoietic system and exocrine pancreas in early infancy, which is characterized by multi-organ involvement, variable manifestations and poor prognosis. Since the clinical complexity and uncertain outcome of PS, the ability to early diagnose and anticipate disease progression is of great clinical importance. We described a patient with severe anemia and hyperglycinemia at birth was diagnosed with neonatal diabetes mellitus, and later with PS. Genetic testing revealed that a novel mtDNA deletion existed in various non-invasive tissues from the patient. The disease course was monitored by mtDNA deletion heteroplasmy and mtDNA/nucleus DNA genome ratio in different tissues and at different time points, showing a potential genotype-phenotype correlation. Our findings suggest that for patient suspected for PS, it may be therapeutically important to first perform detailed mtDNA analysis on non-invasive tissues at the initial diagnosis and during disease progression.

  2. Mitochondrial and plastid genomes of the colonial green alga Gonium pectorale give insights into the origins of organelle DNA architecture within the volvocales.

    Directory of Open Access Journals (Sweden)

    Takashi Hamaji

    Full Text Available Volvocalean green algae have among the most diverse mitochondrial and plastid DNAs (mtDNAs and ptDNAs from the eukaryotic domain. However, nearly all of the organelle genome data from this group are restricted to unicellular species, like Chlamydomonas reinhardtii, and presently only one multicellular species, the ∼4,000-celled Volvox carteri, has had its organelle DNAs sequenced. The V. carteri organelle genomes are repeat rich, and the ptDNA is the largest plastome ever sequenced. Here, we present the complete mtDNA and ptDNA of the colonial volvocalean Gonium pectorale, which is comprised of ∼16 cells and occupies a phylogenetic position closer to that of V. carteri than C. reinhardtii within the volvocine line. The mtDNA and ptDNA of G. pectorale are circular-mapping AT-rich molecules with respective lengths and coding densities of 16 and 222.6 kilobases and 73 and 44%. They share some features with the organelle DNAs of V. carteri, including palindromic repeats within the plastid compartment, but show more similarities with those of C. reinhardtii, such as a compact mtDNA architecture and relatively low organelle DNA intron contents. Overall, the G. pectorale organelle genomes raise several interesting questions about the origin of linear mitochondrial chromosomes within the Volvocales and the relationship between multicellularity and organelle genome expansion.

  3. Machine learning-based receiver operating characteristic (ROC) curves for crisp and fuzzy classification of DNA microarrays in cancer research.

    Science.gov (United States)

    Peterson, Leif E; Coleman, Matthew A

    2008-01-01

    Receiver operating characteristic (ROC) curves were generated to obtain classification area under the curve (AUC) as a function of feature standardization, fuzzification, and sample size from nine large sets of cancer-related DNA microarrays. Classifiers used included k nearest neighbor (kNN), näive Bayes classifier (NBC), linear discriminant analysis (LDA), quadratic discriminant analysis (QDA), learning vector quantization (LVQ1), logistic regression (LOG), polytomous logistic regression (PLOG), artificial neural networks (ANN), particle swarm optimization (PSO), constricted particle swarm optimization (CPSO), kernel regression (RBF), radial basis function networks (RBFN), gradient descent support vector machines (SVMGD), and least squares support vector machines (SVMLS). For each data set, AUC was determined for a number of combinations of sample size, total sum[-log(p)] of feature t-tests, with and without feature standardization and with (fuzzy) and without (crisp) fuzzification of features. Altogether, a total of 2,123,530 classification runs were made. At the greatest level of sample size, ANN resulted in a fitted AUC of 90%, while PSO resulted in the lowest fitted AUC of 72.1%. AUC values derived from 4NN were the most dependent on sample size, while PSO was the least. ANN depended the most on total statistical significance of features used based on sum[-log(p)], whereas PSO was the least dependent. Standardization of features increased AUC by 8.1% for PSO and -0.2% for QDA, while fuzzification increased AUC by 9.4% for PSO and reduced AUC by 3.8% for QDA. AUC determination in planned microarray experiments without standardization and fuzzification of features will benefit the most if CPSO is used for lower levels of feature significance (i.e., sum[-log(p)] ~ 50) and ANN is used for greater levels of significance (i.e., sum[-log(p)] ~ 500). When only standardization of features is performed, studies are likely to benefit most by using CPSO for low levels

  4. (Ubi)quitin' the h2bit: recent insights into the roles of H2B ubiquitylation in DNA replication and transcription.

    Science.gov (United States)

    Wright, Duncan E; Kao, Cheng-Fu

    2015-01-01

    The reversible ubiquitylation of histone H2B has long been known to regulate gene transcription, and is now understood to modulate DNA replication as well. In this review, we describe how recent, genome-wide analyses have demonstrated that this histone mark has further reaching effects on transcription and replication than once thought. We also consider the ongoing efforts to elucidate the molecular mechanisms by which H2B ubiquitylation affects processes on the DNA template, and outline the various hypothetical scenarios.

  5. Evolution of the bomolochiform superfamily complex (Copepoda: Cyclopoida): new insights from ssrDNA and morphology, and origin of Umazuracolids from polychaete-infesting ancestors rejected.

    Science.gov (United States)

    Huys, Rony; Fatih, Farrah; Ohtsuka, Susumu; Llewellyn-Hughes, Julia

    2012-01-01

    Poecilostome cyclopoids are among the most morphologically diverse copepods, having established symbiotic relationships with teleosts, elasmobranchs and invertebrate hosts belonging to no fewer than 14 marine phyla. Many parasitic lineages display radically divergent body plans and on that basis have traditionally been placed at higher taxonomic rank than they deserve. The most recent example is the monotypic family Umazuracolidae, established for a derived fish parasite with bomolochiform affinities. Phylogenetic analysis of complete ssrDNA (18S) sequences of 44 species belonging to 21 families of cyclopoid copepods shows that there is no support for the familial distinctiveness of the Umazuracolidae. Both maximum parsimony tree reconstruction and Bayesian inference, operating under the GTR+I+Γ model of nucleotide substitution, unambiguously placed Umazuracola elongatus in the Taeniacanthidae within the predominantly fish parasitic bomolochiform complex, refuting the original suggestion of a shared most recent common ancestry with polychaete symbionts. The phylogenies also revealed that the bomolochiform families and the Clausidiidae (and allies) form a monophyletic group, the clausidiiform complex, with high nodal support under both methods. Bayesian inference suggested a diphyletic origin of the "Poecilostomatoida" with the clausidiiform family-group holding a basal position while the traditional cyclopoid families form a monophyletic group in apposition to a second poecilostomatoid clade; however, maximum parsimony results were equivocal, depending on outgroup selection. Scrutiny of the morphological characters diagnosing the monotypic families Tegobomolochidae and Tuccidae demonstrated that they merely represent derived lineages within more inclusive taxa, the former being related to a group of nostril-inhabiting genera within the Bomolochidae, the latter forming the sistergroup of Taeniacanthodes within the Taeniacanthidae. The taeniacanthid genus

  6. Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation.

    Science.gov (United States)

    Wang, Xiaotong; Li, Qiye; Lian, Jinmin; Li, Li; Jin, Lijun; Cai, Huimin; Xu, Fei; Qi, Haigang; Zhang, Linlin; Wu, Fucun; Meng, Jie; Que, Huayong; Fang, Xiaodong; Guo, Ximing; Zhang, Guofan

    2014-12-16

    Studies of DNA methylomes in a wide range of eukaryotes have revealed both conserved and divergent characteristics of DNA methylation among phylogenetic groups. However, data on invertebrates particularly molluscs are limited, which hinders our understanding of the evolution of DNA methylation in metazoa. The sequencing of the Pacific oyster Crassostrea gigas genome provides an opportunity for genome-wide profiling of DNA methylation in this model mollusc. Homologous searches against the C. gigas genome identified functional orthologs for key genes involved in DNA methylation: DNMT1, DNMT2, DNMT3, MBD2/3 and UHRF1. Whole-genome bisulfite sequencing (BS-seq) of the oyster's mantle tissues revealed that more than 99% methylation modification was restricted to cytosines in CpG context and methylated CpGs accumulated in the bodies of genes that were moderately expressed. Young repeat elements were another major targets of CpG methylation in oysters. Comparison with other invertebrate methylomes suggested that the 5'-end bias of gene body methylation and the negative correlation between gene body methylation and gene length were the derived features probably limited to the insect lineage. Interestingly, phylostratigraphic analysis showed that CpG methylation preferentially targeted genes originating in the common ancestor of eukaryotes rather than the oldest genes originating in the common ancestor of cellular organisms. Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these 'relatively young' genes was critical for the origin and radiation of eukaryotes.

  7. Insight into the binding of a non-toxic, self-assembling aromatic tripeptide with ct-DNA: Spectroscopic and viscositic studies

    Directory of Open Access Journals (Sweden)

    Soumi Biswas

    2017-09-01

    Full Text Available The report describes the synthesis, self-association and DNA binding studies of an aromatic tripeptide H-Phe-Phe-Phe-OH (FFF. The peptide backbone adopts β—sheet conformation both in solid and solution. In aqueous solution, FFF self-assembles to form nanostructured aggregates. Interactions of this peptide with calf-thymus DNA (ct-DNA have been studied using various biophysical techniques including ultraviolet (UV absorption spectroscopy, fluorescence spectroscopy and circular dichroism (CD spectroscopy. The value of mean binding constant calculated from UV and fluorescence spectroscopic data is (2.914 ± 0.74 x 103 M−1 which is consistent with an external binding mode. Fluorescence intercalator displacement (FID assay, iodide quenching study, viscosity measurement and thermal denaturation study of DNA further confirm the groove binding mode of peptide, FFF with ct-DNA. MTT cell survival assay reveals very low cytotoxicity of the peptide toward human lung carcinoma cell line A549.

  8. Fine-tuning alkyne cycloadditions: Insights into photochemistry responsible for the double-strand DNA cleavage via structural perturbations in diaryl alkyne conjugates

    Directory of Open Access Journals (Sweden)

    Igor V. Alabugin

    2011-06-01

    Full Text Available Hybrid molecules combining photoactivated aryl acetylenes and a dicationic lysine moiety cause the most efficient double-strand (ds DNA cleavage known to date for a small molecule. In order to test the connection between the alkylating ability and the DNA-damaging properties of these compounds, we investigated the photoreactivity of three isomeric aryl–tetrafluoropyridinyl (TFP alkynes with amide substituents in different positions (o-, m-, and p- toward a model π-system. Reactions with 1,4-cyclohexadiene (1,4-CHD were used to probe the alkylating properties of the triplet excited states in these three isomers whilst Stern–Volmer quenching experiments were used to investigate the kinetics of photoinduced electron transfer (PET. The three analogous isomeric lysine conjugates cleaved DNA with different efficiencies (34, 15, and 0% of ds DNA cleavage for p-, m-, and o-substituted lysine conjugates, respectively consistent with the alkylating ability of the respective acetamides. The significant protecting effect of the hydroxyl radical and singlet oxygen scavengers to DNA cleavage was shown only with m-lysine conjugate. All three isomeric lysine conjugates inhibited human melanoma cell growth under photoactivation: The p-conjugate had the lowest CC50 (50% cell cytotoxicity value of 1.49 × 10−7 M.

  9. Structural and mutational analyses of Deinococcus radiodurans UvrA2 provide insight into DNA binding and damage recognition by UvrAs.

    Science.gov (United States)

    Timmins, Joanna; Gordon, Elspeth; Caria, Sofia; Leonard, Gordon; Acajjaoui, Samira; Kuo, Mei-Shiue; Monchois, Vincent; McSweeney, Sean

    2009-04-15

    UvrA proteins are key actors in DNA damage repair and play an essential role in prokaryotic nucleotide excision repair (NER), a pathway that is unique in its ability to remove a broad spectrum of DNA lesions. Understanding the DNA binding and damage recognition activities of the UvrA family is a critical component for establishing the molecular basis of this process. Here we report the structure of the class II UvrA2 from Deinococcus radiodurans in two crystal forms. These structures, coupled with mutational analyses and comparison with the crystal structure of class I UvrA from Bacillus stearothermophilus, suggest a previously unsuspected role for the identified insertion domains of UvrAs in both DNA binding and damage recognition. Taken together, the available information suggests a model for how UvrA interacts with DNA and thus sheds new light on the molecular mechanisms underlying the role of UvrA in the early steps of NER.

  10. [The validation of kit of reagents for quantitative detection of DNA of human cytomegalovirus in biological material using polymerase chain reaction technique in real time operation mode].

    Science.gov (United States)

    Sil'veĭstrova, O Iu; Domonova, É A; Shipulina, O Iu

    2014-04-01

    The validation of kit of reagents destined to detection and quantitative evaluation of DNA of human cytomegalovirus in biological material using polymerase chain reaction technique in real time operation mode was implemented. The comparison was made against international WHO standard--The first WHO international standard for human cytomegalovirus to implement measures the kit of reagents "AmpliSens CMV-screen/monitor-FL" and standard sample of enterprise DNA HCMV (The central research institute of epidemiology of Rospotrebnadzor) was applied. The fivefold dilution of international WHO standard and standard sample of enterprise were carried out in concentrations of DNA HCMV from 106 to 102. The arrangement of polymerase chain reaction and analysis of results were implemented using programed amplifier with system of detection of fluorescent signal in real-time mode "Rotor-Gene Q" ("Qiagen", Germany). In the total of three series of experiments, all stages of polymerase chain reaction study included, the coefficient of translation of quantitative evaluation of DNA HCMV from copy/ml to ME/ml equal to 0.6 was introduced for this kit of reagents.

  11. Temperature-induced melting of double-stranded DNA in the absence and presence of covalently bonded antitumour drugs: insight from molecular dynamics simulations.

    Science.gov (United States)

    Bueren-Calabuig, Juan A; Giraudon, Christophe; Galmarini, Carlos M; Egly, Jean Marc; Gago, Federico

    2011-10-01

    The difference in melting temperature of a double-stranded (ds) DNA molecule in the absence and presence of bound ligands can provide experimental information about the stabilization brought about by ligand binding. By simulating the dynamic behaviour of a duplex of sequence 5'-d(TAATAACGGATTATT)·5'-d(AATAATCCGTTATTA) in 0.1 M NaCl aqueous solution at 400 K, we have characterized in atomic detail its complete thermal denaturation profile in PM01183. Progressive helix unzipping was clearly interspersed with some reannealing events, which were most noticeable in the oligonucleotides containing the monoadducts, which maintained an average of 6 bp in the central region at the end of the simulations. These significant differences attest to the demonstrated ability of these drugs to stabilize dsDNA, stall replication and transcription forks, and recruit DNA repair proteins. This stabilization, quantified here in terms of undisrupted base pairs, supports the view that these monoadducts can functionally mimic a DNA interstrand crosslink.

  12. Structure of the Full-Length Human RPA14/32 Complex Gives Insights Into the Mechanism of DNA Binding And Complex Formation

    Energy Technology Data Exchange (ETDEWEB)

    Deng, X.; Habel, J.E.; Kabaleeswaran, V.; Snell, E.H.; Wold, M.S.; Borgstahl, G.E.O.

    2009-06-03

    Replication protein A (RPA) is the ubiquitous, eukaryotic single-stranded DNA (ssDNA) binding protein and is essential for DNA replication, recombination, and repair. Here, crystal structures of the soluble RPA heterodimer, composed of the RPA14 and RPA32 subunits, have been determined for the full-length protein in multiple crystal forms. In all crystals, the electron density for the N-terminal (residues 1--42) and C-terminal (residues 175--270) regions of RPA32 is weak and of poor quality indicating that these regions are disordered and/or assume multiple positions in the crystals. Hence, the RPA32 N terminus, that is hyperphosphorylated in a cell-cycle-dependent manner and in response to DNA damaging agents, appears to be inherently disordered in the unphosphorylated state. The C-terminal, winged helix-loop-helix, protein-protein interaction domain adopts several conformations perhaps to facilitate its interaction with various proteins. Although the ordered regions of RPA14/32 resemble the previously solved protease-resistant core crystal structure, the quaternary structures between the heterodimers are quite different. Thus, the four-helix bundle quaternary assembly noted in the original core structure is unlikely to be related to the quaternary structure of the intact heterotrimer. An organic ligand binding site between subunits RPA14 and RPA32 was identified to bind dioxane. Comparison of the ssDNA binding surfaces of RPA70 with RPA14/32 showed that the lower affinity of RPA14/32 can be attributed to a shallower binding crevice with reduced positive electrostatic charge.

  13. Structural, energetic and tautomeric properties of the T·T∗/T∗·T DNA mismatch involving mutagenic tautomer of thymine: A QM and QTAIM insight

    Science.gov (United States)

    Brovarets', Ol'ha O.; Zhurakivsky, Roman O.; Hovorun, Dmytro M.

    2014-01-01

    It was revealed by thorough study of the T·T∗ (C1) ↔ T∗·T (C1) tautomerisation via the synchronous concerted double proton transfer (DPT) through the TS (C2v) that the T·T∗/T∗·T H-bonded mismatch is dynamically stable non-planar complex with a lifetime 1.6 × 10-10 s. The 5 key points were firstly detected and completely investigated along the intrinsic reaction coordinate of the DPT tautomerisation. The reported data allow us to suggest that the T∗ mutagenic tautomer of the thymine (T) is shared with approximately equal probability between two DNA strands during the dissociation of the mispair by DNA polymerase.

  14. Rescue of a Plant Negative-Strand RNA Virus from Cloned cDNA: Insights into Enveloped Plant Virus Movement and Morphogenesis

    OpenAIRE

    Qiang Wang; Xiaonan Ma; ShaSha Qian; Xin Zhou; Kai Sun; Xiaolan Chen; Xueping Zhou; Jackson, Andrew O.; Zhenghe Li

    2015-01-01

    Reverse genetics systems have been established for all major groups of plant DNA and positive-strand RNA viruses, and our understanding of their infection cycles and pathogenesis has benefitted enormously from use of these approaches. However, technical difficulties have heretofore hampered applications of reverse genetics to plant negative-strand RNA (NSR) viruses. Here, we report recovery of infectious virus from cloned cDNAs of a model plant NSR, Sonchus yellow net rhabdovirus (SYNV). The ...

  15. Insights into dynamic mitotic chromatin organization through the NIMA kinase suppressor SonC, a chromatin-associated protein involved in the DNA damage response.

    Science.gov (United States)

    Larson, Jennifer R; Facemyer, Eric M; Shen, Kuo-Fang; Ukil, Leena; Osmani, Stephen A

    2014-01-01

    The nuclear pore complex proteins SonA and SonB, the orthologs of mammalian RAE1 and NUP98, respectively, were identified in Aspergillus nidulans as cold-sensitive suppressors of a temperature-sensitive allele of the essential mitotic NIMA kinase (nimA1). Subsequent analyses found that sonB1 mutants exhibit temperature-dependent DNA damage sensitivity. To understand this pathway further, we performed a genetic screen to isolate additional conditional DNA damage-sensitive suppressors of nimA1. We identified two new alleles of SonA and four intragenic nimA mutations that suppress the temperature sensitivity of the nimA1 mutant. In addition, we identified SonC, a previously unstudied binuclear zinc cluster protein involved with NIMA and the DNA damage response. Like sonA and sonB, sonC is an essential gene. SonC localizes to nuclei and partially disperses during mitosis. When the nucleolar organizer region (NOR) undergoes mitotic condensation and removal from the nucleolus, nuclear SonC and histone H1 localize in a mutually exclusive manner with H1 being removed from the NOR region and SonC being absent from the end of the chromosome beyond the NOR. This region of chromatin is adjacent to a cluster of nuclear pore complexes to which NIMA localizes last during its progression around the nuclear envelope during initiation of mitosis. The results genetically extend the NIMA regulatory system to include a protein with selective large-scale chromatin location observed during mitosis. The data suggest a model in which NIMA and SonC, its new chromatin-associated suppressor, might help to orchestrate global chromatin states during mitosis and the DNA damage response.

  16. Temperature-induced melting of double-stranded DNA in the absence and presence of covalently bonded antitumour drugs: insight from molecular dynamics simulations

    OpenAIRE

    Bueren-Calabuig, J. A.; Giraudon, C.; Galmarini, C M; Egly, J M; Gago, F.

    2011-01-01

    The difference in melting temperature of a double-stranded (ds) DNA molecule in the absence and presence of bound ligands can provide experimental information about the stabilization brought about by ligand binding. By simulating the dynamic behaviour of a duplex of sequence 5′-d(TAATAACGGATTATT)·5′-d(AATAATCCGTTATTA) in 0.1 M NaCl aqueous solution at 400 K, we have characterized in atomic detail its complete thermal denaturation profile in

  17. Cysteine Mutational Studies Provide Insight into a Thiol-Based Redox Switch Mechanism of Metal and DNA Binding in FurA from Anabaena sp. PCC 7120

    Science.gov (United States)

    Botello-Morte, Laura; Pellicer, Silvia; Sein-Echaluce, Violeta C.; Contreras, Lellys M.; Neira, José Luis; Abián, Olga; Velázquez-Campoy, Adrián; Peleato, María Luisa; Fillat, María F.

    2016-01-01

    Abstract Aims: The ferric uptake regulator (Fur) is the main transcriptional regulator of genes involved in iron homeostasis in most prokaryotes. FurA from Anabaena sp. PCC 7120 contains five cysteine residues, four of them arranged in two redox-active CXXC motifs. The protein needs not only metal but also reducing conditions to remain fully active in vitro. Through a mutational study of the cysteine residues present in FurA, we have investigated their involvement in metal and DNA binding. Results: Residue C101 that belongs to a conserved CXXC motif plays an essential role in both metal and DNA binding activities in vitro. Substitution of C101 by serine impairs DNA and metal binding abilities of FurA. Isothermal titration calorimetry measurements show that the redox state of C101 is responsible for the protein ability to coordinate the metal corepressor. Moreover, the redox state of C101 varies with the presence or absence of C104 or C133, suggesting that the environments of these cysteines are mutually interdependent. Innovation: We propose that C101 is part of a thiol/disulfide redox switch that determines FurA ability to bind the metal corepressor. Conclusion: This mechanism supports a novel feature of a Fur protein that emerges as a regulator, which connects the response to changes in the intracellular redox state and iron management in cyanobacteria. Antioxid. Redox Signal. 24, 173–185. PMID:26414804

  18. Fusion tyrosine kinase NPM-ALK Deregulates MSH2 and suppresses DNA mismatch repair function novel insights into a potent oncoprotein.

    Science.gov (United States)

    Young, Leah C; Bone, Kathleen M; Wang, Peng; Wu, Fang; Adam, Benjamin A; Hegazy, Samar; Gelebart, Pascal; Holovati, Jelena; Li, Liang; Andrew, Susan E; Lai, Raymond

    2011-07-01

    The fusion tyrosine kinase NPM-ALK is central to the pathogenesis of ALK-positive anaplastic large cell lymphoma (ALK(+)ALCL). We recently identified that MSH2, a key DNA mismatch repair (MMR) protein integral to the suppression of tumorigenesis, is an NPM-ALK-interacting protein. In this study, we found in vitro evidence that enforced expression of NPM-ALK in HEK293 cells suppressed MMR function. Correlating with these findings, six of nine ALK(+)ALCL tumors displayed evidence of microsatellite instability, as opposed to none of the eight normal DNA control samples (P = 0.007, Student's t-test). Using co-immunoprecipitation, we found that increasing levels of NPM-ALK expression in HEK293 cells resulted in decreased levels of MSH6 bound to MSH2, whereas MSH2·NPM-ALK binding was increased. The NPM-ALK·MSH2 interaction was dependent on the activation/autophosphorylation of NPM-ALK, and the Y191 residue of NPM-ALK was a crucial site for this interaction and NPM-ALK-mediated MMR suppression. MSH2 was found to be tyrosine phosphorylated in the presence of NPM-ALK. Finally, NPM-ALK impeded the expected DNA damage-induced translocation of MSH2 out of the cytoplasm. To conclude, our data support a model in which the suppression of MMR by NPM-ALK is attributed to its ability to interfere with normal MSH2 biochemistry and function.

  19. Solution structure of a 2:1 complex of anticancer drug XR5944 with TFF1 estrogen response element: insights into DNA recognition by a bis-intercalator.

    Science.gov (United States)

    Lin, Clement; Mathad, Raveendra I; Zhang, Zhenjiang; Sidell, Neil; Yang, Danzhou

    2014-05-01

    XR5944, a deoxyribonucleic acid (DNA) bis-intercalator with potent anticancer activity, can bind the estrogen response element (ERE) sequence to inhibit estrogen receptor-α activities. This novel mechanism of action may be useful for overcoming drug resistance to currently available antiestrogen treatments, all of which target the hormone-receptor complex. Here we report the nuclear magnetic resonance solution structure of the 2:1 complex of XR5944 with the naturally occurring TFF1-ERE, which exhibits important and unexpected features. In both drug-DNA complexes, XR5944 binds strongly at one intercalation site but weakly at the second site. The sites of intercalation within a native promoter sequence appear to be context and sequence dependent. The binding of one drug molecule influences the binding site of the second. Our structures underscore the fact that the DNA binding of a bis-intercalator is directional and different from the simple addition of two single intercalation sites. Our study suggests that improved XR5944 bis-intercalators targeting ERE may be designed through optimization of aminoalkyl linker and intercalation moieties at the weak binding sites. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Detoxification of olefinic epoxides and nucleotide excision repair of epoxide-mediated DNA damage: Insights from animal models examining human sensitivity to 1,3-butadiene.

    Science.gov (United States)

    Wickliffe, Jeffrey K; Herring, Stacy M; Hallberg, Lance M; Galbert, Lori A; Masters, Oscar E; Ammenheuser, Marinel M; Xie, Jingwu; Friedberg, Errol C; Lloyd, R Stephen; Abdel-Rahman, Sherif Z; Ward, Jonathan B

    2007-03-20

    1,3-Butadiene (BD) is a well-documented mutagen and carcinogen in rodents and is currently classified as a probable carcinogen in humans. Studies investigating workers exposed to BD indicate that, in some plants, there may be an increased genetic risk, and that polymorphisms in biotransformation and DNA repair proteins may modulate genetic susceptibility. To investigate the role of genetic polymorphisms in microsomal epoxide hydrolase (mEH) or nucleotide excision repair (NER) in contributing to the mutagenicity of BD, we conducted a series of experiments in which mice lacking mEH or NER activity were exposed to BD by inhalation or to the reactive epoxide metabolites of BD (epoxybutene-EB or diepoxybutane-DEB) by i.p. injection. Genetic susceptibility was measured using the Hprt cloning assay. Both deficient strains of mouse were significantly more sensitive to the mutagenic effects of BD and the injected epoxides. These studies provide support for the critical role that mEH plays in the biotransformation of BD, and the role that NER plays in maintaining genomic integrity following exposure to BD. Additional studies are needed to examine the importance of base excision repair (BER) in maintaining genomic integrity, the differential formation of DNA and protein adducts in deficient strains, and the potential for enhanced sensitivity to BD genotoxicity in mice either lacking or deficient in both biotransformation and DNA repair activity.

  1. Local chromatin microenvironment determines DNMT activity : from DNA methyltransferase to DNA demethylase or DNA dehydroxymethylase

    NARCIS (Netherlands)

    van der Wijst, Monique G. P.; Venkiteswaran, Muralidhar; Chen, Hui; Xu, Guo-Liang; Plosch, Torsten; Rots, Marianne G.

    2015-01-01

    Insights on active DNA demethylation disproved the original assumption that DNA methylation is a stable epigenetic modification. Interestingly, mammalian DNA methyltransferases 3A and 3B (DNMT-3A and -3B) have also been reported to induce active DNA demethylation, in addition to their well-known fun

  2. Double positivity for HPV DNA/p16 in tonsillar and base of tongue cancer improves prognostication: Insights from a large population-based study.

    Science.gov (United States)

    Garnaes, Emilie; Frederiksen, Kirsten; Kiss, Katalin; Andersen, Luise; Therkildsen, Marianne H; Franzmann, Maria B; Specht, Lena; Andersen, Elo; Norrild, Bodil; Kjaer, Susanne K; von Buchwald, Christian

    2016-12-01

    The aim was to explore the overall survival (OS) for palatine tonsillar squamous cell carcinoma (TSCC), subdivided, according to certainty of tonsillar tumour origin, into specified tonsillar squamous cell carcinomas (STSCCs) and nonspecified tonsillar squamous cell carcinomas (NSTSCCs), and base of tongue squamous cell carcinoma (BSCC) when stratifying for HPV DNA status, p16 expression and combined HPV/p16 status. We included all patients (n = 797) diagnosed with TSCCs and BSCCs in Eastern Denmark as registered in the Danish Head and Neck Cancer Group (DAHANCA) database and the Danish Pathology Databank, 2000-2010. Patients were treated according to national guidelines (radiotherapy +/- concomitant cisplatin). All specimens were analysed using HPV DNA PCR and p16 immunohistochemistry. Clinical information was retrieved from the DAHANCA database and the Danish National Patient Registry. Information on vital status was obtained from the Danish Civil Registration System. We observed improved OS for HPV+/p16+ BSCCs compared to HPV-/p16- (hazard ratio for death [HR], 0.15; 95% CI, 0.09-0.24). Among STSCCs, HPV+/p16+ showed the lowest HR (0.19, 95% CI, 0.13-0.29); whereas, HPV-/p16+ showed an intermediate HR (0.39; 95% CI, 0.22-0.70). For NSTSCCs, HPV+/p16+ and HPV-/p16+ showed similar OS (HRs, 0.39; 95% CI, 0.26-0.59; and 0.48; 95% CI, 0.24-0.95, respectively). Combined HPV+/p16+ was a significantly better prognostic marker in BSCCs and STSCCs than HPV DNA and p16, alone (all p-values p16 (p = 0.53), alone. In conclusion, double positivity for HPV/p16 in conjunction with the certainty of tumour site improved prognosis.

  3. Sequence-specific binding of recombinant Zbed4 to DNA: insights into Zbed4 participation in gene transcription and its association with other proteins.

    Science.gov (United States)

    Mokhonov, Vladislav V; Theendakara, Veena P; Gribanova, Yekaterina E; Ahmedli, Novruz B; Farber, Debora B

    2012-01-01

    Zbed4, a member of the BED subclass of Zinc-finger proteins, is expressed in cone photoreceptors and glial Müller cells of human retina whereas it is only present in Müller cells of mouse retina. To characterize structural and functional properties of Zbed4, enough amounts of purified protein were needed. Thus, recombinant Zbed4 was expressed in E. coli and its refolding conditions optimized for the production of homogenous and functionally active protein. Zbed4's secondary structure, determined by circular dichroism spectroscopy, showed that this protein contains 32% α-helices, 18% β-sheets, 20% turns and 30% unordered structures. CASTing was used to identify the target sites of Zbed4 in DNA. The majority of the DNA fragments obtained contained poly-Gs and some of them had, in addition, the core signature of GC boxes; a few clones had only GC-boxes. With electrophoretic mobility shift assays we demonstrated that Zbed4 binds both not only to DNA and but also to RNA oligonucleotides with very high affinity, interacting with poly-G tracts that have a minimum of 5 Gs; its binding to and GC-box consensus sequences. However, the latter binding depends on the GC-box flanking nucleotides. We also found that Zbed4 interacts in Y79 retinoblastoma cells with nuclear and cytoplasmic proteins Scaffold Attachment Factor B1 (SAFB1), estrogen receptor alpha (ERα), and cellular myosin 9 (MYH9), as shown with immunoprecipitation and mass spectrometry studies as well as gel overlay assays. In addition, immunostaining corroborated the co-localization of Zbed4 with these proteins. Most importantly, in vitro experiments using constructs containing promoters of genes directing expression of the luciferase gene, showed that Zbed4 transactivates the transcription of those promoters with poly-G tracts.

  4. Cysteine Mutational Studies Provide Insight into a Thiol-Based Redox Switch Mechanism of Metal and DNA Binding in FurA from Anabaena sp. PCC 7120

    OpenAIRE

    Botello-Morte, Laura; Pellicer, Silvia; Sein-Echaluce, Violeta C.; Contreras, Lellys M.; Neira, José Luis; Abián, Olga; Velázquez-Campoy, Adrián; Peleato, María Luisa; Fillat, María F; Bes, María Teresa

    2016-01-01

    Aims: The ferric uptake regulator (Fur) is the main transcriptional regulator of genes involved in iron homeostasis in most prokaryotes. FurA from Anabaena sp. PCC 7120 contains five cysteine residues, four of them arranged in two redox-active CXXC motifs. The protein needs not only metal but also reducing conditions to remain fully active in vitro. Through a mutational study of the cysteine residues present in FurA, we have investigated their involvement in metal and DNA binding. Results: Re...

  5. The GC-Rich Mitochondrial and Plastid Genomes of the Green Alga Coccomyxa Give Insight into the Evolution of Organelle DNA Nucleotide Landscape

    Energy Technology Data Exchange (ETDEWEB)

    Smith, David Roy; Burki, Fabien; Yamada, Takashi; Grimwood, Jane; Grigoriev, Igor V.; Van Etten, James L.; Keeling, Patrick J.

    2011-05-13

    Most of the available mitochondrial and plastid genome sequences are biased towards adenine and thymine (AT) over guanine and cytosine (GC). Examples of GC-rich organelle DNAs are limited to a small but eclectic list of species, including certain green algae. Here, to gain insight in the evolution of organelle nucleotide landscape, we present the GC-rich mitochondrial and plastid DNAs from the trebouxiophyte green alga Coccomyxa sp. C-169. We compare these sequences with other GC-rich organelle DNAs and argue that the forces biasing them towards G and C are nonadaptive and linked to the metabolic and/or life history features of this species. The Coccomyxa organelle genomes are also used for phylogenetic analyses, which highlight the complexities in trying to resolve the interrelationships among the core chlorophyte green algae, but ultimately favour a sister relationship between the Ulvophyceae and Chlorophyceae, with the Trebouxiophyceae branching at the base of the chlorophyte crown.

  6. Insights into the initiation of JC virus DNA replication derived from the crystal structure of the T-antigen origin binding domain.

    Directory of Open Access Journals (Sweden)

    Gretchen Meinke

    2014-02-01

    Full Text Available JC virus is a member of the Polyomavirus family of DNA tumor viruses and the causative agent of progressive multifocal leukoencephalopathy (PML. PML is a disease that occurs primarily in people who are immunocompromised and is usually fatal. As with other Polyomavirus family members, the replication of JC virus (JCV DNA is dependent upon the virally encoded protein T-antigen. To further our understanding of JCV replication, we have determined the crystal structure of the origin-binding domain (OBD of JCV T-antigen. This structure provides the first molecular understanding of JCV T-ag replication functions; for example, it suggests how the JCV T-ag OBD site-specifically binds to the major groove of GAGGC sequences in the origin. Furthermore, these studies suggest how the JCV OBDs interact during subsequent oligomerization events. We also report that the OBD contains a novel "pocket"; which sequesters the A1 & B2 loops of neighboring molecules. Mutagenesis of a residue in the pocket associated with the JCV T-ag OBD interfered with viral replication. Finally, we report that relative to the SV40 OBD, the surface of the JCV OBD contains one hemisphere that is highly conserved and one that is highly variable.

  7. Ancient mtDNA analysis of early 16(th century Caribbean cattle provides insight into founding populations of New World creole cattle breeds.

    Directory of Open Access Journals (Sweden)

    Camilla F Speller

    Full Text Available The Columbian Exchange resulted in a widespread movement of humans, plants and animals between the Old and New Worlds. The late 15(th to early 16(th century transfer of cattle from the Iberian Peninsula and Canary Islands to the Caribbean laid the foundation for the development of American creole cattle (Bos taurus breeds. Genetic analyses of modern cattle from the Americas reveal a mixed ancestry of European, African and Indian origins. Recent debate in the genetic literature centers on the 'African' haplogroup T1 and its subhaplogroups, alternatively tying their origins to the initial Spanish herds, and/or from subsequent movements of taurine cattle through the African slave trade. We examine this problem through ancient DNA analysis of early 16(th century cattle bone from Sevilla la Nueva, the first Spanish colony in Jamaica. In spite of poor DNA preservation, both T3 and T1 haplogroups were identified in the cattle remains, confirming the presence of T1 in the earliest Spanish herds. The absence, however, of "African-derived American" haplotypes (AA/T1c1a1 in the Sevilla la Nueva sample, leaves open the origins of this sub-haplogroup in contemporary Caribbean cattle.

  8. SUMO-1 possesses DNA binding activity

    Directory of Open Access Journals (Sweden)

    Wieruszeski Jean-Michel

    2010-05-01

    Full Text Available Abstract Background Conjugation of small ubiquitin-related modifiers (SUMOs is a frequent post-translational modification of proteins. SUMOs can also temporally associate with protein-targets via SUMO binding motifs (SBMs. Protein sumoylation has been identified as an important regulatory mechanism especially in the regulation of transcription and the maintenance of genome stability. The precise molecular mechanisms by which SUMO conjugation and association act are, however, not understood. Findings Using NMR spectroscopy and protein-DNA cross-linking experiments, we demonstrate here that SUMO-1 can specifically interact with dsDNA in a sequence-independent fashion. We also show that SUMO-1 binding to DNA can compete with other protein-DNA interactions at the example of the regulatory domain of Thymine-DNA Glycosylase and, based on these competition studies, estimate the DNA binding constant of SUMO1 in the range 1 mM. Conclusion This finding provides an important insight into how SUMO-1 might exert its activity. SUMO-1 might play a general role in destabilizing DNA bound protein complexes thereby operating in a bottle-opener way of fashion, explaining its pivotal role in regulating the activity of many central transcription and DNA repair complexes.

  9. A long-standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope

    DEFF Research Database (Denmark)

    Lorenzen, Eline; Masembe, Charles; Arctander, Peter;

    2010-01-01

    East Africa could result from colonization following extinction from the region. Only two other dated African ungulate phylogenies have been published, applying different methods, and the similarity of dates obtained from the three distinct approaches indicates a significant event c. 200 ka, which left....... Phylogeographic analysis of the common eland antelope, Taurotragus oryx (Bovidae), was used to assess these hypotheses and the existence of genetic signatures of Pleistocene climate change. Location The sub-Saharan savanna biome of East and southern Africa. Methods Mitochondrial DNA control-region fragments (414......-based methods and a calibrated fossil root of 1.6 Ma for the split between the common eland and the giant eland, Taurotragus derbianus. Results Two major phylogeographic lineages comprising East and southern African localities, respectively, were separated by a net nucleotide distance of 4.7%. A third...

  10. A new phylogeny and environmental DNA insight into paramyxids: an increasingly important but enigmatic clade of protistan parasites of marine invertebrates.

    Science.gov (United States)

    Ward, Georgia M; Bennett, Martyn; Bateman, Kelly; Stentiford, Grant D; Kerr, Rose; Feist, Stephen W; Williams, Suzanne T; Berney, Cedric; Bass, David

    2016-09-01

    Paramyxida is an order of rhizarian protists that parasitise marine molluscs, annelids and crustaceans. They include notifiable pathogens (Marteilia spp.) of bivalves and other taxa of economic significance for shellfish production. The diversity of paramyxids is poorly known, particularly outside of commercially important hosts, and their phylogenetic position is unclear due to their extremely divergent 18S rDNA sequences. However, novel paramyxean lineages are increasingly being detected in a wide range of invertebrate hosts, and interest in the group is growing, marked by the first 'Paramyxean Working Group' Meeting held in Spain in February 2015. We review the diversity, host affiliations, and geographical ranges of all known paramyxids, present a comprehensive phylogeny of the order and clarify its taxonomy. Our phylogenetic analyses confirm the separate status of four genera: Paramarteilia, Marteilioides, Paramyxa and Marteilia. Further, as including M. granula in Marteilia would make the genus paraphyletic we suggest transferring this species to a new genus, Eomarteilia. We present sequence data for Paramyxa nephtys comb. n., a parasite of polychaete worms, providing morphological data for a clade of otherwise environmental sequences, sister to Marteilioides. Light and electron microscopy analyses show strong similarities with both Paramyxa and Paramyxoides, and we further discuss the validity of those two genera. We provide histological and electron microscopic data for Paramarteilia orchestiae, the type species of that genus originally described from the amphipod Orchestia; in situ hybridisation shows that Paramarteilia also infects crab species. We present, to our knowledge, the first known results of a paramyxid-specific environmental DNA survey of environmental (filtered water, sediment, etc.) and organismally-derived samples, revealing new lineages and showing that paramyxids are associated with a wider range of hosts and habitat types than previously

  11. Study of criteria influencing the success rate of DNA swabs in operational conditions: A contribution to an evidence-based approach to crime scene investigation and triage.

    Science.gov (United States)

    Baechler, S

    2016-01-01

    DNA is nowadays swabbed routinely to investigate serious and volume crimes, but research remains scarce when it comes to determining the criteria that may impact the success rate of DNA swabs taken on different surfaces and situations. To investigate these criteria in fully operational conditions, DNA analysis results of 4772 swabs taken by the forensic unit of a police department in Western Switzerland over a 2.5-year period (2012-2014) in volume crime cases were considered. A representative and random sample of 1236 swab analyses was extensively examined and codified, describing several criteria such as whether the swabbing was performed at the scene or in the lab, the zone of the scene where it was performed, the kind of object or surface that was swabbed, whether the target specimen was a touch surface or a biological fluid, and whether the swab targeted a single surface or combined different surfaces. The impact of each criterion and of their combination was assessed in regard to the success rate of DNA analysis, measured through the quality of the resulting profile, and whether the profile resulted in a hit in the national database or not. Results show that some situations-such as swabs taken on door and window handles for instance-have a higher success rate than average swabs. Conversely, other situations lead to a marked decrease in the success rate, which should discourage further analyses of such swabs. Results also confirm that targeting a DNA swab on a single surface is preferable to swabbing different surfaces with the intent to aggregate cells deposited by the offender. Such results assist in predicting the chance that the analysis of a swab taken in a given situation will lead to a positive result. The study could therefore inform an evidence-based approach to decision-making at the crime scene (what to swab or not) and at the triage step (what to analyse or not), contributing thus to save resource and increase the efficiency of forensic science

  12. Pathogen quantitation in complex matrices: a multi-operator comparison of DNA extraction methods with a novel assessment of PCR inhibition.

    Directory of Open Access Journals (Sweden)

    Alessandra Pontiroli

    Full Text Available BACKGROUND: Mycobacterium bovis is the aetiological agent of bovine tuberculosis (bTB, an important recrudescent zoonosis, significantly increasing in British herds in recent years. Wildlife reservoirs have been identified for this disease but the mode of transmission to cattle remains unclear. There is evidence that viable M. bovis cells can survive in soil and faeces for over a year. METHODOLOGY/PRINCIPAL FINDINGS: We report a multi-operator blinded trial for a rigorous comparison of five DNA extraction methods from a variety of soil and faecal samples to assess recovery of M. bovis via real-time PCR detection. The methods included four commercial kits: the QIAamp Stool Mini kit with a pre-treatment step, the FastDNA® Spin kit, the UltraClean™ and PowerSoil™ soil kits and a published manual method based on phenol:chloroform purification, termed Griffiths. M. bovis BCG Pasteur spiked samples were extracted by four operators and evaluated using a specific real-time PCR assay. A novel inhibition control assay was used alongside spectrophotometric ratios to monitor the level of inhibitory compounds affecting PCR, DNA yield, and purity. There were statistically significant differences in M. bovis detection between methods of extraction and types of environmental samples; no significant differences were observed between operators. Processing times and costs were also evaluated. To improve M. bovis detection further, the two best performing methods, FastDNA® Spin kit and Griffiths, were optimised and the ABI TaqMan environmental PCR Master mix was adopted, leading to improved sensitivities. CONCLUSIONS: M. bovis was successfully detected in all environmental samples; DNA extraction using FastDNA® Spin kit was the most sensitive method with highest recoveries from all soil types tested. For troublesome faecal samples, we have used and recommend an improved assay based on a reduced volume, resulting in detection limits of 4.25×10(5 cells g(-1

  13. Geophysical and magneto-structural study of the Maâdna structure (Talemzane, Algeria): Insights on its age and origin

    Science.gov (United States)

    Lamali, A.; Rochette, P.; Merabet, N.; Abtout, A.; Maouche, S.; Gattacceca, J.; Ferrière, L.; Hamoudi, M.; Meziane, E. H.; Ayache, M.

    2016-12-01

    The Maâdna structure is located approximately 400 km south of Algiers (33°19' N, 4°19' E) and emplaced in Upper-Cretaceous to Eocene limestones. Although accepted as an impact crater on the basis of alleged observations of shock-diagnostic features such as planar deformation features (PDFs) in quartz grains, previous works were limited and further studies are desirable to ascertain the structure formation process and its age. For this purpose, the crater was investigated using a multidisciplinary approach including field observations, detailed cartography of the different geological and structural units, geophysical surveys, anisotropy of magnetic susceptibility, paleomagnetism, and petrography of the collected samples. We found that the magnetic and gravimetric profiles highlight a succession of positive and negative anomalies, ones that might indicate the occurrence of a causative material which is at least in part identical. Geophysical analysis and modeling suggest the presence of this material within the crater at a depth of about 100 m below the surface. Using soil magnetic susceptibility measurements, the shallowest magnetized zone in the central part of the crater is identified as a recently deposited material. Paleomagnetic and rock magnetic experiments combined with petrographic observations show that detrital hematite is the main magnetic carrier although often associated with magnetite. A primary magnetization is inferred from a stable remanence with both normal and reverse directions, carried by these two minerals. Although this is supposed to be a chemical remagnetization, its normal polarity nature is considered to be a Pliocene component, subsequent to the crater formation. The pole falls onto the Miocene-Pliocene part of the African Apparent Polar Wander Path (APWP). Consequently, we estimate the formation of the Maâdna crater to have occurred during the time period extending from the Late Miocene to the Early Pliocene. Unfortunately, our field

  14. Analysis of pigmented villonodular synovitis with genome-wide complementary DNA microarray and tissue array technology reveals insight into potential novel therapeutic approaches.

    Science.gov (United States)

    Finis, Katharina; Sültmann, Holger; Ruschhaupt, Markus; Buness, Andreas; Helmchen, Birgit; Kuner, Ruprecht; Gross, Marie-Luise; Fink, Bernd; Schirmacher, Peter; Poustka, Annemarie; Berger, Irina

    2006-03-01

    To characterize the gene expression profile and determine potential diagnostic markers and therapeutic targets in pigmented villonodular synovitis (PVNS). Gene expression patterns in 11 patients with PVNS, 18 patients with rheumatoid arthritis (RA), and 19 patients with osteoarthritis (OA) were investigated using genome-wide complementary DNA microarrays. Validation of differentially expressed genes was performed by real-time quantitative polymerase chain reaction and immunohistochemical analysis on tissue arrays (80 patients with PVNS, 51 patients with RA, and 20 patients with OA). The gene expression profile in PVNS was clearly distinct from those in RA and OA. One hundred forty-one up-regulated genes and 47 down-regulated genes were found in PVNS compared with RA, and 153 up-regulated genes and 89 down-regulated genes were found in PVNS compared with OA (fold change > or = 1.5; Q PVNS were involved in apoptosis regulation, matrix degradation, and inflammation (ALOX5AP, ATP6V1B2, CD53, CHI3L1, CTSL, CXCR4, HSPA8, HSPCA, LAPTM5, MMP9, MOAP1, and SPP1). The gene expression signature in PVNS is similar to that of activated macrophages and is consistent with the local destructive course of the disease. The gene and protein expression patterns suggest that the ongoing proliferation in PVNS is sustained by apoptosis resistance. This result suggests the possibility of a potential novel therapeutic intervention against PVNS.

  15. West Eurasian mtDNA lineages in India: an insight into the spread of the Dravidian language and the origins of the caste system.

    Science.gov (United States)

    Palanichamy, Malliya Gounder; Mitra, Bikash; Zhang, Cai-Ling; Debnath, Monojit; Li, Gui-Mei; Wang, Hua-Wei; Agrawal, Suraksha; Chaudhuri, Tapas Kumar; Zhang, Ya-Ping

    2015-06-01

    There is no indication from the previous mtDNA studies that west Eurasian-specific subclades have evolved within India and played a role in the spread of languages and the origins of the caste system. To address these issues, we have screened 14,198 individuals (4208 from this study) and analyzed 112 mitogenomes (41 new sequences) to trace west Eurasian maternal ancestry. This has led to the identification of two autochthonous subhaplogroups--HV14a1 and U1a1a4, which are likely to have originated in the Dravidian-speaking populations approximately 10.5-17.9 thousand years ago (kya). The carriers of these maternal lineages might have settled in South India during the time of the spread of the Dravidian language. In addition to this, we have identified several subsets of autochthonous U7 lineages, including U7a1, U7a2b, U7a3, U7a6, U7a7, and U7c, which seem to have originated particularly in the higher-ranked caste populations in relatively recent times (2.6-8.0 kya with an average of 5.7 kya). These lineages have provided crucial clues to the differentiation of the caste system that has occurred during the recent past and possibly, this might have been influenced by the Indo-Aryan migration. The remaining west Eurasian lineages observed in the higher-ranked caste groups, like the Brahmins, were found to cluster with populations who possibly arrived from west Asia during more recent times.

  16. Consumer Insights

    Institute of Scientific and Technical Information of China (English)

    JANKOT

    2004-01-01

    Fang Jun, the head of consumer and market insights of Unilever Shanghai, has summarized his early life as a market in two sentences: rush about to study market changes;act all day to observe consumer behavior. And now?"Tell stories, conduct interviews and piece together different data; calculate numbers,build models and write reports."

  17. On the origins of the tetraploid Bromus species (section Bromus, Poaceae): insights from internal transcribed spacer sequences of nuclear ribosomal DNA.

    Science.gov (United States)

    Ainouche, M L; Bayer, R J

    1997-10-01

    The internal transcribed spacer (ITS) region of nuclear ribosomal DNA from 22 diploid and tetraploid annual Bromus species of section Bromus (Poaceae) and three species belonging to other Bromus sections, Bromus catharticus (section Ceratochloa), Bromus anomalus (section Pnigma), and Bromus sterilis (section Genea), were investigated by PCR amplification and direct sequencing. The length of the ITS-1 region varied from 215 to 218 bp, and that of the ITS-2 region from 215 to 216 bp, in the species analyzed. ITS-1 was more variable and provided more informative sites (49) than ITS-2 (32). No variation was encountered within species. In pairwise comparison among species of section Bromus, sequence divergence ranged from 0.0 to 8.0% for the combined ITS-1 and ITS-2 regions. Parsimony analysis using Avena longiglumis and Hordeum vulgare as outgroups resulted in well-resolved phylogenetic trees and showed that section Bromus is monophyletic according to the species analyzed outside of the section. The analysis clarified the phylogenetic relationships among monogenomic (diploid) species. Introduction of the allotetraploid species did not change the general topology of the trees obtained using only the diploid species. Although some tetraploid-diploid species relationships will have to be clarified with faster evolving markers, the ITS sequences are shown to be useful for assessing evolutionary relationships among closely related Bromus species, as well as for clarifying taxonomic problems in previously controversial cases (e.g., Bromus alopecuros and Bromus caroli-henrici). New hypotheses are proposed concerning the origin of several allotetraploid species. For example, it is shown that the tetraploid Bromus hordeaceus diverged earlier than all other species of section Bromus, excluding the diploid B. caroli-henrici, which is found to be basal in this group. The tetraploid Bromus arenarius, which was considered a hybrid between sections Bromus and Genea, and the

  18. Insights into the Genetic Relationships and Breeding Patterns of the African Tea Germplasm Based on nSSR Markers and cpDNA Sequences.

    Science.gov (United States)

    Wambulwa, Moses C; Meegahakumbura, Muditha K; Kamunya, Samson; Muchugi, Alice; Möller, Michael; Liu, Jie; Xu, Jian-Chu; Ranjitkar, Sailesh; Li, De-Zhu; Gao, Lian-Ming

    2016-01-01

    Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (H S) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study represents

  19. The Effect of Different Operations Modes on Science Capabilities During the 2010 Desert-RATS Test: Insights from the Geologist Crewmembers

    Science.gov (United States)

    Bleacher, Jacob E.; Hurtado, Jose M., Jr.; Young, Kelsey E.; Rice, James W., Jr.; Garry, W. Brent

    2011-01-01

    The 2010 Desert RATS field test utilized two Space Exploration Vehicles (prototype planetary rovers) and four crewmembers (2 per rover) to conduct a geologic traverse across northern Arizona while testing continuous and twice-per-day communications paired with operation modes of separating and exploring individually (Divide & Conquer) and exploring together (Lead & Follow), respectively. This report provides qualitative conclusions from the geologist crewmembers involved in this test as to how these modes of communications and operations affected our ability to conduct field geology. Each mode of communication and operation provided beneficial capabilities that might be further explored for future Human Spaceflight Missions to other solar system objects. We find that more frequent interactions between crews and an Apollo-style Science Team on the Earth best enables scientific progress during human exploration. However, during multiple vehicle missions, this communication with an Earth-based team of scientists, who represent "more minds on the problem", should not come at the exclusion of (or significantly decrease) communication between the crewmembers in different vehicles who have the "eyes on the ground". Inter-crew communications improved when discussions with a backroom were infrequent. Both aspects are critical and cannot be mutually exclusive. Increased vehicle separation distances best enable encounters with multiple geologic units. However, seemingly redundant visits by multiple vehicles to the same feature can be utilized to provide improved process-related observations about the development and modification of the local terrain. We consider the value of data management, transfer, and accessibility to be the most important lesson learned. Crews and backrooms should have access to all data and related interpretations within the mission in as close to real-time conditions as possible. This ensures that while on another planetary surface, crewmembers are as

  20. Insights into the relationships of Palearctic and Nearctic lymnaeids (Mollusca : Gastropoda by rDNA ITS-2 sequencing and phylogeny of stagnicoline intermediate host species of Fasciola hepatica

    Directory of Open Access Journals (Sweden)

    Bargues M.D.

    2003-09-01

    Full Text Available Fascioliasis by Fasciola hepatica is the vector-borne disease presenting the widest latitudinal, longitudinal and altitudinal distribution known. F. hepatica shows a great adaptation power to new environmental conditions which is the consequence of its own capacities together with the adaptation and colonization abilities of its specific vector hosts, freshwater snails of the family Lymnaeidae. Several lymnaeid species only considered as secondary contributors to the liver fluke transmission have, however, played a very important role in the geographic expansion of this disease. Many of them belong to the so-called "stagnicoline" type group. Stagnicolines have, therefore, a very important applied interest in the Holarctic region, to which they are geographically restricted. The present knowledge on the genetics of stagnicolines and on their parasite-host interrelationships is, however, far from being sufficient. The present paper analyses the relationships between Palaearctic and Nearctic stagnicoline species on the base of the new light furnished by the results obtained in nuclear rDNA ITS-2 sequencing and corresponding phylogenetic studies of the lymnaeid taxa Lymnaea (Stagnicola occulta, L. (S. palustris palustris (topotype specimens and L.(S. p. turricula from Europe. Natural infections with F. hepatica have been reported in all of them. Surprisingly, ITS-2 length and G C content of L. occulta were similar and perfectly fitted within the respective ranges known in North American stagnicolines. Nucleotide differences and genetic distances were higher between L. occulta and the other European stagnicolines than between L. occulta and the North American ones. The ITS-2 sequence of L. p. turricula from Poland differed from the other genotypes known from turricula in Europe. The phylogenetic trees using the maximum-parsimony, distance and maximum-likelihood methods confirmed (i the inclusion of L. occulta in the branch of North American

  1. Soft X-ray imaging and spectromicroscopy: new insights in chemical state and morphology of the key components in operating fuel-cells.

    Science.gov (United States)

    Bozzini, Benedetto; Abyaneh, Majid Kazemian; Amati, Matteo; Gianoncelli, Alessandra; Gregoratti, Luca; Kaulich, Burkhard; Kiskinova, Maya

    2012-08-13

    Fuel cells are one of the most appealing environmentally friendly devices for the effective conversion of chemical energy into electricity and heat, but still there are key barriers to their broad commercialization. In addition to efficiency, a major challenge of fuel-cell technology is the durability of the key components (interconnects, electrodes, and electrolytes) that can be subject to corrosion or undesired morphology and chemical changes occurring under operating conditions. The complementary capabilities of synchrotron-based soft X-ray microscopes in terms of imaging, spectroscopy, spatial and time resolution, and variable probing depths are opening unique opportunities to shed light on the multiple processes occurring in these complex systems at microscopic length scales. This type of information is prerequisite for understanding and controlling the performance and durability of such devices. This paper reviews the most recent efforts in the implementation of these methods for exploring the evolving structure and chemical composition of some key fuel cell components. Recent achievements are illustrated by selected results obtained with simplified versions of proton-exchange fuel-cells (PEFC) and solid-oxide fuel-cells (SOFC), which allow in situ monitoring of the redox reactions resulting in: 1) undesired deposits at interconnects and electrodes (PEFC); 2) material interactions at the electrode-electrolyte interface (PEFC); 3) release of corrosion products to the electrolyte phase (PEFC, and 4) mass-transport processes and structural changes occurring at the high operation temperatures of SOFC and promoted by the polarization.

  2. Insights on the High-Temperature Operational Limits of ZrO2-Y2O3 TBCs Manufactured via Air Plasma Spray

    Science.gov (United States)

    Lima, Rogerio S.; Marple, Basil R.

    2017-02-01

    The effective high-temperature operation limit of a ZrO2-7-8 wt.%Y2O3 (YSZ) thermal barrier coating (TBC) manufactured via air plasma spray (APS) is considered to be 1300 °C. This is related to the metastable tetragonal t'-phase formed during the rapid quenching of the YSZ particles during spraying. The t'-phase transforms into the equilibrium tetragonal and cubic phases at temperatures ≥ 1300 °C, which can lead to the formation of the monoclinic phase of YSZ upon cooling to room temperature. This formation of the monoclinic phase is accompanied by a volume expansion that leads to TBC failure due to extensive micro-cracking. To further investigate this limitation, an APS YSZ TBC was sprayed on a CMSX-4 substrate. By using a thermal (laser) gradient cyclic testing, a temperature gradient was generated across the TBC/substrate system. The YSZ T-front and substrate backside T-back temperature levels were 1500 and 1000 °C, respectively. In cycle conditions (5-min or 1-h hot and 2-min cool), no TBC failure has been observed. This behavior was partially attributed to the unexpected absence of the monoclinic phase of the YSZ in the cycled coatings. Although preliminary, these results are promising regarding increasing the effective high-temperature operational limits of APS YSZ TBCs.

  3. Biogenic hydrogen conversion of de-oiled jatropha waste via anaerobic sequencing batch reactor operation: process performance, microbial insights, and CO2 reduction efficiency.

    Science.gov (United States)

    Kumar, Gopalakrishnan; Lin, Chiu-Yue

    2014-01-01

    We report the semicontinuous, direct (anaerobic sequencing batch reactor operation) hydrogen fermentation of de-oiled jatropha waste (DJW). The effect of hydraulic retention time (HRT) was studied and results show that the stable and peak hydrogen production rate of 1.48 L/L ∗ d and hydrogen yield of 8.7 mL H2/g volatile solid added were attained when the reactor was operated at HRT 2 days (d) with a DJW concentration of 200 g/L, temperature 55 °C, and pH 6.5. Reduced HRT enhanced the production performance until 1.75 d. Further reduction has lowered the process efficiency in terms of biogas production and hydrogen gas content. The effluent from hydrogen fermentor was utilized for methane fermentation in batch reactors using pig slurry and cow dung as seed sources. The results revealed that pig slurry was a feasible seed source for methane generation. Peak methane production rate of 0.43 L CH4/L ∗ d and methane yield of 20.5 mL CH4/g COD were observed at substrate concentration of 10 g COD/L, temperature 30 °C, and pH 7.0. PCR-DGGE analysis revealed that combination of cellulolytic and fermentative bacteria were present in the hydrogen producing ASBR.

  4. Biogenic Hydrogen Conversion of De-Oiled Jatropha Waste via Anaerobic Sequencing Batch Reactor Operation: Process Performance, Microbial Insights, and CO2 Reduction Efficiency

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Kumar

    2014-01-01

    Full Text Available We report the semicontinuous, direct (anaerobic sequencing batch reactor operation hydrogen fermentation of de-oiled jatropha waste (DJW. The effect of hydraulic retention time (HRT was studied and results show that the stable and peak hydrogen production rate of 1.48 L/L*d and hydrogen yield of 8.7 mL H2/g volatile solid added were attained when the reactor was operated at HRT 2 days (d with a DJW concentration of 200 g/L, temperature 55°C, and pH 6.5. Reduced HRT enhanced the production performance until 1.75 d. Further reduction has lowered the process efficiency in terms of biogas production and hydrogen gas content. The effluent from hydrogen fermentor was utilized for methane fermentation in batch reactors using pig slurry and cow dung as seed sources. The results revealed that pig slurry was a feasible seed source for methane generation. Peak methane production rate of 0.43 L CH4/L*d and methane yield of 20.5 mL CH4/g COD were observed at substrate concentration of 10 g COD/L, temperature 30°C, and pH 7.0. PCR-DGGE analysis revealed that combination of celluloytic and fermentative bacteria were present in the hydrogen producing ASBR.

  5. Hindering the strand passage reaction of human topoisomerase IIalpha without disturbing DNA cleavage, ATP hydrolysis, or the operation of the N-terminal clamp

    DEFF Research Database (Denmark)

    Oestergaard, Vibe H; Giangiacomo, Laura; Bjergbaek, Lotte

    2004-01-01

    , the enzyme fails to decatenate and relax DNA, even though it is fully capable of ATP hydrolysis, closure of the N-terminal clamp, and DNA cleavage. The cleavage activity is increased, suggesting that the transducer domain has a role in regulating DNA cleavage. Furthermore, the enzyme has retained a tendency...... to increase DNA cleavage upon nucleotide binding and also responds to DNA with elevated ATP hydrolysis. However, the DNA-mediated increase in ATP hydrolysis is lower than that obtained with the wild-type enzyme but similar to that of a cleavage-deficient topoisomerase IIalpha enzyme. Our results strongly...... suggest that the strand passage event is required for efficient DNA stimulation of topoisomerase II-mediated ATP hydrolysis, whereas the stimulation occurs independent of the DNA cleavage reaction per se. A comparison of the strand passage deficient-enzyme described here and the cleavage-deficient enzyme...

  6. Comparing the role of selective and divided attention in the composite face effect: Insights from Attention Operating Characteristic (AOC) plots and cross-contingency correlations.

    Science.gov (United States)

    Fitousi, Daniel

    2016-03-01

    Composite faces combine the top half of one face with the bottom half of another to create a compelling illusion of a new face. Evidence for holistic processing with composite faces comes primarily from a matching procedure in a selective attention task. In the present study, a dual-task approach has been employed to study whether composite faces reflect genuine holistic (i.e., fusion of parts) or non-holistic processing strategies (i.e., switching, resource sharing). This has been accomplished by applying the Attention Operation Characteristic methodology (AOC, Sperling & Melchner, 1978a, 1978b) and cross-contingency correlations (Bonnel & Prinzmetal, 1998) to composite faces. Overall, the results converged on the following conclusions: (a) observers can voluntarily allocate differential amounts of attention to the top and bottom parts in both spatially aligned and misaligned composite faces, (b) the interaction between composite face halves is due to attentional limitations, not due to switching or fusion strategies, and (c) the processing of aligned and misaligned composite faces is quantitatively and qualitatively similar. Taken together, these results challenge the holistic interpretation of the composite face illusion.

  7. Left-handed DNA crossovers. Implications for DNA-DNA recognition and structural alterations.

    Science.gov (United States)

    Timsit, Y; Shatzky-Schwartz, M; Shakked, Z

    1999-02-01

    The close approach of DNA segments participates in many biological functions including DNA condensation and DNA processing. Previous crystallographic studies have shown that B-DNA self-fitting by mutual groove-backbone interaction produces right-handed DNA crossovers. These structures have opened new perspectives on the role of close DNA-DNA interactions in the architecture and activity the DNA molecule. In the present study, the analysis of the crystal packing of two B-DNA decamer duplexes d(CCIIICCCGG) and d(CCGCCGGCGG) reveals the existence of new modes of DNA crossing. Symmetric left-handed crossovers are produced by mutual fitting of DNA grooves at the crossing point. New sequence patterns contribute to stabilize longitudinal fitting of the sugar-phosphate backbone into the major groove. In addition, the close approach of DNA segments greatly influences the DNA conformation in a sequence dependent manner. This study provides new insights into the role of DNA sequence and structure in DNA-DNA recognition. In providing detailed molecular views of DNA crossovers of opposite chirality, this study can also help to elucidate the role of symmetry and chirality in the recognition of complex DNA structures by protein dimers or tetramers, such as topoisomerase II and recombinase enzymes. These results are discussed in the context of the possible relationships between DNA condensation and DNA processing.

  8. The Escherichia coli metallo-regulator RcnR represses rcnA and rcnR transcription through binding on a shared operator site: Insights into regulatory specificity towards nickel and cobalt.

    Science.gov (United States)

    Blaha, Didier; Arous, Safia; Blériot, Camille; Dorel, Corinne; Mandrand-Berthelot, Marie-Andrée; Rodrigue, Agnès

    2011-03-01

    RcnA is an efflux pump responsible for Ni and Co detoxification in Escherichia coli. The expression of rcnA is induced by Ni and Co via the metallo-regulator RcnR. In the present work, the functioning of the promoter-operator region of rcnR and rcnA was investigated using primer extension and DNAse I footprinting experiments. We show that the promoters of rcnR and rcnA are convergent and that apo-RcnR binds on symmetrically located sequences in this intergenic region. Moreover, RcnR DNA binding is specifically modulated by one Ni or Co equivalent and not by other metals. In addition to rcnA, RcnR controls expression of its own gene in response to Ni and Co, but the two genes are differentially expressed.

  9. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  10. DNA vaccines and intradermal vaccination by DNA tattooing.

    Science.gov (United States)

    Oosterhuis, K; van den Berg, J H; Schumacher, T N; Haanen, J B A G

    2012-01-01

    Over the past two decades, DNA vaccination has been developed as a method for the induction of immune responses. However, in spite of high expectations based on their efficacy in preclinical models, immunogenicity of first generation DNA vaccines in clinical trials was shown to be poor, and no DNA vaccines have yet been licensed for human use. In recent years significant progress has been made in the development of second generation DNA vaccines and DNA vaccine delivery methods. Here we review the key characteristics of DNA vaccines as compared to other vaccine platforms, and recent insights into the prerequisites for induction of immune responses by DNA vaccines will be discussed. We illustrate the development of second generation DNA vaccines with the description of DNA tattooing as a novel DNA delivery method. This technique has shown great promise both in a small animal model and in non-human primates and is currently under clinical evaluation.

  11. DNA topology and transcription

    Science.gov (United States)

    Kouzine, Fedor; Levens, David; Baranello, Laura

    2014-01-01

    Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions. PMID:24755522

  12. DNA topology and transcription.

    Science.gov (United States)

    Kouzine, Fedor; Levens, David; Baranello, Laura

    2014-01-01

    Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions.

  13. Authenticity in ancient DNA studies

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Willerslev, Eske

    2006-01-01

    Ancient DNA studies represent a powerful tool that can be used to obtain genetic insights into the past. However, despite the publication of large numbers of apparently successful ancient DNA studies, a number of problems exist with the field that are often ignored. Therefore, questions exist as ...

  14. Authenticity in ancient DNA studies

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Willerslev, Eske

    2006-01-01

    Ancient DNA studies represent a powerful tool that can be used to obtain genetic insights into the past. However, despite the publication of large numbers of apparently successful ancient DNA studies, a number of problems exist with the field that are often ignored. Therefore, questions exist as ...

  15. [Uracil-DNA glycosylases].

    Science.gov (United States)

    Pytel, Dariusz; Słupianek, Artur; Ksiazek, Dominika; Skórski, Tomasz; Błasiak, Janusz

    2008-01-01

    Uracil is one of four nitrogen bases, most frequently found in normal RNA. Uracyl can be found also in DNA as a result of enzymatic or non-enzymatic deamination of cytosine as well as misincorporation of dUMP instead of dTMP during DNA replication. Uracil from DNA can be removed by DNA repair enzymes with apirymidine site as an intermediate. However, if uracil is not removed from DNA a pair C:G in parental DNA can be changed into a T:A pair in the daughter DNA molecule. Therefore, uracil in DNA may lead to a mutation. Uracil in DNA, similarly to thymine, forms energetically most favorable hydrogen bonds with adenine, therefore uracil does not change the coding properties of DNA. Uracil in DNA is recognized by uracil DNA glycosylase (UDGs), which initiates DNA base excision repair, leading to removing of uracil from DNA and replacing it by thymine or cytosine, when arose as a result of cytosine deamination. Eukaryotes have at least four nuclear UDGs: UNG2, SMUG1, TDG i MBD4, while UNG1 operates in the mitochondrium. UNG2 is involved in DNA repair associated with DNA replication and interacts with PCNA and RPA proteins. Uracil can also be an intermediate product in the process of antigen-dependent antibody diversification in B lymphocytes. Enzymatic deamination of viral DNA by host cells can be a defense mechanism against viral infection, including HIV-1. UNG2, MBD4 and TDG glycosylases may cooperate with mismatch repair proteins and TDG can be involved in nucleotide excision repair system.

  16. New insights on the role of the gamma-herpesvirus uracil-DNA glycosylase leucine loop revealed by the structure of the Epstein-Barr virus enzyme in complex with an inhibitor protein.

    Science.gov (United States)

    Géoui, Thibault; Buisson, Marlyse; Tarbouriech, Nicolas; Burmeister, Wim Pascal

    2007-02-09

    Epstein-Barr virus (EBV) is a human gamma-herpesvirus. Within its 86 open reading frame containing genome, two enzymes avoiding uracil incorporation into DNA can be found: uracil triphosphate hydrolase and uracil-DNA glycosylase (UNG). The latter one excises uracil bases that are due to cytosine deamination or uracil misincorporation from double-stranded DNA substrates. The EBV enzyme belongs to family 1 UNGs. We solved the three-dimensional structure of EBV UNG in complex with the uracil-DNA glycosylase inhibitor protein (Ugi) from bacteriophage PBS-2 at a resolution of 2.3 A by X-ray crystallography. The structure of EBV UNG encoded by the BKRF3 reading frame shows the excellent global structural conservation within the solved examples of family 1 enzymes. Four out of the five catalytic motifs are completely conserved, whereas the fifth one, the leucine loop, carries a seven residue insertion. Despite this insertion, catalytic constants of EBV UNG are similar to those of other UNGs. Modelling of the EBV UNG-DNA complex shows that the longer leucine loop still contacts DNA and is likely to fulfil its role of DNA binding and deformation differently than the enzymes with previously solved structures. We could show that despite the evolutionary distance of EBV UNG from the natural host protein, bacteriophage Ugi binds with an inhibitory constant of 8 nM to UNG. This is due to an excellent specificity of Ugi for conserved elements of UNG, four of them corresponding to catalytic motifs and a fifth one corresponding to an important beta-turn structuring the catalytic site.

  17. DNA damage and carcinogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Stelow, R B

    1980-01-01

    Although cancer may arise as a result of many different types of molecular changes, there is little reason to doubt that changes to DNA are one of the more important ones in cancer initiation. Although DNA repair mechanisms seem able to eliminate a very large fraction of deleterious changes to DNA, we not only have little insight into the molecular mechanisms involved in such repair, but have a negligible amount of information to permit us to estimate the shape of dose response relations at low doses. The case of skin cancer is a special one, in that the average population is exposed to sufficient solar uv so that the effects of small increments in uv dose may be estimated. An approximate 85% reduction in DNA repair increases skin cancer incidence 10/sup 4/ fold.

  18. Operating room manager game

    NARCIS (Netherlands)

    Hans, Erwin W.; Nieberg, Tim

    2007-01-01

    The operating room (OR) department of a hospital forms the heart of the organization, where the single largest cost is incurred. This document presents and reports on the “Operating Room Manager Game,” developed to give insight into managing a large hospital's OR department at various levels of cont

  19. Kohler's Insight Revisited.

    Science.gov (United States)

    Windholtz, George

    1985-01-01

    Psychology textbooks frequently present Wolfgang Kohler's two-stick experiment with chimpanzees as having demonstrated insight in learning. Studies that replicated Kohler's work support his findings but not his interpretation in terms of insightful solution. The uncritical inclusion of Kohler's insight interpretation in texts is not warranted in…

  20. Duplication in DNA Sequences

    Science.gov (United States)

    Ito, Masami; Kari, Lila; Kincaid, Zachary; Seki, Shinnosuke

    The duplication and repeat-deletion operations are the basis of a formal language theoretic model of errors that can occur during DNA replication. During DNA replication, subsequences of a strand of DNA may be copied several times (resulting in duplications) or skipped (resulting in repeat-deletions). As formal language operations, iterated duplication and repeat-deletion of words and languages have been well studied in the literature. However, little is known about single-step duplications and repeat-deletions. In this paper, we investigate several properties of these operations, including closure properties of language families in the Chomsky hierarchy and equations involving these operations. We also make progress toward a characterization of regular languages that are generated by duplicating a regular language.

  1. A dnaN plasmid shuffle strain for rapid in vivo analysis of mutant Escherichia coli β clamps provides insight into the role of clamp in umuDC-mediated cold sensitivity.

    Directory of Open Access Journals (Sweden)

    Vignesh M P Babu

    Full Text Available The E. coli umuDC gene products participate in two temporally distinct roles: UmuD2C acts in a DNA damage checkpoint control, while UmuD'2C, also known as DNA polymerase V (Pol V, catalyzes replication past DNA lesions via a process termed translesion DNA synthesis. These different roles of the umuDC gene products are managed in part by the dnaN-encoded β sliding clamp protein. Co-overexpression of the β clamp and Pol V severely blocked E. coli growth at 30°C. We previously used a genetic assay that was independent of the ability of β clamp to support E. coli viability to isolate 8 mutant clamp proteins (βQ61K, βS107L, βD150N, βG157S, βV170M, βE202K, βM204K and βP363S that failed to block growth at 30°C when co-overexpressed with Pol V. It was unknown whether these mutant clamps were capable of supporting E. coli viability and normal umuDC functions in vivo. The goals of this study were to answer these questions. To this end, we developed a novel dnaN plasmid shuffle assay. Using this assay, βD150N and βP363S were unable to support E. coli viability. The remaining 6 mutant clamps, each of which supported viability, were indistinguishable from β+ with respect to umuDC functions in vivo. In light of these findings, we analyzed phenotypes of strains overexpressing either β clamp or Pol V alone. The strain overexpressing β+, but not those expressing mutant β clamps, displayed slowed growth irrespective of the incubation temperature. Moreover, growth of the Pol V-expressing strain was modestly slowed at 30°, but not 42°C. Taken together, these results suggest the mutant clamps were identified due to their inability to slow growth rather than an inability to interact with Pol V. They further suggest that cold sensitivity is due, at least in part, to the combination of their individual effects on growth at 30°C.

  2. A dnaN plasmid shuffle strain for rapid in vivo analysis of mutant Escherichia coli β clamps provides insight into the role of clamp in umuDC-mediated cold sensitivity.

    Science.gov (United States)

    Babu, Vignesh M P; Sutton, Mark D

    2014-01-01

    The E. coli umuDC gene products participate in two temporally distinct roles: UmuD2C acts in a DNA damage checkpoint control, while UmuD'2C, also known as DNA polymerase V (Pol V), catalyzes replication past DNA lesions via a process termed translesion DNA synthesis. These different roles of the umuDC gene products are managed in part by the dnaN-encoded β sliding clamp protein. Co-overexpression of the β clamp and Pol V severely blocked E. coli growth at 30°C. We previously used a genetic assay that was independent of the ability of β clamp to support E. coli viability to isolate 8 mutant clamp proteins (βQ61K, βS107L, βD150N, βG157S, βV170M, βE202K, βM204K and βP363S) that failed to block growth at 30°C when co-overexpressed with Pol V. It was unknown whether these mutant clamps were capable of supporting E. coli viability and normal umuDC functions in vivo. The goals of this study were to answer these questions. To this end, we developed a novel dnaN plasmid shuffle assay. Using this assay, βD150N and βP363S were unable to support E. coli viability. The remaining 6 mutant clamps, each of which supported viability, were indistinguishable from β+ with respect to umuDC functions in vivo. In light of these findings, we analyzed phenotypes of strains overexpressing either β clamp or Pol V alone. The strain overexpressing β+, but not those expressing mutant β clamps, displayed slowed growth irrespective of the incubation temperature. Moreover, growth of the Pol V-expressing strain was modestly slowed at 30°, but not 42°C. Taken together, these results suggest the mutant clamps were identified due to their inability to slow growth rather than an inability to interact with Pol V. They further suggest that cold sensitivity is due, at least in part, to the combination of their individual effects on growth at 30°C.

  3. Does the tautomeric status of the adenine bases change upon the dissociation of the A*·A(syn) Topal-Fresco DNA mismatch? A combined QM and QTAIM atomistic insight.

    Science.gov (United States)

    Brovarets', Ol'ha O; Zhurakivsky, Roman O; Hovorun, Dmytro M

    2014-02-28

    We have scrupulously explored the tautomerisation mechanism via the double proton transfer of the A*·A(syn) Topal-Fresco base mispair (C(s) symmetry), formed by the imino and amino tautomers of the adenine DNA base in the anti- and syn-conformations, respectively, bridging quantum-mechanical calculations with Bader's quantum theory of atoms in molecules. It was found that the A*·A(syn) ↔ A·A*(syn) tautomerisation is the asynchronous concerted process. It was established that the A*·A(syn) DNA mismatch is stabilized by the N6H···N6 (6.35) and N1H···N7 (6.17) hydrogen (H) bonds, whereas the A·A*(syn) base mispair (Cs) by the N6H···N6 (8.82) and N7H···N1 (9.78) H-bonds and the C8H···HC2 HH-bond (0.30 kcal mol(-1)). Using the sweeps of the energies of the intermolecular H-bonds, it was observed that the N6H···N6 and N1H···N7/N7H···N1 H-bonds are anti-cooperative and mutually weaken each other in the A*·A(syn) and A·A*(syn) mispairs. It was revealed that the A·A*(syn) DNA mismatch is a dynamically unstable structure with a short lifetime of 1.12 × 10(-13) s and any of its 6 low-frequency intermolecular vibrations can develop during this period of time. This observation makes it impossible to change the tautomeric status of the A bases upon the dissociation of the A*·A(syn) base mispair into the monomers during DNA replication.

  4. What Controls DNA Looping?

    Directory of Open Access Journals (Sweden)

    Pamela J. Perez

    2014-08-01

    Full Text Available The looping of DNA provides a means of communication between sequentially distant genomic sites that operate in tandem to express, copy, and repair the information encoded in the DNA base sequence. The short loops implicated in the expression of bacterial genes suggest that molecular factors other than the naturally stiff double helix are involved in bringing the interacting sites into close spatial proximity. New computational techniques that take direct account of the three-dimensional structures and fluctuations of protein and DNA allow us to examine the likely means of enhancing such communication. Here, we describe the application of these approaches to the looping of a 92 base-pair DNA segment between the headpieces of the tetrameric Escherichia coli Lac repressor protein. The distortions of the double helix induced by a second protein—the nonspecific nucleoid protein HU—increase the computed likelihood of looping by several orders of magnitude over that of DNA alone. Large-scale deformations of the repressor, sequence-dependent features in the DNA loop, and deformability of the DNA operators also enhance looping, although to lesser degrees. The correspondence between the predicted looping propensities and the ease of looping derived from gene-expression and single-molecule measurements lends credence to the derived structural picture.

  5. Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY–DNA (W-Box Complex Interaction in Tomato (Solanum lycopersicum L.. A Computational Approach

    Directory of Open Access Journals (Sweden)

    Mohd Aamir

    2017-05-01

    Full Text Available The WRKY transcription factors (TFs, play crucial role in plant defense response against various abiotic and biotic stresses. The role of WRKY3 and WRKY4 genes in plant defense response against necrotrophic pathogens is well-reported. However, their functional annotation in tomato is largely unknown. In the present work, we have characterized the structural and functional attributes of the two identified tomato WRKY transcription factors, WRKY3 (SlWRKY3, and WRKY4 (SlWRKY4 using computational approaches. Arabidopsis WRKY3 (AtWRKY3: NP_178433 and WRKY4 (AtWRKY4: NP_172849 protein sequences were retrieved from TAIR database and protein BLAST was done for finding their sequential homologs in tomato. Sequence alignment, phylogenetic classification, and motif composition analysis revealed the remarkable sequential variation between, these two WRKYs. The tomato WRKY3 and WRKY4 clusters with Solanum pennellii showing the monophyletic origin and evolution from their wild homolog. The functional domain region responsible for sequence specific DNA-binding occupied in both proteins were modeled [using AtWRKY4 (PDB ID:1WJ2 and AtWRKY1 (PDBID:2AYD as template protein structures] through homology modeling using Discovery Studio 3.0. The generated models were further evaluated for their accuracy and reliability based on qualitative and quantitative parameters. The modeled proteins were found to satisfy all the crucial energy parameters and showed acceptable Ramachandran statistics when compared to the experimentally resolved NMR solution structures and/or X-Ray diffracted crystal structures (templates. The superimposition of the functional WRKY domains from SlWRKY3 and SlWRKY4 revealed remarkable structural similarity. The sequence specific DNA binding for two WRKYs was explored through DNA-protein interaction using Hex Docking server. The interaction studies found that SlWRKY4 binds with the W-box DNA through WRKYGQK with Tyr408, Arg409, and Lys419 with the

  6. Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition.

    Science.gov (United States)

    Knudsen, Berith E; Bergmark, Lasse; Munk, Patrick; Lukjancenko, Oksana; Priemé, Anders; Aarestrup, Frank M; Pamp, Sünje J

    2016-01-01

    Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs. Here, we compare in a stepwise approach a total of eight commercially available DNA extraction kits and 16 procedures based on these for three specimen types (human feces, pig feces, and hospital sewage). We assess DNA extraction using spike-in controls and different types of beads for bead beating, facilitating cell lysis. We evaluate DNA concentration, purity, and stability and microbial community composition using 16S rRNA gene sequencing and for selected samples using shotgun metagenomic sequencing. Our results suggest that inferred community composition was dependent on inherent specimen properties as well as DNA extraction method. We further show that bead beating or enzymatic treatment can increase the extraction of DNA from Gram-positive bacteria. Final DNA quantities could be increased by isolating DNA from a larger volume of cell lysate than that in standard protocols. Based on this insight, we designed an improved DNA isolation procedure optimized for microbiome genomics that can be used for the three examined specimen types and potentially also for other biological specimens. A standard operating procedure is available from https://dx.doi.org/10.6084/m9.figshare.3475406. IMPORTANCE Sequencing-based analyses of microbiomes may lead to a breakthrough in our understanding of the microbial worlds associated with humans

  7. Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells.

    Science.gov (United States)

    Hensel, Zach; Weng, Xiaoli; Lagda, Arvin Cesar; Xiao, Jie

    2013-01-01

    DNA looping mediated by transcription factors plays critical roles in prokaryotic gene regulation. The "genetic switch" of bacteriophage λ determines whether a prophage stays incorporated in the E. coli chromosome or enters the lytic cycle of phage propagation and cell lysis. Past studies have shown that long-range DNA interactions between the operator sequences O(R) and O(L) (separated by 2.3 kb), mediated by the λ repressor CI (accession number P03034), play key roles in regulating the λ switch. In vitro, it was demonstrated that DNA segments harboring the operator sequences formed loops in the presence of CI, but CI-mediated DNA looping has not been directly visualized in vivo, hindering a deep understanding of the corresponding dynamics in realistic cellular environments. We report a high-resolution, single-molecule imaging method to probe CI-mediated DNA looping in live E. coli cells. We labeled two DNA loci with differently colored fluorescent fusion proteins and tracked their separations in real time with ∼40 nm accuracy, enabling the first direct analysis of transcription-factor-mediated DNA looping in live cells. Combining looping measurements with measurements of CI expression levels in different operator mutants, we show quantitatively that DNA looping activates transcription and enhances repression. Further, we estimated the upper bound of the rate of conformational change from the unlooped to the looped state, and discuss how chromosome compaction may impact looping kinetics. Our results provide insights into transcription-factor-mediated DNA looping in a variety of operator and CI mutant backgrounds in vivo, and our methodology can be applied to a broad range of questions regarding chromosome conformations in prokaryotes and higher organisms.

  8. Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells.

    Directory of Open Access Journals (Sweden)

    Zach Hensel

    Full Text Available DNA looping mediated by transcription factors plays critical roles in prokaryotic gene regulation. The "genetic switch" of bacteriophage λ determines whether a prophage stays incorporated in the E. coli chromosome or enters the lytic cycle of phage propagation and cell lysis. Past studies have shown that long-range DNA interactions between the operator sequences O(R and O(L (separated by 2.3 kb, mediated by the λ repressor CI (accession number P03034, play key roles in regulating the λ switch. In vitro, it was demonstrated that DNA segments harboring the operator sequences formed loops in the presence of CI, but CI-mediated DNA looping has not been directly visualized in vivo, hindering a deep understanding of the corresponding dynamics in realistic cellular environments. We report a high-resolution, single-molecule imaging method to probe CI-mediated DNA looping in live E. coli cells. We labeled two DNA loci with differently colored fluorescent fusion proteins and tracked their separations in real time with ∼40 nm accuracy, enabling the first direct analysis of transcription-factor-mediated DNA looping in live cells. Combining looping measurements with measurements of CI expression levels in different operator mutants, we show quantitatively that DNA looping activates transcription and enhances repression. Further, we estimated the upper bound of the rate of conformational change from the unlooped to the looped state, and discuss how chromosome compaction may impact looping kinetics. Our results provide insights into transcription-factor-mediated DNA looping in a variety of operator and CI mutant backgrounds in vivo, and our methodology can be applied to a broad range of questions regarding chromosome conformations in prokaryotes and higher organisms.

  9. New insights into estrogenic regulation of O(6)-methylguanine DNA-methyltransferase (MGMT) in human breast cancer cells: Co-degradation of ER-α and MGMT proteins by fulvestrant or O(6)-benzylguanine indicates fresh avenues for therapy.

    Science.gov (United States)

    Paranjpe, Ameya; Bailey, Nathan I; Konduri, Santhi; Bobustuc, George C; Ali-Osman, Francis; Yusuf, Mohd A; Punganuru, Surendra R; Madala, Hanumantha Rao; Basak, Debasish; Mostofa, Agm; Srivenugopal, Kalkunte S

    2016-09-01

    Endocrine therapy using estrogen receptor-α (ER-α) antagonists for attenuating horm2one-driven cell proliferation is a major treatment modality for breast cancers. To exploit any DNA repair deficiencies associated with endocrine therapy, we investigated the functional and physical interactions of ER-α with O(6)-methylguanine DNA methyltransferase (MGMT), a unique DNA repair protein that confers tumor resistance to various anticancer alkylating agents. The ER-α -positive breast cancer cell lines (MCF-7, T47D) and ER- negative cell lines (MDAMB-468, MDAMB-231), and established inhibitors of ER-α and MGMT, namely, ICI-182,780 (Faslodex) and O(6)-benzylguanine, respectively, were used to study MGMT- ER interactions. The MGMT gene promoter was found to harbor one full and two half estrogen-responsive elements (EREs) and two antioxidant-responsive elements (AREs). MGMT expression was upregulated by estrogen, downregulated by tamoxifen in Western blot and promoter-linked reporter assays. Similarly, both transient and stable transfections of Nrf-2 (nuclear factor-erythroid 2-related factor-2) increased the levels of MGMT protein and activity 3 to 4-fold reflecting novel regulatory nodes for this drug-resistance determinant. Of the different ER-α antagonists tested, the pure anti-estrogen fulvestrant was most potent in inhibiting the MGMT activity in a dose, time and ER-α dependent manner, similar to O(6)-benzylguanine. Interestingly, fulvestrant exposure led to a degradation of both ER-α and MGMT proteins and O(6)-benzylguanine also induced a specific loss of ER-α and MGMT proteins in MCF-7 and T47D breast cancer cells with similar kinetics. Immunoprecipitation revealed a specific association of ER-α and MGMT proteins in breast cancer cells. Furthermore, silencing of MGMT gene expression triggered a decrease in the levels of both MGMT and ER-α proteins. The involvement of proteasome in the drug-induced degradation of both proteins was also demonstrated

  10. New insights into estrogenic regulation of O6-methylguanine DNA-methyltransferase (MGMT) in human breast cancer cells: Co-degradation of ER-α and MGMT proteins by fulvestrant or O6-benzylguanine indicates fresh avenues for therapy

    Science.gov (United States)

    Paranjpe, Ameya; Bailey, Nathan I.; Konduri, Santhi; Bobustuc, George C.; Ali-Osman, Francis; Yusuf, Mohd. A.; Punganuru, Surendra R.; Madala, Hanumantha Rao; Basak, Debasish; Mostofa, AGM; Srivenugopal, Kalkunte S.

    2016-01-01

    Abstract Endocrine therapy using estrogen receptor-α (ER-α) antagonists for attenuating horm2one-driven cell proliferation is a major treatment modality for breast cancers. To exploit any DNA repair deficiencies associated with endocrine therapy, we investigated the functional and physical interactions of ER-α with O6-methylguanine DNA methyltransferase (MGMT), a unique DNA repair protein that confers tumor resistance to various anticancer alkylating agents. The ER-α -positive breast cancer cell lines (MCF-7, T47D) and ER- negative cell lines (MDAMB-468, MDAMB-231), and established inhibitors of ER-α and MGMT, namely, ICI-182,780 (Faslodex) and O6-benzylguanine, respectively, were used to study MGMT- ER interactions. The MGMT gene promoter was found to harbor one full and two half estrogen-responsive elements (EREs) and two antioxidant-responsive elements (AREs). MGMT expression was upregulated by estrogen, downregulated by tamoxifen in Western blot and promoter-linked reporter assays. Similarly, both transient and stable transfections of Nrf-2 (nuclear factor-erythroid 2-related factor-2) increased the levels of MGMT protein and activity 3 to 4-fold reflecting novel regulatory nodes for this drug-resistance determinant. Of the different ER-α antagonists tested, the pure anti-estrogen fulvestrant was most potent in inhibiting the MGMT activity in a dose, time and ER-α dependent manner, similar to O6-benzylguanine. Interestingly, fulvestrant exposure led to a degradation of both ER-α and MGMT proteins and O6-benzylguanine also induced a specific loss of ER-α and MGMT proteins in MCF-7 and T47D breast cancer cells with similar kinetics. Immunoprecipitation revealed a specific association of ER-α and MGMT proteins in breast cancer cells. Furthermore, silencing of MGMT gene expression triggered a decrease in the levels of both MGMT and ER-α proteins. The involvement of proteasome in the drug-induced degradation of both proteins was also demonstrated

  11. DNA Nanotechnology

    Science.gov (United States)

    Taniguchi, Masateru; Kawai, Tomoji

    2002-11-01

    DNA is one candidate of promising molecules for molecular electronic devices, since it has the double helix structure with pi-electron bases for electron transport, the address at 0.4 nm intervals, and the self-assembly. Electrical conductivity and nanostructure of DNA and modified DNA molecules are investigated in order to research the application of DNA in nanoelectronic devices. It has been revealed that DNA is a wide-gap semiconductor in the absence of doping. The conductivity of DNA has been controlled by chemical doping, electric field doping, and photo-doping. It has found that Poly(dG)[middle dot]Poly(dC) has the best conductivity and can function as a conducting nanowire. The pattern of DNA network is controlled by changing the concentration of the DNA solution.

  12. Mechanistic insights into a novel chromone-appended Cu(II) anticancer drug entity: in vitro binding profile with DNA/RNA substrates and cytotoxic activity against MCF-7 and HepG2 cancer cells.

    Science.gov (United States)

    Yousuf, Imtiyaz; Arjmand, Farukh; Tabassum, Sartaj; Toupet, Loic; Khan, Rais Ahmad; Siddiqui, Maqsood Ahmad

    2015-06-14

    A new chromone-appended Cu(ii) drug entity () was designed and synthesized as a potential anticancer chemotherapeutic agent. The structural elucidation was carried out thoroughly by elemental analysis, FT-IR, EPR, ESI-MS and single crystal X-ray crystallography. Complex resulted from the in situ methoxylation reaction of the 3-formylchromone ligand and its subsequent complexation with the copper nitrate salt in a 2 : 1 ratio, respectively. crystallized in the monoclinic P21/c space group possessing the lattice parameters, a = 8.75 Å, b = 5.07 Å, c = 26.22 Å, α = γ = 90°, β = 96.3° per unit cell. Furthermore, in vitro interaction studies of with ct-DNA and tRNA were carried out which suggested more avid binding propensity towards the RNA target via intercalative mode, which was reflected from its Kb, K and Ksv values. The gel electrophoretic mobility assay was carried out on the pBR322 plasmid DNA substrate, to ascertain the cleaving ability and the mechanistic pathway in the presence of additives, and the results revealed the efficient cleaving ability of via the oxidative pathway. In vitro cell growth inhibition via the MTT assay was carried out to evaluate the cytotoxicity of complex and IC50 values were found to be in the range of 5-10 μg mL(-1) in HepG2 and MCF-7 cancer cell lines, which were found to be much lower than the IC50 values of previously reported similar Cu(ii) complexes. Additionally, in the presence of , reactive oxygen species (ROS) and thiobarbituric acid reactive substance (TBARS) levels in the tested cancer cell lines increased significantly, coupled with reduced glutathione (GSH) levels. Thus, our results suggested that ROS plays an important role in cell apoptosis induced by the Cu(ii) complex and validates its potential to act as a robust anticancer drug entity.

  13. DNA Methylation

    OpenAIRE

    Alokail, Majed S.; Alenad, Amal M.

    2015-01-01

    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication e...

  14. Bending the Rules of Transcriptional Repression: Tightly Looped DNA Directly Represses T7 RNA Polymerase

    OpenAIRE

    Lionberger, Troy A.; Meyhöfer, Edgar

    2010-01-01

    From supercoiled DNA to the tight loops of DNA formed by some gene repressors, DNA in cells is often highly bent. Despite evidence that transcription by RNA polymerase (RNAP) is affected in systems where DNA is deformed significantly, the mechanistic details underlying the relationship between polymerase function and mechanically stressed DNA remain unclear. Seeking to gain additional insight into the regulatory consequences of highly bent DNA, we hypothesize that tightly looping DNA is alone...

  15. DNA Sequential Logic Gate Using Two-Ring DNA.

    Science.gov (United States)

    Zhang, Cheng; Shen, Linjing; Liang, Chao; Dong, Yafei; Yang, Jing; Xu, Jin

    2016-04-13

    Sequential DNA detection is a fundamental issue for elucidating the interactive relationships among complex gene systems. Here, a sequential logic DNA gate was achieved by utilizing the two-ring DNA structure, with the ability to recognize "before" and "after" triggering sequences of DNA signals. By taking advantage of a "loop-open" mechanism, separations of two-ring DNAs were controlled. Three triggering pathways with different sequential DNA treatments were distinguished by comparing fluorescent outputs. Programmed nanoparticle arrangement guided by "interlocked" two-ring DNA was also constructed to demonstrate the achievement of designed nanostrucutres. Such sequential logic DNA operation may guide future molecular sensors to monitor more complex gene network in biological systems.

  16. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  17. Uncovering unseen fungal diversity from plant DNA banks

    Directory of Open Access Journals (Sweden)

    Erin M. Datlof

    2017-08-01

    Full Text Available Throughout the world DNA banks are used as storage repositories for genetic diversity of organisms ranging from plants to insects to mammals. Designed to preserve the genetic information for organisms of interest, these banks also indirectly preserve organisms’ associated microbiomes, including fungi associated with plant tissues. Studies of fungal biodiversity lag far behind those of macroorganisms, such as plants, and estimates of global fungal richness are still widely debated. Utilizing previously collected specimens to study patterns of fungal diversity could significantly increase our understanding of overall patterns of biodiversity from snapshots in time. Here, we investigated the fungi inhabiting the phylloplane among species of the endemic Hawaiian plant genus, Clermontia (Campanulaceae. Utilizing next generation DNA amplicon sequencing, we uncovered approximately 1,780 fungal operational taxonomic units from just 20 DNA bank samples collected throughout the main Hawaiian Islands. Using these historical samples, we tested the macroecological pattern of decreasing community similarity with decreasing geographic proximity. We found a significant distance decay pattern among Clermontia associated fungal communities. This study provides the first insights into elucidating patterns of microbial diversity through the use of DNA bank repository samples.

  18. Insights into the strategies used by related group II introns to adapt successfully for the colonisation of a bacterial genome.

    Science.gov (United States)

    Martínez-Rodríguez, Laura; García-Rodríguez, Fernando M; Molina-Sánchez, María Dolores; Toro, Nicolás; Martínez-Abarca, Francisco

    2014-01-01

    Group II introns are self-splicing RNAs and site-specific mobile retroelements found in bacterial and organellar genomes. The group II intron RmInt1 is present at high copy number in Sinorhizobium meliloti species, and has a multifunctional intron-encoded protein (IEP) with reverse transcriptase/maturase activities, but lacking the DNA-binding and endonuclease domains. We characterized two RmInt1-related group II introns RmInt2 from S. meliloti strain GR4 and Sr.md.I1 from S. medicae strain WSM419 in terms of splicing and mobility activities. We used both wild-type and engineered intron-donor constructs based on ribozyme ΔORF-coding sequence derivatives, and we determined the DNA target requirements for RmInt2, the element most distantly related to RmInt1. The excision and mobility patterns of intron-donor constructs expressing different combinations of IEP and intron RNA provided experimental evidence for the co-operation of IEPs and intron RNAs from related elements in intron splicing and, in some cases, in intron homing. We were also able to identify the DNA target regions recognized by these IEPs lacking the DNA endonuclease domain. Our results provide new insight into the versatility of related group II introns and the possible co-operation between these elements to facilitate the colonization of bacterial genomes.

  19. Single-molecule studies of DNA transcription using atomic force microscopy

    Science.gov (United States)

    Billingsley, Daniel J.; Bonass, William A.; Crampton, Neal; Kirkham, Jennifer; Thomson, Neil H.

    2012-04-01

    Atomic force microscopy (AFM) can detect single biomacromolecules with a high signal-to-noise ratio on atomically flat biocompatible support surfaces, such as mica. Contrast arises from the innate forces and therefore AFM does not require imaging contrast agents, leading to sample preparation that is relatively straightforward. The ability of AFM to operate in hydrated environments, including humid air and aqueous buffers, allows structure and function of biological and biomolecular systems to be retained. These traits of the AFM are ensuring that it is being increasingly used to study deoxyribonucleic acid (DNA) structure and DNA-protein interactions down to the secondary structure level. This report focuses in particular on reviewing the applications of AFM to the study of DNA transcription in reductionist single-molecule bottom-up approaches. The technique has allowed new insights into the interactions between ribonucleic acid (RNA) polymerase to be gained and enabled quantification of some aspects of the transcription process, such as promoter location, DNA wrapping and elongation. More recently, the trend is towards studying the interactions of more than one enzyme operating on a single DNA template. These methods begin to reveal the mechanics of gene expression at the single-molecule level and will enable us to gain greater understanding of how the genome is transcribed and translated into the proteome.

  20. Insights into the Genetic Relationships and Breeding Patterns of the African Tea Germplasm (Camellia sinensis (L. O. Kuntze Based on nSSR Markers and cpDNA Sequences

    Directory of Open Access Journals (Sweden)

    Lianming Gao

    2016-08-01

    Full Text Available Africa is one of the key centres of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships and breeding patterns of tea accessions collected from eight countries in Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (HS estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica respectively, as well as an admixed mosaic group whose individuals were defined as hybrids of F2 and BC generation with high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centres corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA and East Africa (Tea Research Foundation of Kenya, TRFK. Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centres, TRFCA and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study

  1. Glass slides to DNA microarrays

    Directory of Open Access Journals (Sweden)

    Samuel D Conzone

    2004-03-01

    Full Text Available A tremendous interest in deoxyribonucleic acid (DNA characterization tools was spurred by the mapping and sequencing of the human genome. New tools were needed, beginning in the early 1990s, to cope with the unprecedented amount of genomic information that was being discovered. Such needs led to the development of DNA microarrays; tiny gene-based sensors traditionally prepared on coated glass microscope slides. The following review is intended to provide historical insight into the advent of the DNA microarray, followed by a description of the technology from both the application and fabrication points of view. Finally, the unmet challenges and needs associated with DNA microarrays will be described to define areas of potential future developments for the materials researcher.

  2. Ancient DNA from marine mammals

    DEFF Research Database (Denmark)

    Foote, Andrew David; Hofreiter, Michael; Morin, Philip A.

    2012-01-01

    Marine mammals have long generation times and broad, difficult to sample distributions, which makes inferring evolutionary and demographic changes using field studies of extant populations challenging. However, molecular analyses from sub-fossil or historical materials of marine mammals...... such as bone, tooth, baleen, skin, fur, whiskers and scrimshaw using ancient DNA (aDNA) approaches provide an oppor- tunity for investigating such changes over evolutionary and ecological timescales. Here, we review the application of aDNA techniques to the study of marine mammals. Most of the studies have...... in distribution and range of marine mammal species; we review these studies and discuss the limitations of such ‘presence only’ studies. Combining aDNA data with stable isotopes can provide further insights into changes in ecology and we review past studies and suggest future potential applications. We also...

  3. Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair.

    Science.gov (United States)

    Chen, Xi; Zhong, Shijun; Zhu, Xiao; Dziegielewska, Barbara; Ellenberger, Tom; Wilson, Gerald M; MacKerell, Alexander D; Tomkinson, Alan E

    2008-05-01

    Based on the crystal structure of human DNA ligase I complexed with nicked DNA, computer-aided drug design was used to identify compounds in a database of 1.5 million commercially available low molecular weight chemicals that were predicted to bind to a DNA-binding pocket within the DNA-binding domain of DNA ligase I, thereby inhibiting DNA joining. Ten of 192 candidates specifically inhibited purified human DNA ligase I. Notably, a subset of these compounds was also active against the other human DNA ligases. Three compounds that differed in their specificity for the three human DNA ligases were analyzed further. L82 inhibited DNA ligase I, L67 inhibited DNA ligases I and III, and L189 inhibited DNA ligases I, III, and IV in DNA joining assays with purified proteins and in cell extract assays of DNA replication, base excision repair, and nonhomologous end-joining. L67 and L189 are simple competitive inhibitors with respect to nicked DNA, whereas L82 is an uncompetitive inhibitor that stabilized complex formation between DNA ligase I and nicked DNA. In cell culture assays, L82 was cytostatic whereas L67 and L189 were cytotoxic. Concordant with their ability to inhibit DNA repair in vitro, subtoxic concentrations of L67 and L189 significantly increased the cytotoxicity of DNA-damaging agents. Interestingly, the ligase inhibitors specifically sensitized cancer cells to DNA damage. Thus, these novel human DNA ligase inhibitors will not only provide insights into the cellular function of these enzymes but also serve as lead compounds for the development of anticancer agents.

  4. Inside PixInsight

    CERN Document Server

    Keller, Warren A

    2016-01-01

    In this book, Warren Keller reveals the secrets of astro-image processing software PixInsight in a practical and easy to follow manner, allowing the reader to produce stunning astrophotographs from even mediocre data. As the first comprehensive post-processing platform to be created by astro-imagers for astro-imagers, it has for many, replaced the generic graphics editors as the software of choice. With clear instructions from Keller, astrophotographers can get the most from its tools to create amazing images. Capable of complex post-processing routines, PixInsight is also an advanced pre-processing software, through which astrophotographers calibrate and stack their exposures into completed master files.This is the most comprehensive resource on PixInsight to date. With screenshots to help illustrate the process, it is a vital guide.

  5. Linking strategic flexibility and operational efficiency: the mediating role of ambidextrous operational capabilities

    NARCIS (Netherlands)

    S. Kortmann; C. Gelhard; C. Zimmermann; F.T. Piller

    2014-01-01

    We elucidate the important, though complex, relationship between strategic flexibility and operational efficiency. We incorporate insights from the dynamic resource-based view, ambidexterity literature and managerial practice to explain how two ambidextrous operational capabilities, i.e., mass custo

  6. Linking strategic flexibility and operational efficiency: the mediating role of ambidextrous operational capabilities

    NARCIS (Netherlands)

    Kortmann, S.; Gelhard, C.; Zimmermann, C.; Piller, F.T.

    2014-01-01

    We elucidate the important, though complex, relationship between strategic flexibility and operational efficiency. We incorporate insights from the dynamic resource-based view, ambidexterity literature and managerial practice to explain how two ambidextrous operational capabilities, i.e., mass

  7. Dreaming and insight

    Directory of Open Access Journals (Sweden)

    Christopher L Edwards

    2013-12-01

    Full Text Available This paper addresses claims that dreams can be a source of personal insight. Whereas there has been anecdotal backing for such claims, there is now tangential support from findings of the facilitative effect of sleep on cognitive insight, and of REM sleep in particular on emotional memory consolidation. Furthermore, the presence in dreams of metaphorical representations of waking life indicates the possibility of novel insight as an emergent feature of such metaphorical mappings. In order to assess whether personal insight can occur as a result of the consideration of dream content, 11 dream group discussion sessions were conducted which followed the Ullman Dream Appreciation technique, one session for each of 11 participants (10 females, 1 male; mean age = 19.2 years. Self-ratings of deepened self-perception and personal gains from participation in the group sessions showed that the Ullman technique is an effective procedure for establishing connections between dream content and recent waking life experiences, although wake life sources were found for only 14% of dream report text. The mean Exploration-Insight score on the Gains from Dream Interpretation questionnaire was very high and comparable to outcomes from the well-established Hill (1996 therapist-led dream interpretation method. This score was associated between-subjects with pre-group positive Attitude Toward Dreams. The need to distinguish ‘aha’ experiences as a result of discovering a waking life source for part of a dream, from ‘aha’ experiences of personal insight as a result of considering dream content, is discussed. Difficulties are described in designing a control condition to which the dream report condition can be compared.

  8. Dreaming and insight.

    Science.gov (United States)

    Edwards, Christopher L; Ruby, Perrine M; Malinowski, Josie E; Bennett, Paul D; Blagrove, Mark T

    2013-01-01

    This paper addresses claims that dreams can be a source of personal insight. Whereas there has been anecdotal backing for such claims, there is now tangential support from findings of the facilitative effect of sleep on cognitive insight, and of REM sleep in particular on emotional memory consolidation. Furthermore, the presence in dreams of metaphorical representations of waking life indicates the possibility of novel insight as an emergent feature of such metaphorical mappings. In order to assess whether personal insight can occur as a result of the consideration of dream content, 11 dream group discussion sessions were conducted which followed the Ullman Dream Appreciation technique, one session for each of 11 participants (10 females, 1 male; mean age = 19.2 years). Self-ratings of deepened self-perception and personal gains from participation in the group sessions showed that the Ullman technique is an effective procedure for establishing connections between dream content and recent waking life experiences, although wake life sources were found for only 14% of dream report text. The mean Exploration-Insight score on the Gains from Dream Interpretation questionnaire was very high and comparable to outcomes from the well-established Hill (1996) therapist-led dream interpretation method. This score was associated between-subjects with pre-group positive Attitude Toward Dreams (ATD). The need to distinguish "aha" experiences as a result of discovering a waking life source for part of a dream, from "aha" experiences of personal insight as a result of considering dream content, is discussed. Difficulties are described in designing a control condition to which the dream report condition can be compared.

  9. Dreaming and insight

    Science.gov (United States)

    Edwards, Christopher L.; Ruby, Perrine M.; Malinowski, Josie E.; Bennett, Paul D.; Blagrove, Mark T.

    2013-01-01

    This paper addresses claims that dreams can be a source of personal insight. Whereas there has been anecdotal backing for such claims, there is now tangential support from findings of the facilitative effect of sleep on cognitive insight, and of REM sleep in particular on emotional memory consolidation. Furthermore, the presence in dreams of metaphorical representations of waking life indicates the possibility of novel insight as an emergent feature of such metaphorical mappings. In order to assess whether personal insight can occur as a result of the consideration of dream content, 11 dream group discussion sessions were conducted which followed the Ullman Dream Appreciation technique, one session for each of 11 participants (10 females, 1 male; mean age = 19.2 years). Self-ratings of deepened self-perception and personal gains from participation in the group sessions showed that the Ullman technique is an effective procedure for establishing connections between dream content and recent waking life experiences, although wake life sources were found for only 14% of dream report text. The mean Exploration-Insight score on the Gains from Dream Interpretation questionnaire was very high and comparable to outcomes from the well-established Hill (1996) therapist-led dream interpretation method. This score was associated between-subjects with pre-group positive Attitude Toward Dreams (ATD). The need to distinguish “aha” experiences as a result of discovering a waking life source for part of a dream, from “aha” experiences of personal insight as a result of considering dream content, is discussed. Difficulties are described in designing a control condition to which the dream report condition can be compared. PMID:24550849

  10. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  11. GOES-R: Satellite Insight

    Science.gov (United States)

    Fitzpatrick, Austin J.; Leon, Nancy J.; Novati, Alexander; Lincoln, Laura K.; Fisher, Diane K.

    2012-01-01

    GOES-R: Satellite Insight seeks to bring awareness of the GOES-R (Geostationary Operational Environmental Satellite -- R Series) satellite currently in development to an audience of all ages on the emerging medium of mobile games. The iPhone app (Satellite Insight) was created for the GOES-R Program. The app describes in simple terms the types of data products that can be produced from GOES-R measurements. The game is easy to learn, yet challenging for all audiences. It includes educational content and a path to further information about GOESR, its technology, and the benefits of the data it collects. The game features action-puzzle game play in which the player must prevent an overflow of data by matching falling blocks that represent different types of GOES-R data. The game adds more different types of data blocks over time, as long as the player can prevent a data overflow condition. Points are awarded for matches, and players can compete with themselves to beat their highest score.

  12. OpenGL Insights

    CERN Document Server

    Cozzi, Patrick

    2012-01-01

    Get Real-World Insight from Experienced Professionals in the OpenGL Community With OpenGL, OpenGL ES, and WebGL, real-time rendering is becoming available everywhere, from AAA games to mobile phones to web pages. Assembling contributions from experienced developers, vendors, researchers, and educators, OpenGL Insights presents real-world techniques for intermediate and advanced OpenGL, OpenGL ES, and WebGL developers. Go Beyond the Basics The book thoroughly covers a range of topics, including OpenGL 4.2 and recent extensions. It explains how to optimize for mobile devices, explores the design

  13. PDA: Pooled DNA analyzer

    Directory of Open Access Journals (Sweden)

    Lin Chin-Yu

    2006-04-01

    Full Text Available Abstract Background Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer, to analyze pooled DNA data. Results We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB® language, but it can also be executed on a Windows system without installing the MATLAB®. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples. Conclusion PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm.

  14. Outsourcing/Offshoring Insights

    DEFF Research Database (Denmark)

    Tate, Wendy; Bals, Lydia

    2017-01-01

    Findings: Both the geographical and governance dimensions are part of the rightshoring decision which is an important conceptual foundation for this special issue, as it invited insightful pieces on all of these phenomena (e.g. outsourcing, insourcing, offshoring, reshoring), acknowledging that t...

  15. The INSIGHT SEIS VBB Experiment

    Science.gov (United States)

    Tillier, S.; De Raucourt, S.; Lognonne, P. H.; Banerdt, B.; Mimoun, D.; Giardini, D.; Christensen, U. R.; Pike, W. T.; Zweifel, P.; Mance, D.; Bierwirth, M.; Laudet, P.; Perez, R.; Kerjean, L.; Hurst, K. J.; Mocquet, A.; Garcia, R. F.

    2012-12-01

    The SEIS experiment is the primary payload of the Interior Structure investigation using Seismology and Heat Transport (INSIGHT) Mission Proposal, submitted to NASA in the frame of the 2010 Discovery program, and selected for a competitive phase A study, together with two other projects. The objective of the INSIGHT SEIS experiment is the determination of the deep internal structure of Mars. In particular, geophysical parameters of first importance, such as the state (liquid/solid) and size of the core, structure of the mantle, shape of discontinuities, thickness of the crust will be determined by the experiment. It will measure seismic activity in a very broad band of signal, from the tidal frequencies (0.05 mHz) up to the short period frequencies (50 Hz), to address the widest range of scientific questions, from the state of the core to the meteoritic impact and quake rates. The instrument integrates a Very Broad Band (VBB) 3 axis seismometer, completed by another trihedron of MEMS short period seismometers, environmental sensors for pressure, wind and temperature, The sensors will be deployed on the Martian ground by a robotic arm from a Phoenix-type lander platform and protected by a wind and thermal shield. The sensor assembly, which contains all seismic sensors, the leveling system, as well as house-keeping and temperature measurements, will be deployed on the soil in order to allow the best possible mechanical coupling with the ground motion. The wind and thermal shield, the sensors' specific containers (vacuum sphere for VBBs) and a passive thermal compensation system will achieve a very high protection of the VBB against temperature and pressure variations, allowing the sensor to operate in the rough Martian thermal environment while reaching a deection threshold below 10-9 ms-2 Hz-1/2 in the VBB bandwidth. A dedicated electronics will manage the overall experiment and ultra-low noise, space qualified 24 bits A/D converters will perform the acquisition

  16. Remote Operations Control Center (ROCC)

    Science.gov (United States)

    1997-01-01

    Students at Rensselaer Polytechnic Institute (RPI) in Troy, NY, monitor the progress of the Isothermal Dendritic Growth Experiment (IDGE) during the U.S. Microgravity Payload-4 (USMP-4) mission (STS-87, Nov. 19 - Dec. 5, 1997). Remote Operation Control Center (ROCC) like this one will become more common during operations with International Space Station. IDGE, flown on three Space Shuttle missions, is yielding new insights into virtually all industrially relevant metal and alloy forming operations. Photo credit: Renssenlaer Polythnic Institute (RPI)

  17. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  18. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  19. DNA adductomics.

    Science.gov (United States)

    Balbo, Silvia; Turesky, Robert J; Villalta, Peter W

    2014-03-17

    Systems toxicology is a broad-based approach to describe many of the toxicological features that occur within a living system under stress or subjected to exogenous or endogenous exposures. The ultimate goal is to capture an overview of all exposures and the ensuing biological responses of the body. The term exposome has been employed to refer to the totality of all exposures, and systems toxicology investigates how the exposome influences health effects and consequences of exposures over a lifetime. The tools to advance systems toxicology include high-throughput transcriptomics, proteomics, metabolomics, and adductomics, which is still in its infancy. A well-established methodology for the comprehensive measurement of DNA damage resulting from every day exposures is not fully developed. During the past several decades, the (32)P-postlabeling technique has been employed to screen the damage to DNA induced by multiple classes of genotoxicants; however, more robust, specific, and quantitative methods have been sought to identify and quantify DNA adducts. Although triple quadrupole and ion trap mass spectrometry, particularly when using multistage scanning (LC-MS(n)), have shown promise in the field of DNA adductomics, it is anticipated that high-resolution and accurate-mass LC-MS(n) instrumentation will play a major role in assessing global DNA damage. Targeted adductomics should also benefit greatly from improved triple quadrupole technology. Once the analytical MS methods are fully mature, DNA adductomics along with other -omics tools will contribute greatly to the field of systems toxicology.

  20. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  1. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  2. Death: 'nothing' gives insight.

    Science.gov (United States)

    Ettema, Eric J

    2013-08-01

    According to a widely accepted belief, we cannot know our own death--death means 'nothing' to us. At first sight, the meaning of 'nothing' just implies the negation or absence of 'something'. Death then simply refers to the negation or absence of life. As a consequence, however, death has no meaning of itself. This leads to an ontological paradox in which death is both acknowledged and denied: death is … nothing. In this article, I investigate whether insight into the ontological paradox of the nothingness of death can contribute to a good end-of-life. By analysing Aquinas', Heidegger's and Derrida's understanding of death as nothingness, I explore how giving meaning to death on different ontological levels connects to, and at the same time provides resistance against, the harsh reality of death. By doing so, I intend to demonstrate that insight into the nothingness of death can count as a framework for a meaningful dealing with death.

  3. World energy insight 2011

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2011-11-15

    The World Energy Insight 2011 is the official publication of the World Energy Council. It includes interviews, articles and case studies from a distinguished panel of World Energy Council Officers, CEOs, government ministers, academics and opinion formers from all areas of the energy sector and provides perspectives from around the globe. Government, industry and NGO's offer both policy and technology perspectives. The insights within this publication add to the work that WEC is doing to provide the forum for energy leaders, along with the on-going WEC studies and programmes on Energy Policies, 2050 Energy Scenarios, Energy Resources & Technologies, Energy for Urban Innovation, Rules Of Energy Trade and Global Energy Access.

  4. The politics of insight.

    Science.gov (United States)

    Salvi, Carola; Cristofori, Irene; Grafman, Jordan; Beeman, Mark

    2016-01-01

    Previous studies showed that liberals and conservatives differ in cognitive style. Liberals are more flexible, and tolerant of complexity and novelty, whereas conservatives are more rigid, are more resistant to change, and prefer clear answers. We administered a set of compound remote associate problems, a task extensively used to differentiate problem-solving styles (via insight or analysis). Using this task, several researches have proven that self-reports, which differentiate between insight and analytic problem-solving, are reliable and are associated with two different neural circuits. In our research we found that participants self-identifying with distinct political orientations demonstrated differences in problem-solving strategy. Liberals solved significantly more problems via insight instead of in a step-by-step analytic fashion. Our findings extend previous observations that self-identified political orientations reflect differences in cognitive styles. More specifically, we show that type of political orientation is associated with problem-solving strategy. The data converge with previous neurobehavioural and cognitive studies indicating a link between cognitive style and the psychological mechanisms that mediate political beliefs.

  5. DNA and RNA sensor

    Institute of Scientific and Technical Information of China (English)

    LIU; Tao; LIN; Lin; ZHAO; Hong; JIANG; Long

    2005-01-01

    This review summarizes recent advances in DNA sensor. Major areas of DNA sensor covered in this review include immobilization methods of DNA, general techniques of DNA detection and application of nanoparticles in DNA sensor.

  6. What Is Mitochondrial DNA?

    Science.gov (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  7. DNA detection by THz pumping

    Energy Technology Data Exchange (ETDEWEB)

    Chernev, A. L. [Russian Academy of Sciences, St. Petersburg Academic University—Nanotechnology Research and Education Centre (Russian Federation); Bagraev, N. T.; Klyachkin, L. E. [Russian Academy of Sciences, Ioffe Physicotechnical Institute (Russian Federation); Emelyanov, A. K.; Dubina, M. V. [Russian Academy of Sciences, St. Petersburg Academic University—Nanotechnology Research and Education Centre (Russian Federation)

    2015-07-15

    DNA semiconductor detection and sequencing is considered to be the most promising approach for future discoveries in genome and proteome research which is dramatically dependent on the challenges faced by semiconductor nanotechnologies. DNA pH-sensing with ion-sensitive field effect transistor (ISFET) is well-known to be a successfully applied electronic platform for genetic research. However this method lacks fundamentally in chemical specificity. Here we develop the first ever silicon nanosandwich pump device, which provides both the excitation of DNA fragments’ self-resonant modes and the feedback for current-voltage measurements at room temperature. This device allows direct detection of singlestranded label-free oligonucleotides by measuring their THz frequency response in aqueous solution. These results provide a new insight into the nanobioelectronics for the future real-time technologies of direct gene observations.

  8. DNA Computer; Present and Future

    Directory of Open Access Journals (Sweden)

    Amir Abbaszadeh Sori

    2014-06-01

    Full Text Available DNA computers use strands of DNA to perform computing operations. The computer consists of two types of strands – the instruction strands and the input data strands. The instruction strands splice together the input data strands to generate the desired output data strand. DNA computing holds out the promise of important and significant connections between computers and living systems, as well as promising massively parallel computations. Before these promises are fulfilled, however, important challenges related to errors and practicality has to be addressed. On the other hand, new directions toward a synthesis of molecular evolution and DNA computing might circumvent the problems that have hindered development, so far. This paper represent present and future DNA computer.

  9. Single Molecule Bioelectronics and Their Application to Amplification-Free Measurement of DNA Lengths.

    Science.gov (United States)

    Gül, O Tolga; Pugliese, Kaitlin M; Choi, Yongki; Sims, Patrick C; Pan, Deng; Rajapakse, Arith J; Weiss, Gregory A; Collins, Philip G

    2016-06-24

    As biosensing devices shrink smaller and smaller, they approach a scale in which single molecule electronic sensing becomes possible. Here, we review the operation of single-enzyme transistors made using single-walled carbon nanotubes. These novel hybrid devices transduce the motions and catalytic activity of a single protein into an electronic signal for real-time monitoring of the protein's activity. Analysis of these electronic signals reveals new insights into enzyme function and proves the electronic technique to be complementary to other single-molecule methods based on fluorescence. As one example of the nanocircuit technique, we have studied the Klenow Fragment (KF) of DNA polymerase I as it catalytically processes single-stranded DNA templates. The fidelity of DNA polymerases makes them a key component in many DNA sequencing techniques, and here we demonstrate that KF nanocircuits readily resolve DNA polymerization with single-base sensitivity. Consequently, template lengths can be directly counted from electronic recordings of KF's base-by-base activity. After measuring as few as 20 copies, the template length can be determined with <1 base pair resolution, and different template lengths can be identified and enumerated in solutions containing template mixtures.

  10. Endocycling cells do not apoptose in response to DNA rereplication genotoxic stress.

    Science.gov (United States)

    Mehrotra, Sonam; Maqbool, Shahina B; Kolpakas, Alexis; Murnen, Katherine; Calvi, Brian R

    2008-11-15

    Initiation of DNA replication at origins more than once per cell cycle results in rereplication and has been implicated in cancer. Here we use Drosophila to examine the checkpoint responses to rereplication in a developmental context. We find that increased Double-parked (Dup), the Drosophila ortholog of Cdt1, results in rereplication and DNA damage. In most cells, this rereplication triggers caspase activation and apoptotic cell death mediated by both p53-dependent and -independent pathways. Elevated Dup also caused DNA damage in endocycling cells, which switch to a G/S cycle during normal development, indicating that rereplication and the endocycling DNA reduplication program are distinct processes. Unexpectedly, however, endocycling cells do not apoptose regardless of tissue type. Our combined evidence suggests that endocycling apoptosis is repressed in part because proapoptotic gene promoters are silenced. Normal endocycling cells had DNA lesions near heterochromatin, which increased after rereplication, explaining why endocycling cells must constantly repress the genotoxic apoptotic response. Our results reveal a novel regulation of apoptosis in development and new insights into the little-understood endocycle. Similar mechanisms may operate during vertebrate development, with implications for cancer predisposition in certain tissues.

  11. Single Molecule Bioelectronics and Their Application to Amplification-Free Measurement of DNA Lengths

    Directory of Open Access Journals (Sweden)

    O. Tolga Gül

    2016-06-01

    Full Text Available As biosensing devices shrink smaller and smaller, they approach a scale in which single molecule electronic sensing becomes possible. Here, we review the operation of single-enzyme transistors made using single-walled carbon nanotubes. These novel hybrid devices transduce the motions and catalytic activity of a single protein into an electronic signal for real-time monitoring of the protein’s activity. Analysis of these electronic signals reveals new insights into enzyme function and proves the electronic technique to be complementary to other single-molecule methods based on fluorescence. As one example of the nanocircuit technique, we have studied the Klenow Fragment (KF of DNA polymerase I as it catalytically processes single-stranded DNA templates. The fidelity of DNA polymerases makes them a key component in many DNA sequencing techniques, and here we demonstrate that KF nanocircuits readily resolve DNA polymerization with single-base sensitivity. Consequently, template lengths can be directly counted from electronic recordings of KF’s base-by-base activity. After measuring as few as 20 copies, the template length can be determined with <1 base pair resolution, and different template lengths can be identified and enumerated in solutions containing template mixtures.

  12. DNA vaccines

    Science.gov (United States)

    Gregersen, Jens-Peter

    2001-12-01

    Immunization by genes encoding immunogens, rather than with the immunogen itself, has opened up new possibilities for vaccine research and development and offers chances for new applications and indications for future vaccines. The underlying mechanisms of antigen processing, immune presentation and regulation of immune responses raise high expectations for new and more effective prophylactic or therapeutic vaccines, particularly for vaccines against chronic or persistent infectious diseases and tumors. Our current knowledge and experience of DNA vaccination is summarized and critically reviewed with particular attention to basic immunological mechanisms, the construction of plasmids, screening for protective immunogens to be encoded by these plasmids, modes of application, pharmacokinetics, safety and immunotoxicological aspects. DNA vaccines have the potential to accelerate the research phase of new vaccines and to improve the chances of success, since finding new immunogens with the desired properties is at least technically less demanding than for conventional vaccines. However, on the way to innovative vaccine products, several hurdles have to be overcome. The efficacy of DNA vaccines in humans appears to be much less than indicated by early studies in mice. Open questions remain concerning the persistence and distribution of inoculated plasmid DNA in vivo, its potential to express antigens inappropriately, or the potentially deleterious ability to insert genes into the host cell's genome. Furthermore, the possibility of inducing immunotolerance or autoimmune diseases also needs to be investigated more thoroughly, in order to arrive at a well-founded consensus, which justifies the widespread application of DNA vaccines in a healthy population.

  13. DNA nanotechnology

    Directory of Open Access Journals (Sweden)

    Nadrian C Seeman

    2003-01-01

    We are all aware that the DNA found in cells is a double helix consisting of two antiparallel strands held together by specific hydrogen-bonded base pairs; adenine (A always pairs with thymine (T, and guanine (G always pairs with cytosine (C. The specificity of this base pairing and the ability to ensure that it occurs in this fashion (and not some other1 is key to the use of DNA in materials applications. The double helical arrangement of the two molecules leads to a linear helix axis, linear not in the geometrical sense of being a straight line, but in the topological sense of being unbranched. Genetic engineers discovered in the 1970s how to splice together pieces of DNA to add new genes to DNA molecules2, and synthetic chemists worked out convenient syntheses for short pieces of DNA (up to ∼100–150 units in the 1980s3. Regardless of the impact of these technologies on biological systems, hooking together linear molecules leads only to longer linear molecules, with circles, knots, and catenanes perhaps resulting from time to time.

  14. Ocorrência de custos ocultos em operações de serviços: insights sobre observação em uma sociedade de economia mista no Brasil Occurrence of hidden costs in service operations: insights into a publicly held company

    Directory of Open Access Journals (Sweden)

    Paulo César Pereira da Silva

    2011-01-01

    related to identification, checking, and measurement of the costs generated during the production of the final product. The main objective of this article is to verify the occurrence of hidden costs of services rendered by a public company controlled by the Paraiba State government in Brazil. The occurrence of hidden costs incurred by this corporation was verified in terms of the most common organizational malfunctioning such as: waiting time, useless motion, overpay, overconsumption, rework, occupational accidents, absenteeism, idleness, and litigations. This study was based on semi-structured interviews conducted with workstation operators and in loco observation of workers' activities. It is important to highlight the occurrence of hidden costs that are not accounted by the traditional cost systems and their intangibility, which is not recognized by productivity measurement models, for example, the Soniano Model (SON, 1991. The approach to investigate hidden costs used in this study was based on the theoretical foundation developed by Savall and Zardet (1991. The research results indicated the occurrence of hidden costs, mainly derived from malfunctioning related to rework, waiting time, high staff turnover, and stress. In addition, it was verified that among the most common hidden costs observed, rework, and waiting time, identified in virtually all sectors, are the ones that affect the most the proper functioning of the organization.

  15. An anti-DNA antibody prefers damaged dsDNA over native.

    Science.gov (United States)

    Akberova, N I; Zhmurov, A A; Nevzorova, T A; Litvinov, R I

    2017-01-01

    DNA-protein interactions, including DNA-antibody complexes, have both fundamental and practical significance. In particular, antibodies against double-stranded DNA play an important role in the pathogenesis of autoimmune diseases. Elucidation of structural mechanisms of an antigen recognition and interaction of anti-DNA antibodies provides a basis for understanding the role of DNA-containing immune complexes in human pathologies and for new treatments. Here we used Molecular Dynamic simulations of bimolecular complexes of a segment of dsDNA with a monoclonal anti-DNA antibody's Fab-fragment to obtain detailed structural and physical characteristics of the dynamic intermolecular interactions. Using a computationally modified crystal structure of a Fab-DNA complex (PDB: 3VW3), we studied in silico equilibrium Molecular Dynamics of the Fab-fragment associated with two homologous dsDNA fragments, containing or not containing dimerized thymine, a product of DNA photodamage. The Fab-fragment interactions with the thymine dimer-containing DNA was thermodynamically more stable than with the native DNA. The amino acid residues constituting a paratope and the complementary nucleotide epitopes for both Fab-DNA constructs were identified. Stacking and electrostatic interactions were shown to play the main role in the antibody-dsDNA contacts, while hydrogen bonds were less significant. The aggregate of data show that the chemically modified dsDNA (containing a covalent thymine dimer) has a higher affinity toward the antibody and forms a stronger immune complex. These findings provide a mechanistic insight into formation and properties of the pathogenic anti-DNA antibodies in autoimmune diseases, such as systemic lupus erythematosus, associated with skin photosensibilization and DNA photodamage.

  16. Chloroplast DNA phylogeography and cytotype geography in autopolyploid Plantago media

    NARCIS (Netherlands)

    Van Dijk, P.J.; Bakx-Schotman, Tanja

    1997-01-01

    In order to gain insight into the causes of parapatric diploid and tetraploid distributions in Plantago media chloroplast DNA (cpDNA) restriction site polymorphism was studied in 36 European populations. Parapatric distributions are often explained by adaptive differences between cytotypes to an und

  17. DNA origami nanopores for controlling DNA translocation.

    Science.gov (United States)

    Hernández-Ainsa, Silvia; Bell, Nicholas A W; Thacker, Vivek V; Göpfrich, Kerstin; Misiunas, Karolis; Fuentes-Perez, Maria Eugenia; Moreno-Herrero, Fernando; Keyser, Ulrich F

    2013-07-23

    We combine DNA origami structures with glass nanocapillaries to reversibly form hybrid DNA origami nanopores. Trapping of the DNA origami onto the nanocapillary is proven by imaging fluorescently labeled DNA origami structures and simultaneous ionic current measurements of the trapping events. We then show two applications highlighting the versatility of these DNA origami nanopores. First, by tuning the pore size we can control the folding of dsDNA molecules ("physical control"). Second, we show that the specific introduction of binding sites in the DNA origami nanopore allows selective detection of ssDNA as a function of the DNA sequence ("chemical control").

  18. Modeling for Insights

    Energy Technology Data Exchange (ETDEWEB)

    Jacob J. Jacobson; Gretchen Matthern

    2007-04-01

    System Dynamics is a computer-aided approach to evaluating the interrelationships of different components and activities within complex systems. Recently, System Dynamics models have been developed in areas such as policy design, biological and medical modeling, energy and the environmental analysis, and in various other areas in the natural and social sciences. The real power of System Dynamic modeling is gaining insights into total system behavior as time, and system parameters are adjusted and the effects are visualized in real time. System Dynamic models allow decision makers and stakeholders to explore long-term behavior and performance of complex systems, especially in the context of dynamic processes and changing scenarios without having to wait decades to obtain field data or risk failure if a poor management or design approach is used. The Idaho National Laboratory recently has been developing a System Dynamic model of the US Nuclear Fuel Cycle. The model is intended to be used to identify and understand interactions throughout the entire nuclear fuel cycle and suggest sustainable development strategies. This paper describes the basic framework of the current model and presents examples of useful insights gained from the model thus far with respect to sustainable development of nuclear power.

  19. Establishing Operational Access: Insights from the Past for the Future

    Science.gov (United States)

    2014-06-01

    49 Dolman, Pure Strategy, 153. 50 Rosen, Winning the next War, 52. 26 through proxies and observe self -imposed limits, such as...they gained valuable confidence and regional esteem for initiating and surviving an offensive against a more advanced foe. The IDF and IAF...Canal were buried in concrete bunkers and arrayed in carefully prepared, symmetric sites based on precise calculations of coverage areas.35 Any

  20. Smart Pricing: Linking Pricing Decisions with Operational Insights

    NARCIS (Netherlands)

    M. Fleischmann (Moritz); J.M. Hall (Joseph); D.F. Pyke (David)

    2003-01-01

    textabstractThe past decade has seen a virtual explosion of information about customers and their preferences. This information potentially allows companies to increase their revenues, in particular since modern technology enables price changes to be effected at minimal cost. At the same time, compa

  1. Enhancing Civilian Protection in Peace Operations: Insights from Africa

    Science.gov (United States)

    2010-09-01

    survival) or maximalist (the enjoyment of rights) terms and hence as a concept that contains many interconnected layers. Ideally, civilians would be...promoting Enabling conditions Enjoyment of human rights Provision of basic necessities Physical protection from imminent violence Figure 1. The...who displayed “no particular respect for anybody and essentially work to their own unruly/ drunk /drugged tune.” They were, he concluded, “a very

  2. Smart Pricing: Linking Pricing Decisions with Operational Insights

    NARCIS (Netherlands)

    M. Fleischmann (Moritz); J.M. Hall (Joseph); D.F. Pyke (David)

    2003-01-01

    textabstractThe past decade has seen a virtual explosion of information about customers and their preferences. This information potentially allows companies to increase their revenues, in particular since modern technology enables price changes to be effected at minimal cost. At the same time, compa

  3. Operational amplifiers

    CERN Document Server

    Dostal, Jiri

    1993-01-01

    This book provides the reader with the practical knowledge necessary to select and use operational amplifier devices. It presents an extensive treatment of applications and a practically oriented, unified theory of operational circuits.Provides the reader with practical knowledge necessary to select and use operational amplifier devices. Presents an extensive treatment of applications and a practically oriented, unified theory of operational circuits

  4. Divalent counterion-induced condensation of triple-strand DNA.

    Science.gov (United States)

    Qiu, Xiangyun; Parsegian, V Adrian; Rau, Donald C

    2010-12-14

    Understanding and manipulation of the forces assembling DNA/RNA helices have broad implications for biology, medicine, and physics. One subject of significance is the attractive force between dsDNA mediated by polycations of valence ≥ 3. Despite extensive studies, the physical origin of the "like-charge attraction" remains unsettled among competing theories. Here we show that triple-strand DNA (tsDNA), a more highly charged helix than dsDNA, is precipitated by alkaline-earth divalent cations that are unable to condense dsDNA. We further show that our observation is general by examining several cations (Mg(2+), Ba(2+), and Ca(2+)) and two distinct tsDNA constructs. Cation-condensed tsDNA forms ordered hexagonal arrays that redissolve upon adding monovalent salts. Forces between tsDNA helices, measured by osmotic stress, follow the form of hydration forces observed with condensed dsDNA. Probing a well-defined system of point-like cations and tsDNAs with more evenly spaced helical charges, the counterintuitive observation that the more highly charged tsDNA (vs. dsDNA) is condensed by cations of lower valence provides new insights into theories of polyelectrolytes and the biological and pathological roles of tsDNA. Cations and tsDNAs also hold promise as a model system for future studies of DNA-DNA interactions and electrostatic interactions in general.

  5. Nucleotide Metabolism and DNA Replication.

    Science.gov (United States)

    Warner, Digby F; Evans, Joanna C; Mizrahi, Valerie

    2014-10-01

    The development and application of a highly versatile suite of tools for mycobacterial genetics, coupled with widespread use of "omics" approaches to elucidate the structure, function, and regulation of mycobacterial proteins, has led to spectacular advances in our understanding of the metabolism and physiology of mycobacteria. In this article, we provide an update on nucleotide metabolism and DNA replication in mycobacteria, highlighting key findings from the past 10 to 15 years. In the first section, we focus on nucleotide metabolism, ranging from the biosynthesis, salvage, and interconversion of purine and pyrimidine ribonucleotides to the formation of deoxyribonucleotides. The second part of the article is devoted to DNA replication, with a focus on replication initiation and elongation, as well as DNA unwinding. We provide an overview of replication fidelity and mutation rates in mycobacteria and summarize evidence suggesting that DNA replication occurs during states of low metabolic activity, and conclude by suggesting directions for future research to address key outstanding questions. Although this article focuses primarily on observations from Mycobacterium tuberculosis, it is interspersed, where appropriate, with insights from, and comparisons with, other mycobacterial species as well as better characterized bacterial models such as Escherichia coli. Finally, a common theme underlying almost all studies of mycobacterial metabolism is the potential to identify and validate functions or pathways that can be exploited for tuberculosis drug discovery. In this context, we have specifically highlighted those processes in mycobacterial DNA replication that might satisfy this critical requirement.

  6. The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics

    Science.gov (United States)

    Biebricher, Andreas S.; Heller, Iddo; Roijmans, Roel F. H.; Hoekstra, Tjalle P.; Peterman, Erwin J. G.; Wuite, Gijs J. L.

    2015-01-01

    DNA intercalators are widely used as fluorescent probes to visualize DNA and DNA transactions in vivo and in vitro. It is well known that they perturb DNA structure and stability, which can in turn influence DNA-processing by proteins. Here we elucidate this perturbation by combining single-dye fluorescence microscopy with force spectroscopy and measuring the kinetics of DNA intercalation by the mono- and bis-intercalating cyanine dyes SYTOX Orange, SYTOX Green, SYBR Gold, YO-PRO-1, YOYO-1 and POPO-3. We show that their DNA-binding affinity is mainly governed by a strongly tension-dependent dissociation rate. These rates can be tuned over a range of seven orders of magnitude by changing DNA tension, intercalating species and ionic strength. We show that optimizing these rates minimizes the impact of intercalators on strand separation and enzymatic activity. These new insights provide handles for the improved use of intercalators as DNA probes with minimal perturbation and maximal efficacy. PMID:26084388

  7. Insights on STEM Careers

    Energy Technology Data Exchange (ETDEWEB)

    Wendelberger, Joanne Roth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2014-11-05

    This presentation will provide career advice for individuals seeking to go beyond just having a job to building a successful career in the areas of Science, Technology, Engineering, and Mathematics. Careful planning can be used to turn a job into a springboard for professional advancement and personal satisfaction. Topics to be addressed include setting priorities, understanding career ladders, making tough choices, overcoming stereotypes and assumptions by others, networking, developing a professional identify, and balancing a career with family and other personal responsibilities. Insights on the transition from individual technical work to leadership will also be provided. The author will draw upon experiences gained in academic, industrial, and government laboratory settings, as well as extensive professional service and community involvement.

  8. DNA nanostructure immobilization to lithographic DNA arrays

    Science.gov (United States)

    Negrete, Omar D.

    Although DNA is well known for its genetic role in biology, DNA has also been sought-after as a material for the self-assembly of biological and electronic devices. Examples of DNA nanostructure construction include DNA tiled self-assembly and DNA Origami, where by controlling the sequence and concentration of DNA molecules, the rational design of geometric DNA nanostructures is possible. The assembly of DNA nanostructures takes place in solution and thus they are in disorder and require further organization to construct circuitry or devices. Hence, it is essential for future applications of this technology to develop methods to direct the placement of DNA nanostructures on a surface. To address this challenge my research examines the use of DNA microarrays to capture DNA nanostructures via DNA hybridization. Modern DNA arrays offer a high-density of sequence-specific molecular recognition sites where the addressable placement of DNA nanostructures can be achieved. Using Maskless Array Synthesizer (MAS) technology, I have characterized photolithographic DNA arrays for the hybridization of DNA complexes like large DNA molecules (> 1 kb), DNA-gold nanoparticle conjugates, and DNA Origami. Although modern photolithographic DNA arrays can possess a high-density of sequence (106/cm2), the printed DNA areas are on the order of tens of microns. Thus, I have also developed a method to reduce the DNA array spot size to nanoscale dimensions through the combined use of electron beam lithography with photolithographic DNA synthesis. This work addresses the key elements towards developing a surface patterning technology that takes advantage of DNA base-pairing for both molecular sub-assembly and surface patterning.

  9. Insights into business student's book

    CERN Document Server

    Lannon, Michael; Trappe, Tonya

    1993-01-01

    With Challenging reading and listening texts from a range of authentic business sources, New Insights into Business will really engage your students. The thorough language and vocabulary syllabus together with the strong focus on business skills development gives students everything they need to function effectively in the workplace. New Insights into Business is a self-contained course and is also an ideal follow-on to First Insights into Business.

  10. DNA curvature and flexibility in vitro and in vivo

    Science.gov (United States)

    Peters, Justin P.; Maher, L. James

    2014-01-01

    It has been more than 50 years since the elucidation of the structure of double-helical DNA. Despite active research and progress in DNA biology and biochemistry, much remains to be learned in the field of DNA biophysics. Predicting the sequence-dependent curvature and flexibility of DNA is difficult. Applicability of the conventional worm-like chain polymer model of DNA has been challenged. The fundamental forces responsible for the remarkable resistance of DNA to bending and twisting remain controversial. The apparent “softening” of DNA measured in vivo in the presence of kinking proteins and superhelical strain is incompletely understood. New methods and insights are being applied to these problems. This review places current work on DNA biophysics in historical context and illustrates the ongoing interplay between theory and experiment in this exciting field. PMID:20478077

  11. Damage, DNA Repair, Aging, and Neurodegeneration

    Science.gov (United States)

    Maynard, Scott; Fang, Evandro Fei; Scheibye-Knudsen, Morten; Croteau, Deborah L.; Bohr, Vilhelm A.

    2017-01-01

    Aging in mammals is accompanied by a progressive atrophy of tissues and organs, and stochastic damage accumulation to the macromolecules DNA, RNA, proteins, and lipids. The sequence of the human genome represents our genetic blueprint, and accumulating evidence suggests that loss of genomic maintenance may causally contribute to aging. Distinct evidence for a role of imperfect DNA repair in aging is that several premature aging syndromes have underlying genetic DNA repair defects. Accumulation of DNA damage may be particularly prevalent in the central nervous system owing to the low DNA repair capacity in postmitotic brain tissue. It is generally believed that the cumulative effects of the deleterious changes that occur in aging, mostly after the reproductive phase, contribute to species-specific rates of aging. In addition to nuclear DNA damage contributions to aging, there is also abundant evidence for a causative link between mitochondrial DNA damage and the major phenotypes associated with aging. Understanding the mechanistic basis for the association of DNA damage and DNA repair with aging and age-related diseases, such as neurodegeneration, would give insight into contravening age-related diseases and promoting a healthy life span. PMID:26385091

  12. A bouquet of DNA structures: Emerging diversity

    Directory of Open Access Journals (Sweden)

    Mahima Kaushik

    2016-03-01

    Full Text Available Structural polymorphism of DNA has constantly been evolving from the time of illustration of the double helical model of DNA by Watson and Crick. A variety of non-canonical DNA structures have constantly been documented across the globe. DNA attracted worldwide attention as a carrier of genetic information. In addition to the classical Watson–Crick duplex, DNA can actually adopt diverse structures during its active participation in cellular processes like replication, transcription, recombination and repair. Structures like hairpin, cruciform, triplex, G-triplex, quadruplex, i-motif and other alternative non-canonical DNA structures have been studied at length and have also shown their in vivo occurrence. This review mainly focuses on non-canonical structures adopted by DNA oligonucleotides which have certain prerequisites for their formation in terms of sequence, its length, number and orientation of strands along with varied solution conditions. This conformational polymorphism of DNA might be the basis of different functional properties of a specific set of DNA sequences, further giving some insights for various extremely complicated biological phenomena. Many of these structures have already shown their linkages with diseases like cancer and genetic disorders, hence making them an extremely striking target for structure-specific drug designing and therapeutic applications.

  13. Construction of DNA logic gates utilizing a H+/Ag+ induced i-motif structure.

    Science.gov (United States)

    Shi, Yunhua; Sun, Hongxia; Xiang, Junfeng; Chen, Hongbo; Yang, Qianfan; Guan, Aijiao; Li, Qian; Yu, Lijia; Tang, Yalin

    2014-12-18

    A simple technology to construct diverse DNA logic gates (OR and INHIBIT) has been designed utilizing a H(+) and/or Ag(+) induced i-motif structure. The logic gates are easily controlled and also show a real time response towards inputs. The research provides a new insight for designing DNA logic gates using an i-motif DNA structure.

  14. Rethinking transcription coupled DNA repair.

    Science.gov (United States)

    Kamarthapu, Venu; Nudler, Evgeny

    2015-04-01

    Nucleotide excision repair (NER) is an evolutionarily conserved, multistep process that can detect a wide variety of DNA lesions. Transcription coupled repair (TCR) is a subpathway of NER that repairs the transcribed DNA strand faster than the rest of the genome. RNA polymerase (RNAP) stalled at DNA lesions mediates the recruitment of NER enzymes to the damage site. In this review we focus on a newly identified bacterial TCR pathway in which the NER enzyme UvrD, in conjunction with NusA, plays a major role in initiating the repair process. We discuss the tradeoff between the new and conventional models of TCR, how and when each pathway operates to repair DNA damage, and the necessity of pervasive transcription in maintaining genome integrity. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. DNA origami: Nanorobots grab cellular control

    Science.gov (United States)

    Elbaz, Johann; Willner, Itamar

    2012-04-01

    Self-assembled barrel-like DNA nanostructures carrying active payloads and pre-programmed with logic operations to reconfigure in response to cell-surface cues can trigger a variety of intracellular functions.

  16. Competition for DNA binding sites using Promega DNA IQ™ paramagnetic beads.

    Science.gov (United States)

    Frégeau, Chantal J; De Moors, Anick

    2012-09-01

    The Promega DNA IQ™ system is easily amenable to automation and has been an integral part of standard operating procedures for many forensic laboratories including those of the Royal Canadian Mounted Police (RCMP) since 2004. Due to some failure to extract DNA from samples that should have produced DNA using our validated automated DNA IQ™-based protocol, the competition for binding sites on the DNA IQ™ magnetic beads was more closely examined. Heme from heavily blooded samples interfered slightly with DNA binding. Increasing the concentration of Proteinase K during lysis of these samples did not enhance DNA recovery. However, diluting the sample lysate following lysis prior to DNA extraction overcame the reduction in DNA yield and preserved portions of the lysates for subsequent manual or automated extraction. Dye/chemicals from black denim lysates competed for binding sites on the DNA IQ™ beads and significantly reduced DNA recovery. Increasing the size or number of black denim cuttings during lysis had a direct adverse effect on DNA yield from various blood volumes. The dilution approach was successful on these samples and permitted the extraction of high DNA yields. Alternatively, shortening the incubation time for cell lysis to 30 min instead of the usual overnight at 56 °C prevented competition from black denim dye/chemicals and increased DNA yields.

  17. A toolbox for generating single-stranded DNA in optical tweezers experiments.

    Science.gov (United States)

    Candelli, Andrea; Hoekstra, Tjalle P; Farge, Geraldine; Gross, Peter; Peterman, Erwin J G; Wuite, Gijs J L

    2013-09-01

    Essential genomic transactions such as DNA-damage repair and DNA replication take place on single-stranded DNA (ssDNA) or require specific single-stranded/double-stranded DNA (ssDNA/dsDNA) junctions (SDSJ). A significant challenge in single-molecule studies of DNA-protein interactions using optical trapping is the design and generation of appropriate DNA templates. In contrast to dsDNA, only a limited toolbox is available for the generation of ssDNA constructs for optical tweezers experiments. Here, we present several kinds of DNA templates suitable for single-molecule experiments requiring segments of ssDNA of several kilobases in length. These different biotinylated dsDNA templates can be tethered between optically trapped microspheres and can, by the subsequent use of force-induced DNA melting, be converted into partial or complete ssDNA molecules. We systematically investigated the time scale and efficiency of force-induced melting at different ionic strengths for DNA molecules of different sequences and lengths. Furthermore, we quantified the impact of microspheres of different sizes on the lifetime of ssDNA tethers in optical tweezers experiments. Together, these experiments provide deeper insights into the variables that impact the production of ssDNA for single molecules studies and represent a starting point for further optimization of DNA templates that permit the investigation of protein binding and kinetics on ssDNA. Copyright © 2013 Wiley Periodicals, Inc.

  18. Operational calculus

    CERN Document Server

    Boehme, Thomas K

    1987-01-01

    Operational Calculus, Volume II is a methodical presentation of operational calculus. An outline of the general theory of linear differential equations with constant coefficients is presented. Integral operational calculus and advanced topics in operational calculus, including locally integrable functions and convergence in the space of operators, are also discussed. Formulas and tables are included.Comprised of four sections, this volume begins with a discussion on the general theory of linear differential equations with constant coefficients, focusing on such topics as homogeneous and non-ho

  19. Operating systems

    CERN Document Server

    Tsichritzis, Dionysios C; Rheinboldt, Werner

    1974-01-01

    Operating Systems deals with the fundamental concepts and principles that govern the behavior of operating systems. Many issues regarding the structure of operating systems, including the problems of managing processes, processors, and memory, are examined. Various aspects of operating systems are also discussed, from input-output and files to security, protection, reliability, design methods, performance evaluation, and implementation methods.Comprised of 10 chapters, this volume begins with an overview of what constitutes an operating system, followed by a discussion on the definition and pr

  20. Error-resilient DNA computation

    Energy Technology Data Exchange (ETDEWEB)

    Karp, R.M.; Kenyon, C.; Waarts, O. [Univ. of California, Berkeley, CA (United States)

    1996-12-31

    The DNA model of computation, with test tubes of DNA molecules encoding bit sequences, is based on three primitives, Extract-A-Bit, which splits a test tube into two test tubes according to the value of a particular bit x, Merge-Two-Tubes and Detect-Emptiness. Perfect operations can test the satisfiability of any boolean formula in linear time. However, in reality the Extract operation is faulty; it misclassifies a certain proportion of the strands. We consider the following problem: given an algorithm based on perfect Extract, Merge and Detect operations, convert it to one that works correctly with high probability when the Extract operation is faulty. The fundamental problem in such a conversion is to construct a sequence of faulty Extracts and perfect Merges that simulates a highly reliable Extract operation. We first determine (up to a small constant factor) the minimum number of faulty Extract operations inherently required to simulate a highly reliable Extract operation. We then go on to derive a general method for converting any algorithm based on error-free operations to an error-resilient one, and give optimal error-resilient algorithms for realizing simple n-variable boolean functions such as Conjunction, Disjunction and Parity.

  1. Schwartz operators

    Science.gov (United States)

    Keyl, M.; Kiukas, J.; Werner, R. F.

    2016-05-01

    In this paper, we introduce Schwartz operators as a non-commutative analog of Schwartz functions and provide a detailed discussion of their properties. We equip them, in particular, with a number of different (but equivalent) families of seminorms which turns the space of Schwartz operators into a Fréchet space. The study of the topological dual leads to non-commutative tempered distributions which are discussed in detail as well. We show, in particular, that the latter can be identified with a certain class of quadratic forms, therefore making operations like products with bounded (and also some unbounded) operators and quantum harmonic analysis available to objects which are otherwise too singular for being a Hilbert space operator. Finally, we show how the new methods can be applied by studying operator moment problems and convergence properties of fluctuation operators.

  2. Transition Operators

    CERN Document Server

    Alcock-Zeilinger, Judith

    2016-01-01

    In this paper, we give a generic algorithm of the transition operators between Hermitian Young projection operators corresponding to equivalent irreducible representations of SU(N), using the compact expressions of Hermitian Young projection operators derived in a companion paper. We show that the Hermitian Young projection operators together with their transition operators constitute a fully orthogonal basis for the algebra of invariants of $V^{\\otimes m}$ that exhibits a systematically simplified multiplication table. We discuss the full algebra of invariants over $V^{\\otimes 3}$ and $V^{\\otimes 4}$ as explicit examples. In our presentation we make use of various standard concepts such as Young projection operators, Clebsch-Gordan operators, and invariants (in birdtrack notation). We tie these perspectives together and use them to shed light on each other.

  3. Insight with hands and things

    DEFF Research Database (Denmark)

    Vallée-Tourangeau, Frédéric; Steffensen, S. V.; Vallée-Tourangeau, Gaëlle

    2016-01-01

    Two experiments examined whether different task ecologies influenced insight problem solving. The 17 animals problem was employed, a pure insight problem. Its initial formulation encourages the application of a direct arithmetic solution, but its solution requires the spatial arrangement of sets...

  4. Cognitive insight: A systematic review.

    Science.gov (United States)

    Van Camp, L S C; Sabbe, B G C; Oldenburg, J F E

    2017-07-01

    Cognitive insight is the ability to re-evaluate thoughts and beliefs in order to make thoughtful conclusions. It differs from clinical insight, as it focuses on more general metacognitive processes. Therefore, it could be relevant to diverse disorders and non-clinical subjects. There is a growing body of research on cognitive insight in individuals with and without psychosis. This review has summarised the current state of the art regarding this topic. We conclude that while cognitive insight in its current form seems valid for use in individuals with psychosis, it is less so for individuals without psychosis. Additionally, higher cognitive insight not always leads to better psychological functioning. For instance, higher levels of self-reflection are often associated with depressive mood. We therefore recommend the sub-components of cognitive insight to be studied separately. Also, it is unclear what position cognitive insight takes within the spectrum of metacognitive processes and how it relates to other self-related concepts that have been defined previously in literature. Combining future and past research on cognitive insight and its analogue concepts will help in the formation of a uniform definition that fits all subjects discussed here. Copyright © 2017. Published by Elsevier Ltd.

  5. Systemic sclerosis: Recent insights.

    Science.gov (United States)

    Elhai, Muriel; Avouac, Jérôme; Kahan, André; Allanore, Yannick

    2015-05-01

    Systemic sclerosis is an orphan connective tissue disease characterized by alterations of the microvasculature, disturbances of the immune system and massive deposition of collagen and other matrix substances in the skin and internal organs. A major achievement of the recent years has been the validation of new classification criteria, allowing earlier diagnosis and earlier treatment of systemic sclerosis, before irreversible fibrosis and organ damage appeared ("window of opportunity"). Raynaud's phenomenon is usually the first sign of the disease and is considered as the main sentinel sign for the identification of very early systemic sclerosis. Systemic sclerosis is clinically heterogeneous and disease course remains unpredictable. Its prognosis depends on cardiopulmonary involvement and recent studies aim to identify serum or genetic biomarkers predictive of severe organ involvement. Moreover, the prospective follow-up of large cohorts has provided and will offer critical material to identify strong prognostic factors. Whereas the outcomes of vascular manifestations of the disease has been recently improved due to targeted therapy, recent data have highlighted that mortality has not changed over the past 40 years. This reflects the absence of efficacy of current available drugs to counteract the fibrotic process. Nevertheless, several targeted immunity therapies, commonly with proven efficacy in other immune diseases, are about to be investigated in systemic sclerosis. Indeed, promising results in small and open studies have been reported. This article deals with recent insights into classification criteria, pathogenesis, organ involvements, outcome and current and possible future therapeutic options in systemic sclerosis.

  6. O insight em psiquiatria

    Directory of Open Access Journals (Sweden)

    Ana Margarida P. Cardoso

    2008-12-01

    Full Text Available O sinal de que algo está a acontecer contribui para que o paciente reconheça que alguma coisa de estranho se está a passar consigo. Este reconhecimento faz com que o sujeito possa desempenhar uma função activa e seja um elemento colaborante do seu processo de recuperação. Cada doença apresenta, contudo, diferentes sintomas, uma vez que cada doença psiquiátrica consiste em diferentes perturbações com diversos efeitos sobre o funcionamento mental. Desta maneira, o fenómeno do insight que é registado em cada doença é diferente e expressa-se sob diferentes formas, não somente devido às manifestações clínicas da doença mas também devido às características individuais do sujeito.

  7. JavaScript DNA translator: DNA-aligned protein translations.

    Science.gov (United States)

    Perry, William L

    2002-12-01

    There are many instances in molecular biology when it is necessary to identify ORFs in a DNA sequence. While programs exist for displaying protein translations in multiple ORFs in alignment with a DNA sequence, they are often expensive, exist as add-ons to software that must be purchased, or are only compatible with a particular operating system. JavaScript DNA Translator is a shareware application written in JavaScript, a scripting language interpreted by the Netscape Communicator and Internet Explorer Web browsers, which makes it compatible with several different operating systems. While the program uses a familiar Web page interface, it requires no connection to the Internet since calculations are performed on the user's own computer. The program analyzes one or multiple DNA sequences and generates translations in up to six reading frames aligned to a DNA sequence, in addition to displaying translations as separate sequences in FASTA format. ORFs within a reading frame can also be displayed as separate sequences. Flexible formatting options are provided, including the ability to hide ORFs below a minimum size specified by the user. The program is available free of charge at the BioTechniques Software Library (www.Biotechniques.com).

  8. Compressive Sensing DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Richard G. Baraniuk

    2009-01-01

    Full Text Available Compressive sensing microarrays (CSMs are DNA-based sensors that operate using group testing and compressive sensing (CS principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization times are allowed.

  9. Diagnostic accuracy of insight intraoral film on dental caries

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Young Nam; Lee, Byung Do [Wonkwang University College of Medicine, Iksan (Korea, Republic of); Lee, Sang Rae [Kyunghee University College of Medicine, Seoul (Korea, Republic of)

    2004-03-15

    To compare the diagnostic accuracy of Kodak Insight film with other intra-oral films in the detection of dental caries. Periapical radiographs of 99 extracted human teeth with sound proximal surfaces and interproximal artificial cavities were made on Kodak Ultra speed, Ektaspeed, Agfa Ektaspeed and Kodak Insight films and automatically processed. Six dentists examined the presence of dental caries using a five-point confidence rating scale and compared the diagnostic accuracy by ROC (Receiver Operating Characteristic) analysis and ANOVA test. The sensitivity of Kodak Ultra speed, Ektaspeed, Agfa Ektaspeed and Insight film were 0.84, 0.77, 0.75 and 0.79 respectively. The specificity of Kodak Ultra speed, Ektaspeed, Agfa Ektaspeed and Insight film were 0.97, 0.95, 0.96 and 0.94 respectively. The mean ROC areas (Az) of Kodak Ultra speed, Ektaspeed, Agfa Ektaspeed and Insight film were 0.917, 0.910, 0.894, 0.909 respectively. There was no significant differences between Az of Insight film and other films (p = 0.178). Theses results suggested that Kodak Insight film have the comparative diagnostic accuracy of dental caries with Ultraspeed and Ektaspeed films. (77)

  10. DNA nanostructure meets nanofabrication.

    Science.gov (United States)

    Zhang, Guomei; Surwade, Sumedh P; Zhou, Feng; Liu, Haitao

    2013-04-07

    Recent advances in DNA nanotechnology have made it possible to construct DNA nanostructures of almost arbitrary shapes with 2-3 nm of precision in their dimensions. These DNA nanostructures are ideal templates for bottom-up nanofabrication. This review highlights the challenges and recent advances in three areas that are directly related to DNA-based nanofabrication: (1) fabrication of large scale DNA nanostructures; (2) pattern transfer from DNA nanostructure to an inorganic substrate; and (3) directed assembly of DNA nanostructures.

  11. Spacecraft operations

    CERN Document Server

    Sellmaier, Florian; Schmidhuber, Michael

    2015-01-01

    The book describes the basic concepts of spaceflight operations, for both, human and unmanned missions. The basic subsystems of a space vehicle are explained in dedicated chapters, the relationship of spacecraft design and the very unique space environment are laid out. Flight dynamics are taught as well as ground segment requirements. Mission operations are divided into preparation including management aspects, execution and planning. Deep space missions and space robotic operations are included as special cases. The book is based on a course held at the German Space Operation Center (GSOC).

  12. Conventional and nanotechniques for DNA methylation profiling.

    Science.gov (United States)

    Shanmuganathan, Rajasree; Basheer, Nazeema B; Amirthalingam, Laxmi; Muthukumar, Harshiny; Kaliaperumal, Rajendran; Shanmugam, Kumaran

    2013-01-01

    DNA methylation is critical for gene silencing and is associated with the incidence of many diseases, including cancer. Underlying molecular mechanisms of human diseases and tissue-specific gene expression have been elucidated based on DNA methylation studies. This review highlights the advantages and drawbacks of various methylation screening techniques: blotting, genomic sequencing, bisulfite sequencing, methylation-specific PCR, methylated DNA immunoprecipitation, microarray analysis, matrix-assisted laser desorption ionization time-of-flight mass spectroscopy, nanowire transistor detection procedure, quantum dot-based nanoassay, single-molecule real-time detection, fluorimetric assay, electrochemical detection, and atomic force spectroscopy. The review provides insight for selecting a method or a combination of methods for DNA methylation analysis. Convergence of conventional and contemporary nanotechniques to enumerate methylation at specific CpG sites of oncogene would fill the gap in diagnosis of cancer.

  13. Collaborations between CpG sites in DNA methylation

    Science.gov (United States)

    Song, You; Ren, Honglei; Lei, Jinzhi

    2017-08-01

    DNA methylation patterns have profound impacts on genome stability, gene expression and development. The molecular base of DNA methylation patterns has long been focused at single CpG sites level. Here, we construct a kinetic model of DNA methylation with collaborations between CpG sites, from which a correlation function was established based on experimental data. The function consists of three parts that suggest three possible sources of the correlation: movement of enzymes along DNA, collaboration between DNA methylation and nucleosome modification, and global enzyme concentrations within a cell. Moreover, the collaboration strength between DNA methylation and nucleosome modification is universal for mouse early embryo cells. The obtained correlation function provides insightful understanding for the mechanisms of inheritance of DNA methylation patterns.

  14. Insights into distinct regulatory modes of nucleosome positioning

    Directory of Open Access Journals (Sweden)

    Feng Jihua

    2009-12-01

    Full Text Available Abstract Background The nucleosome is the fundamental unit of eukaryotic genomes. Experimental evidence suggests that the genomic DNA sequence and a variety of protein factors contribute to nucleosome positioning in vivo. However, how nucleosome positioning is determined locally is still largely unknown. Results We found that transcription factor binding sites (TFBSs with particular nucleosomal contexts show a preference to reside on specific chromosomes. We identified four typical gene classes associated with distinct regulatory modes of nucleosome positioning, and further showed that they are distinguished by transcriptional regulation patterns. The first mode involves the cooperativity between chromatin remodeling and stable transcription factor (TF-DNA binding that is linked to high intrinsic DNA binding affinities, evicting nucleosomes from favorable DNA sequences. The second is the DNA-encoded low nucleosome occupancy that is associated with high gene activity. The third is through chromatin remodeling and histone acetylation, sliding nucleosomes along DNA. This mode is linked to more cryptic sites for TF binding. The last consists of the nucleosome-enriched organization driven by other factors that overrides nucleosome sequence preferences. In addition, we showed that high polymerase II (Pol II occupancy is associated with high nucleosome occupancy around the transcription start site (TSS. Conclusions We identified four different regulatory modes of nucleosome positioning and gave insights into mechanisms that specify promoter nucleosome location. We suggest two distinct modes of recruitment of Pol II, which are selectively employed by different genes.

  15. Recent Neurobiological Insights into the Concept of Insight in Psychosis.

    Science.gov (United States)

    Mythri, Starlin Vijay; Sanjay, Y

    2016-01-01

    The concept of insight in psychosis has been an interesting area in clinical psychiatry for well over a century with a surge in research interest over the past 25 years. Moreover, the past 5 years have been particularly fruitful in deciphering its neurobiological underpinnings. This article presents the development of the concept of insight in psychosis and reviews the current neurobiological research findings in this area.

  16. Recent Neurobiological Insights into the Concept of Insight in Psychosis

    Science.gov (United States)

    Mythri, Starlin Vijay; Sanjay, Y

    2016-01-01

    The concept of insight in psychosis has been an interesting area in clinical psychiatry for well over a century with a surge in research interest over the past 25 years. Moreover, the past 5 years have been particularly fruitful in deciphering its neurobiological underpinnings. This article presents the development of the concept of insight in psychosis and reviews the current neurobiological research findings in this area. PMID:27335512

  17. QPSO-based adaptive DNA computing algorithm.

    Science.gov (United States)

    Karakose, Mehmet; Cigdem, Ugur

    2013-01-01

    DNA (deoxyribonucleic acid) computing that is a new computation model based on DNA molecules for information storage has been increasingly used for optimization and data analysis in recent years. However, DNA computing algorithm has some limitations in terms of convergence speed, adaptability, and effectiveness. In this paper, a new approach for improvement of DNA computing is proposed. This new approach aims to perform DNA computing algorithm with adaptive parameters towards the desired goal using quantum-behaved particle swarm optimization (QPSO). Some contributions provided by the proposed QPSO based on adaptive DNA computing algorithm are as follows: (1) parameters of population size, crossover rate, maximum number of operations, enzyme and virus mutation rate, and fitness function of DNA computing algorithm are simultaneously tuned for adaptive process, (2) adaptive algorithm is performed using QPSO algorithm for goal-driven progress, faster operation, and flexibility in data, and (3) numerical realization of DNA computing algorithm with proposed approach is implemented in system identification. Two experiments with different systems were carried out to evaluate the performance of the proposed approach with comparative results. Experimental results obtained with Matlab and FPGA demonstrate ability to provide effective optimization, considerable convergence speed, and high accuracy according to DNA computing algorithm.

  18. QPSO-Based Adaptive DNA Computing Algorithm

    Directory of Open Access Journals (Sweden)

    Mehmet Karakose

    2013-01-01

    Full Text Available DNA (deoxyribonucleic acid computing that is a new computation model based on DNA molecules for information storage has been increasingly used for optimization and data analysis in recent years. However, DNA computing algorithm has some limitations in terms of convergence speed, adaptability, and effectiveness. In this paper, a new approach for improvement of DNA computing is proposed. This new approach aims to perform DNA computing algorithm with adaptive parameters towards the desired goal using quantum-behaved particle swarm optimization (QPSO. Some contributions provided by the proposed QPSO based on adaptive DNA computing algorithm are as follows: (1 parameters of population size, crossover rate, maximum number of operations, enzyme and virus mutation rate, and fitness function of DNA computing algorithm are simultaneously tuned for adaptive process, (2 adaptive algorithm is performed using QPSO algorithm for goal-driven progress, faster operation, and flexibility in data, and (3 numerical realization of DNA computing algorithm with proposed approach is implemented in system identification. Two experiments with different systems were carried out to evaluate the performance of the proposed approach with comparative results. Experimental results obtained with Matlab and FPGA demonstrate ability to provide effective optimization, considerable convergence speed, and high accuracy according to DNA computing algorithm.

  19. Involvement of DNA ligase III and ribonuclease H1 in mitochondrial DNA replication in cultured human cells.

    Science.gov (United States)

    Ruhanen, Heini; Ushakov, Kathy; Yasukawa, Takehiro

    2011-12-01

    Recent evidence suggests that coupled leading and lagging strand DNA synthesis operates in mammalian mitochondrial DNA (mtDNA) replication, but the factors involved in lagging strand synthesis are largely uncharacterised. We investigated the effect of knockdown of the candidate proteins in cultured human cells under conditions where mtDNA appears to replicate chiefly via coupled leading and lagging strand DNA synthesis to restore the copy number of mtDNA to normal levels after transient mtDNA depletion. DNA ligase III knockdown attenuated the recovery of mtDNA copy number and appeared to cause single strand nicks in replicating mtDNA molecules, suggesting the involvement of DNA ligase III in Okazaki fragment ligation in human mitochondria. Knockdown of ribonuclease (RNase) H1 completely prevented the mtDNA copy number restoration, and replication intermediates with increased single strand nicks were readily observed. On the other hand, knockdown of neither flap endonuclease 1 (FEN1) nor DNA2 affected mtDNA replication. These findings imply that RNase H1 is indispensable for the progression of mtDNA synthesis through removing RNA primers from Okazaki fragments. In the nucleus, Okazaki fragments are ligated by DNA ligase I, and the RNase H2 is involved in Okazaki fragment processing. This study thus proposes that the mitochondrial replication system utilises distinct proteins, DNA ligase III and RNase H1, for Okazaki fragment maturation.

  20. Temperature effect on DNA molecular wires

    Science.gov (United States)

    Bui, Christopher Minh

    The demand of technology and information today has further pushed the fabrication process of nanotechnology, yet there are limits and obstacles set by the primary laws of physics. Therefore, researchers are pursuing alternative technologies. Deoxyribonucleic acids (DNA) molecular wire is one advantageous option due to its unique characteristics including self-assembly and naturally small; size. This thesis reports the temperature effect on the electrical properties of a double-stranded ?-DNA molecular wire. The data will help expand the DNA wire application and functionality. Thus, the data supports the charge hopping theory on DNA electrical conductivity. Diverse amount of literatures has demonstrated that DNA experiences a biochemical alteration when exposed under different temperature conditions. This change will also cause a change in the electrical properties. In this research, DNA will hang between two gold covered microelectrodes with a distance of 10 to 12 microns. The microelectrodes are fabricated through negative lithography techniques. Then, the samples were exposed to a numerous range of temperature from 25°C to 180°C and went through varying cycles of heating and cooling. The experimental results revealed that the DNA experienced a hysteresis like behavior where the impedance differed between the heating and cooling phase. The impedance of the DNA molecular wire increased when exposed to higher temperature. Furthermore, the impedance stops increasing after a certain amount of heat cycles before the DNA structure failed. The biology and thermodynamics of the DNA wire was analyzed due to the temperature hysteresis effect. The melting temperature and the bond dissociation temperature were evaluated to determine the cause of the impedance trends. The studies and analysis of the temperature effect provided certain insights towards the charge hopping transport mechanism. The thesis concludes with possible applications relating to the temperature effect of

  1. The DNA damage response during mitosis.

    Science.gov (United States)

    Heijink, Anne Margriet; Krajewska, Małgorzata; van Vugt, Marcel A T M

    2013-10-01

    Cells are equipped with a cell-intrinsic signaling network called the DNA damage response (DDR). This signaling network recognizes DNA lesions and initiates various downstream pathways to coordinate a cell cycle arrest with the repair of the damaged DNA. Alternatively, the DDR can mediate clearance of affected cells that are beyond repair through apoptosis or senescence. The DDR can be activated in response to DNA damage throughout the cell cycle, although the extent of DDR signaling is different in each cell cycle phase. Especially in response to DNA double strand breaks, only a very marginal response was observed during mitosis. Early on it was recognized that cells which are irradiated during mitosis continued division without repairing broken chromosomes. Although these initial observations indicated diminished DNA repair and lack of an acute DNA damage-induced cell cycle arrest, insight into the mechanistic re-wiring of DDR signaling during mitosis was only recently provided. Different mechanisms appear to be at play to inactivate specific signaling axes of the DDR network in mitosis. Importantly, mitotic cells not simply inactivate the entire DDR, but appear to mark their DNA damage for repair after mitotic exit. Since the treatment of cancer frequently involves agents that induce DNA damage as well as agents that block mitotic progression, it is clinically relevant to obtain a better understanding of how cancer cells deal with DNA damage during interphase versus mitosis. In this review, the molecular details concerning DDR signaling during mitosis as well as the consequences of encountering DNA damage during mitosis for cellular fate are discussed.

  2. The DNA damage response during mitosis

    Energy Technology Data Exchange (ETDEWEB)

    Heijink, Anne Margriet; Krajewska, Małgorzata; Vugt, Marcel A.T.M. van, E-mail: m.vugt@umcg.nl

    2013-10-15

    Cells are equipped with a cell-intrinsic signaling network called the DNA damage response (DDR). This signaling network recognizes DNA lesions and initiates various downstream pathways to coordinate a cell cycle arrest with the repair of the damaged DNA. Alternatively, the DDR can mediate clearance of affected cells that are beyond repair through apoptosis or senescence. The DDR can be activated in response to DNA damage throughout the cell cycle, although the extent of DDR signaling is different in each cell cycle phase. Especially in response to DNA double strand breaks, only a very marginal response was observed during mitosis. Early on it was recognized that cells which are irradiated during mitosis continued division without repairing broken chromosomes. Although these initial observations indicated diminished DNA repair and lack of an acute DNA damage-induced cell cycle arrest, insight into the mechanistic re-wiring of DDR signaling during mitosis was only recently provided. Different mechanisms appear to be at play to inactivate specific signaling axes of the DDR network in mitosis. Importantly, mitotic cells not simply inactivate the entire DDR, but appear to mark their DNA damage for repair after mitotic exit. Since the treatment of cancer frequently involves agents that induce DNA damage as well as agents that block mitotic progression, it is clinically relevant to obtain a better understanding of how cancer cells deal with DNA damage during interphase versus mitosis. In this review, the molecular details concerning DDR signaling during mitosis as well as the consequences of encountering DNA damage during mitosis for cellular fate are discussed.

  3. DNA damage response and Autophagy: a meaningful partnership

    Directory of Open Access Journals (Sweden)

    ARISTIDES G ELIOPOULOS

    2016-11-01

    Full Text Available Autophagy and the DNA damage response (DDR are biological processes essential for cellular and organismal homeostasis. Herein we summarize and discuss emerging evidence linking DDR to autophagy. We highlight published data suggesting that autophagy is activated by DNA damage and is required for several functional outcomes of DDR signaling, including repair of DNA lesions, senescence, cell death, and cytokine secretion. Uncovering the mechanisms by which autophagy and DDR are intertwined provides novel insight into the pathobiology of conditions associated with accumulation of DNA damage, including cancer and aging, and novel concepts for the development of improved therapeutic strategies against these pathologies.

  4. DNA replication origin activation in space and time.

    Science.gov (United States)

    Fragkos, Michalis; Ganier, Olivier; Coulombe, Philippe; Méchali, Marcel

    2015-06-01

    DNA replication begins with the assembly of pre-replication complexes (pre-RCs) at thousands of DNA replication origins during the G1 phase of the cell cycle. At the G1-S-phase transition, pre-RCs are converted into pre-initiation complexes, in which the replicative helicase is activated, leading to DNA unwinding and initiation of DNA synthesis. However, only a subset of origins are activated during any S phase. Recent insights into the mechanisms underlying this choice reveal how flexibility in origin usage and temporal activation are linked to chromosome structure and organization, cell growth and differentiation, and replication stress.

  5. Caged DNA does not aggregate in high ionic strength solutions.

    Science.gov (United States)

    Trubetskoy, V S; Loomis, A; Slattum, P M; Hagstrom, J E; Budker, V G; Wolff, J A

    1999-01-01

    The assembly of DNA into compact particles that do not aggregate in physiologic salt solution occurs naturally in chromatin and viral particles but has been challenging to duplicate using artificial constructs. Cross-linking amino-containing polycations in the presence of DNA with bisimidoester cross-linker leads to the formation of caged DNA particles that are stable in salt solutions. This first demonstration of caged DNA provides insight into how natural condensation processes avoid aggregation and a promising avenue for developing nonviral gene therapy vectors.

  6. Operation REDWING

    Science.gov (United States)

    1956-07-31

    only 16mm cinemascope films would be available after 1 August 1956t Act- tion was taken to modify the screens of the Terrace and Starlite theaters...approximately 900, was in operation throughout the interim and operational period. The Starlite Theater, which seats approximately 600, opened in

  7. OPERATION ASKARI

    African Journals Online (AJOL)

    operation using conventional arms against Swapo Plan, while they were still massed in their .... stationed there was no real threat to our planned operation. the idea was to sow confusion in the minds ...... A four by four transport vehi- cle, based ...

  8. Operational Sequencing

    DEFF Research Database (Denmark)

    Nielsen, Thomas Rosendal; Hustvedt, Kjersti

    2016-01-01

    by Bakhtinian theory, Brian Edmiston developed a solution to this in the 1990s: the principle of ‘dialogic sequencing’. Aiming to escape the conflict between relativism and absolutism, we present an alternative to Edmiston’s approach, based on Niklas Luhmann’s theory of ‘operational closure’: operational...

  9. Business & Operations

    Science.gov (United States)

    Agron, Joe

    2007-01-01

    This article presents an interview with John D. Musso, executive director of the Association of School Business Officials (ASBO) International. Musso talks about trends and issues that will most affect school business and operations in 2007 and beyond. Despite the challenges facing school operations, he believes that the key to being successful at…

  10. Operation crosscheck

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, F. C.

    1964-11-06

    This report consists of three sections covering the three major areas of Lawrence Livermore Laboratory`s participation in Operation Crosscheck. These areas are: Diagnostic Aircraft; Radiochemical Sampling; and Device Assembly and Handling, Barbers Point. The information contained in these sections has been extracted from Crosscheck post-operation reports.

  11. Operational Amplifiers.

    Science.gov (United States)

    Foxcroft, G. E.

    1986-01-01

    Addresses the introduction of low cost equipment into high school and college physical science classes. Examines the properties of an "ideal" operational amplifier and discusses how it might be used under saturated and non-saturated conditions. Notes the action of a "real" operational amplifier. (TW)

  12. DNA packaging induced by micellar aggregates: a novel in vitro DNA condensation system.

    Science.gov (United States)

    Ghirlando, R; Wachtel, E J; Arad, T; Minsky, A

    1992-08-11

    Evidence for a conceptually novel DNA packaging process is presented. X-ray scattering, electron microscopy, and circular dichroism measurements indicate that in the presence of positively charged micellar aggregates and flexible anionic polymers, such as negatively charged polypeptides or single-stranded RNA species, a complex is formed in which DNA molecules are partially embedded within a micellar scaffold and partially condensed into highly packed chiral structures. Based on studies of micelle-DNA and micelle-flexible anionic polymer systems, as well as on the known effects of a high charge density upon the micellar organization, a DNA packaging model is proposed. According to this model, the DNA induces the elongation of the micelles into rodlike aggregates, forming a closely packed matrix in which the DNA molecules are immobilized. In contrast, the flexible anionic polymers stabilize clusters of spherical micelles which are proposed to effect a capping of the rodlike micelles, thus arresting their elongation and creating surfactant-free segments of the DNA that are able to converge and collapse. Thus, unlike other in vitro DNA packaging systems, in which condensation follows encounters between charge-neutralized DNA molecules, a prepackaging phase where the DNA is immobilized within a matrix is proposed in this case. Cellular and nuclear membranes have been implicated in DNA packaging processes in vivo, and negatively charged polyelectrolytes were shown to be involved in the processes. These observations, combined with the basic tenets of the DNA condensation system described here, allow for the progression to the study of more elaborate model systems and thus might lead to insights into the nature and roles of the intricate in vivo DNA-membrane complexes.

  13. Probing DNA-DNA Interactions with a Combination of Quadruple-Trap Optical Tweezers and Microfluidics.

    Science.gov (United States)

    Brouwer, Ineke; King, Graeme A; Heller, Iddo; Biebricher, Andreas S; Peterman, Erwin J G; Wuite, Gijs J L

    2017-01-01

    DNA metabolism and DNA compaction in vivo involve frequent interactions of remote DNA segments, mediated by proteins. In order to gain insight into such interactions, quadruple-trap optical tweezers have been developed. This technique provides an unprecedented degree of control through the ability to independently manipulate two DNA molecules in three dimensions. In this way, discrete regions of different DNA molecules can be brought into contact with one another, with a well-defined spatial configuration. At the same time, the tension and extension of the DNA molecules can be monitored. Furthermore, combining quadruple-trap optical tweezers with microfluidics makes fast buffer exchange possible, which is important for in situ generation of the dual DNA-protein constructs needed for these kinds of experiments. In this way, processes such as protein-mediated inter-DNA bridging can be studied with unprecedented control. This chapter provides a step-by-step description of how to perform a dual DNA manipulation experiment using combined quadruple-trap optical tweezers and microfluidics.

  14. Dynamics and Control of DNA Sequence Amplification

    CERN Document Server

    Marimuthu, Karthikeyan

    2014-01-01

    DNA amplification is the process of replication of a specified DNA sequence \\emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction (PCR) as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal tempe...

  15. Trends in operations strategy research

    Directory of Open Access Journals (Sweden)

    Ana Beatriz Lopes de Sousa Jabbour

    2009-12-01

    Full Text Available This article aims to identify research approaches in operations strategy research, with regards its content. From a systematic literature review we highlight the main definitions of operations strategy and discussions on competitive priorities and then, present the main focuses of the articles published in reputable journals nationally and internationally. It was identified that studies on the operations strategy followed in general the direction of relating the influence and the alignment of competitive priorities for structural and infrastructure decisions. And there are initiatives of studies, which derive from that, to relate the operations strategy in the context of supply chain, which in future may be an important trend. The results of this article bring insights on research trends in a subject with constant interest from researchers in the field of operations management.

  16. Dynamics of DNA in vitro evolution

    Institute of Scientific and Technical Information of China (English)

    Xiaojing Yang; Xili Liu; Chunbo Lou; Qi Ouyang

    2009-01-01

    In vitro evolution has become a very important research area in recent years. From a practical point of view, it provides a powerful and reliable tool for engineering functional molecules (DNA, RNA or proteins) in reasonably short periods of time. From a theoretical point of view, since in vitro evolution is analogous to natural evolution in many respects, the study of the dynamic details of in vitro evolution may provide some instructive insights into the process of evolution. In this review, we summarize current theoretical and exper-imental studies, including several efforts made by our group, on the dynamics of DNA in vitro evolution.

  17. DNA ligase I, the replicative DNA ligase.

    Science.gov (United States)

    Howes, Timothy R L; Tomkinson, Alan E

    2012-01-01

    Multiple DNA ligation events are required to join the Okazaki fragments generated during lagging strand DNA synthesis. In eukaryotes, this is primarily carried out by members of the DNA ligase I family. The C-terminal catalytic region of these enzymes is composed of three domains: a DNA binding domain, an adenylation domain and an OB-fold domain. In the absence of DNA, these domains adopt an extended structure but transition into a compact ring structure when they engage a DNA nick, with each of the domains contacting the DNA. The non-catalytic N-terminal region of eukaryotic DNA ligase I is responsible for the specific participation of these enzymes in DNA replication. This proline-rich unstructured region contains the nuclear localization signal and a PCNA interaction motif that is critical for localization to replication foci and efficient joining of Okazaki fragments. DNA ligase I initially engages the PCNA trimer via this interaction motif which is located at the extreme N-terminus of this flexible region. It is likely that this facilitates an additional interaction between the DNA binding domain and the PCNA ring. The similar size and shape of the rings formed by the PCNA trimer and the DNA ligase I catalytic region when it engages a DNA nick suggest that these proteins interact to form a double-ring structure during the joining of Okazaki fragments. DNA ligase I also interacts with replication factor C, the factor that loads the PCNA trimeric ring onto DNA. This interaction, which is regulated by phosphorylation of the non-catalytic N-terminus of DNA ligase I, also appears to be critical for DNA replication.

  18. Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture.

    Science.gov (United States)

    Mayanagi, Kouta; Kiyonari, Shinichi; Saito, Mihoko; Shirai, Tsuyoshi; Ishino, Yoshizumi; Morikawa, Kosuke

    2009-03-24

    The 3D structure of the ternary complex, consisting of DNA ligase, the proliferating cell nuclear antigen (PCNA) clamp, and DNA, was investigated by single-particle analysis. This report presents the structural view, where the crescent-shaped DNA ligase with 3 distinct domains surrounds the central DNA duplex, encircled by the closed PCNA ring, thus forming a double-layer structure with dual contacts between the 2 proteins. The relative orientations of the DNA ligase domains, which remarkably differ from those of the known crystal structures, suggest that a large domain rearrangement occurs upon ternary complex formation. A second contact was found between the PCNA ring and the middle adenylation domain of the DNA ligase. Notably, the map revealed a substantial DNA tilt from the PCNA ring axis. This structure allows us to propose a switching mechanism for the replication factors operating on the PCNA ring.

  19. Reactor operation

    CERN Document Server

    Shaw, J

    2013-01-01

    Reactor Operation covers the theoretical aspects and design information of nuclear reactors. This book is composed of nine chapters that also consider their control, calibration, and experimentation.The opening chapters present the general problems of reactor operation and the principles of reactor control and operation. The succeeding chapters deal with the instrumentation, start-up, pre-commissioning, and physical experiments of nuclear reactors. The remaining chapters are devoted to the control rod calibrations and temperature coefficient measurements in the reactor. These chapters also exp

  20. Operator programs and operator processes

    NARCIS (Netherlands)

    Bergstra, J.A.; Walters, P.

    2003-01-01

    We define a notion of program which is not a computer program but an operator program: a detailed description of actions performed and decisions taken by a human operator (computer user) performing a task to achieve a goal in a simple setting consisting of that user, one or more computers and a

  1. Operator programs and operator processes

    NARCIS (Netherlands)

    Bergstra, J.A.; Walters, P.

    2003-01-01

    We define a notion of program which is not a computer program but an operator program: a detailed description of actions performed and decisions taken by a human operator (computer user) performing a task to achieve a goal in a simple setting consisting of that user, one or more computers and a work

  2. Self-assembly programming of DNA polyominoes.

    Science.gov (United States)

    Ong, Hui San; Syafiq-Rahim, Mohd; Kasim, Noor Hayaty Abu; Firdaus-Raih, Mohd; Ramlan, Effirul Ikhwan

    2016-10-20

    Fabrication of functional DNA nanostructures operating at a cellular level has been accomplished through molecular programming techniques such as DNA origami and single-stranded tiles (SST). During implementation, restrictive and constraint dependent designs are enforced to ensure conformity is attainable. We propose a concept of DNA polyominoes that promotes flexibility in molecular programming. The fabrication of complex structures is achieved through self-assembly of distinct heterogeneous shapes (i.e., self-organised optimisation among competing DNA basic shapes) with total flexibility during the design and assembly phases. In this study, the plausibility of the approach is validated using the formation of multiple 3×4 DNA network fabricated from five basic DNA shapes with distinct configurations (monomino, tromino and tetrominoes). Computational tools to aid the design of compatible DNA shapes and the structure assembly assessment are presented. The formations of the desired structures were validated using Atomic Force Microscopy (AFM) imagery. Five 3×4 DNA networks were successfully constructed using combinatorics of these five distinct DNA heterogeneous shapes. Our findings revealed that the construction of DNA supra-structures could be achieved using a more natural-like orchestration as compared to the rigid and restrictive conventional approaches adopted previously.

  3. Recognition of Local DNA Structures by p53 Protein.

    Science.gov (United States)

    Brázda, Václav; Coufal, Jan

    2017-02-10

    p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells.

  4. Net Operations

    Institute of Scientific and Technical Information of China (English)

    蒋昌俊; 吴哲辉

    1992-01-01

    Two kinds of net operations.addition and Cartesian production of P/T nets,are introduced.They are defined on the set of underlying net of P/T systems.The conditions for preserving structural properties of Petri net after these operations are discussed.It is shown that the set of P/T nets forms and Abelian group for net addition operation and the inverse net of a P/T net in usual meaning of net theory is exactly the inverse of this P/T net as an element of the P/T net group;and that the set of P/T nets forms an Abelian ring for net addition and Caresian product operations.

  5. Operable Units

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of operable unit data from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times and...

  6. Operator theory

    CERN Document Server

    2015-01-01

    A one-sentence definition of operator theory could be: The study of (linear) continuous operations between topological vector spaces, these being in general (but not exclusively) Fréchet, Banach, or Hilbert spaces (or their duals). Operator theory is thus a very wide field, with numerous facets, both applied and theoretical. There are deep connections with complex analysis, functional analysis, mathematical physics, and electrical engineering, to name a few. Fascinating new applications and directions regularly appear, such as operator spaces, free probability, and applications to Clifford analysis. In our choice of the sections, we tried to reflect this diversity. This is a dynamic ongoing project, and more sections are planned, to complete the picture. We hope you enjoy the reading, and profit from this endeavor.

  7. Insights in Public Health

    Science.gov (United States)

    Choy, Lehua B; Smith, Heidi Hansen; Espiritu, Justine; Higa, Earl; Lee, Thomas; Maddock, Jay

    2015-01-01

    Abstract In 2011, a small pilot bike share program was established in the town core of Kailua, Hawai‘i, with funding from the Hawai‘i State Department of Health. The Kailua system consisted of two stations with 12 bicycles, and the goal was to secure additional funding to expand the station network in the future. Community feedback consistently indicated support for the bike share program. However, system metrics showed low levels of usage, averaging 41.5 rides per month (2011–2014). From observational data, users were primarily tourists. With minimal local staff, the bike share program had limited resources for promotion and education, which may have hindered potential use by local residents. Management of station operations and bike maintenance were additional, ongoing barriers to success. Despite the challenges, the pilot bike share program was valuable in several ways. It introduced the bike share concept to Hawai‘i, thereby helping to build awareness and connect an initial network of stakeholders. Furthermore, the pilot bike share program informed the development of a larger bike share program for urban Honolulu. As limited information exists in the literature about the experiences of smaller bike share programs and their unique considerations, this article shares lessons learned for other communities interested in starting similar bike share programs. PMID:26535166

  8. Chiroplasmonic DNA-based nanostructures

    Science.gov (United States)

    Cecconello, Alessandro; Besteiro, Lucas V.; Govorov, Alexander O.; Willner, Itamar

    2017-09-01

    Chiroplasmonic properties of nanoparticles, organized using DNA-based nanostructures, have attracted both theoretical and experimental interest. Theory suggests that the circular dichroism spectra accompanying chiroplasmonic nanoparticle assemblies are controlled by the sizes, shapes, geometries and interparticle distances of the nanoparticles. In this Review, we present different methods to assemble chiroplasmonic nanoparticle or nanorod systems using DNA scaffolds, and we discuss the operations of dynamically reconfigurable chiroplasmonic nanostructures. The chiroplasmonic properties of the different systems are characterized by circular dichroism and further supported by high-resolution transmission electron microscopy or cryo-transmission electron microscopy imaging and theoretical modelling. We also outline the applications of chiroplasmonic assemblies, including their use as DNA-sensing platforms and as functional systems for information processing and storage. Finally, future perspectives in applying chiroplasmonic nanoparticles as waveguides for selective information transfer and their use as ensembles for chiroselective synthesis are discussed. Specifically, we highlight the upscaling of the systems to device-like configurations.

  9. Multiplication operators on the Bergman space

    CERN Document Server

    Guo, Kunyu

    2015-01-01

    This book deals with various aspects of commutants and reducing subspaces of multiplication operators on the Bergman space, along with relevant von Neumann algebras generated by these operators, which have been the focus of considerable attention from the authors and other experts in recent years. The book reviews past developments and offers insights into cutting-edge developments in the study of multiplication operators. It also provides commentary and comparisons to stimulate research in this area.

  10. Sperm DNA oxidative damage and DNA adducts

    Science.gov (United States)

    Jeng, Hueiwang Anna; Pan, Chih-Hong; Chao, Mu-Rong; Lin, Wen-Yi

    2015-01-01

    The objective of this study was to investigate DNA damage and adducts in sperm from coke oven workers who have been exposed to polycyclic aromatic hydrocarbons. A longitudinal study was conducted with repeated measurements during spermatogenesis. Coke-oven workers (n=112) from a coke-oven plant served the PAH-exposed group, while administrators and security personnel (n=67) served the control. Routine semen parameters (concentration, motility, vitality, and morphology) were analyzed simultaneously; the assessment of sperm DNA integrity endpoints included DNA fragmentation, bulky DNA adducts, and 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dGuo). The degree of sperm DNA fragmentation was measured using the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay and sperm chromatin structure assay (SCSA). The PAH-exposed group had a significant increase in bulky DNA adducts and 8-oxo-dGuo compared to the control subjects (Ps = 0.002 and 0.045, respectively). Coke oven workers' percentages of DNA fragmentation and denaturation from the PAH-exposed group were not significantly different from those of the control subjects (Ps = 0.232 and 0.245, respectively). Routine semen parameters and DNA integrity endpoints were not correlated. Concentrations of 8-oxo-dGuo were positively correlated with percentages of DNA fragmentation measured by both TUNEL and SCSA (Ps = 0.045 and 0.034, respectively). However, the concentrations of 8-oxo-dGuo and percentages of DNA fragmentation did not correlate with concentrations of bulky DNA adducts. In summary, coke oven workers with chronic exposure to PAHs experienced decreased sperm DNA integrity. Oxidative stress could contribute to the degree of DNA fragmentation. Bulky DNA adducts may be independent of the formation of DNA fragmentation and oxidative adducts in sperm. Monitoring sperm DNA integrity is recommended as a part of the process of assessing the impact of occupational and environmental toxins on

  11. Synthesis of DNA

    Science.gov (United States)

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  12. Crystal structure of a DNA catalyst.

    Science.gov (United States)

    Ponce-Salvatierra, Almudena; Wawrzyniak-Turek, Katarzyna; Steuerwald, Ulrich; Höbartner, Claudia; Pena, Vladimir

    2016-01-14

    Catalysis in biology is restricted to RNA (ribozymes) and protein enzymes, but synthetic biomolecular catalysts can also be made of DNA (deoxyribozymes) or synthetic genetic polymers. In vitro selection from synthetic random DNA libraries identified DNA catalysts for various chemical reactions beyond RNA backbone cleavage. DNA-catalysed reactions include RNA and DNA ligation in various topologies, hydrolytic cleavage and photorepair of DNA, as well as reactions of peptides and small molecules. In spite of comprehensive biochemical studies of DNA catalysts for two decades, fundamental mechanistic understanding of their function is lacking in the absence of three-dimensional models at atomic resolution. Early attempts to solve the crystal structure of an RNA-cleaving deoxyribozyme resulted in a catalytically irrelevant nucleic acid fold. Here we report the crystal structure of the RNA-ligating deoxyribozyme 9DB1 (ref. 14) at 2.8 Å resolution. The structure captures the ligation reaction in the post-catalytic state, revealing a compact folding unit stabilized by numerous tertiary interactions, and an unanticipated organization of the catalytic centre. Structure-guided mutagenesis provided insights into the basis for regioselectivity of the ligation reaction and allowed remarkable manipulation of substrate recognition and reaction rate. Moreover, the structure highlights how the specific properties of deoxyribose are reflected in the backbone conformation of the DNA catalyst, in support of its intricate three-dimensional organization. The structural principles underlying the catalytic ability of DNA elucidate differences and similarities in DNA versus RNA catalysts, which is relevant for comprehending the privileged position of folded RNA in the prebiotic world and in current organisms.

  13. Insights in Public Health

    Science.gov (United States)

    Whelen, A Christian; Kitagawa, Kent; Maddock, Jay; Hayes, Donald; St John, Tonya Lowery; Rajan, Ranjani

    2013-01-01

    Chronically understaffed public health laboratories depend on a decreasing number of employees who must assume broader responsibilities in order to sustain essential functions for the many clients the laboratories support. Prospective scientists considering a career in public health are often not aware of the requirements associated with working in a laboratory regulated by the Clinical Laboratory Improvement Amendments (CLIA). The purpose of this pilot internship was two-fold; introduce students to operations in a regulated laboratory early enough in their academics so that they could make good career decisions, and evaluate internship methodology as one possible solution to workforce shortages. Four interns were recruited from three different local universities, and were paired with an experienced State Laboratories Division (SLD) staff mentor. Students performed tasks that demonstrated the importance of CLIA regulations for 10–15 hours per week over a 14 week period. Students also attended several directed group sessions on regulatory lab practice and quality systems. Both interns and mentors were surveyed periodically during the semester. Surveys of mentors and interns indicated overall positive experiences. One-on-one pairing of experienced public health professionals and students seems to be a mutually beneficial arrangement. Interns reported that they would participate if the internship was lower paid, unpaid, or for credit only. The internship appeared to be an effective tool to expose students to employment in CLIA-regulated laboratories, and potentially help address public health laboratory staffing shortfalls. Longer term follow up with multiple classes of interns may provide a more informed assessment. PMID:23386992

  14. A new DNA algorithm to solve graph coloring problem

    Institute of Scientific and Technical Information of China (English)

    Jiang Xingpeng; Li Yin; Meng Ya; Meng Dazhi

    2007-01-01

    Using a small quantity of DNA molecules and little experimental time to solve complex problems successfully is a goal of DNA computing. Some NP-hard problems have been solved by DNA computing with lower time complexity than conventional computing.However, this advantage often brings higher space complexity and needs a large number of DNA encoding molecules. One example is graph coloring problem. Current DNA algorithms need exponentially increasing DNA encoding strands with the growing of problem size.Here we propose a new DNA algorithm of graph coloring problem based on the proof of four-color theorem. This algorithm has good properties of needing a relatively small number of operations in polynomial time and needing a small number of DNA encoding molecules (we need only 6R DNA encoding molecules if the number of regions in a graph is R ).

  15. Molecular DNA switches and DNA chips

    Science.gov (United States)

    Sabanayagam, Chandran R.; Berkey, Cristin; Lavi, Uri; Cantor, Charles R.; Smith, Cassandra L.

    1999-06-01

    We present an assay to detect single-nucleotide polymorphisms on a chip using molecular DNA switches and isothermal rolling- circle amplification. The basic principle behind the switch is an allele-specific oligonucleotide circularization, mediated by DNA ligase. A DNA switch is closed when perfect hybridization between the probe oligonucleotide and target DNA allows ligase to covalently circularize the probe. Mismatches around the ligation site prevent probe circularization, resulting in an open switch. DNA polymerase is then used to preferentially amplify the closed switches, via rolling-circle amplification. The stringency of the molecular switches yields 102 - 103 fold discrimination between matched and mismatched sequences.

  16. Kinetics of DNA tile dimerization.

    Science.gov (United States)

    Jiang, Shuoxing; Yan, Hao; Liu, Yan

    2014-06-24

    Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

  17. DNA detection using recombination proteins.

    Directory of Open Access Journals (Sweden)

    Olaf Piepenburg

    2006-07-01

    Full Text Available DNA amplification is essential to most nucleic acid testing strategies, but established techniques require sophisticated equipment or complex experimental procedures, and their uptake outside specialised laboratories has been limited. Our novel approach, recombinase polymerase amplification (RPA, couples isothermal recombinase-driven primer targeting of template material with strand-displacement DNA synthesis. It achieves exponential amplification with no need for pretreatment of sample DNA. Reactions are sensitive, specific, and rapid and operate at constant low temperature. We have also developed a probe-based detection system. Key aspects of the combined RPA amplification/detection process are illustrated by a test for the pathogen methicillin-resistant Staphylococcus aureus. The technology proves to be sensitive to fewer than ten copies of genomic DNA. Furthermore, products can be detected in a simple sandwich assay, thereby establishing an instrument-free DNA testing system. This unique combination of properties is a significant advance in the development of portable and widely accessible nucleic acid-based tests.

  18. Isothermal hybridization kinetics of DNA assembly of two-dimensional DNA origami.

    Science.gov (United States)

    Song, Jie; Zhang, Zhao; Zhang, Shuai; Liu, Lei; Li, Qiang; Xie, Erqing; Gothelf, Kurt Vesterager; Besenbacher, Flemming; Dong, Mingdong

    2013-09-09

    The Watson-Crick base-pairing with specificity and predictability makes DNA molecules suitable for building versatile nanoscale structures and devices, and the DNA origami method enables researchers to incorporate more complexities into DNA-based devices. Thermally controlled atomic force microscopy in combination with nanomechanical spectroscopy with forces controlled in the pico Newton (pN) range as a novel technique is introduced to directly investigate the kinetics of multistrand DNA hybridization events on DNA origami nanopores under defined isothermal conditions. For the synthesis of DNA nanostructures under isothermal conditions at 60 °C, a higher hybridization rate, fewer defects, and a higher stability are achieved compared to room-temperature studies. By quantifying the assembly times for filling pores in origami structures at several constant temperatures, the fill factors show a consistent exponential increase over time. Furthermore, the local hybridization rate can be accelerated by adding a higher concentration of the staples. The new insight gained on the kinetics of staple-scaffold hybridization on the synthesis of two dimensional DNA origami structures may open up new routes and ideas for designing DNA assembly systems with increased potential for their application.

  19. Single-molecule visualization of ROS-induced DNA damage in large DNA molecules.

    Science.gov (United States)

    Lee, Jinyong; Kim, Yongkyun; Lim, Sangyong; Jo, Kyubong

    2016-02-07

    We present a single molecule visualization approach for the quantitative analysis of reactive oxygen species (ROS) induced DNA damage, such as base oxidation and single stranded breaks in large DNA molecules. We utilized the Fenton reaction to generate DNA damage with subsequent enzymatic treatment using a mixture of three types of glycosylases to remove oxidized bases, and then fluorescent labeling on damaged lesions via nick translation. This single molecule analytical platform provided the capability to count one or two damaged sites per λ DNA molecule (48.5 kb), which were reliably dependent on the concentrations of hydrogen peroxide and ferrous ion at the micromolar level. More importantly, the labeled damaged sites that were visualized under a microscope provided positional information, which offered the capability of comparing DNA damaged sites with the in silico genomic map to reveal sequence specificity that GTGR is more sensitive to oxidative damage. Consequently, single DNA molecule analysis provides a sensitive analytical platform for ROS-induced DNA damage and suggests an interesting biochemical insight that the genome primarily active during the lysogenic cycle may have less probability for oxidative DNA damage.

  20. Applied Operations Research: Operator's Assistant

    Science.gov (United States)

    Cole, Stuart K.

    2015-01-01

    NASA operates high value critical equipment (HVCE) that requires trouble shooting, periodic maintenance and continued monitoring by Operations staff. The complexity HVCE and information required to maintain and trouble shoot HVCE to assure continued mission success as paper is voluminous. Training on new HVCE is commensurate with the need for equipment maintenance. LaRC Research Directorate has undertaken a proactive research to support Operations staff by initiation of the development and prototyping an electronic computer based portable maintenance aid (Operator's Assistant). This research established a goal with multiple objectives and a working prototype was developed. The research identified affordable solutions; constraints; demonstrated use of commercial off the shelf software; use of the US Coast Guard maintenance solution; NASA Procedure Representation Language; and the identification of computer system strategies; where these demonstrations and capabilities support the Operator, and maintenance. The results revealed validation against measures of effectiveness and overall proved a substantial training and capability sustainment tool. The research indicated that the OA could be deployed operationally at the LaRC Compressor Station with an expectation of satisfactorily results and to obtain additional lessons learned prior to deployment at other LaRC Research Directorate Facilities. The research revealed projected cost and time savings.

  1. Diet-related DNA adduct formation in relation to carcinogenesis.

    Science.gov (United States)

    Hemeryck, Lieselot Y; Vanhaecke, Lynn

    2016-08-01

    The human diet contributes significantly to the initiation and promotion of carcinogenesis. It has become clear that the human diet contains several groups of natural foodborne chemicals that are at least in part responsible for the genotoxic, mutagenic, and carcinogenic potential of certain foodstuffs. Electrophilic chemicals are prone to attack nucleophilic sites in DNA, resulting in the formation of altered nucleobases, also known as DNA adducts. Since DNA adduct formation is believed to signal the onset of chemically induced carcinogenesis, the DNA adduct-inducing potential of certain foodstuffs has been investigated to gain more insight into diet-related pathways of carcinogenesis. Many studies have investigated diet-related DNA adduct formation. This review summarizes work on known or suspected dietary carcinogens and the role of DNA adduct formation in hypothesized carcinogenesis pathways.

  2. Understanding Insight in the Context of Q

    Science.gov (United States)

    Coghlan, David

    2012-01-01

    In Revans' learning formula, L = P + Q, Q represents "questioning insight", by which Revans means that insight comes out of the process of questioning programmed knowledge (P) in the light of experience. We typically focus on the content of an insight rather than on the act of insight. Drawing primarily on the work of Bernard Lonergan this paper…

  3. A bipedal DNA motor that travels back and forth between two DNA origami tiles.

    Science.gov (United States)

    Liber, Miran; Tomov, Toma E; Tsukanov, Roman; Berger, Yaron; Nir, Eyal

    2015-02-04

    In this work, the successful operation of a dynamic DNA device constructed from two DNA origami building blocks is reported. The device includes a bipedal walker that strides back and forth between the two origami tiles. Two different DNA origami tiles are first prepared separately; they are then joined together in a controlled manner by a set of DNA strands to form a stable track in high yield as confirmed by single-molecule fluorescence (SMF). Second, a bipedal DNA motor, initially attached to one of the two origami units and operated by sequential interaction with "fuel" and "antifuel" DNA strands, moves from one origami tile to another and then back again. The operational yield, measured by SMF, was similar to that of a motor operating on a similar track embedded in a single origami tile, confirming that the transfer across the junction from one tile to the other does not result in dissociation that is any more than that of steps on a single tile. These results demonstrate that moving parts can reliably travel from one origami unit to another, and it demonstrates the feasibility of dynamic DNA molecular machines that are made of more than a single origami building block. This study is a step toward the development of motors that can stride over micrometer distances.

  4. A model for the mechanism of strand passage by DNA gyrase

    DEFF Research Database (Denmark)

    Kampranis, S C; Bates, A D; Maxwell, A

    1999-01-01

    The mechanism of type II DNA topoisomerases involves the formation of an enzyme-operated gate in one double-stranded DNA segment and the passage of another segment through this gate. DNA gyrase is the only type II topoisomerase able to introduce negative supercoils into DNA, a feature that requir...

  5. Approaching the Distinction between Intuition and Insight.

    Science.gov (United States)

    Zhang, Zhonglu; Lei, Yi; Li, Hong

    2016-01-01

    Intuition and insight share similar cognitive and neural basis. Though, there are still some essential differences between the two. Here in this short review, we discriminated between intuition, and insight in two aspects. First, intuition, and insight are toward different aspects of information processing. Whereas intuition involves judgment about "yes or no," insight is related to "what" is the solution. Second, tacit knowledge play different roles in between intuition and insight. On the one hand, tacit knowledge is conducive to intuitive judgment. On the other hand, tacit knowledge may first impede but later facilitate insight occurrence. Furthermore, we share theoretical, and methodological views on how to access the distinction between intuition and insight.

  6. International operations networks

    CERN Document Server

    Farooq, Sami; Cheng, Yang

    2014-01-01

    Although the area of International Manufacturing Network (IMN) and International Operations Network (ION) has received considerable attention in the literature, most of studies appear multifaceted and interdisciplinary, and thereby require thorough investigation from both academic and practical perspectives, in order to deepen our related understanding. The book seeks advanced contributions that will combine theoretical insights and empirical experience by offering a detailed examination of IMN and, further, ION from various perspectives. This book can be used as a reference material for scholarpractitioners, business executives, and university researchers who need to deepen their understanding on the importance and influence of IMN and ION as well as their development. The book is important because there are few reference/resource materials available related to IMN and ION.

  7. Conceptualizing operations strategy processes

    DEFF Research Database (Denmark)

    Rytter, Niels Gorm; Boer, Harry; Koch, Christian

    2007-01-01

    Purpose - The purpose of this paper is to present insights into operations strategy (OS) in practice. It outlines a conceptualization and model of OS processes and, based on findings from an in-depth and longitudinal case study, contributes to further development of extant OS models and methods...... which presently mainly focus on OS content, as distinct from process issues. DesignImethodology/approach - The methodology combines action research and a longitudinal single site case study of OS processes in practice. Findings - The paper conceptualises an OS process as: events of dialogue and action...... provides a useful tool for describing and analyzing real-time OS processes unfolding in practice. Research limitations/implications - The research is based on a single case, which limits the generalizability of the findings. Practical implications - The findings suggest that, in order to obtain successful...

  8. Operator product expansion algebra

    Energy Technology Data Exchange (ETDEWEB)

    Holland, Jan [CPHT, Ecole Polytechnique, Paris-Palaiseau (France)

    2014-07-01

    The Operator Product Expansion (OPE) is a theoretical tool for studying the short distance behaviour of products of local quantum fields. Over the past 40 years, the OPE has not only found widespread computational application in high-energy physics, but, on a more conceptual level, it also encodes fundamental information on algebraic structures underlying quantum field theories. I review new insights into the status and properties of the OPE within Euclidean perturbation theory, addressing in particular the topics of convergence and ''factorisation'' of the expansion. Further, I present a formula for the ''deformation'' of the OPE algebra caused by a quartic interaction. This formula can be used to set up a novel iterative scheme for the perturbative computation of OPE coefficients, based solely on the zeroth order coefficients (and renormalisation conditions) as initial input.

  9. Risk Insights Gained from Fire Incidents

    Energy Technology Data Exchange (ETDEWEB)

    Kazarians, Mardy; Nowlen, Steven P.

    1999-06-10

    There now exist close to 20 years of history in the application of Probabilistic Risk Assessment (PRA) for the analysis of fire risk at nuclear power plants. The current methods are based on various assumptions regarding fire phenomena, the impact of fire on equipment and operator response, and the overall progression of a fire event from initiation through final resolution. Over this same time period, a number of significant fire incidents have occurred at nuclear power plants around the world. Insights gained from US experience have been used in US studies as the statistical basis for establishing fire initiation frequencies both as a function of the plant area and the initiating fire source.To a lesser extent, the fire experience has also been used to assess the general severity and duration of fires. However, aside from these statistical analyses, the incidents have rarely been scrutinized in detail to verify the underlying assumptions of fire PRAs. This paper discusses an effort, under which a set of fire incidents are being reviewed in order to gain insights directly relevant to the methods, data, and assumptions that form the basis for current fire PRAs. The paper focuses on the objectives of the effort, the specific fire events being reviews methodology, and anticipated follow-on activities.

  10. Hysteresis in pressure-driven DNA denaturation.

    Directory of Open Access Journals (Sweden)

    Enrique Hernández-Lemus

    Full Text Available In the past, a great deal of attention has been drawn to thermal driven denaturation processes. In recent years, however, the discovery of stress-induced denaturation, observed at the one-molecule level, has revealed new insights into the complex phenomena involved in the thermo-mechanics of DNA function. Understanding the effect of local pressure variations in DNA stability is thus an appealing topic. Such processes as cellular stress, dehydration, and changes in the ionic strength of the medium could explain local pressure changes that will affect the molecular mechanics of DNA and hence its stability. In this work, a theory that accounts for hysteresis in pressure-driven DNA denaturation is proposed. We here combine an irreversible thermodynamic approach with an equation of state based on the Poisson-Boltzmann cell model. The latter one provides a good description of the osmotic pressure over a wide range of DNA concentrations. The resulting theoretical framework predicts, in general, the process of denaturation and, in particular, hysteresis curves for a DNA sequence in terms of system parameters such as salt concentration, density of DNA molecules and temperature in addition to structural and configurational states of DNA. Furthermore, this formalism can be naturally extended to more complex situations, for example, in cases where the host medium is made up of asymmetric salts or in the description of the (helical-like charge distribution along the DNA molecule. Moreover, since this study incorporates the effect of pressure through a thermodynamic analysis, much of what is known from temperature-driven experiments will shed light on the pressure-induced melting issue.

  11. Operational Circulars

    CERN Multimedia

    2003-01-01

    Operational Circular N° 4 - April 2003 Conditions for use by members of the CERN personnel of vehicles belonging to or rented by CERN - This circular has been drawn up. Operational Circular N° 5 - October 2000 Use of CERN computing facilities - Further details on the personal use of CERN computing facilities Operational Circular N° 5 and its Subsidiary Rules http://cern.ch/ComputingRules defines the rules for the use of CERN computing facilities. One of the basic principles governing such use is that it must come within the professional duties of the user concerned, as defined by the user's divisional hierarchy. However, personal use of the computing facilities is tolerated or allowed provided : a) It is in compliance with Operational Circular N° 5 and not detrimental to official duties, including those of other users; b) the frequency and duration is limited and there is a negligible use of CERN resources; c) it does not constitute a political, commercial and/or profit-making activity; d) it is not...

  12. Operative links

    DEFF Research Database (Denmark)

    Wistoft, Karen

    2010-01-01

    as networks: second, a semantic perspective on discourses and concepts of health, and, third, a health pedagogical perspective on participation, intervention, and roles. This paper argues for the importance of 'operative links' between different levels in health strategies. It is proposed that such links...

  13. Operation Context

    DEFF Research Database (Denmark)

    Stüben, Henning; Tietjen, Anne

    2006-01-01

    Abstract: This paper seeks to challenge the notion of context from an operational perspective. Can we grasp the forces that shape the complex conditions for an architectural or urban design within the notion of context? By shifting the gaze towards the agency of architecture, contextual analysis...

  14. Increased sensitivity of DNA damage response-deficient cells to stimulated microgravity-induced DNA lesions.

    Directory of Open Access Journals (Sweden)

    Nan Li

    Full Text Available Microgravity is a major stress factor that astronauts have to face in space. In the past, the effects of microgravity on genomic DNA damage were studied, and it seems that the effect on genomic DNA depends on cell types and the length of exposure time to microgravity or simulated microgravity (SMG. In this study we used mouse embryonic stem (MES and mouse embryonic fibroblast (MEF cells to assess the effects of SMG on DNA lesions. To acquire the insight into potential mechanisms by which cells resist and/or adapt to SMG, we also included Rad9-deleted MES and Mdc1-deleted MEF cells in addition to wild type cells in this study. We observed significant SMG-induced DNA double strand breaks (DSBs in Rad9-/- MES and Mdc1-/- MEF cells but not in their corresponding wild type cells. A similar pattern of DNA single strand break or modifications was also observed in Rad9-/- MES. As the exposure to SMG was prolonged, Rad9-/- MES cells adapted to the SMG disturbance by reducing the induced DNA lesions. The induced DNA lesions in Rad9-/- MES were due to SMG-induced reactive oxygen species (ROS. Interestingly, Mdc1-/- MEF cells were only partially adapted to the SMG disturbance. That is, the induced DNA lesions were reduced over time, but did not return to the control level while ROS returned to a control level. In addition, ROS was only partially responsible for the induced DNA lesions in Mdc1-/- MEF cells. Taken together, these data suggest that SMG is a weak genomic DNA stress and can aggravate genomic instability in cells with DNA damage response (DDR defects.

  15. Heterogeneous dynamics in DNA site discrimination by the structurally homologous DNA-binding domains of ETS-family transcription factors.

    Science.gov (United States)

    He, Gaofei; Tolic, Ana; Bashkin, James K; Poon, Gregory M K

    2015-04-30

    The ETS family of transcription factors exemplifies current uncertainty in how eukaryotic genetic regulators with overlapping DNA sequence preferences achieve target site specificity. PU.1 and Ets-1 represent archetypes for studying site discrimination by ETS proteins because their DNA-binding domains are the most divergent in sequence, yet they share remarkably superimposable DNA-bound structures. To gain insight into the contrasting thermodynamics and kinetics of DNA recognition by these two proteins, we investigated the structure and dynamics of site discrimination by their DNA-binding domains. Electrophoretic mobilities of complexes formed by the two homologs with circularly permuted binding sites showed significant dynamic differences only for DNA complexes of PU.1. Free solution measurements by dynamic light scattering showed PU.1 to be more dynamic than Ets-1; moreover, dynamic changes are strongly coupled to site discrimination by PU.1, but not Ets-1. Interrogation of the protein/DNA interface by DNA footprinting showed similar accessibility to dimethyl sulfate for PU.1/DNA and Ets-1/DNA complexes, indicating that the dynamics of PU.1/DNA complexes reside primarily outside that interface. An information-based analysis of the two homologs' binding motifs suggests a role for dynamic coupling in PU.1's ability to enforce a more stringent sequence preference than Ets-1 and its proximal sequence homologs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways.

    Science.gov (United States)

    Suksombat, Sukrit; Khafizov, Rustem; Kozlov, Alexander G; Lohman, Timothy M; Chemla, Yann R

    2015-08-25

    Escherichia coli single-stranded (ss)DNA binding (SSB) protein mediates genome maintenance processes by regulating access to ssDNA. This homotetrameric protein wraps ssDNA in multiple distinct binding modes that may be used selectively in different DNA processes, and whose detailed wrapping topologies remain speculative. Here, we used single-molecule force and fluorescence spectroscopy to investigate E. coli SSB binding to ssDNA. Stretching a single ssDNA-SSB complex reveals discrete states that correlate with known binding modes, the likely ssDNA conformations and diffusion dynamics in each, and the kinetic pathways by which the protein wraps ssDNA and is dissociated. The data allow us to construct an energy landscape for the ssDNA-SSB complex, revealing that unwrapping energy costs increase the more ssDNA is unraveled. Our findings provide insights into the mechanism by which proteins gain access to ssDNA bound by SSB, as demonstrated by experiments in which SSB is displaced by the E. coli recombinase RecA.

  17. Entropy involved in fidelity of DNA replication

    CERN Document Server

    Arias-Gonzalez, J Ricardo

    2012-01-01

    Information has an entropic character which can be analyzed within the Statistical Theory in molecular systems. R. Landauer and C.H. Bennett showed that a logical copy can be carried out in the limit of no dissipation if the computation is performed sufficiently slowly. Structural and recent single-molecule assays have provided dynamic details of polymerase machinery with insight into information processing. We introduce a rigorous characterization of Shannon Information in biomolecular systems and apply it to DNA replication in the limit of no dissipation. Specifically, we devise an equilibrium pathway in DNA replication to determine the entropy generated in copying the information from a DNA template in the absence of friction. Both the initial state, the free nucleotides randomly distributed in certain concentrations, and the final state, a polymerized strand, are mesoscopic equilibrium states for the nucleotide distribution. We use empirical stacking free energies to calculate the probabilities of incorpo...

  18. On the electrostatics of DNA in chromatin

    Directory of Open Access Journals (Sweden)

    Klemen Bohinc

    2016-02-01

    Full Text Available We examine the interaction between DNA molecules immersed in an aqueous solution of oppositely charged, trivalent spermidine molecules. The DNA molecules are modeled as planar, likecharged surfaces immersed in an aqueous solution of multivalent, rod-like ions consisting of rigidly bonded point charges. An approximate field theory is used to determine the properties of this system from the weak to the intermediate through to the strong coupling regimes. In the weak coupling limit, the interaction between the charged surfaces is only repulsive, whereas in the intermediate coupling regime, the rod-like ions with spatial charge distribution can induce attractive force between the charged surfaces. In the strong coupling limit, the inter-ionic charge correlations induce attractive interaction at short separations between the surfaces. This theoretical study can give new insights in the problem of interaction between DNA molecules mediated by trivalent spermidine molecules.

  19. Thermal denaturation of A-DNA

    Science.gov (United States)

    Valle-Orero, J.; Wildes, A. R.; Theodorakopoulos, N.; Cuesta-López, S.; Garden, J.-L.; Danilkin, S.; Peyrard, M.

    2014-11-01

    The DNA molecule can take various conformational forms. Investigations focus mainly on the so-called ‘B-form’, schematically drawn in the famous paper by Watson and Crick [1]. This is the usual form of DNA in a biological environment and is the only form that is stable in an aqueous environment. Other forms, however, can teach us much about DNA. They have the same nucleotide base pairs for ‘building blocks’ as B-DNA, but with different relative positions, and studying these forms gives insight into the interactions between elements under conditions far from equilibrium in the B-form. Studying the thermal denaturation is particularly interesting because it provides a direct probe of those interactions which control the growth of the fluctuations when the ‘melting’ temperature is approached. Here we report such a study on the ‘A-form’ using calorimetry and neutron scattering. We show that it can be carried further than a similar study on B-DNA, requiring the improvement of thermodynamic models for DNA.

  20. Your Lung Operation: After Your Operation

    Medline Plus

    Full Text Available ... Surgeons Education Patients and Family Skills Programs Your Lung Operation Your Lung Operation DVD After Your Operation Back to Your Lung Operation Your Lung Operation DVD Welcome Your Lung ...

  1. Insights from a Math Phobic.

    Science.gov (United States)

    Dodd, Anne Wescott

    1992-01-01

    The author's personal experiences in overcoming mathematics anxiety provide insights into how teachers can create a classroom environment to help students develop self-confidence by assessing students' feelings, using cooperative-learning techniques, showing more patience, and having students write about their experiences. (MDH)

  2. Global China Insights December 2013

    NARCIS (Netherlands)

    Segers, Rien T.; Havinga, Marieke; Fischer, Ingrid

    2013-01-01

    Journal in which the Groningen Confucius Institute (GCI) shares different perspectives on China and provides insights into China from as many different aspects as possible. GCI aims to provide a full view of real China to the readers as well as featuring international and comprehensive perspectives,

  3. New Insights into Behavioral Finance

    NARCIS (Netherlands)

    G. Baltussen (Guido)

    2008-01-01

    textabstractThis thesis applies insights from psychology and other behavioral sciences to overcome the shortcomings of the traditional finance approach (which assumes that agents and markets are rational) and improves our understanding of financial markets and its participants. More specific, this t

  4. Investigating Insight as Sudden Learning

    Science.gov (United States)

    Ash, Ivan K.; Jee, Benjamin D.; Wiley, Jennifer

    2012-01-01

    Gestalt psychologists proposed two distinct learning mechanisms. Associative learning occurs gradually through the repeated co-occurrence of external stimuli or memories. Insight learning occurs suddenly when people discover new relationships within their prior knowledge as a result of reasoning or problem solving processes that re-organize or…

  5. Global China Insights June 2014

    NARCIS (Netherlands)

    Ingrid Fischer; Rien T. Segers

    2013-01-01

    Journal in which the Groningen Confucius Institute (GCI) shares different perspectives on China and provides insights into China from as many different aspects as possible. GCI aims to provide a full view of real China to the readers as well as featuring international and comprehensive perspectives,

  6. Non-equilibrium Dynamics of DNA Nanotubes

    Science.gov (United States)

    Hariadi, Rizal Fajar

    nanotubes with an irreversible energy consumption reaction, analogous to nucleotide hydrolysis in actin and microtubule polymerization. Finally, we integrated the DNA strand displacement circuits with DNA nanotube polymerization to achieve programmable kinetic control of behavior within artificial cytoskeleton. Our synthetic approach may provide insights into natural cytoskeleton dynamics, such as minimal architectural or reaction mechanism requirements for non-equilibrium behaviors including treadmilling and dynamic instability. The outgrowth of DNA nanotechnology beyond its own boundaries, serving as a general model system for biomolecular dynamics, can lead to an understanding of molecular processes that advances both basic and applied sciences.

  7. Chromatin challenges during DNA replication and repair

    DEFF Research Database (Denmark)

    Groth, Anja; Rocha, Walter; Verreault, Alain

    2007-01-01

    Inheritance and maintenance of the DNA sequence and its organization into chromatin are central for eukaryotic life. To orchestrate DNA-replication and -repair processes in the context of chromatin is a challenge, both in terms of accessibility and maintenance of chromatin organization. To meet...... the challenge of maintenance, cells have evolved efficient nucleosome-assembly pathways and chromatin-maturation mechanisms that reproduce chromatin organization in the wake of DNA replication and repair. The aim of this Review is to describe how these pathways operate and to highlight how the epigenetic...

  8. Operation Poorman

    Energy Technology Data Exchange (ETDEWEB)

    Pruvost, N.; Tsitouras, J.

    1981-03-18

    The objectives of Operation Poorman were to design and build a portable seismic system and to set up and use this system in a cold-weather environment. The equipment design uses current technology to achieve a low-power, lightweight system that is configured into three modules. The system was deployed in Alaska during wintertime, and the results provide a basis for specifying a mission-ready seismic verification system.

  9. Joint Operations

    Science.gov (United States)

    2006-09-17

    Unified Task Force (UNITAF) Somalia was formed with forces from France, Italy, Canada, Belgium, Egypt , Turkey, Saudi Arabia, and the United States...military presence, open-source intelligence ( OSINT ) may be the best immediately available information to prepare US forces to operate in a foreign...country. OSINT from radio broadcasts, newspapers, and periodicals often provide tip-offs for HUMINT and other intelligence and information collection

  10. Insights into the regulation of transcription by scanning force microscopy.

    Science.gov (United States)

    Dame, R T; Wyman, C; Goosen, N

    2003-12-01

    The scanning force microscope (SFM) is a valuable tool for the structural analysis of complexes between protein(s) and DNA. In recent years the application of scanning force microscopy to the field of transcription regulation has been reported in numerous studies. Using this technique, novel insights could be obtained into the architecture and dynamics of complexes, which are relevant to the transcription process and the mechanisms by which this process is regulated. In this article an overview is given of SFM studies addressing, in particular, topics in the field of transcription in prokaryotic organisms.

  11. Insight and analysis problem solving in microbes to machines.

    Science.gov (United States)

    Clark, Kevin B

    2015-11-01

    A key feature for obtaining solutions to difficult problems, insight is oftentimes vaguely regarded as a special discontinuous intellectual process and/or a cognitive restructuring of problem representation or goal approach. However, this nearly century-old state of art devised by the Gestalt tradition to explain the non-analytical or non-trial-and-error, goal-seeking aptitude of primate mentality tends to neglect problem-solving capabilities of lower animal phyla, Kingdoms other than Animalia, and advancing smart computational technologies built from biological, artificial, and composite media. Attempting to provide an inclusive, precise definition of insight, two major criteria of insight, discontinuous processing and problem restructuring, are here reframed using terminology and statistical mechanical properties of computational complexity classes. Discontinuous processing becomes abrupt state transitions in algorithmic/heuristic outcomes or in types of algorithms/heuristics executed by agents using classical and/or quantum computational models. And problem restructuring becomes combinatorial reorganization of resources, problem-type substitution, and/or exchange of computational models. With insight bounded by computational complexity, humans, ciliated protozoa, and complex technological networks, for example, show insight when restructuring time requirements, combinatorial complexity, and problem type to solve polynomial and nondeterministic polynomial decision problems. Similar effects are expected from other problem types, supporting the idea that insight might be an epiphenomenon of analytical problem solving and consequently a larger information processing framework. Thus, this computational complexity definition of insight improves the power, external and internal validity, and reliability of operational parameters with which to classify, investigate, and produce the phenomenon for computational agents ranging from microbes to man-made devices.

  12. CRISPR-Cas adaptation: insights into the mechanism of action.

    Science.gov (United States)

    Amitai, Gil; Sorek, Rotem

    2016-02-01

    Since the first demonstration that CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against phages and plasmids, numerous studies have yielded key insights into the molecular mechanisms governing how these systems attack and degrade foreign DNA. However, the molecular mechanisms underlying the adaptation stage, in which new immunological memory is formed, have until recently represented a major unresolved question. In this Progress article, we discuss recent discoveries that have shown both how foreign DNA is identified by the CRISPR-Cas adaptation machinery and the molecular basis for its integration into the chromosome to form an immunological memory. Furthermore, we describe the roles of each of the specific CRISPR-Cas components that are involved in memory formation, and consider current models for their evolutionary origin.

  13. DNA strand generation for DNA computing by using a multi-objective differential evolution algorithm.

    Science.gov (United States)

    Chaves-González, José M; Vega-Rodríguez, Miguel A

    2014-02-01

    In this paper, we use an adapted multi-objective version of the differential evolution (DE) metaheuristics for the design and generation of reliable DNA libraries that can be used for computation. DNA sequence design is a very relevant task in many recent research fields, e.g. nanotechnology or DNA computing. Specifically, DNA computing is a new computational model which uses DNA molecules as information storage and their possible biological interactions as processing operators. Therefore, the possible reactions and interactions among molecules must be strictly controlled to prevent incorrect computations. The design of reliable DNA libraries for bio-molecular computing is an NP-hard combinatorial problem which involves many heterogeneous and conflicting design criteria. For this reason, we modelled DNA sequence design as a multiobjective optimization problem and we solved it by using an adapted multi-objective version of DE metaheuristics. Seven different bio-chemical design criteria have been simultaneously considered to obtain high quality DNA sequences which are suitable for molecular computing. Furthermore, we have developed the multiobjective standard fast non-dominated sorting genetic algorithm (NSGA-II) in order to perform a formal comparative study by using multi-objective indicators. Additionally, we have also compared our results with other relevant results published in the literature. We conclude that our proposal is a promising approach which is able to generate reliable real-world DNA sequences that significantly improve other DNA libraries previously published in the literature.

  14. Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4.

    Science.gov (United States)

    Wu, Peï-Yu; Frit, Philippe; Meesala, SriLakshmi; Dauvillier, Stéphanie; Modesti, Mauro; Andres, Sara N; Huang, Ying; Sekiguchi, JoAnn; Calsou, Patrick; Salles, Bernard; Junop, Murray S

    2009-06-01

    Nonhomologous end-joining represents the major pathway used by human cells to repair DNA double-strand breaks. It relies on the XRCC4/DNA ligase IV complex to reseal DNA strands. Here we report the high-resolution crystal structure of human XRCC4 bound to the carboxy-terminal tandem BRCT repeat of DNA ligase IV. The structure differs from the homologous Saccharomyces cerevisiae complex and reveals an extensive DNA ligase IV binding interface formed by a helix-loop-helix structure within the inter-BRCT linker region, as well as significant interactions involving the second BRCT domain, which induces a kink in the tail region of XRCC4. We further demonstrate that interaction with the second BRCT domain of DNA ligase IV is necessary for stable binding to XRCC4 in cells, as well as to achieve efficient dominant-negative effects resulting in radiosensitization after ectopic overexpression of DNA ligase IV fragments in human fibroblasts. Together our findings provide unanticipated insight for understanding the physical and functional architecture of the nonhomologous end-joining ligation complex.

  15. Structural and Functional Interaction Between the Human DNA Repair Proteins DNA ligase IV and XRCC4

    Energy Technology Data Exchange (ETDEWEB)

    Wu, P.; Meesala, S; Dauvillier, S; Modesti, M; Andres, S; Huang, Y; Sekiguchi, J; Calsou, P; Salles, B; Junop, M

    2009-01-01

    Nonhomologous end-joining represents the major pathway used by human cells to repair DNA double-strand breaks. It relies on the XRCC4/DNA ligase IV complex to reseal DNA strands. Here we report the high-resolution crystal structure of human XRCC4 bound to the carboxy-terminal tandem BRCT repeat of DNA ligase IV. The structure differs from the homologous Saccharomyces cerevisiae complex and reveals an extensive DNA ligase IV binding interface formed by a helix-loop-helix structure within the inter-BRCT linker region, as well as significant interactions involving the second BRCT domain, which induces a kink in the tail region of XRCC4. We further demonstrate that interaction with the second BRCT domain of DNA ligase IV is necessary for stable binding to XRCC4 in cells, as well as to achieve efficient dominant-negative effects resulting in radiosensitization after ectopic overexpression of DNA ligase IV fragments in human fibroblasts. Together our findings provide unanticipated insight for understanding the physical and functional architecture of the nonhomologous end-joining ligation complex.

  16. Altofrequency SNPs of mitochondrial DNA in 26 Han Chinese

    Institute of Scientific and Technical Information of China (English)

    LUO Yong-jun; GAO Wen-xiang; GAO Yu-qi; CHEN Jian; TAN Xiao-ling; LIU Xin; CHEN Hai-hua

    2007-01-01

    Objective:To explore the possible mitochondrial DNA (mtDNA) polymorphism in Han Chinese.Methods:The complete mitochondrial genome of 26 unrelated healthy Han Chinese were extracted and sequenced.Results:The mtDNA nucleotide sites (2 706,7 028,8 860,11 719,and 15 326)were found totally different from the Revised Cambridge Reference Sequence (rCRS).These single nucleotide polymorphisms (SNPs) were 2 706 A→G,7 028 C→T,8 860 A→G,11 719 G→A,15 326 A→G.Conclusion:These findings provide new insights into the characteristics of Han Chinese mitochondrial genetic diversity.

  17. Single DNA molecular manipulation with atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    L(U) Jun-Hong; WU Shi-Ying; ZHANG Yi; HU Jun; LI Min-Qian

    2004-01-01

    Nanomanipulation of DNA molecules or other biomolecules to form artificial patterns or structures at nanometer scale has potential applications in the construction of molecular devices in future industries. It may also lead to new insights into the interesting properties and behavior of this fantastic nature-selected molecule at the single-molecular level. Here we present a special method based on the combination of macroscopic "molecular combing" and microscopic "molecular cutting" to manipulate DNA molecules and form complex patterns at nanometer scale on solid surfaces. A possible strategy for ordered DNA sequencing based on this nanomanipulation technique has also been proposed.

  18. Environmental DNA for wildlife biology and biodiversity monitoring

    DEFF Research Database (Denmark)

    Bohmann, Kristine; Evans, Alice; Gilbert, M. Thomas P.

    2014-01-01

    Extraction and identification of DNA from an environmental sample has proven noteworthy recently in detecting and monitoring not only common species, but also those that are endangered, invasive, or elusive. Particular attributes of so-called environmental DNA (eDNA) analysis render it a potent...... tool for elucidating mechanistic insights in ecological and evolutionary processes. Foremost among these is an improved ability to explore ecosystem-level processes, the generation of quantitative indices for analyses of species, community diversity, and dynamics, and novel opportunities through...

  19. DNA fragmentation in apoptosis

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Cleavage of chromosomal DNA into oligonucleosomal size fragments is an integral part of apoptosis. Elegant biochemical work identified the DNA fragmentation factor (DFF) as a major apoptotic endonuclease for DNA fragmentation in vitro. Genetic studies in mice support the importance of DFF in DNA fragmentation and possibly in apoptosis in vivo. Recent work also suggests the existence of additional endonucleases for DNA degradation. Understanding the roles of individual endonucleases in apoptosis, and how they might coordinate to degrade DNA in different tissues during normal development and homeostasis, as well as in various diseased states, will be a major research focus in the near future.

  20. ex vivo DNA assembly

    Directory of Open Access Journals (Sweden)

    Adam B Fisher

    2013-10-01

    Full Text Available Even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. Advances in cloning techniques have resulted in powerful in vitro and in vivo assembly of DNA. However, monetary and time costs have limited these approaches. Here, we report an ex vivo DNA assembly method that uses cellular lysates derived from a commonly used laboratory strain of Escherichia coli for joining double-stranded DNA with short end homologies embedded within inexpensive primers. This method concurrently shortens the time and decreases costs associated with current DNA assembly methods.

  1. Dynamics and control of DNA sequence amplification

    Energy Technology Data Exchange (ETDEWEB)

    Marimuthu, Karthikeyan [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Chakrabarti, Raj, E-mail: raj@pmc-group.com, E-mail: rajc@andrew.cmu.edu [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Division of Fundamental Research, PMC Advanced Technology, Mount Laurel, New Jersey 08054 (United States)

    2014-10-28

    DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.

  2. Extracellular DNA: the tip of root defenses?

    Science.gov (United States)

    Hawes, Martha C; Curlango-Rivera, Gilberto; Wen, Fushi; White, Gerard J; Vanetten, Hans D; Xiong, Zhongguo

    2011-06-01

    This review discusses how extracellular DNA (exDNA) might function in plant defense, and at what level(s) of innate immunity this process might operate. A new role for extracellular factors in mammalian defense has been described in a series of studies. These studies reveal that cells including neutrophils, eosinophils, and mast cells produce 'extracellular traps' (ETs) consisting of histone-linked exDNA. When pathogens are attracted to such ETs, they are trapped and killed. When the exDNA component of ETs is degraded, trapping is impaired and resistance against invasion is reduced. Conversely, mutation of microbial genes encoding exDNases that degrade exDNA results in loss of virulence. This discovery that exDNases are virulence factors opens new avenues for disease control. In plants, exDNA is required for defense of the root tip. Innate immunity-related proteins are among a group of >100 proteins secreted from the root cap and root border cell populations. Direct tests revealed that exDNA also is rapidly synthesized and exported from the root tip. When this exDNA is degraded by the endonuclease DNase 1, root tip resistance to fungal infection is lost; when the polymeric structure is degraded more slowly, by the exonuclease BAL31, loss of resistance to fungal infection is delayed accordingly. The results suggest that root border cells may function in a manner analogous to that which occurs in mammalian cells.

  3. Programmed DNA Self-Assembly and Logic Circuits

    Science.gov (United States)

    Li, Wei

    DNA is a unique, highly programmable and addressable biomolecule. Due to its reliable and predictable base recognition behavior, uniform structural properties, and extraordinary stability, DNA molecules are desirable substrates for biological computation and nanotechnology. The field of DNA computation has gained considerable attention due to the possibility of exploiting the massive parallelism that is inherent in natural systems to solve computational problems. This dissertation focuses on building novel types of computational DNA systems based on both DNA reaction networks and DNA nanotechnology. A series of related research projects are presented here. First, a novel, three-input majority logic gate based on DNA strand displacement reactions was constructed. Here, the three inputs in the majority gate have equal priority, and the output will be true if any two of the inputs are true. We subsequently designed and realized a complex, 5-input majority logic gate. By controlling two of the five inputs, the complex gate is capable of realizing every combination of OR and AND gates of the other 3 inputs. Next, we constructed a half adder, which is a basic arithmetic unit, from DNA strand operated XOR and AND gates. The aim of these two projects was to develop novel types of DNA logic gates to enrich the DNA computation toolbox, and to examine plausible ways to implement large scale DNA logic circuits. The third project utilized a two dimensional DNA origami frame shaped structure with a hollow interior where DNA hybridization seeds were selectively positioned to control the assembly of small DNA tile building blocks. The small DNA tiles were directed to fill the hollow interior of the DNA origami frame, guided through sticky end interactions at prescribed positions. This research shed light on the fundamental behavior of DNA based self-assembling systems, and provided the information necessary to build programmed nanodisplays based on the self-assembly of DNA.

  4. A Parallel Biological Optimization Algorithm to Solve the Unbalanced Assignment Problem Based on DNA Molecular Computing.

    Science.gov (United States)

    Wang, Zhaocai; Pu, Jun; Cao, Liling; Tan, Jian

    2015-10-23

    The unbalanced assignment problem (UAP) is to optimally resolve the problem of assigning n jobs to m individuals (m parallel DNA algorithm for solving the unbalanced assignment problem using DNA molecular operations. We reasonably design flexible-length DNA strands representing different jobs and individuals, take appropriate steps, and get the solutions of the UAP in the proper length range and O(mn) time. We extend the application of DNA molecular operations and simultaneity to simplify the complexity of the computation.

  5. DnaN clamp zones provide a platform for spatiotemporal coupling of mismatch detection to DNA replication.

    Science.gov (United States)

    Lenhart, Justin S; Sharma, Anushi; Hingorani, Manju M; Simmons, Lyle A

    2013-02-01

    Mismatch repair (MMR) increases the fidelity of DNA replication by identifying and correcting replication errors. Processivity clamps are vital components of DNA replication and MMR, yet the mechanism and extent to which they participate in MMR remains unclear. We investigated the role of the Bacillus subtilis processivity clamp DnaN, and found that it serves as a platform for mismatch detection and coupling of repair to DNA replication. By visualizing functional MutS fluorescent fusions in vivo, we find that MutS forms foci independent of mismatch detection at sites of replication (i.e. the replisome). These MutS foci are directed to the replisome by DnaN clamp zones that aid mismatch detection by targeting the search to nascent DNA. Following mismatch detection, MutS disengages from the replisome, facilitating repair. We tested the functional importance of DnaN-mediated mismatch detection for MMR, and found that it accounts for 90% of repair. This high dependence on DnaN can be bypassed by increasing MutS concentration within the cell, indicating a secondary mode of detection in vivo whereby MutS directly finds mismatches without associating with the replisome. Overall, our results provide new insight into the mechanism by which DnaN couples mismatch recognition to DNA replication in living cells.

  6. Spectroscopic and molecular docking studies on chlorambucil interaction with DNA.

    Science.gov (United States)

    Charak, Sonika; Shandilya, Manish; Tyagi, Gunjan; Mehrotra, Ranjana

    2012-11-01

    Chlorambucil (CMB) is an anticancer drug used for the treatment of variety of cancers. Structural and conformational changes associated with DNA after binding with CMB were explored using spectroscopic techniques to get insight into the mechanism of action of CMB at molecular level. Different molar ratios of CMB-DNA complex were prepared with constant DNA concentration under physiological conditions. FTIR spectroscopy, UV-visible spectroscopy, CD spectroscopy and molecular docking studies were employed to determine the binding site and binding constant of CMB with DNA. The results show CMB binds DNA through nitrogenous bases (thymine, guanine and cytosine). The binding constant was calculated to be 1.3 × 10³ M⁻¹, which suggests weak binding of CMB with DNA double helix. FTIR and CD results show that CMB do not disturb native B-conformation of DNA and it continues to remain in its B conformation even at higher concentrations of CMB. The molecular docking results are in corroboration with our experimental results and provides structural insight into the interaction site. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Quantum quadratic operators and processes

    CERN Document Server

    Mukhamedov, Farrukh

    2015-01-01

    Covering both classical and quantum approaches, this unique and self-contained book presents the most recent developments in the theory of quadratic stochastic operators and their Markov and related processes. The asymptotic behavior of dynamical systems generated by classical and quantum quadratic operators is investigated and various properties of quantum quadratic operators are studied, providing an insight into the construction of quantum channels. This book is suitable as a textbook for an advanced undergraduate/graduate level course or summer school in quantum dynamical systems. It can also be used as a reference book by researchers looking for interesting  problems to work on, or useful techniques and discussions of particular problems. Since it includes the latest developments in the fields of quadratic dynamical systems, Markov processes and quantum stochastic processes, researchers at all levels are likely to find the book inspiring and useful.

  8. Force induced DNA melting

    Energy Technology Data Exchange (ETDEWEB)

    Santosh, Mogurampelly; Maiti, Prabal K [Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore-12 (India)], E-mail: santosh@physics.iisc.ernet.in, E-mail: maiti@physics.iisc.ernet.in

    2009-01-21

    When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates by roughly twice its initial contour length at a pulling force of about 70 pN. The transition to this highly overstretched form of DNA is very cooperative. Applying a force perpendicular to the DNA axis (unzipping), double-strand DNA can also be separated into two single-stranded DNA, this being a fundamental process in DNA replication. We study the DNA overstretching and unzipping transition using fully atomistic molecular dynamics (MD) simulations and argue that the conformational changes of double-strand DNA associated with either of the above mentioned processes can be viewed as force induced DNA melting. As the force at one end of the DNA is increased the DNA starts melting abruptly/smoothly above a critical force depending on the pulling direction. The critical force f{sub m}, at which DNA melts completely decreases as the temperature of the system is increased. The melting force in the case of unzipping is smaller compared to the melting force when the DNA is pulled along the helical axis. In the case of melting through unzipping, the double-strand separation has jumps which correspond to the different energy minima arising due to sequence of different base pairs. The fraction of Watson-Crick base pair hydrogen bond breaking as a function of force does not show smooth and continuous behavior and consists of plateaus followed by sharp jumps.

  9. DNA damage and autophagy

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely [Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583 (United States); Panayiotidis, Mihalis I. [School of Community Health Sciences, University of Nevada, Reno, NV 89557 (United States); Franco, Rodrigo, E-mail: rfrancocruz2@unl.edu [Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583 (United States)

    2011-06-03

    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  10. Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1.

    Science.gov (United States)

    Zhou, Xianglian; Ren, Wendan; Bharath, Sakshibeedu R; Tang, Xuhua; He, Yang; Chen, Chen; Liu, Zhou; Li, Dewang; Song, Haiwei

    2016-03-01

    Pif1 is a conserved SF1B DNA helicase involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. Here, we report the structures of the helicase domain of human Pif1 and Bacteroides sp Pif1 (BaPif1) in complex with ADP-AlF4(-) and two different single-stranded DNAs (ssDNAs). The wedge region equivalent to the β hairpin in other SF1B DNA helicases folds into an extended loop followed by an α helix. The Pif1 signature motif of BaPif1 interacts with the wedge region and a short helix in order to stabilize these ssDNA binding elements, therefore indirectly exerting its functional role. Domain 2B of BaPif1 undergoes a large conformational change upon concomitant binding of ATP and ssDNA, which is critical for Pif1's activities. BaPif1 cocrystallized with a tailed dsDNA and ADP-AlF4(-), resulting in a bound ssDNA bent nearly 90° at the ssDNA/dsDNA junction. The conformational snapshots of BaPif1 provide insights into the mechanism governing the helicase activity of Pif1. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  11. SCIENCE CHINA In-Sight

    Institute of Scientific and Technical Information of China (English)

    HE ShiGang

    2010-01-01

    @@ 2010 celebrates the 60th anniversary of this journal.From this issue, the journal features a brand new section: 'In-Sight'.Equivalent to the Cutting Edge of the Cell, News and Views of the Nature and Perspective of the Science, 'In-Sight' provides a forum for discussions about science and science policies in China, the history and future development of this journal and the highlights of scientific progresses published in the current issue.

  12. Theoretical Insight into Shocked Gases

    Energy Technology Data Exchange (ETDEWEB)

    Leiding, Jeffery Allen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-09-29

    I present the results of statistical mechanical calculations on shocked molecular gases. This work provides insight into the general behavior of shock Hugoniots of gas phase molecular targets with varying initial pressures. The dissociation behavior of the molecules is emphasized. Impedance matching calculations are performed to determine the maximum degree of dissociation accessible for a given flyer velocity as a function of initial gas pressure.

  13. Binary electrokinetic separation of target DNA from background DNA primers.

    Energy Technology Data Exchange (ETDEWEB)

    James, Conrad D.; Derzon, Mark Steven

    2005-10-01

    This report contains the summary of LDRD project 91312, titled ''Binary Electrokinetic Separation of Target DNA from Background DNA Primers''. This work is the first product of a collaboration with Columbia University and the Northeast BioDefense Center of Excellence. In conjunction with Ian Lipkin's lab, we are developing a technique to reduce false positive events, due to the detection of unhybridized reporter molecules, in a sensitive and multiplexed detection scheme for nucleic acids developed by the Lipkin lab. This is the most significant problem in the operation of their capability. As they are developing the tools for rapidly detecting the entire panel of hemorrhagic fevers this technology will immediately serve an important national need. The goal of this work was to attempt to separate nucleic acid from a preprocessed sample. We demonstrated the preconcentration of kilobase-pair length double-stranded DNA targets, and observed little preconcentration of 60 base-pair length single-stranded DNA probes. These objectives were accomplished in microdevice formats that are compatible with larger detection systems for sample pre-processing. Combined with Columbia's expertise, this technology would enable a unique, fast, and potentially compact method for detecting/identifying genetically-modified organisms and multiplexed rapid nucleic acid identification. Another competing approach is the DARPA funded IRIS Pharmaceutical TIGER platform which requires many hours for operation, and an 800k$ piece of equipment that fills a room. The Columbia/SNL system could provide a result in 30 minutes, at the cost of a few thousand dollars for the platform, and would be the size of a shoebox or smaller.

  14. Developing DNA nanotechnology using single-molecule fluorescence.

    Science.gov (United States)

    Tsukanov, Roman; Tomov, Toma E; Liber, Miran; Berger, Yaron; Nir, Eyal

    2014-06-17

    CONSPECTUS: An important effort in the DNA nanotechnology field is focused on the rational design and manufacture of molecular structures and dynamic devices made of DNA. As is the case for other technologies that deal with manipulation of matter, rational development requires high quality and informative feedback on the building blocks and final products. For DNA nanotechnology such feedback is typically provided by gel electrophoresis, atomic force microscopy (AFM), and transmission electron microscopy (TEM). These analytical tools provide excellent structural information; however, usually they do not provide high-resolution dynamic information. For the development of DNA-made dynamic devices such as machines, motors, robots, and computers this constitutes a major problem. Bulk-fluorescence techniques are capable of providing dynamic information, but because only ensemble averaged information is obtained, the technique may not adequately describe the dynamics in the context of complex DNA devices. The single-molecule fluorescence (SMF) technique offers a unique combination of capabilities that make it an excellent tool for guiding the development of DNA-made devices. The technique has been increasingly used in DNA nanotechnology, especially for the analysis of structure, dynamics, integrity, and operation of DNA-made devices; however, its capabilities are not yet sufficiently familiar to the community. The purpose of this Account is to demonstrate how different SMF tools can be utilized for the development of DNA devices and for structural dynamic investigation of biomolecules in general and DNA molecules in particular. Single-molecule diffusion-based Förster resonance energy transfer and alternating laser excitation (sm-FRET/ALEX) and immobilization-based total internal reflection fluorescence (TIRF) techniques are briefly described and demonstrated. To illustrate the many applications of SMF to DNA nanotechnology, examples of SMF studies of DNA hairpins and

  15. Stability and dynamics of membrane-spanning DNA nanopores

    Science.gov (United States)

    Maingi, Vishal; Burns, Jonathan R.; Uusitalo, Jaakko J.; Howorka, Stefan; Marrink, Siewert J.; Sansom, Mark S. P.

    2017-03-01

    Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine.

  16. Operational excellence in logistics and supply chains

    OpenAIRE

    2015-01-01

    This volume contains research contributions by an international group of authors focusing on innovative models to optimize logistics and supply chains at an operational level. They address process efficiency and data-related aspects. Supply chain security insights are also given.

  17. DNA tagged microparticles

    Energy Technology Data Exchange (ETDEWEB)

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  18. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  19. DNA computing models

    CERN Document Server

    Ignatova, Zoya; Zimmermann, Karl-Heinz

    2008-01-01

    In this excellent text, the reader is given a comprehensive introduction to the field of DNA computing. The book emphasizes computational methods to tackle central problems of DNA computing, such as controlling living cells, building patterns, and generating nanomachines.

  20. Forensic DNA and bioinformatics

    National Research Council Canada - National Science Library

    Bianchi, Lucia; Liò, Pietro

    The field of forensic science is increasingly based on biomolecular data and many European countries are establishing forensic databases to store DNA profiles of crime scenes of known offenders and apply DNA testing...

  1. DNA tagged microparticles

    Science.gov (United States)

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  2. Operator-based metric for nuclear operations automation assessment

    Energy Technology Data Exchange (ETDEWEB)

    Zacharias, G.L.; Miao, A.X.; Kalkan, A. [Charles River Analytics Inc., Cambridge, MA (United States)] [and others

    1995-04-01

    Continuing advances in real-time computational capabilities will support enhanced levels of smart automation and AI-based decision-aiding systems in the nuclear power plant (NPP) control room of the future. To support development of these aids, we describe in this paper a research tool, and more specifically, a quantitative metric, to assess the impact of proposed automation/aiding concepts in a manner that can account for a number of interlinked factors in the control room environment. In particular, we describe a cognitive operator/plant model that serves as a framework for integrating the operator`s information-processing capabilities with his procedural knowledge, to provide insight as to how situations are assessed by the operator, decisions made, procedures executed, and communications conducted. Our focus is on the situation assessment (SA) behavior of the operator, the development of a quantitative metric reflecting overall operator awareness, and the use of this metric in evaluating automation/aiding options. We describe the results of a model-based simulation of a selected emergency scenario, and metric-based evaluation of a range of contemplated NPP control room automation/aiding options. The results demonstrate the feasibility of model-based analysis of contemplated control room enhancements, and highlight the need for empirical validation.

  3. Suspended Operations

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    A ship from China’s State Oceanic Administration (SOA) evaluates ConocoPhillips’s clean-up efforts in the Bohai Bay on September 2.That day, the SOA ordered the U.S. oil giant to cease all operations on the Penglai 19-3 Oilfield after the company failed to plug leaks in the oilfield by the administration’s August 31 deadline.The oil leaking from the oilfield caused by ConocoPhillips at the Penglai 19-3 Oilfield in the Bohai Bay was first spotted in June. The oil has since spread to beaches in China’s Hebei and Liaoning provinces, causing huge losses in the provinces’ tourism and aquatic farming industries.On September 7, ConocoPhillips said it will establish a fund to compensate victims of the oil spill in line with Chinese laws and to benefit the general environment of the Bohai Bay.

  4. Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores.

    Science.gov (United States)

    Shrestha, Prakash; Emura, Tomoko; Koirala, Deepak; Cui, Yunxi; Hidaka, Kumi; Maximuck, William J; Endo, Masayuki; Sugiyama, Hiroshi; Mao, Hanbin

    2016-08-19

    DNA nanoassemblies have demonstrated wide applications in various fields including nanomaterials, drug delivery and biosensing. In DNA origami, single-stranded DNA template is shaped into desired nanostructure by DNA staples that form Holliday junctions with the template. Limited by current methodologies, however, mechanical properties of DNA origami structures have not been adequately characterized, which hinders further applications of these materials. Using laser tweezers, here, we have described two mechanical properties of DNA nanoassemblies represented by DNA nanotubes, DNA nanopyramids and DNA nanotiles. First, mechanical stability of DNA origami structures is determined by the effective density of Holliday junctions along a particular stress direction. Second, mechanical isomerization observed between two conformations of DNA nanotubes at 10-35 pN has been ascribed to the collective actions of individual Holliday junctions, which are only possible in DNA origami with rotational symmetric arrangements of Holliday junctions, such as those in DNA nanotubes. Our results indicate that Holliday junctions control mechanical behaviors of DNA nanoassemblies. Therefore, they can be considered as 'mechanophores' that sustain mechanical properties of origami nanoassemblies. The mechanical properties observed here provide insights for designing better DNA nanostructures. In addition, the unprecedented mechanical isomerization process brings new strategies for the development of nano-sensors and actuators.

  5. Click chemistry with DNA

    OpenAIRE

    El-Sagheer, Afaf H.; Brown, Tom

    2010-01-01

    The advent of click chemistry has led to an influx of new ideas in the nucleic acids field. The copper catalysed alkyne–azide cycloaddition (CuAAC) reaction is the method of choice for DNA click chemistry due to its remarkable efficiency. It has been used to label oligonucleotides with fluorescent dyes, sugars, peptides and other reporter groups, to cyclise DNA, to synthesise DNA catenanes, to join oligonucleotides to PNA, and to produce analogues of DNA with modified nucleobases and backbone...

  6. Crystal structure of peroxide stress regulator from Streptococcus pyogenes provides functional insights into the mechanism of oxidative stress sensing.

    Science.gov (United States)

    Makthal, Nishanth; Rastegari, Sheila; Sanson, Misu; Ma, Zhen; Olsen, Randall J; Helmann, John D; Musser, James M; Kumaraswami, Muthiah

    2013-06-21

    Regulation of oxidative stress responses by the peroxide stress regulator (PerR) is critical for the in vivo fitness and virulence of group A Streptococcus. To elucidate the molecular mechanism of DNA binding, peroxide sensing, and gene regulation by PerR, we performed biochemical and structural characterization of PerR. Sequence-specific DNA binding by PerR does not require regulatory metal occupancy. However, metal binding promotes higher affinity PerR-DNA interactions. PerR metallated with iron directly senses peroxide stress and dissociates from operator sequences. The crystal structure revealed that PerR exists as a homodimer with two metal-binding sites per subunit as follows: a structural zinc site and a regulatory metal site that is occupied in the crystals by nickel. The regulatory metal-binding site in PerR involves a previously unobserved HXH motif located in its unique N-terminal extension. Mutational analysis of the regulatory site showed that the PerR metal ligands are involved in regulatory metal binding, and integrity of this site is critical for group A Streptococcus virulence. Interestingly, the metal-binding HXH motif is not present in the structurally characterized members of ferric uptake regulator (Fur) family but is fully conserved among PerR from the genus Streptococcus. Thus, it is likely that the PerR orthologs from streptococci share a common mechanism of metal binding, peroxide sensing, and gene regulation that is different from that of well characterized PerR from Bacillus subtilis. Together, our findings provide key insights into the peroxide sensing and regulation of the oxidative stress-adaptive responses by the streptococcal subfamily of PerR.

  7. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  8. Quantifying the Qualitative: Measuring the Insight Experience

    Science.gov (United States)

    Jarman, Matthew S.

    2014-01-01

    No scales currently exist that measure variability in the insight experience. Two scales were created to measure two factors hypothesized to be key drivers of the insight experience: insight radicality (i.e., perceived deviation between previous and new problem representations) and restructuring experience (i.e., the subjective experience of the…

  9. Three-Dimensional DNA Nanostructures Assembled from DNA Star Motifs.

    Science.gov (United States)

    Tian, Cheng; Zhang, Chuan

    2017-01-01

    Tile-based DNA self-assembly is a promising method in DNA nanotechnology and has produced a wide range of nanostructures by using a small set of unique DNA strands. DNA star motif, as one of DNA tiles, has been employed to assemble varieties of symmetric one-, two-, three-dimensional (1, 2, 3D) DNA nanostructures. Herein, we describe the design principles, assembly methods, and characterization methods of 3D DNA nanostructures assembled from the DNA star motifs.

  10. The SEIS InSight VBB Experiment

    Science.gov (United States)

    Nebut, T.; Lognonne, P. H.; Banerdt, W. B.; De Raucourt, S.; Beyneix, J.; Dandonneau, P. A.; Gabsi, T.; Robert, O.; Tillier, S.; Hurst, K. J.; Mimoun, D.; Christensen, U. R.; Bierwierth, M.; Roll, R.; Pike, W. T.; Calcutt, S. B.; Giardini, D.; Mance, D.; Zweifel, P.; Laudet, P.; Kerjean, L.; Perez, R.

    2013-12-01

    Introduction: The SEIS experiment is the primary payload of the Interior Structure Investigation using Seismology and Heat Transport (InSight) mission selected by NASA in August 2012 to be the next Mars mission. The objective of the InSight SEIS experiment is the determination of the deep internal structure of Mars. In particular, geophysical parameters of first importance, such as the state (liquid/solid) and size of the core, structure of the mantle, shape of discontinui-ties and thickness of the crust will be determined by the experiment. It will measure seismic activity over a very broad frequency band, from tidal frequencies (0.05 mHz) up to high frequencies (50 Hz), to address a wide range of scientific questions, from the state of the core to the meteoritic impact rate, marsquake rate and the response of the planet to the Phobos tide. Description of the instrument: The instrument includes notably a Very Broad Band (VBB) 3 axis seis-mometer which is developed by the ';Institut du Globe de Paris' (IPGP) under the funding of CNES. The sensor assembly, which also contains a MEMS short-period seismometer, will be deployed on the Martian ground by a robotic arm from a Phoenix-type lander platform and will be protected by a wind and thermal shield. The wind and thermal shield,together with a vacuum sphere and a passive compensation system will achieve a very high protection of the VBB against temperature and pressure variations, allowing the sensor to operate in the rough Martian thermal environment while reaching a detection threshold below 10-9 ms-2 Hz-1/2 in the VBB bandwidth. Conclusion: Performance has been demonstrated with previous prototypes and the SEIS experiment of the InSight mission will therefore provide high-quality seismic signal acquisition and associated seismic information during one martian year. The delivery of the payload is planned for the end of 2014 and the launch is in March 2016 SEIS deployed on the ground next to the lander Single

  11. Eukaryotic transcriptomics in silico: optimizing cDNA-AFLP efficiency.

    Science.gov (United States)

    Stölting, Kai N; Gort, Gerrit; Wüst, Christian; Wilson, Anthony B

    2009-11-30

    Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP) is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. In spite of the frequent application of this method, studies on the optimization of the cDNA-AFLP assay design are rare and have typically been taxonomically restricted. Here, we model cDNA-AFLPs on all 92 eukaryotic species for which cDNA pools are currently available, using all combinations of eight restriction enzymes standard in cDNA-AFLP screens. In silco simulations reveal that cDNA pool coverage is largely determined by the choice of individual restriction enzymes and that, through the choice of optimal enzyme combinations, coverage can be increased from cDNA pool coverage for particular enzyme combinations, indicating that our recommendations should be applicable to most eukaryotic systems. We also explore the relationship between the average observed fragment number per selective AFLP-PCR reaction and the size of the underlying cDNA pool, and show how AFLP experiments can be used to estimate the number of genes expressed in a target tissue. The insights gained from in silico screening of cDNA-AFLPs from a broad sampling of eukaryotes provide a set of guidelines that should help to substantially increase the efficiency of future cDNA-AFLP experiments in eukaryotes. In silico simulations also suggest a novel use of cDNA-AFLP screens to determine the number of transcripts expressed in a target tissue, an application that should be invaluable as next-generation sequencing technologies are adapted for differential display.

  12. Ultrafast exciton transfers in DNA and its nonlinear optical spectroscopy

    OpenAIRE

    Kim, Hyeon-Deuk; Tanimura, Yoshitaka; Cho, Minhaeng

    2008-01-01

    We have calculated the nonlinear response function of a DNA duplex helix including the contributions from the exciton population and coherence transfers by developing an appropriate exciton theory as well as by utilizing a projector operator technique. As a representative example of DNA double helices, the B-form (dA)10-(dT)10 is considered in detail. The Green functions of the exciton population and coherence transfer processes were obtained by developing the DNA exciton Hamiltonian. This en...

  13. Genetic and environmental influence on DNA strand break repair: a twin study

    DEFF Research Database (Denmark)

    Garm, Christian; Moreno-Villanueva, Maria; Bürkle, Alexander

    2013-01-01

    factors are likely to influence DNA repair capacity. In order to gain more insight into the genetic and environmental contribution to the molecular basis of DNA repair, we have performed a human twin study, where we focused on the consequences of some of the most abundant types of DNA damage (single......Accumulation of DNA damage deriving from exogenous and endogenous sources has significant consequences for cellular survival, and is implicated in aging, cancer, and neurological diseases. Different DNA repair pathways have evolved in order to maintain genomic stability. Genetic and environmental......-strand breaks), and some of the most hazardous lesions (DNA double-strand breaks). DNA damage signaling response (Gamma-H2AX signaling), relative amount of endogenous damage, and DNA-strand break repair capacities were studied in peripheral blood mononuclear cells from 198 twins (94 monozygotic and 104...

  14. Pitfalls in the analysis of ancient human mtDNA

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The retrieval of DNA from ancient human specimens is not always successful owing to DNA deterioration and contamination although it is vital to provide new insights into the genetic structure of ancient people and to reconstruct the past history. Normally, only short DNA fragments can be retrieved from the ancient specimens. How to identify the authenticity of DNA obtained and to uncover the information it contained are difficult. We employed the ancient mtDNAs reported from Central Asia (including Xinjiang, China) as an example to discern potentially extraneous DNA contamination based on the updated mtDNA phylogeny derived from mtDNA control region, coding region, as well as complete sequence information. Our results demonstrated that many mtDNAs reported are more or less problematic. Starting from a reliable mtDNA phylogeney and combining the available modern data into analysis, one can ascertain the authenticity of the ancient DNA, distinguish the potential errors in a data set, and efficiently decipher the meager information it harbored. The reappraisal of the mtDNAs with the age of more than 2000 years from Central Asia gave support to the suggestion of extensively (pre)historical gene admixture in this region.

  15. Using DNA Computing in Classification

    National Research Council Canada - National Science Library

    Abd El-Menem Abd El-Bary; Roshdy AbdelRassoul; Aya Mohamed El-Ebshihy

    2016-01-01

    ... to demonstrate better accuracy and predict some objects for example boys. In addition the explanation of DNA computing, Boolean Circuit using DNA, Molecular Beacons, also DNA logic gates and some applications using DNA computing...

  16. Fast phylogenetic DNA barcoding

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Willerslev, Eske

    2008-01-01

    We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect...... DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria...... for determining the taxonomic level at which a particular DNA sequence can be assigned....

  17. DNA-Mediated Electrochemistry

    Science.gov (United States)

    Gorodetsky, Alon A.; Buzzeo, Marisa C.

    2009-01-01

    The base pair stack of DNA has been demonstrated as a medium for long range charge transport chemistry both in solution and at DNA-modified surfaces. This chemistry is exquisitely sensitive to structural perturbations in the base pair stack as occur with lesions, single base mismatches, and protein binding. We have exploited this sensitivity for the development of reliable electrochemical assays based on DNA charge transport at self-assembled DNA monolayers. Here we discuss the characteristic features, applications, and advantages of DNA-mediated electrochemistry. PMID:18980370

  18. Archaeal DNA replication.

    Science.gov (United States)

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed.

  19. Racemic DNA crystallography.

    Science.gov (United States)

    Mandal, Pradeep K; Collie, Gavin W; Kauffmann, Brice; Huc, Ivan

    2014-12-22

    Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA.

  20. Ionisation clusters at DNA level: experimental modelling

    Energy Technology Data Exchange (ETDEWEB)

    Pszona, S.; Kula, J

    2002-07-01

    The importance of initial clustered damage to DNA is a hypothesis, which has to be approached also from physical modelling of the initial products of single charged particle interaction with DNA. A new tool for such studies, presented here, is based on modelling of the ionisation patterns resulting from a single charged particle crossing a nitrogen cavity of nanometre size. The nanometre size sites equivalent in unit density to DNA and nucleosome, have been modelled in a device, called a Jet Counter, consisting of a pulse operated valve which inject nitrogen in the form of an expansion jet into a interaction chamber. The distributions of the number of ions in a cluster created by a single alpha particle of 4.6 MeV along 0.15 nm to 13 nm size in nitrogen have been measured. A new descriptor of radiation action at DNA level is proposed. (author)

  1. Enantiospecific kinking of DNA by a partially intercalating metal complex

    KAUST Repository

    Reymer, Anna

    2012-01-01

    Opposite enantiomers of [Ru(phenanthroline) 3] 2+ affect the persistence length of DNA differently, a long speculated effect of helix kinking. Our molecular dynamics simulations confirm a substantial change of duplex secondary structure produced by wedge-intercalation of one but not the other enantiomer. This effect is exploited by several classes of DNA operative proteins. © The Royal Society of Chemistry 2012.

  2. DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch

    DEFF Research Database (Denmark)

    Norregaard, Kamilla; Andersson, Magnus; Sneppen, Kim

    2013-01-01

    Bacteriophage λ stably maintains its dormant prophage state but efficiently enters lytic development in response to DNA damage. The mediator of these processes is the λ repressor protein, CI, and its interactions with λ operator DNA. This λ switch is a model on the basis of which epigenetic switch...

  3. DNA barcoding for plants.

    Science.gov (United States)

    de Vere, Natasha; Rich, Tim C G; Trinder, Sarah A; Long, Charlotte

    2015-01-01

    DNA barcoding uses specific regions of DNA in order to identify species. Initiatives are taking place around the world to generate DNA barcodes for all groups of living organisms and to make these data publically available in order to help understand, conserve, and utilize the world's biodiversity. For land plants the core DNA barcode markers are two sections of coding regions within the chloroplast, part of the genes, rbcL and matK. In order to create high quality databases, each plant that is DNA barcoded needs to have a herbarium voucher that accompanies the rbcL and matK DNA sequences. The quality of the DNA sequences, the primers used, and trace files should also be accessible to users of the data. Multiple individuals should be DNA barcoded for each species in order to check for errors and allow for intraspecific variation. The world's herbaria provide a rich resource of already preserved and identified material and these can be used for DNA barcoding as well as by collecting fresh samples from the wild. These protocols describe the whole DNA barcoding process, from the collection of plant material from the wild or from the herbarium, how to extract and amplify the DNA, and how to check the quality of the data after sequencing.

  4. Interface Layering Phenomena in Capacitance Detection of DNA with Biochips

    Directory of Open Access Journals (Sweden)

    Sandro Carrara

    2007-02-01

    Full Text Available Reliable DNA detection is of great importance for the development of the Lab-on-chip technology. The effort of the most recent projects on this field is to integrate all necessary operations, such as sample preparation (mixing, PCR amplification together with the sensor user for DNA detection. Among the different ways to sense the DNA hybridization, fluorescence based detection has been favored by the market. However, fluorescence based approaches require that the DNA targets are labeled by means of chromophores. As an alternative label-free DNA detection method, capacitance detection was recently proposed by different authors. While this effect has been successfully demonstrated by several groups, the model used for data analysis is far too simple to describe the real behavior of a DNA sensor. The aim of the present paper is to propose a different electrochemical model to describe DNA capacitance detection.

  5. Development of fluorescent methods for DNA methyltransferase assay

    Science.gov (United States)

    Li, Yueying; Zou, Xiaoran; Ma, Fei; Tang, Bo; Zhang, Chun-yang

    2017-03-01

    DNA methylation modified by DNA methyltransferase (MTase) plays an important role in regulating gene transcription, cell growth and proliferation. The aberrant DNA MTase activity may lead to a variety of human diseases including cancers. Therefore, accurate and sensitive detection of DNA MTase activity is crucial to biomedical research, clinical diagnostics and therapy. However, conventional DNA MTase assays often suffer from labor-intensive operations and time-consuming procedures. Alternatively, fluorescent methods have significant advantages of simplicity and high sensitivity, and have been widely applied for DNA MTase assay. In this review, we summarize the recent advances in the development of fluorescent methods for DNA MTase assay. These emerging methods include amplification-free and the amplification-assisted assays. Moreover, we discuss the challenges and future directions of this area.

  6. DNA: Structure and function

    DEFF Research Database (Denmark)

    Sinden, Richard R.; E. Pearson, Christopher; N. Potaman, Vladimir

    1998-01-01

    for a long period of time before its information is accessed by the cell. Although DNA plays a critical role as an informational storage molecule, it is by no means as unexciting as a computer tape or disk drive. The structure of the DNA described by Watson and Crick in 1953 is a right handed helix of two......This chapter discusses the structure and function of DNA. DNA occupies a critical role in cells, because it is the source of all intrinsic genetic information. Chemically, DNA is a very stable molecule, a characteristic important for a macromolecule that may have to persist in an intact form...... individual antiparallel DNA strands. Hydrogen bonds provide specificity that allows pairing between the complementary bases (A.T and G.C) in opposite strands. Base stacking occurs near the center of the DNA helix and provides a great deal of stability to the helix (in addition to hydrogen bonding). The sugar...

  7. Biophysics of DNA

    CERN Document Server

    Vologodskii, Alexander

    2015-01-01

    Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

  8. DNA fragmentation in spermatozoa

    DEFF Research Database (Denmark)

    Rex, A S; Aagaard, J.; Fedder, J

    2017-01-01

    Sperm DNA Fragmentation has been extensively studied for more than a decade. In the 1940s the uniqueness of the spermatozoa protein complex which stabilizes the DNA was discovered. In the fifties and sixties, the association between unstable chromatin structure and subfertility was investigated....... In the seventies, the impact of induced DNA damage was investigated. In the 1980s the concept of sperm DNA fragmentation as related to infertility was introduced as well as the first DNA fragmentation test: the Sperm Chromatin Structure Assay (SCSA). The terminal deoxynucleotidyl transferase nick end labelling...... (TUNEL) test followed by others was introduced in the nineties. The association between DNA fragmentation in spermatozoa and pregnancy loss has been extensively investigated spurring the need for a therapeutic tool for these patients. This gave rise to an increased interest in the aetiology of DNA damage...

  9. Takotsubo Syndrome: Insights from Japan.

    Science.gov (United States)

    Akashi, Yoshihiro J; Ishihara, Masaharu

    2016-10-01

    We report the history and new insights of takotsubo syndrome based on the achievements that Japanese researchers have contributed and summarize the evidence originally presented from Japan. Takotsubo syndrome is a newly described heart failure characterized by transient left ventricular dysfunction. We should be aware of this entity as a syndrome, not actual cardiomyopathy. Japanese researchers focus on the experimental approaches for clinical diagnosis and treatment of takotsubo syndrome. As representatives from a country originally naming this syndrome takotsubo, a global registry for takotsubo syndrome including Japan should be established. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. [DNA methylation and epigenetics].

    Science.gov (United States)

    Vaniushin, B F

    2006-09-01

    In eukaryotic cells, nuclear DNA is subject to enzymatic methylation with the formation of 5-methylcytosine residues, mostly within the CG and CNG sequences. In plants and animals this DNA methylation is species-, tissue-, and organelle-specific. It changes (decreases) with age and is regulated by hormones. On the other hand, genome methylation can control hormonal signal. Replicative and post-replicative DNA methylation types are distinguished. They are mediated by multiple DNA methyltransferases with different site-specificity. Replication is accompanied by the appearance of hemimethylated DNA sites. Pronounced asymmetry of the DNA strand methylation disappears to the end of the cell cycle. A model of methylation-regulated DNA replication is proposed. DNA methylation controls all genetic processes in the cell (replication, transcription, DNA repair, recombination, and gene transposition). It is the mechanism of cell differentiation, gene discrimination and silencing. In animals, suppression of DNA methylation stops development (embryogenesis), switches on apoptosis, and is usually lethal. Disruption of DNA methylation pattern results in the malignant cell transformation and serves as one of the early diagnostic features of carcinogenesis. In malignant cell the pattern of DNA methylation, as well as the set of DNA methyltransferase activities, differs from that in normal cell. In plants inhibition of DNA methylation is accompanied by the induction of seed storage and florescence genes. In eukaryotes one and the same gene can be simultaneously methylated both at cytosine and adenine residues. It can be thus suggested, that the plant cell contains at least two different, and probably, interdependent systems of DNA methylation. The first eukaryotic adenine DNA methyltransferase was isolated from plants. This enzyme methylates DNA with the formation of N6-methyladenine residues in the sequence TGATCA (TGATCA-->TGm6ATCA). Plants possess AdoMet-dependent endonucleases

  11. Novel DNA probes for sensitive DNA detection

    OpenAIRE

    Richardson, James Alistair

    2010-01-01

    The ability to detect and interrogate DNA sequences allows further understanding and\\ud diagnosis of genetic disease. The ability to perform such analysis of genetic material\\ud requires highly selective and reliable technologies. Furthermore techniques which can use\\ud simple and cheap equipment allow the use of such technologies for point of care analysis.\\ud \\ud Described in this thesis are two novel DNA probe systems designed for mutation\\ud discrimination and sequence recognition of PCR ...

  12. Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.

    Science.gov (United States)

    Laponogov, Ivan; Veselkov, Dennis A; Crevel, Isabelle M-T; Pan, Xiao-Su; Fisher, L Mark; Sanderson, Mark R

    2013-11-01

    Type II topoisomerases regulate DNA supercoiling and chromosome segregation. They act as ATP-operated clamps that capture a DNA duplex and pass it through a transient DNA break in a second DNA segment via the sequential opening and closure of ATPase-, G-DNA- and C-gates. Here, we present the first 'open clamp' structures of a 3-gate topoisomerase II-DNA complex, the seminal complex engaged in DNA recognition and capture. A high-resolution structure was solved for a (full-length ParE-ParC55)2 dimer of Streptococcus pneumoniae topoisomerase IV bound to two DNA molecules: a closed DNA gate in a B-A-B form double-helical conformation and a second B-form duplex associated with closed C-gate helices at a novel site neighbouring the catalytically important β-pinwheel DNA-binding domain. The protein N gate is present in an 'arms-wide-open' state with the undimerized N-terminal ParE ATPase domains connected to TOPRIM domains via a flexible joint and folded back allowing ready access both for gate and transported DNA segments and cleavage-stabilizing antibacterial drugs. The structure shows the molecular conformations of all three gates at 3.7 Å, the highest resolution achieved for the full complex to date, and illuminates the mechanism of DNA capture and transport by a type II topoisomerase.

  13. Serial DNA relay in DNA logic gates by electrical fusion and mechanical splitting of droplets

    Science.gov (United States)

    Kawano, Ryuji; Takinoue, Masahiro; Osaki, Toshihisa; Kamiya, Koki; Miki, Norihisa

    2017-01-01

    DNA logic circuits utilizing DNA hybridization and/or enzymatic reactions have drawn increasing attention for their potential applications in the diagnosis and treatment of cellular diseases. The compartmentalization of such a system into a microdroplet considerably helps to precisely regulate local interactions and reactions between molecules. In this study, we introduced a relay approach for enabling the transfer of DNA from one droplet to another to implement multi-step sequential logic operations. We proposed electrical fusion and mechanical splitting of droplets to facilitate the DNA flow at the inputs, logic operation, output, and serial connection between two logic gates. We developed Negative-OR operations integrated by a serial connection of the OR gate and NOT gate incorporated in a series of droplets. The four types of input defined by the presence/absence of DNA in the input droplet pair were correctly reflected in the readout at the Negative-OR gate. The proposed approach potentially allows for serial and parallel logic operations that could be used for complex diagnostic applications. PMID:28700641

  14. Theory of mind correlates with clinical insight but not cognitive insight in patients with schizophrenia.

    Science.gov (United States)

    Zhang, Qi; Li, Xu; Parker, Giverny J; Hong, Xiao-Hong; Wang, Yi; Lui, Simon S Y; Neumann, David L; Cheung, Eric F C; Shum, David H K; Chan, Raymond C K

    2016-03-30

    Research on the relationship between insight and social cognition, in particular Theory of Mind (ToM), in schizophrenia has yielded mixed findings to date. Very few studies, however, have assessed both clinical insight and cognitive insight when examining their relationships with ToM in schizophrenia. The current study thus investigated the relationship between clinical insight, cognitive insight, and ToM in a sample of 56 patients with schizophrenia and 30 healthy controls. Twenty-seven patients were classified as low in clinical insight according to their scores on the 'insight' item (G12) of the Positive and Negative Syndrome Scale (PANSS). Moreover, cognitive insight and ToM were assessed with the Beck Cognitive Insight Scale (BCIS) and the Yoni task, respectively. The results indicated that patients with poor clinical insight performed worse on tasks of second-order cognitive and affective ToM, while the ToM performance of patients with high clinical insight was equivalent to that of healthy controls. Furthermore, while clinical insight was correlated with ToM and clinical symptoms, cognitive insight did not correlate with clinical insight, ToM, or clinical symptoms. Clinical insight thus appears to be an important factor related to ToM in schizophrenia.

  15. Video prototype of the interactive operating theatre

    DEFF Research Database (Denmark)

    2004-01-01

    Building capture and access (C&A) applications for use in the operation theatre differs greatly from C&A applications built to support other settings e.g. meeting rooms or classrooms. Based on field studies of surgical operations, this paper explores how to design C&A applications for the operation...... theatre. Based on the findings from our field work, we have built the ActiveTheatre, a C&A prototype. ActiveTheatre is built to support collaboration in and around the operating theatre, to capture events instead of automatically capturing eve- rything, and to be integrated with existing applications...... already present in the operation theatre. The ActiveTheatre prototype has been developed in close co- operation with surgeons and nurses at a local hospital. The work on the proto- type and our initial evaluations have provided an insight into how to design, capture and access applications that are going...

  16. Insight with hands and things.

    Science.gov (United States)

    Vallée-Tourangeau, Frédéric; Steffensen, Sune Vork; Vallée-Tourangeau, Gaëlle; Sirota, Miroslav

    2016-10-01

    Two experiments examined whether different task ecologies influenced insight problem solving. The 17 animals problem was employed, a pure insight problem. Its initial formulation encourages the application of a direct arithmetic solution, but its solution requires the spatial arrangement of sets involving some degree of overlap. Participants were randomly allocated to either a tablet condition where they could use a stylus and an electronic tablet to sketch a solution or a model building condition where participants were given material with which to build enclosures and figurines. In both experiments, participants were much more likely to develop a working solution in the model building condition. The difference in performance elicited by different task ecologies was unrelated to individual differences in working memory, actively open-minded thinking, or need for cognition (Experiment 1), although individual differences in creativity were correlated with problem solving success in Experiment 2. The discussion focuses on the implications of these findings for the prevailing metatheoretical commitment to methodological individualism that places the individual as the ontological locus of cognition.

  17. Genomic and Biochemical Insights into the Specificity of ETS Transcription Factors

    Science.gov (United States)

    Hollenhorst, Peter C.; McIntosh, Lawrence P.; Graves, Barbara J.

    2017-01-01

    ETS proteins are a group of evolutionarily related, DNA-binding transcriptional factors. These proteins direct gene expression in diverse normal and disease states by binding to specific promoters and enhancers and facilitating assembly of other components of the transcriptional machinery. The highly conserved DNA-binding ETS domain defines the family and is responsible for specific recognition of a common sequence motif, 5′-GGA(A/T)-3′. Attaining specificity for biological regulation in such a family is thus a conundrum. We present the current knowledge of routes to functional diversity and DNA binding specificity, including divergent properties of the conserved ETS and PNT domains, the involvement of flanking structured and unstructured regions appended to these dynamic domains, posttranslational modifications, and protein partnerships with other DNA-binding proteins and coregulators. The review emphasizes recent advances from biochemical and biophysical approaches, as well as insights from genomic studies that detect ETS-factor occupancy in living cells. PMID:21548782

  18. 5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases

    Science.gov (United States)

    Le Bihan, Yann-Vaï; Angeles Izquierdo, Maria; Coste, Franck; Aller, Pierre; Culard, Françoise; Gehrke, Tim H.; Essalhi, Kadija; Carell, Thomas; Castaing, Bertrand

    2011-01-01

    DNA base-damage recognition in the base excision repair (BER) is a process operating on a wide variety of alkylated, oxidized and degraded bases. DNA glycosylases are the key enzymes which initiate the BER pathway by recognizing and excising the base damages guiding the damaged DNA through repair synthesis. We report here biochemical and structural evidence for the irreversible entrapment of DNA glycosylases by 5-hydroxy-5-methylhydantoin, an oxidized thymine lesion. The first crystal structure of a suicide complex between DNA glycosylase and unrepaired DNA has been solved. In this structure, the formamidopyrimidine-(Fapy) DNA glycosylase from Lactococcus lactis (LlFpg/LlMutM) is covalently bound to the hydantoin carbanucleoside-containing DNA. Coupling a structural approach by solving also the crystal structure of the non-covalent complex with site directed mutagenesis, this atypical suicide reaction mechanism was elucidated. It results from the nucleophilic attack of the catalytic N-terminal proline of LlFpg on the C5-carbon of the base moiety of the hydantoin lesion. The biological significance of this finding is discussed. PMID:21486746

  19. ATM Dependent Silencing Links Nucleolar Chromatin Reorganization to DNA Damage Recognition.

    Science.gov (United States)

    Harding, Shane M; Boiarsky, Jonathan A; Greenberg, Roger A

    2015-10-13

    Resolution of DNA double-strand breaks (DSBs) is essential for the suppression of genome instability. DSB repair in transcriptionally active genomic regions represents a unique challenge that is associated with ataxia telangiectasia mutated (ATM) kinase-mediated transcriptional silencing. Despite emerging insights into the underlying mechanisms, how DSB silencing connects to DNA repair remains undefined. We observe that silencing within the rDNA depends on persistent DSBs. Non-homologous end-joining was the predominant mode of DSB repair allowing transcription to resume. ATM-dependent rDNA silencing in the presence of persistent DSBs led to the large-scale reorganization of nucleolar architecture, with movement of damaged chromatin to nucleolar cap regions. These findings identify ATM-dependent temporal and spatial control of DNA repair and provide insights into how communication between DSB signaling and ongoing transcription promotes genome integrity.

  20. ATM Dependent Silencing Links Nucleolar Chromatin Reorganization to DNA Damage Recognition

    Directory of Open Access Journals (Sweden)

    Shane M. Harding

    2015-10-01

    Full Text Available Resolution of DNA double-strand breaks (DSBs is essential for the suppression of genome instability. DSB repair in transcriptionally active genomic regions represents a unique challenge that is associated with ataxia telangiectasia mutated (ATM kinase-mediated transcriptional silencing. Despite emerging insights into the underlying mechanisms, how DSB silencing connects to DNA repair remains undefined. We observe that silencing within the rDNA depends on persistent DSBs. Non-homologous end-joining was the predominant mode of DSB repair allowing transcription to resume. ATM-dependent rDNA silencing in the presence of persistent DSBs led to the large-scale reorganization of nucleolar architecture, with movement of damaged chromatin to nucleolar cap regions. These findings identify ATM-dependent temporal and spatial control of DNA repair and provide insights into how communication between DSB signaling and ongoing transcription promotes genome integrity.